From 506d60f0e188723ddc91c26824b41ac7034df3fe Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Thu, 4 Sep 2008 13:34:15 +0000
Subject: [PATCH] merge from 2_4_Release branch

---
 help/html/jalviewjnlp.html                         |   38 +-
 src/MCview/AppletPDBCanvas.java                    |  264 +-
 src/MCview/AppletPDBViewer.java                    |   72 +-
 src/MCview/Atom.java                               |   41 +-
 src/MCview/Bond.java                               |  160 +-
 src/MCview/MCMatrix.java                           |  346 +-
 src/MCview/PDBCanvas.java                          |  287 +-
 src/MCview/PDBChain.java                           |  214 +-
 src/MCview/PDBViewer.java                          |  158 +-
 src/MCview/PDBfile.java                            |   65 +-
 src/MCview/Residue.java                            |  101 +-
 src/MCview/Zsort.java                              |  148 +-
 src/com/stevesoft/pat/AmpersandRule.java           |   59 +-
 src/com/stevesoft/pat/Any.java                     |  110 +-
 src/com/stevesoft/pat/BackG.java                   |   93 +-
 src/com/stevesoft/pat/BackMatch.java               |  114 +-
 src/com/stevesoft/pat/BackRefRule.java             |   78 +-
 src/com/stevesoft/pat/Backup.java                  |  106 +-
 src/com/stevesoft/pat/BasicStringBufferLike.java   |   45 +-
 src/com/stevesoft/pat/Bits.java                    | 6136 +++++++-------
 src/com/stevesoft/pat/Boundary.java                |  181 +-
 src/com/stevesoft/pat/Bracket.java                 |  175 +-
 src/com/stevesoft/pat/CaseMgr.java                 | 8816 ++++++++++----------
 src/com/stevesoft/pat/ChangeRule.java              |   97 +-
 src/com/stevesoft/pat/CodeRule.java                |   65 +-
 src/com/stevesoft/pat/Ctrl.java                    |  332 +-
 src/com/stevesoft/pat/Custom.java                  |  124 +-
 src/com/stevesoft/pat/CustomEndpoint.java          |   87 +-
 src/com/stevesoft/pat/DirFileRegex.java            |   61 +-
 src/com/stevesoft/pat/DotMulti.java                |  414 +-
 src/com/stevesoft/pat/End.java                     |  141 +-
 src/com/stevesoft/pat/FastBracket.java             |  512 +-
 src/com/stevesoft/pat/FastMulti.java               |  340 +-
 src/com/stevesoft/pat/FileRegex.java               |  616 +-
 src/com/stevesoft/pat/Group.java                   |  152 +-
 src/com/stevesoft/pat/LeftRule.java                |   61 +-
 src/com/stevesoft/pat/Multi.java                   |  175 +-
 src/com/stevesoft/pat/MultiMin.java                |   43 +-
 src/com/stevesoft/pat/Multi_stage2.java            |  313 +-
 src/com/stevesoft/pat/NoPattern.java               |   66 +-
 src/com/stevesoft/pat/NonDirFileRegex.java         |   61 +-
 src/com/stevesoft/pat/NotImplementedError.java     |   33 +-
 src/com/stevesoft/pat/NullPattern.java             |   74 +-
 src/com/stevesoft/pat/NullRule.java                |   58 +-
 src/com/stevesoft/pat/Or.java                      |  257 +-
 src/com/stevesoft/pat/OrMark.java                  |  145 +-
 src/com/stevesoft/pat/PartialBuffer.java           |  215 +-
 src/com/stevesoft/pat/Pattern.java                 |  574 +-
 src/com/stevesoft/pat/PatternSub.java              |   33 +-
 src/com/stevesoft/pat/PopRule.java                 |   47 +-
 src/com/stevesoft/pat/Prop.java                    |  148 +-
 src/com/stevesoft/pat/Pthings.java                 |   82 +-
 src/com/stevesoft/pat/PushRule.java                |   97 +-
 src/com/stevesoft/pat/RBuffer.java                 |   99 +-
 src/com/stevesoft/pat/Range.java                   |  195 +-
 src/com/stevesoft/pat/RegOpt.java                  |  917 +-
 src/com/stevesoft/pat/RegRes.java                  |  575 +-
 src/com/stevesoft/pat/RegSyntax.java               |   59 +-
 src/com/stevesoft/pat/RegSyntaxError.java          |   82 +-
 src/com/stevesoft/pat/Regex.java                   | 4114 ++++-----
 src/com/stevesoft/pat/RegexReader.java             |  634 +-
 src/com/stevesoft/pat/RegexTokenizer.java          |  332 +-
 src/com/stevesoft/pat/RegexWriter.java             |  543 +-
 src/com/stevesoft/pat/ReplaceRule.java             |  798 +-
 src/com/stevesoft/pat/Replacer.java                |  724 +-
 src/com/stevesoft/pat/RightRule.java               |   60 +-
 src/com/stevesoft/pat/Rthings.java                 |  120 +-
 src/com/stevesoft/pat/RuleHolder.java              |   85 +-
 src/com/stevesoft/pat/Skip.java                    |  382 +-
 src/com/stevesoft/pat/Skip2.java                   |  112 +-
 src/com/stevesoft/pat/SkipBMH.java                 |  550 +-
 src/com/stevesoft/pat/Skipped.java                 |  110 +-
 src/com/stevesoft/pat/SpecialRule.java             |   37 +-
 src/com/stevesoft/pat/Start.java                   |  114 +-
 src/com/stevesoft/pat/StrPos.java                  |  367 +-
 src/com/stevesoft/pat/StringBufferLike.java        |  182 +-
 src/com/stevesoft/pat/StringLike.java              |   91 +-
 src/com/stevesoft/pat/StringRule.java              |   76 +-
 src/com/stevesoft/pat/SubMark.java                 |   63 +-
 src/com/stevesoft/pat/TransPat.java                |   96 +-
 src/com/stevesoft/pat/Transformer.java             |  452 +-
 src/com/stevesoft/pat/UniValidator.java            |   49 +-
 src/com/stevesoft/pat/Validator.java               |  145 +-
 src/com/stevesoft/pat/WantMoreTextReplaceRule.java |   57 +-
 src/com/stevesoft/pat/lookAhead.java               |  198 +-
 src/com/stevesoft/pat/oneChar.java                 |  151 +-
 src/com/stevesoft/pat/parsePerl.java               |  752 +-
 src/com/stevesoft/pat/patInf.java                  |   33 +-
 src/com/stevesoft/pat/patInt.java                  |  351 +-
 .../stevesoft/pat/wrap/CharArrayBufferWrap.java    |  107 +-
 src/com/stevesoft/pat/wrap/CharArrayWrap.java      |  149 +-
 .../stevesoft/pat/wrap/RandomAccessFileWrap.java   |  343 +-
 src/com/stevesoft/pat/wrap/StringBufferWrap.java   |   96 +-
 src/com/stevesoft/pat/wrap/StringWrap.java         |  116 +-
 src/com/stevesoft/pat/wrap/WriterWrap.java         |  120 +-
 src/ext/vamsas/IRegistry.java                      |   28 +-
 src/ext/vamsas/IRegistryService.java               |   30 +-
 src/ext/vamsas/IRegistryServiceLocator.java        |   85 +-
 src/ext/vamsas/Jpred.java                          |   39 +-
 src/ext/vamsas/JpredService.java                   |   31 +-
 src/ext/vamsas/JpredServiceLocator.java            |   84 +-
 src/ext/vamsas/JpredSoapBindingStub.java           |  224 +-
 src/ext/vamsas/MuscleWS.java                       |   96 +-
 src/ext/vamsas/MuscleWSService.java                |   86 +-
 src/ext/vamsas/MuscleWSServiceLocator.java         |  417 +-
 src/ext/vamsas/MuscleWSSoapBindingStub.java        |  960 +--
 src/ext/vamsas/RegistryServiceSoapBindingStub.java |  121 +-
 src/ext/vamsas/SeqSearchI.java                     |   46 +-
 src/ext/vamsas/SeqSearchServiceLocator.java        |  286 +-
 src/ext/vamsas/SeqSearchServiceService.java        |   34 +-
 .../vamsas/SeqSearchServiceSoapBindingStub.java    |  835 +-
 src/ext/vamsas/ServiceHandle.java                  |  118 +-
 src/ext/vamsas/ServiceHandles.java                 |   86 +-
 src/jalview/analysis/AAFrequency.java              |  315 +-
 src/jalview/analysis/AlignSeq.java                 |  360 +-
 src/jalview/analysis/AlignmentSorter.java          |  265 +-
 src/jalview/analysis/Conservation.java             |   31 +-
 src/jalview/analysis/CrossRef.java                 |   76 +-
 src/jalview/analysis/Dna.java                      |  270 +-
 src/jalview/analysis/Finder.java                   |   91 +-
 src/jalview/analysis/NJTree.java                   |  517 +-
 src/jalview/analysis/PCA.java                      |  491 +-
 src/jalview/analysis/ParseProperties.java          |  159 +-
 src/jalview/analysis/SeqsetUtils.java              |  174 +-
 src/jalview/analysis/SequenceIdMatcher.java        |  504 +-
 src/jalview/appletgui/APopupMenu.java              |  353 +-
 src/jalview/appletgui/AlignFrame.java              | 1492 ++--
 src/jalview/appletgui/AlignViewport.java           |  280 +-
 src/jalview/appletgui/AlignmentPanel.java          |  120 +-
 src/jalview/appletgui/AnnotationColourChooser.java |  161 +-
 src/jalview/appletgui/AnnotationLabels.java        |  107 +-
 src/jalview/appletgui/AnnotationPanel.java         |  556 +-
 src/jalview/appletgui/AppletJmol.java              |  470 +-
 src/jalview/appletgui/CutAndPasteTransfer.java     |  557 +-
 src/jalview/appletgui/EditNameDialog.java          |  161 +-
 src/jalview/appletgui/EmbmenuFrame.java            |  186 +-
 src/jalview/appletgui/FeatureRenderer.java         |  487 +-
 src/jalview/appletgui/FeatureSettings.java         |  154 +-
 src/jalview/appletgui/Finder.java                  |   59 +-
 src/jalview/appletgui/FontChooser.java             |  550 +-
 src/jalview/appletgui/IdCanvas.java                |  134 +-
 src/jalview/appletgui/IdPanel.java                 |   77 +-
 src/jalview/appletgui/IdwidthAdjuster.java         |  212 +-
 src/jalview/appletgui/JVDialog.java                |  157 +-
 src/jalview/appletgui/OverviewPanel.java           |  904 +-
 src/jalview/appletgui/PCAPanel.java                |   78 +-
 src/jalview/appletgui/PaintRefresher.java          |  457 +-
 src/jalview/appletgui/PairwiseAlignPanel.java      |   68 +-
 src/jalview/appletgui/RedundancyPanel.java         |   86 +-
 src/jalview/appletgui/RotatableCanvas.java         | 1263 +--
 src/jalview/appletgui/ScalePanel.java              |  910 +-
 src/jalview/appletgui/SeqCanvas.java               | 1643 ++--
 src/jalview/appletgui/SeqPanel.java                |  433 +-
 src/jalview/appletgui/SequenceRenderer.java        |  673 +-
 src/jalview/appletgui/SliderPanel.java             |  740 +-
 src/jalview/appletgui/Tooltip.java                 |   57 +-
 src/jalview/appletgui/TreeCanvas.java              |  203 +-
 src/jalview/appletgui/TreePanel.java               |  140 +-
 src/jalview/appletgui/UserDefinedColours.java      | 1195 +--
 src/jalview/bin/Cache.java                         |  330 +-
 src/jalview/bin/Jalview.java                       |  226 +-
 src/jalview/bin/JalviewLite.java                   |   50 +-
 src/jalview/binding/Alignment.java                 |  332 +-
 src/jalview/binding/Annotation.java                |  864 +-
 src/jalview/binding/AnnotationElement.java         |  579 +-
 src/jalview/binding/Colour.java                    |  331 +-
 src/jalview/binding/Feature.java                   |  577 +-
 src/jalview/binding/FeatureSettings.java           |  493 +-
 src/jalview/binding/Features.java                  |  205 +-
 src/jalview/binding/JGroup.java                    | 1484 ++--
 src/jalview/binding/JSeq.java                      | 1253 +--
 src/jalview/binding/JalviewModel.java              |  436 +-
 src/jalview/binding/JalviewModelSequence.java      | 1862 +++--
 src/jalview/binding/JalviewUserColours.java        |  584 +-
 src/jalview/binding/Pdbentry.java                  |  643 +-
 src/jalview/binding/PdbentryItem.java              |  367 +-
 src/jalview/binding/Pdbids.java                    |  205 +-
 src/jalview/binding/Property.java                  |  332 +-
 src/jalview/binding/Sequence.java                  |  205 +-
 src/jalview/binding/SequenceSet.java               | 1037 +--
 src/jalview/binding/SequenceType.java              |  383 +-
 src/jalview/binding/Setting.java                   |  495 +-
 src/jalview/binding/Tree.java                      | 1648 ++--
 src/jalview/binding/UserColourScheme.java          |  206 +-
 src/jalview/binding/UserColours.java               |  333 +-
 src/jalview/binding/VAMSAS.java                    | 1168 +--
 src/jalview/binding/VamsasModel.java               |  204 +-
 src/jalview/binding/Viewport.java                  | 2880 +++----
 src/jalview/commands/ChangeCaseCommand.java        |   37 +-
 src/jalview/commands/CommandI.java                 |   10 +-
 src/jalview/commands/EditCommand.java              |  505 +-
 src/jalview/commands/OrderCommand.java             |   20 +-
 src/jalview/commands/RemoveGapColCommand.java      |   65 +-
 src/jalview/commands/RemoveGapsCommand.java        |   60 +-
 src/jalview/commands/SlideSequencesCommand.java    |   55 +-
 src/jalview/commands/TrimRegionCommand.java        |   48 +-
 src/jalview/datamodel/AlignedCodonFrame.java       |  204 +-
 src/jalview/datamodel/Alignment.java               |  261 +-
 src/jalview/datamodel/AlignmentAnnotation.java     |  315 +-
 src/jalview/datamodel/AlignmentI.java              |  195 +-
 src/jalview/datamodel/AlignmentOrder.java          |  665 +-
 src/jalview/datamodel/AlignmentView.java           | 1053 +--
 src/jalview/datamodel/Annotation.java              |   67 +-
 src/jalview/datamodel/BinaryNode.java              |  585 +-
 src/jalview/datamodel/BinarySequence.java          |   46 +-
 src/jalview/datamodel/CigarArray.java              |   89 +-
 src/jalview/datamodel/CigarBase.java               |  571 +-
 src/jalview/datamodel/CigarCigar.java              |  121 +-
 src/jalview/datamodel/CigarSimple.java             |   96 +-
 src/jalview/datamodel/ColumnSelection.java         |  323 +-
 src/jalview/datamodel/DBRefEntry.java              |  188 +-
 src/jalview/datamodel/DBRefSource.java             |  231 +-
 src/jalview/datamodel/FeatureProperties.java       |   33 +-
 src/jalview/datamodel/GraphLine.java               |   20 +-
 src/jalview/datamodel/HiddenSequences.java         |   30 +-
 src/jalview/datamodel/Mapping.java                 |   90 +-
 src/jalview/datamodel/PDBEntry.java                |   47 +-
 src/jalview/datamodel/Provenance.java              |   95 +-
 src/jalview/datamodel/ProvenanceEntry.java         |  106 +-
 src/jalview/datamodel/SearchResults.java           |   54 +-
 src/jalview/datamodel/SeqCigar.java                |  370 +-
 src/jalview/datamodel/Sequence.java                |   19 +-
 src/jalview/datamodel/SequenceFeature.java         |   87 +-
 src/jalview/datamodel/SequenceGroup.java           |  228 +-
 src/jalview/datamodel/SequenceI.java               |  201 +-
 src/jalview/datamodel/SequenceNode.java            |   93 +-
 src/jalview/datamodel/SequencePoint.java           |   15 +-
 src/jalview/datamodel/UniprotEntry.java            |  191 +-
 src/jalview/datamodel/UniprotFile.java             |   72 +-
 src/jalview/datamodel/UniprotProteinName.java      |   10 +-
 src/jalview/datamodel/UniprotSequence.java         |   92 +-
 src/jalview/datamodel/xdb/embl/BasePosition.java   |   84 +-
 src/jalview/datamodel/xdb/embl/EmblEntry.java      |  151 +-
 src/jalview/datamodel/xdb/embl/EmblError.java      |   50 +-
 src/jalview/datamodel/xdb/embl/EmblFeature.java    |  151 +-
 .../datamodel/xdb/embl/EmblFeatureLocElement.java  |  183 +-
 .../datamodel/xdb/embl/EmblFeatureLocations.java   |  241 +-
 src/jalview/datamodel/xdb/embl/EmblFile.java       |  211 +-
 src/jalview/datamodel/xdb/embl/EmblSequence.java   |  116 +-
 src/jalview/datamodel/xdb/embl/Qualifier.java      |  160 +-
 src/jalview/gui/AlignFrame.java                    | 3067 +++----
 src/jalview/gui/AlignViewport.java                 | 2999 +++----
 src/jalview/gui/AlignmentPanel.java                |  506 +-
 src/jalview/gui/AnnotationColourChooser.java       | 1041 +--
 src/jalview/gui/AnnotationExporter.java            |  117 +-
 src/jalview/gui/AnnotationLabels.java              |  234 +-
 src/jalview/gui/AnnotationPanel.java               |  640 +-
 src/jalview/gui/AppJmol.java                       |  438 +-
 src/jalview/gui/CutAndPasteTransfer.java           |  525 +-
 src/jalview/gui/DasSourceBrowser.java              |  280 +-
 src/jalview/gui/Desktop.java                       |  794 +-
 src/jalview/gui/EPSOptions.java                    |  292 +-
 src/jalview/gui/EditNameDialog.java                |  164 +-
 src/jalview/gui/FeatureRenderer.java               |  544 +-
 src/jalview/gui/FeatureSettings.java               |  586 +-
 src/jalview/gui/Finder.java                        |   93 +-
 src/jalview/gui/FontChooser.java                   |  530 +-
 src/jalview/gui/IProgressIndicator.java            |   35 +-
 src/jalview/gui/IdCanvas.java                      |  966 +--
 src/jalview/gui/IdPanel.java                       |  170 +-
 src/jalview/gui/IdwidthAdjuster.java               |  333 +-
 src/jalview/gui/Jalview2XML.java                   |  462 +-
 src/jalview/gui/Jalview2XML_V1.java                |  230 +-
 src/jalview/gui/OOMWarning.java                    |   79 +
 src/jalview/gui/OverviewPanel.java                 |  905 +-
 src/jalview/gui/PCAPanel.java                      |  190 +-
 src/jalview/gui/PaintRefresher.java                |  487 +-
 src/jalview/gui/PairwiseAlignPanel.java            |   68 +-
 src/jalview/gui/PopupMenu.java                     |  622 +-
 src/jalview/gui/Preferences.java                   |  295 +-
 src/jalview/gui/RedundancyPanel.java               |   85 +-
 src/jalview/gui/RotatableCanvas.java               | 1587 ++--
 src/jalview/gui/ScalePanel.java                    |  137 +-
 src/jalview/gui/ScriptWindow.java                  | 1346 +--
 src/jalview/gui/SeqCanvas.java                     |  378 +-
 src/jalview/gui/SeqPanel.java                      |  495 +-
 src/jalview/gui/SequenceFetcher.java               |   96 +-
 src/jalview/gui/SequenceRenderer.java              |  906 +-
 src/jalview/gui/SliderPanel.java                   |  732 +-
 src/jalview/gui/SplashScreen.java                  |  123 +-
 src/jalview/gui/TextColourChooser.java             |  422 +-
 src/jalview/gui/TreeCanvas.java                    |  414 +-
 src/jalview/gui/TreePanel.java                     |  272 +-
 src/jalview/gui/UserDefinedColours.java            |  270 +-
 src/jalview/gui/UserQuestionnaireCheck.java        |   89 +-
 src/jalview/gui/VamsasApplication.java             |  104 +-
 src/jalview/gui/WebserviceInfo.java                |   10 +-
 src/jalview/io/AMSAFile.java                       |  199 +-
 src/jalview/io/AlignFile.java                      |  108 +-
 src/jalview/io/AnnotationFile.java                 |  336 +-
 src/jalview/io/AppletFormatAdapter.java            |  268 +-
 src/jalview/io/BLCFile.java                        |  139 +-
 src/jalview/io/ClansFile.java                      |   20 +-
 src/jalview/io/ClustalFile.java                    |   56 +-
 src/jalview/io/DBRefFile.java                      |   24 +-
 src/jalview/io/FastaFile.java                      |   94 +-
 src/jalview/io/FeaturesFile.java                   |   49 +-
 src/jalview/io/FileLoader.java                     |   77 +-
 src/jalview/io/FileParse.java                      |  282 +-
 src/jalview/io/FormatAdapter.java                  |  162 +-
 src/jalview/io/HTMLOutput.java                     |  773 +-
 src/jalview/io/IdentifyFile.java                   |  168 +-
 src/jalview/io/JPredFile.java                      |  220 +-
 src/jalview/io/JalviewFileChooser.java             |   95 +-
 src/jalview/io/JalviewFileFilter.java              |  345 +-
 src/jalview/io/JalviewFileView.java                |  222 +-
 src/jalview/io/JnetAnnotationMaker.java            |  143 +-
 src/jalview/io/MSFfile.java                        |  128 +-
 src/jalview/io/MatrixFile.java                     |   39 +-
 src/jalview/io/ModellerDescription.java            |  799 +-
 src/jalview/io/NewickFile.java                     |   56 +-
 src/jalview/io/PIRFile.java                        |   43 +-
 src/jalview/io/PfamFile.java                       |   42 +-
 src/jalview/io/PileUpfile.java                     |   78 +-
 src/jalview/io/StockholmFile.java                  |   63 +-
 src/jalview/io/VamsasAppDatastore.java             |   75 +-
 src/jalview/io/WSWUBlastClient.java                |  609 +-
 src/jalview/io/vamsas/DatastoreItem.java           |  111 +-
 src/jalview/io/vamsas/Dbref.java                   |   99 +-
 src/jalview/io/vamsas/LocalDocSyncObject.java      |   68 +-
 src/jalview/io/vamsas/Rangetype.java               |  131 +-
 src/jalview/io/vamsas/Sequencemapping.java         |  315 +-
 src/jalview/io/vamsas/Tree.java                    |   42 +-
 src/jalview/jbgui/GAlignFrame.java                 |  786 +-
 src/jalview/jbgui/GAlignmentPanel.java             |  234 +-
 src/jalview/jbgui/GCutAndPasteTransfer.java        |  444 +-
 src/jalview/jbgui/GDasSourceBrowser.java           |  109 +-
 src/jalview/jbgui/GDesktop.java                    |  175 +-
 src/jalview/jbgui/GFinder.java                     |   42 +-
 src/jalview/jbgui/GFontChooser.java                |  526 +-
 src/jalview/jbgui/GPCAPanel.java                   |  527 +-
 src/jalview/jbgui/GPairwiseAlignPanel.java         |  184 +-
 src/jalview/jbgui/GPreferences.java                | 1207 +--
 src/jalview/jbgui/GSequenceLink.java               |   57 +-
 src/jalview/jbgui/GSliderPanel.java                |  402 +-
 src/jalview/jbgui/GStructureViewer.java            |  666 +-
 src/jalview/jbgui/GTreePanel.java                  |  511 +-
 src/jalview/jbgui/GUserDefinedColours.java         |  536 +-
 src/jalview/jbgui/GWebserviceInfo.java             |  240 +-
 src/jalview/math/Matrix.java                       | 1708 ++--
 src/jalview/math/RotatableMatrix.java              |  675 +-
 src/jalview/schemabinding/version2/AlcodMap.java   |  359 +-
 src/jalview/schemabinding/version2/Alcodon.java    |  521 +-
 .../schemabinding/version2/AlcodonFrame.java       |  861 +-
 src/jalview/schemabinding/version2/Annotation.java | 1561 ++--
 .../schemabinding/version2/AnnotationColours.java  |  723 +-
 .../schemabinding/version2/AnnotationElement.java  |  679 +-
 src/jalview/schemabinding/version2/Colour.java     |  332 +-
 src/jalview/schemabinding/version2/DBRef.java      |  435 +-
 src/jalview/schemabinding/version2/Feature.java    | 1052 +--
 .../schemabinding/version2/FeatureSettings.java    |  857 +-
 src/jalview/schemabinding/version2/Features.java   |  205 +-
 src/jalview/schemabinding/version2/Group.java      |  398 +-
 .../schemabinding/version2/HiddenColumns.java      |  426 +-
 src/jalview/schemabinding/version2/JGroup.java     | 1772 ++--
 src/jalview/schemabinding/version2/JSeq.java       | 1664 ++--
 .../schemabinding/version2/JalviewModel.java       |  439 +-
 .../version2/JalviewModelSequence.java             | 1896 +++--
 .../schemabinding/version2/JalviewUserColours.java |  587 +-
 .../schemabinding/version2/MapListFrom.java        |  426 +-
 src/jalview/schemabinding/version2/MapListTo.java  |  426 +-
 .../schemabinding/version2/MapListType.java        | 1162 +--
 src/jalview/schemabinding/version2/Mapping.java    |  317 +-
 .../schemabinding/version2/MappingChoice.java      |  335 +-
 src/jalview/schemabinding/version2/OtherData.java  |  334 +-
 src/jalview/schemabinding/version2/Pdbentry.java   |  700 +-
 .../schemabinding/version2/PdbentryItem.java       |  375 +-
 src/jalview/schemabinding/version2/Pdbids.java     |  510 +-
 src/jalview/schemabinding/version2/Property.java   |  334 +-
 src/jalview/schemabinding/version2/Sequence.java   |  608 +-
 .../schemabinding/version2/SequenceSet.java        | 1664 ++--
 .../version2/SequenceSetProperties.java            |  336 +-
 .../schemabinding/version2/SequenceType.java       |  436 +-
 src/jalview/schemabinding/version2/Setting.java    |  592 +-
 .../schemabinding/version2/StructureState.java     |  794 +-
 .../schemabinding/version2/ThresholdLine.java      |  477 +-
 src/jalview/schemabinding/version2/Tree.java       | 1649 ++--
 .../schemabinding/version2/UserColourScheme.java   |  209 +-
 .../schemabinding/version2/UserColours.java        |  335 +-
 src/jalview/schemabinding/version2/VAMSAS.java     |  846 +-
 .../schemabinding/version2/VamsasModel.java        |  205 +-
 src/jalview/schemabinding/version2/Viewport.java   | 3538 ++++----
 .../version2/descriptors/AlcodMapDescriptor.java   |  438 +-
 .../version2/descriptors/AlcodonDescriptor.java    |  528 +-
 .../descriptors/AlcodonFrameDescriptor.java        |  467 +-
 .../descriptors/AnnotationColoursDescriptor.java   |  812 +-
 .../version2/descriptors/AnnotationDescriptor.java | 1432 ++--
 .../descriptors/AnnotationElementDescriptor.java   |  812 +-
 .../version2/descriptors/ColourDescriptor.java     |  434 +-
 .../version2/descriptors/DBRefDescriptor.java      |  590 +-
 .../version2/descriptors/FeatureDescriptor.java    |  987 ++-
 .../descriptors/FeatureSettingsDescriptor.java     |  466 +-
 .../version2/descriptors/FeaturesDescriptor.java   |  282 +-
 .../version2/descriptors/GroupDescriptor.java      |  449 +-
 .../descriptors/HiddenColumnsDescriptor.java       |  462 +-
 .../version2/descriptors/JGroupDescriptor.java     | 1584 ++--
 .../version2/descriptors/JSeqDescriptor.java       | 1046 +--
 .../descriptors/JalviewModelDescriptor.java        |  611 +-
 .../JalviewModelSequenceDescriptor.java            |  826 +-
 .../descriptors/JalviewUserColoursDescriptor.java  |  453 +-
 .../descriptors/MapListFromDescriptor.java         |  464 +-
 .../version2/descriptors/MapListToDescriptor.java  |  464 +-
 .../descriptors/MapListTypeDescriptor.java         |  660 +-
 .../descriptors/MappingChoiceDescriptor.java       |  447 +-
 .../version2/descriptors/MappingDescriptor.java    |  379 +-
 .../version2/descriptors/OtherDataDescriptor.java  |  440 +-
 .../version2/descriptors/PdbentryDescriptor.java   |  613 +-
 .../descriptors/PdbentryItemDescriptor.java        |  394 +-
 .../version2/descriptors/PdbidsDescriptor.java     |  397 +-
 .../version2/descriptors/PropertyDescriptor.java   |  440 +-
 .../version2/descriptors/SequenceDescriptor.java   |  455 +-
 .../descriptors/SequenceSetDescriptor.java         |  825 +-
 .../SequenceSetPropertiesDescriptor.java           |  446 +-
 .../descriptors/SequenceTypeDescriptor.java        |  600 +-
 .../version2/descriptors/SettingDescriptor.java    |  641 +-
 .../descriptors/StructureStateDescriptor.java      |  823 +-
 .../descriptors/ThresholdLineDescriptor.java       |  524 +-
 .../version2/descriptors/TreeDescriptor.java       | 1649 ++--
 .../descriptors/UserColourSchemeDescriptor.java    |  283 +-
 .../descriptors/UserColoursDescriptor.java         |  436 +-
 .../version2/descriptors/VAMSASDescriptor.java     |  478 +-
 .../descriptors/VamsasModelDescriptor.java         |  282 +-
 .../version2/descriptors/ViewportDescriptor.java   | 3206 +++----
 src/jalview/schemes/AnnotationColourGradient.java  |  457 +-
 src/jalview/schemes/Blosum62ColourScheme.java      |  183 +-
 src/jalview/schemes/BuriedColourScheme.java        |  104 +-
 src/jalview/schemes/ClustalxColourScheme.java      |  178 +-
 src/jalview/schemes/ColourSchemeI.java             |   86 +-
 src/jalview/schemes/ColourSchemeProperty.java      |   12 +-
 src/jalview/schemes/Consensus.java                 |   32 +-
 src/jalview/schemes/HelixColourScheme.java         |   71 +-
 src/jalview/schemes/HydrophobicColourScheme.java   |  104 +-
 src/jalview/schemes/NucleotideColourScheme.java    |  175 +-
 src/jalview/schemes/PIDColourScheme.java           |  187 +-
 src/jalview/schemes/ResidueColourScheme.java       |  552 +-
 src/jalview/schemes/ResidueProperties.java         |  577 +-
 src/jalview/schemes/ScoreColourScheme.java         |  247 +-
 src/jalview/schemes/ScoreMatrix.java               |   36 +-
 src/jalview/schemes/StrandColourScheme.java        |  104 +-
 src/jalview/schemes/TaylorColourScheme.java        |   55 +-
 src/jalview/schemes/TurnColourScheme.java          |  104 +-
 src/jalview/schemes/UserColourScheme.java          |   37 +-
 src/jalview/schemes/ZappoColourScheme.java         |   15 +-
 src/jalview/structure/SequenceListener.java        |   10 +-
 src/jalview/structure/StructureListener.java       |   66 +-
 src/jalview/structure/StructureMapping.java        |  199 +-
 .../structure/StructureSelectionManager.java       |   14 +-
 src/jalview/structure/VamsasListener.java          |   18 +
 src/jalview/util/BrowserLauncher.java              | 1821 ++--
 src/jalview/util/Comparison.java                   |  462 +-
 src/jalview/util/DBRefUtils.java                   |  526 +-
 src/jalview/util/Format.java                       | 1809 ++--
 src/jalview/util/ImageMaker.java                   |  376 +-
 src/jalview/util/MapList.java                      |   51 +-
 src/jalview/util/Platform.java                     |   24 +-
 src/jalview/util/QuickSort.java                    |   31 +-
 src/jalview/util/ShiftList.java                    |   47 +-
 src/jalview/util/TableSorter.java                  |  184 +-
 src/jalview/util/UrlLink.java                      |   20 +-
 src/jalview/ws/DBRefFetcher.java                   |   65 +-
 src/jalview/ws/DasSequenceFeatureFetcher.java      |  181 +-
 src/jalview/ws/Discoverer.java                     |  314 +-
 src/jalview/ws/JPredClient.java                    |  241 +-
 src/jalview/ws/JPredThread.java                    |  375 +-
 src/jalview/ws/MsaWSClient.java                    |  141 +-
 src/jalview/ws/MsaWSThread.java                    | 1435 ++--
 src/jalview/ws/SeqSearchWSClient.java              |  610 +-
 src/jalview/ws/SeqSearchWSThread.java              | 1346 +--
 src/jalview/ws/SequenceFetcher.java                |  153 +-
 src/jalview/ws/WSClient.java                       |   93 +-
 src/jalview/ws/WSClientI.java                      |   23 +-
 src/jalview/ws/WSThread.java                       |  929 ++-
 src/jalview/ws/dbsources/DasSequenceSource.java    |  100 +-
 .../ws/dbsources/EbiFileRetrievedProxy.java        |   31 +-
 src/jalview/ws/dbsources/EmblCdsSouce.java         |   36 +-
 src/jalview/ws/dbsources/EmblSource.java           |   54 +-
 src/jalview/ws/dbsources/EmblXmlSource.java        |  149 +-
 src/jalview/ws/dbsources/GeneDbSource.java         |   20 +-
 src/jalview/ws/dbsources/Pdb.java                  |   86 +-
 src/jalview/ws/dbsources/Pfam.java                 |  121 +-
 src/jalview/ws/dbsources/PfamFull.java             |   31 +-
 src/jalview/ws/dbsources/PfamSeed.java             |   32 +-
 src/jalview/ws/dbsources/Uniprot.java              |   75 +-
 src/jalview/ws/dbsources/UnprotName.java           |   33 +-
 .../dbsources/das/DasSequenceSourceListener.java   |   94 +-
 src/jalview/ws/ebi/EBIFetchClient.java             |  475 +-
 src/jalview/ws/seqfetcher/ASequenceFetcher.java    |   70 +-
 src/jalview/ws/seqfetcher/DbSourceProxy.java       |   80 +-
 src/jalview/ws/seqfetcher/DbSourceProxyImpl.java   |   58 +-
 .../biojava/dasobert/das/DAS_FeatureRetrieve.java  |  171 +-
 .../biojava/dasobert/das/DAS_Feature_Handler.java  |  262 +-
 .../biojava/dasobert/das/DAS_Sequence_Handler.java |  240 +-
 src/org/biojava/dasobert/das/FeatureThread.java    |   43 +-
 src/org/biojava/dasobert/das/SequenceThread.java   |  447 +-
 src/org/biojava/dasobert/das2/Das2Capability.java  |    5 +-
 .../biojava/dasobert/das2/Das2CapabilityImpl.java  |    9 +-
 src/org/biojava/dasobert/das2/Das2Source.java      |   12 +-
 src/org/biojava/dasobert/das2/Das2SourceImpl.java  |   18 +-
 .../biojava/dasobert/das2/DasSourceConverter.java  |   23 +-
 .../dasobert/das2/io/DAS2SourceHandler.java        |   60 +-
 .../dasobert/das2/io/DasSourceReaderImpl.java      |   51 +-
 .../biojava/dasobert/dasregistry/Das1Source.java   |  124 +-
 .../dasregistry/DasCoordSysComparator.java         |   22 +-
 .../dasobert/dasregistry/DasCoordinateSystem.java  |   38 +-
 .../biojava/dasobert/dasregistry/DasSource.java    |   65 +-
 .../dasobert/dasregistry/DasSourceComparator.java  |   69 +-
 .../dasobert/eventmodel/AbstractDasEvent.java      |   23 +-
 .../biojava/dasobert/eventmodel/FeatureEvent.java  |   52 +-
 .../dasobert/eventmodel/FeatureListener.java       |   17 +-
 .../dasobert/eventmodel/ObjectListener.java        |   18 +-
 .../biojava/dasobert/eventmodel/SequenceEvent.java |   19 +-
 .../dasobert/eventmodel/SequenceListener.java      |   40 +-
 .../dasobert/feature/AbstractFeatureTrack.java     |  410 +-
 .../biojava/dasobert/feature/AbstractSegment.java  |  363 +-
 .../dasobert/feature/FeatureComparator.java        |   76 +-
 .../dasobert/feature/FeatureMapComparator.java     |   59 +-
 src/org/biojava/dasobert/feature/FeatureTrack.java |  176 +-
 .../dasobert/feature/FeatureTrackConverter.java    |  924 +-
 .../biojava/dasobert/feature/FeatureTrackImpl.java |   67 +-
 .../biojava/dasobert/feature/HistogramFeature.java |  135 +-
 .../biojava/dasobert/feature/HistogramSegment.java |   70 +-
 src/org/biojava/dasobert/feature/Segment.java      |   72 +-
 .../dasobert/feature/SegmentComparator.java        |   30 +-
 src/org/biojava/dasobert/feature/SegmentImpl.java  |   97 +-
 src/org/jibble/epsgraphics/EpsDocument.java        |  533 +-
 src/org/jibble/epsgraphics/EpsException.java       |   53 +-
 src/org/jibble/epsgraphics/EpsGraphics2D.java      | 2887 ++++---
 src/uk/ac/ebi/picr/model/CrossReference.java       |  580 +-
 .../ac/ebi/picr/model/CrossReference_Helper.java   |  180 +-
 src/uk/ac/ebi/picr/model/UPEntry.java              |  493 +-
 src/uk/ac/ebi/picr/model/UPEntry_Helper.java       |  148 +-
 src/uk/ac/ebi/www/Data.java                        |   51 +-
 src/uk/ac/ebi/www/InputParams.java                 |  145 +-
 src/uk/ac/ebi/www/WSFile.java                      |   51 +-
 src/uk/ac/ebi/www/WSWUBlast.java                   |   18 +-
 src/uk/ac/ebi/www/WSWUBlastService.java            |    7 +-
 src/uk/ac/ebi/www/WSWUBlastServiceLocator.java     |   59 +-
 src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java    |  267 +-
 .../AccessionMapperBindingStub.java                |  588 +-
 .../AccessionMapperInterface.java                  |   18 +-
 .../AccessionMapperService.java                    |   11 +-
 .../AccessionMapperServiceLocator.java             |  275 +-
 src/vamsas/IMsaWS.java                             |   23 +-
 src/vamsas/objects/simple/Alignment.java           |  281 +-
 src/vamsas/objects/simple/Alignment_Helper.java    |  128 +-
 src/vamsas/objects/simple/JpredResult.java         |   56 +-
 src/vamsas/objects/simple/JpredResult_Helper.java  |   56 +-
 src/vamsas/objects/simple/MsaResult.java           |  251 +-
 src/vamsas/objects/simple/MsaResult_Helper.java    |  165 +-
 src/vamsas/objects/simple/Msfalignment.java        |   55 +-
 src/vamsas/objects/simple/Msfalignment_Helper.java |   56 +-
 src/vamsas/objects/simple/Object.java              |   86 +-
 src/vamsas/objects/simple/Object_Helper.java       |   95 +-
 src/vamsas/objects/simple/Result.java              |  658 +-
 src/vamsas/objects/simple/Result_Helper.java       |  216 +-
 src/vamsas/objects/simple/Secstructpred.java       |   43 +-
 .../objects/simple/Secstructpred_Helper.java       |   54 +-
 src/vamsas/objects/simple/SeqSearchResult.java     |  325 +-
 .../objects/simple/SeqSearchResult_Helper.java     |  139 +-
 src/vamsas/objects/simple/Sequence.java            |  190 +-
 src/vamsas/objects/simple/SequenceSet.java         |  152 +-
 src/vamsas/objects/simple/SequenceSet_Helper.java  |  106 +-
 src/vamsas/objects/simple/Sequence_Helper.java     |  117 +-
 src/vamsas/objects/simple/WsJobId.java             |  184 +-
 src/vamsas/objects/simple/WsJobId_Helper.java      |  117 +-
 utils/.cvsignore                                   |    1 +
 utils/help2Website.java                            |  208 +-
 567 files changed, 115183 insertions(+), 104310 deletions(-)
 create mode 100644 src/jalview/gui/OOMWarning.java
 create mode 100644 utils/.cvsignore

diff --git a/help/html/jalviewjnlp.html b/help/html/jalviewjnlp.html
index 9be4e4b..b966dcd 100755
--- a/help/html/jalviewjnlp.html
+++ b/help/html/jalviewjnlp.html
@@ -29,31 +29,31 @@
   &lt;resources&gt;
   &lt;!-- <em>the additional memory parameters are here</em> --&gt;
   &lt;j2se version="1.4+" initial-heap-size="500M" max-heap-size="1000M"/&gt;
-    &lt;jar href="http://www.jalview.org/webstart/jalview.jar" download="eager" main="false"/&gt;
-    &lt;jar href="http://www.jalview.org/webstart/activation.jar" download="eager" main="false"/&gt;
-    &lt;jar href="http://www.jalview.org/webstart/axis.jar" download="eager" main="false"/&gt;
-    &lt;jar href="http://www.jalview.org/webstart/castor-0.9.6-xml.jar" download="eager" main="false"/&gt;
-    &lt;jar href="http://www.jalview.org/webstart/commons-discovery.jar" download="eager" main="false"/&gt;
-    &lt;jar href="http://www.jalview.org/webstart/commons-logging.jar" download="eager" main="false"/&gt;
-    &lt;jar href="http://www.jalview.org/webstart/jaxrpc.jar" download="eager" main="false"/&gt;
-    &lt;jar href="http://www.jalview.org/webstart/jhall.jar" download="eager" main="false"/&gt;
-    &lt;jar href="http://www.jalview.org/webstart/log4j-1.2.8.jar" download="eager" main="false"/&gt;
-    &lt;jar href="http://www.jalview.org/webstart/mail.jar" download="eager" main="false"/&gt;
-    &lt;jar href="http://www.jalview.org/webstart/regex.jar" download="eager" main="false"/&gt;
-    &lt;jar href="http://www.jalview.org/webstart/saaj.jar" download="eager" main="false"/&gt;
-    &lt;jar href="http://www.jalview.org/webstart/wsdl4j.jar" download="eager" main="false"/&gt;
-    &lt;jar href="http://www.jalview.org/webstart/xercesImpl.jar" download="eager" main="false"/&gt;
-    &lt;jar href="http://www.jalview.org/webstart/xml-apis.jar" download="eager" main="false"/&gt;
-    &lt;property name="jalview.version" value="2.07"/&gt;
+    &lt;jar href="jalview.jar"/&gt;
+		&lt;jar href="Jmol-11.0.2.jar"/&gt;
+		&lt;jar href="activation.jar"/&gt;
+		&lt;jar href="axis.jar"/&gt;
+		&lt;jar href="castor-1.1-cycle-xml.jar"/&gt;
+		&lt;jar href="commons-discovery.jar"/&gt;
+		&lt;jar href="commons-logging.jar"/&gt;
+		&lt;jar href="jaxrpc.jar"/&gt;
+		&lt;jar href="jhall.jar"/&gt;
+		&lt;jar href="log4j-1.2.8.jar"/&gt;
+		&lt;jar href="mail.jar"/&gt;
+		&lt;jar href="regex.jar"/&gt;
+		&lt;jar href="saaj.jar"/&gt;
+		&lt;jar href="vamsas-client.jar"/&gt;
+		&lt;jar href="wsdl4j.jar"/&gt;
+		&lt;jar href="xercesImpl.jar"/&gt;
+		&lt;jar href="xml-apis.jar"/&gt;
+		&lt;property name="jalview.version" value="2.4"/&gt;
   &lt;/resources&gt;
   &lt;application-desc main-class="jalview.bin.Jalview"/&gt;
 &lt;/jnlp&gt;
 </pre>
 <address>
 <a
-href="mailto:help@{removeeveryother}.jalview.{removeeveryother}.org">jalview
-help</a>
+href="http://www.jalview.org/mailman/listinfo/jalview-discuss">If you have problems, send an email to jalview-discuss</a>
 </address>
 </body>
 </html>
-
diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
index 73ed7a7..390e20f 100755
--- a/src/MCview/AppletPDBCanvas.java
+++ b/src/MCview/AppletPDBCanvas.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -31,61 +31,102 @@ import jalview.datamodel.*;
 import jalview.appletgui.*;
 import jalview.structure.*;
 
-public class AppletPDBCanvas
-    extends Panel implements MouseListener, MouseMotionListener, StructureListener
+public class AppletPDBCanvas extends Panel implements MouseListener,
+        MouseMotionListener, StructureListener
 {
 
   MCMatrix idmat = new MCMatrix(3, 3);
+
   MCMatrix objmat = new MCMatrix(3, 3);
+
   boolean redrawneeded = true;
+
   int omx = 0;
+
   int mx = 0;
+
   int omy = 0;
+
   int my = 0;
+
   public PDBfile pdb;
+
   PDBEntry pdbentry;
+
   int bsize;
+
   Image img;
+
   Graphics ig;
+
   Dimension prefsize;
+
   float[] centre = new float[3];
+
   float[] width = new float[3];
+
   float maxwidth;
+
   float scale;
+
   String inStr;
+
   String inType;
+
   boolean bysequence = true;
+
   boolean depthcue = true;
+
   boolean wire = false;
+
   boolean bymolecule = false;
+
   boolean zbuffer = true;
+
   boolean dragging;
+
   int xstart;
+
   int xend;
+
   int ystart;
+
   int yend;
+
   int xmid;
+
   int ymid;
+
   Font font = new Font("Helvetica", Font.PLAIN, 10);
-  public SequenceI [] sequence;
+
+  public SequenceI[] sequence;
+
   final StringBuffer mappingDetails = new StringBuffer();
+
   String appletToolTip = null;
+
   int toolx, tooly;
+
   PDBChain mainchain;
+
   Vector highlightRes;
+
   boolean pdbAction = false;
+
   Bond highlightBond1, highlightBond2;
+
   boolean errorLoading = false;
+
   boolean seqColoursReady = false;
+
   FeatureRenderer fr;
+
   AlignmentPanel ap;
+
   StructureSelectionManager ssm;
 
-  public AppletPDBCanvas(PDBEntry pdbentry,
-                         SequenceI[] seq,
-                         String [] chains,
-                         AlignmentPanel ap,
-                         String protocol)
+  public AppletPDBCanvas(PDBEntry pdbentry, SequenceI[] seq,
+          String[] chains, AlignmentPanel ap, String protocol)
 
   {
     this.ap = ap;
@@ -94,13 +135,14 @@ public class AppletPDBCanvas
 
     ssm = StructureSelectionManager.getStructureSelectionManager();
 
-    try{
+    try
+    {
       pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol);
 
-      if(protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
-       pdbentry.setFile("INLINE"+pdb.id);
+      if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+        pdbentry.setFile("INLINE" + pdb.id);
 
-    }catch(Exception ex)
+    } catch (Exception ex)
     {
       ex.printStackTrace();
       return;
@@ -119,25 +161,24 @@ public class AppletPDBCanvas
     int seqstart = 0;
     int seqend = 0;
 
-    //JUST DEAL WITH ONE SEQUENCE FOR NOW
+    // JUST DEAL WITH ONE SEQUENCE FOR NOW
     SequenceI sequence = seq[0];
 
     for (int i = 0; i < pdb.chains.size(); i++)
     {
 
-      mappingDetails.append("\n\nPDB Sequence is :\nSequence = " +
-                            ( (PDBChain) pdb.chains.elementAt(i)).sequence.
-                            getSequenceAsString());
-      mappingDetails.append("\nNo of residues = " +
-                            ( (PDBChain) pdb.chains.elementAt(i)).residues.size() +
-                            "\n\n");
+      mappingDetails.append("\n\nPDB Sequence is :\nSequence = "
+              + ((PDBChain) pdb.chains.elementAt(i)).sequence
+                      .getSequenceAsString());
+      mappingDetails.append("\nNo of residues = "
+              + ((PDBChain) pdb.chains.elementAt(i)).residues.size()
+              + "\n\n");
 
       // Now lets compare the sequences to get
       // the start and end points.
       // Align the sequence to the pdb
-      AlignSeq as = new AlignSeq(sequence,
-                                 ( (PDBChain) pdb.chains.elementAt(i)).sequence,
-                                 "pep");
+      AlignSeq as = new AlignSeq(sequence, ((PDBChain) pdb.chains
+              .elementAt(i)).sequence, "pep");
       as.calcScoreMatrix();
       as.traceAlignment();
       PrintStream ps = new PrintStream(System.out)
@@ -164,7 +205,7 @@ public class AppletPDBCanvas
         pdbend = as.seq2end;
         seqstart = as.seq1start + sequence.getStart() - 1;
         seqend = as.seq1end + sequence.getEnd() - 1;
-       }
+      }
 
       mappingDetails.append("\nPDB start/end " + pdbstart + " " + pdbend);
       mappingDetails.append("\nSEQ start/end " + seqstart + " " + seqend);
@@ -177,12 +218,12 @@ public class AppletPDBCanvas
     mainchain.seqstart = seqstart;
     mainchain.seqend = seqend;
     mainchain.isVisible = true;
-  //  mainchain.makeExactMapping(maxAlignseq, sequence);
-  //  mainchain.transferRESNUMFeatures(sequence, null);
+    // mainchain.makeExactMapping(maxAlignseq, sequence);
+    // mainchain.transferRESNUMFeatures(sequence, null);
     this.pdb = pdb;
     this.prefsize = new Dimension(getSize().width, getSize().height);
 
-    //Initialize the matrices to identity
+    // Initialize the matrices to identity
     for (int i = 0; i < 3; i++)
     {
       for (int j = 0; j < 3; j++)
@@ -220,6 +261,7 @@ public class AppletPDBCanvas
   }
 
   Vector visiblebonds;
+
   void setupBonds()
   {
     seqColoursReady = false;
@@ -228,9 +270,9 @@ public class AppletPDBCanvas
 
     for (int ii = 0; ii < pdb.chains.size(); ii++)
     {
-      if ( ( (PDBChain) pdb.chains.elementAt(ii)).isVisible)
+      if (((PDBChain) pdb.chains.elementAt(ii)).isVisible)
       {
-        Vector tmp = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
+        Vector tmp = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
 
         for (int i = 0; i < tmp.size(); i++)
         {
@@ -249,9 +291,9 @@ public class AppletPDBCanvas
     float[] max = new float[3];
     float[] min = new float[3];
 
-    max[0] = (float) - 1e30;
-    max[1] = (float) - 1e30;
-    max[2] = (float) - 1e30;
+    max[0] = (float) -1e30;
+    max[1] = (float) -1e30;
+    max[2] = (float) -1e30;
 
     min[0] = (float) 1e30;
     min[1] = (float) 1e30;
@@ -259,9 +301,9 @@ public class AppletPDBCanvas
 
     for (int ii = 0; ii < pdb.chains.size(); ii++)
     {
-      if ( ( (PDBChain) pdb.chains.elementAt(ii)).isVisible)
+      if (((PDBChain) pdb.chains.elementAt(ii)).isVisible)
       {
-        Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
+        Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
 
         for (int i = 0; i < bonds.size(); i++)
         {
@@ -386,25 +428,25 @@ public class AppletPDBCanvas
 
     int bsize = 0;
 
-    //Find centre coordinate
+    // Find centre coordinate
     for (int ii = 0; ii < pdb.chains.size(); ii++)
     {
-      if ( ( (PDBChain) pdb.chains.elementAt(ii)).isVisible)
+      if (((PDBChain) pdb.chains.elementAt(ii)).isVisible)
       {
-        Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
+        Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
 
         bsize += bonds.size();
 
         for (int i = 0; i < bonds.size(); i++)
         {
-          xtot = xtot + ( (Bond) bonds.elementAt(i)).start[0] +
-              ( (Bond) bonds.elementAt(i)).end[0];
+          xtot = xtot + ((Bond) bonds.elementAt(i)).start[0]
+                  + ((Bond) bonds.elementAt(i)).end[0];
 
-          ytot = ytot + ( (Bond) bonds.elementAt(i)).start[1] +
-              ( (Bond) bonds.elementAt(i)).end[1];
+          ytot = ytot + ((Bond) bonds.elementAt(i)).start[1]
+                  + ((Bond) bonds.elementAt(i)).end[1];
 
-          ztot = ztot + ( (Bond) bonds.elementAt(i)).start[2] +
-              ( (Bond) bonds.elementAt(i)).end[2];
+          ztot = ztot + ((Bond) bonds.elementAt(i)).start[2]
+                  + ((Bond) bonds.elementAt(i)).end[2];
         }
       }
     }
@@ -435,10 +477,10 @@ public class AppletPDBCanvas
       return;
     }
 
-    //Only create the image at the beginning -
-    //this saves much memory usage
-    if ( (img == null) || (prefsize.width != getSize().width) ||
-        (prefsize.height != getSize().height))
+    // Only create the image at the beginning -
+    // this saves much memory usage
+    if ((img == null) || (prefsize.width != getSize().width)
+            || (prefsize.height != getSize().height))
     {
 
       try
@@ -451,8 +493,7 @@ public class AppletPDBCanvas
         ig = img.getGraphics();
 
         redrawneeded = true;
-      }
-      catch (Exception ex)
+      } catch (Exception ex)
       {
         ex.printStackTrace();
       }
@@ -490,8 +531,6 @@ public class AppletPDBCanvas
     repaint();
   }
 
-
-
   // This method has been taken out of PDBChain to allow
   // Applet and Application specific sequence renderers to be used
   void colourBySequence()
@@ -536,7 +575,7 @@ public class AppletPDBCanvas
             {
               if (mapping[m].getSequence() == sequence[s])
               {
-                int pos = mapping[m].getSeqPos(tmp.at1.resNumber)-1;
+                int pos = mapping[m].getSeqPos(tmp.at1.resNumber) - 1;
                 if (pos > 0)
                 {
                   pos = sequence[s].findIndex(pos);
@@ -544,11 +583,10 @@ public class AppletPDBCanvas
                   if (showFeatures)
                   {
                     tmp.startCol = fr.findFeatureColour(tmp.startCol,
-                                                        sequence[s],
-                                                        pos);
+                            sequence[s], pos);
                   }
                 }
-                pos = mapping[m].getSeqPos(tmp.at2.resNumber)-1;
+                pos = mapping[m].getSeqPos(tmp.at2.resNumber) - 1;
                 if (pos > 0)
                 {
                   pos = sequence[s].findIndex(pos);
@@ -556,8 +594,7 @@ public class AppletPDBCanvas
                   if (showFeatures)
                   {
                     tmp.endCol = fr.findFeatureColour(tmp.endCol,
-                                                        sequence[s],
-                                                        pos);
+                            sequence[s], pos);
                   }
                 }
 
@@ -570,6 +607,7 @@ public class AppletPDBCanvas
   }
 
   Zsort zsort;
+
   public void drawScene(Graphics g)
   {
     if (zbuffer)
@@ -587,15 +625,11 @@ public class AppletPDBCanvas
     {
       tmpBond = (Bond) visiblebonds.elementAt(i);
 
-      xstart = (int) ( ( (tmpBond.start[0] - centre[0]) * scale) +
-                      (getSize().width / 2));
-      ystart = (int) ( ( (centre[1] - tmpBond.start[1] ) * scale) +
-                      (getSize().height / 2));
+      xstart = (int) (((tmpBond.start[0] - centre[0]) * scale) + (getSize().width / 2));
+      ystart = (int) (((centre[1] - tmpBond.start[1]) * scale) + (getSize().height / 2));
 
-      xend = (int) ( ( (tmpBond.end[0] - centre[0]) * scale) +
-                    (getSize().width / 2));
-      yend = (int) ( ( (centre[1] - tmpBond.end[1] ) * scale) +
-                    (getSize().height / 2));
+      xend = (int) (((tmpBond.end[0] - centre[0]) * scale) + (getSize().width / 2));
+      yend = (int) (((centre[1] - tmpBond.end[1]) * scale) + (getSize().height / 2));
 
       xmid = (xend + xstart) / 2;
       ymid = (yend + ystart) / 2;
@@ -677,7 +711,7 @@ public class AppletPDBCanvas
   {
     if (!wire)
     {
-      if ( ( (float) Math.abs(y2 - y1) / (float) Math.abs(x2 - x1)) < 0.5)
+      if (((float) Math.abs(y2 - y1) / (float) Math.abs(x2 - x1)) < 0.5)
       {
         g.drawLine(x1, y1, x2, y2);
         g.drawLine(x1 + 1, y1 + 1, x2 + 1, y2 + 1);
@@ -793,13 +827,14 @@ public class AppletPDBCanvas
       toolx = e.getX();
       tooly = e.getY();
 
-      appletToolTip = chain.id + ":" + fatom.resNumber + " " + fatom.resName;
+      appletToolTip = chain.id + ":" + fatom.resNumber + " "
+              + fatom.resName;
       redrawneeded = true;
       repaint();
     }
     else
     {
-      mouseOverStructure(-1, chain!=null?chain.id:null);
+      mouseOverStructure(-1, chain != null ? chain.id : null);
       appletToolTip = null;
       redrawneeded = true;
       repaint();
@@ -828,33 +863,33 @@ public class AppletPDBCanvas
     MCMatrix objmat = new MCMatrix(3, 3);
     objmat.setIdentity();
 
-    if ( (evt.getModifiers() & Event.META_MASK) != 0)
+    if ((evt.getModifiers() & Event.META_MASK) != 0)
     {
-      objmat.rotatez( (float) ( (mx - omx)));
+      objmat.rotatez((float) ((mx - omx)));
     }
     else
     {
-      objmat.rotatex( (float) ( (omy - my)));
-      objmat.rotatey( (float) ( (omx - mx)));
+      objmat.rotatex((float) ((omy - my)));
+      objmat.rotatey((float) ((omx - mx)));
     }
 
-    //Alter the bonds
+    // Alter the bonds
     for (int ii = 0; ii < pdb.chains.size(); ii++)
     {
-      Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
+      Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
 
       for (int i = 0; i < bonds.size(); i++)
       {
         Bond tmpBond = (Bond) bonds.elementAt(i);
 
-        //Translate the bond so the centre is 0,0,0
-        tmpBond.translate( -centre[0], -centre[1], -centre[2]);
+        // Translate the bond so the centre is 0,0,0
+        tmpBond.translate(-centre[0], -centre[1], -centre[2]);
 
-        //Now apply the rotation matrix
+        // Now apply the rotation matrix
         tmpBond.start = objmat.vectorMultiply(tmpBond.start);
         tmpBond.end = objmat.vectorMultiply(tmpBond.end);
 
-        //Now translate back again
+        // Now translate back again
         tmpBond.translate(centre[0], centre[1], centre[2]);
       }
     }
@@ -886,7 +921,7 @@ public class AppletPDBCanvas
 
       if (chain.isVisible)
       {
-        Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
+        Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
 
         for (int i = 0; i < bonds.size(); i++)
         {
@@ -913,10 +948,8 @@ public class AppletPDBCanvas
 
     if (n == 1)
     {
-      int xstart = (int) ( ( (b.start[0] - centre[0]) * scale) +
-                          (getSize().width / 2));
-      int ystart = (int) ( ( (centre[1] - b.start[1]) * scale) +
-                          (getSize().height / 2));
+      int xstart = (int) (((b.start[0] - centre[0]) * scale) + (getSize().width / 2));
+      int ystart = (int) (((centre[1] - b.start[1]) * scale) + (getSize().height / 2));
 
       g.setColor(Color.red);
       g.drawString(b.at1.resName + "-" + b.at1.resNumber, xstart, ystart);
@@ -924,10 +957,8 @@ public class AppletPDBCanvas
 
     if (n == 2)
     {
-      int xstart = (int) ( ( (b.end[0] - centre[0]) * scale) +
-                          (getSize().width / 2));
-      int ystart = (int) ( ( (centre[1] - b.end[1]) * scale) +
-                          (getSize().height / 2));
+      int xstart = (int) (((b.end[0] - centre[0]) * scale) + (getSize().width / 2));
+      int ystart = (int) (((centre[1] - b.end[1]) * scale) + (getSize().height / 2));
 
       g.setColor(Color.red);
       g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart);
@@ -935,6 +966,7 @@ public class AppletPDBCanvas
   }
 
   int foundchain = -1;
+
   public Atom findAtom(int x, int y)
   {
     Atom fatom = null;
@@ -949,19 +981,17 @@ public class AppletPDBCanvas
 
       if (chain.isVisible)
       {
-        Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
+        Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
 
         for (int i = 0; i < bonds.size(); i++)
         {
           tmpBond = (Bond) bonds.elementAt(i);
 
-          truex = (int) ( ( (tmpBond.start[0] - centre[0]) * scale) +
-                         (getSize().width / 2));
+          truex = (int) (((tmpBond.start[0] - centre[0]) * scale) + (getSize().width / 2));
 
           if (Math.abs(truex - x) <= 2)
           {
-            int truey = (int) ( ( (centre[1] - tmpBond.start[1] ) * scale) +
-                               (getSize().height / 2));
+            int truey = (int) (((centre[1] - tmpBond.start[1]) * scale) + (getSize().height / 2));
 
             if (Math.abs(truey - y) <= 2)
             {
@@ -974,13 +1004,11 @@ public class AppletPDBCanvas
 
         // Still here? Maybe its the last bond
 
-        truex = (int) ( ( (tmpBond.end[0] - centre[0]) * scale) +
-                       (getSize().width / 2));
+        truex = (int) (((tmpBond.end[0] - centre[0]) * scale) + (getSize().width / 2));
 
         if (Math.abs(truex - x) <= 2)
         {
-          int truey = (int) ( ( (tmpBond.end[1] - centre[1]) * scale) +
-                             (getSize().height / 2));
+          int truey = (int) (((tmpBond.end[1] - centre[1]) * scale) + (getSize().height / 2));
 
           if (Math.abs(truey - y) <= 2)
           {
@@ -992,7 +1020,7 @@ public class AppletPDBCanvas
 
       }
 
-      if (fatom != null) //)&& chain.ds != null)
+      if (fatom != null) // )&& chain.ds != null)
       {
         chain = (PDBChain) pdb.chains.elementAt(foundchain);
       }
@@ -1013,8 +1041,7 @@ public class AppletPDBCanvas
       return;
     }
 
-    if (highlightRes != null
-        && highlightRes.contains( (ii - 1) + ""))
+    if (highlightRes != null && highlightRes.contains((ii - 1) + ""))
     {
       return;
     }
@@ -1071,36 +1098,36 @@ public class AppletPDBCanvas
     setupBonds();
   }
 
-
-  //////////////////////////////////
-  ///StructureListener
+  // ////////////////////////////////
+  // /StructureListener
   public String getPdbFile()
   {
     return pdbentry.getFile();
   }
 
-
   String lastMessage;
+
   public void mouseOverStructure(int pdbResNum, String chain)
   {
-      if (lastMessage == null || !lastMessage.equals(pdbResNum+chain))
-        ssm.mouseOverStructure(pdbResNum, chain, pdbentry.getFile());
+    if (lastMessage == null || !lastMessage.equals(pdbResNum + chain))
+      ssm.mouseOverStructure(pdbResNum, chain, pdbentry.getFile());
 
-      lastMessage = pdbResNum+chain;
+    lastMessage = pdbResNum + chain;
   }
 
   StringBuffer resetLastRes = new StringBuffer();
+
   StringBuffer eval = new StringBuffer();
 
-  public void highlightAtom(int atomIndex, int pdbResNum, String chain, String pdbfile)
+  public void highlightAtom(int atomIndex, int pdbResNum, String chain,
+          String pdbfile)
   {
     if (!seqColoursReady)
     {
       return;
     }
 
-    if (highlightRes != null
-        && highlightRes.contains( (atomIndex - 1) + ""))
+    if (highlightRes != null && highlightRes.contains((atomIndex - 1) + ""))
     {
       return;
     }
@@ -1145,14 +1172,14 @@ public class AppletPDBCanvas
     repaint();
   }
 
-
-  public Color getColour(int atomIndex, int pdbResNum, String chain, String pdbfile)
+  public Color getColour(int atomIndex, int pdbResNum, String chain,
+          String pdbfile)
   {
     return Color.white;
-   // if (!pdbfile.equals(pdbentry.getFile()))
-   //   return null;
+    // if (!pdbfile.equals(pdbentry.getFile()))
+    // return null;
 
-    //return new Color(viewer.getAtomArgb(atomIndex));
+    // return new Color(viewer.getAtomArgb(atomIndex));
   }
 
   public void updateColours(Object source)
@@ -1162,5 +1189,4 @@ public class AppletPDBCanvas
     repaint();
   }
 
-
 }
diff --git a/src/MCview/AppletPDBViewer.java b/src/MCview/AppletPDBViewer.java
index fc8478d..8299abc 100755
--- a/src/MCview/AppletPDBViewer.java
+++ b/src/MCview/AppletPDBViewer.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -25,23 +25,18 @@ import jalview.appletgui.*;
 import jalview.datamodel.*;
 import jalview.schemes.*;
 
-
-public class AppletPDBViewer
-    extends EmbmenuFrame implements ActionListener, ItemListener
+public class AppletPDBViewer extends EmbmenuFrame implements
+        ActionListener, ItemListener
 {
   AppletPDBCanvas pdbcanvas;
 
-  public AppletPDBViewer(PDBEntry pdbentry,
-                         SequenceI[] seq,
-                         String [] chains,
-                         AlignmentPanel ap,
-                         String protocol)
+  public AppletPDBViewer(PDBEntry pdbentry, SequenceI[] seq,
+          String[] chains, AlignmentPanel ap, String protocol)
   {
     try
     {
       jbInit();
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       ex.printStackTrace();
     }
@@ -51,26 +46,23 @@ public class AppletPDBViewer
     embedMenuIfNeeded(pdbcanvas);
     add(pdbcanvas, BorderLayout.CENTER);
 
-    StringBuffer title = new StringBuffer(seq[0].getName()
-                                          + ":"
-                                          + pdbcanvas.pdbentry.getFile());
+    StringBuffer title = new StringBuffer(seq[0].getName() + ":"
+            + pdbcanvas.pdbentry.getFile());
 
     jalview.bin.JalviewLite.addFrame(this, title.toString(), 400, 400);
 
   }
 
-
-
   public void actionPerformed(ActionEvent evt)
   {
     if (evt.getSource() == mapping)
     {
-      jalview.appletgui.CutAndPasteTransfer cap
-          = new jalview.appletgui.CutAndPasteTransfer(false, null);
+      jalview.appletgui.CutAndPasteTransfer cap = new jalview.appletgui.CutAndPasteTransfer(
+              false, null);
       Frame frame = new Frame();
       frame.add(cap);
-      jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping", 500,
-                                       600);
+      jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping",
+              500, 600);
       cap.setText(pdbcanvas.mappingDetails.toString());
 
     }
@@ -138,7 +130,7 @@ public class AppletPDBViewer
     }
     else if (evt.getSource() == wire)
     {
-          pdbcanvas.wire = !pdbcanvas.wire;
+      pdbcanvas.wire = !pdbcanvas.wire;
     }
     else if (evt.getSource() == depth)
     {
@@ -152,8 +144,7 @@ public class AppletPDBViewer
     pdbcanvas.repaint();
   }
 
-  private void jbInit()
-      throws Exception
+  private void jbInit() throws Exception
   {
     setMenuBar(jMenuBar1);
     fileMenu.setLabel("File");
@@ -196,7 +187,8 @@ public class AppletPDBViewer
     jMenuBar1.add(fileMenu);
     jMenuBar1.add(coloursMenu);
     jMenuBar1.add(viewMenu);
-    fileMenu.add(mapping); ;
+    fileMenu.add(mapping);
+    ;
 
     coloursMenu.add(seqButton);
     coloursMenu.add(chain);
@@ -217,32 +209,48 @@ public class AppletPDBViewer
   }
 
   MenuBar jMenuBar1 = new MenuBar();
+
   Menu fileMenu = new Menu();
+
   Menu coloursMenu = new Menu();
+
   MenuItem mapping = new MenuItem();
+
   CheckboxGroup bg = new CheckboxGroup();
+
   CheckboxMenuItem wire = new CheckboxMenuItem();
+
   CheckboxMenuItem depth = new CheckboxMenuItem();
+
   CheckboxMenuItem zbuffer = new CheckboxMenuItem();
 
   MenuItem charge = new MenuItem();
+
   MenuItem hydro = new MenuItem();
+
   MenuItem chain = new MenuItem();
+
   MenuItem seqButton = new MenuItem();
 
   CheckboxMenuItem allchains = new CheckboxMenuItem();
+
   Menu viewMenu = new Menu();
+
   MenuItem turn = new MenuItem();
+
   MenuItem strand = new MenuItem();
+
   MenuItem helix = new MenuItem();
+
   MenuItem taylor = new MenuItem();
+
   MenuItem zappo = new MenuItem();
-  MenuItem buried = new MenuItem();
-  MenuItem user = new MenuItem();
 
+  MenuItem buried = new MenuItem();
 
-//End StructureListener
-////////////////////////////
+  MenuItem user = new MenuItem();
 
+  // End StructureListener
+  // //////////////////////////
 
 }
diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index e22b94e..e69e1ce 100755
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -23,21 +23,37 @@ import java.awt.*;
 public class Atom
 {
   public float x;
+
   public float y;
+
   public float z;
+
   public int number;
+
   public String name;
+
   public String resName;
+
   public int resNumber;
+
   public char insCode = ' ';
+
   public String resNumIns = null;
+
   public int type;
+
   Color color = Color.lightGray;
+
   public String chain;
+
   public int alignmentMapping = -1;
+
   public int atomIndex;
-  public float occupancy=0;
-  public float tfactor=0;
+
+  public float occupancy = 0;
+
+  public float tfactor = 0;
+
   public boolean isSelected = false;
 
   public Atom(String str)
@@ -56,8 +72,9 @@ public class Atom
     this.x = (float) (new Float(str.substring(30, 38).trim()).floatValue());
     this.y = (float) (new Float(str.substring(38, 46).trim()).floatValue());
     this.z = (float) (new Float(str.substring(47, 55).trim()).floatValue());
-    occupancy = (float) (new Float(str.substring(54,60).trim()).floatValue());
-    tfactor = (float) (new Float(str.substring(60,66).trim()).floatValue());
+    occupancy = (float) (new Float(str.substring(54, 60).trim())
+            .floatValue());
+    tfactor = (float) (new Float(str.substring(60, 66).trim()).floatValue());
   }
 
   public Atom(float x, float y, float z)
@@ -66,7 +83,7 @@ public class Atom
     this.y = y;
     this.z = z;
   }
-  //  public void setColor(Color col) {
-  //      this.color = col;
-  //  }
+  // public void setColor(Color col) {
+  // this.color = col;
+  // }
 }
diff --git a/src/MCview/Bond.java b/src/MCview/Bond.java
index 8e95c1b..cc5e67c 100755
--- a/src/MCview/Bond.java
+++ b/src/MCview/Bond.java
@@ -1,80 +1,80 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package MCview;
-
-import java.awt.*;
-
-public class Bond
-{
-  float[] start;
-  float[] end;
-  Color startCol = Color.lightGray;
-  Color endCol = Color.lightGray;
-  public Atom at1;
-  public Atom at2;
-
-  public Bond(float[] start, float[] end, Atom at1, Atom at2)
-  {
-    this.start = start;
-    this.end = end;
-    this.startCol = at1.color;
-    this.endCol = at2.color;
-    this.at1 = at1;
-    this.at2 = at2;
-  }
-
-  /*  public Bond(Bond bond) {
-        this.start = new float[3];
-
-        this.start[0] = bond.start[0];
-        this.start[1] = bond.start[1];
-        this.start[2] = bond.start[2];
-
-        this.end = new float[3];
-
-        this.end[0] = bond.end[0];
-        this.end[1] = bond.end[1];
-        this.end[2] = bond.end[2];
-
-        this.startCol = bond.startCol;
-        this.endCol = bond.endCol;
-    }
-
-    public float length() {
-        float len = ((end[0] - start[0]) * (end[0] - start[0])) +
-            ((end[1] - start[1]) * (end[1] - start[1])) +
-            ((end[2] - start[2]) * (end[2] - start[2]));
-
-        len = (float) (Math.sqrt(len));
-
-        return len;
-    }*/
-
-  public void translate(float x, float y, float z)
-  {
-    start[0] = (start[0] + x);
-    end[0] = (end[0] + x);
-
-    start[1] = (start[1] + y);
-    end[1] = (end[1] + y);
-
-    start[2] = (start[2] + z);
-    end[2] = (end[2] + z);
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package MCview;
+
+import java.awt.*;
+
+public class Bond
+{
+  float[] start;
+
+  float[] end;
+
+  Color startCol = Color.lightGray;
+
+  Color endCol = Color.lightGray;
+
+  public Atom at1;
+
+  public Atom at2;
+
+  public Bond(float[] start, float[] end, Atom at1, Atom at2)
+  {
+    this.start = start;
+    this.end = end;
+    this.startCol = at1.color;
+    this.endCol = at2.color;
+    this.at1 = at1;
+    this.at2 = at2;
+  }
+
+  /*
+   * public Bond(Bond bond) { this.start = new float[3];
+   * 
+   * this.start[0] = bond.start[0]; this.start[1] = bond.start[1]; this.start[2] =
+   * bond.start[2];
+   * 
+   * this.end = new float[3];
+   * 
+   * this.end[0] = bond.end[0]; this.end[1] = bond.end[1]; this.end[2] =
+   * bond.end[2];
+   * 
+   * this.startCol = bond.startCol; this.endCol = bond.endCol; }
+   * 
+   * public float length() { float len = ((end[0] - start[0]) * (end[0] -
+   * start[0])) + ((end[1] - start[1]) * (end[1] - start[1])) + ((end[2] -
+   * start[2]) * (end[2] - start[2]));
+   * 
+   * len = (float) (Math.sqrt(len));
+   * 
+   * return len; }
+   */
+
+  public void translate(float x, float y, float z)
+  {
+    start[0] = (start[0] + x);
+    end[0] = (end[0] + x);
+
+    start[1] = (start[1] + y);
+    end[1] = (end[1] + y);
+
+    start[2] = (start[2] + z);
+    end[2] = (end[2] + z);
+  }
+}
diff --git a/src/MCview/MCMatrix.java b/src/MCview/MCMatrix.java
index 9eba886..1b9a2d8 100755
--- a/src/MCview/MCMatrix.java
+++ b/src/MCview/MCMatrix.java
@@ -1,171 +1,175 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package MCview;
-
-public class MCMatrix
-{
-  float[][] matrix;
-  float[][] tmp;
-  float mycos;
-  float mysin;
-  float myconst = (float) (Math.PI / 180);
-
-  public MCMatrix(int rows, int cols)
-  {
-    matrix = new float[rows][cols];
-    tmp = new float[rows][cols];
-  }
-
-  public void addElement(int i, int j, float value)
-  {
-    matrix[i][j] = value;
-  }
-
-  public void rotatex(float degrees)
-  {
-    mycos = (float) (Math.cos(degrees * myconst));
-    mysin = (float) (Math.sin(degrees * myconst));
-
-    tmp[0][0] = 1;
-    tmp[0][1] = 0;
-    tmp[0][2] = 0;
-    tmp[1][0] = 0;
-    tmp[1][1] = mycos;
-    tmp[1][2] = mysin;
-    tmp[2][0] = 0;
-    tmp[2][1] = -mysin;
-    tmp[2][2] = mycos;
-    preMultiply(tmp);
-  }
-
-  public void rotatez(float degrees)
-  {
-    mycos = (float) (Math.cos(degrees * myconst));
-    mysin = (float) (Math.sin(degrees * myconst));
-
-    tmp[0][0] = mycos;
-    tmp[0][1] = -mysin;
-    tmp[0][2] = 0;
-    tmp[1][0] = mysin;
-    tmp[1][1] = mycos;
-    tmp[1][2] = 0;
-    tmp[2][0] = 0;
-    tmp[2][1] = 0;
-    tmp[2][2] = 1;
-
-    preMultiply(tmp);
-  }
-
-  public void rotatey(float degrees)
-  {
-    mycos = (float) (Math.cos(degrees * myconst));
-    mysin = (float) (Math.sin(degrees * myconst));
-
-    tmp[0][0] = mycos;
-    tmp[0][1] = 0;
-    tmp[0][2] = -mysin;
-    tmp[1][0] = 0;
-    tmp[1][1] = 1;
-    tmp[1][2] = 0;
-    tmp[2][0] = mysin;
-    tmp[2][1] = 0;
-    tmp[2][2] = mycos;
-
-    preMultiply(tmp);
-  }
-
-  public float[] vectorMultiply(float[] vect)
-  {
-    float[] temp = new float[3];
-
-    temp[0] = vect[0];
-    temp[1] = vect[1];
-    temp[2] = vect[2];
-
-    for (int i = 0; i < 3; i++)
-    {
-      temp[i] = ( (float) matrix[i][0] * vect[0]) +
-          ( (float) matrix[i][1] * vect[1]) +
-          ( (float) matrix[i][2] * vect[2]);
-    }
-
-    vect[0] = temp[0];
-    vect[1] = temp[1];
-    vect[2] = temp[2];
-
-    return vect;
-  }
-
-  public void preMultiply(float[][] mat)
-  {
-    float[][] tmp = new float[3][3];
-
-    for (int i = 0; i < 3; i++)
-    {
-      for (int j = 0; j < 3; j++)
-      {
-        tmp[i][j] = (mat[i][0] * matrix[0][j]) +
-            (mat[i][1] * matrix[1][j]) + (mat[i][2] * matrix[2][j]);
-      }
-    }
-
-    for (int i = 0; i < 3; i++)
-    {
-      for (int j = 0; j < 3; j++)
-      {
-        matrix[i][j] = tmp[i][j];
-      }
-    }
-  }
-
-  public void postMultiply(float[][] mat)
-  {
-    float[][] tmp = new float[3][3];
-
-    for (int i = 0; i < 3; i++)
-    {
-      for (int j = 0; j < 3; j++)
-      {
-        tmp[i][j] = (matrix[i][0] * mat[0][j]) +
-            (matrix[i][1] * mat[1][j]) + (matrix[i][2] * mat[2][j]);
-      }
-    }
-
-    for (int i = 0; i < 3; i++)
-    {
-      for (int j = 0; j < 3; j++)
-      {
-        matrix[i][j] = tmp[i][j];
-      }
-    }
-  }
-
-  public void setIdentity()
-  {
-    matrix[0][0] = 1;
-    matrix[1][1] = 1;
-    matrix[2][2] = 1;
-    matrix[0][1] = 0;
-    matrix[0][2] = 0;
-    matrix[1][0] = 0;
-    matrix[1][2] = 0;
-    matrix[2][0] = 0;
-    matrix[2][1] = 0;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package MCview;
+
+public class MCMatrix
+{
+  float[][] matrix;
+
+  float[][] tmp;
+
+  float mycos;
+
+  float mysin;
+
+  float myconst = (float) (Math.PI / 180);
+
+  public MCMatrix(int rows, int cols)
+  {
+    matrix = new float[rows][cols];
+    tmp = new float[rows][cols];
+  }
+
+  public void addElement(int i, int j, float value)
+  {
+    matrix[i][j] = value;
+  }
+
+  public void rotatex(float degrees)
+  {
+    mycos = (float) (Math.cos(degrees * myconst));
+    mysin = (float) (Math.sin(degrees * myconst));
+
+    tmp[0][0] = 1;
+    tmp[0][1] = 0;
+    tmp[0][2] = 0;
+    tmp[1][0] = 0;
+    tmp[1][1] = mycos;
+    tmp[1][2] = mysin;
+    tmp[2][0] = 0;
+    tmp[2][1] = -mysin;
+    tmp[2][2] = mycos;
+    preMultiply(tmp);
+  }
+
+  public void rotatez(float degrees)
+  {
+    mycos = (float) (Math.cos(degrees * myconst));
+    mysin = (float) (Math.sin(degrees * myconst));
+
+    tmp[0][0] = mycos;
+    tmp[0][1] = -mysin;
+    tmp[0][2] = 0;
+    tmp[1][0] = mysin;
+    tmp[1][1] = mycos;
+    tmp[1][2] = 0;
+    tmp[2][0] = 0;
+    tmp[2][1] = 0;
+    tmp[2][2] = 1;
+
+    preMultiply(tmp);
+  }
+
+  public void rotatey(float degrees)
+  {
+    mycos = (float) (Math.cos(degrees * myconst));
+    mysin = (float) (Math.sin(degrees * myconst));
+
+    tmp[0][0] = mycos;
+    tmp[0][1] = 0;
+    tmp[0][2] = -mysin;
+    tmp[1][0] = 0;
+    tmp[1][1] = 1;
+    tmp[1][2] = 0;
+    tmp[2][0] = mysin;
+    tmp[2][1] = 0;
+    tmp[2][2] = mycos;
+
+    preMultiply(tmp);
+  }
+
+  public float[] vectorMultiply(float[] vect)
+  {
+    float[] temp = new float[3];
+
+    temp[0] = vect[0];
+    temp[1] = vect[1];
+    temp[2] = vect[2];
+
+    for (int i = 0; i < 3; i++)
+    {
+      temp[i] = ((float) matrix[i][0] * vect[0])
+              + ((float) matrix[i][1] * vect[1])
+              + ((float) matrix[i][2] * vect[2]);
+    }
+
+    vect[0] = temp[0];
+    vect[1] = temp[1];
+    vect[2] = temp[2];
+
+    return vect;
+  }
+
+  public void preMultiply(float[][] mat)
+  {
+    float[][] tmp = new float[3][3];
+
+    for (int i = 0; i < 3; i++)
+    {
+      for (int j = 0; j < 3; j++)
+      {
+        tmp[i][j] = (mat[i][0] * matrix[0][j]) + (mat[i][1] * matrix[1][j])
+                + (mat[i][2] * matrix[2][j]);
+      }
+    }
+
+    for (int i = 0; i < 3; i++)
+    {
+      for (int j = 0; j < 3; j++)
+      {
+        matrix[i][j] = tmp[i][j];
+      }
+    }
+  }
+
+  public void postMultiply(float[][] mat)
+  {
+    float[][] tmp = new float[3][3];
+
+    for (int i = 0; i < 3; i++)
+    {
+      for (int j = 0; j < 3; j++)
+      {
+        tmp[i][j] = (matrix[i][0] * mat[0][j]) + (matrix[i][1] * mat[1][j])
+                + (matrix[i][2] * mat[2][j]);
+      }
+    }
+
+    for (int i = 0; i < 3; i++)
+    {
+      for (int j = 0; j < 3; j++)
+      {
+        matrix[i][j] = tmp[i][j];
+      }
+    }
+  }
+
+  public void setIdentity()
+  {
+    matrix[0][0] = 1;
+    matrix[1][1] = 1;
+    matrix[2][2] = 1;
+    matrix[0][1] = 0;
+    matrix[0][2] = 0;
+    matrix[1][0] = 0;
+    matrix[1][2] = 0;
+    matrix[2][0] = 0;
+    matrix[2][1] = 0;
+  }
+}
diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java
index 79871e8..ccc359b 100755
--- a/src/MCview/PDBCanvas.java
+++ b/src/MCview/PDBCanvas.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -31,58 +31,95 @@ import jalview.datamodel.*;
 import jalview.gui.*;
 import jalview.structure.*;
 
-public class PDBCanvas
-    extends JPanel implements MouseListener, MouseMotionListener, StructureListener
+public class PDBCanvas extends JPanel implements MouseListener,
+        MouseMotionListener, StructureListener
 {
   boolean redrawneeded = true;
+
   int omx = 0;
+
   int mx = 0;
+
   int omy = 0;
+
   int my = 0;
+
   public PDBfile pdb;
+
   PDBEntry pdbentry;
+
   int bsize;
+
   Image img;
+
   Graphics ig;
+
   Dimension prefsize;
+
   float[] centre = new float[3];
+
   float[] width = new float[3];
+
   float maxwidth;
+
   float scale;
+
   String inStr;
+
   String inType;
+
   boolean bysequence = true;
+
   boolean depthcue = true;
+
   boolean wire = false;
+
   boolean bymolecule = false;
+
   boolean zbuffer = true;
+
   boolean dragging;
+
   int xstart;
+
   int xend;
+
   int ystart;
+
   int yend;
+
   int xmid;
+
   int ymid;
+
   Font font = new Font("Helvetica", Font.PLAIN, 10);
+
   jalview.gui.SeqCanvas seqcanvas;
-  public SequenceI [] sequence;
+
+  public SequenceI[] sequence;
+
   final StringBuffer mappingDetails = new StringBuffer();
+
   PDBChain mainchain;
+
   Vector highlightRes;
+
   boolean pdbAction = false;
+
   boolean seqColoursReady = false;
+
   jalview.gui.FeatureRenderer fr;
+
   Color backgroundColour = Color.black;
+
   AlignmentPanel ap;
+
   StructureSelectionManager ssm;
-  String errorMessage;
 
+  String errorMessage;
 
-  void init(PDBEntry pdbentry,
-                         SequenceI[] seq,
-                         String [] chains,
-                         AlignmentPanel ap,
-                         String protocol)
+  void init(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
+          AlignmentPanel ap, String protocol)
   {
     this.ap = ap;
     this.pdbentry = pdbentry;
@@ -90,21 +127,22 @@ public class PDBCanvas
 
     ssm = StructureSelectionManager.getStructureSelectionManager();
 
-    try{
+    try
+    {
       pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol);
 
-      if(protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
-       pdbentry.setFile("INLINE"+pdb.id);
+      if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+        pdbentry.setFile("INLINE" + pdb.id);
 
-    }catch(Exception ex)
+    } catch (Exception ex)
     {
       ex.printStackTrace();
       return;
     }
 
-    if(pdb==null)
+    if (pdb == null)
     {
-      errorMessage = "Error loading file: "+pdbentry.getId();
+      errorMessage = "Error loading file: " + pdbentry.getId();
       return;
     }
     pdbentry.setId(pdb.id);
@@ -120,25 +158,24 @@ public class PDBCanvas
     int seqstart = 0;
     int seqend = 0;
 
-    //JUST DEAL WITH ONE SEQUENCE FOR NOW
+    // JUST DEAL WITH ONE SEQUENCE FOR NOW
     SequenceI sequence = seq[0];
 
     for (int i = 0; i < pdb.chains.size(); i++)
     {
 
-      mappingDetails.append("\n\nPDB Sequence is :\nSequence = " +
-                            ( (PDBChain) pdb.chains.elementAt(i)).sequence.
-                            getSequenceAsString());
-      mappingDetails.append("\nNo of residues = " +
-                            ( (PDBChain) pdb.chains.elementAt(i)).residues.size() +
-                            "\n\n");
+      mappingDetails.append("\n\nPDB Sequence is :\nSequence = "
+              + ((PDBChain) pdb.chains.elementAt(i)).sequence
+                      .getSequenceAsString());
+      mappingDetails.append("\nNo of residues = "
+              + ((PDBChain) pdb.chains.elementAt(i)).residues.size()
+              + "\n\n");
 
       // Now lets compare the sequences to get
       // the start and end points.
       // Align the sequence to the pdb
-      AlignSeq as = new AlignSeq(sequence,
-                                 ( (PDBChain) pdb.chains.elementAt(i)).sequence,
-                                 "pep");
+      AlignSeq as = new AlignSeq(sequence, ((PDBChain) pdb.chains
+              .elementAt(i)).sequence, "pep");
       as.calcScoreMatrix();
       as.traceAlignment();
       PrintStream ps = new PrintStream(System.out)
@@ -182,7 +219,6 @@ public class PDBCanvas
     this.pdb = pdb;
     this.prefsize = new Dimension(getSize().width, getSize().height);
 
-
     addMouseMotionListener(this);
     addMouseListener(this);
 
@@ -207,6 +243,7 @@ public class PDBCanvas
   }
 
   Vector visiblebonds;
+
   void setupBonds()
   {
     seqColoursReady = false;
@@ -215,9 +252,9 @@ public class PDBCanvas
 
     for (int ii = 0; ii < pdb.chains.size(); ii++)
     {
-      if ( ( (PDBChain) pdb.chains.elementAt(ii)).isVisible)
+      if (((PDBChain) pdb.chains.elementAt(ii)).isVisible)
       {
-        Vector tmp = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
+        Vector tmp = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
 
         for (int i = 0; i < tmp.size(); i++)
         {
@@ -237,9 +274,9 @@ public class PDBCanvas
     float[] max = new float[3];
     float[] min = new float[3];
 
-    max[0] = (float) - 1e30;
-    max[1] = (float) - 1e30;
-    max[2] = (float) - 1e30;
+    max[0] = (float) -1e30;
+    max[1] = (float) -1e30;
+    max[2] = (float) -1e30;
 
     min[0] = (float) 1e30;
     min[1] = (float) 1e30;
@@ -247,9 +284,9 @@ public class PDBCanvas
 
     for (int ii = 0; ii < pdb.chains.size(); ii++)
     {
-      if ( ( (PDBChain) pdb.chains.elementAt(ii)).isVisible)
+      if (((PDBChain) pdb.chains.elementAt(ii)).isVisible)
       {
-        Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
+        Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
 
         for (int i = 0; i < bonds.size(); i++)
         {
@@ -318,9 +355,10 @@ public class PDBCanvas
       }
     }
     /*
-             System.out.println("xmax " + max[0] + " min " + min[0]);
-             System.out.println("ymax " + max[1] + " min " + min[1]);
-             System.out.println("zmax " + max[2] + " min " + min[2]);*/
+     * System.out.println("xmax " + max[0] + " min " + min[0]);
+     * System.out.println("ymax " + max[1] + " min " + min[1]);
+     * System.out.println("zmax " + max[2] + " min " + min[2]);
+     */
 
     width[0] = (float) Math.abs(max[0] - min[0]);
     width[1] = (float) Math.abs(max[1] - min[1]);
@@ -378,25 +416,25 @@ public class PDBCanvas
 
     int bsize = 0;
 
-    //Find centre coordinate
+    // Find centre coordinate
     for (int ii = 0; ii < pdb.chains.size(); ii++)
     {
-      if ( ( (PDBChain) pdb.chains.elementAt(ii)).isVisible)
+      if (((PDBChain) pdb.chains.elementAt(ii)).isVisible)
       {
-        Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
+        Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
 
         bsize += bonds.size();
 
         for (int i = 0; i < bonds.size(); i++)
         {
-          xtot = xtot + ( (Bond) bonds.elementAt(i)).start[0] +
-              ( (Bond) bonds.elementAt(i)).end[0];
+          xtot = xtot + ((Bond) bonds.elementAt(i)).start[0]
+                  + ((Bond) bonds.elementAt(i)).end[0];
 
-          ytot = ytot + ( (Bond) bonds.elementAt(i)).start[1] +
-              ( (Bond) bonds.elementAt(i)).end[1];
+          ytot = ytot + ((Bond) bonds.elementAt(i)).start[1]
+                  + ((Bond) bonds.elementAt(i)).end[1];
 
-          ztot = ztot + ( (Bond) bonds.elementAt(i)).start[2] +
-              ( (Bond) bonds.elementAt(i)).end[2];
+          ztot = ztot + ((Bond) bonds.elementAt(i)).start[2]
+                  + ((Bond) bonds.elementAt(i)).end[2];
         }
       }
     }
@@ -410,21 +448,19 @@ public class PDBCanvas
   {
     super.paintComponent(g);
 
-    if (!seqColoursReady || errorMessage!=null)
+    if (!seqColoursReady || errorMessage != null)
     {
       g.setColor(Color.black);
       g.setFont(new Font("Verdana", Font.BOLD, 14));
-      g.drawString(errorMessage==null?
-                   "Retrieving PDB data....":errorMessage,
-                   20, getHeight() / 2);
+      g.drawString(errorMessage == null ? "Retrieving PDB data...."
+              : errorMessage, 20, getHeight() / 2);
       return;
     }
 
-    //Only create the image at the beginning -
-    //this saves much memory usage
-    if ( (img == null)
-        || (prefsize.width != getWidth())
-        || (prefsize.height != getHeight()))
+    // Only create the image at the beginning -
+    // this saves much memory usage
+    if ((img == null) || (prefsize.width != getWidth())
+            || (prefsize.height != getHeight()))
 
     {
       prefsize.width = getWidth();
@@ -436,7 +472,7 @@ public class PDBCanvas
       Graphics2D ig2 = (Graphics2D) ig;
 
       ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-                           RenderingHints.VALUE_ANTIALIAS_ON);
+              RenderingHints.VALUE_ANTIALIAS_ON);
 
       redrawneeded = true;
     }
@@ -473,7 +509,6 @@ public class PDBCanvas
     repaint();
   }
 
-
   // This method has been taken out of PDBChain to allow
   // Applet and Application specific sequence renderers to be used
   void colourBySequence()
@@ -518,7 +553,7 @@ public class PDBCanvas
             {
               if (mapping[m].getSequence() == sequence[s])
               {
-                int pos = mapping[m].getSeqPos(tmp.at1.resNumber)-1;
+                int pos = mapping[m].getSeqPos(tmp.at1.resNumber) - 1;
                 if (pos > 0)
                 {
                   pos = sequence[s].findIndex(pos);
@@ -526,11 +561,10 @@ public class PDBCanvas
                   if (showFeatures)
                   {
                     tmp.startCol = fr.findFeatureColour(tmp.startCol,
-                                                        sequence[s],
-                                                        pos);
+                            sequence[s], pos);
                   }
                 }
-                pos = mapping[m].getSeqPos(tmp.at2.resNumber)-1;
+                pos = mapping[m].getSeqPos(tmp.at2.resNumber) - 1;
                 if (pos > 0)
                 {
                   pos = sequence[s].findIndex(pos);
@@ -538,8 +572,7 @@ public class PDBCanvas
                   if (showFeatures)
                   {
                     tmp.endCol = fr.findFeatureColour(tmp.endCol,
-                                                        sequence[s],
-                                                        pos);
+                            sequence[s], pos);
                   }
                 }
 
@@ -552,6 +585,7 @@ public class PDBCanvas
   }
 
   Zsort zsort;
+
   public void drawScene(Graphics g)
   {
     if (zbuffer)
@@ -569,15 +603,11 @@ public class PDBCanvas
     {
       tmpBond = (Bond) visiblebonds.elementAt(i);
 
-      xstart = (int) ( ( (tmpBond.start[0] - centre[0]) * scale) +
-                      (getWidth() / 2));
-      ystart = (int) ( ( (centre[1] - tmpBond.start[1] ) * scale) +
-                      (getHeight() / 2));
+      xstart = (int) (((tmpBond.start[0] - centre[0]) * scale) + (getWidth() / 2));
+      ystart = (int) (((centre[1] - tmpBond.start[1]) * scale) + (getHeight() / 2));
 
-      xend = (int) ( ( (tmpBond.end[0] - centre[0]) * scale) +
-                    (getWidth() / 2));
-      yend = (int) ( ( (centre[1] - tmpBond.end[1] ) * scale) +
-                    (getHeight() / 2));
+      xend = (int) (((tmpBond.end[0] - centre[0]) * scale) + (getWidth() / 2));
+      yend = (int) (((centre[1] - tmpBond.end[1]) * scale) + (getHeight() / 2));
 
       xmid = (xend + xstart) / 2;
       ymid = (yend + ystart) / 2;
@@ -641,13 +671,15 @@ public class PDBCanvas
 
       if (highlightBond1 != null && highlightBond1 == tmpBond)
       {
-        g.setColor(tmpBond.endCol.brighter().brighter().brighter().brighter());
+        g.setColor(tmpBond.endCol.brighter().brighter().brighter()
+                .brighter());
         drawLine(g, xmid, ymid, xend, yend);
       }
 
       if (highlightBond2 != null && highlightBond2 == tmpBond)
       {
-        g.setColor(tmpBond.startCol.brighter().brighter().brighter().brighter());
+        g.setColor(tmpBond.startCol.brighter().brighter().brighter()
+                .brighter());
         drawLine(g, xstart, ystart, xmid, ymid);
       }
 
@@ -659,7 +691,7 @@ public class PDBCanvas
   {
     if (!wire)
     {
-      if ( ( (float) Math.abs(y2 - y1) / (float) Math.abs(x2 - x1)) < 0.5)
+      if (((float) Math.abs(y2 - y1) / (float) Math.abs(x2 - x1)) < 0.5)
       {
         g.drawLine(x1, y1, x2, y2);
         g.drawLine(x1 + 1, y1 + 1, x2 + 1, y2 + 1);
@@ -772,24 +804,27 @@ public class PDBCanvas
 
     if (fatom != null)
     {
-      this.setToolTipText(chain.id + ":" + fatom.resNumber + " " +
-                          fatom.resName);
+      this.setToolTipText(chain.id + ":" + fatom.resNumber + " "
+              + fatom.resName);
     }
     else
     {
-      mouseOverStructure(-1, chain!=null?chain.id:null);
+      mouseOverStructure(-1, chain != null ? chain.id : null);
       this.setToolTipText(null);
     }
   }
 
   public void mouseClicked(MouseEvent e)
-  {}
+  {
+  }
 
   public void mouseEntered(MouseEvent e)
-  {}
+  {
+  }
 
   public void mouseExited(MouseEvent e)
-  {}
+  {
+  }
 
   public void mouseDragged(MouseEvent evt)
   {
@@ -801,33 +836,33 @@ public class PDBCanvas
     MCMatrix objmat = new MCMatrix(3, 3);
     objmat.setIdentity();
 
-    if ( (evt.getModifiers() & Event.META_MASK) != 0)
+    if ((evt.getModifiers() & Event.META_MASK) != 0)
     {
-      objmat.rotatez( (float) ( (mx - omx)));
+      objmat.rotatez((float) ((mx - omx)));
     }
     else
     {
-      objmat.rotatex( (float) ( (my - omy)));
-      objmat.rotatey( (float) ( (omx - mx)));
+      objmat.rotatex((float) ((my - omy)));
+      objmat.rotatey((float) ((omx - mx)));
     }
 
-    //Alter the bonds
+    // Alter the bonds
     for (int ii = 0; ii < pdb.chains.size(); ii++)
     {
-      Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
+      Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
 
       for (int i = 0; i < bonds.size(); i++)
       {
         Bond tmpBond = (Bond) bonds.elementAt(i);
 
-        //Translate the bond so the centre is 0,0,0
-        tmpBond.translate( -centre[0], -centre[1], -centre[2]);
+        // Translate the bond so the centre is 0,0,0
+        tmpBond.translate(-centre[0], -centre[1], -centre[2]);
 
-        //Now apply the rotation matrix
+        // Now apply the rotation matrix
         tmpBond.start = objmat.vectorMultiply(tmpBond.start);
         tmpBond.end = objmat.vectorMultiply(tmpBond.end);
 
-        //Now translate back again
+        // Now translate back again
         tmpBond.translate(centre[0], centre[1], centre[2]);
       }
     }
@@ -859,7 +894,7 @@ public class PDBCanvas
 
       if (chain.isVisible)
       {
-        Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
+        Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
 
         for (int i = 0; i < bonds.size(); i++)
         {
@@ -886,26 +921,23 @@ public class PDBCanvas
     g.setColor(Color.red);
     if (n == 1)
     {
-      int xstart = (int) ( ( (b.start[0] - centre[0]) * scale) +
-                          (getWidth() / 2));
-      int ystart = (int) ( ( (centre[1] - b.start[1] ) * scale) +
-                          (getHeight() / 2));
+      int xstart = (int) (((b.start[0] - centre[0]) * scale) + (getWidth() / 2));
+      int ystart = (int) (((centre[1] - b.start[1]) * scale) + (getHeight() / 2));
 
       g.drawString(b.at1.resName + "-" + b.at1.resNumber, xstart, ystart);
     }
 
     if (n == 2)
     {
-      int xstart = (int) ( ( (b.end[0] - centre[0]) * scale) +
-                          (getWidth() / 2));
-      int ystart = (int) ( ( (centre[1] - b.end[1] ) * scale) +
-                          (getHeight() / 2));
+      int xstart = (int) (((b.end[0] - centre[0]) * scale) + (getWidth() / 2));
+      int ystart = (int) (((centre[1] - b.end[1]) * scale) + (getHeight() / 2));
 
       g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart);
     }
   }
 
   int foundchain = -1;
+
   public Atom findAtom(int x, int y)
   {
     Atom fatom = null;
@@ -920,19 +952,17 @@ public class PDBCanvas
 
       if (chain.isVisible)
       {
-        Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
+        Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
 
         for (int i = 0; i < bonds.size(); i++)
         {
           tmpBond = (Bond) bonds.elementAt(i);
 
-          truex = (int) ( ( (tmpBond.start[0] - centre[0]) * scale) +
-                         (getWidth() / 2));
+          truex = (int) (((tmpBond.start[0] - centre[0]) * scale) + (getWidth() / 2));
 
           if (Math.abs(truex - x) <= 2)
           {
-            int truey = (int) ( ( (centre[1] - tmpBond.start[1] ) * scale) +
-                               (getHeight() / 2));
+            int truey = (int) (((centre[1] - tmpBond.start[1]) * scale) + (getHeight() / 2));
 
             if (Math.abs(truey - y) <= 2)
             {
@@ -945,13 +975,11 @@ public class PDBCanvas
 
         // Still here? Maybe its the last bond
 
-        truex = (int) ( ( (tmpBond.end[0] - centre[0]) * scale) +
-                       (getWidth() / 2));
+        truex = (int) (((tmpBond.end[0] - centre[0]) * scale) + (getWidth() / 2));
 
         if (Math.abs(truex - x) <= 2)
         {
-          int truey = (int) ( ( (tmpBond.end[1] - centre[1]) * scale) +
-                             (getHeight() / 2));
+          int truey = (int) (((tmpBond.end[1] - centre[1]) * scale) + (getHeight() / 2));
 
           if (Math.abs(truey - y) <= 2)
           {
@@ -963,7 +991,7 @@ public class PDBCanvas
 
       }
 
-      if (fatom != null) //)&& chain.ds != null)
+      if (fatom != null) // )&& chain.ds != null)
       {
         chain = (PDBChain) pdb.chains.elementAt(foundchain);
       }
@@ -973,6 +1001,7 @@ public class PDBCanvas
   }
 
   Bond highlightBond1, highlightBond2;
+
   public void highlightRes(int ii)
   {
     if (!seqColoursReady)
@@ -980,8 +1009,7 @@ public class PDBCanvas
       return;
     }
 
-    if (highlightRes != null
-        && highlightRes.contains( (ii - 1) + ""))
+    if (highlightRes != null && highlightRes.contains((ii - 1) + ""))
     {
       return;
     }
@@ -1038,35 +1066,36 @@ public class PDBCanvas
     setupBonds();
   }
 
-  //////////////////////////////////
-  ///StructureListener
+  // ////////////////////////////////
+  // /StructureListener
   public String getPdbFile()
   {
     return pdbentry.getFile();
   }
 
-
   String lastMessage;
+
   public void mouseOverStructure(int pdbResNum, String chain)
   {
-      if (lastMessage == null || !lastMessage.equals(pdbResNum+chain))
-        ssm.mouseOverStructure(pdbResNum, chain, pdbentry.getFile());
+    if (lastMessage == null || !lastMessage.equals(pdbResNum + chain))
+      ssm.mouseOverStructure(pdbResNum, chain, pdbentry.getFile());
 
-      lastMessage = pdbResNum+chain;
+    lastMessage = pdbResNum + chain;
   }
 
   StringBuffer resetLastRes = new StringBuffer();
+
   StringBuffer eval = new StringBuffer();
 
-  public void highlightAtom(int atomIndex, int pdbResNum, String chain, String pdbfile)
+  public void highlightAtom(int atomIndex, int pdbResNum, String chain,
+          String pdbfile)
   {
     if (!seqColoursReady)
     {
       return;
     }
 
-    if (highlightRes != null
-        && highlightRes.contains( (atomIndex - 1) + ""))
+    if (highlightRes != null && highlightRes.contains((atomIndex - 1) + ""))
     {
       return;
     }
@@ -1111,14 +1140,14 @@ public class PDBCanvas
     repaint();
   }
 
-
-  public Color getColour(int atomIndex, int pdbResNum, String chain, String pdbfile)
+  public Color getColour(int atomIndex, int pdbResNum, String chain,
+          String pdbfile)
   {
     return Color.white;
-   // if (!pdbfile.equals(pdbentry.getFile()))
-   //   return null;
+    // if (!pdbfile.equals(pdbentry.getFile()))
+    // return null;
 
-    //return new Color(viewer.getAtomArgb(atomIndex));
+    // return new Color(viewer.getAtomArgb(atomIndex));
   }
 
   public void updateColours(Object source)
diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 30712f2..c1c586a 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -33,19 +33,33 @@ public class PDBChain
    * SequenceFeature group for PDB File features added to sequences
    */
   private static final String PDBFILEFEATURE = "PDBFile";
+
   private static final String IEASTATUS = "IEA:jalview";
+
   public String id;
+
   public Vector bonds = new Vector();
+
   public Vector atoms = new Vector();
+
   public Vector residues = new Vector();
+
   public int offset;
+
   public Sequence sequence;
+
   public boolean isVisible = true;
+
   public int pdbstart = 0;
+
   public int pdbend = 0;
+
   public int seqstart = 0;
+
   public int seqend = 0;
+
   public String pdbid = "";
+
   public PDBChain(String pdbid, String id)
   {
     this.pdbid = pdbid.toLowerCase();
@@ -58,9 +72,9 @@ public class PDBChain
 
     for (int i = 0; i < bonds.size(); i++)
     {
-      tmp = tmp + ( (Bond) bonds.elementAt(i)).at1.resName + " " +
-          ( (Bond) bonds.elementAt(i)).at1.resNumber + " " + offset +
-          "\n";
+      tmp = tmp + ((Bond) bonds.elementAt(i)).at1.resName + " "
+              + ((Bond) bonds.elementAt(i)).at1.resNumber + " " + offset
+              + "\n";
     }
 
     return tmp;
@@ -95,16 +109,21 @@ public class PDBChain
       }
     }
   }
+
   /**
-   * copy over the RESNUM seqfeatures from the internal chain sequence to the mapped sequence
+   * copy over the RESNUM seqfeatures from the internal chain sequence to the
+   * mapped sequence
+   * 
    * @param seq
-   * @param status The Status of the transferred annotation
+   * @param status
+   *                The Status of the transferred annotation
    * @return the features added to sq (or its dataset)
    */
-  public SequenceFeature[] transferRESNUMFeatures(SequenceI seq, String status)
+  public SequenceFeature[] transferRESNUMFeatures(SequenceI seq,
+          String status)
   {
     SequenceI sq = seq;
-    while (sq!=null && sq.getDatasetSequence()!=null)
+    while (sq != null && sq.getDatasetSequence() != null)
     {
       sq = sq.getDatasetSequence();
       if (sq == sequence)
@@ -114,11 +133,10 @@ public class PDBChain
     }
     /**
      * Remove any existing features for this chain if they exist ?
-     * SequenceFeature[] seqsfeatures=seq.getSequenceFeatures();
-        int totfeat=seqsfeatures.length;
-        // Remove any features for this exact chain ?
-        for (int i=0; i<seqsfeatures.length; i++) {
-        } */
+     * SequenceFeature[] seqsfeatures=seq.getSequenceFeatures(); int
+     * totfeat=seqsfeatures.length; // Remove any features for this exact chain ?
+     * for (int i=0; i<seqsfeatures.length; i++) { }
+     */
     if (status == null)
     {
       status = PDBChain.IEASTATUS;
@@ -129,16 +147,15 @@ public class PDBChain
       if (features[i].getFeatureGroup().equals(pdbid))
       {
         SequenceFeature tx = new SequenceFeature(features[i]);
-        tx.setBegin(1 +
-                    ( (Atom) ( (Residue) residues.elementAt(tx.getBegin() - offset)).
-                     atoms.elementAt(0)).alignmentMapping);
-        tx.setEnd(1 +
-                  ( (Atom) ( (Residue) residues.elementAt(tx.getEnd() - offset)).
-                   atoms.elementAt(0)).alignmentMapping);
-        tx.setStatus(status +
-                     ( (tx.getStatus() == null || tx.getStatus().length() == 0) ?
-                      "" : ":" + tx.getStatus()));
-        if (tx.begin!=0 && tx.end!=0)
+        tx.setBegin(1 + ((Atom) ((Residue) residues.elementAt(tx.getBegin()
+                - offset)).atoms.elementAt(0)).alignmentMapping);
+        tx.setEnd(1 + ((Atom) ((Residue) residues.elementAt(tx.getEnd()
+                - offset)).atoms.elementAt(0)).alignmentMapping);
+        tx
+                .setStatus(status
+                        + ((tx.getStatus() == null || tx.getStatus()
+                                .length() == 0) ? "" : ":" + tx.getStatus()));
+        if (tx.begin != 0 && tx.end != 0)
           sq.addSequenceFeature(tx);
       }
     }
@@ -154,7 +171,7 @@ public class PDBChain
       Atom at1 = tmpres.findAtom("CA");
       Atom at2 = tmpres2.findAtom("CA");
 
-      if ( (at1 != null) && (at2 != null))
+      if ((at1 != null) && (at2 != null))
       {
         if (at1.chain.equals(at2.chain))
         {
@@ -204,16 +221,16 @@ public class PDBChain
       }
 
       Vector resAtoms = new Vector();
-      //Add atoms to a vector while the residue number
-      //remains the same as the first atom's resNumber (res)
-      while ( (resNumber == res) && (i < atoms.size()))
+      // Add atoms to a vector while the residue number
+      // remains the same as the first atom's resNumber (res)
+      while ((resNumber == res) && (i < atoms.size()))
       {
-        resAtoms.addElement( (Atom) atoms.elementAt(i));
+        resAtoms.addElement((Atom) atoms.elementAt(i));
         i++;
 
         if (i < atoms.size())
         {
-          resNumber = ( (Atom) atoms.elementAt(i)).resNumber;
+          resNumber = ((Atom) atoms.elementAt(i)).resNumber;
         }
         else
         {
@@ -221,38 +238,34 @@ public class PDBChain
         }
       }
 
-      //We need this to keep in step with the outer for i = loop
+      // We need this to keep in step with the outer for i = loop
       i--;
 
-      //Make a new Residue object with the new atoms vector
+      // Make a new Residue object with the new atoms vector
       residues.addElement(new Residue(resAtoms, resNumber - 1, count));
 
       Residue tmpres = (Residue) residues.lastElement();
       Atom tmpat = (Atom) tmpres.atoms.elementAt(0);
       // Make A new SequenceFeature for the current residue numbering
-      SequenceFeature sf =
-          new SequenceFeature("RESNUM",
-                              tmpat.resName + ":" + tmpat.resNumIns + " " +
-                              pdbid + id,
-                              "", offset + count, offset + count,
-                              pdbid);
-
-      //MCview.PDBChain.PDBFILEFEATURE);
+      SequenceFeature sf = new SequenceFeature("RESNUM", tmpat.resName
+              + ":" + tmpat.resNumIns + " " + pdbid + id, "", offset
+              + count, offset + count, pdbid);
+
+      // MCview.PDBChain.PDBFILEFEATURE);
       resFeatures.addElement(sf);
       resAnnotation.addElement(new Annotation(tmpat.tfactor));
       // Keep totting up the sequence
       if (ResidueProperties.getAA3Hash().get(tmpat.resName) == null)
       {
         seq.append("X");
-        //  System.err.println("PDBReader:Null aa3Hash for " +
-        //     tmpat.resName);
+        // System.err.println("PDBReader:Null aa3Hash for " +
+        // tmpat.resName);
       }
       else
       {
 
-        seq.append(ResidueProperties.aa[ ( (Integer) ResidueProperties.
-                                          getAA3Hash()
-                                          .get(tmpat.resName)).intValue()]);
+        seq.append(ResidueProperties.aa[((Integer) ResidueProperties
+                .getAA3Hash().get(tmpat.resName)).intValue()]);
       }
       count++;
     }
@@ -262,25 +275,31 @@ public class PDBChain
       id = " ";
     }
 
-    sequence = new Sequence(id, seq.toString(), offset, resNumber - 1); // Note: resNumber-offset ~= seq.size()
-    //  System.out.println("PDB Sequence is :\nSequence = " + seq);
-    //   System.out.println("No of residues = " + residues.size());
+    sequence = new Sequence(id, seq.toString(), offset, resNumber - 1); // Note:
+                                                                        // resNumber-offset
+                                                                        // ~=
+                                                                        // seq.size()
+    // System.out.println("PDB Sequence is :\nSequence = " + seq);
+    // System.out.println("No of residues = " + residues.size());
     for (i = 0, iSize = resFeatures.size(); i < iSize; i++)
     {
-      sequence.addSequenceFeature( (SequenceFeature) resFeatures.elementAt(i));
+      sequence.addSequenceFeature((SequenceFeature) resFeatures
+              .elementAt(i));
       resFeatures.setElementAt(null, i);
     }
     Annotation[] annots = new Annotation[resAnnotation.size()];
-    float max=0;
-    for (i=0,iSize=annots.length; i<iSize; i++)
+    float max = 0;
+    for (i = 0, iSize = annots.length; i < iSize; i++)
     {
       annots[i] = (Annotation) resAnnotation.elementAt(i);
-      if (annots[i].value>max)
+      if (annots[i].value > max)
         max = annots[i].value;
       resAnnotation.setElementAt(null, i);
     }
-    AlignmentAnnotation tfactorann = new AlignmentAnnotation("PDB.CATempFactor","CA Temperature Factor for "+sequence.getName(),
-            annots, 0, max, AlignmentAnnotation.LINE_GRAPH);
+    AlignmentAnnotation tfactorann = new AlignmentAnnotation(
+            "PDB.CATempFactor", "CA Temperature Factor for "
+                    + sequence.getName(), annots, 0, max,
+            AlignmentAnnotation.LINE_GRAPH);
     tfactorann.setSequenceRef(sequence);
     sequence.addAlignmentAnnotation(tfactorann);
   }
@@ -293,13 +312,13 @@ public class PDBChain
       {
         Bond b = (Bond) bonds.elementAt(i);
 
-        if (b.at1.resName.equalsIgnoreCase("ASP") ||
-            b.at1.resName.equalsIgnoreCase("GLU"))
+        if (b.at1.resName.equalsIgnoreCase("ASP")
+                || b.at1.resName.equalsIgnoreCase("GLU"))
         {
           b.startCol = Color.red;
         }
-        else if (b.at1.resName.equalsIgnoreCase("LYS") ||
-                 b.at1.resName.equalsIgnoreCase("ARG"))
+        else if (b.at1.resName.equalsIgnoreCase("LYS")
+                || b.at1.resName.equalsIgnoreCase("ARG"))
         {
           b.startCol = Color.blue;
         }
@@ -312,13 +331,13 @@ public class PDBChain
           b.startCol = Color.lightGray;
         }
 
-        if (b.at2.resName.equalsIgnoreCase("ASP") ||
-            b.at2.resName.equalsIgnoreCase("GLU"))
+        if (b.at2.resName.equalsIgnoreCase("ASP")
+                || b.at2.resName.equalsIgnoreCase("GLU"))
         {
           b.endCol = Color.red;
         }
-        else if (b.at2.resName.equalsIgnoreCase("LYS") ||
-                 b.at2.resName.equalsIgnoreCase("ARG"))
+        else if (b.at2.resName.equalsIgnoreCase("LYS")
+                || b.at2.resName.equalsIgnoreCase("ARG"))
         {
           b.endCol = Color.blue;
         }
@@ -330,8 +349,7 @@ public class PDBChain
         {
           b.endCol = Color.lightGray;
         }
-      }
-      catch (Exception e)
+      } catch (Exception e)
       {
         Bond b = (Bond) bonds.elementAt(i);
         b.startCol = Color.gray;
@@ -350,16 +368,15 @@ public class PDBChain
       {
         b = (Bond) bonds.elementAt(i);
 
-        index = ( (Integer) ResidueProperties.aa3Hash.get(b.at1.
-            resName)).intValue();
+        index = ((Integer) ResidueProperties.aa3Hash.get(b.at1.resName))
+                .intValue();
         b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0));
 
-        index = ( (Integer) ResidueProperties.aa3Hash.get(b.at2.resName)).
-            intValue();
+        index = ((Integer) ResidueProperties.aa3Hash.get(b.at2.resName))
+                .intValue();
         b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0));
 
-      }
-      catch (Exception e)
+      } catch (Exception e)
       {
         b = (Bond) bonds.elementAt(i);
         b.startCol = Color.gray;
@@ -378,7 +395,8 @@ public class PDBChain
     }
   }
 
-  public AlignmentAnnotation[] transferResidueAnnotation(SequenceI seq, String status)
+  public AlignmentAnnotation[] transferResidueAnnotation(SequenceI seq,
+          String status)
   {
     AlignmentAnnotation[] transferred = null;
 
@@ -387,41 +405,49 @@ public class PDBChain
   }
 
   /**
-   * copy any sequence annotation onto the sequence mapped using the provided StructureMapping
+   * copy any sequence annotation onto the sequence mapped using the provided
+   * StructureMapping
+   * 
    * @param mapping
    */
   public void transferResidueAnnotation(StructureMapping mapping)
   {
     SequenceI sq = mapping.getSequence();
-    if (sq!=null)
+    if (sq != null)
     {
-      if (sequence!=null && sequence.getAnnotation()!=null)
+      if (sequence != null && sequence.getAnnotation() != null)
       {
 
       }
-      float min=-1,max=0;
-      Annotation[] an=new Annotation[sq.getEnd()-sq.getStart()+1];
-      for (int i=sq.getStart(),j=sq.getEnd(),k=0; i<=j; i++,k++)
+      float min = -1, max = 0;
+      Annotation[] an = new Annotation[sq.getEnd() - sq.getStart() + 1];
+      for (int i = sq.getStart(), j = sq.getEnd(), k = 0; i <= j; i++, k++)
       {
-        int prn = mapping.getPDBResNum(k+1);
+        int prn = mapping.getPDBResNum(k + 1);
 
-        an[k] = new Annotation((float)prn);
-        if (min==-1)
+        an[k] = new Annotation((float) prn);
+        if (min == -1)
         {
-          min=k;
-          max=k;
-        } else {
-          if (min>k)
+          min = k;
+          max = k;
+        }
+        else
+        {
+          if (min > k)
+          {
+            min = k;
+          }
+          else if (max < k)
           {
-            min=k;
-          } else
-            if (max<k)
-            {
-              max=k;
-            }
+            max = k;
+          }
         }
       }
-      sq.addAlignmentAnnotation(new AlignmentAnnotation("PDB.RESNUM", "PDB Residue Numbering for "+this.pdbid+":"+this.id, an, (float)min,(float)max, AlignmentAnnotation.LINE_GRAPH));
+      sq
+              .addAlignmentAnnotation(new AlignmentAnnotation("PDB.RESNUM",
+                      "PDB Residue Numbering for " + this.pdbid + ":"
+                              + this.id, an, (float) min, (float) max,
+                      AlignmentAnnotation.LINE_GRAPH));
     }
   }
 }
diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java
index e586707..dda04a8 100755
--- a/src/MCview/PDBViewer.java
+++ b/src/MCview/PDBViewer.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -31,8 +31,7 @@ import jalview.ws.ebi.EBIFetchClient;
 
 import java.awt.BorderLayout;
 
-public class PDBViewer
-    extends JInternalFrame implements Runnable
+public class PDBViewer extends JInternalFrame implements Runnable
 {
 
   /**
@@ -41,17 +40,19 @@ public class PDBViewer
   PDBCanvas pdbcanvas;
 
   PDBEntry pdbentry;
-  SequenceI[]seq;
-  String[]chains;
+
+  SequenceI[] seq;
+
+  String[] chains;
+
   AlignmentPanel ap;
+
   String protocol;
+
   String tmpPDBFile;
 
-  public PDBViewer(PDBEntry pdbentry,
-                   SequenceI[] seq,
-                   String[] chains,
-                   AlignmentPanel ap,
-                   String protocol)
+  public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
+          AlignmentPanel ap, String protocol)
 
   {
     this.pdbentry = pdbentry;
@@ -63,16 +64,13 @@ public class PDBViewer
     try
     {
       jbInit();
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       ex.printStackTrace();
     }
 
-
-    StringBuffer title = new StringBuffer(seq[0].getName()
-                                          + ":"
-                                          + pdbentry.getFile());
+    StringBuffer title = new StringBuffer(seq[0].getName() + ":"
+            + pdbentry.getFile());
 
     pdbcanvas = new PDBCanvas();
 
@@ -84,12 +82,11 @@ public class PDBViewer
       {
         tmpPDBFile = pdbentry.getFile();
         PDBfile pdbfile = new PDBfile(tmpPDBFile,
-                                      jalview.io.AppletFormatAdapter.FILE);
+                jalview.io.AppletFormatAdapter.FILE);
 
         pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
 
-      }
-      catch (java.io.IOException ex)
+      } catch (java.io.IOException ex)
       {
         ex.printStackTrace();
       }
@@ -100,8 +97,6 @@ public class PDBViewer
       worker.start();
     }
 
-
-
     if (pdbentry.getProperty() != null)
     {
       if (pdbentry.getProperty().get("method") != null)
@@ -125,20 +120,18 @@ public class PDBViewer
       EBIFetchClient ebi = new EBIFetchClient();
       String query = "pdb:" + pdbentry.getId();
       pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw")
-                       .getAbsolutePath());
+              .getAbsolutePath());
 
-      if(pdbentry.getFile()!=null)
+      if (pdbentry.getFile() != null)
         pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
-      pdbcanvas.errorMessage = "Error retrieving file: "+pdbentry.getId();
+      pdbcanvas.errorMessage = "Error retrieving file: " + pdbentry.getId();
       ex.printStackTrace();
     }
   }
 
-  private void jbInit()
-      throws Exception
+  private void jbInit() throws Exception
   {
     this.addKeyListener(new KeyAdapter()
     {
@@ -353,32 +346,33 @@ public class PDBViewer
 
     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
     {
-      java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
-          getUserColourSchemes().keys();
+      java.util.Enumeration userColours = jalview.gui.UserDefinedColours
+              .getUserColourSchemes().keys();
 
       while (userColours.hasMoreElements())
       {
         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
-            userColours.
-            nextElement().toString());
+                userColours.nextElement().toString());
         radioItem.setName("USER_DEFINED");
         radioItem.addMouseListener(new MouseAdapter()
         {
           public void mousePressed(MouseEvent evt)
           {
-            if (evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
+            if (evt.isControlDown()
+                    || SwingUtilities.isRightMouseButton(evt))
             {
-              radioItem.removeActionListener(radioItem.getActionListeners()[0]);
-
-              int option = JOptionPane.showInternalConfirmDialog(jalview.gui.
-                  Desktop.desktop,
-                  "Remove from default list?",
-                  "Remove user defined colour",
-                  JOptionPane.YES_NO_OPTION);
+              radioItem
+                      .removeActionListener(radioItem.getActionListeners()[0]);
+
+              int option = JOptionPane.showInternalConfirmDialog(
+                      jalview.gui.Desktop.desktop,
+                      "Remove from default list?",
+                      "Remove user defined colour",
+                      JOptionPane.YES_NO_OPTION);
               if (option == JOptionPane.YES_OPTION)
               {
-                jalview.gui.UserDefinedColours.removeColourFromDefaults(
-                    radioItem.getText());
+                jalview.gui.UserDefinedColours
+                        .removeColourFromDefaults(radioItem.getText());
                 coloursMenu.remove(radioItem);
               }
               else
@@ -413,36 +407,60 @@ public class PDBViewer
   }
 
   JMenuBar jMenuBar1 = new JMenuBar();
+
   JMenu fileMenu = new JMenu();
+
   JMenu coloursMenu = new JMenu();
+
   JMenu saveMenu = new JMenu();
+
   JMenuItem png = new JMenuItem();
+
   JMenuItem eps = new JMenuItem();
+
   JMenuItem mapping = new JMenuItem();
+
   JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
+
   JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
+
   JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
+
   JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
 
   JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
+
   JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
+
   JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
+
   JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
+
   JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
+
   JRadioButtonMenuItem zappo = new JRadioButtonMenuItem();
+
   JRadioButtonMenuItem user = new JRadioButtonMenuItem();
+
   JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
+
   JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
+
   JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
+
   JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
+
   JMenu viewMenu = new JMenu();
+
   JMenuItem background = new JMenuItem();
+
   JMenuItem savePDB = new JMenuItem();
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void eps_actionPerformed(ActionEvent e)
   {
@@ -451,8 +469,9 @@ public class PDBViewer
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void png_actionPerformed(ActionEvent e)
   {
@@ -468,19 +487,14 @@ public class PDBViewer
 
     if (type == jalview.util.ImageMaker.PNG)
     {
-      im = new jalview.util.ImageMaker(this,
-                                       jalview.util.ImageMaker.PNG,
-                                       "Make PNG image from view",
-                                       width, height,
-                                       null, null);
+      im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
+              "Make PNG image from view", width, height, null, null);
     }
     else
     {
-      im = new jalview.util.ImageMaker(this,
-                                       jalview.util.ImageMaker.EPS,
-                                       "Make EPS file from view",
-                                       width, height,
-                                       null, this.getTitle());
+      im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
+              "Make EPS file from view", width, height, null, this
+                      .getTitle());
     }
 
     if (im.getGraphics() != null)
@@ -560,7 +574,6 @@ public class PDBViewer
     pdbcanvas.setAllchainsVisible(allchains.getState());
   }
 
-
   public void zappo_actionPerformed(ActionEvent e)
   {
     pdbcanvas.bysequence = false;
@@ -613,12 +626,12 @@ public class PDBViewer
   {
     if (e.getActionCommand().equals("User Defined..."))
     {
-     // new UserDefinedColours(pdbcanvas, null);
+      // new UserDefinedColours(pdbcanvas, null);
     }
     else
     {
-      UserColourScheme udc = (UserColourScheme) UserDefinedColours.
-          getUserColourSchemes().get(e.getActionCommand());
+      UserColourScheme udc = (UserColourScheme) UserDefinedColours
+              .getUserColourSchemes().get(e.getActionCommand());
 
       pdbcanvas.pdb.setColours(udc);
       pdbcanvas.redrawneeded = true;
@@ -629,8 +642,7 @@ public class PDBViewer
   public void background_actionPerformed(ActionEvent e)
   {
     java.awt.Color col = JColorChooser.showDialog(this,
-                                                  "Select Background Colour",
-                                                  pdbcanvas.backgroundColour);
+            "Select Background Colour", pdbcanvas.backgroundColour);
 
     if (col != null)
     {
@@ -642,9 +654,8 @@ public class PDBViewer
 
   public void savePDB_actionPerformed(ActionEvent e)
   {
-    JalviewFileChooser chooser = new JalviewFileChooser(
-        jalview.bin.Cache.getProperty(
-            "LAST_DIRECTORY"));
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+            .getProperty("LAST_DIRECTORY"));
 
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle("Save PDB File");
@@ -661,18 +672,15 @@ public class PDBViewer
 
         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
         String data;
-        while ( (data = in.readLine()) != null)
+        while ((data = in.readLine()) != null)
         {
-          if (
-              ! (data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1)
-              )
+          if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
           {
             out.println(data);
           }
         }
         out.close();
-      }
-      catch (Exception ex)
+      } catch (Exception ex)
       {
         ex.printStackTrace();
       }
diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index e5ad565..5fd3d10 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -26,18 +26,18 @@ import java.awt.*;
 import jalview.datamodel.*;
 import jalview.io.FileParse;
 
-public class PDBfile
-    extends jalview.io.AlignFile
+public class PDBfile extends jalview.io.AlignFile
 {
   public Vector chains;
+
   public String id;
 
   /**
    * set to true to add chain alignment annotation as visible annotation.
    */
-  boolean VisibleChainAnnotation=false;
-  public PDBfile(String inFile, String inType)
-      throws IOException
+  boolean VisibleChainAnnotation = false;
+
+  public PDBfile(String inFile, String inType) throws IOException
   {
     super(inFile, inType);
   }
@@ -52,11 +52,10 @@ public class PDBfile
     return null;
   }
 
-  public void parse()
-      throws IOException
+  public void parse() throws IOException
   {
-    // TODO set the filename sensibly 
-    id = (inFile==null) ? "PDBFILE" : inFile.getName();
+    // TODO set the filename sensibly
+    id = (inFile == null) ? "PDBFILE" : inFile.getName();
     try
     {
       chains = new Vector();
@@ -67,7 +66,7 @@ public class PDBfile
       boolean terFlag = false;
 
       int index = 0;
-      while ( (line = nextLine()) != null)
+      while ((line = nextLine()) != null)
       {
         if (line.indexOf("HEADER") == 0)
         {
@@ -94,12 +93,11 @@ public class PDBfile
           break;
         }
         if (line.indexOf("ATOM") == 0
-            || (line.indexOf("HETATM") == 0 && !terFlag)
-            )
+                || (line.indexOf("HETATM") == 0 && !terFlag))
         {
           terFlag = false;
 
-          //Jalview is only interested in CA bonds????
+          // Jalview is only interested in CA bonds????
           if (!line.substring(12, 15).trim().equals("CA"))
           {
             continue;
@@ -130,8 +128,7 @@ public class PDBfile
       }
       for (int i = 0; i < chains.size(); i++)
       {
-        SequenceI dataset = ( (PDBChain) chains.elementAt(i)).
-            sequence;
+        SequenceI dataset = ((PDBChain) chains.elementAt(i)).sequence;
         dataset.setName(id + "|" + dataset.getName());
         PDBEntry entry = new PDBEntry();
         entry.setId(id);
@@ -140,20 +137,21 @@ public class PDBfile
           entry.setFile(inFile.getAbsolutePath());
         }
         dataset.addPDBId(entry);
-        SequenceI chainseq = dataset.deriveSequence(); // PDBChain objects maintain reference to dataset
+        SequenceI chainseq = dataset.deriveSequence(); // PDBChain objects
+                                                        // maintain reference to
+                                                        // dataset
         seqs.addElement(chainseq);
         AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
-        if (chainannot!=null)
+        if (chainannot != null)
         {
-          for (int ai=0; ai<chainannot.length; ai++)
+          for (int ai = 0; ai < chainannot.length; ai++)
           {
-            chainannot[ai].visible=VisibleChainAnnotation;
+            chainannot[ai].visible = VisibleChainAnnotation;
             annotations.addElement(chainannot[ai]);
           }
         }
       }
-    }
-    catch (OutOfMemoryError er)
+    } catch (OutOfMemoryError er)
     {
       System.out.println("OUT OF MEMORY LOADING PDB FILE");
       throw new IOException("Out of memory loading PDB File");
@@ -164,7 +162,7 @@ public class PDBfile
   {
     for (int i = 0; i < chains.size(); i++)
     {
-      ( (PDBChain) chains.elementAt(i)).makeResidueList();
+      ((PDBChain) chains.elementAt(i)).makeResidueList();
     }
   }
 
@@ -172,7 +170,7 @@ public class PDBfile
   {
     for (int i = 0; i < chains.size(); i++)
     {
-      ( (PDBChain) chains.elementAt(i)).makeCaBondList();
+      ((PDBChain) chains.elementAt(i)).makeCaBondList();
     }
   }
 
@@ -180,7 +178,7 @@ public class PDBfile
   {
     for (int i = 0; i < chains.size(); i++)
     {
-      if ( ( (PDBChain) chains.elementAt(i)).id.equals(id))
+      if (((PDBChain) chains.elementAt(i)).id.equals(id))
       {
         return (PDBChain) chains.elementAt(i);
       }
@@ -193,7 +191,7 @@ public class PDBfile
   {
     for (int i = 0; i < chains.size(); i++)
     {
-      ( (PDBChain) chains.elementAt(i)).setChargeColours();
+      ((PDBChain) chains.elementAt(i)).setChargeColours();
     }
   }
 
@@ -201,7 +199,7 @@ public class PDBfile
   {
     for (int i = 0; i < chains.size(); i++)
     {
-      ( (PDBChain) chains.elementAt(i)).setChainColours(cs);
+      ((PDBChain) chains.elementAt(i)).setChainColours(cs);
     }
   }
 
@@ -209,9 +207,8 @@ public class PDBfile
   {
     for (int i = 0; i < chains.size(); i++)
     {
-      ( (PDBChain) chains.elementAt(i)).setChainColours(
-          Color.getHSBColor(1.0f / (float) i, .4f, 1.0f)
-          );
+      ((PDBChain) chains.elementAt(i)).setChainColours(Color.getHSBColor(
+              1.0f / (float) i, .4f, 1.0f));
     }
   }
 }
diff --git a/src/MCview/Residue.java b/src/MCview/Residue.java
index e99c746..4516b96 100755
--- a/src/MCview/Residue.java
+++ b/src/MCview/Residue.java
@@ -1,49 +1,52 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package MCview;
-
-import java.util.*;
-
-public class Residue
-{
-  Vector atoms = new Vector();
-  int number;
-  int count;
-  int seqnumber;
-
-  public Residue(Vector atoms, int number, int count)
-  {
-    this.atoms = atoms;
-    this.number = number;
-    this.count = count;
-  }
-
-  public Atom findAtom(String name)
-  {
-    for (int i = 0; i < atoms.size(); i++)
-    {
-      if ( ( (Atom) atoms.elementAt(i)).name.equals(name))
-      {
-        return (Atom) atoms.elementAt(i);
-      }
-    }
-
-    return null;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package MCview;
+
+import java.util.*;
+
+public class Residue
+{
+  Vector atoms = new Vector();
+
+  int number;
+
+  int count;
+
+  int seqnumber;
+
+  public Residue(Vector atoms, int number, int count)
+  {
+    this.atoms = atoms;
+    this.number = number;
+    this.count = count;
+  }
+
+  public Atom findAtom(String name)
+  {
+    for (int i = 0; i < atoms.size(); i++)
+    {
+      if (((Atom) atoms.elementAt(i)).name.equals(name))
+      {
+        return (Atom) atoms.elementAt(i);
+      }
+    }
+
+    return null;
+  }
+}
diff --git a/src/MCview/Zsort.java b/src/MCview/Zsort.java
index f7f2c39..05a1fc9 100755
--- a/src/MCview/Zsort.java
+++ b/src/MCview/Zsort.java
@@ -1,75 +1,73 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package MCview;
-
-import java.util.*;
-
-public class Zsort
-{
-  public void Zsort(Vector bonds)
-  {
-    sort(bonds, 0, bonds.size() - 1);
-  }
-
-  public void sort(Vector bonds, int p, int r)
-  {
-    int q;
-
-    if (p < r)
-    {
-      q = partition(bonds, p, r);
-      sort(bonds, p, q);
-      sort(bonds, q + 1, r);
-    }
-  }
-
-  private int partition(Vector bonds, int p, int r)
-  {
-    float x = ( (Bond) bonds.elementAt(p)).start[2];
-    int i = p - 1;
-    int j = r + 1;
-    Bond tmp;
-    while (true)
-    {
-      do
-      {
-        j--;
-      }
-      while ( (j >= 0) && ( ( (Bond) bonds.elementAt(j)).start[2] > x));
-
-      do
-      {
-        i++;
-      }
-      while ( (i < bonds.size()) &&
-             ( ( (Bond) bonds.elementAt(i)).start[2] < x));
-
-      if (i < j)
-      {
-        tmp = (Bond) bonds.elementAt(i);
-        bonds.setElementAt(bonds.elementAt(j), i);
-        bonds.setElementAt(tmp, j);
-      }
-      else
-      {
-        return j;
-      }
-    }
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package MCview;
+
+import java.util.*;
+
+public class Zsort
+{
+  public void Zsort(Vector bonds)
+  {
+    sort(bonds, 0, bonds.size() - 1);
+  }
+
+  public void sort(Vector bonds, int p, int r)
+  {
+    int q;
+
+    if (p < r)
+    {
+      q = partition(bonds, p, r);
+      sort(bonds, p, q);
+      sort(bonds, q + 1, r);
+    }
+  }
+
+  private int partition(Vector bonds, int p, int r)
+  {
+    float x = ((Bond) bonds.elementAt(p)).start[2];
+    int i = p - 1;
+    int j = r + 1;
+    Bond tmp;
+    while (true)
+    {
+      do
+      {
+        j--;
+      } while ((j >= 0) && (((Bond) bonds.elementAt(j)).start[2] > x));
+
+      do
+      {
+        i++;
+      } while ((i < bonds.size())
+              && (((Bond) bonds.elementAt(i)).start[2] < x));
+
+      if (i < j)
+      {
+        tmp = (Bond) bonds.elementAt(i);
+        bonds.setElementAt(bonds.elementAt(j), i);
+        bonds.setElementAt(tmp, j);
+      }
+      else
+      {
+        return j;
+      }
+    }
+  }
+}
diff --git a/src/com/stevesoft/pat/AmpersandRule.java b/src/com/stevesoft/pat/AmpersandRule.java
index f838ab2..0496a19 100755
--- a/src/com/stevesoft/pat/AmpersandRule.java
+++ b/src/com/stevesoft/pat/AmpersandRule.java
@@ -1,29 +1,30 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-/** This implements the $& element of the second argument to
- * Regex.
- * @see com.stevesoft.pat.ReplaceRule
- */
-public final class AmpersandRule
-    extends ReplaceRule
-{
-  public AmpersandRule()
-  {}
-
-  public void apply(StringBufferLike sb, RegRes res)
-  {
-    sb.append(res.stringMatched());
-  }
-
-  public String toString1()
-  {
-    return "$&";
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+/**
+ * This implements the $& element of the second argument to Regex.
+ * 
+ * @see com.stevesoft.pat.ReplaceRule
+ */
+public final class AmpersandRule extends ReplaceRule
+{
+  public AmpersandRule()
+  {
+  }
+
+  public void apply(StringBufferLike sb, RegRes res)
+  {
+    sb.append(res.stringMatched());
+  }
+
+  public String toString1()
+  {
+    return "$&";
+  }
+}
diff --git a/src/com/stevesoft/pat/Any.java b/src/com/stevesoft/pat/Any.java
index e833662..c97599c 100755
--- a/src/com/stevesoft/pat/Any.java
+++ b/src/com/stevesoft/pat/Any.java
@@ -1,55 +1,55 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-import java.util.*;
-
-/** This is the '.' character in a Pattern.  It
- matches any character. */
-class Any
-    extends Pattern
-{
-  public int matchInternal(int pos, Pthings pt)
-  {
-    if (pos < pt.src.length())
-    {
-      if (pt.dotDoesntMatchCR)
-      {
-        if (pt.src.charAt(pos) != '\n')
-        {
-          return nextMatch(pos + 1, pt);
-        }
-      }
-      else
-      {
-        return nextMatch(pos + 1, pt);
-      }
-    }
-    return -1;
-  }
-
-  public String toString()
-  {
-    return "." + nextString();
-  }
-
-  public patInt minChars()
-  {
-    return new patInt(1);
-  }
-
-  public patInt maxChars()
-  {
-    return new patInt(1);
-  }
-
-  public Pattern clone1(Hashtable h)
-  {
-    return new Any();
-  }
-};
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+import java.util.*;
+
+/**
+ * This is the '.' character in a Pattern. It matches any character.
+ */
+class Any extends Pattern
+{
+  public int matchInternal(int pos, Pthings pt)
+  {
+    if (pos < pt.src.length())
+    {
+      if (pt.dotDoesntMatchCR)
+      {
+        if (pt.src.charAt(pos) != '\n')
+        {
+          return nextMatch(pos + 1, pt);
+        }
+      }
+      else
+      {
+        return nextMatch(pos + 1, pt);
+      }
+    }
+    return -1;
+  }
+
+  public String toString()
+  {
+    return "." + nextString();
+  }
+
+  public patInt minChars()
+  {
+    return new patInt(1);
+  }
+
+  public patInt maxChars()
+  {
+    return new patInt(1);
+  }
+
+  public Pattern clone1(Hashtable h)
+  {
+    return new Any();
+  }
+};
diff --git a/src/com/stevesoft/pat/BackG.java b/src/com/stevesoft/pat/BackG.java
index 72c4c9a..69f7f61 100755
--- a/src/com/stevesoft/pat/BackG.java
+++ b/src/com/stevesoft/pat/BackG.java
@@ -1,46 +1,47 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-import java.util.*;
-
-/** This class represents the \G pattern element. */
-class BackG
-    extends Pattern
-{
-  char c, altc, altc2;
-  int mask;
-  public BackG()
-  {
-  }
-
-  public int matchInternal(int pos, Pthings pt)
-  {
-    return pos == pt.lastPos ? nextMatch(pos, pt) : -1;
-  }
-
-  public String toString()
-  {
-    return "\\G" + nextString();
-  }
-
-  public patInt minChars()
-  {
-    return new patInt(1);
-  }
-
-  public patInt maxChars()
-  {
-    return new patInt(1);
-  }
-
-  Pattern clone1(Hashtable h)
-  {
-    return new BackG();
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+import java.util.*;
+
+/** This class represents the \G pattern element. */
+class BackG extends Pattern
+{
+  char c, altc, altc2;
+
+  int mask;
+
+  public BackG()
+  {
+  }
+
+  public int matchInternal(int pos, Pthings pt)
+  {
+    return pos == pt.lastPos ? nextMatch(pos, pt) : -1;
+  }
+
+  public String toString()
+  {
+    return "\\G" + nextString();
+  }
+
+  public patInt minChars()
+  {
+    return new patInt(1);
+  }
+
+  public patInt maxChars()
+  {
+    return new patInt(1);
+  }
+
+  Pattern clone1(Hashtable h)
+  {
+    return new BackG();
+  }
+}
diff --git a/src/com/stevesoft/pat/BackMatch.java b/src/com/stevesoft/pat/BackMatch.java
index 2eed23b..1b166e9 100755
--- a/src/com/stevesoft/pat/BackMatch.java
+++ b/src/com/stevesoft/pat/BackMatch.java
@@ -1,57 +1,57 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-import java.util.*;
-
-/** Provides the ability to match a backreference from within
- * a Pattern.
- */
-class BackMatch
-    extends Pattern
-{
-  int id;
-  BackMatch(int id)
-  {
-    this.id = id;
-  }
-
-  public String toString()
-  {
-    return "\\" + (id) + nextString();
-  }
-
-  public int matchInternal(int pos, Pthings p)
-  {
-    int i1 = p.marks[id];
-    int i2 = p.marks[id + p.nMarks];
-    int imax = i2 - i1;
-    if (i1 < 0 || imax < 0 || pos + imax > p.src.length())
-    {
-      return -1;
-    }
-    int ns = p.src.length() - pos;
-    if (imax < ns)
-    {
-      ns = imax;
-    }
-    for (int i = 0; i < ns; i++)
-    {
-      if (p.src.charAt(i + i1) != p.src.charAt(pos + i))
-      {
-        return -1;
-      }
-    }
-    return nextMatch(pos + imax, p);
-  }
-
-  Pattern clone1(Hashtable h)
-  {
-    return new BackMatch(id);
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+import java.util.*;
+
+/**
+ * Provides the ability to match a backreference from within a Pattern.
+ */
+class BackMatch extends Pattern
+{
+  int id;
+
+  BackMatch(int id)
+  {
+    this.id = id;
+  }
+
+  public String toString()
+  {
+    return "\\" + (id) + nextString();
+  }
+
+  public int matchInternal(int pos, Pthings p)
+  {
+    int i1 = p.marks[id];
+    int i2 = p.marks[id + p.nMarks];
+    int imax = i2 - i1;
+    if (i1 < 0 || imax < 0 || pos + imax > p.src.length())
+    {
+      return -1;
+    }
+    int ns = p.src.length() - pos;
+    if (imax < ns)
+    {
+      ns = imax;
+    }
+    for (int i = 0; i < ns; i++)
+    {
+      if (p.src.charAt(i + i1) != p.src.charAt(pos + i))
+      {
+        return -1;
+      }
+    }
+    return nextMatch(pos + imax, p);
+  }
+
+  Pattern clone1(Hashtable h)
+  {
+    return new BackMatch(id);
+  }
+}
diff --git a/src/com/stevesoft/pat/BackRefRule.java b/src/com/stevesoft/pat/BackRefRule.java
index 8488ba3..daacbc1 100755
--- a/src/com/stevesoft/pat/BackRefRule.java
+++ b/src/com/stevesoft/pat/BackRefRule.java
@@ -1,38 +1,40 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-/** This method implements the pattern elements $1, $2, etc in
-    a substitution rule. The apply(StringBufferLike sb,RegRes rr) method of this ReplaceRule
-    simply appends the contents of rr.stringMatched(n), where n is
-    the integer supplied to the constructor. */
-public class BackRefRule
-    extends ReplaceRule
-{
-  int n;
-  public BackRefRule(int n)
-  {
-    this.n = n;
-  }
-
-  public void apply(StringBufferLike sb, RegRes res)
-  {
-    String x = res.stringMatched(n);
-    sb.append(x == null ? "" : x);
-  }
-
-  public String toString1()
-  {
-    return "$" + n;
-  }
-
-  public Object clone1()
-  {
-    return new BackRefRule(n);
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+/**
+ * This method implements the pattern elements $1, $2, etc in a substitution
+ * rule. The apply(StringBufferLike sb,RegRes rr) method of this ReplaceRule
+ * simply appends the contents of rr.stringMatched(n), where n is the integer
+ * supplied to the constructor.
+ */
+public class BackRefRule extends ReplaceRule
+{
+  int n;
+
+  public BackRefRule(int n)
+  {
+    this.n = n;
+  }
+
+  public void apply(StringBufferLike sb, RegRes res)
+  {
+    String x = res.stringMatched(n);
+    sb.append(x == null ? "" : x);
+  }
+
+  public String toString1()
+  {
+    return "$" + n;
+  }
+
+  public Object clone1()
+  {
+    return new BackRefRule(n);
+  }
+}
diff --git a/src/com/stevesoft/pat/Backup.java b/src/com/stevesoft/pat/Backup.java
index 31c41c4..1986460 100755
--- a/src/com/stevesoft/pat/Backup.java
+++ b/src/com/stevesoft/pat/Backup.java
@@ -1,52 +1,54 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-import java.util.*;
-
-/** Implements the (?&lt;number) Pattern, where number is
- an integer telling us how far to back up in the Pattern.
- Not in perl 5. It also allows (?&gt;number). */
-class Backup
-    extends Pattern
-{
-  int bk;
-  Backup(int ii)
-  {
-    bk = ii;
-  }
-
-  public String toString()
-  {
-    return "(?" + (bk < 0 ? ">" + ( -bk) : "<" + bk) + ")" + nextString();
-  }
-
-  public int matchInternal(int pos, Pthings pt)
-  {
-    if (pos < bk)
-    {
-      return -1;
-    }
-    return nextMatch(pos - bk, pt);
-  }
-
-  public patInt minChars()
-  {
-    return new patInt( -bk);
-  }
-
-  public patInt maxChars()
-  {
-    return new patInt( -bk);
-  }
-
-  public Pattern clone1(Hashtable h)
-  {
-    return new Backup(bk);
-  }
-};
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+import java.util.*;
+
+/**
+ * Implements the (?&lt;number) Pattern, where number is an integer telling us
+ * how far to back up in the Pattern. Not in perl 5. It also allows
+ * (?&gt;number).
+ */
+class Backup extends Pattern
+{
+  int bk;
+
+  Backup(int ii)
+  {
+    bk = ii;
+  }
+
+  public String toString()
+  {
+    return "(?" + (bk < 0 ? ">" + (-bk) : "<" + bk) + ")" + nextString();
+  }
+
+  public int matchInternal(int pos, Pthings pt)
+  {
+    if (pos < bk)
+    {
+      return -1;
+    }
+    return nextMatch(pos - bk, pt);
+  }
+
+  public patInt minChars()
+  {
+    return new patInt(-bk);
+  }
+
+  public patInt maxChars()
+  {
+    return new patInt(-bk);
+  }
+
+  public Pattern clone1(Hashtable h)
+  {
+    return new Backup(bk);
+  }
+};
diff --git a/src/com/stevesoft/pat/BasicStringBufferLike.java b/src/com/stevesoft/pat/BasicStringBufferLike.java
index 7563703..adb10f1 100755
--- a/src/com/stevesoft/pat/BasicStringBufferLike.java
+++ b/src/com/stevesoft/pat/BasicStringBufferLike.java
@@ -1,22 +1,23 @@
-package //
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-    com.stevesoft.pat;
-
-/** An abstraction of the StringBuffer which only
-    implements a subset of StringBuffer's methods.
- */
-public interface BasicStringBufferLike
-{
-  public void append(char c);
-
-  public void append(String s);
-
-  public StringLike toStringLike();
-
-  public Object unwrap();
-}
+package //
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+com.stevesoft.pat;
+
+/**
+ * An abstraction of the StringBuffer which only implements a subset of
+ * StringBuffer's methods.
+ */
+public interface BasicStringBufferLike
+{
+  public void append(char c);
+
+  public void append(String s);
+
+  public StringLike toStringLike();
+
+  public Object unwrap();
+}
diff --git a/src/com/stevesoft/pat/Bits.java b/src/com/stevesoft/pat/Bits.java
index f26d1fb..05b3d34 100755
--- a/src/com/stevesoft/pat/Bits.java
+++ b/src/com/stevesoft/pat/Bits.java
@@ -1,3096 +1,3040 @@
-package //
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-    com.stevesoft.pat;
-
-public class Bits
-{
-  char[] carray;
-  Bits(char[] carray)
-  {
-    this.carray = carray;
-  }
-
-  public boolean get(int i)
-  {
-    return ( (carray[i >> 4]) & (1 << (i & 15))) != 0;
-  }
-
-  public void set(int i, boolean b)
-  {
-    if (b)
-    {
-      carray[i >> 4] |= (char) 1 << (i & 15);
-    }
-    else
-    {
-      carray[i >> 4] &= (char)~ (1 << (i & 15));
-    }
-  }
-
-  /*
-     public static String n4(char c) {
-    String s = Integer.toHexString(c);
-    while(s.length()<4)
-      s = "0"+s;
-    return s;
-     }
-     static abstract class Tester {
-    abstract boolean test(char c);
-     }
-     public static void main(String[] args) throws Exception {
-    //pw_s.println("  static {");
-    FileWriter fw = new FileWriter("x.out");
-    fw.close();
-    test("upper",new Tester() {
-      boolean test(char c) {
-        return Character.isUpperCase(c);
-      }
-    });
-    test("lower",new Tester() {
-      boolean test(char c) {
-        return Character.isLowerCase(c);
-      }
-    });
-    test("title",new Tester() {
-      boolean test(char c) {
-        return Character.isLowerCase(c);
-      }
-    });
-    test("currency",new Tester() {
-      boolean test(char c) {
-        return Character.getType(c)==Character.CURRENCY_SYMBOL;
-      }
-    });
-    test("decimal_digit",new Tester() {
-      boolean test(char c) {
-        return Character.getType(c)==Character.DECIMAL_DIGIT_NUMBER;
-      }
-    });
-    test("math",new Tester() {
-      boolean test(char c) {
-        return Character.getType(c)==Character.MATH_SYMBOL;
-      }
-    });
-    test("letter",new Tester() {
-      boolean test(char c) {
-        return Character.isLetter(c);
-      }
-    });
-    test("white",new Tester() {
-      boolean test(char c) {
-        return Character.isWhitespace(c);
-      }
-    });
-    test("punct",new Tester() {
-      boolean test(char c) {
-    boolean r = false;
-        switch(Character.getType(c)) {
-        case Character.DASH_PUNCTUATION:
-        case Character.START_PUNCTUATION:
-        case Character.END_PUNCTUATION:
-        case Character.CONNECTOR_PUNCTUATION:
-        case Character.OTHER_PUNCTUATION:
-   r = true;
-   break;
-    default:
-   r = false;
-   break;
-    }
-    return r;
-      }
-    });
-    //pw_s.println("  }");
-    fw = new FileWriter("x.out",true);
-    fw.write(sw.toString());
-    fw.close();
-     }
-     static StringWriter sw = new StringWriter();
-     static PrintWriter pw_s = new PrintWriter(sw,true);
-     public static void test(String var,Tester t) throws Exception {
-
-    char[] ca = new char[(66536 >> 4)+1];
-    Bits b = new Bits(ca);
-    FileWriter fw = new FileWriter("x.out",true);
-    PrintWriter pw = new PrintWriter(fw);
-
-    //pw_s.println("    "+var+"_f();");
-    pw.println("  public static Bits "+var+";");
-    pw.println("  static void "+var+"_f() {");
-    pw.println("    char[] data = new char["+ca.length+"];");
-    pw.println("    "+var+" = new Bits(data);");
-    for(int i=0;i<66536;i++) {
-      char c = (char)i;
-      //b.set(i,Character.getType(c)==Character.CURRENCY_SYMBOL);
-      b.set(i,t.test(c));
-    }
-    for(int i=0;i<ca.length;i++) {
-      if(ca[i] != 0) {
-        pw.println("    data["+i+"]=(char)0x"+n4(ca[i])+";");
-      }
-    }
-    pw.println();
-    pw.println("  }");
-
-    pw.close();
-     }
-   */
-  public static Bits upper;
-  static void upper_f()
-  {
-    char[] data = new char[4159];
-    upper = new Bits(data);
-    data[4] = (char) 0xfffe;
-    data[5] = (char) 0x07ff;
-    data[12] = (char) 0xffff;
-    data[13] = (char) 0x7f7f;
-    data[16] = (char) 0x5555;
-    data[17] = (char) 0x5555;
-    data[18] = (char) 0x5555;
-    data[19] = (char) 0xaa55;
-    data[20] = (char) 0x54aa;
-    data[21] = (char) 0x5555;
-    data[22] = (char) 0x5555;
-    data[23] = (char) 0x2b55;
-    data[24] = (char) 0xced6;
-    data[25] = (char) 0xb1db;
-    data[26] = (char) 0xd2d5;
-    data[27] = (char) 0x11ae;
-    data[28] = (char) 0xa490;
-    data[29] = (char) 0x4aaa;
-    data[30] = (char) 0x5555;
-    data[31] = (char) 0x5412;
-    data[32] = (char) 0x5555;
-    data[33] = (char) 0x0055;
-    data[56] = (char) 0xd740;
-    data[57] = (char) 0xfffe;
-    data[58] = (char) 0x0ffb;
-    data[61] = (char) 0x541c;
-    data[62] = (char) 0x5555;
-    data[64] = (char) 0xdffe;
-    data[65] = (char) 0xffff;
-    data[66] = (char) 0xffff;
-    data[70] = (char) 0x5555;
-    data[71] = (char) 0x5555;
-    data[72] = (char) 0x0001;
-    data[73] = (char) 0x5555;
-    data[74] = (char) 0x5555;
-    data[75] = (char) 0x5555;
-    data[76] = (char) 0x088a;
-    data[77] = (char) 0x5555;
-    data[78] = (char) 0x4555;
-    data[79] = (char) 0x0115;
-    data[83] = (char) 0xfffe;
-    data[84] = (char) 0xffff;
-    data[85] = (char) 0x007f;
-    data[266] = (char) 0xffff;
-    data[267] = (char) 0xffff;
-    data[268] = (char) 0x003f;
-    data[480] = (char) 0x5555;
-    data[481] = (char) 0x5555;
-    data[482] = (char) 0x5555;
-    data[483] = (char) 0x5555;
-    data[484] = (char) 0x5555;
-    data[485] = (char) 0x5555;
-    data[486] = (char) 0x5555;
-    data[487] = (char) 0x5555;
-    data[488] = (char) 0x5555;
-    data[489] = (char) 0x0015;
-    data[490] = (char) 0x5555;
-    data[491] = (char) 0x5555;
-    data[492] = (char) 0x5555;
-    data[493] = (char) 0x5555;
-    data[494] = (char) 0x5555;
-    data[495] = (char) 0x0155;
-    data[496] = (char) 0xff00;
-    data[497] = (char) 0x3f00;
-    data[498] = (char) 0xff00;
-    data[499] = (char) 0xff00;
-    data[500] = (char) 0x3f00;
-    data[501] = (char) 0xaa00;
-    data[502] = (char) 0xff00;
-    data[504] = (char) 0xff00;
-    data[505] = (char) 0xff00;
-    data[506] = (char) 0xff00;
-    data[507] = (char) 0x5f00;
-    data[508] = (char) 0x1f00;
-    data[509] = (char) 0x0f00;
-    data[510] = (char) 0x1f00;
-    data[511] = (char) 0x1f00;
-    data[528] = (char) 0x3884;
-    data[529] = (char) 0x3f27;
-    data[530] = (char) 0x3d50;
-    data[531] = (char) 0x000b;
-    data[4082] = (char) 0xfffe;
-    data[4083] = (char) 0x07ff;
-    data[4100] = (char) 0xfffe;
-    data[4101] = (char) 0x07ff;
-    data[4108] = (char) 0xffff;
-    data[4109] = (char) 0x7f7f;
-    data[4112] = (char) 0x5555;
-    data[4113] = (char) 0x5555;
-    data[4114] = (char) 0x5555;
-    data[4115] = (char) 0xaa55;
-    data[4116] = (char) 0x54aa;
-    data[4117] = (char) 0x5555;
-    data[4118] = (char) 0x5555;
-    data[4119] = (char) 0x2b55;
-    data[4120] = (char) 0xced6;
-    data[4121] = (char) 0xb1db;
-    data[4122] = (char) 0xd2d5;
-    data[4123] = (char) 0x11ae;
-    data[4124] = (char) 0xa490;
-    data[4125] = (char) 0x4aaa;
-    data[4126] = (char) 0x5555;
-    data[4127] = (char) 0x5412;
-    data[4128] = (char) 0x5555;
-    data[4129] = (char) 0x0055;
-    data[4152] = (char) 0xd740;
-    data[4153] = (char) 0xfffe;
-    data[4154] = (char) 0x0ffb;
-    data[4157] = (char) 0x541c;
-    data[4158] = (char) 0x0055;
-
-  }
-
-  public static Bits lower;
-  static void lower_f()
-  {
-    char[] data = new char[4159];
-    lower = new Bits(data);
-    data[6] = (char) 0xfffe;
-    data[7] = (char) 0x07ff;
-    data[10] = (char) 0x0400;
-    data[11] = (char) 0x0420;
-    data[13] = (char) 0x8000;
-    data[14] = (char) 0xffff;
-    data[15] = (char) 0xff7f;
-    data[16] = (char) 0xaaaa;
-    data[17] = (char) 0xaaaa;
-    data[18] = (char) 0xaaaa;
-    data[19] = (char) 0x55aa;
-    data[20] = (char) 0xab55;
-    data[21] = (char) 0xaaaa;
-    data[22] = (char) 0xaaaa;
-    data[23] = (char) 0xd4aa;
-    data[24] = (char) 0x3129;
-    data[25] = (char) 0x4e24;
-    data[26] = (char) 0x292a;
-    data[27] = (char) 0x2651;
-    data[28] = (char) 0x5240;
-    data[29] = (char) 0xb555;
-    data[30] = (char) 0xaaaa;
-    data[31] = (char) 0xa829;
-    data[32] = (char) 0xaaaa;
-    data[33] = (char) 0x00aa;
-    data[37] = (char) 0xffff;
-    data[38] = (char) 0xffff;
-    data[39] = (char) 0xffff;
-    data[40] = (char) 0xffff;
-    data[41] = (char) 0xffff;
-    data[42] = (char) 0x01ff;
-    data[57] = (char) 0x0001;
-    data[58] = (char) 0xf000;
-    data[59] = (char) 0xffff;
-    data[60] = (char) 0x7fff;
-    data[61] = (char) 0x0063;
-    data[62] = (char) 0xaaa8;
-    data[63] = (char) 0x0007;
-    data[67] = (char) 0xffff;
-    data[68] = (char) 0xffff;
-    data[69] = (char) 0xdffe;
-    data[70] = (char) 0xaaaa;
-    data[71] = (char) 0xaaaa;
-    data[72] = (char) 0x0002;
-    data[73] = (char) 0xaaaa;
-    data[74] = (char) 0xaaaa;
-    data[75] = (char) 0xaaaa;
-    data[76] = (char) 0x1114;
-    data[77] = (char) 0xaaaa;
-    data[78] = (char) 0x8aaa;
-    data[79] = (char) 0x022a;
-    data[86] = (char) 0xfffe;
-    data[87] = (char) 0xffff;
-    data[88] = (char) 0x00ff;
-    data[269] = (char) 0xffff;
-    data[270] = (char) 0xffff;
-    data[271] = (char) 0x007f;
-    data[480] = (char) 0xaaaa;
-    data[481] = (char) 0xaaaa;
-    data[482] = (char) 0xaaaa;
-    data[483] = (char) 0xaaaa;
-    data[484] = (char) 0xaaaa;
-    data[485] = (char) 0xaaaa;
-    data[486] = (char) 0xaaaa;
-    data[487] = (char) 0xaaaa;
-    data[488] = (char) 0xaaaa;
-    data[489] = (char) 0x0fea;
-    data[490] = (char) 0xaaaa;
-    data[491] = (char) 0xaaaa;
-    data[492] = (char) 0xaaaa;
-    data[493] = (char) 0xaaaa;
-    data[494] = (char) 0xaaaa;
-    data[495] = (char) 0x02aa;
-    data[496] = (char) 0x00ff;
-    data[497] = (char) 0x003f;
-    data[498] = (char) 0x00ff;
-    data[499] = (char) 0x00ff;
-    data[500] = (char) 0x003f;
-    data[501] = (char) 0x00ff;
-    data[502] = (char) 0x00ff;
-    data[503] = (char) 0x3fff;
-    data[504] = (char) 0x00ff;
-    data[505] = (char) 0x00ff;
-    data[506] = (char) 0x00ff;
-    data[507] = (char) 0x00df;
-    data[508] = (char) 0x00dc;
-    data[509] = (char) 0x00cf;
-    data[510] = (char) 0x00ff;
-    data[511] = (char) 0x00dc;
-    data[519] = (char) 0x8000;
-    data[528] = (char) 0xc400;
-    data[529] = (char) 0x0008;
-    data[530] = (char) 0xc000;
-    data[531] = (char) 0x0010;
-    data[4016] = (char) 0x007f;
-    data[4017] = (char) 0x00f8;
-    data[4084] = (char) 0xfffe;
-    data[4085] = (char) 0x07ff;
-    data[4102] = (char) 0xfffe;
-    data[4103] = (char) 0x07ff;
-    data[4106] = (char) 0x0400;
-    data[4107] = (char) 0x0420;
-    data[4109] = (char) 0x8000;
-    data[4110] = (char) 0xffff;
-    data[4111] = (char) 0xff7f;
-    data[4112] = (char) 0xaaaa;
-    data[4113] = (char) 0xaaaa;
-    data[4114] = (char) 0xaaaa;
-    data[4115] = (char) 0x55aa;
-    data[4116] = (char) 0xab55;
-    data[4117] = (char) 0xaaaa;
-    data[4118] = (char) 0xaaaa;
-    data[4119] = (char) 0xd4aa;
-    data[4120] = (char) 0x3129;
-    data[4121] = (char) 0x4e24;
-    data[4122] = (char) 0x292a;
-    data[4123] = (char) 0x2651;
-    data[4124] = (char) 0x5240;
-    data[4125] = (char) 0xb555;
-    data[4126] = (char) 0xaaaa;
-    data[4127] = (char) 0xa829;
-    data[4128] = (char) 0xaaaa;
-    data[4129] = (char) 0x00aa;
-    data[4133] = (char) 0xffff;
-    data[4134] = (char) 0xffff;
-    data[4135] = (char) 0xffff;
-    data[4136] = (char) 0xffff;
-    data[4137] = (char) 0xffff;
-    data[4138] = (char) 0x01ff;
-    data[4153] = (char) 0x0001;
-    data[4154] = (char) 0xf000;
-    data[4155] = (char) 0xffff;
-    data[4156] = (char) 0x7fff;
-    data[4157] = (char) 0x0063;
-    data[4158] = (char) 0x00a8;
-
-  }
-
-  public static Bits title;
-  static void title_f()
-  {
-    char[] data = new char[4159];
-    title = new Bits(data);
-    data[6] = (char) 0xfffe;
-    data[7] = (char) 0x07ff;
-    data[10] = (char) 0x0400;
-    data[11] = (char) 0x0420;
-    data[13] = (char) 0x8000;
-    data[14] = (char) 0xffff;
-    data[15] = (char) 0xff7f;
-    data[16] = (char) 0xaaaa;
-    data[17] = (char) 0xaaaa;
-    data[18] = (char) 0xaaaa;
-    data[19] = (char) 0x55aa;
-    data[20] = (char) 0xab55;
-    data[21] = (char) 0xaaaa;
-    data[22] = (char) 0xaaaa;
-    data[23] = (char) 0xd4aa;
-    data[24] = (char) 0x3129;
-    data[25] = (char) 0x4e24;
-    data[26] = (char) 0x292a;
-    data[27] = (char) 0x2651;
-    data[28] = (char) 0x5240;
-    data[29] = (char) 0xb555;
-    data[30] = (char) 0xaaaa;
-    data[31] = (char) 0xa829;
-    data[32] = (char) 0xaaaa;
-    data[33] = (char) 0x00aa;
-    data[37] = (char) 0xffff;
-    data[38] = (char) 0xffff;
-    data[39] = (char) 0xffff;
-    data[40] = (char) 0xffff;
-    data[41] = (char) 0xffff;
-    data[42] = (char) 0x01ff;
-    data[57] = (char) 0x0001;
-    data[58] = (char) 0xf000;
-    data[59] = (char) 0xffff;
-    data[60] = (char) 0x7fff;
-    data[61] = (char) 0x0063;
-    data[62] = (char) 0xaaa8;
-    data[63] = (char) 0x0007;
-    data[67] = (char) 0xffff;
-    data[68] = (char) 0xffff;
-    data[69] = (char) 0xdffe;
-    data[70] = (char) 0xaaaa;
-    data[71] = (char) 0xaaaa;
-    data[72] = (char) 0x0002;
-    data[73] = (char) 0xaaaa;
-    data[74] = (char) 0xaaaa;
-    data[75] = (char) 0xaaaa;
-    data[76] = (char) 0x1114;
-    data[77] = (char) 0xaaaa;
-    data[78] = (char) 0x8aaa;
-    data[79] = (char) 0x022a;
-    data[86] = (char) 0xfffe;
-    data[87] = (char) 0xffff;
-    data[88] = (char) 0x00ff;
-    data[269] = (char) 0xffff;
-    data[270] = (char) 0xffff;
-    data[271] = (char) 0x007f;
-    data[480] = (char) 0xaaaa;
-    data[481] = (char) 0xaaaa;
-    data[482] = (char) 0xaaaa;
-    data[483] = (char) 0xaaaa;
-    data[484] = (char) 0xaaaa;
-    data[485] = (char) 0xaaaa;
-    data[486] = (char) 0xaaaa;
-    data[487] = (char) 0xaaaa;
-    data[488] = (char) 0xaaaa;
-    data[489] = (char) 0x0fea;
-    data[490] = (char) 0xaaaa;
-    data[491] = (char) 0xaaaa;
-    data[492] = (char) 0xaaaa;
-    data[493] = (char) 0xaaaa;
-    data[494] = (char) 0xaaaa;
-    data[495] = (char) 0x02aa;
-    data[496] = (char) 0x00ff;
-    data[497] = (char) 0x003f;
-    data[498] = (char) 0x00ff;
-    data[499] = (char) 0x00ff;
-    data[500] = (char) 0x003f;
-    data[501] = (char) 0x00ff;
-    data[502] = (char) 0x00ff;
-    data[503] = (char) 0x3fff;
-    data[504] = (char) 0x00ff;
-    data[505] = (char) 0x00ff;
-    data[506] = (char) 0x00ff;
-    data[507] = (char) 0x00df;
-    data[508] = (char) 0x00dc;
-    data[509] = (char) 0x00cf;
-    data[510] = (char) 0x00ff;
-    data[511] = (char) 0x00dc;
-    data[519] = (char) 0x8000;
-    data[528] = (char) 0xc400;
-    data[529] = (char) 0x0008;
-    data[530] = (char) 0xc000;
-    data[531] = (char) 0x0010;
-    data[4016] = (char) 0x007f;
-    data[4017] = (char) 0x00f8;
-    data[4084] = (char) 0xfffe;
-    data[4085] = (char) 0x07ff;
-    data[4102] = (char) 0xfffe;
-    data[4103] = (char) 0x07ff;
-    data[4106] = (char) 0x0400;
-    data[4107] = (char) 0x0420;
-    data[4109] = (char) 0x8000;
-    data[4110] = (char) 0xffff;
-    data[4111] = (char) 0xff7f;
-    data[4112] = (char) 0xaaaa;
-    data[4113] = (char) 0xaaaa;
-    data[4114] = (char) 0xaaaa;
-    data[4115] = (char) 0x55aa;
-    data[4116] = (char) 0xab55;
-    data[4117] = (char) 0xaaaa;
-    data[4118] = (char) 0xaaaa;
-    data[4119] = (char) 0xd4aa;
-    data[4120] = (char) 0x3129;
-    data[4121] = (char) 0x4e24;
-    data[4122] = (char) 0x292a;
-    data[4123] = (char) 0x2651;
-    data[4124] = (char) 0x5240;
-    data[4125] = (char) 0xb555;
-    data[4126] = (char) 0xaaaa;
-    data[4127] = (char) 0xa829;
-    data[4128] = (char) 0xaaaa;
-    data[4129] = (char) 0x00aa;
-    data[4133] = (char) 0xffff;
-    data[4134] = (char) 0xffff;
-    data[4135] = (char) 0xffff;
-    data[4136] = (char) 0xffff;
-    data[4137] = (char) 0xffff;
-    data[4138] = (char) 0x01ff;
-    data[4153] = (char) 0x0001;
-    data[4154] = (char) 0xf000;
-    data[4155] = (char) 0xffff;
-    data[4156] = (char) 0x7fff;
-    data[4157] = (char) 0x0063;
-    data[4158] = (char) 0x00a8;
-
-  }
-
-  public static Bits currency;
-  static void currency_f()
-  {
-    char[] data = new char[4159];
-    currency = new Bits(data);
-    data[2] = (char) 0x0010;
-    data[10] = (char) 0x003c;
-    data[159] = (char) 0x000c;
-    data[227] = (char) 0x8000;
-    data[522] = (char) 0x1fff;
-    data[4070] = (char) 0x0200;
-    data[4080] = (char) 0x0010;
-    data[4094] = (char) 0x0063;
-    data[4098] = (char) 0x0010;
-    data[4106] = (char) 0x003c;
-
-  }
-
-  public static Bits decimal_digit;
-  static void decimal_digit_f()
-  {
-    char[] data = new char[4159];
-    decimal_digit = new Bits(data);
-    data[3] = (char) 0x03ff;
-    data[102] = (char) 0x03ff;
-    data[111] = (char) 0x03ff;
-    data[150] = (char) 0xffc0;
-    data[158] = (char) 0xffc0;
-    data[166] = (char) 0xffc0;
-    data[174] = (char) 0xffc0;
-    data[182] = (char) 0xffc0;
-    data[190] = (char) 0xff80;
-    data[198] = (char) 0xffc0;
-    data[206] = (char) 0xffc0;
-    data[214] = (char) 0xffc0;
-    data[229] = (char) 0x03ff;
-    data[237] = (char) 0x03ff;
-    data[242] = (char) 0x03ff;
-    data[4081] = (char) 0x03ff;
-    data[4099] = (char) 0x03ff;
-
-  }
-
-  public static Bits math;
-  static void math_f()
-  {
-    char[] data = new char[4159];
-    math = new Bits(data);
-    data[2] = (char) 0x0800;
-    data[3] = (char) 0x7000;
-    data[7] = (char) 0x5000;
-    data[10] = (char) 0x1000;
-    data[11] = (char) 0x0002;
-    data[13] = (char) 0x0080;
-    data[15] = (char) 0x0080;
-    data[516] = (char) 0x0010;
-    data[519] = (char) 0x1c00;
-    data[520] = (char) 0x1c00;
-    data[537] = (char) 0x001f;
-    data[541] = (char) 0x0014;
-    data[544] = (char) 0xffff;
-    data[545] = (char) 0xffff;
-    data[546] = (char) 0xffff;
-    data[547] = (char) 0xffff;
-    data[548] = (char) 0xffff;
-    data[549] = (char) 0xffff;
-    data[550] = (char) 0xffff;
-    data[551] = (char) 0xffff;
-    data[552] = (char) 0xffff;
-    data[553] = (char) 0xffff;
-    data[554] = (char) 0xffff;
-    data[555] = (char) 0xffff;
-    data[556] = (char) 0xffff;
-    data[557] = (char) 0xffff;
-    data[558] = (char) 0xffff;
-    data[559] = (char) 0x0003;
-    data[560] = (char) 0x0f00;
-    data[562] = (char) 0x0003;
-    data[4018] = (char) 0x0200;
-    data[4070] = (char) 0x0074;
-    data[4080] = (char) 0x0800;
-    data[4081] = (char) 0x7000;
-    data[4085] = (char) 0x5000;
-    data[4094] = (char) 0x1f04;
-    data[4098] = (char) 0x0800;
-    data[4099] = (char) 0x7000;
-    data[4103] = (char) 0x5000;
-    data[4106] = (char) 0x1000;
-    data[4107] = (char) 0x0002;
-    data[4109] = (char) 0x0080;
-    data[4111] = (char) 0x0080;
-
-  }
-
-  public static Bits letter;
-  static void letter_f()
-  {
-    char[] data = new char[4159];
-    letter = new Bits(data);
-    data[4] = (char) 0xfffe;
-    data[5] = (char) 0x07ff;
-    data[6] = (char) 0xfffe;
-    data[7] = (char) 0x07ff;
-    data[10] = (char) 0x0400;
-    data[11] = (char) 0x0420;
-    data[12] = (char) 0xffff;
-    data[13] = (char) 0xff7f;
-    data[14] = (char) 0xffff;
-    data[15] = (char) 0xff7f;
-    data[16] = (char) 0xffff;
-    data[17] = (char) 0xffff;
-    data[18] = (char) 0xffff;
-    data[19] = (char) 0xffff;
-    data[20] = (char) 0xffff;
-    data[21] = (char) 0xffff;
-    data[22] = (char) 0xffff;
-    data[23] = (char) 0xffff;
-    data[24] = (char) 0xffff;
-    data[25] = (char) 0xffff;
-    data[26] = (char) 0xffff;
-    data[27] = (char) 0xffff;
-    data[28] = (char) 0xffff;
-    data[29] = (char) 0xffff;
-    data[30] = (char) 0xffff;
-    data[31] = (char) 0xfc3f;
-    data[32] = (char) 0xffff;
-    data[33] = (char) 0x00ff;
-    data[37] = (char) 0xffff;
-    data[38] = (char) 0xffff;
-    data[39] = (char) 0xffff;
-    data[40] = (char) 0xffff;
-    data[41] = (char) 0xffff;
-    data[42] = (char) 0x01ff;
-    data[43] = (char) 0xf9ff;
-    data[44] = (char) 0x0003;
-    data[45] = (char) 0x0003;
-    data[46] = (char) 0x001f;
-    data[55] = (char) 0x0400;
-    data[56] = (char) 0xd740;
-    data[57] = (char) 0xffff;
-    data[58] = (char) 0xfffb;
-    data[59] = (char) 0xffff;
-    data[60] = (char) 0x7fff;
-    data[61] = (char) 0x547f;
-    data[62] = (char) 0xfffd;
-    data[63] = (char) 0x000f;
-    data[64] = (char) 0xdffe;
-    data[65] = (char) 0xffff;
-    data[66] = (char) 0xffff;
-    data[67] = (char) 0xffff;
-    data[68] = (char) 0xffff;
-    data[69] = (char) 0xdffe;
-    data[70] = (char) 0xffff;
-    data[71] = (char) 0xffff;
-    data[72] = (char) 0x0003;
-    data[73] = (char) 0xffff;
-    data[74] = (char) 0xffff;
-    data[75] = (char) 0xffff;
-    data[76] = (char) 0x199f;
-    data[77] = (char) 0xffff;
-    data[78] = (char) 0xcfff;
-    data[79] = (char) 0x033f;
-    data[83] = (char) 0xfffe;
-    data[84] = (char) 0xffff;
-    data[85] = (char) 0x027f;
-    data[86] = (char) 0xfffe;
-    data[87] = (char) 0xffff;
-    data[88] = (char) 0x00ff;
-    data[93] = (char) 0xffff;
-    data[94] = (char) 0x07ff;
-    data[95] = (char) 0x0007;
-    data[98] = (char) 0xfffe;
-    data[99] = (char) 0x07ff;
-    data[100] = (char) 0x07ff;
-    data[103] = (char) 0xfffe;
-    data[104] = (char) 0xffff;
-    data[105] = (char) 0xffff;
-    data[106] = (char) 0xffff;
-    data[107] = (char) 0x7cff;
-    data[108] = (char) 0x7fff;
-    data[109] = (char) 0x002f;
-    data[110] = (char) 0x0060;
-    data[144] = (char) 0xffe0;
-    data[145] = (char) 0xffff;
-    data[146] = (char) 0xffff;
-    data[147] = (char) 0x23ff;
-    data[149] = (char) 0xff00;
-    data[150] = (char) 0x0003;
-    data[152] = (char) 0x9fe0;
-    data[153] = (char) 0xfff9;
-    data[154] = (char) 0xfdff;
-    data[155] = (char) 0x03c5;
-    data[157] = (char) 0xb000;
-    data[158] = (char) 0x0003;
-    data[159] = (char) 0x0003;
-    data[160] = (char) 0x87e0;
-    data[161] = (char) 0xfff9;
-    data[162] = (char) 0xfdff;
-    data[163] = (char) 0x036d;
-    data[165] = (char) 0x5e00;
-    data[167] = (char) 0x001c;
-    data[168] = (char) 0xafe0;
-    data[169] = (char) 0xfffb;
-    data[170] = (char) 0xfdff;
-    data[171] = (char) 0x23ed;
-    data[174] = (char) 0x0001;
-    data[176] = (char) 0x9fe0;
-    data[177] = (char) 0xfff9;
-    data[178] = (char) 0xfdff;
-    data[179] = (char) 0x23cd;
-    data[181] = (char) 0xb000;
-    data[182] = (char) 0x0003;
-    data[184] = (char) 0xc7e0;
-    data[185] = (char) 0xd63d;
-    data[186] = (char) 0xc718;
-    data[187] = (char) 0x03bf;
-    data[192] = (char) 0xdfe0;
-    data[193] = (char) 0xfffd;
-    data[194] = (char) 0xfdff;
-    data[195] = (char) 0x03ef;
-    data[198] = (char) 0x0003;
-    data[200] = (char) 0xdfe0;
-    data[201] = (char) 0xfffd;
-    data[202] = (char) 0xfdff;
-    data[203] = (char) 0x03ef;
-    data[205] = (char) 0x4000;
-    data[206] = (char) 0x0003;
-    data[208] = (char) 0xdfe0;
-    data[209] = (char) 0xfffd;
-    data[210] = (char) 0xfdff;
-    data[211] = (char) 0x03ff;
-    data[214] = (char) 0x0003;
-    data[224] = (char) 0xfffe;
-    data[225] = (char) 0xffff;
-    data[226] = (char) 0x7fff;
-    data[227] = (char) 0x000d;
-    data[228] = (char) 0x007f;
-    data[232] = (char) 0x2596;
-    data[233] = (char) 0xfef0;
-    data[234] = (char) 0x6cae;
-    data[235] = (char) 0x200d;
-    data[236] = (char) 0x005f;
-    data[237] = (char) 0x3000;
-    data[244] = (char) 0xfeff;
-    data[245] = (char) 0xffff;
-    data[246] = (char) 0x03ff;
-    data[266] = (char) 0xffff;
-    data[267] = (char) 0xffff;
-    data[268] = (char) 0x003f;
-    data[269] = (char) 0xffff;
-    data[270] = (char) 0xffff;
-    data[271] = (char) 0x007f;
-    data[272] = (char) 0xffff;
-    data[273] = (char) 0xffff;
-    data[274] = (char) 0xffff;
-    data[275] = (char) 0xffff;
-    data[276] = (char) 0xffff;
-    data[277] = (char) 0x83ff;
-    data[278] = (char) 0xffff;
-    data[279] = (char) 0xffff;
-    data[280] = (char) 0xffff;
-    data[281] = (char) 0xffff;
-    data[282] = (char) 0xff07;
-    data[283] = (char) 0xffff;
-    data[284] = (char) 0xffff;
-    data[285] = (char) 0xffff;
-    data[286] = (char) 0xffff;
-    data[287] = (char) 0x03ff;
-    data[480] = (char) 0xffff;
-    data[481] = (char) 0xffff;
-    data[482] = (char) 0xffff;
-    data[483] = (char) 0xffff;
-    data[484] = (char) 0xffff;
-    data[485] = (char) 0xffff;
-    data[486] = (char) 0xffff;
-    data[487] = (char) 0xffff;
-    data[488] = (char) 0xffff;
-    data[489] = (char) 0x0fff;
-    data[490] = (char) 0xffff;
-    data[491] = (char) 0xffff;
-    data[492] = (char) 0xffff;
-    data[493] = (char) 0xffff;
-    data[494] = (char) 0xffff;
-    data[495] = (char) 0x03ff;
-    data[496] = (char) 0xffff;
-    data[497] = (char) 0x3f3f;
-    data[498] = (char) 0xffff;
-    data[499] = (char) 0xffff;
-    data[500] = (char) 0x3f3f;
-    data[501] = (char) 0xaaff;
-    data[502] = (char) 0xffff;
-    data[503] = (char) 0x3fff;
-    data[504] = (char) 0xffff;
-    data[505] = (char) 0xffff;
-    data[506] = (char) 0xffff;
-    data[507] = (char) 0x5fdf;
-    data[508] = (char) 0x1fdc;
-    data[509] = (char) 0x0fcf;
-    data[510] = (char) 0x1fff;
-    data[511] = (char) 0x1fdc;
-    data[519] = (char) 0x8000;
-    data[528] = (char) 0xfc84;
-    data[529] = (char) 0x3f2f;
-    data[530] = (char) 0xfd50;
-    data[531] = (char) 0x01fb;
-    data[768] = (char) 0x0020;
-    data[771] = (char) 0x003e;
-    data[772] = (char) 0xfffe;
-    data[773] = (char) 0xffff;
-    data[774] = (char) 0xffff;
-    data[775] = (char) 0xffff;
-    data[776] = (char) 0xffff;
-    data[777] = (char) 0x781f;
-    data[778] = (char) 0xfffe;
-    data[779] = (char) 0xffff;
-    data[780] = (char) 0xffff;
-    data[781] = (char) 0xffff;
-    data[782] = (char) 0xffff;
-    data[783] = (char) 0x77ff;
-    data[784] = (char) 0xffe0;
-    data[785] = (char) 0xffff;
-    data[786] = (char) 0x1fff;
-    data[787] = (char) 0xfffe;
-    data[788] = (char) 0xffff;
-    data[789] = (char) 0xffff;
-    data[790] = (char) 0xffff;
-    data[791] = (char) 0xffff;
-    data[792] = (char) 0x7fff;
-    data[1248] = (char) 0xffff;
-    data[1249] = (char) 0xffff;
-    data[1250] = (char) 0xffff;
-    data[1251] = (char) 0xffff;
-    data[1252] = (char) 0xffff;
-    data[1253] = (char) 0xffff;
-    data[1254] = (char) 0xffff;
-    data[1255] = (char) 0xffff;
-    data[1256] = (char) 0xffff;
-    data[1257] = (char) 0xffff;
-    data[1258] = (char) 0xffff;
-    data[1259] = (char) 0xffff;
-    data[1260] = (char) 0xffff;
-    data[1261] = (char) 0xffff;
-    data[1262] = (char) 0xffff;
-    data[1263] = (char) 0xffff;
-    data[1264] = (char) 0xffff;
-    data[1265] = (char) 0xffff;
-    data[1266] = (char) 0xffff;
-    data[1267] = (char) 0xffff;
-    data[1268] = (char) 0xffff;
-    data[1269] = (char) 0xffff;
-    data[1270] = (char) 0xffff;
-    data[1271] = (char) 0xffff;
-    data[1272] = (char) 0xffff;
-    data[1273] = (char) 0xffff;
-    data[1274] = (char) 0xffff;
-    data[1275] = (char) 0xffff;
-    data[1276] = (char) 0xffff;
-    data[1277] = (char) 0xffff;
-    data[1278] = (char) 0xffff;
-    data[1279] = (char) 0xffff;
-    data[1280] = (char) 0xffff;
-    data[1281] = (char) 0xffff;
-    data[1282] = (char) 0xffff;
-    data[1283] = (char) 0xffff;
-    data[1284] = (char) 0xffff;
-    data[1285] = (char) 0xffff;
-    data[1286] = (char) 0xffff;
-    data[1287] = (char) 0xffff;
-    data[1288] = (char) 0xffff;
-    data[1289] = (char) 0xffff;
-    data[1290] = (char) 0xffff;
-    data[1291] = (char) 0xffff;
-    data[1292] = (char) 0xffff;
-    data[1293] = (char) 0xffff;
-    data[1294] = (char) 0xffff;
-    data[1295] = (char) 0xffff;
-    data[1296] = (char) 0xffff;
-    data[1297] = (char) 0xffff;
-    data[1298] = (char) 0xffff;
-    data[1299] = (char) 0xffff;
-    data[1300] = (char) 0xffff;
-    data[1301] = (char) 0xffff;
-    data[1302] = (char) 0xffff;
-    data[1303] = (char) 0xffff;
-    data[1304] = (char) 0xffff;
-    data[1305] = (char) 0xffff;
-    data[1306] = (char) 0xffff;
-    data[1307] = (char) 0xffff;
-    data[1308] = (char) 0xffff;
-    data[1309] = (char) 0xffff;
-    data[1310] = (char) 0xffff;
-    data[1311] = (char) 0xffff;
-    data[1312] = (char) 0xffff;
-    data[1313] = (char) 0xffff;
-    data[1314] = (char) 0xffff;
-    data[1315] = (char) 0xffff;
-    data[1316] = (char) 0xffff;
-    data[1317] = (char) 0xffff;
-    data[1318] = (char) 0xffff;
-    data[1319] = (char) 0xffff;
-    data[1320] = (char) 0xffff;
-    data[1321] = (char) 0xffff;
-    data[1322] = (char) 0xffff;
-    data[1323] = (char) 0xffff;
-    data[1324] = (char) 0xffff;
-    data[1325] = (char) 0xffff;
-    data[1326] = (char) 0xffff;
-    data[1327] = (char) 0xffff;
-    data[1328] = (char) 0xffff;
-    data[1329] = (char) 0xffff;
-    data[1330] = (char) 0xffff;
-    data[1331] = (char) 0xffff;
-    data[1332] = (char) 0xffff;
-    data[1333] = (char) 0xffff;
-    data[1334] = (char) 0xffff;
-    data[1335] = (char) 0xffff;
-    data[1336] = (char) 0xffff;
-    data[1337] = (char) 0xffff;
-    data[1338] = (char) 0xffff;
-    data[1339] = (char) 0xffff;
-    data[1340] = (char) 0xffff;
-    data[1341] = (char) 0xffff;
-    data[1342] = (char) 0xffff;
-    data[1343] = (char) 0xffff;
-    data[1344] = (char) 0xffff;
-    data[1345] = (char) 0xffff;
-    data[1346] = (char) 0xffff;
-    data[1347] = (char) 0xffff;
-    data[1348] = (char) 0xffff;
-    data[1349] = (char) 0xffff;
-    data[1350] = (char) 0xffff;
-    data[1351] = (char) 0xffff;
-    data[1352] = (char) 0xffff;
-    data[1353] = (char) 0xffff;
-    data[1354] = (char) 0xffff;
-    data[1355] = (char) 0xffff;
-    data[1356] = (char) 0xffff;
-    data[1357] = (char) 0xffff;
-    data[1358] = (char) 0xffff;
-    data[1359] = (char) 0xffff;
-    data[1360] = (char) 0xffff;
-    data[1361] = (char) 0xffff;
-    data[1362] = (char) 0xffff;
-    data[1363] = (char) 0xffff;
-    data[1364] = (char) 0xffff;
-    data[1365] = (char) 0xffff;
-    data[1366] = (char) 0xffff;
-    data[1367] = (char) 0xffff;
-    data[1368] = (char) 0xffff;
-    data[1369] = (char) 0xffff;
-    data[1370] = (char) 0xffff;
-    data[1371] = (char) 0xffff;
-    data[1372] = (char) 0xffff;
-    data[1373] = (char) 0xffff;
-    data[1374] = (char) 0xffff;
-    data[1375] = (char) 0xffff;
-    data[1376] = (char) 0xffff;
-    data[1377] = (char) 0xffff;
-    data[1378] = (char) 0xffff;
-    data[1379] = (char) 0xffff;
-    data[1380] = (char) 0xffff;
-    data[1381] = (char) 0xffff;
-    data[1382] = (char) 0xffff;
-    data[1383] = (char) 0xffff;
-    data[1384] = (char) 0xffff;
-    data[1385] = (char) 0xffff;
-    data[1386] = (char) 0xffff;
-    data[1387] = (char) 0xffff;
-    data[1388] = (char) 0xffff;
-    data[1389] = (char) 0xffff;
-    data[1390] = (char) 0xffff;
-    data[1391] = (char) 0xffff;
-    data[1392] = (char) 0xffff;
-    data[1393] = (char) 0xffff;
-    data[1394] = (char) 0xffff;
-    data[1395] = (char) 0xffff;
-    data[1396] = (char) 0xffff;
-    data[1397] = (char) 0xffff;
-    data[1398] = (char) 0xffff;
-    data[1399] = (char) 0xffff;
-    data[1400] = (char) 0xffff;
-    data[1401] = (char) 0xffff;
-    data[1402] = (char) 0xffff;
-    data[1403] = (char) 0xffff;
-    data[1404] = (char) 0xffff;
-    data[1405] = (char) 0xffff;
-    data[1406] = (char) 0xffff;
-    data[1407] = (char) 0xffff;
-    data[1408] = (char) 0xffff;
-    data[1409] = (char) 0xffff;
-    data[1410] = (char) 0xffff;
-    data[1411] = (char) 0xffff;
-    data[1412] = (char) 0xffff;
-    data[1413] = (char) 0xffff;
-    data[1414] = (char) 0xffff;
-    data[1415] = (char) 0xffff;
-    data[1416] = (char) 0xffff;
-    data[1417] = (char) 0xffff;
-    data[1418] = (char) 0xffff;
-    data[1419] = (char) 0xffff;
-    data[1420] = (char) 0xffff;
-    data[1421] = (char) 0xffff;
-    data[1422] = (char) 0xffff;
-    data[1423] = (char) 0xffff;
-    data[1424] = (char) 0xffff;
-    data[1425] = (char) 0xffff;
-    data[1426] = (char) 0xffff;
-    data[1427] = (char) 0xffff;
-    data[1428] = (char) 0xffff;
-    data[1429] = (char) 0xffff;
-    data[1430] = (char) 0xffff;
-    data[1431] = (char) 0xffff;
-    data[1432] = (char) 0xffff;
-    data[1433] = (char) 0xffff;
-    data[1434] = (char) 0xffff;
-    data[1435] = (char) 0xffff;
-    data[1436] = (char) 0xffff;
-    data[1437] = (char) 0xffff;
-    data[1438] = (char) 0xffff;
-    data[1439] = (char) 0xffff;
-    data[1440] = (char) 0xffff;
-    data[1441] = (char) 0xffff;
-    data[1442] = (char) 0xffff;
-    data[1443] = (char) 0xffff;
-    data[1444] = (char) 0xffff;
-    data[1445] = (char) 0xffff;
-    data[1446] = (char) 0xffff;
-    data[1447] = (char) 0xffff;
-    data[1448] = (char) 0xffff;
-    data[1449] = (char) 0xffff;
-    data[1450] = (char) 0xffff;
-    data[1451] = (char) 0xffff;
-    data[1452] = (char) 0xffff;
-    data[1453] = (char) 0xffff;
-    data[1454] = (char) 0xffff;
-    data[1455] = (char) 0xffff;
-    data[1456] = (char) 0xffff;
-    data[1457] = (char) 0xffff;
-    data[1458] = (char) 0xffff;
-    data[1459] = (char) 0xffff;
-    data[1460] = (char) 0xffff;
-    data[1461] = (char) 0xffff;
-    data[1462] = (char) 0xffff;
-    data[1463] = (char) 0xffff;
-    data[1464] = (char) 0xffff;
-    data[1465] = (char) 0xffff;
-    data[1466] = (char) 0xffff;
-    data[1467] = (char) 0xffff;
-    data[1468] = (char) 0xffff;
-    data[1469] = (char) 0xffff;
-    data[1470] = (char) 0xffff;
-    data[1471] = (char) 0xffff;
-    data[1472] = (char) 0xffff;
-    data[1473] = (char) 0xffff;
-    data[1474] = (char) 0xffff;
-    data[1475] = (char) 0xffff;
-    data[1476] = (char) 0xffff;
-    data[1477] = (char) 0xffff;
-    data[1478] = (char) 0xffff;
-    data[1479] = (char) 0xffff;
-    data[1480] = (char) 0xffff;
-    data[1481] = (char) 0xffff;
-    data[1482] = (char) 0xffff;
-    data[1483] = (char) 0xffff;
-    data[1484] = (char) 0xffff;
-    data[1485] = (char) 0xffff;
-    data[1486] = (char) 0xffff;
-    data[1487] = (char) 0xffff;
-    data[1488] = (char) 0xffff;
-    data[1489] = (char) 0xffff;
-    data[1490] = (char) 0xffff;
-    data[1491] = (char) 0xffff;
-    data[1492] = (char) 0xffff;
-    data[1493] = (char) 0xffff;
-    data[1494] = (char) 0xffff;
-    data[1495] = (char) 0xffff;
-    data[1496] = (char) 0xffff;
-    data[1497] = (char) 0xffff;
-    data[1498] = (char) 0xffff;
-    data[1499] = (char) 0xffff;
-    data[1500] = (char) 0xffff;
-    data[1501] = (char) 0xffff;
-    data[1502] = (char) 0xffff;
-    data[1503] = (char) 0xffff;
-    data[1504] = (char) 0xffff;
-    data[1505] = (char) 0xffff;
-    data[1506] = (char) 0xffff;
-    data[1507] = (char) 0xffff;
-    data[1508] = (char) 0xffff;
-    data[1509] = (char) 0xffff;
-    data[1510] = (char) 0xffff;
-    data[1511] = (char) 0xffff;
-    data[1512] = (char) 0xffff;
-    data[1513] = (char) 0xffff;
-    data[1514] = (char) 0xffff;
-    data[1515] = (char) 0xffff;
-    data[1516] = (char) 0xffff;
-    data[1517] = (char) 0xffff;
-    data[1518] = (char) 0xffff;
-    data[1519] = (char) 0xffff;
-    data[1520] = (char) 0xffff;
-    data[1521] = (char) 0xffff;
-    data[1522] = (char) 0xffff;
-    data[1523] = (char) 0xffff;
-    data[1524] = (char) 0xffff;
-    data[1525] = (char) 0xffff;
-    data[1526] = (char) 0xffff;
-    data[1527] = (char) 0xffff;
-    data[1528] = (char) 0xffff;
-    data[1529] = (char) 0xffff;
-    data[1530] = (char) 0xffff;
-    data[1531] = (char) 0xffff;
-    data[1532] = (char) 0xffff;
-    data[1533] = (char) 0xffff;
-    data[1534] = (char) 0xffff;
-    data[1535] = (char) 0xffff;
-    data[1536] = (char) 0xffff;
-    data[1537] = (char) 0xffff;
-    data[1538] = (char) 0xffff;
-    data[1539] = (char) 0xffff;
-    data[1540] = (char) 0xffff;
-    data[1541] = (char) 0xffff;
-    data[1542] = (char) 0xffff;
-    data[1543] = (char) 0xffff;
-    data[1544] = (char) 0xffff;
-    data[1545] = (char) 0xffff;
-    data[1546] = (char) 0xffff;
-    data[1547] = (char) 0xffff;
-    data[1548] = (char) 0xffff;
-    data[1549] = (char) 0xffff;
-    data[1550] = (char) 0xffff;
-    data[1551] = (char) 0xffff;
-    data[1552] = (char) 0xffff;
-    data[1553] = (char) 0xffff;
-    data[1554] = (char) 0xffff;
-    data[1555] = (char) 0xffff;
-    data[1556] = (char) 0xffff;
-    data[1557] = (char) 0xffff;
-    data[1558] = (char) 0xffff;
-    data[1559] = (char) 0xffff;
-    data[1560] = (char) 0xffff;
-    data[1561] = (char) 0xffff;
-    data[1562] = (char) 0xffff;
-    data[1563] = (char) 0xffff;
-    data[1564] = (char) 0xffff;
-    data[1565] = (char) 0xffff;
-    data[1566] = (char) 0xffff;
-    data[1567] = (char) 0xffff;
-    data[1568] = (char) 0xffff;
-    data[1569] = (char) 0xffff;
-    data[1570] = (char) 0xffff;
-    data[1571] = (char) 0xffff;
-    data[1572] = (char) 0xffff;
-    data[1573] = (char) 0xffff;
-    data[1574] = (char) 0xffff;
-    data[1575] = (char) 0xffff;
-    data[1576] = (char) 0xffff;
-    data[1577] = (char) 0xffff;
-    data[1578] = (char) 0xffff;
-    data[1579] = (char) 0xffff;
-    data[1580] = (char) 0xffff;
-    data[1581] = (char) 0xffff;
-    data[1582] = (char) 0xffff;
-    data[1583] = (char) 0xffff;
-    data[1584] = (char) 0xffff;
-    data[1585] = (char) 0xffff;
-    data[1586] = (char) 0xffff;
-    data[1587] = (char) 0xffff;
-    data[1588] = (char) 0xffff;
-    data[1589] = (char) 0xffff;
-    data[1590] = (char) 0xffff;
-    data[1591] = (char) 0xffff;
-    data[1592] = (char) 0xffff;
-    data[1593] = (char) 0xffff;
-    data[1594] = (char) 0xffff;
-    data[1595] = (char) 0xffff;
-    data[1596] = (char) 0xffff;
-    data[1597] = (char) 0xffff;
-    data[1598] = (char) 0xffff;
-    data[1599] = (char) 0xffff;
-    data[1600] = (char) 0xffff;
-    data[1601] = (char) 0xffff;
-    data[1602] = (char) 0xffff;
-    data[1603] = (char) 0xffff;
-    data[1604] = (char) 0xffff;
-    data[1605] = (char) 0xffff;
-    data[1606] = (char) 0xffff;
-    data[1607] = (char) 0xffff;
-    data[1608] = (char) 0xffff;
-    data[1609] = (char) 0xffff;
-    data[1610] = (char) 0xffff;
-    data[1611] = (char) 0xffff;
-    data[1612] = (char) 0xffff;
-    data[1613] = (char) 0xffff;
-    data[1614] = (char) 0xffff;
-    data[1615] = (char) 0xffff;
-    data[1616] = (char) 0xffff;
-    data[1617] = (char) 0xffff;
-    data[1618] = (char) 0xffff;
-    data[1619] = (char) 0xffff;
-    data[1620] = (char) 0xffff;
-    data[1621] = (char) 0xffff;
-    data[1622] = (char) 0xffff;
-    data[1623] = (char) 0xffff;
-    data[1624] = (char) 0xffff;
-    data[1625] = (char) 0xffff;
-    data[1626] = (char) 0xffff;
-    data[1627] = (char) 0xffff;
-    data[1628] = (char) 0xffff;
-    data[1629] = (char) 0xffff;
-    data[1630] = (char) 0xffff;
-    data[1631] = (char) 0xffff;
-    data[1632] = (char) 0xffff;
-    data[1633] = (char) 0xffff;
-    data[1634] = (char) 0xffff;
-    data[1635] = (char) 0xffff;
-    data[1636] = (char) 0xffff;
-    data[1637] = (char) 0xffff;
-    data[1638] = (char) 0xffff;
-    data[1639] = (char) 0xffff;
-    data[1640] = (char) 0xffff;
-    data[1641] = (char) 0xffff;
-    data[1642] = (char) 0xffff;
-    data[1643] = (char) 0xffff;
-    data[1644] = (char) 0xffff;
-    data[1645] = (char) 0xffff;
-    data[1646] = (char) 0xffff;
-    data[1647] = (char) 0xffff;
-    data[1648] = (char) 0xffff;
-    data[1649] = (char) 0xffff;
-    data[1650] = (char) 0xffff;
-    data[1651] = (char) 0xffff;
-    data[1652] = (char) 0xffff;
-    data[1653] = (char) 0xffff;
-    data[1654] = (char) 0xffff;
-    data[1655] = (char) 0xffff;
-    data[1656] = (char) 0xffff;
-    data[1657] = (char) 0xffff;
-    data[1658] = (char) 0xffff;
-    data[1659] = (char) 0xffff;
-    data[1660] = (char) 0xffff;
-    data[1661] = (char) 0xffff;
-    data[1662] = (char) 0xffff;
-    data[1663] = (char) 0xffff;
-    data[1664] = (char) 0xffff;
-    data[1665] = (char) 0xffff;
-    data[1666] = (char) 0xffff;
-    data[1667] = (char) 0xffff;
-    data[1668] = (char) 0xffff;
-    data[1669] = (char) 0xffff;
-    data[1670] = (char) 0xffff;
-    data[1671] = (char) 0xffff;
-    data[1672] = (char) 0xffff;
-    data[1673] = (char) 0xffff;
-    data[1674] = (char) 0xffff;
-    data[1675] = (char) 0xffff;
-    data[1676] = (char) 0xffff;
-    data[1677] = (char) 0xffff;
-    data[1678] = (char) 0xffff;
-    data[1679] = (char) 0xffff;
-    data[1680] = (char) 0xffff;
-    data[1681] = (char) 0xffff;
-    data[1682] = (char) 0xffff;
-    data[1683] = (char) 0xffff;
-    data[1684] = (char) 0xffff;
-    data[1685] = (char) 0xffff;
-    data[1686] = (char) 0xffff;
-    data[1687] = (char) 0xffff;
-    data[1688] = (char) 0xffff;
-    data[1689] = (char) 0xffff;
-    data[1690] = (char) 0xffff;
-    data[1691] = (char) 0xffff;
-    data[1692] = (char) 0xffff;
-    data[1693] = (char) 0xffff;
-    data[1694] = (char) 0xffff;
-    data[1695] = (char) 0xffff;
-    data[1696] = (char) 0xffff;
-    data[1697] = (char) 0xffff;
-    data[1698] = (char) 0xffff;
-    data[1699] = (char) 0xffff;
-    data[1700] = (char) 0xffff;
-    data[1701] = (char) 0xffff;
-    data[1702] = (char) 0xffff;
-    data[1703] = (char) 0xffff;
-    data[1704] = (char) 0xffff;
-    data[1705] = (char) 0xffff;
-    data[1706] = (char) 0xffff;
-    data[1707] = (char) 0xffff;
-    data[1708] = (char) 0xffff;
-    data[1709] = (char) 0xffff;
-    data[1710] = (char) 0xffff;
-    data[1711] = (char) 0xffff;
-    data[1712] = (char) 0xffff;
-    data[1713] = (char) 0xffff;
-    data[1714] = (char) 0xffff;
-    data[1715] = (char) 0xffff;
-    data[1716] = (char) 0xffff;
-    data[1717] = (char) 0xffff;
-    data[1718] = (char) 0xffff;
-    data[1719] = (char) 0xffff;
-    data[1720] = (char) 0xffff;
-    data[1721] = (char) 0xffff;
-    data[1722] = (char) 0xffff;
-    data[1723] = (char) 0xffff;
-    data[1724] = (char) 0xffff;
-    data[1725] = (char) 0xffff;
-    data[1726] = (char) 0xffff;
-    data[1727] = (char) 0xffff;
-    data[1728] = (char) 0xffff;
-    data[1729] = (char) 0xffff;
-    data[1730] = (char) 0xffff;
-    data[1731] = (char) 0xffff;
-    data[1732] = (char) 0xffff;
-    data[1733] = (char) 0xffff;
-    data[1734] = (char) 0xffff;
-    data[1735] = (char) 0xffff;
-    data[1736] = (char) 0xffff;
-    data[1737] = (char) 0xffff;
-    data[1738] = (char) 0xffff;
-    data[1739] = (char) 0xffff;
-    data[1740] = (char) 0xffff;
-    data[1741] = (char) 0xffff;
-    data[1742] = (char) 0xffff;
-    data[1743] = (char) 0xffff;
-    data[1744] = (char) 0xffff;
-    data[1745] = (char) 0xffff;
-    data[1746] = (char) 0xffff;
-    data[1747] = (char) 0xffff;
-    data[1748] = (char) 0xffff;
-    data[1749] = (char) 0xffff;
-    data[1750] = (char) 0xffff;
-    data[1751] = (char) 0xffff;
-    data[1752] = (char) 0xffff;
-    data[1753] = (char) 0xffff;
-    data[1754] = (char) 0xffff;
-    data[1755] = (char) 0xffff;
-    data[1756] = (char) 0xffff;
-    data[1757] = (char) 0xffff;
-    data[1758] = (char) 0xffff;
-    data[1759] = (char) 0xffff;
-    data[1760] = (char) 0xffff;
-    data[1761] = (char) 0xffff;
-    data[1762] = (char) 0xffff;
-    data[1763] = (char) 0xffff;
-    data[1764] = (char) 0xffff;
-    data[1765] = (char) 0xffff;
-    data[1766] = (char) 0xffff;
-    data[1767] = (char) 0xffff;
-    data[1768] = (char) 0xffff;
-    data[1769] = (char) 0xffff;
-    data[1770] = (char) 0xffff;
-    data[1771] = (char) 0xffff;
-    data[1772] = (char) 0xffff;
-    data[1773] = (char) 0xffff;
-    data[1774] = (char) 0xffff;
-    data[1775] = (char) 0xffff;
-    data[1776] = (char) 0xffff;
-    data[1777] = (char) 0xffff;
-    data[1778] = (char) 0xffff;
-    data[1779] = (char) 0xffff;
-    data[1780] = (char) 0xffff;
-    data[1781] = (char) 0xffff;
-    data[1782] = (char) 0xffff;
-    data[1783] = (char) 0xffff;
-    data[1784] = (char) 0xffff;
-    data[1785] = (char) 0xffff;
-    data[1786] = (char) 0xffff;
-    data[1787] = (char) 0xffff;
-    data[1788] = (char) 0xffff;
-    data[1789] = (char) 0xffff;
-    data[1790] = (char) 0xffff;
-    data[1791] = (char) 0xffff;
-    data[1792] = (char) 0xffff;
-    data[1793] = (char) 0xffff;
-    data[1794] = (char) 0xffff;
-    data[1795] = (char) 0xffff;
-    data[1796] = (char) 0xffff;
-    data[1797] = (char) 0xffff;
-    data[1798] = (char) 0xffff;
-    data[1799] = (char) 0xffff;
-    data[1800] = (char) 0xffff;
-    data[1801] = (char) 0xffff;
-    data[1802] = (char) 0xffff;
-    data[1803] = (char) 0xffff;
-    data[1804] = (char) 0xffff;
-    data[1805] = (char) 0xffff;
-    data[1806] = (char) 0xffff;
-    data[1807] = (char) 0xffff;
-    data[1808] = (char) 0xffff;
-    data[1809] = (char) 0xffff;
-    data[1810] = (char) 0xffff;
-    data[1811] = (char) 0xffff;
-    data[1812] = (char) 0xffff;
-    data[1813] = (char) 0xffff;
-    data[1814] = (char) 0xffff;
-    data[1815] = (char) 0xffff;
-    data[1816] = (char) 0xffff;
-    data[1817] = (char) 0xffff;
-    data[1818] = (char) 0xffff;
-    data[1819] = (char) 0xffff;
-    data[1820] = (char) 0xffff;
-    data[1821] = (char) 0xffff;
-    data[1822] = (char) 0xffff;
-    data[1823] = (char) 0xffff;
-    data[1824] = (char) 0xffff;
-    data[1825] = (char) 0xffff;
-    data[1826] = (char) 0xffff;
-    data[1827] = (char) 0xffff;
-    data[1828] = (char) 0xffff;
-    data[1829] = (char) 0xffff;
-    data[1830] = (char) 0xffff;
-    data[1831] = (char) 0xffff;
-    data[1832] = (char) 0xffff;
-    data[1833] = (char) 0xffff;
-    data[1834] = (char) 0xffff;
-    data[1835] = (char) 0xffff;
-    data[1836] = (char) 0xffff;
-    data[1837] = (char) 0xffff;
-    data[1838] = (char) 0xffff;
-    data[1839] = (char) 0xffff;
-    data[1840] = (char) 0xffff;
-    data[1841] = (char) 0xffff;
-    data[1842] = (char) 0xffff;
-    data[1843] = (char) 0xffff;
-    data[1844] = (char) 0xffff;
-    data[1845] = (char) 0xffff;
-    data[1846] = (char) 0xffff;
-    data[1847] = (char) 0xffff;
-    data[1848] = (char) 0xffff;
-    data[1849] = (char) 0xffff;
-    data[1850] = (char) 0xffff;
-    data[1851] = (char) 0xffff;
-    data[1852] = (char) 0xffff;
-    data[1853] = (char) 0xffff;
-    data[1854] = (char) 0xffff;
-    data[1855] = (char) 0xffff;
-    data[1856] = (char) 0xffff;
-    data[1857] = (char) 0xffff;
-    data[1858] = (char) 0xffff;
-    data[1859] = (char) 0xffff;
-    data[1860] = (char) 0xffff;
-    data[1861] = (char) 0xffff;
-    data[1862] = (char) 0xffff;
-    data[1863] = (char) 0xffff;
-    data[1864] = (char) 0xffff;
-    data[1865] = (char) 0xffff;
-    data[1866] = (char) 0xffff;
-    data[1867] = (char) 0xffff;
-    data[1868] = (char) 0xffff;
-    data[1869] = (char) 0xffff;
-    data[1870] = (char) 0xffff;
-    data[1871] = (char) 0xffff;
-    data[1872] = (char) 0xffff;
-    data[1873] = (char) 0xffff;
-    data[1874] = (char) 0xffff;
-    data[1875] = (char) 0xffff;
-    data[1876] = (char) 0xffff;
-    data[1877] = (char) 0xffff;
-    data[1878] = (char) 0xffff;
-    data[1879] = (char) 0xffff;
-    data[1880] = (char) 0xffff;
-    data[1881] = (char) 0xffff;
-    data[1882] = (char) 0xffff;
-    data[1883] = (char) 0xffff;
-    data[1884] = (char) 0xffff;
-    data[1885] = (char) 0xffff;
-    data[1886] = (char) 0xffff;
-    data[1887] = (char) 0xffff;
-    data[1888] = (char) 0xffff;
-    data[1889] = (char) 0xffff;
-    data[1890] = (char) 0xffff;
-    data[1891] = (char) 0xffff;
-    data[1892] = (char) 0xffff;
-    data[1893] = (char) 0xffff;
-    data[1894] = (char) 0xffff;
-    data[1895] = (char) 0xffff;
-    data[1896] = (char) 0xffff;
-    data[1897] = (char) 0xffff;
-    data[1898] = (char) 0xffff;
-    data[1899] = (char) 0xffff;
-    data[1900] = (char) 0xffff;
-    data[1901] = (char) 0xffff;
-    data[1902] = (char) 0xffff;
-    data[1903] = (char) 0xffff;
-    data[1904] = (char) 0xffff;
-    data[1905] = (char) 0xffff;
-    data[1906] = (char) 0xffff;
-    data[1907] = (char) 0xffff;
-    data[1908] = (char) 0xffff;
-    data[1909] = (char) 0xffff;
-    data[1910] = (char) 0xffff;
-    data[1911] = (char) 0xffff;
-    data[1912] = (char) 0xffff;
-    data[1913] = (char) 0xffff;
-    data[1914] = (char) 0xffff;
-    data[1915] = (char) 0xffff;
-    data[1916] = (char) 0xffff;
-    data[1917] = (char) 0xffff;
-    data[1918] = (char) 0xffff;
-    data[1919] = (char) 0xffff;
-    data[1920] = (char) 0xffff;
-    data[1921] = (char) 0xffff;
-    data[1922] = (char) 0xffff;
-    data[1923] = (char) 0xffff;
-    data[1924] = (char) 0xffff;
-    data[1925] = (char) 0xffff;
-    data[1926] = (char) 0xffff;
-    data[1927] = (char) 0xffff;
-    data[1928] = (char) 0xffff;
-    data[1929] = (char) 0xffff;
-    data[1930] = (char) 0xffff;
-    data[1931] = (char) 0xffff;
-    data[1932] = (char) 0xffff;
-    data[1933] = (char) 0xffff;
-    data[1934] = (char) 0xffff;
-    data[1935] = (char) 0xffff;
-    data[1936] = (char) 0xffff;
-    data[1937] = (char) 0xffff;
-    data[1938] = (char) 0xffff;
-    data[1939] = (char) 0xffff;
-    data[1940] = (char) 0xffff;
-    data[1941] = (char) 0xffff;
-    data[1942] = (char) 0xffff;
-    data[1943] = (char) 0xffff;
-    data[1944] = (char) 0xffff;
-    data[1945] = (char) 0xffff;
-    data[1946] = (char) 0xffff;
-    data[1947] = (char) 0xffff;
-    data[1948] = (char) 0xffff;
-    data[1949] = (char) 0xffff;
-    data[1950] = (char) 0xffff;
-    data[1951] = (char) 0xffff;
-    data[1952] = (char) 0xffff;
-    data[1953] = (char) 0xffff;
-    data[1954] = (char) 0xffff;
-    data[1955] = (char) 0xffff;
-    data[1956] = (char) 0xffff;
-    data[1957] = (char) 0xffff;
-    data[1958] = (char) 0xffff;
-    data[1959] = (char) 0xffff;
-    data[1960] = (char) 0xffff;
-    data[1961] = (char) 0xffff;
-    data[1962] = (char) 0xffff;
-    data[1963] = (char) 0xffff;
-    data[1964] = (char) 0xffff;
-    data[1965] = (char) 0xffff;
-    data[1966] = (char) 0xffff;
-    data[1967] = (char) 0xffff;
-    data[1968] = (char) 0xffff;
-    data[1969] = (char) 0xffff;
-    data[1970] = (char) 0xffff;
-    data[1971] = (char) 0xffff;
-    data[1972] = (char) 0xffff;
-    data[1973] = (char) 0xffff;
-    data[1974] = (char) 0xffff;
-    data[1975] = (char) 0xffff;
-    data[1976] = (char) 0xffff;
-    data[1977] = (char) 0xffff;
-    data[1978] = (char) 0xffff;
-    data[1979] = (char) 0xffff;
-    data[1980] = (char) 0xffff;
-    data[1981] = (char) 0xffff;
-    data[1982] = (char) 0xffff;
-    data[1983] = (char) 0xffff;
-    data[1984] = (char) 0xffff;
-    data[1985] = (char) 0xffff;
-    data[1986] = (char) 0xffff;
-    data[1987] = (char) 0xffff;
-    data[1988] = (char) 0xffff;
-    data[1989] = (char) 0xffff;
-    data[1990] = (char) 0xffff;
-    data[1991] = (char) 0xffff;
-    data[1992] = (char) 0xffff;
-    data[1993] = (char) 0xffff;
-    data[1994] = (char) 0xffff;
-    data[1995] = (char) 0xffff;
-    data[1996] = (char) 0xffff;
-    data[1997] = (char) 0xffff;
-    data[1998] = (char) 0xffff;
-    data[1999] = (char) 0xffff;
-    data[2000] = (char) 0xffff;
-    data[2001] = (char) 0xffff;
-    data[2002] = (char) 0xffff;
-    data[2003] = (char) 0xffff;
-    data[2004] = (char) 0xffff;
-    data[2005] = (char) 0xffff;
-    data[2006] = (char) 0xffff;
-    data[2007] = (char) 0xffff;
-    data[2008] = (char) 0xffff;
-    data[2009] = (char) 0xffff;
-    data[2010] = (char) 0xffff;
-    data[2011] = (char) 0xffff;
-    data[2012] = (char) 0xffff;
-    data[2013] = (char) 0xffff;
-    data[2014] = (char) 0xffff;
-    data[2015] = (char) 0xffff;
-    data[2016] = (char) 0xffff;
-    data[2017] = (char) 0xffff;
-    data[2018] = (char) 0xffff;
-    data[2019] = (char) 0xffff;
-    data[2020] = (char) 0xffff;
-    data[2021] = (char) 0xffff;
-    data[2022] = (char) 0xffff;
-    data[2023] = (char) 0xffff;
-    data[2024] = (char) 0xffff;
-    data[2025] = (char) 0xffff;
-    data[2026] = (char) 0xffff;
-    data[2027] = (char) 0xffff;
-    data[2028] = (char) 0xffff;
-    data[2029] = (char) 0xffff;
-    data[2030] = (char) 0xffff;
-    data[2031] = (char) 0xffff;
-    data[2032] = (char) 0xffff;
-    data[2033] = (char) 0xffff;
-    data[2034] = (char) 0xffff;
-    data[2035] = (char) 0xffff;
-    data[2036] = (char) 0xffff;
-    data[2037] = (char) 0xffff;
-    data[2038] = (char) 0xffff;
-    data[2039] = (char) 0xffff;
-    data[2040] = (char) 0xffff;
-    data[2041] = (char) 0xffff;
-    data[2042] = (char) 0xffff;
-    data[2043] = (char) 0xffff;
-    data[2044] = (char) 0xffff;
-    data[2045] = (char) 0xffff;
-    data[2046] = (char) 0xffff;
-    data[2047] = (char) 0xffff;
-    data[2048] = (char) 0xffff;
-    data[2049] = (char) 0xffff;
-    data[2050] = (char) 0xffff;
-    data[2051] = (char) 0xffff;
-    data[2052] = (char) 0xffff;
-    data[2053] = (char) 0xffff;
-    data[2054] = (char) 0xffff;
-    data[2055] = (char) 0xffff;
-    data[2056] = (char) 0xffff;
-    data[2057] = (char) 0xffff;
-    data[2058] = (char) 0xffff;
-    data[2059] = (char) 0xffff;
-    data[2060] = (char) 0xffff;
-    data[2061] = (char) 0xffff;
-    data[2062] = (char) 0xffff;
-    data[2063] = (char) 0xffff;
-    data[2064] = (char) 0xffff;
-    data[2065] = (char) 0xffff;
-    data[2066] = (char) 0xffff;
-    data[2067] = (char) 0xffff;
-    data[2068] = (char) 0xffff;
-    data[2069] = (char) 0xffff;
-    data[2070] = (char) 0xffff;
-    data[2071] = (char) 0xffff;
-    data[2072] = (char) 0xffff;
-    data[2073] = (char) 0xffff;
-    data[2074] = (char) 0xffff;
-    data[2075] = (char) 0xffff;
-    data[2076] = (char) 0xffff;
-    data[2077] = (char) 0xffff;
-    data[2078] = (char) 0xffff;
-    data[2079] = (char) 0xffff;
-    data[2080] = (char) 0xffff;
-    data[2081] = (char) 0xffff;
-    data[2082] = (char) 0xffff;
-    data[2083] = (char) 0xffff;
-    data[2084] = (char) 0xffff;
-    data[2085] = (char) 0xffff;
-    data[2086] = (char) 0xffff;
-    data[2087] = (char) 0xffff;
-    data[2088] = (char) 0xffff;
-    data[2089] = (char) 0xffff;
-    data[2090] = (char) 0xffff;
-    data[2091] = (char) 0xffff;
-    data[2092] = (char) 0xffff;
-    data[2093] = (char) 0xffff;
-    data[2094] = (char) 0xffff;
-    data[2095] = (char) 0xffff;
-    data[2096] = (char) 0xffff;
-    data[2097] = (char) 0xffff;
-    data[2098] = (char) 0xffff;
-    data[2099] = (char) 0xffff;
-    data[2100] = (char) 0xffff;
-    data[2101] = (char) 0xffff;
-    data[2102] = (char) 0xffff;
-    data[2103] = (char) 0xffff;
-    data[2104] = (char) 0xffff;
-    data[2105] = (char) 0xffff;
-    data[2106] = (char) 0xffff;
-    data[2107] = (char) 0xffff;
-    data[2108] = (char) 0xffff;
-    data[2109] = (char) 0xffff;
-    data[2110] = (char) 0xffff;
-    data[2111] = (char) 0xffff;
-    data[2112] = (char) 0xffff;
-    data[2113] = (char) 0xffff;
-    data[2114] = (char) 0xffff;
-    data[2115] = (char) 0xffff;
-    data[2116] = (char) 0xffff;
-    data[2117] = (char) 0xffff;
-    data[2118] = (char) 0xffff;
-    data[2119] = (char) 0xffff;
-    data[2120] = (char) 0xffff;
-    data[2121] = (char) 0xffff;
-    data[2122] = (char) 0xffff;
-    data[2123] = (char) 0xffff;
-    data[2124] = (char) 0xffff;
-    data[2125] = (char) 0xffff;
-    data[2126] = (char) 0xffff;
-    data[2127] = (char) 0xffff;
-    data[2128] = (char) 0xffff;
-    data[2129] = (char) 0xffff;
-    data[2130] = (char) 0xffff;
-    data[2131] = (char) 0xffff;
-    data[2132] = (char) 0xffff;
-    data[2133] = (char) 0xffff;
-    data[2134] = (char) 0xffff;
-    data[2135] = (char) 0xffff;
-    data[2136] = (char) 0xffff;
-    data[2137] = (char) 0xffff;
-    data[2138] = (char) 0xffff;
-    data[2139] = (char) 0xffff;
-    data[2140] = (char) 0xffff;
-    data[2141] = (char) 0xffff;
-    data[2142] = (char) 0xffff;
-    data[2143] = (char) 0xffff;
-    data[2144] = (char) 0xffff;
-    data[2145] = (char) 0xffff;
-    data[2146] = (char) 0xffff;
-    data[2147] = (char) 0xffff;
-    data[2148] = (char) 0xffff;
-    data[2149] = (char) 0xffff;
-    data[2150] = (char) 0xffff;
-    data[2151] = (char) 0xffff;
-    data[2152] = (char) 0xffff;
-    data[2153] = (char) 0xffff;
-    data[2154] = (char) 0xffff;
-    data[2155] = (char) 0xffff;
-    data[2156] = (char) 0xffff;
-    data[2157] = (char) 0xffff;
-    data[2158] = (char) 0xffff;
-    data[2159] = (char) 0xffff;
-    data[2160] = (char) 0xffff;
-    data[2161] = (char) 0xffff;
-    data[2162] = (char) 0xffff;
-    data[2163] = (char) 0xffff;
-    data[2164] = (char) 0xffff;
-    data[2165] = (char) 0xffff;
-    data[2166] = (char) 0xffff;
-    data[2167] = (char) 0xffff;
-    data[2168] = (char) 0xffff;
-    data[2169] = (char) 0xffff;
-    data[2170] = (char) 0xffff;
-    data[2171] = (char) 0xffff;
-    data[2172] = (char) 0xffff;
-    data[2173] = (char) 0xffff;
-    data[2174] = (char) 0xffff;
-    data[2175] = (char) 0xffff;
-    data[2176] = (char) 0xffff;
-    data[2177] = (char) 0xffff;
-    data[2178] = (char) 0xffff;
-    data[2179] = (char) 0xffff;
-    data[2180] = (char) 0xffff;
-    data[2181] = (char) 0xffff;
-    data[2182] = (char) 0xffff;
-    data[2183] = (char) 0xffff;
-    data[2184] = (char) 0xffff;
-    data[2185] = (char) 0xffff;
-    data[2186] = (char) 0xffff;
-    data[2187] = (char) 0xffff;
-    data[2188] = (char) 0xffff;
-    data[2189] = (char) 0xffff;
-    data[2190] = (char) 0xffff;
-    data[2191] = (char) 0xffff;
-    data[2192] = (char) 0xffff;
-    data[2193] = (char) 0xffff;
-    data[2194] = (char) 0xffff;
-    data[2195] = (char) 0xffff;
-    data[2196] = (char) 0xffff;
-    data[2197] = (char) 0xffff;
-    data[2198] = (char) 0xffff;
-    data[2199] = (char) 0xffff;
-    data[2200] = (char) 0xffff;
-    data[2201] = (char) 0xffff;
-    data[2202] = (char) 0xffff;
-    data[2203] = (char) 0xffff;
-    data[2204] = (char) 0xffff;
-    data[2205] = (char) 0xffff;
-    data[2206] = (char) 0xffff;
-    data[2207] = (char) 0xffff;
-    data[2208] = (char) 0xffff;
-    data[2209] = (char) 0xffff;
-    data[2210] = (char) 0xffff;
-    data[2211] = (char) 0xffff;
-    data[2212] = (char) 0xffff;
-    data[2213] = (char) 0xffff;
-    data[2214] = (char) 0xffff;
-    data[2215] = (char) 0xffff;
-    data[2216] = (char) 0xffff;
-    data[2217] = (char) 0xffff;
-    data[2218] = (char) 0xffff;
-    data[2219] = (char) 0xffff;
-    data[2220] = (char) 0xffff;
-    data[2221] = (char) 0xffff;
-    data[2222] = (char) 0xffff;
-    data[2223] = (char) 0xffff;
-    data[2224] = (char) 0xffff;
-    data[2225] = (char) 0xffff;
-    data[2226] = (char) 0xffff;
-    data[2227] = (char) 0xffff;
-    data[2228] = (char) 0xffff;
-    data[2229] = (char) 0xffff;
-    data[2230] = (char) 0xffff;
-    data[2231] = (char) 0xffff;
-    data[2232] = (char) 0xffff;
-    data[2233] = (char) 0xffff;
-    data[2234] = (char) 0xffff;
-    data[2235] = (char) 0xffff;
-    data[2236] = (char) 0xffff;
-    data[2237] = (char) 0xffff;
-    data[2238] = (char) 0xffff;
-    data[2239] = (char) 0xffff;
-    data[2240] = (char) 0xffff;
-    data[2241] = (char) 0xffff;
-    data[2242] = (char) 0xffff;
-    data[2243] = (char) 0xffff;
-    data[2244] = (char) 0xffff;
-    data[2245] = (char) 0xffff;
-    data[2246] = (char) 0xffff;
-    data[2247] = (char) 0xffff;
-    data[2248] = (char) 0xffff;
-    data[2249] = (char) 0xffff;
-    data[2250] = (char) 0xffff;
-    data[2251] = (char) 0xffff;
-    data[2252] = (char) 0xffff;
-    data[2253] = (char) 0xffff;
-    data[2254] = (char) 0xffff;
-    data[2255] = (char) 0xffff;
-    data[2256] = (char) 0xffff;
-    data[2257] = (char) 0xffff;
-    data[2258] = (char) 0xffff;
-    data[2259] = (char) 0xffff;
-    data[2260] = (char) 0xffff;
-    data[2261] = (char) 0xffff;
-    data[2262] = (char) 0xffff;
-    data[2263] = (char) 0xffff;
-    data[2264] = (char) 0xffff;
-    data[2265] = (char) 0xffff;
-    data[2266] = (char) 0xffff;
-    data[2267] = (char) 0xffff;
-    data[2268] = (char) 0xffff;
-    data[2269] = (char) 0xffff;
-    data[2270] = (char) 0xffff;
-    data[2271] = (char) 0xffff;
-    data[2272] = (char) 0xffff;
-    data[2273] = (char) 0xffff;
-    data[2274] = (char) 0xffff;
-    data[2275] = (char) 0xffff;
-    data[2276] = (char) 0xffff;
-    data[2277] = (char) 0xffff;
-    data[2278] = (char) 0xffff;
-    data[2279] = (char) 0xffff;
-    data[2280] = (char) 0xffff;
-    data[2281] = (char) 0xffff;
-    data[2282] = (char) 0xffff;
-    data[2283] = (char) 0xffff;
-    data[2284] = (char) 0xffff;
-    data[2285] = (char) 0xffff;
-    data[2286] = (char) 0xffff;
-    data[2287] = (char) 0xffff;
-    data[2288] = (char) 0xffff;
-    data[2289] = (char) 0xffff;
-    data[2290] = (char) 0xffff;
-    data[2291] = (char) 0xffff;
-    data[2292] = (char) 0xffff;
-    data[2293] = (char) 0xffff;
-    data[2294] = (char) 0xffff;
-    data[2295] = (char) 0xffff;
-    data[2296] = (char) 0xffff;
-    data[2297] = (char) 0xffff;
-    data[2298] = (char) 0xffff;
-    data[2299] = (char) 0xffff;
-    data[2300] = (char) 0xffff;
-    data[2301] = (char) 0xffff;
-    data[2302] = (char) 0xffff;
-    data[2303] = (char) 0xffff;
-    data[2304] = (char) 0xffff;
-    data[2305] = (char) 0xffff;
-    data[2306] = (char) 0xffff;
-    data[2307] = (char) 0xffff;
-    data[2308] = (char) 0xffff;
-    data[2309] = (char) 0xffff;
-    data[2310] = (char) 0xffff;
-    data[2311] = (char) 0xffff;
-    data[2312] = (char) 0xffff;
-    data[2313] = (char) 0xffff;
-    data[2314] = (char) 0xffff;
-    data[2315] = (char) 0xffff;
-    data[2316] = (char) 0xffff;
-    data[2317] = (char) 0xffff;
-    data[2318] = (char) 0xffff;
-    data[2319] = (char) 0xffff;
-    data[2320] = (char) 0xffff;
-    data[2321] = (char) 0xffff;
-    data[2322] = (char) 0xffff;
-    data[2323] = (char) 0xffff;
-    data[2324] = (char) 0xffff;
-    data[2325] = (char) 0xffff;
-    data[2326] = (char) 0xffff;
-    data[2327] = (char) 0xffff;
-    data[2328] = (char) 0xffff;
-    data[2329] = (char) 0xffff;
-    data[2330] = (char) 0xffff;
-    data[2331] = (char) 0xffff;
-    data[2332] = (char) 0xffff;
-    data[2333] = (char) 0xffff;
-    data[2334] = (char) 0xffff;
-    data[2335] = (char) 0xffff;
-    data[2336] = (char) 0xffff;
-    data[2337] = (char) 0xffff;
-    data[2338] = (char) 0xffff;
-    data[2339] = (char) 0xffff;
-    data[2340] = (char) 0xffff;
-    data[2341] = (char) 0xffff;
-    data[2342] = (char) 0xffff;
-    data[2343] = (char) 0xffff;
-    data[2344] = (char) 0xffff;
-    data[2345] = (char) 0xffff;
-    data[2346] = (char) 0xffff;
-    data[2347] = (char) 0xffff;
-    data[2348] = (char) 0xffff;
-    data[2349] = (char) 0xffff;
-    data[2350] = (char) 0xffff;
-    data[2351] = (char) 0xffff;
-    data[2352] = (char) 0xffff;
-    data[2353] = (char) 0xffff;
-    data[2354] = (char) 0xffff;
-    data[2355] = (char) 0xffff;
-    data[2356] = (char) 0xffff;
-    data[2357] = (char) 0xffff;
-    data[2358] = (char) 0xffff;
-    data[2359] = (char) 0xffff;
-    data[2360] = (char) 0xffff;
-    data[2361] = (char) 0xffff;
-    data[2362] = (char) 0xffff;
-    data[2363] = (char) 0xffff;
-    data[2364] = (char) 0xffff;
-    data[2365] = (char) 0xffff;
-    data[2366] = (char) 0xffff;
-    data[2367] = (char) 0xffff;
-    data[2368] = (char) 0xffff;
-    data[2369] = (char) 0xffff;
-    data[2370] = (char) 0xffff;
-    data[2371] = (char) 0xffff;
-    data[2372] = (char) 0xffff;
-    data[2373] = (char) 0xffff;
-    data[2374] = (char) 0xffff;
-    data[2375] = (char) 0xffff;
-    data[2376] = (char) 0xffff;
-    data[2377] = (char) 0xffff;
-    data[2378] = (char) 0xffff;
-    data[2379] = (char) 0xffff;
-    data[2380] = (char) 0xffff;
-    data[2381] = (char) 0xffff;
-    data[2382] = (char) 0xffff;
-    data[2383] = (char) 0xffff;
-    data[2384] = (char) 0xffff;
-    data[2385] = (char) 0xffff;
-    data[2386] = (char) 0xffff;
-    data[2387] = (char) 0xffff;
-    data[2388] = (char) 0xffff;
-    data[2389] = (char) 0xffff;
-    data[2390] = (char) 0xffff;
-    data[2391] = (char) 0xffff;
-    data[2392] = (char) 0xffff;
-    data[2393] = (char) 0xffff;
-    data[2394] = (char) 0xffff;
-    data[2395] = (char) 0xffff;
-    data[2396] = (char) 0xffff;
-    data[2397] = (char) 0xffff;
-    data[2398] = (char) 0xffff;
-    data[2399] = (char) 0xffff;
-    data[2400] = (char) 0xffff;
-    data[2401] = (char) 0xffff;
-    data[2402] = (char) 0xffff;
-    data[2403] = (char) 0xffff;
-    data[2404] = (char) 0xffff;
-    data[2405] = (char) 0xffff;
-    data[2406] = (char) 0xffff;
-    data[2407] = (char) 0xffff;
-    data[2408] = (char) 0xffff;
-    data[2409] = (char) 0xffff;
-    data[2410] = (char) 0xffff;
-    data[2411] = (char) 0xffff;
-    data[2412] = (char) 0xffff;
-    data[2413] = (char) 0xffff;
-    data[2414] = (char) 0xffff;
-    data[2415] = (char) 0xffff;
-    data[2416] = (char) 0xffff;
-    data[2417] = (char) 0xffff;
-    data[2418] = (char) 0xffff;
-    data[2419] = (char) 0xffff;
-    data[2420] = (char) 0xffff;
-    data[2421] = (char) 0xffff;
-    data[2422] = (char) 0xffff;
-    data[2423] = (char) 0xffff;
-    data[2424] = (char) 0xffff;
-    data[2425] = (char) 0xffff;
-    data[2426] = (char) 0xffff;
-    data[2427] = (char) 0xffff;
-    data[2428] = (char) 0xffff;
-    data[2429] = (char) 0xffff;
-    data[2430] = (char) 0xffff;
-    data[2431] = (char) 0xffff;
-    data[2432] = (char) 0xffff;
-    data[2433] = (char) 0xffff;
-    data[2434] = (char) 0xffff;
-    data[2435] = (char) 0xffff;
-    data[2436] = (char) 0xffff;
-    data[2437] = (char) 0xffff;
-    data[2438] = (char) 0xffff;
-    data[2439] = (char) 0xffff;
-    data[2440] = (char) 0xffff;
-    data[2441] = (char) 0xffff;
-    data[2442] = (char) 0xffff;
-    data[2443] = (char) 0xffff;
-    data[2444] = (char) 0xffff;
-    data[2445] = (char) 0xffff;
-    data[2446] = (char) 0xffff;
-    data[2447] = (char) 0xffff;
-    data[2448] = (char) 0xffff;
-    data[2449] = (char) 0xffff;
-    data[2450] = (char) 0xffff;
-    data[2451] = (char) 0xffff;
-    data[2452] = (char) 0xffff;
-    data[2453] = (char) 0xffff;
-    data[2454] = (char) 0xffff;
-    data[2455] = (char) 0xffff;
-    data[2456] = (char) 0xffff;
-    data[2457] = (char) 0xffff;
-    data[2458] = (char) 0xffff;
-    data[2459] = (char) 0xffff;
-    data[2460] = (char) 0xffff;
-    data[2461] = (char) 0xffff;
-    data[2462] = (char) 0xffff;
-    data[2463] = (char) 0xffff;
-    data[2464] = (char) 0xffff;
-    data[2465] = (char) 0xffff;
-    data[2466] = (char) 0xffff;
-    data[2467] = (char) 0xffff;
-    data[2468] = (char) 0xffff;
-    data[2469] = (char) 0xffff;
-    data[2470] = (char) 0xffff;
-    data[2471] = (char) 0xffff;
-    data[2472] = (char) 0xffff;
-    data[2473] = (char) 0xffff;
-    data[2474] = (char) 0xffff;
-    data[2475] = (char) 0xffff;
-    data[2476] = (char) 0xffff;
-    data[2477] = (char) 0xffff;
-    data[2478] = (char) 0xffff;
-    data[2479] = (char) 0xffff;
-    data[2480] = (char) 0xffff;
-    data[2481] = (char) 0xffff;
-    data[2482] = (char) 0xffff;
-    data[2483] = (char) 0xffff;
-    data[2484] = (char) 0xffff;
-    data[2485] = (char) 0xffff;
-    data[2486] = (char) 0xffff;
-    data[2487] = (char) 0xffff;
-    data[2488] = (char) 0xffff;
-    data[2489] = (char) 0xffff;
-    data[2490] = (char) 0xffff;
-    data[2491] = (char) 0xffff;
-    data[2492] = (char) 0xffff;
-    data[2493] = (char) 0xffff;
-    data[2494] = (char) 0xffff;
-    data[2495] = (char) 0xffff;
-    data[2496] = (char) 0xffff;
-    data[2497] = (char) 0xffff;
-    data[2498] = (char) 0xffff;
-    data[2499] = (char) 0xffff;
-    data[2500] = (char) 0xffff;
-    data[2501] = (char) 0xffff;
-    data[2502] = (char) 0xffff;
-    data[2503] = (char) 0xffff;
-    data[2504] = (char) 0xffff;
-    data[2505] = (char) 0xffff;
-    data[2506] = (char) 0xffff;
-    data[2507] = (char) 0xffff;
-    data[2508] = (char) 0xffff;
-    data[2509] = (char) 0xffff;
-    data[2510] = (char) 0xffff;
-    data[2511] = (char) 0xffff;
-    data[2512] = (char) 0xffff;
-    data[2513] = (char) 0xffff;
-    data[2514] = (char) 0xffff;
-    data[2515] = (char) 0xffff;
-    data[2516] = (char) 0xffff;
-    data[2517] = (char) 0xffff;
-    data[2518] = (char) 0xffff;
-    data[2519] = (char) 0xffff;
-    data[2520] = (char) 0xffff;
-    data[2521] = (char) 0xffff;
-    data[2522] = (char) 0xffff;
-    data[2523] = (char) 0xffff;
-    data[2524] = (char) 0xffff;
-    data[2525] = (char) 0xffff;
-    data[2526] = (char) 0xffff;
-    data[2527] = (char) 0xffff;
-    data[2528] = (char) 0xffff;
-    data[2529] = (char) 0xffff;
-    data[2530] = (char) 0xffff;
-    data[2531] = (char) 0xffff;
-    data[2532] = (char) 0xffff;
-    data[2533] = (char) 0xffff;
-    data[2534] = (char) 0xffff;
-    data[2535] = (char) 0xffff;
-    data[2536] = (char) 0xffff;
-    data[2537] = (char) 0xffff;
-    data[2538] = (char) 0xffff;
-    data[2539] = (char) 0xffff;
-    data[2540] = (char) 0xffff;
-    data[2541] = (char) 0xffff;
-    data[2542] = (char) 0xffff;
-    data[2543] = (char) 0xffff;
-    data[2544] = (char) 0xffff;
-    data[2545] = (char) 0xffff;
-    data[2546] = (char) 0xffff;
-    data[2547] = (char) 0xffff;
-    data[2548] = (char) 0xffff;
-    data[2549] = (char) 0xffff;
-    data[2550] = (char) 0xffff;
-    data[2551] = (char) 0xffff;
-    data[2552] = (char) 0xffff;
-    data[2553] = (char) 0xffff;
-    data[2554] = (char) 0x003f;
-    data[2752] = (char) 0xffff;
-    data[2753] = (char) 0xffff;
-    data[2754] = (char) 0xffff;
-    data[2755] = (char) 0xffff;
-    data[2756] = (char) 0xffff;
-    data[2757] = (char) 0xffff;
-    data[2758] = (char) 0xffff;
-    data[2759] = (char) 0xffff;
-    data[2760] = (char) 0xffff;
-    data[2761] = (char) 0xffff;
-    data[2762] = (char) 0xffff;
-    data[2763] = (char) 0xffff;
-    data[2764] = (char) 0xffff;
-    data[2765] = (char) 0xffff;
-    data[2766] = (char) 0xffff;
-    data[2767] = (char) 0xffff;
-    data[2768] = (char) 0xffff;
-    data[2769] = (char) 0xffff;
-    data[2770] = (char) 0xffff;
-    data[2771] = (char) 0xffff;
-    data[2772] = (char) 0xffff;
-    data[2773] = (char) 0xffff;
-    data[2774] = (char) 0xffff;
-    data[2775] = (char) 0xffff;
-    data[2776] = (char) 0xffff;
-    data[2777] = (char) 0xffff;
-    data[2778] = (char) 0xffff;
-    data[2779] = (char) 0xffff;
-    data[2780] = (char) 0xffff;
-    data[2781] = (char) 0xffff;
-    data[2782] = (char) 0xffff;
-    data[2783] = (char) 0xffff;
-    data[2784] = (char) 0xffff;
-    data[2785] = (char) 0xffff;
-    data[2786] = (char) 0xffff;
-    data[2787] = (char) 0xffff;
-    data[2788] = (char) 0xffff;
-    data[2789] = (char) 0xffff;
-    data[2790] = (char) 0xffff;
-    data[2791] = (char) 0xffff;
-    data[2792] = (char) 0xffff;
-    data[2793] = (char) 0xffff;
-    data[2794] = (char) 0xffff;
-    data[2795] = (char) 0xffff;
-    data[2796] = (char) 0xffff;
-    data[2797] = (char) 0xffff;
-    data[2798] = (char) 0xffff;
-    data[2799] = (char) 0xffff;
-    data[2800] = (char) 0xffff;
-    data[2801] = (char) 0xffff;
-    data[2802] = (char) 0xffff;
-    data[2803] = (char) 0xffff;
-    data[2804] = (char) 0xffff;
-    data[2805] = (char) 0xffff;
-    data[2806] = (char) 0xffff;
-    data[2807] = (char) 0xffff;
-    data[2808] = (char) 0xffff;
-    data[2809] = (char) 0xffff;
-    data[2810] = (char) 0xffff;
-    data[2811] = (char) 0xffff;
-    data[2812] = (char) 0xffff;
-    data[2813] = (char) 0xffff;
-    data[2814] = (char) 0xffff;
-    data[2815] = (char) 0xffff;
-    data[2816] = (char) 0xffff;
-    data[2817] = (char) 0xffff;
-    data[2818] = (char) 0xffff;
-    data[2819] = (char) 0xffff;
-    data[2820] = (char) 0xffff;
-    data[2821] = (char) 0xffff;
-    data[2822] = (char) 0xffff;
-    data[2823] = (char) 0xffff;
-    data[2824] = (char) 0xffff;
-    data[2825] = (char) 0xffff;
-    data[2826] = (char) 0xffff;
-    data[2827] = (char) 0xffff;
-    data[2828] = (char) 0xffff;
-    data[2829] = (char) 0xffff;
-    data[2830] = (char) 0xffff;
-    data[2831] = (char) 0xffff;
-    data[2832] = (char) 0xffff;
-    data[2833] = (char) 0xffff;
-    data[2834] = (char) 0xffff;
-    data[2835] = (char) 0xffff;
-    data[2836] = (char) 0xffff;
-    data[2837] = (char) 0xffff;
-    data[2838] = (char) 0xffff;
-    data[2839] = (char) 0xffff;
-    data[2840] = (char) 0xffff;
-    data[2841] = (char) 0xffff;
-    data[2842] = (char) 0xffff;
-    data[2843] = (char) 0xffff;
-    data[2844] = (char) 0xffff;
-    data[2845] = (char) 0xffff;
-    data[2846] = (char) 0xffff;
-    data[2847] = (char) 0xffff;
-    data[2848] = (char) 0xffff;
-    data[2849] = (char) 0xffff;
-    data[2850] = (char) 0xffff;
-    data[2851] = (char) 0xffff;
-    data[2852] = (char) 0xffff;
-    data[2853] = (char) 0xffff;
-    data[2854] = (char) 0xffff;
-    data[2855] = (char) 0xffff;
-    data[2856] = (char) 0xffff;
-    data[2857] = (char) 0xffff;
-    data[2858] = (char) 0xffff;
-    data[2859] = (char) 0xffff;
-    data[2860] = (char) 0xffff;
-    data[2861] = (char) 0xffff;
-    data[2862] = (char) 0xffff;
-    data[2863] = (char) 0xffff;
-    data[2864] = (char) 0xffff;
-    data[2865] = (char) 0xffff;
-    data[2866] = (char) 0xffff;
-    data[2867] = (char) 0xffff;
-    data[2868] = (char) 0xffff;
-    data[2869] = (char) 0xffff;
-    data[2870] = (char) 0xffff;
-    data[2871] = (char) 0xffff;
-    data[2872] = (char) 0xffff;
-    data[2873] = (char) 0xffff;
-    data[2874] = (char) 0xffff;
-    data[2875] = (char) 0xffff;
-    data[2876] = (char) 0xffff;
-    data[2877] = (char) 0xffff;
-    data[2878] = (char) 0xffff;
-    data[2879] = (char) 0xffff;
-    data[2880] = (char) 0xffff;
-    data[2881] = (char) 0xffff;
-    data[2882] = (char) 0xffff;
-    data[2883] = (char) 0xffff;
-    data[2884] = (char) 0xffff;
-    data[2885] = (char) 0xffff;
-    data[2886] = (char) 0xffff;
-    data[2887] = (char) 0xffff;
-    data[2888] = (char) 0xffff;
-    data[2889] = (char) 0xffff;
-    data[2890] = (char) 0xffff;
-    data[2891] = (char) 0xffff;
-    data[2892] = (char) 0xffff;
-    data[2893] = (char) 0xffff;
-    data[2894] = (char) 0xffff;
-    data[2895] = (char) 0xffff;
-    data[2896] = (char) 0xffff;
-    data[2897] = (char) 0xffff;
-    data[2898] = (char) 0xffff;
-    data[2899] = (char) 0xffff;
-    data[2900] = (char) 0xffff;
-    data[2901] = (char) 0xffff;
-    data[2902] = (char) 0xffff;
-    data[2903] = (char) 0xffff;
-    data[2904] = (char) 0xffff;
-    data[2905] = (char) 0xffff;
-    data[2906] = (char) 0xffff;
-    data[2907] = (char) 0xffff;
-    data[2908] = (char) 0xffff;
-    data[2909] = (char) 0xffff;
-    data[2910] = (char) 0xffff;
-    data[2911] = (char) 0xffff;
-    data[2912] = (char) 0xffff;
-    data[2913] = (char) 0xffff;
-    data[2914] = (char) 0xffff;
-    data[2915] = (char) 0xffff;
-    data[2916] = (char) 0xffff;
-    data[2917] = (char) 0xffff;
-    data[2918] = (char) 0xffff;
-    data[2919] = (char) 0xffff;
-    data[2920] = (char) 0xffff;
-    data[2921] = (char) 0xffff;
-    data[2922] = (char) 0xffff;
-    data[2923] = (char) 0xffff;
-    data[2924] = (char) 0xffff;
-    data[2925] = (char) 0xffff;
-    data[2926] = (char) 0xffff;
-    data[2927] = (char) 0xffff;
-    data[2928] = (char) 0xffff;
-    data[2929] = (char) 0xffff;
-    data[2930] = (char) 0xffff;
-    data[2931] = (char) 0xffff;
-    data[2932] = (char) 0xffff;
-    data[2933] = (char) 0xffff;
-    data[2934] = (char) 0xffff;
-    data[2935] = (char) 0xffff;
-    data[2936] = (char) 0xffff;
-    data[2937] = (char) 0xffff;
-    data[2938] = (char) 0xffff;
-    data[2939] = (char) 0xffff;
-    data[2940] = (char) 0xffff;
-    data[2941] = (char) 0xffff;
-    data[2942] = (char) 0xffff;
-    data[2943] = (char) 0xffff;
-    data[2944] = (char) 0xffff;
-    data[2945] = (char) 0xffff;
-    data[2946] = (char) 0xffff;
-    data[2947] = (char) 0xffff;
-    data[2948] = (char) 0xffff;
-    data[2949] = (char) 0xffff;
-    data[2950] = (char) 0xffff;
-    data[2951] = (char) 0xffff;
-    data[2952] = (char) 0xffff;
-    data[2953] = (char) 0xffff;
-    data[2954] = (char) 0xffff;
-    data[2955] = (char) 0xffff;
-    data[2956] = (char) 0xffff;
-    data[2957] = (char) 0xffff;
-    data[2958] = (char) 0xffff;
-    data[2959] = (char) 0xffff;
-    data[2960] = (char) 0xffff;
-    data[2961] = (char) 0xffff;
-    data[2962] = (char) 0xffff;
-    data[2963] = (char) 0xffff;
-    data[2964] = (char) 0xffff;
-    data[2965] = (char) 0xffff;
-    data[2966] = (char) 0xffff;
-    data[2967] = (char) 0xffff;
-    data[2968] = (char) 0xffff;
-    data[2969] = (char) 0xffff;
-    data[2970] = (char) 0xffff;
-    data[2971] = (char) 0xffff;
-    data[2972] = (char) 0xffff;
-    data[2973] = (char) 0xffff;
-    data[2974] = (char) 0xffff;
-    data[2975] = (char) 0xffff;
-    data[2976] = (char) 0xffff;
-    data[2977] = (char) 0xffff;
-    data[2978] = (char) 0xffff;
-    data[2979] = (char) 0xffff;
-    data[2980] = (char) 0xffff;
-    data[2981] = (char) 0xffff;
-    data[2982] = (char) 0xffff;
-    data[2983] = (char) 0xffff;
-    data[2984] = (char) 0xffff;
-    data[2985] = (char) 0xffff;
-    data[2986] = (char) 0xffff;
-    data[2987] = (char) 0xffff;
-    data[2988] = (char) 0xffff;
-    data[2989] = (char) 0xffff;
-    data[2990] = (char) 0xffff;
-    data[2991] = (char) 0xffff;
-    data[2992] = (char) 0xffff;
-    data[2993] = (char) 0xffff;
-    data[2994] = (char) 0xffff;
-    data[2995] = (char) 0xffff;
-    data[2996] = (char) 0xffff;
-    data[2997] = (char) 0xffff;
-    data[2998] = (char) 0xffff;
-    data[2999] = (char) 0xffff;
-    data[3000] = (char) 0xffff;
-    data[3001] = (char) 0xffff;
-    data[3002] = (char) 0xffff;
-    data[3003] = (char) 0xffff;
-    data[3004] = (char) 0xffff;
-    data[3005] = (char) 0xffff;
-    data[3006] = (char) 0xffff;
-    data[3007] = (char) 0xffff;
-    data[3008] = (char) 0xffff;
-    data[3009] = (char) 0xffff;
-    data[3010] = (char) 0xffff;
-    data[3011] = (char) 0xffff;
-    data[3012] = (char) 0xffff;
-    data[3013] = (char) 0xffff;
-    data[3014] = (char) 0xffff;
-    data[3015] = (char) 0xffff;
-    data[3016] = (char) 0xffff;
-    data[3017] = (char) 0xffff;
-    data[3018] = (char) 0xffff;
-    data[3019] = (char) 0xffff;
-    data[3020] = (char) 0xffff;
-    data[3021] = (char) 0xffff;
-    data[3022] = (char) 0xffff;
-    data[3023] = (char) 0xffff;
-    data[3024] = (char) 0xffff;
-    data[3025] = (char) 0xffff;
-    data[3026] = (char) 0xffff;
-    data[3027] = (char) 0xffff;
-    data[3028] = (char) 0xffff;
-    data[3029] = (char) 0xffff;
-    data[3030] = (char) 0xffff;
-    data[3031] = (char) 0xffff;
-    data[3032] = (char) 0xffff;
-    data[3033] = (char) 0xffff;
-    data[3034] = (char) 0xffff;
-    data[3035] = (char) 0xffff;
-    data[3036] = (char) 0xffff;
-    data[3037] = (char) 0xffff;
-    data[3038] = (char) 0xffff;
-    data[3039] = (char) 0xffff;
-    data[3040] = (char) 0xffff;
-    data[3041] = (char) 0xffff;
-    data[3042] = (char) 0xffff;
-    data[3043] = (char) 0xffff;
-    data[3044] = (char) 0xffff;
-    data[3045] = (char) 0xffff;
-    data[3046] = (char) 0xffff;
-    data[3047] = (char) 0xffff;
-    data[3048] = (char) 0xffff;
-    data[3049] = (char) 0xffff;
-    data[3050] = (char) 0xffff;
-    data[3051] = (char) 0xffff;
-    data[3052] = (char) 0xffff;
-    data[3053] = (char) 0xffff;
-    data[3054] = (char) 0xffff;
-    data[3055] = (char) 0xffff;
-    data[3056] = (char) 0xffff;
-    data[3057] = (char) 0xffff;
-    data[3058] = (char) 0xffff;
-    data[3059] = (char) 0xffff;
-    data[3060] = (char) 0xffff;
-    data[3061] = (char) 0xffff;
-    data[3062] = (char) 0xffff;
-    data[3063] = (char) 0xffff;
-    data[3064] = (char) 0xffff;
-    data[3065] = (char) 0xffff;
-    data[3066] = (char) 0xffff;
-    data[3067] = (char) 0xffff;
-    data[3068] = (char) 0xffff;
-    data[3069] = (char) 0xffff;
-    data[3070] = (char) 0xffff;
-    data[3071] = (char) 0xffff;
-    data[3072] = (char) 0xffff;
-    data[3073] = (char) 0xffff;
-    data[3074] = (char) 0xffff;
-    data[3075] = (char) 0xffff;
-    data[3076] = (char) 0xffff;
-    data[3077] = (char) 0xffff;
-    data[3078] = (char) 0xffff;
-    data[3079] = (char) 0xffff;
-    data[3080] = (char) 0xffff;
-    data[3081] = (char) 0xffff;
-    data[3082] = (char) 0xffff;
-    data[3083] = (char) 0xffff;
-    data[3084] = (char) 0xffff;
-    data[3085] = (char) 0xffff;
-    data[3086] = (char) 0xffff;
-    data[3087] = (char) 0xffff;
-    data[3088] = (char) 0xffff;
-    data[3089] = (char) 0xffff;
-    data[3090] = (char) 0xffff;
-    data[3091] = (char) 0xffff;
-    data[3092] = (char) 0xffff;
-    data[3093] = (char) 0xffff;
-    data[3094] = (char) 0xffff;
-    data[3095] = (char) 0xffff;
-    data[3096] = (char) 0xffff;
-    data[3097] = (char) 0xffff;
-    data[3098] = (char) 0xffff;
-    data[3099] = (char) 0xffff;
-    data[3100] = (char) 0xffff;
-    data[3101] = (char) 0xffff;
-    data[3102] = (char) 0xffff;
-    data[3103] = (char) 0xffff;
-    data[3104] = (char) 0xffff;
-    data[3105] = (char) 0xffff;
-    data[3106] = (char) 0xffff;
-    data[3107] = (char) 0xffff;
-    data[3108] = (char) 0xffff;
-    data[3109] = (char) 0xffff;
-    data[3110] = (char) 0xffff;
-    data[3111] = (char) 0xffff;
-    data[3112] = (char) 0xffff;
-    data[3113] = (char) 0xffff;
-    data[3114] = (char) 0xffff;
-    data[3115] = (char) 0xffff;
-    data[3116] = (char) 0xffff;
-    data[3117] = (char) 0xffff;
-    data[3118] = (char) 0xffff;
-    data[3119] = (char) 0xffff;
-    data[3120] = (char) 0xffff;
-    data[3121] = (char) 0xffff;
-    data[3122] = (char) 0xffff;
-    data[3123] = (char) 0xffff;
-    data[3124] = (char) 0xffff;
-    data[3125] = (char) 0xffff;
-    data[3126] = (char) 0xffff;
-    data[3127] = (char) 0xffff;
-    data[3128] = (char) 0xffff;
-    data[3129] = (char) 0xffff;
-    data[3130] = (char) 0xffff;
-    data[3131] = (char) 0xffff;
-    data[3132] = (char) 0xffff;
-    data[3133] = (char) 0xffff;
-    data[3134] = (char) 0xffff;
-    data[3135] = (char) 0xffff;
-    data[3136] = (char) 0xffff;
-    data[3137] = (char) 0xffff;
-    data[3138] = (char) 0xffff;
-    data[3139] = (char) 0xffff;
-    data[3140] = (char) 0xffff;
-    data[3141] = (char) 0xffff;
-    data[3142] = (char) 0xffff;
-    data[3143] = (char) 0xffff;
-    data[3144] = (char) 0xffff;
-    data[3145] = (char) 0xffff;
-    data[3146] = (char) 0xffff;
-    data[3147] = (char) 0xffff;
-    data[3148] = (char) 0xffff;
-    data[3149] = (char) 0xffff;
-    data[3150] = (char) 0xffff;
-    data[3151] = (char) 0xffff;
-    data[3152] = (char) 0xffff;
-    data[3153] = (char) 0xffff;
-    data[3154] = (char) 0xffff;
-    data[3155] = (char) 0xffff;
-    data[3156] = (char) 0xffff;
-    data[3157] = (char) 0xffff;
-    data[3158] = (char) 0xffff;
-    data[3159] = (char) 0xffff;
-    data[3160] = (char) 0xffff;
-    data[3161] = (char) 0xffff;
-    data[3162] = (char) 0xffff;
-    data[3163] = (char) 0xffff;
-    data[3164] = (char) 0xffff;
-    data[3165] = (char) 0xffff;
-    data[3166] = (char) 0xffff;
-    data[3167] = (char) 0xffff;
-    data[3168] = (char) 0xffff;
-    data[3169] = (char) 0xffff;
-    data[3170] = (char) 0xffff;
-    data[3171] = (char) 0xffff;
-    data[3172] = (char) 0xffff;
-    data[3173] = (char) 0xffff;
-    data[3174] = (char) 0xffff;
-    data[3175] = (char) 0xffff;
-    data[3176] = (char) 0xffff;
-    data[3177] = (char) 0xffff;
-    data[3178] = (char) 0xffff;
-    data[3179] = (char) 0xffff;
-    data[3180] = (char) 0xffff;
-    data[3181] = (char) 0xffff;
-    data[3182] = (char) 0xffff;
-    data[3183] = (char) 0xffff;
-    data[3184] = (char) 0xffff;
-    data[3185] = (char) 0xffff;
-    data[3186] = (char) 0xffff;
-    data[3187] = (char) 0xffff;
-    data[3188] = (char) 0xffff;
-    data[3189] = (char) 0xffff;
-    data[3190] = (char) 0xffff;
-    data[3191] = (char) 0xffff;
-    data[3192] = (char) 0xffff;
-    data[3193] = (char) 0xffff;
-    data[3194] = (char) 0xffff;
-    data[3195] = (char) 0xffff;
-    data[3196] = (char) 0xffff;
-    data[3197] = (char) 0xffff;
-    data[3198] = (char) 0xffff;
-    data[3199] = (char) 0xffff;
-    data[3200] = (char) 0xffff;
-    data[3201] = (char) 0xffff;
-    data[3202] = (char) 0xffff;
-    data[3203] = (char) 0xffff;
-    data[3204] = (char) 0xffff;
-    data[3205] = (char) 0xffff;
-    data[3206] = (char) 0xffff;
-    data[3207] = (char) 0xffff;
-    data[3208] = (char) 0xffff;
-    data[3209] = (char) 0xffff;
-    data[3210] = (char) 0xffff;
-    data[3211] = (char) 0xffff;
-    data[3212] = (char) 0xffff;
-    data[3213] = (char) 0xffff;
-    data[3214] = (char) 0xffff;
-    data[3215] = (char) 0xffff;
-    data[3216] = (char) 0xffff;
-    data[3217] = (char) 0xffff;
-    data[3218] = (char) 0xffff;
-    data[3219] = (char) 0xffff;
-    data[3220] = (char) 0xffff;
-    data[3221] = (char) 0xffff;
-    data[3222] = (char) 0xffff;
-    data[3223] = (char) 0xffff;
-    data[3224] = (char) 0xffff;
-    data[3225] = (char) 0xffff;
-    data[3226] = (char) 0xffff;
-    data[3227] = (char) 0xffff;
-    data[3228] = (char) 0xffff;
-    data[3229] = (char) 0xffff;
-    data[3230] = (char) 0xffff;
-    data[3231] = (char) 0xffff;
-    data[3232] = (char) 0xffff;
-    data[3233] = (char) 0xffff;
-    data[3234] = (char) 0xffff;
-    data[3235] = (char) 0xffff;
-    data[3236] = (char) 0xffff;
-    data[3237] = (char) 0xffff;
-    data[3238] = (char) 0xffff;
-    data[3239] = (char) 0xffff;
-    data[3240] = (char) 0xffff;
-    data[3241] = (char) 0xffff;
-    data[3242] = (char) 0xffff;
-    data[3243] = (char) 0xffff;
-    data[3244] = (char) 0xffff;
-    data[3245] = (char) 0xffff;
-    data[3246] = (char) 0xffff;
-    data[3247] = (char) 0xffff;
-    data[3248] = (char) 0xffff;
-    data[3249] = (char) 0xffff;
-    data[3250] = (char) 0xffff;
-    data[3251] = (char) 0xffff;
-    data[3252] = (char) 0xffff;
-    data[3253] = (char) 0xffff;
-    data[3254] = (char) 0xffff;
-    data[3255] = (char) 0xffff;
-    data[3256] = (char) 0xffff;
-    data[3257] = (char) 0xffff;
-    data[3258] = (char) 0xffff;
-    data[3259] = (char) 0xffff;
-    data[3260] = (char) 0xffff;
-    data[3261] = (char) 0xffff;
-    data[3262] = (char) 0xffff;
-    data[3263] = (char) 0xffff;
-    data[3264] = (char) 0xffff;
-    data[3265] = (char) 0xffff;
-    data[3266] = (char) 0xffff;
-    data[3267] = (char) 0xffff;
-    data[3268] = (char) 0xffff;
-    data[3269] = (char) 0xffff;
-    data[3270] = (char) 0xffff;
-    data[3271] = (char) 0xffff;
-    data[3272] = (char) 0xffff;
-    data[3273] = (char) 0xffff;
-    data[3274] = (char) 0xffff;
-    data[3275] = (char) 0xffff;
-    data[3276] = (char) 0xffff;
-    data[3277] = (char) 0xffff;
-    data[3278] = (char) 0xffff;
-    data[3279] = (char) 0xffff;
-    data[3280] = (char) 0xffff;
-    data[3281] = (char) 0xffff;
-    data[3282] = (char) 0xffff;
-    data[3283] = (char) 0xffff;
-    data[3284] = (char) 0xffff;
-    data[3285] = (char) 0xffff;
-    data[3286] = (char) 0xffff;
-    data[3287] = (char) 0xffff;
-    data[3288] = (char) 0xffff;
-    data[3289] = (char) 0xffff;
-    data[3290] = (char) 0xffff;
-    data[3291] = (char) 0xffff;
-    data[3292] = (char) 0xffff;
-    data[3293] = (char) 0xffff;
-    data[3294] = (char) 0xffff;
-    data[3295] = (char) 0xffff;
-    data[3296] = (char) 0xffff;
-    data[3297] = (char) 0xffff;
-    data[3298] = (char) 0xffff;
-    data[3299] = (char) 0xffff;
-    data[3300] = (char) 0xffff;
-    data[3301] = (char) 0xffff;
-    data[3302] = (char) 0xffff;
-    data[3303] = (char) 0xffff;
-    data[3304] = (char) 0xffff;
-    data[3305] = (char) 0xffff;
-    data[3306] = (char) 0xffff;
-    data[3307] = (char) 0xffff;
-    data[3308] = (char) 0xffff;
-    data[3309] = (char) 0xffff;
-    data[3310] = (char) 0xffff;
-    data[3311] = (char) 0xffff;
-    data[3312] = (char) 0xffff;
-    data[3313] = (char) 0xffff;
-    data[3314] = (char) 0xffff;
-    data[3315] = (char) 0xffff;
-    data[3316] = (char) 0xffff;
-    data[3317] = (char) 0xffff;
-    data[3318] = (char) 0xffff;
-    data[3319] = (char) 0xffff;
-    data[3320] = (char) 0xffff;
-    data[3321] = (char) 0xffff;
-    data[3322] = (char) 0xffff;
-    data[3323] = (char) 0xffff;
-    data[3324] = (char) 0xffff;
-    data[3325] = (char) 0xffff;
-    data[3326] = (char) 0xffff;
-    data[3327] = (char) 0xffff;
-    data[3328] = (char) 0xffff;
-    data[3329] = (char) 0xffff;
-    data[3330] = (char) 0xffff;
-    data[3331] = (char) 0xffff;
-    data[3332] = (char) 0xffff;
-    data[3333] = (char) 0xffff;
-    data[3334] = (char) 0xffff;
-    data[3335] = (char) 0xffff;
-    data[3336] = (char) 0xffff;
-    data[3337] = (char) 0xffff;
-    data[3338] = (char) 0xffff;
-    data[3339] = (char) 0xffff;
-    data[3340] = (char) 0xffff;
-    data[3341] = (char) 0xffff;
-    data[3342] = (char) 0xffff;
-    data[3343] = (char) 0xffff;
-    data[3344] = (char) 0xffff;
-    data[3345] = (char) 0xffff;
-    data[3346] = (char) 0xffff;
-    data[3347] = (char) 0xffff;
-    data[3348] = (char) 0xffff;
-    data[3349] = (char) 0xffff;
-    data[3350] = (char) 0xffff;
-    data[3351] = (char) 0xffff;
-    data[3352] = (char) 0xffff;
-    data[3353] = (char) 0xffff;
-    data[3354] = (char) 0xffff;
-    data[3355] = (char) 0xffff;
-    data[3356] = (char) 0xffff;
-    data[3357] = (char) 0xffff;
-    data[3358] = (char) 0xffff;
-    data[3359] = (char) 0xffff;
-    data[3360] = (char) 0xffff;
-    data[3361] = (char) 0xffff;
-    data[3362] = (char) 0xffff;
-    data[3363] = (char) 0xffff;
-    data[3364] = (char) 0xffff;
-    data[3365] = (char) 0xffff;
-    data[3366] = (char) 0xffff;
-    data[3367] = (char) 0xffff;
-    data[3368] = (char) 0xffff;
-    data[3369] = (char) 0xffff;
-    data[3370] = (char) 0xffff;
-    data[3371] = (char) 0xffff;
-    data[3372] = (char) 0xffff;
-    data[3373] = (char) 0xffff;
-    data[3374] = (char) 0xffff;
-    data[3375] = (char) 0xffff;
-    data[3376] = (char) 0xffff;
-    data[3377] = (char) 0xffff;
-    data[3378] = (char) 0xffff;
-    data[3379] = (char) 0xffff;
-    data[3380] = (char) 0xffff;
-    data[3381] = (char) 0xffff;
-    data[3382] = (char) 0xffff;
-    data[3383] = (char) 0xffff;
-    data[3384] = (char) 0xffff;
-    data[3385] = (char) 0xffff;
-    data[3386] = (char) 0xffff;
-    data[3387] = (char) 0xffff;
-    data[3388] = (char) 0xffff;
-    data[3389] = (char) 0xffff;
-    data[3390] = (char) 0xffff;
-    data[3391] = (char) 0xffff;
-    data[3392] = (char) 0xffff;
-    data[3393] = (char) 0xffff;
-    data[3394] = (char) 0xffff;
-    data[3395] = (char) 0xffff;
-    data[3396] = (char) 0xffff;
-    data[3397] = (char) 0xffff;
-    data[3398] = (char) 0xffff;
-    data[3399] = (char) 0xffff;
-    data[3400] = (char) 0xffff;
-    data[3401] = (char) 0xffff;
-    data[3402] = (char) 0xffff;
-    data[3403] = (char) 0xffff;
-    data[3404] = (char) 0xffff;
-    data[3405] = (char) 0xffff;
-    data[3406] = (char) 0xffff;
-    data[3407] = (char) 0xffff;
-    data[3408] = (char) 0xffff;
-    data[3409] = (char) 0xffff;
-    data[3410] = (char) 0xffff;
-    data[3411] = (char) 0xffff;
-    data[3412] = (char) 0xffff;
-    data[3413] = (char) 0xffff;
-    data[3414] = (char) 0xffff;
-    data[3415] = (char) 0xffff;
-    data[3416] = (char) 0xffff;
-    data[3417] = (char) 0xffff;
-    data[3418] = (char) 0xffff;
-    data[3419] = (char) 0xffff;
-    data[3420] = (char) 0xffff;
-    data[3421] = (char) 0xffff;
-    data[3422] = (char) 0xffff;
-    data[3423] = (char) 0xffff;
-    data[3424] = (char) 0xffff;
-    data[3425] = (char) 0xffff;
-    data[3426] = (char) 0xffff;
-    data[3427] = (char) 0xffff;
-    data[3428] = (char) 0xffff;
-    data[3429] = (char) 0xffff;
-    data[3430] = (char) 0xffff;
-    data[3431] = (char) 0xffff;
-    data[3432] = (char) 0xffff;
-    data[3433] = (char) 0xffff;
-    data[3434] = (char) 0xffff;
-    data[3435] = (char) 0xffff;
-    data[3436] = (char) 0xffff;
-    data[3437] = (char) 0xffff;
-    data[3438] = (char) 0xffff;
-    data[3439] = (char) 0xffff;
-    data[3440] = (char) 0xffff;
-    data[3441] = (char) 0xffff;
-    data[3442] = (char) 0xffff;
-    data[3443] = (char) 0xffff;
-    data[3444] = (char) 0xffff;
-    data[3445] = (char) 0xffff;
-    data[3446] = (char) 0xffff;
-    data[3447] = (char) 0xffff;
-    data[3448] = (char) 0xffff;
-    data[3449] = (char) 0xffff;
-    data[3450] = (char) 0x000f;
-    data[3984] = (char) 0xffff;
-    data[3985] = (char) 0xffff;
-    data[3986] = (char) 0xffff;
-    data[3987] = (char) 0xffff;
-    data[3988] = (char) 0xffff;
-    data[3989] = (char) 0xffff;
-    data[3990] = (char) 0xffff;
-    data[3991] = (char) 0xffff;
-    data[3992] = (char) 0xffff;
-    data[3993] = (char) 0xffff;
-    data[3994] = (char) 0xffff;
-    data[3995] = (char) 0xffff;
-    data[3996] = (char) 0xffff;
-    data[3997] = (char) 0xffff;
-    data[3998] = (char) 0xffff;
-    data[3999] = (char) 0xffff;
-    data[4000] = (char) 0xffff;
-    data[4001] = (char) 0xffff;
-    data[4002] = (char) 0x3fff;
-    data[4016] = (char) 0x007f;
-    data[4017] = (char) 0x80f8;
-    data[4018] = (char) 0xfdff;
-    data[4019] = (char) 0x5f7f;
-    data[4020] = (char) 0xffdb;
-    data[4021] = (char) 0xffff;
-    data[4022] = (char) 0xffff;
-    data[4023] = (char) 0xffff;
-    data[4024] = (char) 0xffff;
-    data[4025] = (char) 0xffff;
-    data[4026] = (char) 0xffff;
-    data[4027] = (char) 0x0003;
-    data[4029] = (char) 0xfff8;
-    data[4030] = (char) 0xffff;
-    data[4031] = (char) 0xffff;
-    data[4032] = (char) 0xffff;
-    data[4033] = (char) 0xffff;
-    data[4034] = (char) 0xffff;
-    data[4035] = (char) 0xffff;
-    data[4036] = (char) 0xffff;
-    data[4037] = (char) 0xffff;
-    data[4038] = (char) 0xffff;
-    data[4039] = (char) 0xffff;
-    data[4040] = (char) 0xffff;
-    data[4041] = (char) 0xffff;
-    data[4042] = (char) 0xffff;
-    data[4043] = (char) 0xffff;
-    data[4044] = (char) 0xffff;
-    data[4045] = (char) 0xffff;
-    data[4046] = (char) 0xffff;
-    data[4047] = (char) 0xffff;
-    data[4048] = (char) 0xffff;
-    data[4049] = (char) 0xffff;
-    data[4050] = (char) 0xffff;
-    data[4051] = (char) 0x3fff;
-    data[4053] = (char) 0xffff;
-    data[4054] = (char) 0xffff;
-    data[4055] = (char) 0xffff;
-    data[4056] = (char) 0xffff;
-    data[4057] = (char) 0xfffc;
-    data[4058] = (char) 0xffff;
-    data[4059] = (char) 0xffff;
-    data[4060] = (char) 0x00ff;
-    data[4063] = (char) 0x0fff;
-    data[4071] = (char) 0xffd7;
-    data[4072] = (char) 0xffff;
-    data[4073] = (char) 0xffff;
-    data[4074] = (char) 0xffff;
-    data[4075] = (char) 0xffff;
-    data[4076] = (char) 0xffff;
-    data[4077] = (char) 0xffff;
-    data[4078] = (char) 0xffff;
-    data[4079] = (char) 0x1fff;
-    data[4082] = (char) 0xfffe;
-    data[4083] = (char) 0x07ff;
-    data[4084] = (char) 0xfffe;
-    data[4085] = (char) 0x07ff;
-    data[4086] = (char) 0xffc0;
-    data[4087] = (char) 0xffff;
-    data[4088] = (char) 0xffff;
-    data[4089] = (char) 0xffff;
-    data[4090] = (char) 0xffff;
-    data[4091] = (char) 0x7fff;
-    data[4092] = (char) 0xfcfc;
-    data[4093] = (char) 0x1cfc;
-    data[4100] = (char) 0xfffe;
-    data[4101] = (char) 0x07ff;
-    data[4102] = (char) 0xfffe;
-    data[4103] = (char) 0x07ff;
-    data[4106] = (char) 0x0400;
-    data[4107] = (char) 0x0420;
-    data[4108] = (char) 0xffff;
-    data[4109] = (char) 0xff7f;
-    data[4110] = (char) 0xffff;
-    data[4111] = (char) 0xff7f;
-    data[4112] = (char) 0xffff;
-    data[4113] = (char) 0xffff;
-    data[4114] = (char) 0xffff;
-    data[4115] = (char) 0xffff;
-    data[4116] = (char) 0xffff;
-    data[4117] = (char) 0xffff;
-    data[4118] = (char) 0xffff;
-    data[4119] = (char) 0xffff;
-    data[4120] = (char) 0xffff;
-    data[4121] = (char) 0xffff;
-    data[4122] = (char) 0xffff;
-    data[4123] = (char) 0xffff;
-    data[4124] = (char) 0xffff;
-    data[4125] = (char) 0xffff;
-    data[4126] = (char) 0xffff;
-    data[4127] = (char) 0xfc3f;
-    data[4128] = (char) 0xffff;
-    data[4129] = (char) 0x00ff;
-    data[4133] = (char) 0xffff;
-    data[4134] = (char) 0xffff;
-    data[4135] = (char) 0xffff;
-    data[4136] = (char) 0xffff;
-    data[4137] = (char) 0xffff;
-    data[4138] = (char) 0x01ff;
-    data[4139] = (char) 0xf9ff;
-    data[4140] = (char) 0x0003;
-    data[4141] = (char) 0x0003;
-    data[4142] = (char) 0x001f;
-    data[4151] = (char) 0x0400;
-    data[4152] = (char) 0xd740;
-    data[4153] = (char) 0xffff;
-    data[4154] = (char) 0xfffb;
-    data[4155] = (char) 0xffff;
-    data[4156] = (char) 0x7fff;
-    data[4157] = (char) 0x547f;
-    data[4158] = (char) 0x00fd;
-
-  }
-
-  public static Bits white;
-  static void white_f()
-  {
-    char[] data = new char[4159];
-    white = new Bits(data);
-    data[0] = (char) 0x3e00;
-    data[1] = (char) 0xf000;
-    data[2] = (char) 0x0001;
-    data[512] = (char) 0x0fff;
-    data[514] = (char) 0x0300;
-    data[768] = (char) 0x0001;
-    data[4096] = (char) 0x3e00;
-    data[4097] = (char) 0xf000;
-    data[4098] = (char) 0x0001;
-
-  }
-
-  public static Bits punct;
-  static void punct_f()
-  {
-    char[] data = new char[4159];
-    punct = new Bits(data);
-    data[2] = (char) 0xf7ee;
-    data[3] = (char) 0x8c00;
-    data[4] = (char) 0x0001;
-    data[5] = (char) 0xb800;
-    data[7] = (char) 0x2800;
-    data[10] = (char) 0x2802;
-    data[11] = (char) 0x8880;
-    data[55] = (char) 0x4030;
-    data[56] = (char) 0x0080;
-    data[85] = (char) 0xfc00;
-    data[88] = (char) 0x0200;
-    data[91] = (char) 0x4000;
-    data[92] = (char) 0x0009;
-    data[95] = (char) 0x0018;
-    data[96] = (char) 0x1000;
-    data[97] = (char) 0x8800;
-    data[102] = (char) 0x3c00;
-    data[109] = (char) 0x0010;
-    data[150] = (char) 0x0030;
-    data[151] = (char) 0x0001;
-    data[226] = (char) 0x8000;
-    data[229] = (char) 0x0c00;
-    data[234] = (char) 0x8000;
-    data[240] = (char) 0xfff0;
-    data[241] = (char) 0x0007;
-    data[243] = (char) 0x3c00;
-    data[248] = (char) 0x0020;
-    data[271] = (char) 0x0800;
-    data[513] = (char) 0xffff;
-    data[514] = (char) 0x00ff;
-    data[515] = (char) 0xffff;
-    data[516] = (char) 0x006f;
-    data[519] = (char) 0x6000;
-    data[520] = (char) 0x6000;
-    data[562] = (char) 0x0600;
-    data[768] = (char) 0xff4e;
-    data[769] = (char) 0xfff3;
-    data[771] = (char) 0x0001;
-    data[783] = (char) 0x0800;
-    data[4051] = (char) 0xc000;
-    data[4067] = (char) 0xffff;
-    data[4068] = (char) 0xfe1f;
-    data[4069] = (char) 0xfff7;
-    data[4070] = (char) 0x0d0b;
-    data[4080] = (char) 0xf7ee;
-    data[4081] = (char) 0x8c00;
-    data[4082] = (char) 0x0001;
-    data[4083] = (char) 0xb800;
-    data[4085] = (char) 0x2800;
-    data[4086] = (char) 0x003e;
-    data[4098] = (char) 0xf7ee;
-    data[4099] = (char) 0x8c00;
-    data[4100] = (char) 0x0001;
-    data[4101] = (char) 0xb800;
-    data[4103] = (char) 0x2800;
-    data[4106] = (char) 0x2802;
-    data[4107] = (char) 0x8880;
-    data[4151] = (char) 0x4030;
-    data[4152] = (char) 0x0080;
-
-  }
-}
+package //
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+com.stevesoft.pat;
+
+public class Bits
+{
+  char[] carray;
+
+  Bits(char[] carray)
+  {
+    this.carray = carray;
+  }
+
+  public boolean get(int i)
+  {
+    return ((carray[i >> 4]) & (1 << (i & 15))) != 0;
+  }
+
+  public void set(int i, boolean b)
+  {
+    if (b)
+    {
+      carray[i >> 4] |= (char) 1 << (i & 15);
+    }
+    else
+    {
+      carray[i >> 4] &= (char) ~(1 << (i & 15));
+    }
+  }
+
+  /*
+   * public static String n4(char c) { String s = Integer.toHexString(c);
+   * while(s.length()<4) s = "0"+s; return s; } static abstract class Tester {
+   * abstract boolean test(char c); } public static void main(String[] args)
+   * throws Exception { //pw_s.println(" static {"); FileWriter fw = new
+   * FileWriter("x.out"); fw.close(); test("upper",new Tester() { boolean
+   * test(char c) { return Character.isUpperCase(c); } }); test("lower",new
+   * Tester() { boolean test(char c) { return Character.isLowerCase(c); } });
+   * test("title",new Tester() { boolean test(char c) { return
+   * Character.isLowerCase(c); } }); test("currency",new Tester() { boolean
+   * test(char c) { return Character.getType(c)==Character.CURRENCY_SYMBOL; }
+   * }); test("decimal_digit",new Tester() { boolean test(char c) { return
+   * Character.getType(c)==Character.DECIMAL_DIGIT_NUMBER; } }); test("math",new
+   * Tester() { boolean test(char c) { return
+   * Character.getType(c)==Character.MATH_SYMBOL; } }); test("letter",new
+   * Tester() { boolean test(char c) { return Character.isLetter(c); } });
+   * test("white",new Tester() { boolean test(char c) { return
+   * Character.isWhitespace(c); } }); test("punct",new Tester() { boolean
+   * test(char c) { boolean r = false; switch(Character.getType(c)) { case
+   * Character.DASH_PUNCTUATION: case Character.START_PUNCTUATION: case
+   * Character.END_PUNCTUATION: case Character.CONNECTOR_PUNCTUATION: case
+   * Character.OTHER_PUNCTUATION: r = true; break; default: r = false; break; }
+   * return r; } }); //pw_s.println(" }"); fw = new FileWriter("x.out",true);
+   * fw.write(sw.toString()); fw.close(); } static StringWriter sw = new
+   * StringWriter(); static PrintWriter pw_s = new PrintWriter(sw,true); public
+   * static void test(String var,Tester t) throws Exception {
+   * 
+   * char[] ca = new char[(66536 >> 4)+1]; Bits b = new Bits(ca); FileWriter fw =
+   * new FileWriter("x.out",true); PrintWriter pw = new PrintWriter(fw);
+   * 
+   * //pw_s.println(" "+var+"_f();"); pw.println(" public static Bits
+   * "+var+";"); pw.println(" static void "+var+"_f() {"); pw.println(" char[]
+   * data = new char["+ca.length+"];"); pw.println(" "+var+" = new
+   * Bits(data);"); for(int i=0;i<66536;i++) { char c = (char)i;
+   * //b.set(i,Character.getType(c)==Character.CURRENCY_SYMBOL);
+   * b.set(i,t.test(c)); } for(int i=0;i<ca.length;i++) { if(ca[i] != 0) {
+   * pw.println(" data["+i+"]=(char)0x"+n4(ca[i])+";"); } } pw.println();
+   * pw.println(" }");
+   * 
+   * pw.close(); }
+   */
+  public static Bits upper;
+
+  static void upper_f()
+  {
+    char[] data = new char[4159];
+    upper = new Bits(data);
+    data[4] = (char) 0xfffe;
+    data[5] = (char) 0x07ff;
+    data[12] = (char) 0xffff;
+    data[13] = (char) 0x7f7f;
+    data[16] = (char) 0x5555;
+    data[17] = (char) 0x5555;
+    data[18] = (char) 0x5555;
+    data[19] = (char) 0xaa55;
+    data[20] = (char) 0x54aa;
+    data[21] = (char) 0x5555;
+    data[22] = (char) 0x5555;
+    data[23] = (char) 0x2b55;
+    data[24] = (char) 0xced6;
+    data[25] = (char) 0xb1db;
+    data[26] = (char) 0xd2d5;
+    data[27] = (char) 0x11ae;
+    data[28] = (char) 0xa490;
+    data[29] = (char) 0x4aaa;
+    data[30] = (char) 0x5555;
+    data[31] = (char) 0x5412;
+    data[32] = (char) 0x5555;
+    data[33] = (char) 0x0055;
+    data[56] = (char) 0xd740;
+    data[57] = (char) 0xfffe;
+    data[58] = (char) 0x0ffb;
+    data[61] = (char) 0x541c;
+    data[62] = (char) 0x5555;
+    data[64] = (char) 0xdffe;
+    data[65] = (char) 0xffff;
+    data[66] = (char) 0xffff;
+    data[70] = (char) 0x5555;
+    data[71] = (char) 0x5555;
+    data[72] = (char) 0x0001;
+    data[73] = (char) 0x5555;
+    data[74] = (char) 0x5555;
+    data[75] = (char) 0x5555;
+    data[76] = (char) 0x088a;
+    data[77] = (char) 0x5555;
+    data[78] = (char) 0x4555;
+    data[79] = (char) 0x0115;
+    data[83] = (char) 0xfffe;
+    data[84] = (char) 0xffff;
+    data[85] = (char) 0x007f;
+    data[266] = (char) 0xffff;
+    data[267] = (char) 0xffff;
+    data[268] = (char) 0x003f;
+    data[480] = (char) 0x5555;
+    data[481] = (char) 0x5555;
+    data[482] = (char) 0x5555;
+    data[483] = (char) 0x5555;
+    data[484] = (char) 0x5555;
+    data[485] = (char) 0x5555;
+    data[486] = (char) 0x5555;
+    data[487] = (char) 0x5555;
+    data[488] = (char) 0x5555;
+    data[489] = (char) 0x0015;
+    data[490] = (char) 0x5555;
+    data[491] = (char) 0x5555;
+    data[492] = (char) 0x5555;
+    data[493] = (char) 0x5555;
+    data[494] = (char) 0x5555;
+    data[495] = (char) 0x0155;
+    data[496] = (char) 0xff00;
+    data[497] = (char) 0x3f00;
+    data[498] = (char) 0xff00;
+    data[499] = (char) 0xff00;
+    data[500] = (char) 0x3f00;
+    data[501] = (char) 0xaa00;
+    data[502] = (char) 0xff00;
+    data[504] = (char) 0xff00;
+    data[505] = (char) 0xff00;
+    data[506] = (char) 0xff00;
+    data[507] = (char) 0x5f00;
+    data[508] = (char) 0x1f00;
+    data[509] = (char) 0x0f00;
+    data[510] = (char) 0x1f00;
+    data[511] = (char) 0x1f00;
+    data[528] = (char) 0x3884;
+    data[529] = (char) 0x3f27;
+    data[530] = (char) 0x3d50;
+    data[531] = (char) 0x000b;
+    data[4082] = (char) 0xfffe;
+    data[4083] = (char) 0x07ff;
+    data[4100] = (char) 0xfffe;
+    data[4101] = (char) 0x07ff;
+    data[4108] = (char) 0xffff;
+    data[4109] = (char) 0x7f7f;
+    data[4112] = (char) 0x5555;
+    data[4113] = (char) 0x5555;
+    data[4114] = (char) 0x5555;
+    data[4115] = (char) 0xaa55;
+    data[4116] = (char) 0x54aa;
+    data[4117] = (char) 0x5555;
+    data[4118] = (char) 0x5555;
+    data[4119] = (char) 0x2b55;
+    data[4120] = (char) 0xced6;
+    data[4121] = (char) 0xb1db;
+    data[4122] = (char) 0xd2d5;
+    data[4123] = (char) 0x11ae;
+    data[4124] = (char) 0xa490;
+    data[4125] = (char) 0x4aaa;
+    data[4126] = (char) 0x5555;
+    data[4127] = (char) 0x5412;
+    data[4128] = (char) 0x5555;
+    data[4129] = (char) 0x0055;
+    data[4152] = (char) 0xd740;
+    data[4153] = (char) 0xfffe;
+    data[4154] = (char) 0x0ffb;
+    data[4157] = (char) 0x541c;
+    data[4158] = (char) 0x0055;
+
+  }
+
+  public static Bits lower;
+
+  static void lower_f()
+  {
+    char[] data = new char[4159];
+    lower = new Bits(data);
+    data[6] = (char) 0xfffe;
+    data[7] = (char) 0x07ff;
+    data[10] = (char) 0x0400;
+    data[11] = (char) 0x0420;
+    data[13] = (char) 0x8000;
+    data[14] = (char) 0xffff;
+    data[15] = (char) 0xff7f;
+    data[16] = (char) 0xaaaa;
+    data[17] = (char) 0xaaaa;
+    data[18] = (char) 0xaaaa;
+    data[19] = (char) 0x55aa;
+    data[20] = (char) 0xab55;
+    data[21] = (char) 0xaaaa;
+    data[22] = (char) 0xaaaa;
+    data[23] = (char) 0xd4aa;
+    data[24] = (char) 0x3129;
+    data[25] = (char) 0x4e24;
+    data[26] = (char) 0x292a;
+    data[27] = (char) 0x2651;
+    data[28] = (char) 0x5240;
+    data[29] = (char) 0xb555;
+    data[30] = (char) 0xaaaa;
+    data[31] = (char) 0xa829;
+    data[32] = (char) 0xaaaa;
+    data[33] = (char) 0x00aa;
+    data[37] = (char) 0xffff;
+    data[38] = (char) 0xffff;
+    data[39] = (char) 0xffff;
+    data[40] = (char) 0xffff;
+    data[41] = (char) 0xffff;
+    data[42] = (char) 0x01ff;
+    data[57] = (char) 0x0001;
+    data[58] = (char) 0xf000;
+    data[59] = (char) 0xffff;
+    data[60] = (char) 0x7fff;
+    data[61] = (char) 0x0063;
+    data[62] = (char) 0xaaa8;
+    data[63] = (char) 0x0007;
+    data[67] = (char) 0xffff;
+    data[68] = (char) 0xffff;
+    data[69] = (char) 0xdffe;
+    data[70] = (char) 0xaaaa;
+    data[71] = (char) 0xaaaa;
+    data[72] = (char) 0x0002;
+    data[73] = (char) 0xaaaa;
+    data[74] = (char) 0xaaaa;
+    data[75] = (char) 0xaaaa;
+    data[76] = (char) 0x1114;
+    data[77] = (char) 0xaaaa;
+    data[78] = (char) 0x8aaa;
+    data[79] = (char) 0x022a;
+    data[86] = (char) 0xfffe;
+    data[87] = (char) 0xffff;
+    data[88] = (char) 0x00ff;
+    data[269] = (char) 0xffff;
+    data[270] = (char) 0xffff;
+    data[271] = (char) 0x007f;
+    data[480] = (char) 0xaaaa;
+    data[481] = (char) 0xaaaa;
+    data[482] = (char) 0xaaaa;
+    data[483] = (char) 0xaaaa;
+    data[484] = (char) 0xaaaa;
+    data[485] = (char) 0xaaaa;
+    data[486] = (char) 0xaaaa;
+    data[487] = (char) 0xaaaa;
+    data[488] = (char) 0xaaaa;
+    data[489] = (char) 0x0fea;
+    data[490] = (char) 0xaaaa;
+    data[491] = (char) 0xaaaa;
+    data[492] = (char) 0xaaaa;
+    data[493] = (char) 0xaaaa;
+    data[494] = (char) 0xaaaa;
+    data[495] = (char) 0x02aa;
+    data[496] = (char) 0x00ff;
+    data[497] = (char) 0x003f;
+    data[498] = (char) 0x00ff;
+    data[499] = (char) 0x00ff;
+    data[500] = (char) 0x003f;
+    data[501] = (char) 0x00ff;
+    data[502] = (char) 0x00ff;
+    data[503] = (char) 0x3fff;
+    data[504] = (char) 0x00ff;
+    data[505] = (char) 0x00ff;
+    data[506] = (char) 0x00ff;
+    data[507] = (char) 0x00df;
+    data[508] = (char) 0x00dc;
+    data[509] = (char) 0x00cf;
+    data[510] = (char) 0x00ff;
+    data[511] = (char) 0x00dc;
+    data[519] = (char) 0x8000;
+    data[528] = (char) 0xc400;
+    data[529] = (char) 0x0008;
+    data[530] = (char) 0xc000;
+    data[531] = (char) 0x0010;
+    data[4016] = (char) 0x007f;
+    data[4017] = (char) 0x00f8;
+    data[4084] = (char) 0xfffe;
+    data[4085] = (char) 0x07ff;
+    data[4102] = (char) 0xfffe;
+    data[4103] = (char) 0x07ff;
+    data[4106] = (char) 0x0400;
+    data[4107] = (char) 0x0420;
+    data[4109] = (char) 0x8000;
+    data[4110] = (char) 0xffff;
+    data[4111] = (char) 0xff7f;
+    data[4112] = (char) 0xaaaa;
+    data[4113] = (char) 0xaaaa;
+    data[4114] = (char) 0xaaaa;
+    data[4115] = (char) 0x55aa;
+    data[4116] = (char) 0xab55;
+    data[4117] = (char) 0xaaaa;
+    data[4118] = (char) 0xaaaa;
+    data[4119] = (char) 0xd4aa;
+    data[4120] = (char) 0x3129;
+    data[4121] = (char) 0x4e24;
+    data[4122] = (char) 0x292a;
+    data[4123] = (char) 0x2651;
+    data[4124] = (char) 0x5240;
+    data[4125] = (char) 0xb555;
+    data[4126] = (char) 0xaaaa;
+    data[4127] = (char) 0xa829;
+    data[4128] = (char) 0xaaaa;
+    data[4129] = (char) 0x00aa;
+    data[4133] = (char) 0xffff;
+    data[4134] = (char) 0xffff;
+    data[4135] = (char) 0xffff;
+    data[4136] = (char) 0xffff;
+    data[4137] = (char) 0xffff;
+    data[4138] = (char) 0x01ff;
+    data[4153] = (char) 0x0001;
+    data[4154] = (char) 0xf000;
+    data[4155] = (char) 0xffff;
+    data[4156] = (char) 0x7fff;
+    data[4157] = (char) 0x0063;
+    data[4158] = (char) 0x00a8;
+
+  }
+
+  public static Bits title;
+
+  static void title_f()
+  {
+    char[] data = new char[4159];
+    title = new Bits(data);
+    data[6] = (char) 0xfffe;
+    data[7] = (char) 0x07ff;
+    data[10] = (char) 0x0400;
+    data[11] = (char) 0x0420;
+    data[13] = (char) 0x8000;
+    data[14] = (char) 0xffff;
+    data[15] = (char) 0xff7f;
+    data[16] = (char) 0xaaaa;
+    data[17] = (char) 0xaaaa;
+    data[18] = (char) 0xaaaa;
+    data[19] = (char) 0x55aa;
+    data[20] = (char) 0xab55;
+    data[21] = (char) 0xaaaa;
+    data[22] = (char) 0xaaaa;
+    data[23] = (char) 0xd4aa;
+    data[24] = (char) 0x3129;
+    data[25] = (char) 0x4e24;
+    data[26] = (char) 0x292a;
+    data[27] = (char) 0x2651;
+    data[28] = (char) 0x5240;
+    data[29] = (char) 0xb555;
+    data[30] = (char) 0xaaaa;
+    data[31] = (char) 0xa829;
+    data[32] = (char) 0xaaaa;
+    data[33] = (char) 0x00aa;
+    data[37] = (char) 0xffff;
+    data[38] = (char) 0xffff;
+    data[39] = (char) 0xffff;
+    data[40] = (char) 0xffff;
+    data[41] = (char) 0xffff;
+    data[42] = (char) 0x01ff;
+    data[57] = (char) 0x0001;
+    data[58] = (char) 0xf000;
+    data[59] = (char) 0xffff;
+    data[60] = (char) 0x7fff;
+    data[61] = (char) 0x0063;
+    data[62] = (char) 0xaaa8;
+    data[63] = (char) 0x0007;
+    data[67] = (char) 0xffff;
+    data[68] = (char) 0xffff;
+    data[69] = (char) 0xdffe;
+    data[70] = (char) 0xaaaa;
+    data[71] = (char) 0xaaaa;
+    data[72] = (char) 0x0002;
+    data[73] = (char) 0xaaaa;
+    data[74] = (char) 0xaaaa;
+    data[75] = (char) 0xaaaa;
+    data[76] = (char) 0x1114;
+    data[77] = (char) 0xaaaa;
+    data[78] = (char) 0x8aaa;
+    data[79] = (char) 0x022a;
+    data[86] = (char) 0xfffe;
+    data[87] = (char) 0xffff;
+    data[88] = (char) 0x00ff;
+    data[269] = (char) 0xffff;
+    data[270] = (char) 0xffff;
+    data[271] = (char) 0x007f;
+    data[480] = (char) 0xaaaa;
+    data[481] = (char) 0xaaaa;
+    data[482] = (char) 0xaaaa;
+    data[483] = (char) 0xaaaa;
+    data[484] = (char) 0xaaaa;
+    data[485] = (char) 0xaaaa;
+    data[486] = (char) 0xaaaa;
+    data[487] = (char) 0xaaaa;
+    data[488] = (char) 0xaaaa;
+    data[489] = (char) 0x0fea;
+    data[490] = (char) 0xaaaa;
+    data[491] = (char) 0xaaaa;
+    data[492] = (char) 0xaaaa;
+    data[493] = (char) 0xaaaa;
+    data[494] = (char) 0xaaaa;
+    data[495] = (char) 0x02aa;
+    data[496] = (char) 0x00ff;
+    data[497] = (char) 0x003f;
+    data[498] = (char) 0x00ff;
+    data[499] = (char) 0x00ff;
+    data[500] = (char) 0x003f;
+    data[501] = (char) 0x00ff;
+    data[502] = (char) 0x00ff;
+    data[503] = (char) 0x3fff;
+    data[504] = (char) 0x00ff;
+    data[505] = (char) 0x00ff;
+    data[506] = (char) 0x00ff;
+    data[507] = (char) 0x00df;
+    data[508] = (char) 0x00dc;
+    data[509] = (char) 0x00cf;
+    data[510] = (char) 0x00ff;
+    data[511] = (char) 0x00dc;
+    data[519] = (char) 0x8000;
+    data[528] = (char) 0xc400;
+    data[529] = (char) 0x0008;
+    data[530] = (char) 0xc000;
+    data[531] = (char) 0x0010;
+    data[4016] = (char) 0x007f;
+    data[4017] = (char) 0x00f8;
+    data[4084] = (char) 0xfffe;
+    data[4085] = (char) 0x07ff;
+    data[4102] = (char) 0xfffe;
+    data[4103] = (char) 0x07ff;
+    data[4106] = (char) 0x0400;
+    data[4107] = (char) 0x0420;
+    data[4109] = (char) 0x8000;
+    data[4110] = (char) 0xffff;
+    data[4111] = (char) 0xff7f;
+    data[4112] = (char) 0xaaaa;
+    data[4113] = (char) 0xaaaa;
+    data[4114] = (char) 0xaaaa;
+    data[4115] = (char) 0x55aa;
+    data[4116] = (char) 0xab55;
+    data[4117] = (char) 0xaaaa;
+    data[4118] = (char) 0xaaaa;
+    data[4119] = (char) 0xd4aa;
+    data[4120] = (char) 0x3129;
+    data[4121] = (char) 0x4e24;
+    data[4122] = (char) 0x292a;
+    data[4123] = (char) 0x2651;
+    data[4124] = (char) 0x5240;
+    data[4125] = (char) 0xb555;
+    data[4126] = (char) 0xaaaa;
+    data[4127] = (char) 0xa829;
+    data[4128] = (char) 0xaaaa;
+    data[4129] = (char) 0x00aa;
+    data[4133] = (char) 0xffff;
+    data[4134] = (char) 0xffff;
+    data[4135] = (char) 0xffff;
+    data[4136] = (char) 0xffff;
+    data[4137] = (char) 0xffff;
+    data[4138] = (char) 0x01ff;
+    data[4153] = (char) 0x0001;
+    data[4154] = (char) 0xf000;
+    data[4155] = (char) 0xffff;
+    data[4156] = (char) 0x7fff;
+    data[4157] = (char) 0x0063;
+    data[4158] = (char) 0x00a8;
+
+  }
+
+  public static Bits currency;
+
+  static void currency_f()
+  {
+    char[] data = new char[4159];
+    currency = new Bits(data);
+    data[2] = (char) 0x0010;
+    data[10] = (char) 0x003c;
+    data[159] = (char) 0x000c;
+    data[227] = (char) 0x8000;
+    data[522] = (char) 0x1fff;
+    data[4070] = (char) 0x0200;
+    data[4080] = (char) 0x0010;
+    data[4094] = (char) 0x0063;
+    data[4098] = (char) 0x0010;
+    data[4106] = (char) 0x003c;
+
+  }
+
+  public static Bits decimal_digit;
+
+  static void decimal_digit_f()
+  {
+    char[] data = new char[4159];
+    decimal_digit = new Bits(data);
+    data[3] = (char) 0x03ff;
+    data[102] = (char) 0x03ff;
+    data[111] = (char) 0x03ff;
+    data[150] = (char) 0xffc0;
+    data[158] = (char) 0xffc0;
+    data[166] = (char) 0xffc0;
+    data[174] = (char) 0xffc0;
+    data[182] = (char) 0xffc0;
+    data[190] = (char) 0xff80;
+    data[198] = (char) 0xffc0;
+    data[206] = (char) 0xffc0;
+    data[214] = (char) 0xffc0;
+    data[229] = (char) 0x03ff;
+    data[237] = (char) 0x03ff;
+    data[242] = (char) 0x03ff;
+    data[4081] = (char) 0x03ff;
+    data[4099] = (char) 0x03ff;
+
+  }
+
+  public static Bits math;
+
+  static void math_f()
+  {
+    char[] data = new char[4159];
+    math = new Bits(data);
+    data[2] = (char) 0x0800;
+    data[3] = (char) 0x7000;
+    data[7] = (char) 0x5000;
+    data[10] = (char) 0x1000;
+    data[11] = (char) 0x0002;
+    data[13] = (char) 0x0080;
+    data[15] = (char) 0x0080;
+    data[516] = (char) 0x0010;
+    data[519] = (char) 0x1c00;
+    data[520] = (char) 0x1c00;
+    data[537] = (char) 0x001f;
+    data[541] = (char) 0x0014;
+    data[544] = (char) 0xffff;
+    data[545] = (char) 0xffff;
+    data[546] = (char) 0xffff;
+    data[547] = (char) 0xffff;
+    data[548] = (char) 0xffff;
+    data[549] = (char) 0xffff;
+    data[550] = (char) 0xffff;
+    data[551] = (char) 0xffff;
+    data[552] = (char) 0xffff;
+    data[553] = (char) 0xffff;
+    data[554] = (char) 0xffff;
+    data[555] = (char) 0xffff;
+    data[556] = (char) 0xffff;
+    data[557] = (char) 0xffff;
+    data[558] = (char) 0xffff;
+    data[559] = (char) 0x0003;
+    data[560] = (char) 0x0f00;
+    data[562] = (char) 0x0003;
+    data[4018] = (char) 0x0200;
+    data[4070] = (char) 0x0074;
+    data[4080] = (char) 0x0800;
+    data[4081] = (char) 0x7000;
+    data[4085] = (char) 0x5000;
+    data[4094] = (char) 0x1f04;
+    data[4098] = (char) 0x0800;
+    data[4099] = (char) 0x7000;
+    data[4103] = (char) 0x5000;
+    data[4106] = (char) 0x1000;
+    data[4107] = (char) 0x0002;
+    data[4109] = (char) 0x0080;
+    data[4111] = (char) 0x0080;
+
+  }
+
+  public static Bits letter;
+
+  static void letter_f()
+  {
+    char[] data = new char[4159];
+    letter = new Bits(data);
+    data[4] = (char) 0xfffe;
+    data[5] = (char) 0x07ff;
+    data[6] = (char) 0xfffe;
+    data[7] = (char) 0x07ff;
+    data[10] = (char) 0x0400;
+    data[11] = (char) 0x0420;
+    data[12] = (char) 0xffff;
+    data[13] = (char) 0xff7f;
+    data[14] = (char) 0xffff;
+    data[15] = (char) 0xff7f;
+    data[16] = (char) 0xffff;
+    data[17] = (char) 0xffff;
+    data[18] = (char) 0xffff;
+    data[19] = (char) 0xffff;
+    data[20] = (char) 0xffff;
+    data[21] = (char) 0xffff;
+    data[22] = (char) 0xffff;
+    data[23] = (char) 0xffff;
+    data[24] = (char) 0xffff;
+    data[25] = (char) 0xffff;
+    data[26] = (char) 0xffff;
+    data[27] = (char) 0xffff;
+    data[28] = (char) 0xffff;
+    data[29] = (char) 0xffff;
+    data[30] = (char) 0xffff;
+    data[31] = (char) 0xfc3f;
+    data[32] = (char) 0xffff;
+    data[33] = (char) 0x00ff;
+    data[37] = (char) 0xffff;
+    data[38] = (char) 0xffff;
+    data[39] = (char) 0xffff;
+    data[40] = (char) 0xffff;
+    data[41] = (char) 0xffff;
+    data[42] = (char) 0x01ff;
+    data[43] = (char) 0xf9ff;
+    data[44] = (char) 0x0003;
+    data[45] = (char) 0x0003;
+    data[46] = (char) 0x001f;
+    data[55] = (char) 0x0400;
+    data[56] = (char) 0xd740;
+    data[57] = (char) 0xffff;
+    data[58] = (char) 0xfffb;
+    data[59] = (char) 0xffff;
+    data[60] = (char) 0x7fff;
+    data[61] = (char) 0x547f;
+    data[62] = (char) 0xfffd;
+    data[63] = (char) 0x000f;
+    data[64] = (char) 0xdffe;
+    data[65] = (char) 0xffff;
+    data[66] = (char) 0xffff;
+    data[67] = (char) 0xffff;
+    data[68] = (char) 0xffff;
+    data[69] = (char) 0xdffe;
+    data[70] = (char) 0xffff;
+    data[71] = (char) 0xffff;
+    data[72] = (char) 0x0003;
+    data[73] = (char) 0xffff;
+    data[74] = (char) 0xffff;
+    data[75] = (char) 0xffff;
+    data[76] = (char) 0x199f;
+    data[77] = (char) 0xffff;
+    data[78] = (char) 0xcfff;
+    data[79] = (char) 0x033f;
+    data[83] = (char) 0xfffe;
+    data[84] = (char) 0xffff;
+    data[85] = (char) 0x027f;
+    data[86] = (char) 0xfffe;
+    data[87] = (char) 0xffff;
+    data[88] = (char) 0x00ff;
+    data[93] = (char) 0xffff;
+    data[94] = (char) 0x07ff;
+    data[95] = (char) 0x0007;
+    data[98] = (char) 0xfffe;
+    data[99] = (char) 0x07ff;
+    data[100] = (char) 0x07ff;
+    data[103] = (char) 0xfffe;
+    data[104] = (char) 0xffff;
+    data[105] = (char) 0xffff;
+    data[106] = (char) 0xffff;
+    data[107] = (char) 0x7cff;
+    data[108] = (char) 0x7fff;
+    data[109] = (char) 0x002f;
+    data[110] = (char) 0x0060;
+    data[144] = (char) 0xffe0;
+    data[145] = (char) 0xffff;
+    data[146] = (char) 0xffff;
+    data[147] = (char) 0x23ff;
+    data[149] = (char) 0xff00;
+    data[150] = (char) 0x0003;
+    data[152] = (char) 0x9fe0;
+    data[153] = (char) 0xfff9;
+    data[154] = (char) 0xfdff;
+    data[155] = (char) 0x03c5;
+    data[157] = (char) 0xb000;
+    data[158] = (char) 0x0003;
+    data[159] = (char) 0x0003;
+    data[160] = (char) 0x87e0;
+    data[161] = (char) 0xfff9;
+    data[162] = (char) 0xfdff;
+    data[163] = (char) 0x036d;
+    data[165] = (char) 0x5e00;
+    data[167] = (char) 0x001c;
+    data[168] = (char) 0xafe0;
+    data[169] = (char) 0xfffb;
+    data[170] = (char) 0xfdff;
+    data[171] = (char) 0x23ed;
+    data[174] = (char) 0x0001;
+    data[176] = (char) 0x9fe0;
+    data[177] = (char) 0xfff9;
+    data[178] = (char) 0xfdff;
+    data[179] = (char) 0x23cd;
+    data[181] = (char) 0xb000;
+    data[182] = (char) 0x0003;
+    data[184] = (char) 0xc7e0;
+    data[185] = (char) 0xd63d;
+    data[186] = (char) 0xc718;
+    data[187] = (char) 0x03bf;
+    data[192] = (char) 0xdfe0;
+    data[193] = (char) 0xfffd;
+    data[194] = (char) 0xfdff;
+    data[195] = (char) 0x03ef;
+    data[198] = (char) 0x0003;
+    data[200] = (char) 0xdfe0;
+    data[201] = (char) 0xfffd;
+    data[202] = (char) 0xfdff;
+    data[203] = (char) 0x03ef;
+    data[205] = (char) 0x4000;
+    data[206] = (char) 0x0003;
+    data[208] = (char) 0xdfe0;
+    data[209] = (char) 0xfffd;
+    data[210] = (char) 0xfdff;
+    data[211] = (char) 0x03ff;
+    data[214] = (char) 0x0003;
+    data[224] = (char) 0xfffe;
+    data[225] = (char) 0xffff;
+    data[226] = (char) 0x7fff;
+    data[227] = (char) 0x000d;
+    data[228] = (char) 0x007f;
+    data[232] = (char) 0x2596;
+    data[233] = (char) 0xfef0;
+    data[234] = (char) 0x6cae;
+    data[235] = (char) 0x200d;
+    data[236] = (char) 0x005f;
+    data[237] = (char) 0x3000;
+    data[244] = (char) 0xfeff;
+    data[245] = (char) 0xffff;
+    data[246] = (char) 0x03ff;
+    data[266] = (char) 0xffff;
+    data[267] = (char) 0xffff;
+    data[268] = (char) 0x003f;
+    data[269] = (char) 0xffff;
+    data[270] = (char) 0xffff;
+    data[271] = (char) 0x007f;
+    data[272] = (char) 0xffff;
+    data[273] = (char) 0xffff;
+    data[274] = (char) 0xffff;
+    data[275] = (char) 0xffff;
+    data[276] = (char) 0xffff;
+    data[277] = (char) 0x83ff;
+    data[278] = (char) 0xffff;
+    data[279] = (char) 0xffff;
+    data[280] = (char) 0xffff;
+    data[281] = (char) 0xffff;
+    data[282] = (char) 0xff07;
+    data[283] = (char) 0xffff;
+    data[284] = (char) 0xffff;
+    data[285] = (char) 0xffff;
+    data[286] = (char) 0xffff;
+    data[287] = (char) 0x03ff;
+    data[480] = (char) 0xffff;
+    data[481] = (char) 0xffff;
+    data[482] = (char) 0xffff;
+    data[483] = (char) 0xffff;
+    data[484] = (char) 0xffff;
+    data[485] = (char) 0xffff;
+    data[486] = (char) 0xffff;
+    data[487] = (char) 0xffff;
+    data[488] = (char) 0xffff;
+    data[489] = (char) 0x0fff;
+    data[490] = (char) 0xffff;
+    data[491] = (char) 0xffff;
+    data[492] = (char) 0xffff;
+    data[493] = (char) 0xffff;
+    data[494] = (char) 0xffff;
+    data[495] = (char) 0x03ff;
+    data[496] = (char) 0xffff;
+    data[497] = (char) 0x3f3f;
+    data[498] = (char) 0xffff;
+    data[499] = (char) 0xffff;
+    data[500] = (char) 0x3f3f;
+    data[501] = (char) 0xaaff;
+    data[502] = (char) 0xffff;
+    data[503] = (char) 0x3fff;
+    data[504] = (char) 0xffff;
+    data[505] = (char) 0xffff;
+    data[506] = (char) 0xffff;
+    data[507] = (char) 0x5fdf;
+    data[508] = (char) 0x1fdc;
+    data[509] = (char) 0x0fcf;
+    data[510] = (char) 0x1fff;
+    data[511] = (char) 0x1fdc;
+    data[519] = (char) 0x8000;
+    data[528] = (char) 0xfc84;
+    data[529] = (char) 0x3f2f;
+    data[530] = (char) 0xfd50;
+    data[531] = (char) 0x01fb;
+    data[768] = (char) 0x0020;
+    data[771] = (char) 0x003e;
+    data[772] = (char) 0xfffe;
+    data[773] = (char) 0xffff;
+    data[774] = (char) 0xffff;
+    data[775] = (char) 0xffff;
+    data[776] = (char) 0xffff;
+    data[777] = (char) 0x781f;
+    data[778] = (char) 0xfffe;
+    data[779] = (char) 0xffff;
+    data[780] = (char) 0xffff;
+    data[781] = (char) 0xffff;
+    data[782] = (char) 0xffff;
+    data[783] = (char) 0x77ff;
+    data[784] = (char) 0xffe0;
+    data[785] = (char) 0xffff;
+    data[786] = (char) 0x1fff;
+    data[787] = (char) 0xfffe;
+    data[788] = (char) 0xffff;
+    data[789] = (char) 0xffff;
+    data[790] = (char) 0xffff;
+    data[791] = (char) 0xffff;
+    data[792] = (char) 0x7fff;
+    data[1248] = (char) 0xffff;
+    data[1249] = (char) 0xffff;
+    data[1250] = (char) 0xffff;
+    data[1251] = (char) 0xffff;
+    data[1252] = (char) 0xffff;
+    data[1253] = (char) 0xffff;
+    data[1254] = (char) 0xffff;
+    data[1255] = (char) 0xffff;
+    data[1256] = (char) 0xffff;
+    data[1257] = (char) 0xffff;
+    data[1258] = (char) 0xffff;
+    data[1259] = (char) 0xffff;
+    data[1260] = (char) 0xffff;
+    data[1261] = (char) 0xffff;
+    data[1262] = (char) 0xffff;
+    data[1263] = (char) 0xffff;
+    data[1264] = (char) 0xffff;
+    data[1265] = (char) 0xffff;
+    data[1266] = (char) 0xffff;
+    data[1267] = (char) 0xffff;
+    data[1268] = (char) 0xffff;
+    data[1269] = (char) 0xffff;
+    data[1270] = (char) 0xffff;
+    data[1271] = (char) 0xffff;
+    data[1272] = (char) 0xffff;
+    data[1273] = (char) 0xffff;
+    data[1274] = (char) 0xffff;
+    data[1275] = (char) 0xffff;
+    data[1276] = (char) 0xffff;
+    data[1277] = (char) 0xffff;
+    data[1278] = (char) 0xffff;
+    data[1279] = (char) 0xffff;
+    data[1280] = (char) 0xffff;
+    data[1281] = (char) 0xffff;
+    data[1282] = (char) 0xffff;
+    data[1283] = (char) 0xffff;
+    data[1284] = (char) 0xffff;
+    data[1285] = (char) 0xffff;
+    data[1286] = (char) 0xffff;
+    data[1287] = (char) 0xffff;
+    data[1288] = (char) 0xffff;
+    data[1289] = (char) 0xffff;
+    data[1290] = (char) 0xffff;
+    data[1291] = (char) 0xffff;
+    data[1292] = (char) 0xffff;
+    data[1293] = (char) 0xffff;
+    data[1294] = (char) 0xffff;
+    data[1295] = (char) 0xffff;
+    data[1296] = (char) 0xffff;
+    data[1297] = (char) 0xffff;
+    data[1298] = (char) 0xffff;
+    data[1299] = (char) 0xffff;
+    data[1300] = (char) 0xffff;
+    data[1301] = (char) 0xffff;
+    data[1302] = (char) 0xffff;
+    data[1303] = (char) 0xffff;
+    data[1304] = (char) 0xffff;
+    data[1305] = (char) 0xffff;
+    data[1306] = (char) 0xffff;
+    data[1307] = (char) 0xffff;
+    data[1308] = (char) 0xffff;
+    data[1309] = (char) 0xffff;
+    data[1310] = (char) 0xffff;
+    data[1311] = (char) 0xffff;
+    data[1312] = (char) 0xffff;
+    data[1313] = (char) 0xffff;
+    data[1314] = (char) 0xffff;
+    data[1315] = (char) 0xffff;
+    data[1316] = (char) 0xffff;
+    data[1317] = (char) 0xffff;
+    data[1318] = (char) 0xffff;
+    data[1319] = (char) 0xffff;
+    data[1320] = (char) 0xffff;
+    data[1321] = (char) 0xffff;
+    data[1322] = (char) 0xffff;
+    data[1323] = (char) 0xffff;
+    data[1324] = (char) 0xffff;
+    data[1325] = (char) 0xffff;
+    data[1326] = (char) 0xffff;
+    data[1327] = (char) 0xffff;
+    data[1328] = (char) 0xffff;
+    data[1329] = (char) 0xffff;
+    data[1330] = (char) 0xffff;
+    data[1331] = (char) 0xffff;
+    data[1332] = (char) 0xffff;
+    data[1333] = (char) 0xffff;
+    data[1334] = (char) 0xffff;
+    data[1335] = (char) 0xffff;
+    data[1336] = (char) 0xffff;
+    data[1337] = (char) 0xffff;
+    data[1338] = (char) 0xffff;
+    data[1339] = (char) 0xffff;
+    data[1340] = (char) 0xffff;
+    data[1341] = (char) 0xffff;
+    data[1342] = (char) 0xffff;
+    data[1343] = (char) 0xffff;
+    data[1344] = (char) 0xffff;
+    data[1345] = (char) 0xffff;
+    data[1346] = (char) 0xffff;
+    data[1347] = (char) 0xffff;
+    data[1348] = (char) 0xffff;
+    data[1349] = (char) 0xffff;
+    data[1350] = (char) 0xffff;
+    data[1351] = (char) 0xffff;
+    data[1352] = (char) 0xffff;
+    data[1353] = (char) 0xffff;
+    data[1354] = (char) 0xffff;
+    data[1355] = (char) 0xffff;
+    data[1356] = (char) 0xffff;
+    data[1357] = (char) 0xffff;
+    data[1358] = (char) 0xffff;
+    data[1359] = (char) 0xffff;
+    data[1360] = (char) 0xffff;
+    data[1361] = (char) 0xffff;
+    data[1362] = (char) 0xffff;
+    data[1363] = (char) 0xffff;
+    data[1364] = (char) 0xffff;
+    data[1365] = (char) 0xffff;
+    data[1366] = (char) 0xffff;
+    data[1367] = (char) 0xffff;
+    data[1368] = (char) 0xffff;
+    data[1369] = (char) 0xffff;
+    data[1370] = (char) 0xffff;
+    data[1371] = (char) 0xffff;
+    data[1372] = (char) 0xffff;
+    data[1373] = (char) 0xffff;
+    data[1374] = (char) 0xffff;
+    data[1375] = (char) 0xffff;
+    data[1376] = (char) 0xffff;
+    data[1377] = (char) 0xffff;
+    data[1378] = (char) 0xffff;
+    data[1379] = (char) 0xffff;
+    data[1380] = (char) 0xffff;
+    data[1381] = (char) 0xffff;
+    data[1382] = (char) 0xffff;
+    data[1383] = (char) 0xffff;
+    data[1384] = (char) 0xffff;
+    data[1385] = (char) 0xffff;
+    data[1386] = (char) 0xffff;
+    data[1387] = (char) 0xffff;
+    data[1388] = (char) 0xffff;
+    data[1389] = (char) 0xffff;
+    data[1390] = (char) 0xffff;
+    data[1391] = (char) 0xffff;
+    data[1392] = (char) 0xffff;
+    data[1393] = (char) 0xffff;
+    data[1394] = (char) 0xffff;
+    data[1395] = (char) 0xffff;
+    data[1396] = (char) 0xffff;
+    data[1397] = (char) 0xffff;
+    data[1398] = (char) 0xffff;
+    data[1399] = (char) 0xffff;
+    data[1400] = (char) 0xffff;
+    data[1401] = (char) 0xffff;
+    data[1402] = (char) 0xffff;
+    data[1403] = (char) 0xffff;
+    data[1404] = (char) 0xffff;
+    data[1405] = (char) 0xffff;
+    data[1406] = (char) 0xffff;
+    data[1407] = (char) 0xffff;
+    data[1408] = (char) 0xffff;
+    data[1409] = (char) 0xffff;
+    data[1410] = (char) 0xffff;
+    data[1411] = (char) 0xffff;
+    data[1412] = (char) 0xffff;
+    data[1413] = (char) 0xffff;
+    data[1414] = (char) 0xffff;
+    data[1415] = (char) 0xffff;
+    data[1416] = (char) 0xffff;
+    data[1417] = (char) 0xffff;
+    data[1418] = (char) 0xffff;
+    data[1419] = (char) 0xffff;
+    data[1420] = (char) 0xffff;
+    data[1421] = (char) 0xffff;
+    data[1422] = (char) 0xffff;
+    data[1423] = (char) 0xffff;
+    data[1424] = (char) 0xffff;
+    data[1425] = (char) 0xffff;
+    data[1426] = (char) 0xffff;
+    data[1427] = (char) 0xffff;
+    data[1428] = (char) 0xffff;
+    data[1429] = (char) 0xffff;
+    data[1430] = (char) 0xffff;
+    data[1431] = (char) 0xffff;
+    data[1432] = (char) 0xffff;
+    data[1433] = (char) 0xffff;
+    data[1434] = (char) 0xffff;
+    data[1435] = (char) 0xffff;
+    data[1436] = (char) 0xffff;
+    data[1437] = (char) 0xffff;
+    data[1438] = (char) 0xffff;
+    data[1439] = (char) 0xffff;
+    data[1440] = (char) 0xffff;
+    data[1441] = (char) 0xffff;
+    data[1442] = (char) 0xffff;
+    data[1443] = (char) 0xffff;
+    data[1444] = (char) 0xffff;
+    data[1445] = (char) 0xffff;
+    data[1446] = (char) 0xffff;
+    data[1447] = (char) 0xffff;
+    data[1448] = (char) 0xffff;
+    data[1449] = (char) 0xffff;
+    data[1450] = (char) 0xffff;
+    data[1451] = (char) 0xffff;
+    data[1452] = (char) 0xffff;
+    data[1453] = (char) 0xffff;
+    data[1454] = (char) 0xffff;
+    data[1455] = (char) 0xffff;
+    data[1456] = (char) 0xffff;
+    data[1457] = (char) 0xffff;
+    data[1458] = (char) 0xffff;
+    data[1459] = (char) 0xffff;
+    data[1460] = (char) 0xffff;
+    data[1461] = (char) 0xffff;
+    data[1462] = (char) 0xffff;
+    data[1463] = (char) 0xffff;
+    data[1464] = (char) 0xffff;
+    data[1465] = (char) 0xffff;
+    data[1466] = (char) 0xffff;
+    data[1467] = (char) 0xffff;
+    data[1468] = (char) 0xffff;
+    data[1469] = (char) 0xffff;
+    data[1470] = (char) 0xffff;
+    data[1471] = (char) 0xffff;
+    data[1472] = (char) 0xffff;
+    data[1473] = (char) 0xffff;
+    data[1474] = (char) 0xffff;
+    data[1475] = (char) 0xffff;
+    data[1476] = (char) 0xffff;
+    data[1477] = (char) 0xffff;
+    data[1478] = (char) 0xffff;
+    data[1479] = (char) 0xffff;
+    data[1480] = (char) 0xffff;
+    data[1481] = (char) 0xffff;
+    data[1482] = (char) 0xffff;
+    data[1483] = (char) 0xffff;
+    data[1484] = (char) 0xffff;
+    data[1485] = (char) 0xffff;
+    data[1486] = (char) 0xffff;
+    data[1487] = (char) 0xffff;
+    data[1488] = (char) 0xffff;
+    data[1489] = (char) 0xffff;
+    data[1490] = (char) 0xffff;
+    data[1491] = (char) 0xffff;
+    data[1492] = (char) 0xffff;
+    data[1493] = (char) 0xffff;
+    data[1494] = (char) 0xffff;
+    data[1495] = (char) 0xffff;
+    data[1496] = (char) 0xffff;
+    data[1497] = (char) 0xffff;
+    data[1498] = (char) 0xffff;
+    data[1499] = (char) 0xffff;
+    data[1500] = (char) 0xffff;
+    data[1501] = (char) 0xffff;
+    data[1502] = (char) 0xffff;
+    data[1503] = (char) 0xffff;
+    data[1504] = (char) 0xffff;
+    data[1505] = (char) 0xffff;
+    data[1506] = (char) 0xffff;
+    data[1507] = (char) 0xffff;
+    data[1508] = (char) 0xffff;
+    data[1509] = (char) 0xffff;
+    data[1510] = (char) 0xffff;
+    data[1511] = (char) 0xffff;
+    data[1512] = (char) 0xffff;
+    data[1513] = (char) 0xffff;
+    data[1514] = (char) 0xffff;
+    data[1515] = (char) 0xffff;
+    data[1516] = (char) 0xffff;
+    data[1517] = (char) 0xffff;
+    data[1518] = (char) 0xffff;
+    data[1519] = (char) 0xffff;
+    data[1520] = (char) 0xffff;
+    data[1521] = (char) 0xffff;
+    data[1522] = (char) 0xffff;
+    data[1523] = (char) 0xffff;
+    data[1524] = (char) 0xffff;
+    data[1525] = (char) 0xffff;
+    data[1526] = (char) 0xffff;
+    data[1527] = (char) 0xffff;
+    data[1528] = (char) 0xffff;
+    data[1529] = (char) 0xffff;
+    data[1530] = (char) 0xffff;
+    data[1531] = (char) 0xffff;
+    data[1532] = (char) 0xffff;
+    data[1533] = (char) 0xffff;
+    data[1534] = (char) 0xffff;
+    data[1535] = (char) 0xffff;
+    data[1536] = (char) 0xffff;
+    data[1537] = (char) 0xffff;
+    data[1538] = (char) 0xffff;
+    data[1539] = (char) 0xffff;
+    data[1540] = (char) 0xffff;
+    data[1541] = (char) 0xffff;
+    data[1542] = (char) 0xffff;
+    data[1543] = (char) 0xffff;
+    data[1544] = (char) 0xffff;
+    data[1545] = (char) 0xffff;
+    data[1546] = (char) 0xffff;
+    data[1547] = (char) 0xffff;
+    data[1548] = (char) 0xffff;
+    data[1549] = (char) 0xffff;
+    data[1550] = (char) 0xffff;
+    data[1551] = (char) 0xffff;
+    data[1552] = (char) 0xffff;
+    data[1553] = (char) 0xffff;
+    data[1554] = (char) 0xffff;
+    data[1555] = (char) 0xffff;
+    data[1556] = (char) 0xffff;
+    data[1557] = (char) 0xffff;
+    data[1558] = (char) 0xffff;
+    data[1559] = (char) 0xffff;
+    data[1560] = (char) 0xffff;
+    data[1561] = (char) 0xffff;
+    data[1562] = (char) 0xffff;
+    data[1563] = (char) 0xffff;
+    data[1564] = (char) 0xffff;
+    data[1565] = (char) 0xffff;
+    data[1566] = (char) 0xffff;
+    data[1567] = (char) 0xffff;
+    data[1568] = (char) 0xffff;
+    data[1569] = (char) 0xffff;
+    data[1570] = (char) 0xffff;
+    data[1571] = (char) 0xffff;
+    data[1572] = (char) 0xffff;
+    data[1573] = (char) 0xffff;
+    data[1574] = (char) 0xffff;
+    data[1575] = (char) 0xffff;
+    data[1576] = (char) 0xffff;
+    data[1577] = (char) 0xffff;
+    data[1578] = (char) 0xffff;
+    data[1579] = (char) 0xffff;
+    data[1580] = (char) 0xffff;
+    data[1581] = (char) 0xffff;
+    data[1582] = (char) 0xffff;
+    data[1583] = (char) 0xffff;
+    data[1584] = (char) 0xffff;
+    data[1585] = (char) 0xffff;
+    data[1586] = (char) 0xffff;
+    data[1587] = (char) 0xffff;
+    data[1588] = (char) 0xffff;
+    data[1589] = (char) 0xffff;
+    data[1590] = (char) 0xffff;
+    data[1591] = (char) 0xffff;
+    data[1592] = (char) 0xffff;
+    data[1593] = (char) 0xffff;
+    data[1594] = (char) 0xffff;
+    data[1595] = (char) 0xffff;
+    data[1596] = (char) 0xffff;
+    data[1597] = (char) 0xffff;
+    data[1598] = (char) 0xffff;
+    data[1599] = (char) 0xffff;
+    data[1600] = (char) 0xffff;
+    data[1601] = (char) 0xffff;
+    data[1602] = (char) 0xffff;
+    data[1603] = (char) 0xffff;
+    data[1604] = (char) 0xffff;
+    data[1605] = (char) 0xffff;
+    data[1606] = (char) 0xffff;
+    data[1607] = (char) 0xffff;
+    data[1608] = (char) 0xffff;
+    data[1609] = (char) 0xffff;
+    data[1610] = (char) 0xffff;
+    data[1611] = (char) 0xffff;
+    data[1612] = (char) 0xffff;
+    data[1613] = (char) 0xffff;
+    data[1614] = (char) 0xffff;
+    data[1615] = (char) 0xffff;
+    data[1616] = (char) 0xffff;
+    data[1617] = (char) 0xffff;
+    data[1618] = (char) 0xffff;
+    data[1619] = (char) 0xffff;
+    data[1620] = (char) 0xffff;
+    data[1621] = (char) 0xffff;
+    data[1622] = (char) 0xffff;
+    data[1623] = (char) 0xffff;
+    data[1624] = (char) 0xffff;
+    data[1625] = (char) 0xffff;
+    data[1626] = (char) 0xffff;
+    data[1627] = (char) 0xffff;
+    data[1628] = (char) 0xffff;
+    data[1629] = (char) 0xffff;
+    data[1630] = (char) 0xffff;
+    data[1631] = (char) 0xffff;
+    data[1632] = (char) 0xffff;
+    data[1633] = (char) 0xffff;
+    data[1634] = (char) 0xffff;
+    data[1635] = (char) 0xffff;
+    data[1636] = (char) 0xffff;
+    data[1637] = (char) 0xffff;
+    data[1638] = (char) 0xffff;
+    data[1639] = (char) 0xffff;
+    data[1640] = (char) 0xffff;
+    data[1641] = (char) 0xffff;
+    data[1642] = (char) 0xffff;
+    data[1643] = (char) 0xffff;
+    data[1644] = (char) 0xffff;
+    data[1645] = (char) 0xffff;
+    data[1646] = (char) 0xffff;
+    data[1647] = (char) 0xffff;
+    data[1648] = (char) 0xffff;
+    data[1649] = (char) 0xffff;
+    data[1650] = (char) 0xffff;
+    data[1651] = (char) 0xffff;
+    data[1652] = (char) 0xffff;
+    data[1653] = (char) 0xffff;
+    data[1654] = (char) 0xffff;
+    data[1655] = (char) 0xffff;
+    data[1656] = (char) 0xffff;
+    data[1657] = (char) 0xffff;
+    data[1658] = (char) 0xffff;
+    data[1659] = (char) 0xffff;
+    data[1660] = (char) 0xffff;
+    data[1661] = (char) 0xffff;
+    data[1662] = (char) 0xffff;
+    data[1663] = (char) 0xffff;
+    data[1664] = (char) 0xffff;
+    data[1665] = (char) 0xffff;
+    data[1666] = (char) 0xffff;
+    data[1667] = (char) 0xffff;
+    data[1668] = (char) 0xffff;
+    data[1669] = (char) 0xffff;
+    data[1670] = (char) 0xffff;
+    data[1671] = (char) 0xffff;
+    data[1672] = (char) 0xffff;
+    data[1673] = (char) 0xffff;
+    data[1674] = (char) 0xffff;
+    data[1675] = (char) 0xffff;
+    data[1676] = (char) 0xffff;
+    data[1677] = (char) 0xffff;
+    data[1678] = (char) 0xffff;
+    data[1679] = (char) 0xffff;
+    data[1680] = (char) 0xffff;
+    data[1681] = (char) 0xffff;
+    data[1682] = (char) 0xffff;
+    data[1683] = (char) 0xffff;
+    data[1684] = (char) 0xffff;
+    data[1685] = (char) 0xffff;
+    data[1686] = (char) 0xffff;
+    data[1687] = (char) 0xffff;
+    data[1688] = (char) 0xffff;
+    data[1689] = (char) 0xffff;
+    data[1690] = (char) 0xffff;
+    data[1691] = (char) 0xffff;
+    data[1692] = (char) 0xffff;
+    data[1693] = (char) 0xffff;
+    data[1694] = (char) 0xffff;
+    data[1695] = (char) 0xffff;
+    data[1696] = (char) 0xffff;
+    data[1697] = (char) 0xffff;
+    data[1698] = (char) 0xffff;
+    data[1699] = (char) 0xffff;
+    data[1700] = (char) 0xffff;
+    data[1701] = (char) 0xffff;
+    data[1702] = (char) 0xffff;
+    data[1703] = (char) 0xffff;
+    data[1704] = (char) 0xffff;
+    data[1705] = (char) 0xffff;
+    data[1706] = (char) 0xffff;
+    data[1707] = (char) 0xffff;
+    data[1708] = (char) 0xffff;
+    data[1709] = (char) 0xffff;
+    data[1710] = (char) 0xffff;
+    data[1711] = (char) 0xffff;
+    data[1712] = (char) 0xffff;
+    data[1713] = (char) 0xffff;
+    data[1714] = (char) 0xffff;
+    data[1715] = (char) 0xffff;
+    data[1716] = (char) 0xffff;
+    data[1717] = (char) 0xffff;
+    data[1718] = (char) 0xffff;
+    data[1719] = (char) 0xffff;
+    data[1720] = (char) 0xffff;
+    data[1721] = (char) 0xffff;
+    data[1722] = (char) 0xffff;
+    data[1723] = (char) 0xffff;
+    data[1724] = (char) 0xffff;
+    data[1725] = (char) 0xffff;
+    data[1726] = (char) 0xffff;
+    data[1727] = (char) 0xffff;
+    data[1728] = (char) 0xffff;
+    data[1729] = (char) 0xffff;
+    data[1730] = (char) 0xffff;
+    data[1731] = (char) 0xffff;
+    data[1732] = (char) 0xffff;
+    data[1733] = (char) 0xffff;
+    data[1734] = (char) 0xffff;
+    data[1735] = (char) 0xffff;
+    data[1736] = (char) 0xffff;
+    data[1737] = (char) 0xffff;
+    data[1738] = (char) 0xffff;
+    data[1739] = (char) 0xffff;
+    data[1740] = (char) 0xffff;
+    data[1741] = (char) 0xffff;
+    data[1742] = (char) 0xffff;
+    data[1743] = (char) 0xffff;
+    data[1744] = (char) 0xffff;
+    data[1745] = (char) 0xffff;
+    data[1746] = (char) 0xffff;
+    data[1747] = (char) 0xffff;
+    data[1748] = (char) 0xffff;
+    data[1749] = (char) 0xffff;
+    data[1750] = (char) 0xffff;
+    data[1751] = (char) 0xffff;
+    data[1752] = (char) 0xffff;
+    data[1753] = (char) 0xffff;
+    data[1754] = (char) 0xffff;
+    data[1755] = (char) 0xffff;
+    data[1756] = (char) 0xffff;
+    data[1757] = (char) 0xffff;
+    data[1758] = (char) 0xffff;
+    data[1759] = (char) 0xffff;
+    data[1760] = (char) 0xffff;
+    data[1761] = (char) 0xffff;
+    data[1762] = (char) 0xffff;
+    data[1763] = (char) 0xffff;
+    data[1764] = (char) 0xffff;
+    data[1765] = (char) 0xffff;
+    data[1766] = (char) 0xffff;
+    data[1767] = (char) 0xffff;
+    data[1768] = (char) 0xffff;
+    data[1769] = (char) 0xffff;
+    data[1770] = (char) 0xffff;
+    data[1771] = (char) 0xffff;
+    data[1772] = (char) 0xffff;
+    data[1773] = (char) 0xffff;
+    data[1774] = (char) 0xffff;
+    data[1775] = (char) 0xffff;
+    data[1776] = (char) 0xffff;
+    data[1777] = (char) 0xffff;
+    data[1778] = (char) 0xffff;
+    data[1779] = (char) 0xffff;
+    data[1780] = (char) 0xffff;
+    data[1781] = (char) 0xffff;
+    data[1782] = (char) 0xffff;
+    data[1783] = (char) 0xffff;
+    data[1784] = (char) 0xffff;
+    data[1785] = (char) 0xffff;
+    data[1786] = (char) 0xffff;
+    data[1787] = (char) 0xffff;
+    data[1788] = (char) 0xffff;
+    data[1789] = (char) 0xffff;
+    data[1790] = (char) 0xffff;
+    data[1791] = (char) 0xffff;
+    data[1792] = (char) 0xffff;
+    data[1793] = (char) 0xffff;
+    data[1794] = (char) 0xffff;
+    data[1795] = (char) 0xffff;
+    data[1796] = (char) 0xffff;
+    data[1797] = (char) 0xffff;
+    data[1798] = (char) 0xffff;
+    data[1799] = (char) 0xffff;
+    data[1800] = (char) 0xffff;
+    data[1801] = (char) 0xffff;
+    data[1802] = (char) 0xffff;
+    data[1803] = (char) 0xffff;
+    data[1804] = (char) 0xffff;
+    data[1805] = (char) 0xffff;
+    data[1806] = (char) 0xffff;
+    data[1807] = (char) 0xffff;
+    data[1808] = (char) 0xffff;
+    data[1809] = (char) 0xffff;
+    data[1810] = (char) 0xffff;
+    data[1811] = (char) 0xffff;
+    data[1812] = (char) 0xffff;
+    data[1813] = (char) 0xffff;
+    data[1814] = (char) 0xffff;
+    data[1815] = (char) 0xffff;
+    data[1816] = (char) 0xffff;
+    data[1817] = (char) 0xffff;
+    data[1818] = (char) 0xffff;
+    data[1819] = (char) 0xffff;
+    data[1820] = (char) 0xffff;
+    data[1821] = (char) 0xffff;
+    data[1822] = (char) 0xffff;
+    data[1823] = (char) 0xffff;
+    data[1824] = (char) 0xffff;
+    data[1825] = (char) 0xffff;
+    data[1826] = (char) 0xffff;
+    data[1827] = (char) 0xffff;
+    data[1828] = (char) 0xffff;
+    data[1829] = (char) 0xffff;
+    data[1830] = (char) 0xffff;
+    data[1831] = (char) 0xffff;
+    data[1832] = (char) 0xffff;
+    data[1833] = (char) 0xffff;
+    data[1834] = (char) 0xffff;
+    data[1835] = (char) 0xffff;
+    data[1836] = (char) 0xffff;
+    data[1837] = (char) 0xffff;
+    data[1838] = (char) 0xffff;
+    data[1839] = (char) 0xffff;
+    data[1840] = (char) 0xffff;
+    data[1841] = (char) 0xffff;
+    data[1842] = (char) 0xffff;
+    data[1843] = (char) 0xffff;
+    data[1844] = (char) 0xffff;
+    data[1845] = (char) 0xffff;
+    data[1846] = (char) 0xffff;
+    data[1847] = (char) 0xffff;
+    data[1848] = (char) 0xffff;
+    data[1849] = (char) 0xffff;
+    data[1850] = (char) 0xffff;
+    data[1851] = (char) 0xffff;
+    data[1852] = (char) 0xffff;
+    data[1853] = (char) 0xffff;
+    data[1854] = (char) 0xffff;
+    data[1855] = (char) 0xffff;
+    data[1856] = (char) 0xffff;
+    data[1857] = (char) 0xffff;
+    data[1858] = (char) 0xffff;
+    data[1859] = (char) 0xffff;
+    data[1860] = (char) 0xffff;
+    data[1861] = (char) 0xffff;
+    data[1862] = (char) 0xffff;
+    data[1863] = (char) 0xffff;
+    data[1864] = (char) 0xffff;
+    data[1865] = (char) 0xffff;
+    data[1866] = (char) 0xffff;
+    data[1867] = (char) 0xffff;
+    data[1868] = (char) 0xffff;
+    data[1869] = (char) 0xffff;
+    data[1870] = (char) 0xffff;
+    data[1871] = (char) 0xffff;
+    data[1872] = (char) 0xffff;
+    data[1873] = (char) 0xffff;
+    data[1874] = (char) 0xffff;
+    data[1875] = (char) 0xffff;
+    data[1876] = (char) 0xffff;
+    data[1877] = (char) 0xffff;
+    data[1878] = (char) 0xffff;
+    data[1879] = (char) 0xffff;
+    data[1880] = (char) 0xffff;
+    data[1881] = (char) 0xffff;
+    data[1882] = (char) 0xffff;
+    data[1883] = (char) 0xffff;
+    data[1884] = (char) 0xffff;
+    data[1885] = (char) 0xffff;
+    data[1886] = (char) 0xffff;
+    data[1887] = (char) 0xffff;
+    data[1888] = (char) 0xffff;
+    data[1889] = (char) 0xffff;
+    data[1890] = (char) 0xffff;
+    data[1891] = (char) 0xffff;
+    data[1892] = (char) 0xffff;
+    data[1893] = (char) 0xffff;
+    data[1894] = (char) 0xffff;
+    data[1895] = (char) 0xffff;
+    data[1896] = (char) 0xffff;
+    data[1897] = (char) 0xffff;
+    data[1898] = (char) 0xffff;
+    data[1899] = (char) 0xffff;
+    data[1900] = (char) 0xffff;
+    data[1901] = (char) 0xffff;
+    data[1902] = (char) 0xffff;
+    data[1903] = (char) 0xffff;
+    data[1904] = (char) 0xffff;
+    data[1905] = (char) 0xffff;
+    data[1906] = (char) 0xffff;
+    data[1907] = (char) 0xffff;
+    data[1908] = (char) 0xffff;
+    data[1909] = (char) 0xffff;
+    data[1910] = (char) 0xffff;
+    data[1911] = (char) 0xffff;
+    data[1912] = (char) 0xffff;
+    data[1913] = (char) 0xffff;
+    data[1914] = (char) 0xffff;
+    data[1915] = (char) 0xffff;
+    data[1916] = (char) 0xffff;
+    data[1917] = (char) 0xffff;
+    data[1918] = (char) 0xffff;
+    data[1919] = (char) 0xffff;
+    data[1920] = (char) 0xffff;
+    data[1921] = (char) 0xffff;
+    data[1922] = (char) 0xffff;
+    data[1923] = (char) 0xffff;
+    data[1924] = (char) 0xffff;
+    data[1925] = (char) 0xffff;
+    data[1926] = (char) 0xffff;
+    data[1927] = (char) 0xffff;
+    data[1928] = (char) 0xffff;
+    data[1929] = (char) 0xffff;
+    data[1930] = (char) 0xffff;
+    data[1931] = (char) 0xffff;
+    data[1932] = (char) 0xffff;
+    data[1933] = (char) 0xffff;
+    data[1934] = (char) 0xffff;
+    data[1935] = (char) 0xffff;
+    data[1936] = (char) 0xffff;
+    data[1937] = (char) 0xffff;
+    data[1938] = (char) 0xffff;
+    data[1939] = (char) 0xffff;
+    data[1940] = (char) 0xffff;
+    data[1941] = (char) 0xffff;
+    data[1942] = (char) 0xffff;
+    data[1943] = (char) 0xffff;
+    data[1944] = (char) 0xffff;
+    data[1945] = (char) 0xffff;
+    data[1946] = (char) 0xffff;
+    data[1947] = (char) 0xffff;
+    data[1948] = (char) 0xffff;
+    data[1949] = (char) 0xffff;
+    data[1950] = (char) 0xffff;
+    data[1951] = (char) 0xffff;
+    data[1952] = (char) 0xffff;
+    data[1953] = (char) 0xffff;
+    data[1954] = (char) 0xffff;
+    data[1955] = (char) 0xffff;
+    data[1956] = (char) 0xffff;
+    data[1957] = (char) 0xffff;
+    data[1958] = (char) 0xffff;
+    data[1959] = (char) 0xffff;
+    data[1960] = (char) 0xffff;
+    data[1961] = (char) 0xffff;
+    data[1962] = (char) 0xffff;
+    data[1963] = (char) 0xffff;
+    data[1964] = (char) 0xffff;
+    data[1965] = (char) 0xffff;
+    data[1966] = (char) 0xffff;
+    data[1967] = (char) 0xffff;
+    data[1968] = (char) 0xffff;
+    data[1969] = (char) 0xffff;
+    data[1970] = (char) 0xffff;
+    data[1971] = (char) 0xffff;
+    data[1972] = (char) 0xffff;
+    data[1973] = (char) 0xffff;
+    data[1974] = (char) 0xffff;
+    data[1975] = (char) 0xffff;
+    data[1976] = (char) 0xffff;
+    data[1977] = (char) 0xffff;
+    data[1978] = (char) 0xffff;
+    data[1979] = (char) 0xffff;
+    data[1980] = (char) 0xffff;
+    data[1981] = (char) 0xffff;
+    data[1982] = (char) 0xffff;
+    data[1983] = (char) 0xffff;
+    data[1984] = (char) 0xffff;
+    data[1985] = (char) 0xffff;
+    data[1986] = (char) 0xffff;
+    data[1987] = (char) 0xffff;
+    data[1988] = (char) 0xffff;
+    data[1989] = (char) 0xffff;
+    data[1990] = (char) 0xffff;
+    data[1991] = (char) 0xffff;
+    data[1992] = (char) 0xffff;
+    data[1993] = (char) 0xffff;
+    data[1994] = (char) 0xffff;
+    data[1995] = (char) 0xffff;
+    data[1996] = (char) 0xffff;
+    data[1997] = (char) 0xffff;
+    data[1998] = (char) 0xffff;
+    data[1999] = (char) 0xffff;
+    data[2000] = (char) 0xffff;
+    data[2001] = (char) 0xffff;
+    data[2002] = (char) 0xffff;
+    data[2003] = (char) 0xffff;
+    data[2004] = (char) 0xffff;
+    data[2005] = (char) 0xffff;
+    data[2006] = (char) 0xffff;
+    data[2007] = (char) 0xffff;
+    data[2008] = (char) 0xffff;
+    data[2009] = (char) 0xffff;
+    data[2010] = (char) 0xffff;
+    data[2011] = (char) 0xffff;
+    data[2012] = (char) 0xffff;
+    data[2013] = (char) 0xffff;
+    data[2014] = (char) 0xffff;
+    data[2015] = (char) 0xffff;
+    data[2016] = (char) 0xffff;
+    data[2017] = (char) 0xffff;
+    data[2018] = (char) 0xffff;
+    data[2019] = (char) 0xffff;
+    data[2020] = (char) 0xffff;
+    data[2021] = (char) 0xffff;
+    data[2022] = (char) 0xffff;
+    data[2023] = (char) 0xffff;
+    data[2024] = (char) 0xffff;
+    data[2025] = (char) 0xffff;
+    data[2026] = (char) 0xffff;
+    data[2027] = (char) 0xffff;
+    data[2028] = (char) 0xffff;
+    data[2029] = (char) 0xffff;
+    data[2030] = (char) 0xffff;
+    data[2031] = (char) 0xffff;
+    data[2032] = (char) 0xffff;
+    data[2033] = (char) 0xffff;
+    data[2034] = (char) 0xffff;
+    data[2035] = (char) 0xffff;
+    data[2036] = (char) 0xffff;
+    data[2037] = (char) 0xffff;
+    data[2038] = (char) 0xffff;
+    data[2039] = (char) 0xffff;
+    data[2040] = (char) 0xffff;
+    data[2041] = (char) 0xffff;
+    data[2042] = (char) 0xffff;
+    data[2043] = (char) 0xffff;
+    data[2044] = (char) 0xffff;
+    data[2045] = (char) 0xffff;
+    data[2046] = (char) 0xffff;
+    data[2047] = (char) 0xffff;
+    data[2048] = (char) 0xffff;
+    data[2049] = (char) 0xffff;
+    data[2050] = (char) 0xffff;
+    data[2051] = (char) 0xffff;
+    data[2052] = (char) 0xffff;
+    data[2053] = (char) 0xffff;
+    data[2054] = (char) 0xffff;
+    data[2055] = (char) 0xffff;
+    data[2056] = (char) 0xffff;
+    data[2057] = (char) 0xffff;
+    data[2058] = (char) 0xffff;
+    data[2059] = (char) 0xffff;
+    data[2060] = (char) 0xffff;
+    data[2061] = (char) 0xffff;
+    data[2062] = (char) 0xffff;
+    data[2063] = (char) 0xffff;
+    data[2064] = (char) 0xffff;
+    data[2065] = (char) 0xffff;
+    data[2066] = (char) 0xffff;
+    data[2067] = (char) 0xffff;
+    data[2068] = (char) 0xffff;
+    data[2069] = (char) 0xffff;
+    data[2070] = (char) 0xffff;
+    data[2071] = (char) 0xffff;
+    data[2072] = (char) 0xffff;
+    data[2073] = (char) 0xffff;
+    data[2074] = (char) 0xffff;
+    data[2075] = (char) 0xffff;
+    data[2076] = (char) 0xffff;
+    data[2077] = (char) 0xffff;
+    data[2078] = (char) 0xffff;
+    data[2079] = (char) 0xffff;
+    data[2080] = (char) 0xffff;
+    data[2081] = (char) 0xffff;
+    data[2082] = (char) 0xffff;
+    data[2083] = (char) 0xffff;
+    data[2084] = (char) 0xffff;
+    data[2085] = (char) 0xffff;
+    data[2086] = (char) 0xffff;
+    data[2087] = (char) 0xffff;
+    data[2088] = (char) 0xffff;
+    data[2089] = (char) 0xffff;
+    data[2090] = (char) 0xffff;
+    data[2091] = (char) 0xffff;
+    data[2092] = (char) 0xffff;
+    data[2093] = (char) 0xffff;
+    data[2094] = (char) 0xffff;
+    data[2095] = (char) 0xffff;
+    data[2096] = (char) 0xffff;
+    data[2097] = (char) 0xffff;
+    data[2098] = (char) 0xffff;
+    data[2099] = (char) 0xffff;
+    data[2100] = (char) 0xffff;
+    data[2101] = (char) 0xffff;
+    data[2102] = (char) 0xffff;
+    data[2103] = (char) 0xffff;
+    data[2104] = (char) 0xffff;
+    data[2105] = (char) 0xffff;
+    data[2106] = (char) 0xffff;
+    data[2107] = (char) 0xffff;
+    data[2108] = (char) 0xffff;
+    data[2109] = (char) 0xffff;
+    data[2110] = (char) 0xffff;
+    data[2111] = (char) 0xffff;
+    data[2112] = (char) 0xffff;
+    data[2113] = (char) 0xffff;
+    data[2114] = (char) 0xffff;
+    data[2115] = (char) 0xffff;
+    data[2116] = (char) 0xffff;
+    data[2117] = (char) 0xffff;
+    data[2118] = (char) 0xffff;
+    data[2119] = (char) 0xffff;
+    data[2120] = (char) 0xffff;
+    data[2121] = (char) 0xffff;
+    data[2122] = (char) 0xffff;
+    data[2123] = (char) 0xffff;
+    data[2124] = (char) 0xffff;
+    data[2125] = (char) 0xffff;
+    data[2126] = (char) 0xffff;
+    data[2127] = (char) 0xffff;
+    data[2128] = (char) 0xffff;
+    data[2129] = (char) 0xffff;
+    data[2130] = (char) 0xffff;
+    data[2131] = (char) 0xffff;
+    data[2132] = (char) 0xffff;
+    data[2133] = (char) 0xffff;
+    data[2134] = (char) 0xffff;
+    data[2135] = (char) 0xffff;
+    data[2136] = (char) 0xffff;
+    data[2137] = (char) 0xffff;
+    data[2138] = (char) 0xffff;
+    data[2139] = (char) 0xffff;
+    data[2140] = (char) 0xffff;
+    data[2141] = (char) 0xffff;
+    data[2142] = (char) 0xffff;
+    data[2143] = (char) 0xffff;
+    data[2144] = (char) 0xffff;
+    data[2145] = (char) 0xffff;
+    data[2146] = (char) 0xffff;
+    data[2147] = (char) 0xffff;
+    data[2148] = (char) 0xffff;
+    data[2149] = (char) 0xffff;
+    data[2150] = (char) 0xffff;
+    data[2151] = (char) 0xffff;
+    data[2152] = (char) 0xffff;
+    data[2153] = (char) 0xffff;
+    data[2154] = (char) 0xffff;
+    data[2155] = (char) 0xffff;
+    data[2156] = (char) 0xffff;
+    data[2157] = (char) 0xffff;
+    data[2158] = (char) 0xffff;
+    data[2159] = (char) 0xffff;
+    data[2160] = (char) 0xffff;
+    data[2161] = (char) 0xffff;
+    data[2162] = (char) 0xffff;
+    data[2163] = (char) 0xffff;
+    data[2164] = (char) 0xffff;
+    data[2165] = (char) 0xffff;
+    data[2166] = (char) 0xffff;
+    data[2167] = (char) 0xffff;
+    data[2168] = (char) 0xffff;
+    data[2169] = (char) 0xffff;
+    data[2170] = (char) 0xffff;
+    data[2171] = (char) 0xffff;
+    data[2172] = (char) 0xffff;
+    data[2173] = (char) 0xffff;
+    data[2174] = (char) 0xffff;
+    data[2175] = (char) 0xffff;
+    data[2176] = (char) 0xffff;
+    data[2177] = (char) 0xffff;
+    data[2178] = (char) 0xffff;
+    data[2179] = (char) 0xffff;
+    data[2180] = (char) 0xffff;
+    data[2181] = (char) 0xffff;
+    data[2182] = (char) 0xffff;
+    data[2183] = (char) 0xffff;
+    data[2184] = (char) 0xffff;
+    data[2185] = (char) 0xffff;
+    data[2186] = (char) 0xffff;
+    data[2187] = (char) 0xffff;
+    data[2188] = (char) 0xffff;
+    data[2189] = (char) 0xffff;
+    data[2190] = (char) 0xffff;
+    data[2191] = (char) 0xffff;
+    data[2192] = (char) 0xffff;
+    data[2193] = (char) 0xffff;
+    data[2194] = (char) 0xffff;
+    data[2195] = (char) 0xffff;
+    data[2196] = (char) 0xffff;
+    data[2197] = (char) 0xffff;
+    data[2198] = (char) 0xffff;
+    data[2199] = (char) 0xffff;
+    data[2200] = (char) 0xffff;
+    data[2201] = (char) 0xffff;
+    data[2202] = (char) 0xffff;
+    data[2203] = (char) 0xffff;
+    data[2204] = (char) 0xffff;
+    data[2205] = (char) 0xffff;
+    data[2206] = (char) 0xffff;
+    data[2207] = (char) 0xffff;
+    data[2208] = (char) 0xffff;
+    data[2209] = (char) 0xffff;
+    data[2210] = (char) 0xffff;
+    data[2211] = (char) 0xffff;
+    data[2212] = (char) 0xffff;
+    data[2213] = (char) 0xffff;
+    data[2214] = (char) 0xffff;
+    data[2215] = (char) 0xffff;
+    data[2216] = (char) 0xffff;
+    data[2217] = (char) 0xffff;
+    data[2218] = (char) 0xffff;
+    data[2219] = (char) 0xffff;
+    data[2220] = (char) 0xffff;
+    data[2221] = (char) 0xffff;
+    data[2222] = (char) 0xffff;
+    data[2223] = (char) 0xffff;
+    data[2224] = (char) 0xffff;
+    data[2225] = (char) 0xffff;
+    data[2226] = (char) 0xffff;
+    data[2227] = (char) 0xffff;
+    data[2228] = (char) 0xffff;
+    data[2229] = (char) 0xffff;
+    data[2230] = (char) 0xffff;
+    data[2231] = (char) 0xffff;
+    data[2232] = (char) 0xffff;
+    data[2233] = (char) 0xffff;
+    data[2234] = (char) 0xffff;
+    data[2235] = (char) 0xffff;
+    data[2236] = (char) 0xffff;
+    data[2237] = (char) 0xffff;
+    data[2238] = (char) 0xffff;
+    data[2239] = (char) 0xffff;
+    data[2240] = (char) 0xffff;
+    data[2241] = (char) 0xffff;
+    data[2242] = (char) 0xffff;
+    data[2243] = (char) 0xffff;
+    data[2244] = (char) 0xffff;
+    data[2245] = (char) 0xffff;
+    data[2246] = (char) 0xffff;
+    data[2247] = (char) 0xffff;
+    data[2248] = (char) 0xffff;
+    data[2249] = (char) 0xffff;
+    data[2250] = (char) 0xffff;
+    data[2251] = (char) 0xffff;
+    data[2252] = (char) 0xffff;
+    data[2253] = (char) 0xffff;
+    data[2254] = (char) 0xffff;
+    data[2255] = (char) 0xffff;
+    data[2256] = (char) 0xffff;
+    data[2257] = (char) 0xffff;
+    data[2258] = (char) 0xffff;
+    data[2259] = (char) 0xffff;
+    data[2260] = (char) 0xffff;
+    data[2261] = (char) 0xffff;
+    data[2262] = (char) 0xffff;
+    data[2263] = (char) 0xffff;
+    data[2264] = (char) 0xffff;
+    data[2265] = (char) 0xffff;
+    data[2266] = (char) 0xffff;
+    data[2267] = (char) 0xffff;
+    data[2268] = (char) 0xffff;
+    data[2269] = (char) 0xffff;
+    data[2270] = (char) 0xffff;
+    data[2271] = (char) 0xffff;
+    data[2272] = (char) 0xffff;
+    data[2273] = (char) 0xffff;
+    data[2274] = (char) 0xffff;
+    data[2275] = (char) 0xffff;
+    data[2276] = (char) 0xffff;
+    data[2277] = (char) 0xffff;
+    data[2278] = (char) 0xffff;
+    data[2279] = (char) 0xffff;
+    data[2280] = (char) 0xffff;
+    data[2281] = (char) 0xffff;
+    data[2282] = (char) 0xffff;
+    data[2283] = (char) 0xffff;
+    data[2284] = (char) 0xffff;
+    data[2285] = (char) 0xffff;
+    data[2286] = (char) 0xffff;
+    data[2287] = (char) 0xffff;
+    data[2288] = (char) 0xffff;
+    data[2289] = (char) 0xffff;
+    data[2290] = (char) 0xffff;
+    data[2291] = (char) 0xffff;
+    data[2292] = (char) 0xffff;
+    data[2293] = (char) 0xffff;
+    data[2294] = (char) 0xffff;
+    data[2295] = (char) 0xffff;
+    data[2296] = (char) 0xffff;
+    data[2297] = (char) 0xffff;
+    data[2298] = (char) 0xffff;
+    data[2299] = (char) 0xffff;
+    data[2300] = (char) 0xffff;
+    data[2301] = (char) 0xffff;
+    data[2302] = (char) 0xffff;
+    data[2303] = (char) 0xffff;
+    data[2304] = (char) 0xffff;
+    data[2305] = (char) 0xffff;
+    data[2306] = (char) 0xffff;
+    data[2307] = (char) 0xffff;
+    data[2308] = (char) 0xffff;
+    data[2309] = (char) 0xffff;
+    data[2310] = (char) 0xffff;
+    data[2311] = (char) 0xffff;
+    data[2312] = (char) 0xffff;
+    data[2313] = (char) 0xffff;
+    data[2314] = (char) 0xffff;
+    data[2315] = (char) 0xffff;
+    data[2316] = (char) 0xffff;
+    data[2317] = (char) 0xffff;
+    data[2318] = (char) 0xffff;
+    data[2319] = (char) 0xffff;
+    data[2320] = (char) 0xffff;
+    data[2321] = (char) 0xffff;
+    data[2322] = (char) 0xffff;
+    data[2323] = (char) 0xffff;
+    data[2324] = (char) 0xffff;
+    data[2325] = (char) 0xffff;
+    data[2326] = (char) 0xffff;
+    data[2327] = (char) 0xffff;
+    data[2328] = (char) 0xffff;
+    data[2329] = (char) 0xffff;
+    data[2330] = (char) 0xffff;
+    data[2331] = (char) 0xffff;
+    data[2332] = (char) 0xffff;
+    data[2333] = (char) 0xffff;
+    data[2334] = (char) 0xffff;
+    data[2335] = (char) 0xffff;
+    data[2336] = (char) 0xffff;
+    data[2337] = (char) 0xffff;
+    data[2338] = (char) 0xffff;
+    data[2339] = (char) 0xffff;
+    data[2340] = (char) 0xffff;
+    data[2341] = (char) 0xffff;
+    data[2342] = (char) 0xffff;
+    data[2343] = (char) 0xffff;
+    data[2344] = (char) 0xffff;
+    data[2345] = (char) 0xffff;
+    data[2346] = (char) 0xffff;
+    data[2347] = (char) 0xffff;
+    data[2348] = (char) 0xffff;
+    data[2349] = (char) 0xffff;
+    data[2350] = (char) 0xffff;
+    data[2351] = (char) 0xffff;
+    data[2352] = (char) 0xffff;
+    data[2353] = (char) 0xffff;
+    data[2354] = (char) 0xffff;
+    data[2355] = (char) 0xffff;
+    data[2356] = (char) 0xffff;
+    data[2357] = (char) 0xffff;
+    data[2358] = (char) 0xffff;
+    data[2359] = (char) 0xffff;
+    data[2360] = (char) 0xffff;
+    data[2361] = (char) 0xffff;
+    data[2362] = (char) 0xffff;
+    data[2363] = (char) 0xffff;
+    data[2364] = (char) 0xffff;
+    data[2365] = (char) 0xffff;
+    data[2366] = (char) 0xffff;
+    data[2367] = (char) 0xffff;
+    data[2368] = (char) 0xffff;
+    data[2369] = (char) 0xffff;
+    data[2370] = (char) 0xffff;
+    data[2371] = (char) 0xffff;
+    data[2372] = (char) 0xffff;
+    data[2373] = (char) 0xffff;
+    data[2374] = (char) 0xffff;
+    data[2375] = (char) 0xffff;
+    data[2376] = (char) 0xffff;
+    data[2377] = (char) 0xffff;
+    data[2378] = (char) 0xffff;
+    data[2379] = (char) 0xffff;
+    data[2380] = (char) 0xffff;
+    data[2381] = (char) 0xffff;
+    data[2382] = (char) 0xffff;
+    data[2383] = (char) 0xffff;
+    data[2384] = (char) 0xffff;
+    data[2385] = (char) 0xffff;
+    data[2386] = (char) 0xffff;
+    data[2387] = (char) 0xffff;
+    data[2388] = (char) 0xffff;
+    data[2389] = (char) 0xffff;
+    data[2390] = (char) 0xffff;
+    data[2391] = (char) 0xffff;
+    data[2392] = (char) 0xffff;
+    data[2393] = (char) 0xffff;
+    data[2394] = (char) 0xffff;
+    data[2395] = (char) 0xffff;
+    data[2396] = (char) 0xffff;
+    data[2397] = (char) 0xffff;
+    data[2398] = (char) 0xffff;
+    data[2399] = (char) 0xffff;
+    data[2400] = (char) 0xffff;
+    data[2401] = (char) 0xffff;
+    data[2402] = (char) 0xffff;
+    data[2403] = (char) 0xffff;
+    data[2404] = (char) 0xffff;
+    data[2405] = (char) 0xffff;
+    data[2406] = (char) 0xffff;
+    data[2407] = (char) 0xffff;
+    data[2408] = (char) 0xffff;
+    data[2409] = (char) 0xffff;
+    data[2410] = (char) 0xffff;
+    data[2411] = (char) 0xffff;
+    data[2412] = (char) 0xffff;
+    data[2413] = (char) 0xffff;
+    data[2414] = (char) 0xffff;
+    data[2415] = (char) 0xffff;
+    data[2416] = (char) 0xffff;
+    data[2417] = (char) 0xffff;
+    data[2418] = (char) 0xffff;
+    data[2419] = (char) 0xffff;
+    data[2420] = (char) 0xffff;
+    data[2421] = (char) 0xffff;
+    data[2422] = (char) 0xffff;
+    data[2423] = (char) 0xffff;
+    data[2424] = (char) 0xffff;
+    data[2425] = (char) 0xffff;
+    data[2426] = (char) 0xffff;
+    data[2427] = (char) 0xffff;
+    data[2428] = (char) 0xffff;
+    data[2429] = (char) 0xffff;
+    data[2430] = (char) 0xffff;
+    data[2431] = (char) 0xffff;
+    data[2432] = (char) 0xffff;
+    data[2433] = (char) 0xffff;
+    data[2434] = (char) 0xffff;
+    data[2435] = (char) 0xffff;
+    data[2436] = (char) 0xffff;
+    data[2437] = (char) 0xffff;
+    data[2438] = (char) 0xffff;
+    data[2439] = (char) 0xffff;
+    data[2440] = (char) 0xffff;
+    data[2441] = (char) 0xffff;
+    data[2442] = (char) 0xffff;
+    data[2443] = (char) 0xffff;
+    data[2444] = (char) 0xffff;
+    data[2445] = (char) 0xffff;
+    data[2446] = (char) 0xffff;
+    data[2447] = (char) 0xffff;
+    data[2448] = (char) 0xffff;
+    data[2449] = (char) 0xffff;
+    data[2450] = (char) 0xffff;
+    data[2451] = (char) 0xffff;
+    data[2452] = (char) 0xffff;
+    data[2453] = (char) 0xffff;
+    data[2454] = (char) 0xffff;
+    data[2455] = (char) 0xffff;
+    data[2456] = (char) 0xffff;
+    data[2457] = (char) 0xffff;
+    data[2458] = (char) 0xffff;
+    data[2459] = (char) 0xffff;
+    data[2460] = (char) 0xffff;
+    data[2461] = (char) 0xffff;
+    data[2462] = (char) 0xffff;
+    data[2463] = (char) 0xffff;
+    data[2464] = (char) 0xffff;
+    data[2465] = (char) 0xffff;
+    data[2466] = (char) 0xffff;
+    data[2467] = (char) 0xffff;
+    data[2468] = (char) 0xffff;
+    data[2469] = (char) 0xffff;
+    data[2470] = (char) 0xffff;
+    data[2471] = (char) 0xffff;
+    data[2472] = (char) 0xffff;
+    data[2473] = (char) 0xffff;
+    data[2474] = (char) 0xffff;
+    data[2475] = (char) 0xffff;
+    data[2476] = (char) 0xffff;
+    data[2477] = (char) 0xffff;
+    data[2478] = (char) 0xffff;
+    data[2479] = (char) 0xffff;
+    data[2480] = (char) 0xffff;
+    data[2481] = (char) 0xffff;
+    data[2482] = (char) 0xffff;
+    data[2483] = (char) 0xffff;
+    data[2484] = (char) 0xffff;
+    data[2485] = (char) 0xffff;
+    data[2486] = (char) 0xffff;
+    data[2487] = (char) 0xffff;
+    data[2488] = (char) 0xffff;
+    data[2489] = (char) 0xffff;
+    data[2490] = (char) 0xffff;
+    data[2491] = (char) 0xffff;
+    data[2492] = (char) 0xffff;
+    data[2493] = (char) 0xffff;
+    data[2494] = (char) 0xffff;
+    data[2495] = (char) 0xffff;
+    data[2496] = (char) 0xffff;
+    data[2497] = (char) 0xffff;
+    data[2498] = (char) 0xffff;
+    data[2499] = (char) 0xffff;
+    data[2500] = (char) 0xffff;
+    data[2501] = (char) 0xffff;
+    data[2502] = (char) 0xffff;
+    data[2503] = (char) 0xffff;
+    data[2504] = (char) 0xffff;
+    data[2505] = (char) 0xffff;
+    data[2506] = (char) 0xffff;
+    data[2507] = (char) 0xffff;
+    data[2508] = (char) 0xffff;
+    data[2509] = (char) 0xffff;
+    data[2510] = (char) 0xffff;
+    data[2511] = (char) 0xffff;
+    data[2512] = (char) 0xffff;
+    data[2513] = (char) 0xffff;
+    data[2514] = (char) 0xffff;
+    data[2515] = (char) 0xffff;
+    data[2516] = (char) 0xffff;
+    data[2517] = (char) 0xffff;
+    data[2518] = (char) 0xffff;
+    data[2519] = (char) 0xffff;
+    data[2520] = (char) 0xffff;
+    data[2521] = (char) 0xffff;
+    data[2522] = (char) 0xffff;
+    data[2523] = (char) 0xffff;
+    data[2524] = (char) 0xffff;
+    data[2525] = (char) 0xffff;
+    data[2526] = (char) 0xffff;
+    data[2527] = (char) 0xffff;
+    data[2528] = (char) 0xffff;
+    data[2529] = (char) 0xffff;
+    data[2530] = (char) 0xffff;
+    data[2531] = (char) 0xffff;
+    data[2532] = (char) 0xffff;
+    data[2533] = (char) 0xffff;
+    data[2534] = (char) 0xffff;
+    data[2535] = (char) 0xffff;
+    data[2536] = (char) 0xffff;
+    data[2537] = (char) 0xffff;
+    data[2538] = (char) 0xffff;
+    data[2539] = (char) 0xffff;
+    data[2540] = (char) 0xffff;
+    data[2541] = (char) 0xffff;
+    data[2542] = (char) 0xffff;
+    data[2543] = (char) 0xffff;
+    data[2544] = (char) 0xffff;
+    data[2545] = (char) 0xffff;
+    data[2546] = (char) 0xffff;
+    data[2547] = (char) 0xffff;
+    data[2548] = (char) 0xffff;
+    data[2549] = (char) 0xffff;
+    data[2550] = (char) 0xffff;
+    data[2551] = (char) 0xffff;
+    data[2552] = (char) 0xffff;
+    data[2553] = (char) 0xffff;
+    data[2554] = (char) 0x003f;
+    data[2752] = (char) 0xffff;
+    data[2753] = (char) 0xffff;
+    data[2754] = (char) 0xffff;
+    data[2755] = (char) 0xffff;
+    data[2756] = (char) 0xffff;
+    data[2757] = (char) 0xffff;
+    data[2758] = (char) 0xffff;
+    data[2759] = (char) 0xffff;
+    data[2760] = (char) 0xffff;
+    data[2761] = (char) 0xffff;
+    data[2762] = (char) 0xffff;
+    data[2763] = (char) 0xffff;
+    data[2764] = (char) 0xffff;
+    data[2765] = (char) 0xffff;
+    data[2766] = (char) 0xffff;
+    data[2767] = (char) 0xffff;
+    data[2768] = (char) 0xffff;
+    data[2769] = (char) 0xffff;
+    data[2770] = (char) 0xffff;
+    data[2771] = (char) 0xffff;
+    data[2772] = (char) 0xffff;
+    data[2773] = (char) 0xffff;
+    data[2774] = (char) 0xffff;
+    data[2775] = (char) 0xffff;
+    data[2776] = (char) 0xffff;
+    data[2777] = (char) 0xffff;
+    data[2778] = (char) 0xffff;
+    data[2779] = (char) 0xffff;
+    data[2780] = (char) 0xffff;
+    data[2781] = (char) 0xffff;
+    data[2782] = (char) 0xffff;
+    data[2783] = (char) 0xffff;
+    data[2784] = (char) 0xffff;
+    data[2785] = (char) 0xffff;
+    data[2786] = (char) 0xffff;
+    data[2787] = (char) 0xffff;
+    data[2788] = (char) 0xffff;
+    data[2789] = (char) 0xffff;
+    data[2790] = (char) 0xffff;
+    data[2791] = (char) 0xffff;
+    data[2792] = (char) 0xffff;
+    data[2793] = (char) 0xffff;
+    data[2794] = (char) 0xffff;
+    data[2795] = (char) 0xffff;
+    data[2796] = (char) 0xffff;
+    data[2797] = (char) 0xffff;
+    data[2798] = (char) 0xffff;
+    data[2799] = (char) 0xffff;
+    data[2800] = (char) 0xffff;
+    data[2801] = (char) 0xffff;
+    data[2802] = (char) 0xffff;
+    data[2803] = (char) 0xffff;
+    data[2804] = (char) 0xffff;
+    data[2805] = (char) 0xffff;
+    data[2806] = (char) 0xffff;
+    data[2807] = (char) 0xffff;
+    data[2808] = (char) 0xffff;
+    data[2809] = (char) 0xffff;
+    data[2810] = (char) 0xffff;
+    data[2811] = (char) 0xffff;
+    data[2812] = (char) 0xffff;
+    data[2813] = (char) 0xffff;
+    data[2814] = (char) 0xffff;
+    data[2815] = (char) 0xffff;
+    data[2816] = (char) 0xffff;
+    data[2817] = (char) 0xffff;
+    data[2818] = (char) 0xffff;
+    data[2819] = (char) 0xffff;
+    data[2820] = (char) 0xffff;
+    data[2821] = (char) 0xffff;
+    data[2822] = (char) 0xffff;
+    data[2823] = (char) 0xffff;
+    data[2824] = (char) 0xffff;
+    data[2825] = (char) 0xffff;
+    data[2826] = (char) 0xffff;
+    data[2827] = (char) 0xffff;
+    data[2828] = (char) 0xffff;
+    data[2829] = (char) 0xffff;
+    data[2830] = (char) 0xffff;
+    data[2831] = (char) 0xffff;
+    data[2832] = (char) 0xffff;
+    data[2833] = (char) 0xffff;
+    data[2834] = (char) 0xffff;
+    data[2835] = (char) 0xffff;
+    data[2836] = (char) 0xffff;
+    data[2837] = (char) 0xffff;
+    data[2838] = (char) 0xffff;
+    data[2839] = (char) 0xffff;
+    data[2840] = (char) 0xffff;
+    data[2841] = (char) 0xffff;
+    data[2842] = (char) 0xffff;
+    data[2843] = (char) 0xffff;
+    data[2844] = (char) 0xffff;
+    data[2845] = (char) 0xffff;
+    data[2846] = (char) 0xffff;
+    data[2847] = (char) 0xffff;
+    data[2848] = (char) 0xffff;
+    data[2849] = (char) 0xffff;
+    data[2850] = (char) 0xffff;
+    data[2851] = (char) 0xffff;
+    data[2852] = (char) 0xffff;
+    data[2853] = (char) 0xffff;
+    data[2854] = (char) 0xffff;
+    data[2855] = (char) 0xffff;
+    data[2856] = (char) 0xffff;
+    data[2857] = (char) 0xffff;
+    data[2858] = (char) 0xffff;
+    data[2859] = (char) 0xffff;
+    data[2860] = (char) 0xffff;
+    data[2861] = (char) 0xffff;
+    data[2862] = (char) 0xffff;
+    data[2863] = (char) 0xffff;
+    data[2864] = (char) 0xffff;
+    data[2865] = (char) 0xffff;
+    data[2866] = (char) 0xffff;
+    data[2867] = (char) 0xffff;
+    data[2868] = (char) 0xffff;
+    data[2869] = (char) 0xffff;
+    data[2870] = (char) 0xffff;
+    data[2871] = (char) 0xffff;
+    data[2872] = (char) 0xffff;
+    data[2873] = (char) 0xffff;
+    data[2874] = (char) 0xffff;
+    data[2875] = (char) 0xffff;
+    data[2876] = (char) 0xffff;
+    data[2877] = (char) 0xffff;
+    data[2878] = (char) 0xffff;
+    data[2879] = (char) 0xffff;
+    data[2880] = (char) 0xffff;
+    data[2881] = (char) 0xffff;
+    data[2882] = (char) 0xffff;
+    data[2883] = (char) 0xffff;
+    data[2884] = (char) 0xffff;
+    data[2885] = (char) 0xffff;
+    data[2886] = (char) 0xffff;
+    data[2887] = (char) 0xffff;
+    data[2888] = (char) 0xffff;
+    data[2889] = (char) 0xffff;
+    data[2890] = (char) 0xffff;
+    data[2891] = (char) 0xffff;
+    data[2892] = (char) 0xffff;
+    data[2893] = (char) 0xffff;
+    data[2894] = (char) 0xffff;
+    data[2895] = (char) 0xffff;
+    data[2896] = (char) 0xffff;
+    data[2897] = (char) 0xffff;
+    data[2898] = (char) 0xffff;
+    data[2899] = (char) 0xffff;
+    data[2900] = (char) 0xffff;
+    data[2901] = (char) 0xffff;
+    data[2902] = (char) 0xffff;
+    data[2903] = (char) 0xffff;
+    data[2904] = (char) 0xffff;
+    data[2905] = (char) 0xffff;
+    data[2906] = (char) 0xffff;
+    data[2907] = (char) 0xffff;
+    data[2908] = (char) 0xffff;
+    data[2909] = (char) 0xffff;
+    data[2910] = (char) 0xffff;
+    data[2911] = (char) 0xffff;
+    data[2912] = (char) 0xffff;
+    data[2913] = (char) 0xffff;
+    data[2914] = (char) 0xffff;
+    data[2915] = (char) 0xffff;
+    data[2916] = (char) 0xffff;
+    data[2917] = (char) 0xffff;
+    data[2918] = (char) 0xffff;
+    data[2919] = (char) 0xffff;
+    data[2920] = (char) 0xffff;
+    data[2921] = (char) 0xffff;
+    data[2922] = (char) 0xffff;
+    data[2923] = (char) 0xffff;
+    data[2924] = (char) 0xffff;
+    data[2925] = (char) 0xffff;
+    data[2926] = (char) 0xffff;
+    data[2927] = (char) 0xffff;
+    data[2928] = (char) 0xffff;
+    data[2929] = (char) 0xffff;
+    data[2930] = (char) 0xffff;
+    data[2931] = (char) 0xffff;
+    data[2932] = (char) 0xffff;
+    data[2933] = (char) 0xffff;
+    data[2934] = (char) 0xffff;
+    data[2935] = (char) 0xffff;
+    data[2936] = (char) 0xffff;
+    data[2937] = (char) 0xffff;
+    data[2938] = (char) 0xffff;
+    data[2939] = (char) 0xffff;
+    data[2940] = (char) 0xffff;
+    data[2941] = (char) 0xffff;
+    data[2942] = (char) 0xffff;
+    data[2943] = (char) 0xffff;
+    data[2944] = (char) 0xffff;
+    data[2945] = (char) 0xffff;
+    data[2946] = (char) 0xffff;
+    data[2947] = (char) 0xffff;
+    data[2948] = (char) 0xffff;
+    data[2949] = (char) 0xffff;
+    data[2950] = (char) 0xffff;
+    data[2951] = (char) 0xffff;
+    data[2952] = (char) 0xffff;
+    data[2953] = (char) 0xffff;
+    data[2954] = (char) 0xffff;
+    data[2955] = (char) 0xffff;
+    data[2956] = (char) 0xffff;
+    data[2957] = (char) 0xffff;
+    data[2958] = (char) 0xffff;
+    data[2959] = (char) 0xffff;
+    data[2960] = (char) 0xffff;
+    data[2961] = (char) 0xffff;
+    data[2962] = (char) 0xffff;
+    data[2963] = (char) 0xffff;
+    data[2964] = (char) 0xffff;
+    data[2965] = (char) 0xffff;
+    data[2966] = (char) 0xffff;
+    data[2967] = (char) 0xffff;
+    data[2968] = (char) 0xffff;
+    data[2969] = (char) 0xffff;
+    data[2970] = (char) 0xffff;
+    data[2971] = (char) 0xffff;
+    data[2972] = (char) 0xffff;
+    data[2973] = (char) 0xffff;
+    data[2974] = (char) 0xffff;
+    data[2975] = (char) 0xffff;
+    data[2976] = (char) 0xffff;
+    data[2977] = (char) 0xffff;
+    data[2978] = (char) 0xffff;
+    data[2979] = (char) 0xffff;
+    data[2980] = (char) 0xffff;
+    data[2981] = (char) 0xffff;
+    data[2982] = (char) 0xffff;
+    data[2983] = (char) 0xffff;
+    data[2984] = (char) 0xffff;
+    data[2985] = (char) 0xffff;
+    data[2986] = (char) 0xffff;
+    data[2987] = (char) 0xffff;
+    data[2988] = (char) 0xffff;
+    data[2989] = (char) 0xffff;
+    data[2990] = (char) 0xffff;
+    data[2991] = (char) 0xffff;
+    data[2992] = (char) 0xffff;
+    data[2993] = (char) 0xffff;
+    data[2994] = (char) 0xffff;
+    data[2995] = (char) 0xffff;
+    data[2996] = (char) 0xffff;
+    data[2997] = (char) 0xffff;
+    data[2998] = (char) 0xffff;
+    data[2999] = (char) 0xffff;
+    data[3000] = (char) 0xffff;
+    data[3001] = (char) 0xffff;
+    data[3002] = (char) 0xffff;
+    data[3003] = (char) 0xffff;
+    data[3004] = (char) 0xffff;
+    data[3005] = (char) 0xffff;
+    data[3006] = (char) 0xffff;
+    data[3007] = (char) 0xffff;
+    data[3008] = (char) 0xffff;
+    data[3009] = (char) 0xffff;
+    data[3010] = (char) 0xffff;
+    data[3011] = (char) 0xffff;
+    data[3012] = (char) 0xffff;
+    data[3013] = (char) 0xffff;
+    data[3014] = (char) 0xffff;
+    data[3015] = (char) 0xffff;
+    data[3016] = (char) 0xffff;
+    data[3017] = (char) 0xffff;
+    data[3018] = (char) 0xffff;
+    data[3019] = (char) 0xffff;
+    data[3020] = (char) 0xffff;
+    data[3021] = (char) 0xffff;
+    data[3022] = (char) 0xffff;
+    data[3023] = (char) 0xffff;
+    data[3024] = (char) 0xffff;
+    data[3025] = (char) 0xffff;
+    data[3026] = (char) 0xffff;
+    data[3027] = (char) 0xffff;
+    data[3028] = (char) 0xffff;
+    data[3029] = (char) 0xffff;
+    data[3030] = (char) 0xffff;
+    data[3031] = (char) 0xffff;
+    data[3032] = (char) 0xffff;
+    data[3033] = (char) 0xffff;
+    data[3034] = (char) 0xffff;
+    data[3035] = (char) 0xffff;
+    data[3036] = (char) 0xffff;
+    data[3037] = (char) 0xffff;
+    data[3038] = (char) 0xffff;
+    data[3039] = (char) 0xffff;
+    data[3040] = (char) 0xffff;
+    data[3041] = (char) 0xffff;
+    data[3042] = (char) 0xffff;
+    data[3043] = (char) 0xffff;
+    data[3044] = (char) 0xffff;
+    data[3045] = (char) 0xffff;
+    data[3046] = (char) 0xffff;
+    data[3047] = (char) 0xffff;
+    data[3048] = (char) 0xffff;
+    data[3049] = (char) 0xffff;
+    data[3050] = (char) 0xffff;
+    data[3051] = (char) 0xffff;
+    data[3052] = (char) 0xffff;
+    data[3053] = (char) 0xffff;
+    data[3054] = (char) 0xffff;
+    data[3055] = (char) 0xffff;
+    data[3056] = (char) 0xffff;
+    data[3057] = (char) 0xffff;
+    data[3058] = (char) 0xffff;
+    data[3059] = (char) 0xffff;
+    data[3060] = (char) 0xffff;
+    data[3061] = (char) 0xffff;
+    data[3062] = (char) 0xffff;
+    data[3063] = (char) 0xffff;
+    data[3064] = (char) 0xffff;
+    data[3065] = (char) 0xffff;
+    data[3066] = (char) 0xffff;
+    data[3067] = (char) 0xffff;
+    data[3068] = (char) 0xffff;
+    data[3069] = (char) 0xffff;
+    data[3070] = (char) 0xffff;
+    data[3071] = (char) 0xffff;
+    data[3072] = (char) 0xffff;
+    data[3073] = (char) 0xffff;
+    data[3074] = (char) 0xffff;
+    data[3075] = (char) 0xffff;
+    data[3076] = (char) 0xffff;
+    data[3077] = (char) 0xffff;
+    data[3078] = (char) 0xffff;
+    data[3079] = (char) 0xffff;
+    data[3080] = (char) 0xffff;
+    data[3081] = (char) 0xffff;
+    data[3082] = (char) 0xffff;
+    data[3083] = (char) 0xffff;
+    data[3084] = (char) 0xffff;
+    data[3085] = (char) 0xffff;
+    data[3086] = (char) 0xffff;
+    data[3087] = (char) 0xffff;
+    data[3088] = (char) 0xffff;
+    data[3089] = (char) 0xffff;
+    data[3090] = (char) 0xffff;
+    data[3091] = (char) 0xffff;
+    data[3092] = (char) 0xffff;
+    data[3093] = (char) 0xffff;
+    data[3094] = (char) 0xffff;
+    data[3095] = (char) 0xffff;
+    data[3096] = (char) 0xffff;
+    data[3097] = (char) 0xffff;
+    data[3098] = (char) 0xffff;
+    data[3099] = (char) 0xffff;
+    data[3100] = (char) 0xffff;
+    data[3101] = (char) 0xffff;
+    data[3102] = (char) 0xffff;
+    data[3103] = (char) 0xffff;
+    data[3104] = (char) 0xffff;
+    data[3105] = (char) 0xffff;
+    data[3106] = (char) 0xffff;
+    data[3107] = (char) 0xffff;
+    data[3108] = (char) 0xffff;
+    data[3109] = (char) 0xffff;
+    data[3110] = (char) 0xffff;
+    data[3111] = (char) 0xffff;
+    data[3112] = (char) 0xffff;
+    data[3113] = (char) 0xffff;
+    data[3114] = (char) 0xffff;
+    data[3115] = (char) 0xffff;
+    data[3116] = (char) 0xffff;
+    data[3117] = (char) 0xffff;
+    data[3118] = (char) 0xffff;
+    data[3119] = (char) 0xffff;
+    data[3120] = (char) 0xffff;
+    data[3121] = (char) 0xffff;
+    data[3122] = (char) 0xffff;
+    data[3123] = (char) 0xffff;
+    data[3124] = (char) 0xffff;
+    data[3125] = (char) 0xffff;
+    data[3126] = (char) 0xffff;
+    data[3127] = (char) 0xffff;
+    data[3128] = (char) 0xffff;
+    data[3129] = (char) 0xffff;
+    data[3130] = (char) 0xffff;
+    data[3131] = (char) 0xffff;
+    data[3132] = (char) 0xffff;
+    data[3133] = (char) 0xffff;
+    data[3134] = (char) 0xffff;
+    data[3135] = (char) 0xffff;
+    data[3136] = (char) 0xffff;
+    data[3137] = (char) 0xffff;
+    data[3138] = (char) 0xffff;
+    data[3139] = (char) 0xffff;
+    data[3140] = (char) 0xffff;
+    data[3141] = (char) 0xffff;
+    data[3142] = (char) 0xffff;
+    data[3143] = (char) 0xffff;
+    data[3144] = (char) 0xffff;
+    data[3145] = (char) 0xffff;
+    data[3146] = (char) 0xffff;
+    data[3147] = (char) 0xffff;
+    data[3148] = (char) 0xffff;
+    data[3149] = (char) 0xffff;
+    data[3150] = (char) 0xffff;
+    data[3151] = (char) 0xffff;
+    data[3152] = (char) 0xffff;
+    data[3153] = (char) 0xffff;
+    data[3154] = (char) 0xffff;
+    data[3155] = (char) 0xffff;
+    data[3156] = (char) 0xffff;
+    data[3157] = (char) 0xffff;
+    data[3158] = (char) 0xffff;
+    data[3159] = (char) 0xffff;
+    data[3160] = (char) 0xffff;
+    data[3161] = (char) 0xffff;
+    data[3162] = (char) 0xffff;
+    data[3163] = (char) 0xffff;
+    data[3164] = (char) 0xffff;
+    data[3165] = (char) 0xffff;
+    data[3166] = (char) 0xffff;
+    data[3167] = (char) 0xffff;
+    data[3168] = (char) 0xffff;
+    data[3169] = (char) 0xffff;
+    data[3170] = (char) 0xffff;
+    data[3171] = (char) 0xffff;
+    data[3172] = (char) 0xffff;
+    data[3173] = (char) 0xffff;
+    data[3174] = (char) 0xffff;
+    data[3175] = (char) 0xffff;
+    data[3176] = (char) 0xffff;
+    data[3177] = (char) 0xffff;
+    data[3178] = (char) 0xffff;
+    data[3179] = (char) 0xffff;
+    data[3180] = (char) 0xffff;
+    data[3181] = (char) 0xffff;
+    data[3182] = (char) 0xffff;
+    data[3183] = (char) 0xffff;
+    data[3184] = (char) 0xffff;
+    data[3185] = (char) 0xffff;
+    data[3186] = (char) 0xffff;
+    data[3187] = (char) 0xffff;
+    data[3188] = (char) 0xffff;
+    data[3189] = (char) 0xffff;
+    data[3190] = (char) 0xffff;
+    data[3191] = (char) 0xffff;
+    data[3192] = (char) 0xffff;
+    data[3193] = (char) 0xffff;
+    data[3194] = (char) 0xffff;
+    data[3195] = (char) 0xffff;
+    data[3196] = (char) 0xffff;
+    data[3197] = (char) 0xffff;
+    data[3198] = (char) 0xffff;
+    data[3199] = (char) 0xffff;
+    data[3200] = (char) 0xffff;
+    data[3201] = (char) 0xffff;
+    data[3202] = (char) 0xffff;
+    data[3203] = (char) 0xffff;
+    data[3204] = (char) 0xffff;
+    data[3205] = (char) 0xffff;
+    data[3206] = (char) 0xffff;
+    data[3207] = (char) 0xffff;
+    data[3208] = (char) 0xffff;
+    data[3209] = (char) 0xffff;
+    data[3210] = (char) 0xffff;
+    data[3211] = (char) 0xffff;
+    data[3212] = (char) 0xffff;
+    data[3213] = (char) 0xffff;
+    data[3214] = (char) 0xffff;
+    data[3215] = (char) 0xffff;
+    data[3216] = (char) 0xffff;
+    data[3217] = (char) 0xffff;
+    data[3218] = (char) 0xffff;
+    data[3219] = (char) 0xffff;
+    data[3220] = (char) 0xffff;
+    data[3221] = (char) 0xffff;
+    data[3222] = (char) 0xffff;
+    data[3223] = (char) 0xffff;
+    data[3224] = (char) 0xffff;
+    data[3225] = (char) 0xffff;
+    data[3226] = (char) 0xffff;
+    data[3227] = (char) 0xffff;
+    data[3228] = (char) 0xffff;
+    data[3229] = (char) 0xffff;
+    data[3230] = (char) 0xffff;
+    data[3231] = (char) 0xffff;
+    data[3232] = (char) 0xffff;
+    data[3233] = (char) 0xffff;
+    data[3234] = (char) 0xffff;
+    data[3235] = (char) 0xffff;
+    data[3236] = (char) 0xffff;
+    data[3237] = (char) 0xffff;
+    data[3238] = (char) 0xffff;
+    data[3239] = (char) 0xffff;
+    data[3240] = (char) 0xffff;
+    data[3241] = (char) 0xffff;
+    data[3242] = (char) 0xffff;
+    data[3243] = (char) 0xffff;
+    data[3244] = (char) 0xffff;
+    data[3245] = (char) 0xffff;
+    data[3246] = (char) 0xffff;
+    data[3247] = (char) 0xffff;
+    data[3248] = (char) 0xffff;
+    data[3249] = (char) 0xffff;
+    data[3250] = (char) 0xffff;
+    data[3251] = (char) 0xffff;
+    data[3252] = (char) 0xffff;
+    data[3253] = (char) 0xffff;
+    data[3254] = (char) 0xffff;
+    data[3255] = (char) 0xffff;
+    data[3256] = (char) 0xffff;
+    data[3257] = (char) 0xffff;
+    data[3258] = (char) 0xffff;
+    data[3259] = (char) 0xffff;
+    data[3260] = (char) 0xffff;
+    data[3261] = (char) 0xffff;
+    data[3262] = (char) 0xffff;
+    data[3263] = (char) 0xffff;
+    data[3264] = (char) 0xffff;
+    data[3265] = (char) 0xffff;
+    data[3266] = (char) 0xffff;
+    data[3267] = (char) 0xffff;
+    data[3268] = (char) 0xffff;
+    data[3269] = (char) 0xffff;
+    data[3270] = (char) 0xffff;
+    data[3271] = (char) 0xffff;
+    data[3272] = (char) 0xffff;
+    data[3273] = (char) 0xffff;
+    data[3274] = (char) 0xffff;
+    data[3275] = (char) 0xffff;
+    data[3276] = (char) 0xffff;
+    data[3277] = (char) 0xffff;
+    data[3278] = (char) 0xffff;
+    data[3279] = (char) 0xffff;
+    data[3280] = (char) 0xffff;
+    data[3281] = (char) 0xffff;
+    data[3282] = (char) 0xffff;
+    data[3283] = (char) 0xffff;
+    data[3284] = (char) 0xffff;
+    data[3285] = (char) 0xffff;
+    data[3286] = (char) 0xffff;
+    data[3287] = (char) 0xffff;
+    data[3288] = (char) 0xffff;
+    data[3289] = (char) 0xffff;
+    data[3290] = (char) 0xffff;
+    data[3291] = (char) 0xffff;
+    data[3292] = (char) 0xffff;
+    data[3293] = (char) 0xffff;
+    data[3294] = (char) 0xffff;
+    data[3295] = (char) 0xffff;
+    data[3296] = (char) 0xffff;
+    data[3297] = (char) 0xffff;
+    data[3298] = (char) 0xffff;
+    data[3299] = (char) 0xffff;
+    data[3300] = (char) 0xffff;
+    data[3301] = (char) 0xffff;
+    data[3302] = (char) 0xffff;
+    data[3303] = (char) 0xffff;
+    data[3304] = (char) 0xffff;
+    data[3305] = (char) 0xffff;
+    data[3306] = (char) 0xffff;
+    data[3307] = (char) 0xffff;
+    data[3308] = (char) 0xffff;
+    data[3309] = (char) 0xffff;
+    data[3310] = (char) 0xffff;
+    data[3311] = (char) 0xffff;
+    data[3312] = (char) 0xffff;
+    data[3313] = (char) 0xffff;
+    data[3314] = (char) 0xffff;
+    data[3315] = (char) 0xffff;
+    data[3316] = (char) 0xffff;
+    data[3317] = (char) 0xffff;
+    data[3318] = (char) 0xffff;
+    data[3319] = (char) 0xffff;
+    data[3320] = (char) 0xffff;
+    data[3321] = (char) 0xffff;
+    data[3322] = (char) 0xffff;
+    data[3323] = (char) 0xffff;
+    data[3324] = (char) 0xffff;
+    data[3325] = (char) 0xffff;
+    data[3326] = (char) 0xffff;
+    data[3327] = (char) 0xffff;
+    data[3328] = (char) 0xffff;
+    data[3329] = (char) 0xffff;
+    data[3330] = (char) 0xffff;
+    data[3331] = (char) 0xffff;
+    data[3332] = (char) 0xffff;
+    data[3333] = (char) 0xffff;
+    data[3334] = (char) 0xffff;
+    data[3335] = (char) 0xffff;
+    data[3336] = (char) 0xffff;
+    data[3337] = (char) 0xffff;
+    data[3338] = (char) 0xffff;
+    data[3339] = (char) 0xffff;
+    data[3340] = (char) 0xffff;
+    data[3341] = (char) 0xffff;
+    data[3342] = (char) 0xffff;
+    data[3343] = (char) 0xffff;
+    data[3344] = (char) 0xffff;
+    data[3345] = (char) 0xffff;
+    data[3346] = (char) 0xffff;
+    data[3347] = (char) 0xffff;
+    data[3348] = (char) 0xffff;
+    data[3349] = (char) 0xffff;
+    data[3350] = (char) 0xffff;
+    data[3351] = (char) 0xffff;
+    data[3352] = (char) 0xffff;
+    data[3353] = (char) 0xffff;
+    data[3354] = (char) 0xffff;
+    data[3355] = (char) 0xffff;
+    data[3356] = (char) 0xffff;
+    data[3357] = (char) 0xffff;
+    data[3358] = (char) 0xffff;
+    data[3359] = (char) 0xffff;
+    data[3360] = (char) 0xffff;
+    data[3361] = (char) 0xffff;
+    data[3362] = (char) 0xffff;
+    data[3363] = (char) 0xffff;
+    data[3364] = (char) 0xffff;
+    data[3365] = (char) 0xffff;
+    data[3366] = (char) 0xffff;
+    data[3367] = (char) 0xffff;
+    data[3368] = (char) 0xffff;
+    data[3369] = (char) 0xffff;
+    data[3370] = (char) 0xffff;
+    data[3371] = (char) 0xffff;
+    data[3372] = (char) 0xffff;
+    data[3373] = (char) 0xffff;
+    data[3374] = (char) 0xffff;
+    data[3375] = (char) 0xffff;
+    data[3376] = (char) 0xffff;
+    data[3377] = (char) 0xffff;
+    data[3378] = (char) 0xffff;
+    data[3379] = (char) 0xffff;
+    data[3380] = (char) 0xffff;
+    data[3381] = (char) 0xffff;
+    data[3382] = (char) 0xffff;
+    data[3383] = (char) 0xffff;
+    data[3384] = (char) 0xffff;
+    data[3385] = (char) 0xffff;
+    data[3386] = (char) 0xffff;
+    data[3387] = (char) 0xffff;
+    data[3388] = (char) 0xffff;
+    data[3389] = (char) 0xffff;
+    data[3390] = (char) 0xffff;
+    data[3391] = (char) 0xffff;
+    data[3392] = (char) 0xffff;
+    data[3393] = (char) 0xffff;
+    data[3394] = (char) 0xffff;
+    data[3395] = (char) 0xffff;
+    data[3396] = (char) 0xffff;
+    data[3397] = (char) 0xffff;
+    data[3398] = (char) 0xffff;
+    data[3399] = (char) 0xffff;
+    data[3400] = (char) 0xffff;
+    data[3401] = (char) 0xffff;
+    data[3402] = (char) 0xffff;
+    data[3403] = (char) 0xffff;
+    data[3404] = (char) 0xffff;
+    data[3405] = (char) 0xffff;
+    data[3406] = (char) 0xffff;
+    data[3407] = (char) 0xffff;
+    data[3408] = (char) 0xffff;
+    data[3409] = (char) 0xffff;
+    data[3410] = (char) 0xffff;
+    data[3411] = (char) 0xffff;
+    data[3412] = (char) 0xffff;
+    data[3413] = (char) 0xffff;
+    data[3414] = (char) 0xffff;
+    data[3415] = (char) 0xffff;
+    data[3416] = (char) 0xffff;
+    data[3417] = (char) 0xffff;
+    data[3418] = (char) 0xffff;
+    data[3419] = (char) 0xffff;
+    data[3420] = (char) 0xffff;
+    data[3421] = (char) 0xffff;
+    data[3422] = (char) 0xffff;
+    data[3423] = (char) 0xffff;
+    data[3424] = (char) 0xffff;
+    data[3425] = (char) 0xffff;
+    data[3426] = (char) 0xffff;
+    data[3427] = (char) 0xffff;
+    data[3428] = (char) 0xffff;
+    data[3429] = (char) 0xffff;
+    data[3430] = (char) 0xffff;
+    data[3431] = (char) 0xffff;
+    data[3432] = (char) 0xffff;
+    data[3433] = (char) 0xffff;
+    data[3434] = (char) 0xffff;
+    data[3435] = (char) 0xffff;
+    data[3436] = (char) 0xffff;
+    data[3437] = (char) 0xffff;
+    data[3438] = (char) 0xffff;
+    data[3439] = (char) 0xffff;
+    data[3440] = (char) 0xffff;
+    data[3441] = (char) 0xffff;
+    data[3442] = (char) 0xffff;
+    data[3443] = (char) 0xffff;
+    data[3444] = (char) 0xffff;
+    data[3445] = (char) 0xffff;
+    data[3446] = (char) 0xffff;
+    data[3447] = (char) 0xffff;
+    data[3448] = (char) 0xffff;
+    data[3449] = (char) 0xffff;
+    data[3450] = (char) 0x000f;
+    data[3984] = (char) 0xffff;
+    data[3985] = (char) 0xffff;
+    data[3986] = (char) 0xffff;
+    data[3987] = (char) 0xffff;
+    data[3988] = (char) 0xffff;
+    data[3989] = (char) 0xffff;
+    data[3990] = (char) 0xffff;
+    data[3991] = (char) 0xffff;
+    data[3992] = (char) 0xffff;
+    data[3993] = (char) 0xffff;
+    data[3994] = (char) 0xffff;
+    data[3995] = (char) 0xffff;
+    data[3996] = (char) 0xffff;
+    data[3997] = (char) 0xffff;
+    data[3998] = (char) 0xffff;
+    data[3999] = (char) 0xffff;
+    data[4000] = (char) 0xffff;
+    data[4001] = (char) 0xffff;
+    data[4002] = (char) 0x3fff;
+    data[4016] = (char) 0x007f;
+    data[4017] = (char) 0x80f8;
+    data[4018] = (char) 0xfdff;
+    data[4019] = (char) 0x5f7f;
+    data[4020] = (char) 0xffdb;
+    data[4021] = (char) 0xffff;
+    data[4022] = (char) 0xffff;
+    data[4023] = (char) 0xffff;
+    data[4024] = (char) 0xffff;
+    data[4025] = (char) 0xffff;
+    data[4026] = (char) 0xffff;
+    data[4027] = (char) 0x0003;
+    data[4029] = (char) 0xfff8;
+    data[4030] = (char) 0xffff;
+    data[4031] = (char) 0xffff;
+    data[4032] = (char) 0xffff;
+    data[4033] = (char) 0xffff;
+    data[4034] = (char) 0xffff;
+    data[4035] = (char) 0xffff;
+    data[4036] = (char) 0xffff;
+    data[4037] = (char) 0xffff;
+    data[4038] = (char) 0xffff;
+    data[4039] = (char) 0xffff;
+    data[4040] = (char) 0xffff;
+    data[4041] = (char) 0xffff;
+    data[4042] = (char) 0xffff;
+    data[4043] = (char) 0xffff;
+    data[4044] = (char) 0xffff;
+    data[4045] = (char) 0xffff;
+    data[4046] = (char) 0xffff;
+    data[4047] = (char) 0xffff;
+    data[4048] = (char) 0xffff;
+    data[4049] = (char) 0xffff;
+    data[4050] = (char) 0xffff;
+    data[4051] = (char) 0x3fff;
+    data[4053] = (char) 0xffff;
+    data[4054] = (char) 0xffff;
+    data[4055] = (char) 0xffff;
+    data[4056] = (char) 0xffff;
+    data[4057] = (char) 0xfffc;
+    data[4058] = (char) 0xffff;
+    data[4059] = (char) 0xffff;
+    data[4060] = (char) 0x00ff;
+    data[4063] = (char) 0x0fff;
+    data[4071] = (char) 0xffd7;
+    data[4072] = (char) 0xffff;
+    data[4073] = (char) 0xffff;
+    data[4074] = (char) 0xffff;
+    data[4075] = (char) 0xffff;
+    data[4076] = (char) 0xffff;
+    data[4077] = (char) 0xffff;
+    data[4078] = (char) 0xffff;
+    data[4079] = (char) 0x1fff;
+    data[4082] = (char) 0xfffe;
+    data[4083] = (char) 0x07ff;
+    data[4084] = (char) 0xfffe;
+    data[4085] = (char) 0x07ff;
+    data[4086] = (char) 0xffc0;
+    data[4087] = (char) 0xffff;
+    data[4088] = (char) 0xffff;
+    data[4089] = (char) 0xffff;
+    data[4090] = (char) 0xffff;
+    data[4091] = (char) 0x7fff;
+    data[4092] = (char) 0xfcfc;
+    data[4093] = (char) 0x1cfc;
+    data[4100] = (char) 0xfffe;
+    data[4101] = (char) 0x07ff;
+    data[4102] = (char) 0xfffe;
+    data[4103] = (char) 0x07ff;
+    data[4106] = (char) 0x0400;
+    data[4107] = (char) 0x0420;
+    data[4108] = (char) 0xffff;
+    data[4109] = (char) 0xff7f;
+    data[4110] = (char) 0xffff;
+    data[4111] = (char) 0xff7f;
+    data[4112] = (char) 0xffff;
+    data[4113] = (char) 0xffff;
+    data[4114] = (char) 0xffff;
+    data[4115] = (char) 0xffff;
+    data[4116] = (char) 0xffff;
+    data[4117] = (char) 0xffff;
+    data[4118] = (char) 0xffff;
+    data[4119] = (char) 0xffff;
+    data[4120] = (char) 0xffff;
+    data[4121] = (char) 0xffff;
+    data[4122] = (char) 0xffff;
+    data[4123] = (char) 0xffff;
+    data[4124] = (char) 0xffff;
+    data[4125] = (char) 0xffff;
+    data[4126] = (char) 0xffff;
+    data[4127] = (char) 0xfc3f;
+    data[4128] = (char) 0xffff;
+    data[4129] = (char) 0x00ff;
+    data[4133] = (char) 0xffff;
+    data[4134] = (char) 0xffff;
+    data[4135] = (char) 0xffff;
+    data[4136] = (char) 0xffff;
+    data[4137] = (char) 0xffff;
+    data[4138] = (char) 0x01ff;
+    data[4139] = (char) 0xf9ff;
+    data[4140] = (char) 0x0003;
+    data[4141] = (char) 0x0003;
+    data[4142] = (char) 0x001f;
+    data[4151] = (char) 0x0400;
+    data[4152] = (char) 0xd740;
+    data[4153] = (char) 0xffff;
+    data[4154] = (char) 0xfffb;
+    data[4155] = (char) 0xffff;
+    data[4156] = (char) 0x7fff;
+    data[4157] = (char) 0x547f;
+    data[4158] = (char) 0x00fd;
+
+  }
+
+  public static Bits white;
+
+  static void white_f()
+  {
+    char[] data = new char[4159];
+    white = new Bits(data);
+    data[0] = (char) 0x3e00;
+    data[1] = (char) 0xf000;
+    data[2] = (char) 0x0001;
+    data[512] = (char) 0x0fff;
+    data[514] = (char) 0x0300;
+    data[768] = (char) 0x0001;
+    data[4096] = (char) 0x3e00;
+    data[4097] = (char) 0xf000;
+    data[4098] = (char) 0x0001;
+
+  }
+
+  public static Bits punct;
+
+  static void punct_f()
+  {
+    char[] data = new char[4159];
+    punct = new Bits(data);
+    data[2] = (char) 0xf7ee;
+    data[3] = (char) 0x8c00;
+    data[4] = (char) 0x0001;
+    data[5] = (char) 0xb800;
+    data[7] = (char) 0x2800;
+    data[10] = (char) 0x2802;
+    data[11] = (char) 0x8880;
+    data[55] = (char) 0x4030;
+    data[56] = (char) 0x0080;
+    data[85] = (char) 0xfc00;
+    data[88] = (char) 0x0200;
+    data[91] = (char) 0x4000;
+    data[92] = (char) 0x0009;
+    data[95] = (char) 0x0018;
+    data[96] = (char) 0x1000;
+    data[97] = (char) 0x8800;
+    data[102] = (char) 0x3c00;
+    data[109] = (char) 0x0010;
+    data[150] = (char) 0x0030;
+    data[151] = (char) 0x0001;
+    data[226] = (char) 0x8000;
+    data[229] = (char) 0x0c00;
+    data[234] = (char) 0x8000;
+    data[240] = (char) 0xfff0;
+    data[241] = (char) 0x0007;
+    data[243] = (char) 0x3c00;
+    data[248] = (char) 0x0020;
+    data[271] = (char) 0x0800;
+    data[513] = (char) 0xffff;
+    data[514] = (char) 0x00ff;
+    data[515] = (char) 0xffff;
+    data[516] = (char) 0x006f;
+    data[519] = (char) 0x6000;
+    data[520] = (char) 0x6000;
+    data[562] = (char) 0x0600;
+    data[768] = (char) 0xff4e;
+    data[769] = (char) 0xfff3;
+    data[771] = (char) 0x0001;
+    data[783] = (char) 0x0800;
+    data[4051] = (char) 0xc000;
+    data[4067] = (char) 0xffff;
+    data[4068] = (char) 0xfe1f;
+    data[4069] = (char) 0xfff7;
+    data[4070] = (char) 0x0d0b;
+    data[4080] = (char) 0xf7ee;
+    data[4081] = (char) 0x8c00;
+    data[4082] = (char) 0x0001;
+    data[4083] = (char) 0xb800;
+    data[4085] = (char) 0x2800;
+    data[4086] = (char) 0x003e;
+    data[4098] = (char) 0xf7ee;
+    data[4099] = (char) 0x8c00;
+    data[4100] = (char) 0x0001;
+    data[4101] = (char) 0xb800;
+    data[4103] = (char) 0x2800;
+    data[4106] = (char) 0x2802;
+    data[4107] = (char) 0x8880;
+    data[4151] = (char) 0x4030;
+    data[4152] = (char) 0x0080;
+
+  }
+}
diff --git a/src/com/stevesoft/pat/Boundary.java b/src/com/stevesoft/pat/Boundary.java
index d6481b4..566b20e 100755
--- a/src/com/stevesoft/pat/Boundary.java
+++ b/src/com/stevesoft/pat/Boundary.java
@@ -1,92 +1,89 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-import java.util.*;
-
-/** This class implements the word boundary pattern element: \b. */
-class Boundary
-    extends Pattern
-{
-  public String toString()
-  {
-    return "\\b" + nextString();
-  }
-
-  boolean isAChar(char c)
-  {
-    if (c >= 'a' && c <= 'z')
-    {
-      return true;
-    }
-    if (c >= 'A' && c <= 'Z')
-    {
-      return true;
-    }
-    if (c >= '0' && c <= '9')
-    {
-      return true;
-    }
-    if (c == '_')
-    {
-      return true;
-    }
-    return false;
-  }
-
-  boolean matchLeft(int pos, Pthings pt)
-  {
-    if (pos <= 0)
-    {
-      return true;
-    }
-    if (isAChar(pt.src.charAt(pos))
-        && isAChar(pt.src.charAt(pos - 1)))
-    {
-      return false;
-    }
-    return true;
-  }
-
-  boolean matchRight(int pos, Pthings pt)
-  {
-    if (pos < 0)
-    {
-      return false;
-    }
-    if (pos + 1 >= pt.src.length())
-    {
-      return true;
-    }
-    if (isAChar(pt.src.charAt(pos))
-        && isAChar(pt.src.charAt(pos + 1)))
-    {
-      return false;
-    }
-    return true;
-  }
-
-  public int matchInternal(int pos, Pthings pt)
-  {
-    if (matchRight(pos - 1, pt) || matchLeft(pos, pt))
-    {
-      return nextMatch(pos, pt);
-    }
-    return -1;
-  }
-
-  public patInt maxChars()
-  {
-    return new patInt(0);
-  }
-
-  public Pattern clone1(Hashtable h)
-  {
-    return new Boundary();
-  }
-};
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+import java.util.*;
+
+/** This class implements the word boundary pattern element: \b. */
+class Boundary extends Pattern
+{
+  public String toString()
+  {
+    return "\\b" + nextString();
+  }
+
+  boolean isAChar(char c)
+  {
+    if (c >= 'a' && c <= 'z')
+    {
+      return true;
+    }
+    if (c >= 'A' && c <= 'Z')
+    {
+      return true;
+    }
+    if (c >= '0' && c <= '9')
+    {
+      return true;
+    }
+    if (c == '_')
+    {
+      return true;
+    }
+    return false;
+  }
+
+  boolean matchLeft(int pos, Pthings pt)
+  {
+    if (pos <= 0)
+    {
+      return true;
+    }
+    if (isAChar(pt.src.charAt(pos)) && isAChar(pt.src.charAt(pos - 1)))
+    {
+      return false;
+    }
+    return true;
+  }
+
+  boolean matchRight(int pos, Pthings pt)
+  {
+    if (pos < 0)
+    {
+      return false;
+    }
+    if (pos + 1 >= pt.src.length())
+    {
+      return true;
+    }
+    if (isAChar(pt.src.charAt(pos)) && isAChar(pt.src.charAt(pos + 1)))
+    {
+      return false;
+    }
+    return true;
+  }
+
+  public int matchInternal(int pos, Pthings pt)
+  {
+    if (matchRight(pos - 1, pt) || matchLeft(pos, pt))
+    {
+      return nextMatch(pos, pt);
+    }
+    return -1;
+  }
+
+  public patInt maxChars()
+  {
+    return new patInt(0);
+  }
+
+  public Pattern clone1(Hashtable h)
+  {
+    return new Boundary();
+  }
+};
diff --git a/src/com/stevesoft/pat/Bracket.java b/src/com/stevesoft/pat/Bracket.java
index 175731b..cec8af4 100755
--- a/src/com/stevesoft/pat/Bracket.java
+++ b/src/com/stevesoft/pat/Bracket.java
@@ -1,87 +1,88 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-import java.util.*;
-
-/** The Bracket is a form of the Or class,
- implements the pattern element [  ]. */
-class Bracket
-    extends Or
-{
-  boolean neg;
-  Bracket(boolean n)
-  {
-    neg = n;
-  }
-
-  String leftForm()
-  {
-    if (neg)
-    {
-      return "[^";
-    }
-    else
-    {
-      return "[";
-    }
-  }
-
-  String rightForm()
-  {
-    return "]";
-  }
-
-  String sepForm()
-  {
-    return "";
-  }
-
-  public int matchInternal(int pos, Pthings pt)
-  {
-    if (pos >= pt.src.length())
-    {
-      return -1;
-    }
-    int r = super.matchInternal(pos, pt);
-    if ( (neg && r < 0) || (!neg && r >= 0))
-    {
-      return nextMatch(pos + 1, pt);
-    }
-    return -1;
-  }
-
-  public patInt minChars()
-  {
-    return new patInt(1);
-  }
-
-  public patInt maxChars()
-  {
-    return new patInt(1);
-  }
-
-  public Or addOr(Pattern p)
-  {
-    pv = null;
-    v.addElement(p);
-    p.setParent(null);
-    return this;
-  }
-
-  public Pattern clone1(Hashtable h)
-  {
-    Bracket b = new Bracket(neg);
-    b.v = new Vector();
-    for (int i = 0; i < v.size(); i++)
-    {
-      b.v.addElement( ( (Pattern) v.elementAt(i)).clone1(h));
-    }
-    return b;
-  }
-};
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+import java.util.*;
+
+/**
+ * The Bracket is a form of the Or class, implements the pattern element [ ].
+ */
+class Bracket extends Or
+{
+  boolean neg;
+
+  Bracket(boolean n)
+  {
+    neg = n;
+  }
+
+  String leftForm()
+  {
+    if (neg)
+    {
+      return "[^";
+    }
+    else
+    {
+      return "[";
+    }
+  }
+
+  String rightForm()
+  {
+    return "]";
+  }
+
+  String sepForm()
+  {
+    return "";
+  }
+
+  public int matchInternal(int pos, Pthings pt)
+  {
+    if (pos >= pt.src.length())
+    {
+      return -1;
+    }
+    int r = super.matchInternal(pos, pt);
+    if ((neg && r < 0) || (!neg && r >= 0))
+    {
+      return nextMatch(pos + 1, pt);
+    }
+    return -1;
+  }
+
+  public patInt minChars()
+  {
+    return new patInt(1);
+  }
+
+  public patInt maxChars()
+  {
+    return new patInt(1);
+  }
+
+  public Or addOr(Pattern p)
+  {
+    pv = null;
+    v.addElement(p);
+    p.setParent(null);
+    return this;
+  }
+
+  public Pattern clone1(Hashtable h)
+  {
+    Bracket b = new Bracket(neg);
+    b.v = new Vector();
+    for (int i = 0; i < v.size(); i++)
+    {
+      b.v.addElement(((Pattern) v.elementAt(i)).clone1(h));
+    }
+    return b;
+  }
+};
diff --git a/src/com/stevesoft/pat/CaseMgr.java b/src/com/stevesoft/pat/CaseMgr.java
index ff93f25..393dac9 100755
--- a/src/com/stevesoft/pat/CaseMgr.java
+++ b/src/com/stevesoft/pat/CaseMgr.java
@@ -1,4407 +1,4409 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-/** Encapsulates the Unicode definitions of Upper,
-    Lower, and Title case as defined by <a href="http://www.unicode.org">
-    unicode.org</a>.
-    <p>
-    The performance of the methods found in String
-    and Character is better, but these methods work
-    both in java 1.0 and 1.1.  If it is desirable,
-    either to gain a slight performance increase or
-    to accomodate application specific modifications
-    to the definitions of upper, lower, and title case
-    then it should be a straightforward task to substitute
-    your own methods for these.
- */
-final public class CaseMgr
-{
-  final static boolean java_1_0 = false;
-  /** Convert a character to upper case .*/
-  public static char toUpperCase(char c)
-  {
-    if (java_1_0)
-    {
-      int ret = (int) c;
-      switch (c)
-      {
-        case 97:
-          ret = 65;
-          break;
-        case 98:
-          ret = 66;
-          break;
-        case 99:
-          ret = 67;
-          break;
-        case 100:
-          ret = 68;
-          break;
-        case 101:
-          ret = 69;
-          break;
-        case 102:
-          ret = 70;
-          break;
-        case 103:
-          ret = 71;
-          break;
-        case 104:
-          ret = 72;
-          break;
-        case 105:
-          ret = 73;
-          break;
-        case 106:
-          ret = 74;
-          break;
-        case 107:
-          ret = 75;
-          break;
-        case 108:
-          ret = 76;
-          break;
-        case 109:
-          ret = 77;
-          break;
-        case 110:
-          ret = 78;
-          break;
-        case 111:
-          ret = 79;
-          break;
-        case 112:
-          ret = 80;
-          break;
-        case 113:
-          ret = 81;
-          break;
-        case 114:
-          ret = 82;
-          break;
-        case 115:
-          ret = 83;
-          break;
-        case 116:
-          ret = 84;
-          break;
-        case 117:
-          ret = 85;
-          break;
-        case 118:
-          ret = 86;
-          break;
-        case 119:
-          ret = 87;
-          break;
-        case 120:
-          ret = 88;
-          break;
-        case 121:
-          ret = 89;
-          break;
-        case 122:
-          ret = 90;
-          break;
-        case 224:
-          ret = 192;
-          break;
-        case 225:
-          ret = 193;
-          break;
-        case 226:
-          ret = 194;
-          break;
-        case 227:
-          ret = 195;
-          break;
-        case 228:
-          ret = 196;
-          break;
-        case 229:
-          ret = 197;
-          break;
-        case 230:
-          ret = 198;
-          break;
-        case 231:
-          ret = 199;
-          break;
-        case 232:
-          ret = 200;
-          break;
-        case 233:
-          ret = 201;
-          break;
-        case 234:
-          ret = 202;
-          break;
-        case 235:
-          ret = 203;
-          break;
-        case 236:
-          ret = 204;
-          break;
-        case 237:
-          ret = 205;
-          break;
-        case 238:
-          ret = 206;
-          break;
-        case 239:
-          ret = 207;
-          break;
-        case 240:
-          ret = 208;
-          break;
-        case 241:
-          ret = 209;
-          break;
-        case 242:
-          ret = 210;
-          break;
-        case 243:
-          ret = 211;
-          break;
-        case 244:
-          ret = 212;
-          break;
-        case 245:
-          ret = 213;
-          break;
-        case 246:
-          ret = 214;
-          break;
-        case 248:
-          ret = 216;
-          break;
-        case 249:
-          ret = 217;
-          break;
-        case 250:
-          ret = 218;
-          break;
-        case 251:
-          ret = 219;
-          break;
-        case 252:
-          ret = 220;
-          break;
-        case 253:
-          ret = 221;
-          break;
-        case 254:
-          ret = 222;
-          break;
-        case 255:
-          ret = 376;
-          break;
-        case 257:
-          ret = 256;
-          break;
-        case 259:
-          ret = 258;
-          break;
-        case 261:
-          ret = 260;
-          break;
-        case 263:
-          ret = 262;
-          break;
-        case 265:
-          ret = 264;
-          break;
-        case 267:
-          ret = 266;
-          break;
-        case 269:
-          ret = 268;
-          break;
-        case 271:
-          ret = 270;
-          break;
-        case 273:
-          ret = 272;
-          break;
-        case 275:
-          ret = 274;
-          break;
-        case 277:
-          ret = 276;
-          break;
-        case 279:
-          ret = 278;
-          break;
-        case 281:
-          ret = 280;
-          break;
-        case 283:
-          ret = 282;
-          break;
-        case 285:
-          ret = 284;
-          break;
-        case 287:
-          ret = 286;
-          break;
-        case 289:
-          ret = 288;
-          break;
-        case 291:
-          ret = 290;
-          break;
-        case 293:
-          ret = 292;
-          break;
-        case 295:
-          ret = 294;
-          break;
-        case 297:
-          ret = 296;
-          break;
-        case 299:
-          ret = 298;
-          break;
-        case 301:
-          ret = 300;
-          break;
-        case 303:
-          ret = 302;
-          break;
-        case 305:
-          ret = 73;
-          break;
-        case 307:
-          ret = 306;
-          break;
-        case 309:
-          ret = 308;
-          break;
-        case 311:
-          ret = 310;
-          break;
-        case 314:
-          ret = 313;
-          break;
-        case 316:
-          ret = 315;
-          break;
-        case 318:
-          ret = 317;
-          break;
-        case 320:
-          ret = 319;
-          break;
-        case 322:
-          ret = 321;
-          break;
-        case 324:
-          ret = 323;
-          break;
-        case 326:
-          ret = 325;
-          break;
-        case 328:
-          ret = 327;
-          break;
-        case 331:
-          ret = 330;
-          break;
-        case 333:
-          ret = 332;
-          break;
-        case 335:
-          ret = 334;
-          break;
-        case 337:
-          ret = 336;
-          break;
-        case 339:
-          ret = 338;
-          break;
-        case 341:
-          ret = 340;
-          break;
-        case 343:
-          ret = 342;
-          break;
-        case 345:
-          ret = 344;
-          break;
-        case 347:
-          ret = 346;
-          break;
-        case 349:
-          ret = 348;
-          break;
-        case 351:
-          ret = 350;
-          break;
-        case 353:
-          ret = 352;
-          break;
-        case 355:
-          ret = 354;
-          break;
-        case 357:
-          ret = 356;
-          break;
-        case 359:
-          ret = 358;
-          break;
-        case 361:
-          ret = 360;
-          break;
-        case 363:
-          ret = 362;
-          break;
-        case 365:
-          ret = 364;
-          break;
-        case 367:
-          ret = 366;
-          break;
-        case 369:
-          ret = 368;
-          break;
-        case 371:
-          ret = 370;
-          break;
-        case 373:
-          ret = 372;
-          break;
-        case 375:
-          ret = 374;
-          break;
-        case 378:
-          ret = 377;
-          break;
-        case 380:
-          ret = 379;
-          break;
-        case 382:
-          ret = 381;
-          break;
-        case 383:
-          ret = 83;
-          break;
-        case 387:
-          ret = 386;
-          break;
-        case 389:
-          ret = 388;
-          break;
-        case 392:
-          ret = 391;
-          break;
-        case 396:
-          ret = 395;
-          break;
-        case 402:
-          ret = 401;
-          break;
-        case 409:
-          ret = 408;
-          break;
-        case 417:
-          ret = 416;
-          break;
-        case 419:
-          ret = 418;
-          break;
-        case 421:
-          ret = 420;
-          break;
-        case 424:
-          ret = 423;
-          break;
-        case 429:
-          ret = 428;
-          break;
-        case 432:
-          ret = 431;
-          break;
-        case 436:
-          ret = 435;
-          break;
-        case 438:
-          ret = 437;
-          break;
-        case 441:
-          ret = 440;
-          break;
-        case 445:
-          ret = 444;
-          break;
-        case 453:
-          ret = 452;
-          break;
-        case 454:
-          ret = 452;
-          break;
-        case 456:
-          ret = 455;
-          break;
-        case 457:
-          ret = 455;
-          break;
-        case 459:
-          ret = 458;
-          break;
-        case 460:
-          ret = 458;
-          break;
-        case 462:
-          ret = 461;
-          break;
-        case 464:
-          ret = 463;
-          break;
-        case 466:
-          ret = 465;
-          break;
-        case 468:
-          ret = 467;
-          break;
-        case 470:
-          ret = 469;
-          break;
-        case 472:
-          ret = 471;
-          break;
-        case 474:
-          ret = 473;
-          break;
-        case 476:
-          ret = 475;
-          break;
-        case 479:
-          ret = 478;
-          break;
-        case 481:
-          ret = 480;
-          break;
-        case 483:
-          ret = 482;
-          break;
-        case 485:
-          ret = 484;
-          break;
-        case 487:
-          ret = 486;
-          break;
-        case 489:
-          ret = 488;
-          break;
-        case 491:
-          ret = 490;
-          break;
-        case 493:
-          ret = 492;
-          break;
-        case 495:
-          ret = 494;
-          break;
-        case 498:
-          ret = 497;
-          break;
-        case 499:
-          ret = 497;
-          break;
-        case 501:
-          ret = 500;
-          break;
-        case 507:
-          ret = 506;
-          break;
-        case 509:
-          ret = 508;
-          break;
-        case 511:
-          ret = 510;
-          break;
-        case 513:
-          ret = 512;
-          break;
-        case 515:
-          ret = 514;
-          break;
-        case 517:
-          ret = 516;
-          break;
-        case 519:
-          ret = 518;
-          break;
-        case 521:
-          ret = 520;
-          break;
-        case 523:
-          ret = 522;
-          break;
-        case 525:
-          ret = 524;
-          break;
-        case 527:
-          ret = 526;
-          break;
-        case 529:
-          ret = 528;
-          break;
-        case 531:
-          ret = 530;
-          break;
-        case 533:
-          ret = 532;
-          break;
-        case 535:
-          ret = 534;
-          break;
-        case 595:
-          ret = 385;
-          break;
-        case 596:
-          ret = 390;
-          break;
-        case 598:
-          ret = 393;
-          break;
-        case 599:
-          ret = 394;
-          break;
-        case 600:
-          ret = 398;
-          break;
-        case 601:
-          ret = 399;
-          break;
-        case 603:
-          ret = 400;
-          break;
-        case 608:
-          ret = 403;
-          break;
-        case 611:
-          ret = 404;
-          break;
-        case 616:
-          ret = 407;
-          break;
-        case 617:
-          ret = 406;
-          break;
-        case 623:
-          ret = 412;
-          break;
-        case 626:
-          ret = 413;
-          break;
-        case 643:
-          ret = 425;
-          break;
-        case 648:
-          ret = 430;
-          break;
-        case 650:
-          ret = 433;
-          break;
-        case 651:
-          ret = 434;
-          break;
-        case 658:
-          ret = 439;
-          break;
-        case 940:
-          ret = 902;
-          break;
-        case 941:
-          ret = 904;
-          break;
-        case 942:
-          ret = 905;
-          break;
-        case 943:
-          ret = 906;
-          break;
-        case 945:
-          ret = 913;
-          break;
-        case 946:
-          ret = 914;
-          break;
-        case 947:
-          ret = 915;
-          break;
-        case 948:
-          ret = 916;
-          break;
-        case 949:
-          ret = 917;
-          break;
-        case 950:
-          ret = 918;
-          break;
-        case 951:
-          ret = 919;
-          break;
-        case 952:
-          ret = 920;
-          break;
-        case 953:
-          ret = 921;
-          break;
-        case 954:
-          ret = 922;
-          break;
-        case 955:
-          ret = 923;
-          break;
-        case 956:
-          ret = 924;
-          break;
-        case 957:
-          ret = 925;
-          break;
-        case 958:
-          ret = 926;
-          break;
-        case 959:
-          ret = 927;
-          break;
-        case 960:
-          ret = 928;
-          break;
-        case 961:
-          ret = 929;
-          break;
-        case 963:
-          ret = 931;
-          break;
-        case 964:
-          ret = 932;
-          break;
-        case 965:
-          ret = 933;
-          break;
-        case 966:
-          ret = 934;
-          break;
-        case 967:
-          ret = 935;
-          break;
-        case 968:
-          ret = 936;
-          break;
-        case 969:
-          ret = 937;
-          break;
-        case 970:
-          ret = 938;
-          break;
-        case 971:
-          ret = 939;
-          break;
-        case 972:
-          ret = 908;
-          break;
-        case 973:
-          ret = 910;
-          break;
-        case 974:
-          ret = 911;
-          break;
-        case 976:
-          ret = 914;
-          break;
-        case 977:
-          ret = 920;
-          break;
-        case 981:
-          ret = 934;
-          break;
-        case 982:
-          ret = 928;
-          break;
-        case 995:
-          ret = 994;
-          break;
-        case 997:
-          ret = 996;
-          break;
-        case 999:
-          ret = 998;
-          break;
-        case 1001:
-          ret = 1000;
-          break;
-        case 1003:
-          ret = 1002;
-          break;
-        case 1005:
-          ret = 1004;
-          break;
-        case 1007:
-          ret = 1006;
-          break;
-        case 1008:
-          ret = 922;
-          break;
-        case 1009:
-          ret = 929;
-          break;
-        case 1072:
-          ret = 1040;
-          break;
-        case 1073:
-          ret = 1041;
-          break;
-        case 1074:
-          ret = 1042;
-          break;
-        case 1075:
-          ret = 1043;
-          break;
-        case 1076:
-          ret = 1044;
-          break;
-        case 1077:
-          ret = 1045;
-          break;
-        case 1078:
-          ret = 1046;
-          break;
-        case 1079:
-          ret = 1047;
-          break;
-        case 1080:
-          ret = 1048;
-          break;
-        case 1081:
-          ret = 1049;
-          break;
-        case 1082:
-          ret = 1050;
-          break;
-        case 1083:
-          ret = 1051;
-          break;
-        case 1084:
-          ret = 1052;
-          break;
-        case 1085:
-          ret = 1053;
-          break;
-        case 1086:
-          ret = 1054;
-          break;
-        case 1087:
-          ret = 1055;
-          break;
-        case 1088:
-          ret = 1056;
-          break;
-        case 1089:
-          ret = 1057;
-          break;
-        case 1090:
-          ret = 1058;
-          break;
-        case 1091:
-          ret = 1059;
-          break;
-        case 1092:
-          ret = 1060;
-          break;
-        case 1093:
-          ret = 1061;
-          break;
-        case 1094:
-          ret = 1062;
-          break;
-        case 1095:
-          ret = 1063;
-          break;
-        case 1096:
-          ret = 1064;
-          break;
-        case 1097:
-          ret = 1065;
-          break;
-        case 1098:
-          ret = 1066;
-          break;
-        case 1099:
-          ret = 1067;
-          break;
-        case 1100:
-          ret = 1068;
-          break;
-        case 1101:
-          ret = 1069;
-          break;
-        case 1102:
-          ret = 1070;
-          break;
-        case 1103:
-          ret = 1071;
-          break;
-        case 1105:
-          ret = 1025;
-          break;
-        case 1106:
-          ret = 1026;
-          break;
-        case 1107:
-          ret = 1027;
-          break;
-        case 1108:
-          ret = 1028;
-          break;
-        case 1109:
-          ret = 1029;
-          break;
-        case 1110:
-          ret = 1030;
-          break;
-        case 1111:
-          ret = 1031;
-          break;
-        case 1112:
-          ret = 1032;
-          break;
-        case 1113:
-          ret = 1033;
-          break;
-        case 1114:
-          ret = 1034;
-          break;
-        case 1115:
-          ret = 1035;
-          break;
-        case 1116:
-          ret = 1036;
-          break;
-        case 1118:
-          ret = 1038;
-          break;
-        case 1119:
-          ret = 1039;
-          break;
-        case 1121:
-          ret = 1120;
-          break;
-        case 1123:
-          ret = 1122;
-          break;
-        case 1125:
-          ret = 1124;
-          break;
-        case 1127:
-          ret = 1126;
-          break;
-        case 1129:
-          ret = 1128;
-          break;
-        case 1131:
-          ret = 1130;
-          break;
-        case 1133:
-          ret = 1132;
-          break;
-        case 1135:
-          ret = 1134;
-          break;
-        case 1137:
-          ret = 1136;
-          break;
-        case 1139:
-          ret = 1138;
-          break;
-        case 1141:
-          ret = 1140;
-          break;
-        case 1143:
-          ret = 1142;
-          break;
-        case 1145:
-          ret = 1144;
-          break;
-        case 1147:
-          ret = 1146;
-          break;
-        case 1149:
-          ret = 1148;
-          break;
-        case 1151:
-          ret = 1150;
-          break;
-        case 1153:
-          ret = 1152;
-          break;
-        case 1169:
-          ret = 1168;
-          break;
-        case 1171:
-          ret = 1170;
-          break;
-        case 1173:
-          ret = 1172;
-          break;
-        case 1175:
-          ret = 1174;
-          break;
-        case 1177:
-          ret = 1176;
-          break;
-        case 1179:
-          ret = 1178;
-          break;
-        case 1181:
-          ret = 1180;
-          break;
-        case 1183:
-          ret = 1182;
-          break;
-        case 1185:
-          ret = 1184;
-          break;
-        case 1187:
-          ret = 1186;
-          break;
-        case 1189:
-          ret = 1188;
-          break;
-        case 1191:
-          ret = 1190;
-          break;
-        case 1193:
-          ret = 1192;
-          break;
-        case 1195:
-          ret = 1194;
-          break;
-        case 1197:
-          ret = 1196;
-          break;
-        case 1199:
-          ret = 1198;
-          break;
-        case 1201:
-          ret = 1200;
-          break;
-        case 1203:
-          ret = 1202;
-          break;
-        case 1205:
-          ret = 1204;
-          break;
-        case 1207:
-          ret = 1206;
-          break;
-        case 1209:
-          ret = 1208;
-          break;
-        case 1211:
-          ret = 1210;
-          break;
-        case 1213:
-          ret = 1212;
-          break;
-        case 1215:
-          ret = 1214;
-          break;
-        case 1218:
-          ret = 1217;
-          break;
-        case 1220:
-          ret = 1219;
-          break;
-        case 1224:
-          ret = 1223;
-          break;
-        case 1228:
-          ret = 1227;
-          break;
-        case 1233:
-          ret = 1232;
-          break;
-        case 1235:
-          ret = 1234;
-          break;
-        case 1237:
-          ret = 1236;
-          break;
-        case 1239:
-          ret = 1238;
-          break;
-        case 1241:
-          ret = 1240;
-          break;
-        case 1243:
-          ret = 1242;
-          break;
-        case 1245:
-          ret = 1244;
-          break;
-        case 1247:
-          ret = 1246;
-          break;
-        case 1249:
-          ret = 1248;
-          break;
-        case 1251:
-          ret = 1250;
-          break;
-        case 1253:
-          ret = 1252;
-          break;
-        case 1255:
-          ret = 1254;
-          break;
-        case 1257:
-          ret = 1256;
-          break;
-        case 1259:
-          ret = 1258;
-          break;
-        case 1263:
-          ret = 1262;
-          break;
-        case 1265:
-          ret = 1264;
-          break;
-        case 1267:
-          ret = 1266;
-          break;
-        case 1269:
-          ret = 1268;
-          break;
-        case 1273:
-          ret = 1272;
-          break;
-        case 1377:
-          ret = 1329;
-          break;
-        case 1378:
-          ret = 1330;
-          break;
-        case 1379:
-          ret = 1331;
-          break;
-        case 1380:
-          ret = 1332;
-          break;
-        case 1381:
-          ret = 1333;
-          break;
-        case 1382:
-          ret = 1334;
-          break;
-        case 1383:
-          ret = 1335;
-          break;
-        case 1384:
-          ret = 1336;
-          break;
-        case 1385:
-          ret = 1337;
-          break;
-        case 1386:
-          ret = 1338;
-          break;
-        case 1387:
-          ret = 1339;
-          break;
-        case 1388:
-          ret = 1340;
-          break;
-        case 1389:
-          ret = 1341;
-          break;
-        case 1390:
-          ret = 1342;
-          break;
-        case 1391:
-          ret = 1343;
-          break;
-        case 1392:
-          ret = 1344;
-          break;
-        case 1393:
-          ret = 1345;
-          break;
-        case 1394:
-          ret = 1346;
-          break;
-        case 1395:
-          ret = 1347;
-          break;
-        case 1396:
-          ret = 1348;
-          break;
-        case 1397:
-          ret = 1349;
-          break;
-        case 1398:
-          ret = 1350;
-          break;
-        case 1399:
-          ret = 1351;
-          break;
-        case 1400:
-          ret = 1352;
-          break;
-        case 1401:
-          ret = 1353;
-          break;
-        case 1402:
-          ret = 1354;
-          break;
-        case 1403:
-          ret = 1355;
-          break;
-        case 1404:
-          ret = 1356;
-          break;
-        case 1405:
-          ret = 1357;
-          break;
-        case 1406:
-          ret = 1358;
-          break;
-        case 1407:
-          ret = 1359;
-          break;
-        case 1408:
-          ret = 1360;
-          break;
-        case 1409:
-          ret = 1361;
-          break;
-        case 1410:
-          ret = 1362;
-          break;
-        case 1411:
-          ret = 1363;
-          break;
-        case 1412:
-          ret = 1364;
-          break;
-        case 1413:
-          ret = 1365;
-          break;
-        case 1414:
-          ret = 1366;
-          break;
-        case 7681:
-          ret = 7680;
-          break;
-        case 7683:
-          ret = 7682;
-          break;
-        case 7685:
-          ret = 7684;
-          break;
-        case 7687:
-          ret = 7686;
-          break;
-        case 7689:
-          ret = 7688;
-          break;
-        case 7691:
-          ret = 7690;
-          break;
-        case 7693:
-          ret = 7692;
-          break;
-        case 7695:
-          ret = 7694;
-          break;
-        case 7697:
-          ret = 7696;
-          break;
-        case 7699:
-          ret = 7698;
-          break;
-        case 7701:
-          ret = 7700;
-          break;
-        case 7703:
-          ret = 7702;
-          break;
-        case 7705:
-          ret = 7704;
-          break;
-        case 7707:
-          ret = 7706;
-          break;
-        case 7709:
-          ret = 7708;
-          break;
-        case 7711:
-          ret = 7710;
-          break;
-        case 7713:
-          ret = 7712;
-          break;
-        case 7715:
-          ret = 7714;
-          break;
-        case 7717:
-          ret = 7716;
-          break;
-        case 7719:
-          ret = 7718;
-          break;
-        case 7721:
-          ret = 7720;
-          break;
-        case 7723:
-          ret = 7722;
-          break;
-        case 7725:
-          ret = 7724;
-          break;
-        case 7727:
-          ret = 7726;
-          break;
-        case 7729:
-          ret = 7728;
-          break;
-        case 7731:
-          ret = 7730;
-          break;
-        case 7733:
-          ret = 7732;
-          break;
-        case 7735:
-          ret = 7734;
-          break;
-        case 7737:
-          ret = 7736;
-          break;
-        case 7739:
-          ret = 7738;
-          break;
-        case 7741:
-          ret = 7740;
-          break;
-        case 7743:
-          ret = 7742;
-          break;
-        case 7745:
-          ret = 7744;
-          break;
-        case 7747:
-          ret = 7746;
-          break;
-        case 7749:
-          ret = 7748;
-          break;
-        case 7751:
-          ret = 7750;
-          break;
-        case 7753:
-          ret = 7752;
-          break;
-        case 7755:
-          ret = 7754;
-          break;
-        case 7757:
-          ret = 7756;
-          break;
-        case 7759:
-          ret = 7758;
-          break;
-        case 7761:
-          ret = 7760;
-          break;
-        case 7763:
-          ret = 7762;
-          break;
-        case 7765:
-          ret = 7764;
-          break;
-        case 7767:
-          ret = 7766;
-          break;
-        case 7769:
-          ret = 7768;
-          break;
-        case 7771:
-          ret = 7770;
-          break;
-        case 7773:
-          ret = 7772;
-          break;
-        case 7775:
-          ret = 7774;
-          break;
-        case 7777:
-          ret = 7776;
-          break;
-        case 7779:
-          ret = 7778;
-          break;
-        case 7781:
-          ret = 7780;
-          break;
-        case 7783:
-          ret = 7782;
-          break;
-        case 7785:
-          ret = 7784;
-          break;
-        case 7787:
-          ret = 7786;
-          break;
-        case 7789:
-          ret = 7788;
-          break;
-        case 7791:
-          ret = 7790;
-          break;
-        case 7793:
-          ret = 7792;
-          break;
-        case 7795:
-          ret = 7794;
-          break;
-        case 7797:
-          ret = 7796;
-          break;
-        case 7799:
-          ret = 7798;
-          break;
-        case 7801:
-          ret = 7800;
-          break;
-        case 7803:
-          ret = 7802;
-          break;
-        case 7805:
-          ret = 7804;
-          break;
-        case 7807:
-          ret = 7806;
-          break;
-        case 7809:
-          ret = 7808;
-          break;
-        case 7811:
-          ret = 7810;
-          break;
-        case 7813:
-          ret = 7812;
-          break;
-        case 7815:
-          ret = 7814;
-          break;
-        case 7817:
-          ret = 7816;
-          break;
-        case 7819:
-          ret = 7818;
-          break;
-        case 7821:
-          ret = 7820;
-          break;
-        case 7823:
-          ret = 7822;
-          break;
-        case 7825:
-          ret = 7824;
-          break;
-        case 7827:
-          ret = 7826;
-          break;
-        case 7829:
-          ret = 7828;
-          break;
-        case 7841:
-          ret = 7840;
-          break;
-        case 7843:
-          ret = 7842;
-          break;
-        case 7845:
-          ret = 7844;
-          break;
-        case 7847:
-          ret = 7846;
-          break;
-        case 7849:
-          ret = 7848;
-          break;
-        case 7851:
-          ret = 7850;
-          break;
-        case 7853:
-          ret = 7852;
-          break;
-        case 7855:
-          ret = 7854;
-          break;
-        case 7857:
-          ret = 7856;
-          break;
-        case 7859:
-          ret = 7858;
-          break;
-        case 7861:
-          ret = 7860;
-          break;
-        case 7863:
-          ret = 7862;
-          break;
-        case 7865:
-          ret = 7864;
-          break;
-        case 7867:
-          ret = 7866;
-          break;
-        case 7869:
-          ret = 7868;
-          break;
-        case 7871:
-          ret = 7870;
-          break;
-        case 7873:
-          ret = 7872;
-          break;
-        case 7875:
-          ret = 7874;
-          break;
-        case 7877:
-          ret = 7876;
-          break;
-        case 7879:
-          ret = 7878;
-          break;
-        case 7881:
-          ret = 7880;
-          break;
-        case 7883:
-          ret = 7882;
-          break;
-        case 7885:
-          ret = 7884;
-          break;
-        case 7887:
-          ret = 7886;
-          break;
-        case 7889:
-          ret = 7888;
-          break;
-        case 7891:
-          ret = 7890;
-          break;
-        case 7893:
-          ret = 7892;
-          break;
-        case 7895:
-          ret = 7894;
-          break;
-        case 7897:
-          ret = 7896;
-          break;
-        case 7899:
-          ret = 7898;
-          break;
-        case 7901:
-          ret = 7900;
-          break;
-        case 7903:
-          ret = 7902;
-          break;
-        case 7905:
-          ret = 7904;
-          break;
-        case 7907:
-          ret = 7906;
-          break;
-        case 7909:
-          ret = 7908;
-          break;
-        case 7911:
-          ret = 7910;
-          break;
-        case 7913:
-          ret = 7912;
-          break;
-        case 7915:
-          ret = 7914;
-          break;
-        case 7917:
-          ret = 7916;
-          break;
-        case 7919:
-          ret = 7918;
-          break;
-        case 7921:
-          ret = 7920;
-          break;
-        case 7923:
-          ret = 7922;
-          break;
-        case 7925:
-          ret = 7924;
-          break;
-        case 7927:
-          ret = 7926;
-          break;
-        case 7929:
-          ret = 7928;
-          break;
-        case 7936:
-          ret = 7944;
-          break;
-        case 7937:
-          ret = 7945;
-          break;
-        case 7938:
-          ret = 7946;
-          break;
-        case 7939:
-          ret = 7947;
-          break;
-        case 7940:
-          ret = 7948;
-          break;
-        case 7941:
-          ret = 7949;
-          break;
-        case 7942:
-          ret = 7950;
-          break;
-        case 7943:
-          ret = 7951;
-          break;
-        case 7952:
-          ret = 7960;
-          break;
-        case 7953:
-          ret = 7961;
-          break;
-        case 7954:
-          ret = 7962;
-          break;
-        case 7955:
-          ret = 7963;
-          break;
-        case 7956:
-          ret = 7964;
-          break;
-        case 7957:
-          ret = 7965;
-          break;
-        case 7968:
-          ret = 7976;
-          break;
-        case 7969:
-          ret = 7977;
-          break;
-        case 7970:
-          ret = 7978;
-          break;
-        case 7971:
-          ret = 7979;
-          break;
-        case 7972:
-          ret = 7980;
-          break;
-        case 7973:
-          ret = 7981;
-          break;
-        case 7974:
-          ret = 7982;
-          break;
-        case 7975:
-          ret = 7983;
-          break;
-        case 7984:
-          ret = 7992;
-          break;
-        case 7985:
-          ret = 7993;
-          break;
-        case 7986:
-          ret = 7994;
-          break;
-        case 7987:
-          ret = 7995;
-          break;
-        case 7988:
-          ret = 7996;
-          break;
-        case 7989:
-          ret = 7997;
-          break;
-        case 7990:
-          ret = 7998;
-          break;
-        case 7991:
-          ret = 7999;
-          break;
-        case 8000:
-          ret = 8008;
-          break;
-        case 8001:
-          ret = 8009;
-          break;
-        case 8002:
-          ret = 8010;
-          break;
-        case 8003:
-          ret = 8011;
-          break;
-        case 8004:
-          ret = 8012;
-          break;
-        case 8005:
-          ret = 8013;
-          break;
-        case 8017:
-          ret = 8025;
-          break;
-        case 8019:
-          ret = 8027;
-          break;
-        case 8021:
-          ret = 8029;
-          break;
-        case 8023:
-          ret = 8031;
-          break;
-        case 8032:
-          ret = 8040;
-          break;
-        case 8033:
-          ret = 8041;
-          break;
-        case 8034:
-          ret = 8042;
-          break;
-        case 8035:
-          ret = 8043;
-          break;
-        case 8036:
-          ret = 8044;
-          break;
-        case 8037:
-          ret = 8045;
-          break;
-        case 8038:
-          ret = 8046;
-          break;
-        case 8039:
-          ret = 8047;
-          break;
-        case 8048:
-          ret = 8122;
-          break;
-        case 8049:
-          ret = 8123;
-          break;
-        case 8050:
-          ret = 8136;
-          break;
-        case 8051:
-          ret = 8137;
-          break;
-        case 8052:
-          ret = 8138;
-          break;
-        case 8053:
-          ret = 8139;
-          break;
-        case 8054:
-          ret = 8154;
-          break;
-        case 8055:
-          ret = 8155;
-          break;
-        case 8056:
-          ret = 8184;
-          break;
-        case 8057:
-          ret = 8185;
-          break;
-        case 8058:
-          ret = 8170;
-          break;
-        case 8059:
-          ret = 8171;
-          break;
-        case 8060:
-          ret = 8186;
-          break;
-        case 8061:
-          ret = 8187;
-          break;
-        case 8064:
-          ret = 8072;
-          break;
-        case 8065:
-          ret = 8073;
-          break;
-        case 8066:
-          ret = 8074;
-          break;
-        case 8067:
-          ret = 8075;
-          break;
-        case 8068:
-          ret = 8076;
-          break;
-        case 8069:
-          ret = 8077;
-          break;
-        case 8070:
-          ret = 8078;
-          break;
-        case 8071:
-          ret = 8079;
-          break;
-        case 8080:
-          ret = 8088;
-          break;
-        case 8081:
-          ret = 8089;
-          break;
-        case 8082:
-          ret = 8090;
-          break;
-        case 8083:
-          ret = 8091;
-          break;
-        case 8084:
-          ret = 8092;
-          break;
-        case 8085:
-          ret = 8093;
-          break;
-        case 8086:
-          ret = 8094;
-          break;
-        case 8087:
-          ret = 8095;
-          break;
-        case 8096:
-          ret = 8104;
-          break;
-        case 8097:
-          ret = 8105;
-          break;
-        case 8098:
-          ret = 8106;
-          break;
-        case 8099:
-          ret = 8107;
-          break;
-        case 8100:
-          ret = 8108;
-          break;
-        case 8101:
-          ret = 8109;
-          break;
-        case 8102:
-          ret = 8110;
-          break;
-        case 8103:
-          ret = 8111;
-          break;
-        case 8112:
-          ret = 8120;
-          break;
-        case 8113:
-          ret = 8121;
-          break;
-        case 8115:
-          ret = 8124;
-          break;
-        case 8131:
-          ret = 8140;
-          break;
-        case 8144:
-          ret = 8152;
-          break;
-        case 8145:
-          ret = 8153;
-          break;
-        case 8160:
-          ret = 8168;
-          break;
-        case 8161:
-          ret = 8169;
-          break;
-        case 8165:
-          ret = 8172;
-          break;
-        case 8179:
-          ret = 8188;
-          break;
-        case 8560:
-          ret = 8544;
-          break;
-        case 8561:
-          ret = 8545;
-          break;
-        case 8562:
-          ret = 8546;
-          break;
-        case 8563:
-          ret = 8547;
-          break;
-        case 8564:
-          ret = 8548;
-          break;
-        case 8565:
-          ret = 8549;
-          break;
-        case 8566:
-          ret = 8550;
-          break;
-        case 8567:
-          ret = 8551;
-          break;
-        case 8568:
-          ret = 8552;
-          break;
-        case 8569:
-          ret = 8553;
-          break;
-        case 8570:
-          ret = 8554;
-          break;
-        case 8571:
-          ret = 8555;
-          break;
-        case 8572:
-          ret = 8556;
-          break;
-        case 8573:
-          ret = 8557;
-          break;
-        case 8574:
-          ret = 8558;
-          break;
-        case 8575:
-          ret = 8559;
-          break;
-        case 9424:
-          ret = 9398;
-          break;
-        case 9425:
-          ret = 9399;
-          break;
-        case 9426:
-          ret = 9400;
-          break;
-        case 9427:
-          ret = 9401;
-          break;
-        case 9428:
-          ret = 9402;
-          break;
-        case 9429:
-          ret = 9403;
-          break;
-        case 9430:
-          ret = 9404;
-          break;
-        case 9431:
-          ret = 9405;
-          break;
-        case 9432:
-          ret = 9406;
-          break;
-        case 9433:
-          ret = 9407;
-          break;
-        case 9434:
-          ret = 9408;
-          break;
-        case 9435:
-          ret = 9409;
-          break;
-        case 9436:
-          ret = 9410;
-          break;
-        case 9437:
-          ret = 9411;
-          break;
-        case 9438:
-          ret = 9412;
-          break;
-        case 9439:
-          ret = 9413;
-          break;
-        case 9440:
-          ret = 9414;
-          break;
-        case 9441:
-          ret = 9415;
-          break;
-        case 9442:
-          ret = 9416;
-          break;
-        case 9443:
-          ret = 9417;
-          break;
-        case 9444:
-          ret = 9418;
-          break;
-        case 9445:
-          ret = 9419;
-          break;
-        case 9446:
-          ret = 9420;
-          break;
-        case 9447:
-          ret = 9421;
-          break;
-        case 9448:
-          ret = 9422;
-          break;
-        case 9449:
-          ret = 9423;
-          break;
-        case 65345:
-          ret = 65313;
-          break;
-        case 65346:
-          ret = 65314;
-          break;
-        case 65347:
-          ret = 65315;
-          break;
-        case 65348:
-          ret = 65316;
-          break;
-        case 65349:
-          ret = 65317;
-          break;
-        case 65350:
-          ret = 65318;
-          break;
-        case 65351:
-          ret = 65319;
-          break;
-        case 65352:
-          ret = 65320;
-          break;
-        case 65353:
-          ret = 65321;
-          break;
-        case 65354:
-          ret = 65322;
-          break;
-        case 65355:
-          ret = 65323;
-          break;
-        case 65356:
-          ret = 65324;
-          break;
-        case 65357:
-          ret = 65325;
-          break;
-        case 65358:
-          ret = 65326;
-          break;
-        case 65359:
-          ret = 65327;
-          break;
-        case 65360:
-          ret = 65328;
-          break;
-        case 65361:
-          ret = 65329;
-          break;
-        case 65362:
-          ret = 65330;
-          break;
-        case 65363:
-          ret = 65331;
-          break;
-        case 65364:
-          ret = 65332;
-          break;
-        case 65365:
-          ret = 65333;
-          break;
-        case 65366:
-          ret = 65334;
-          break;
-        case 65367:
-          ret = 65335;
-          break;
-        case 65368:
-          ret = 65336;
-          break;
-        case 65369:
-          ret = 65337;
-          break;
-        case 65370:
-          ret = 65338;
-          break;
-      }
-      return (char) ret;
-    }
-    return Character.toUpperCase(c);
-  }
-
-  /** Convert a character to lower case. */
-  public static char toLowerCase(char c)
-  {
-    if (java_1_0)
-    {
-      int ret = (int) c;
-      switch (c)
-      {
-        case 65:
-          ret = 97;
-          break;
-        case 66:
-          ret = 98;
-          break;
-        case 67:
-          ret = 99;
-          break;
-        case 68:
-          ret = 100;
-          break;
-        case 69:
-          ret = 101;
-          break;
-        case 70:
-          ret = 102;
-          break;
-        case 71:
-          ret = 103;
-          break;
-        case 72:
-          ret = 104;
-          break;
-        case 73:
-          ret = 105;
-          break;
-        case 74:
-          ret = 106;
-          break;
-        case 75:
-          ret = 107;
-          break;
-        case 76:
-          ret = 108;
-          break;
-        case 77:
-          ret = 109;
-          break;
-        case 78:
-          ret = 110;
-          break;
-        case 79:
-          ret = 111;
-          break;
-        case 80:
-          ret = 112;
-          break;
-        case 81:
-          ret = 113;
-          break;
-        case 82:
-          ret = 114;
-          break;
-        case 83:
-          ret = 115;
-          break;
-        case 84:
-          ret = 116;
-          break;
-        case 85:
-          ret = 117;
-          break;
-        case 86:
-          ret = 118;
-          break;
-        case 87:
-          ret = 119;
-          break;
-        case 88:
-          ret = 120;
-          break;
-        case 89:
-          ret = 121;
-          break;
-        case 90:
-          ret = 122;
-          break;
-        case 192:
-          ret = 224;
-          break;
-        case 193:
-          ret = 225;
-          break;
-        case 194:
-          ret = 226;
-          break;
-        case 195:
-          ret = 227;
-          break;
-        case 196:
-          ret = 228;
-          break;
-        case 197:
-          ret = 229;
-          break;
-        case 198:
-          ret = 230;
-          break;
-        case 199:
-          ret = 231;
-          break;
-        case 200:
-          ret = 232;
-          break;
-        case 201:
-          ret = 233;
-          break;
-        case 202:
-          ret = 234;
-          break;
-        case 203:
-          ret = 235;
-          break;
-        case 204:
-          ret = 236;
-          break;
-        case 205:
-          ret = 237;
-          break;
-        case 206:
-          ret = 238;
-          break;
-        case 207:
-          ret = 239;
-          break;
-        case 208:
-          ret = 240;
-          break;
-        case 209:
-          ret = 241;
-          break;
-        case 210:
-          ret = 242;
-          break;
-        case 211:
-          ret = 243;
-          break;
-        case 212:
-          ret = 244;
-          break;
-        case 213:
-          ret = 245;
-          break;
-        case 214:
-          ret = 246;
-          break;
-        case 216:
-          ret = 248;
-          break;
-        case 217:
-          ret = 249;
-          break;
-        case 218:
-          ret = 250;
-          break;
-        case 219:
-          ret = 251;
-          break;
-        case 220:
-          ret = 252;
-          break;
-        case 221:
-          ret = 253;
-          break;
-        case 222:
-          ret = 254;
-          break;
-        case 256:
-          ret = 257;
-          break;
-        case 258:
-          ret = 259;
-          break;
-        case 260:
-          ret = 261;
-          break;
-        case 262:
-          ret = 263;
-          break;
-        case 264:
-          ret = 265;
-          break;
-        case 266:
-          ret = 267;
-          break;
-        case 268:
-          ret = 269;
-          break;
-        case 270:
-          ret = 271;
-          break;
-        case 272:
-          ret = 273;
-          break;
-        case 274:
-          ret = 275;
-          break;
-        case 276:
-          ret = 277;
-          break;
-        case 278:
-          ret = 279;
-          break;
-        case 280:
-          ret = 281;
-          break;
-        case 282:
-          ret = 283;
-          break;
-        case 284:
-          ret = 285;
-          break;
-        case 286:
-          ret = 287;
-          break;
-        case 288:
-          ret = 289;
-          break;
-        case 290:
-          ret = 291;
-          break;
-        case 292:
-          ret = 293;
-          break;
-        case 294:
-          ret = 295;
-          break;
-        case 296:
-          ret = 297;
-          break;
-        case 298:
-          ret = 299;
-          break;
-        case 300:
-          ret = 301;
-          break;
-        case 302:
-          ret = 303;
-          break;
-        case 304:
-          ret = 105;
-          break;
-        case 306:
-          ret = 307;
-          break;
-        case 308:
-          ret = 309;
-          break;
-        case 310:
-          ret = 311;
-          break;
-        case 313:
-          ret = 314;
-          break;
-        case 315:
-          ret = 316;
-          break;
-        case 317:
-          ret = 318;
-          break;
-        case 319:
-          ret = 320;
-          break;
-        case 321:
-          ret = 322;
-          break;
-        case 323:
-          ret = 324;
-          break;
-        case 325:
-          ret = 326;
-          break;
-        case 327:
-          ret = 328;
-          break;
-        case 330:
-          ret = 331;
-          break;
-        case 332:
-          ret = 333;
-          break;
-        case 334:
-          ret = 335;
-          break;
-        case 336:
-          ret = 337;
-          break;
-        case 338:
-          ret = 339;
-          break;
-        case 340:
-          ret = 341;
-          break;
-        case 342:
-          ret = 343;
-          break;
-        case 344:
-          ret = 345;
-          break;
-        case 346:
-          ret = 347;
-          break;
-        case 348:
-          ret = 349;
-          break;
-        case 350:
-          ret = 351;
-          break;
-        case 352:
-          ret = 353;
-          break;
-        case 354:
-          ret = 355;
-          break;
-        case 356:
-          ret = 357;
-          break;
-        case 358:
-          ret = 359;
-          break;
-        case 360:
-          ret = 361;
-          break;
-        case 362:
-          ret = 363;
-          break;
-        case 364:
-          ret = 365;
-          break;
-        case 366:
-          ret = 367;
-          break;
-        case 368:
-          ret = 369;
-          break;
-        case 370:
-          ret = 371;
-          break;
-        case 372:
-          ret = 373;
-          break;
-        case 374:
-          ret = 375;
-          break;
-        case 376:
-          ret = 255;
-          break;
-        case 377:
-          ret = 378;
-          break;
-        case 379:
-          ret = 380;
-          break;
-        case 381:
-          ret = 382;
-          break;
-        case 385:
-          ret = 595;
-          break;
-        case 386:
-          ret = 387;
-          break;
-        case 388:
-          ret = 389;
-          break;
-        case 390:
-          ret = 596;
-          break;
-        case 391:
-          ret = 392;
-          break;
-        case 393:
-          ret = 598;
-          break;
-        case 394:
-          ret = 599;
-          break;
-        case 395:
-          ret = 396;
-          break;
-        case 398:
-          ret = 600;
-          break;
-        case 399:
-          ret = 601;
-          break;
-        case 400:
-          ret = 603;
-          break;
-        case 401:
-          ret = 402;
-          break;
-        case 403:
-          ret = 608;
-          break;
-        case 404:
-          ret = 611;
-          break;
-        case 406:
-          ret = 617;
-          break;
-        case 407:
-          ret = 616;
-          break;
-        case 408:
-          ret = 409;
-          break;
-        case 412:
-          ret = 623;
-          break;
-        case 413:
-          ret = 626;
-          break;
-        case 416:
-          ret = 417;
-          break;
-        case 418:
-          ret = 419;
-          break;
-        case 420:
-          ret = 421;
-          break;
-        case 423:
-          ret = 424;
-          break;
-        case 425:
-          ret = 643;
-          break;
-        case 428:
-          ret = 429;
-          break;
-        case 430:
-          ret = 648;
-          break;
-        case 431:
-          ret = 432;
-          break;
-        case 433:
-          ret = 650;
-          break;
-        case 434:
-          ret = 651;
-          break;
-        case 435:
-          ret = 436;
-          break;
-        case 437:
-          ret = 438;
-          break;
-        case 439:
-          ret = 658;
-          break;
-        case 440:
-          ret = 441;
-          break;
-        case 444:
-          ret = 445;
-          break;
-        case 452:
-          ret = 454;
-          break;
-        case 453:
-          ret = 454;
-          break;
-        case 455:
-          ret = 457;
-          break;
-        case 456:
-          ret = 457;
-          break;
-        case 458:
-          ret = 460;
-          break;
-        case 459:
-          ret = 460;
-          break;
-        case 461:
-          ret = 462;
-          break;
-        case 463:
-          ret = 464;
-          break;
-        case 465:
-          ret = 466;
-          break;
-        case 467:
-          ret = 468;
-          break;
-        case 469:
-          ret = 470;
-          break;
-        case 471:
-          ret = 472;
-          break;
-        case 473:
-          ret = 474;
-          break;
-        case 475:
-          ret = 476;
-          break;
-        case 478:
-          ret = 479;
-          break;
-        case 480:
-          ret = 481;
-          break;
-        case 482:
-          ret = 483;
-          break;
-        case 484:
-          ret = 485;
-          break;
-        case 486:
-          ret = 487;
-          break;
-        case 488:
-          ret = 489;
-          break;
-        case 490:
-          ret = 491;
-          break;
-        case 492:
-          ret = 493;
-          break;
-        case 494:
-          ret = 495;
-          break;
-        case 497:
-          ret = 499;
-          break;
-        case 498:
-          ret = 499;
-          break;
-        case 500:
-          ret = 501;
-          break;
-        case 506:
-          ret = 507;
-          break;
-        case 508:
-          ret = 509;
-          break;
-        case 510:
-          ret = 511;
-          break;
-        case 512:
-          ret = 513;
-          break;
-        case 514:
-          ret = 515;
-          break;
-        case 516:
-          ret = 517;
-          break;
-        case 518:
-          ret = 519;
-          break;
-        case 520:
-          ret = 521;
-          break;
-        case 522:
-          ret = 523;
-          break;
-        case 524:
-          ret = 525;
-          break;
-        case 526:
-          ret = 527;
-          break;
-        case 528:
-          ret = 529;
-          break;
-        case 530:
-          ret = 531;
-          break;
-        case 532:
-          ret = 533;
-          break;
-        case 534:
-          ret = 535;
-          break;
-        case 902:
-          ret = 940;
-          break;
-        case 904:
-          ret = 941;
-          break;
-        case 905:
-          ret = 942;
-          break;
-        case 906:
-          ret = 943;
-          break;
-        case 908:
-          ret = 972;
-          break;
-        case 910:
-          ret = 973;
-          break;
-        case 911:
-          ret = 974;
-          break;
-        case 913:
-          ret = 945;
-          break;
-        case 914:
-          ret = 946;
-          break;
-        case 915:
-          ret = 947;
-          break;
-        case 916:
-          ret = 948;
-          break;
-        case 917:
-          ret = 949;
-          break;
-        case 918:
-          ret = 950;
-          break;
-        case 919:
-          ret = 951;
-          break;
-        case 920:
-          ret = 952;
-          break;
-        case 921:
-          ret = 953;
-          break;
-        case 922:
-          ret = 954;
-          break;
-        case 923:
-          ret = 955;
-          break;
-        case 924:
-          ret = 956;
-          break;
-        case 925:
-          ret = 957;
-          break;
-        case 926:
-          ret = 958;
-          break;
-        case 927:
-          ret = 959;
-          break;
-        case 928:
-          ret = 960;
-          break;
-        case 929:
-          ret = 961;
-          break;
-        case 931:
-          ret = 963;
-          break;
-        case 932:
-          ret = 964;
-          break;
-        case 933:
-          ret = 965;
-          break;
-        case 934:
-          ret = 966;
-          break;
-        case 935:
-          ret = 967;
-          break;
-        case 936:
-          ret = 968;
-          break;
-        case 937:
-          ret = 969;
-          break;
-        case 938:
-          ret = 970;
-          break;
-        case 939:
-          ret = 971;
-          break;
-        case 994:
-          ret = 995;
-          break;
-        case 996:
-          ret = 997;
-          break;
-        case 998:
-          ret = 999;
-          break;
-        case 1000:
-          ret = 1001;
-          break;
-        case 1002:
-          ret = 1003;
-          break;
-        case 1004:
-          ret = 1005;
-          break;
-        case 1006:
-          ret = 1007;
-          break;
-        case 1025:
-          ret = 1105;
-          break;
-        case 1026:
-          ret = 1106;
-          break;
-        case 1027:
-          ret = 1107;
-          break;
-        case 1028:
-          ret = 1108;
-          break;
-        case 1029:
-          ret = 1109;
-          break;
-        case 1030:
-          ret = 1110;
-          break;
-        case 1031:
-          ret = 1111;
-          break;
-        case 1032:
-          ret = 1112;
-          break;
-        case 1033:
-          ret = 1113;
-          break;
-        case 1034:
-          ret = 1114;
-          break;
-        case 1035:
-          ret = 1115;
-          break;
-        case 1036:
-          ret = 1116;
-          break;
-        case 1038:
-          ret = 1118;
-          break;
-        case 1039:
-          ret = 1119;
-          break;
-        case 1040:
-          ret = 1072;
-          break;
-        case 1041:
-          ret = 1073;
-          break;
-        case 1042:
-          ret = 1074;
-          break;
-        case 1043:
-          ret = 1075;
-          break;
-        case 1044:
-          ret = 1076;
-          break;
-        case 1045:
-          ret = 1077;
-          break;
-        case 1046:
-          ret = 1078;
-          break;
-        case 1047:
-          ret = 1079;
-          break;
-        case 1048:
-          ret = 1080;
-          break;
-        case 1049:
-          ret = 1081;
-          break;
-        case 1050:
-          ret = 1082;
-          break;
-        case 1051:
-          ret = 1083;
-          break;
-        case 1052:
-          ret = 1084;
-          break;
-        case 1053:
-          ret = 1085;
-          break;
-        case 1054:
-          ret = 1086;
-          break;
-        case 1055:
-          ret = 1087;
-          break;
-        case 1056:
-          ret = 1088;
-          break;
-        case 1057:
-          ret = 1089;
-          break;
-        case 1058:
-          ret = 1090;
-          break;
-        case 1059:
-          ret = 1091;
-          break;
-        case 1060:
-          ret = 1092;
-          break;
-        case 1061:
-          ret = 1093;
-          break;
-        case 1062:
-          ret = 1094;
-          break;
-        case 1063:
-          ret = 1095;
-          break;
-        case 1064:
-          ret = 1096;
-          break;
-        case 1065:
-          ret = 1097;
-          break;
-        case 1066:
-          ret = 1098;
-          break;
-        case 1067:
-          ret = 1099;
-          break;
-        case 1068:
-          ret = 1100;
-          break;
-        case 1069:
-          ret = 1101;
-          break;
-        case 1070:
-          ret = 1102;
-          break;
-        case 1071:
-          ret = 1103;
-          break;
-        case 1120:
-          ret = 1121;
-          break;
-        case 1122:
-          ret = 1123;
-          break;
-        case 1124:
-          ret = 1125;
-          break;
-        case 1126:
-          ret = 1127;
-          break;
-        case 1128:
-          ret = 1129;
-          break;
-        case 1130:
-          ret = 1131;
-          break;
-        case 1132:
-          ret = 1133;
-          break;
-        case 1134:
-          ret = 1135;
-          break;
-        case 1136:
-          ret = 1137;
-          break;
-        case 1138:
-          ret = 1139;
-          break;
-        case 1140:
-          ret = 1141;
-          break;
-        case 1142:
-          ret = 1143;
-          break;
-        case 1144:
-          ret = 1145;
-          break;
-        case 1146:
-          ret = 1147;
-          break;
-        case 1148:
-          ret = 1149;
-          break;
-        case 1150:
-          ret = 1151;
-          break;
-        case 1152:
-          ret = 1153;
-          break;
-        case 1168:
-          ret = 1169;
-          break;
-        case 1170:
-          ret = 1171;
-          break;
-        case 1172:
-          ret = 1173;
-          break;
-        case 1174:
-          ret = 1175;
-          break;
-        case 1176:
-          ret = 1177;
-          break;
-        case 1178:
-          ret = 1179;
-          break;
-        case 1180:
-          ret = 1181;
-          break;
-        case 1182:
-          ret = 1183;
-          break;
-        case 1184:
-          ret = 1185;
-          break;
-        case 1186:
-          ret = 1187;
-          break;
-        case 1188:
-          ret = 1189;
-          break;
-        case 1190:
-          ret = 1191;
-          break;
-        case 1192:
-          ret = 1193;
-          break;
-        case 1194:
-          ret = 1195;
-          break;
-        case 1196:
-          ret = 1197;
-          break;
-        case 1198:
-          ret = 1199;
-          break;
-        case 1200:
-          ret = 1201;
-          break;
-        case 1202:
-          ret = 1203;
-          break;
-        case 1204:
-          ret = 1205;
-          break;
-        case 1206:
-          ret = 1207;
-          break;
-        case 1208:
-          ret = 1209;
-          break;
-        case 1210:
-          ret = 1211;
-          break;
-        case 1212:
-          ret = 1213;
-          break;
-        case 1214:
-          ret = 1215;
-          break;
-        case 1217:
-          ret = 1218;
-          break;
-        case 1219:
-          ret = 1220;
-          break;
-        case 1223:
-          ret = 1224;
-          break;
-        case 1227:
-          ret = 1228;
-          break;
-        case 1232:
-          ret = 1233;
-          break;
-        case 1234:
-          ret = 1235;
-          break;
-        case 1236:
-          ret = 1237;
-          break;
-        case 1238:
-          ret = 1239;
-          break;
-        case 1240:
-          ret = 1241;
-          break;
-        case 1242:
-          ret = 1243;
-          break;
-        case 1244:
-          ret = 1245;
-          break;
-        case 1246:
-          ret = 1247;
-          break;
-        case 1248:
-          ret = 1249;
-          break;
-        case 1250:
-          ret = 1251;
-          break;
-        case 1252:
-          ret = 1253;
-          break;
-        case 1254:
-          ret = 1255;
-          break;
-        case 1256:
-          ret = 1257;
-          break;
-        case 1258:
-          ret = 1259;
-          break;
-        case 1262:
-          ret = 1263;
-          break;
-        case 1264:
-          ret = 1265;
-          break;
-        case 1266:
-          ret = 1267;
-          break;
-        case 1268:
-          ret = 1269;
-          break;
-        case 1272:
-          ret = 1273;
-          break;
-        case 1329:
-          ret = 1377;
-          break;
-        case 1330:
-          ret = 1378;
-          break;
-        case 1331:
-          ret = 1379;
-          break;
-        case 1332:
-          ret = 1380;
-          break;
-        case 1333:
-          ret = 1381;
-          break;
-        case 1334:
-          ret = 1382;
-          break;
-        case 1335:
-          ret = 1383;
-          break;
-        case 1336:
-          ret = 1384;
-          break;
-        case 1337:
-          ret = 1385;
-          break;
-        case 1338:
-          ret = 1386;
-          break;
-        case 1339:
-          ret = 1387;
-          break;
-        case 1340:
-          ret = 1388;
-          break;
-        case 1341:
-          ret = 1389;
-          break;
-        case 1342:
-          ret = 1390;
-          break;
-        case 1343:
-          ret = 1391;
-          break;
-        case 1344:
-          ret = 1392;
-          break;
-        case 1345:
-          ret = 1393;
-          break;
-        case 1346:
-          ret = 1394;
-          break;
-        case 1347:
-          ret = 1395;
-          break;
-        case 1348:
-          ret = 1396;
-          break;
-        case 1349:
-          ret = 1397;
-          break;
-        case 1350:
-          ret = 1398;
-          break;
-        case 1351:
-          ret = 1399;
-          break;
-        case 1352:
-          ret = 1400;
-          break;
-        case 1353:
-          ret = 1401;
-          break;
-        case 1354:
-          ret = 1402;
-          break;
-        case 1355:
-          ret = 1403;
-          break;
-        case 1356:
-          ret = 1404;
-          break;
-        case 1357:
-          ret = 1405;
-          break;
-        case 1358:
-          ret = 1406;
-          break;
-        case 1359:
-          ret = 1407;
-          break;
-        case 1360:
-          ret = 1408;
-          break;
-        case 1361:
-          ret = 1409;
-          break;
-        case 1362:
-          ret = 1410;
-          break;
-        case 1363:
-          ret = 1411;
-          break;
-        case 1364:
-          ret = 1412;
-          break;
-        case 1365:
-          ret = 1413;
-          break;
-        case 1366:
-          ret = 1414;
-          break;
-        case 4256:
-          ret = 4304;
-          break;
-        case 4257:
-          ret = 4305;
-          break;
-        case 4258:
-          ret = 4306;
-          break;
-        case 4259:
-          ret = 4307;
-          break;
-        case 4260:
-          ret = 4308;
-          break;
-        case 4261:
-          ret = 4309;
-          break;
-        case 4262:
-          ret = 4310;
-          break;
-        case 4263:
-          ret = 4311;
-          break;
-        case 4264:
-          ret = 4312;
-          break;
-        case 4265:
-          ret = 4313;
-          break;
-        case 4266:
-          ret = 4314;
-          break;
-        case 4267:
-          ret = 4315;
-          break;
-        case 4268:
-          ret = 4316;
-          break;
-        case 4269:
-          ret = 4317;
-          break;
-        case 4270:
-          ret = 4318;
-          break;
-        case 4271:
-          ret = 4319;
-          break;
-        case 4272:
-          ret = 4320;
-          break;
-        case 4273:
-          ret = 4321;
-          break;
-        case 4274:
-          ret = 4322;
-          break;
-        case 4275:
-          ret = 4323;
-          break;
-        case 4276:
-          ret = 4324;
-          break;
-        case 4277:
-          ret = 4325;
-          break;
-        case 4278:
-          ret = 4326;
-          break;
-        case 4279:
-          ret = 4327;
-          break;
-        case 4280:
-          ret = 4328;
-          break;
-        case 4281:
-          ret = 4329;
-          break;
-        case 4282:
-          ret = 4330;
-          break;
-        case 4283:
-          ret = 4331;
-          break;
-        case 4284:
-          ret = 4332;
-          break;
-        case 4285:
-          ret = 4333;
-          break;
-        case 4286:
-          ret = 4334;
-          break;
-        case 4287:
-          ret = 4335;
-          break;
-        case 4288:
-          ret = 4336;
-          break;
-        case 4289:
-          ret = 4337;
-          break;
-        case 4290:
-          ret = 4338;
-          break;
-        case 4291:
-          ret = 4339;
-          break;
-        case 4292:
-          ret = 4340;
-          break;
-        case 4293:
-          ret = 4341;
-          break;
-        case 7680:
-          ret = 7681;
-          break;
-        case 7682:
-          ret = 7683;
-          break;
-        case 7684:
-          ret = 7685;
-          break;
-        case 7686:
-          ret = 7687;
-          break;
-        case 7688:
-          ret = 7689;
-          break;
-        case 7690:
-          ret = 7691;
-          break;
-        case 7692:
-          ret = 7693;
-          break;
-        case 7694:
-          ret = 7695;
-          break;
-        case 7696:
-          ret = 7697;
-          break;
-        case 7698:
-          ret = 7699;
-          break;
-        case 7700:
-          ret = 7701;
-          break;
-        case 7702:
-          ret = 7703;
-          break;
-        case 7704:
-          ret = 7705;
-          break;
-        case 7706:
-          ret = 7707;
-          break;
-        case 7708:
-          ret = 7709;
-          break;
-        case 7710:
-          ret = 7711;
-          break;
-        case 7712:
-          ret = 7713;
-          break;
-        case 7714:
-          ret = 7715;
-          break;
-        case 7716:
-          ret = 7717;
-          break;
-        case 7718:
-          ret = 7719;
-          break;
-        case 7720:
-          ret = 7721;
-          break;
-        case 7722:
-          ret = 7723;
-          break;
-        case 7724:
-          ret = 7725;
-          break;
-        case 7726:
-          ret = 7727;
-          break;
-        case 7728:
-          ret = 7729;
-          break;
-        case 7730:
-          ret = 7731;
-          break;
-        case 7732:
-          ret = 7733;
-          break;
-        case 7734:
-          ret = 7735;
-          break;
-        case 7736:
-          ret = 7737;
-          break;
-        case 7738:
-          ret = 7739;
-          break;
-        case 7740:
-          ret = 7741;
-          break;
-        case 7742:
-          ret = 7743;
-          break;
-        case 7744:
-          ret = 7745;
-          break;
-        case 7746:
-          ret = 7747;
-          break;
-        case 7748:
-          ret = 7749;
-          break;
-        case 7750:
-          ret = 7751;
-          break;
-        case 7752:
-          ret = 7753;
-          break;
-        case 7754:
-          ret = 7755;
-          break;
-        case 7756:
-          ret = 7757;
-          break;
-        case 7758:
-          ret = 7759;
-          break;
-        case 7760:
-          ret = 7761;
-          break;
-        case 7762:
-          ret = 7763;
-          break;
-        case 7764:
-          ret = 7765;
-          break;
-        case 7766:
-          ret = 7767;
-          break;
-        case 7768:
-          ret = 7769;
-          break;
-        case 7770:
-          ret = 7771;
-          break;
-        case 7772:
-          ret = 7773;
-          break;
-        case 7774:
-          ret = 7775;
-          break;
-        case 7776:
-          ret = 7777;
-          break;
-        case 7778:
-          ret = 7779;
-          break;
-        case 7780:
-          ret = 7781;
-          break;
-        case 7782:
-          ret = 7783;
-          break;
-        case 7784:
-          ret = 7785;
-          break;
-        case 7786:
-          ret = 7787;
-          break;
-        case 7788:
-          ret = 7789;
-          break;
-        case 7790:
-          ret = 7791;
-          break;
-        case 7792:
-          ret = 7793;
-          break;
-        case 7794:
-          ret = 7795;
-          break;
-        case 7796:
-          ret = 7797;
-          break;
-        case 7798:
-          ret = 7799;
-          break;
-        case 7800:
-          ret = 7801;
-          break;
-        case 7802:
-          ret = 7803;
-          break;
-        case 7804:
-          ret = 7805;
-          break;
-        case 7806:
-          ret = 7807;
-          break;
-        case 7808:
-          ret = 7809;
-          break;
-        case 7810:
-          ret = 7811;
-          break;
-        case 7812:
-          ret = 7813;
-          break;
-        case 7814:
-          ret = 7815;
-          break;
-        case 7816:
-          ret = 7817;
-          break;
-        case 7818:
-          ret = 7819;
-          break;
-        case 7820:
-          ret = 7821;
-          break;
-        case 7822:
-          ret = 7823;
-          break;
-        case 7824:
-          ret = 7825;
-          break;
-        case 7826:
-          ret = 7827;
-          break;
-        case 7828:
-          ret = 7829;
-          break;
-        case 7840:
-          ret = 7841;
-          break;
-        case 7842:
-          ret = 7843;
-          break;
-        case 7844:
-          ret = 7845;
-          break;
-        case 7846:
-          ret = 7847;
-          break;
-        case 7848:
-          ret = 7849;
-          break;
-        case 7850:
-          ret = 7851;
-          break;
-        case 7852:
-          ret = 7853;
-          break;
-        case 7854:
-          ret = 7855;
-          break;
-        case 7856:
-          ret = 7857;
-          break;
-        case 7858:
-          ret = 7859;
-          break;
-        case 7860:
-          ret = 7861;
-          break;
-        case 7862:
-          ret = 7863;
-          break;
-        case 7864:
-          ret = 7865;
-          break;
-        case 7866:
-          ret = 7867;
-          break;
-        case 7868:
-          ret = 7869;
-          break;
-        case 7870:
-          ret = 7871;
-          break;
-        case 7872:
-          ret = 7873;
-          break;
-        case 7874:
-          ret = 7875;
-          break;
-        case 7876:
-          ret = 7877;
-          break;
-        case 7878:
-          ret = 7879;
-          break;
-        case 7880:
-          ret = 7881;
-          break;
-        case 7882:
-          ret = 7883;
-          break;
-        case 7884:
-          ret = 7885;
-          break;
-        case 7886:
-          ret = 7887;
-          break;
-        case 7888:
-          ret = 7889;
-          break;
-        case 7890:
-          ret = 7891;
-          break;
-        case 7892:
-          ret = 7893;
-          break;
-        case 7894:
-          ret = 7895;
-          break;
-        case 7896:
-          ret = 7897;
-          break;
-        case 7898:
-          ret = 7899;
-          break;
-        case 7900:
-          ret = 7901;
-          break;
-        case 7902:
-          ret = 7903;
-          break;
-        case 7904:
-          ret = 7905;
-          break;
-        case 7906:
-          ret = 7907;
-          break;
-        case 7908:
-          ret = 7909;
-          break;
-        case 7910:
-          ret = 7911;
-          break;
-        case 7912:
-          ret = 7913;
-          break;
-        case 7914:
-          ret = 7915;
-          break;
-        case 7916:
-          ret = 7917;
-          break;
-        case 7918:
-          ret = 7919;
-          break;
-        case 7920:
-          ret = 7921;
-          break;
-        case 7922:
-          ret = 7923;
-          break;
-        case 7924:
-          ret = 7925;
-          break;
-        case 7926:
-          ret = 7927;
-          break;
-        case 7928:
-          ret = 7929;
-          break;
-        case 7944:
-          ret = 7936;
-          break;
-        case 7945:
-          ret = 7937;
-          break;
-        case 7946:
-          ret = 7938;
-          break;
-        case 7947:
-          ret = 7939;
-          break;
-        case 7948:
-          ret = 7940;
-          break;
-        case 7949:
-          ret = 7941;
-          break;
-        case 7950:
-          ret = 7942;
-          break;
-        case 7951:
-          ret = 7943;
-          break;
-        case 7960:
-          ret = 7952;
-          break;
-        case 7961:
-          ret = 7953;
-          break;
-        case 7962:
-          ret = 7954;
-          break;
-        case 7963:
-          ret = 7955;
-          break;
-        case 7964:
-          ret = 7956;
-          break;
-        case 7965:
-          ret = 7957;
-          break;
-        case 7976:
-          ret = 7968;
-          break;
-        case 7977:
-          ret = 7969;
-          break;
-        case 7978:
-          ret = 7970;
-          break;
-        case 7979:
-          ret = 7971;
-          break;
-        case 7980:
-          ret = 7972;
-          break;
-        case 7981:
-          ret = 7973;
-          break;
-        case 7982:
-          ret = 7974;
-          break;
-        case 7983:
-          ret = 7975;
-          break;
-        case 7992:
-          ret = 7984;
-          break;
-        case 7993:
-          ret = 7985;
-          break;
-        case 7994:
-          ret = 7986;
-          break;
-        case 7995:
-          ret = 7987;
-          break;
-        case 7996:
-          ret = 7988;
-          break;
-        case 7997:
-          ret = 7989;
-          break;
-        case 7998:
-          ret = 7990;
-          break;
-        case 7999:
-          ret = 7991;
-          break;
-        case 8008:
-          ret = 8000;
-          break;
-        case 8009:
-          ret = 8001;
-          break;
-        case 8010:
-          ret = 8002;
-          break;
-        case 8011:
-          ret = 8003;
-          break;
-        case 8012:
-          ret = 8004;
-          break;
-        case 8013:
-          ret = 8005;
-          break;
-        case 8025:
-          ret = 8017;
-          break;
-        case 8027:
-          ret = 8019;
-          break;
-        case 8029:
-          ret = 8021;
-          break;
-        case 8031:
-          ret = 8023;
-          break;
-        case 8040:
-          ret = 8032;
-          break;
-        case 8041:
-          ret = 8033;
-          break;
-        case 8042:
-          ret = 8034;
-          break;
-        case 8043:
-          ret = 8035;
-          break;
-        case 8044:
-          ret = 8036;
-          break;
-        case 8045:
-          ret = 8037;
-          break;
-        case 8046:
-          ret = 8038;
-          break;
-        case 8047:
-          ret = 8039;
-          break;
-        case 8072:
-          ret = 8064;
-          break;
-        case 8073:
-          ret = 8065;
-          break;
-        case 8074:
-          ret = 8066;
-          break;
-        case 8075:
-          ret = 8067;
-          break;
-        case 8076:
-          ret = 8068;
-          break;
-        case 8077:
-          ret = 8069;
-          break;
-        case 8078:
-          ret = 8070;
-          break;
-        case 8079:
-          ret = 8071;
-          break;
-        case 8088:
-          ret = 8080;
-          break;
-        case 8089:
-          ret = 8081;
-          break;
-        case 8090:
-          ret = 8082;
-          break;
-        case 8091:
-          ret = 8083;
-          break;
-        case 8092:
-          ret = 8084;
-          break;
-        case 8093:
-          ret = 8085;
-          break;
-        case 8094:
-          ret = 8086;
-          break;
-        case 8095:
-          ret = 8087;
-          break;
-        case 8104:
-          ret = 8096;
-          break;
-        case 8105:
-          ret = 8097;
-          break;
-        case 8106:
-          ret = 8098;
-          break;
-        case 8107:
-          ret = 8099;
-          break;
-        case 8108:
-          ret = 8100;
-          break;
-        case 8109:
-          ret = 8101;
-          break;
-        case 8110:
-          ret = 8102;
-          break;
-        case 8111:
-          ret = 8103;
-          break;
-        case 8120:
-          ret = 8112;
-          break;
-        case 8121:
-          ret = 8113;
-          break;
-        case 8122:
-          ret = 8048;
-          break;
-        case 8123:
-          ret = 8049;
-          break;
-        case 8124:
-          ret = 8115;
-          break;
-        case 8136:
-          ret = 8050;
-          break;
-        case 8137:
-          ret = 8051;
-          break;
-        case 8138:
-          ret = 8052;
-          break;
-        case 8139:
-          ret = 8053;
-          break;
-        case 8140:
-          ret = 8131;
-          break;
-        case 8152:
-          ret = 8144;
-          break;
-        case 8153:
-          ret = 8145;
-          break;
-        case 8154:
-          ret = 8054;
-          break;
-        case 8155:
-          ret = 8055;
-          break;
-        case 8168:
-          ret = 8160;
-          break;
-        case 8169:
-          ret = 8161;
-          break;
-        case 8170:
-          ret = 8058;
-          break;
-        case 8171:
-          ret = 8059;
-          break;
-        case 8172:
-          ret = 8165;
-          break;
-        case 8184:
-          ret = 8056;
-          break;
-        case 8185:
-          ret = 8057;
-          break;
-        case 8186:
-          ret = 8060;
-          break;
-        case 8187:
-          ret = 8061;
-          break;
-        case 8188:
-          ret = 8179;
-          break;
-        case 8544:
-          ret = 8560;
-          break;
-        case 8545:
-          ret = 8561;
-          break;
-        case 8546:
-          ret = 8562;
-          break;
-        case 8547:
-          ret = 8563;
-          break;
-        case 8548:
-          ret = 8564;
-          break;
-        case 8549:
-          ret = 8565;
-          break;
-        case 8550:
-          ret = 8566;
-          break;
-        case 8551:
-          ret = 8567;
-          break;
-        case 8552:
-          ret = 8568;
-          break;
-        case 8553:
-          ret = 8569;
-          break;
-        case 8554:
-          ret = 8570;
-          break;
-        case 8555:
-          ret = 8571;
-          break;
-        case 8556:
-          ret = 8572;
-          break;
-        case 8557:
-          ret = 8573;
-          break;
-        case 8558:
-          ret = 8574;
-          break;
-        case 8559:
-          ret = 8575;
-          break;
-        case 9398:
-          ret = 9424;
-          break;
-        case 9399:
-          ret = 9425;
-          break;
-        case 9400:
-          ret = 9426;
-          break;
-        case 9401:
-          ret = 9427;
-          break;
-        case 9402:
-          ret = 9428;
-          break;
-        case 9403:
-          ret = 9429;
-          break;
-        case 9404:
-          ret = 9430;
-          break;
-        case 9405:
-          ret = 9431;
-          break;
-        case 9406:
-          ret = 9432;
-          break;
-        case 9407:
-          ret = 9433;
-          break;
-        case 9408:
-          ret = 9434;
-          break;
-        case 9409:
-          ret = 9435;
-          break;
-        case 9410:
-          ret = 9436;
-          break;
-        case 9411:
-          ret = 9437;
-          break;
-        case 9412:
-          ret = 9438;
-          break;
-        case 9413:
-          ret = 9439;
-          break;
-        case 9414:
-          ret = 9440;
-          break;
-        case 9415:
-          ret = 9441;
-          break;
-        case 9416:
-          ret = 9442;
-          break;
-        case 9417:
-          ret = 9443;
-          break;
-        case 9418:
-          ret = 9444;
-          break;
-        case 9419:
-          ret = 9445;
-          break;
-        case 9420:
-          ret = 9446;
-          break;
-        case 9421:
-          ret = 9447;
-          break;
-        case 9422:
-          ret = 9448;
-          break;
-        case 9423:
-          ret = 9449;
-          break;
-        case 65313:
-          ret = 65345;
-          break;
-        case 65314:
-          ret = 65346;
-          break;
-        case 65315:
-          ret = 65347;
-          break;
-        case 65316:
-          ret = 65348;
-          break;
-        case 65317:
-          ret = 65349;
-          break;
-        case 65318:
-          ret = 65350;
-          break;
-        case 65319:
-          ret = 65351;
-          break;
-        case 65320:
-          ret = 65352;
-          break;
-        case 65321:
-          ret = 65353;
-          break;
-        case 65322:
-          ret = 65354;
-          break;
-        case 65323:
-          ret = 65355;
-          break;
-        case 65324:
-          ret = 65356;
-          break;
-        case 65325:
-          ret = 65357;
-          break;
-        case 65326:
-          ret = 65358;
-          break;
-        case 65327:
-          ret = 65359;
-          break;
-        case 65328:
-          ret = 65360;
-          break;
-        case 65329:
-          ret = 65361;
-          break;
-        case 65330:
-          ret = 65362;
-          break;
-        case 65331:
-          ret = 65363;
-          break;
-        case 65332:
-          ret = 65364;
-          break;
-        case 65333:
-          ret = 65365;
-          break;
-        case 65334:
-          ret = 65366;
-          break;
-        case 65335:
-          ret = 65367;
-          break;
-        case 65336:
-          ret = 65368;
-          break;
-        case 65337:
-          ret = 65369;
-          break;
-        case 65338:
-          ret = 65370;
-          break;
-      }
-      return (char) ret;
-    }
-    return Character.toLowerCase(c);
-  }
-
-  /** Convert a String to title case. */
-  public static String toTitleCase(String s)
-  {
-    StringBuffer sb = new StringBuffer();
-    for (int i = 0; i < s.length(); i++)
-    {
-      sb.append(CaseMgr.toTitleCase(s.charAt(i)));
-    }
-    return sb.toString();
-  }
-
-  /** Convert a String to upper case. */
-  public static String toUpperCase(String s)
-  {
-    StringBuffer sb = new StringBuffer();
-    for (int i = 0; i < s.length(); i++)
-    {
-      sb.append(CaseMgr.toUpperCase(s.charAt(i)));
-    }
-    return sb.toString();
-  }
-
-  /** Convert a String to lower case. */
-  public static String toLowerCase(String s)
-  {
-    StringBuffer sb = new StringBuffer();
-    for (int i = 0; i < s.length(); i++)
-    {
-      sb.append(CaseMgr.toLowerCase(s.charAt(i)));
-    }
-    return sb.toString();
-  }
-
-  /** Convert a character to title case.*/
-  public static char toTitleCase(char c)
-  {
-    if (java_1_0)
-    {
-      int ret = (int) toUpperCase(c);
-      switch (c)
-      {
-        case 452:
-          ret = 453;
-          break;
-        case 453:
-          ret = 453;
-          break;
-        case 454:
-          ret = 453;
-          break;
-        case 455:
-          ret = 456;
-          break;
-        case 456:
-          ret = 456;
-          break;
-        case 457:
-          ret = 456;
-          break;
-        case 458:
-          ret = 459;
-          break;
-        case 459:
-          ret = 459;
-          break;
-        case 460:
-          ret = 459;
-          break;
-        case 497:
-          ret = 498;
-          break;
-        case 498:
-          ret = 498;
-          break;
-        case 499:
-          ret = 498;
-          break;
-      }
-      return (char) ret;
-    }
-    return Character.toTitleCase(c);
-  }
-
-  /** Duplicates the regionMatches routine of String -- but
-      makes use of the definitions of upper, lower, and title
-      case in this class when ignoreCase is set. */
-  public static boolean regionMatches(StringLike s1,
-                                      boolean ign, int i1, StringLike s2,
-                                      int i2, int i3)
-  {
-    int itot = i2 + i3;
-    if (itot > s2.length() || i1 + i3 > s1.length())
-    {
-      return false;
-    }
-    if (!ign)
-    {
-      for (int i = i2; i < itot; i++)
-      {
-        if (s2.charAt(i) != s1.charAt(i1++))
-        {
-          return false;
-        }
-      }
-    }
-    else
-    {
-      for (int i = i2; i < itot; i++)
-      {
-        if (toLowerCase(s2.charAt(i)) != toLowerCase(s1.charAt(i1++)))
-        {
-          return false;
-        }
-      }
-    }
-    return true;
-  }
-
-  /** Duplicates the regionMatches routine of String -- but
-      makes use of the definitions of upper, lower, and title
-      case in this class when ignoreCase is set. */
-  public static boolean regionMatches(String s1,
-                                      boolean ign, int i1, StringLike s2,
-                                      int i2, int i3)
-  {
-    int itot = i2 + i3;
-    if (itot > s2.length() || i1 + i3 > s1.length())
-    {
-      return false;
-    }
-    if (!ign)
-    {
-      for (int i = i2; i < itot; i++)
-      {
-        if (s2.charAt(i) != s1.charAt(i1++))
-        {
-          return false;
-        }
-      }
-    }
-    else
-    {
-      for (int i = i2; i < itot; i++)
-      {
-        if (toLowerCase(s2.charAt(i)) != toLowerCase(s1.charAt(i1++)))
-        {
-          return false;
-        }
-      }
-    }
-    return true;
-  }
-
-  /** Duplicates the regionMatches routine of String -- but
-      makes use of the definitions of upper, lower, and title
-      case in this class when ignoreCase is set. */
-  public static boolean regionMatches(StringLike s1,
-                                      boolean ign, int i1, String s2, int i2,
-                                      int i3)
-  {
-    int itot = i2 + i3;
-    if (itot > s2.length() || i1 + i3 > s1.length())
-    {
-      return false;
-    }
-    if (!ign)
-    {
-      for (int i = i2; i < itot; i++)
-      {
-        if (s2.charAt(i) != s1.charAt(i1++))
-        {
-          return false;
-        }
-      }
-    }
-    else
-    {
-      for (int i = i2; i < itot; i++)
-      {
-        if (toLowerCase(s2.charAt(i)) != toLowerCase(s1.charAt(i1++)))
-        {
-          return false;
-        }
-      }
-    }
-    return true;
-  }
-
-  /** Duplicates the regionMatches routine of String -- but
-      makes use of the definitions of upper, lower, and title
-      case in this class when ignoreCase is set. */
-  public static boolean regionMatches(String s1,
-                                      boolean ign, int i1, String s2, int i2,
-                                      int i3)
-  {
-    int itot = i2 + i3;
-    if (itot > s2.length() || i1 + i3 > s1.length())
-    {
-      return false;
-    }
-    if (!ign)
-    {
-      for (int i = i2; i < itot; i++)
-      {
-        if (s2.charAt(i) != s1.charAt(i1++))
-        {
-          return false;
-        }
-      }
-    }
-    else
-    {
-      for (int i = i2; i < itot; i++)
-      {
-        if (toLowerCase(s2.charAt(i)) != toLowerCase(s1.charAt(i1++)))
-        {
-          return false;
-        }
-      }
-    }
-    return true;
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+/**
+ * Encapsulates the Unicode definitions of Upper, Lower, and Title case as
+ * defined by <a href="http://www.unicode.org"> unicode.org</a>.
+ * <p>
+ * The performance of the methods found in String and Character is better, but
+ * these methods work both in java 1.0 and 1.1. If it is desirable, either to
+ * gain a slight performance increase or to accomodate application specific
+ * modifications to the definitions of upper, lower, and title case then it
+ * should be a straightforward task to substitute your own methods for these.
+ */
+final public class CaseMgr
+{
+  final static boolean java_1_0 = false;
+
+  /** Convert a character to upper case . */
+  public static char toUpperCase(char c)
+  {
+    if (java_1_0)
+    {
+      int ret = (int) c;
+      switch (c)
+      {
+      case 97:
+        ret = 65;
+        break;
+      case 98:
+        ret = 66;
+        break;
+      case 99:
+        ret = 67;
+        break;
+      case 100:
+        ret = 68;
+        break;
+      case 101:
+        ret = 69;
+        break;
+      case 102:
+        ret = 70;
+        break;
+      case 103:
+        ret = 71;
+        break;
+      case 104:
+        ret = 72;
+        break;
+      case 105:
+        ret = 73;
+        break;
+      case 106:
+        ret = 74;
+        break;
+      case 107:
+        ret = 75;
+        break;
+      case 108:
+        ret = 76;
+        break;
+      case 109:
+        ret = 77;
+        break;
+      case 110:
+        ret = 78;
+        break;
+      case 111:
+        ret = 79;
+        break;
+      case 112:
+        ret = 80;
+        break;
+      case 113:
+        ret = 81;
+        break;
+      case 114:
+        ret = 82;
+        break;
+      case 115:
+        ret = 83;
+        break;
+      case 116:
+        ret = 84;
+        break;
+      case 117:
+        ret = 85;
+        break;
+      case 118:
+        ret = 86;
+        break;
+      case 119:
+        ret = 87;
+        break;
+      case 120:
+        ret = 88;
+        break;
+      case 121:
+        ret = 89;
+        break;
+      case 122:
+        ret = 90;
+        break;
+      case 224:
+        ret = 192;
+        break;
+      case 225:
+        ret = 193;
+        break;
+      case 226:
+        ret = 194;
+        break;
+      case 227:
+        ret = 195;
+        break;
+      case 228:
+        ret = 196;
+        break;
+      case 229:
+        ret = 197;
+        break;
+      case 230:
+        ret = 198;
+        break;
+      case 231:
+        ret = 199;
+        break;
+      case 232:
+        ret = 200;
+        break;
+      case 233:
+        ret = 201;
+        break;
+      case 234:
+        ret = 202;
+        break;
+      case 235:
+        ret = 203;
+        break;
+      case 236:
+        ret = 204;
+        break;
+      case 237:
+        ret = 205;
+        break;
+      case 238:
+        ret = 206;
+        break;
+      case 239:
+        ret = 207;
+        break;
+      case 240:
+        ret = 208;
+        break;
+      case 241:
+        ret = 209;
+        break;
+      case 242:
+        ret = 210;
+        break;
+      case 243:
+        ret = 211;
+        break;
+      case 244:
+        ret = 212;
+        break;
+      case 245:
+        ret = 213;
+        break;
+      case 246:
+        ret = 214;
+        break;
+      case 248:
+        ret = 216;
+        break;
+      case 249:
+        ret = 217;
+        break;
+      case 250:
+        ret = 218;
+        break;
+      case 251:
+        ret = 219;
+        break;
+      case 252:
+        ret = 220;
+        break;
+      case 253:
+        ret = 221;
+        break;
+      case 254:
+        ret = 222;
+        break;
+      case 255:
+        ret = 376;
+        break;
+      case 257:
+        ret = 256;
+        break;
+      case 259:
+        ret = 258;
+        break;
+      case 261:
+        ret = 260;
+        break;
+      case 263:
+        ret = 262;
+        break;
+      case 265:
+        ret = 264;
+        break;
+      case 267:
+        ret = 266;
+        break;
+      case 269:
+        ret = 268;
+        break;
+      case 271:
+        ret = 270;
+        break;
+      case 273:
+        ret = 272;
+        break;
+      case 275:
+        ret = 274;
+        break;
+      case 277:
+        ret = 276;
+        break;
+      case 279:
+        ret = 278;
+        break;
+      case 281:
+        ret = 280;
+        break;
+      case 283:
+        ret = 282;
+        break;
+      case 285:
+        ret = 284;
+        break;
+      case 287:
+        ret = 286;
+        break;
+      case 289:
+        ret = 288;
+        break;
+      case 291:
+        ret = 290;
+        break;
+      case 293:
+        ret = 292;
+        break;
+      case 295:
+        ret = 294;
+        break;
+      case 297:
+        ret = 296;
+        break;
+      case 299:
+        ret = 298;
+        break;
+      case 301:
+        ret = 300;
+        break;
+      case 303:
+        ret = 302;
+        break;
+      case 305:
+        ret = 73;
+        break;
+      case 307:
+        ret = 306;
+        break;
+      case 309:
+        ret = 308;
+        break;
+      case 311:
+        ret = 310;
+        break;
+      case 314:
+        ret = 313;
+        break;
+      case 316:
+        ret = 315;
+        break;
+      case 318:
+        ret = 317;
+        break;
+      case 320:
+        ret = 319;
+        break;
+      case 322:
+        ret = 321;
+        break;
+      case 324:
+        ret = 323;
+        break;
+      case 326:
+        ret = 325;
+        break;
+      case 328:
+        ret = 327;
+        break;
+      case 331:
+        ret = 330;
+        break;
+      case 333:
+        ret = 332;
+        break;
+      case 335:
+        ret = 334;
+        break;
+      case 337:
+        ret = 336;
+        break;
+      case 339:
+        ret = 338;
+        break;
+      case 341:
+        ret = 340;
+        break;
+      case 343:
+        ret = 342;
+        break;
+      case 345:
+        ret = 344;
+        break;
+      case 347:
+        ret = 346;
+        break;
+      case 349:
+        ret = 348;
+        break;
+      case 351:
+        ret = 350;
+        break;
+      case 353:
+        ret = 352;
+        break;
+      case 355:
+        ret = 354;
+        break;
+      case 357:
+        ret = 356;
+        break;
+      case 359:
+        ret = 358;
+        break;
+      case 361:
+        ret = 360;
+        break;
+      case 363:
+        ret = 362;
+        break;
+      case 365:
+        ret = 364;
+        break;
+      case 367:
+        ret = 366;
+        break;
+      case 369:
+        ret = 368;
+        break;
+      case 371:
+        ret = 370;
+        break;
+      case 373:
+        ret = 372;
+        break;
+      case 375:
+        ret = 374;
+        break;
+      case 378:
+        ret = 377;
+        break;
+      case 380:
+        ret = 379;
+        break;
+      case 382:
+        ret = 381;
+        break;
+      case 383:
+        ret = 83;
+        break;
+      case 387:
+        ret = 386;
+        break;
+      case 389:
+        ret = 388;
+        break;
+      case 392:
+        ret = 391;
+        break;
+      case 396:
+        ret = 395;
+        break;
+      case 402:
+        ret = 401;
+        break;
+      case 409:
+        ret = 408;
+        break;
+      case 417:
+        ret = 416;
+        break;
+      case 419:
+        ret = 418;
+        break;
+      case 421:
+        ret = 420;
+        break;
+      case 424:
+        ret = 423;
+        break;
+      case 429:
+        ret = 428;
+        break;
+      case 432:
+        ret = 431;
+        break;
+      case 436:
+        ret = 435;
+        break;
+      case 438:
+        ret = 437;
+        break;
+      case 441:
+        ret = 440;
+        break;
+      case 445:
+        ret = 444;
+        break;
+      case 453:
+        ret = 452;
+        break;
+      case 454:
+        ret = 452;
+        break;
+      case 456:
+        ret = 455;
+        break;
+      case 457:
+        ret = 455;
+        break;
+      case 459:
+        ret = 458;
+        break;
+      case 460:
+        ret = 458;
+        break;
+      case 462:
+        ret = 461;
+        break;
+      case 464:
+        ret = 463;
+        break;
+      case 466:
+        ret = 465;
+        break;
+      case 468:
+        ret = 467;
+        break;
+      case 470:
+        ret = 469;
+        break;
+      case 472:
+        ret = 471;
+        break;
+      case 474:
+        ret = 473;
+        break;
+      case 476:
+        ret = 475;
+        break;
+      case 479:
+        ret = 478;
+        break;
+      case 481:
+        ret = 480;
+        break;
+      case 483:
+        ret = 482;
+        break;
+      case 485:
+        ret = 484;
+        break;
+      case 487:
+        ret = 486;
+        break;
+      case 489:
+        ret = 488;
+        break;
+      case 491:
+        ret = 490;
+        break;
+      case 493:
+        ret = 492;
+        break;
+      case 495:
+        ret = 494;
+        break;
+      case 498:
+        ret = 497;
+        break;
+      case 499:
+        ret = 497;
+        break;
+      case 501:
+        ret = 500;
+        break;
+      case 507:
+        ret = 506;
+        break;
+      case 509:
+        ret = 508;
+        break;
+      case 511:
+        ret = 510;
+        break;
+      case 513:
+        ret = 512;
+        break;
+      case 515:
+        ret = 514;
+        break;
+      case 517:
+        ret = 516;
+        break;
+      case 519:
+        ret = 518;
+        break;
+      case 521:
+        ret = 520;
+        break;
+      case 523:
+        ret = 522;
+        break;
+      case 525:
+        ret = 524;
+        break;
+      case 527:
+        ret = 526;
+        break;
+      case 529:
+        ret = 528;
+        break;
+      case 531:
+        ret = 530;
+        break;
+      case 533:
+        ret = 532;
+        break;
+      case 535:
+        ret = 534;
+        break;
+      case 595:
+        ret = 385;
+        break;
+      case 596:
+        ret = 390;
+        break;
+      case 598:
+        ret = 393;
+        break;
+      case 599:
+        ret = 394;
+        break;
+      case 600:
+        ret = 398;
+        break;
+      case 601:
+        ret = 399;
+        break;
+      case 603:
+        ret = 400;
+        break;
+      case 608:
+        ret = 403;
+        break;
+      case 611:
+        ret = 404;
+        break;
+      case 616:
+        ret = 407;
+        break;
+      case 617:
+        ret = 406;
+        break;
+      case 623:
+        ret = 412;
+        break;
+      case 626:
+        ret = 413;
+        break;
+      case 643:
+        ret = 425;
+        break;
+      case 648:
+        ret = 430;
+        break;
+      case 650:
+        ret = 433;
+        break;
+      case 651:
+        ret = 434;
+        break;
+      case 658:
+        ret = 439;
+        break;
+      case 940:
+        ret = 902;
+        break;
+      case 941:
+        ret = 904;
+        break;
+      case 942:
+        ret = 905;
+        break;
+      case 943:
+        ret = 906;
+        break;
+      case 945:
+        ret = 913;
+        break;
+      case 946:
+        ret = 914;
+        break;
+      case 947:
+        ret = 915;
+        break;
+      case 948:
+        ret = 916;
+        break;
+      case 949:
+        ret = 917;
+        break;
+      case 950:
+        ret = 918;
+        break;
+      case 951:
+        ret = 919;
+        break;
+      case 952:
+        ret = 920;
+        break;
+      case 953:
+        ret = 921;
+        break;
+      case 954:
+        ret = 922;
+        break;
+      case 955:
+        ret = 923;
+        break;
+      case 956:
+        ret = 924;
+        break;
+      case 957:
+        ret = 925;
+        break;
+      case 958:
+        ret = 926;
+        break;
+      case 959:
+        ret = 927;
+        break;
+      case 960:
+        ret = 928;
+        break;
+      case 961:
+        ret = 929;
+        break;
+      case 963:
+        ret = 931;
+        break;
+      case 964:
+        ret = 932;
+        break;
+      case 965:
+        ret = 933;
+        break;
+      case 966:
+        ret = 934;
+        break;
+      case 967:
+        ret = 935;
+        break;
+      case 968:
+        ret = 936;
+        break;
+      case 969:
+        ret = 937;
+        break;
+      case 970:
+        ret = 938;
+        break;
+      case 971:
+        ret = 939;
+        break;
+      case 972:
+        ret = 908;
+        break;
+      case 973:
+        ret = 910;
+        break;
+      case 974:
+        ret = 911;
+        break;
+      case 976:
+        ret = 914;
+        break;
+      case 977:
+        ret = 920;
+        break;
+      case 981:
+        ret = 934;
+        break;
+      case 982:
+        ret = 928;
+        break;
+      case 995:
+        ret = 994;
+        break;
+      case 997:
+        ret = 996;
+        break;
+      case 999:
+        ret = 998;
+        break;
+      case 1001:
+        ret = 1000;
+        break;
+      case 1003:
+        ret = 1002;
+        break;
+      case 1005:
+        ret = 1004;
+        break;
+      case 1007:
+        ret = 1006;
+        break;
+      case 1008:
+        ret = 922;
+        break;
+      case 1009:
+        ret = 929;
+        break;
+      case 1072:
+        ret = 1040;
+        break;
+      case 1073:
+        ret = 1041;
+        break;
+      case 1074:
+        ret = 1042;
+        break;
+      case 1075:
+        ret = 1043;
+        break;
+      case 1076:
+        ret = 1044;
+        break;
+      case 1077:
+        ret = 1045;
+        break;
+      case 1078:
+        ret = 1046;
+        break;
+      case 1079:
+        ret = 1047;
+        break;
+      case 1080:
+        ret = 1048;
+        break;
+      case 1081:
+        ret = 1049;
+        break;
+      case 1082:
+        ret = 1050;
+        break;
+      case 1083:
+        ret = 1051;
+        break;
+      case 1084:
+        ret = 1052;
+        break;
+      case 1085:
+        ret = 1053;
+        break;
+      case 1086:
+        ret = 1054;
+        break;
+      case 1087:
+        ret = 1055;
+        break;
+      case 1088:
+        ret = 1056;
+        break;
+      case 1089:
+        ret = 1057;
+        break;
+      case 1090:
+        ret = 1058;
+        break;
+      case 1091:
+        ret = 1059;
+        break;
+      case 1092:
+        ret = 1060;
+        break;
+      case 1093:
+        ret = 1061;
+        break;
+      case 1094:
+        ret = 1062;
+        break;
+      case 1095:
+        ret = 1063;
+        break;
+      case 1096:
+        ret = 1064;
+        break;
+      case 1097:
+        ret = 1065;
+        break;
+      case 1098:
+        ret = 1066;
+        break;
+      case 1099:
+        ret = 1067;
+        break;
+      case 1100:
+        ret = 1068;
+        break;
+      case 1101:
+        ret = 1069;
+        break;
+      case 1102:
+        ret = 1070;
+        break;
+      case 1103:
+        ret = 1071;
+        break;
+      case 1105:
+        ret = 1025;
+        break;
+      case 1106:
+        ret = 1026;
+        break;
+      case 1107:
+        ret = 1027;
+        break;
+      case 1108:
+        ret = 1028;
+        break;
+      case 1109:
+        ret = 1029;
+        break;
+      case 1110:
+        ret = 1030;
+        break;
+      case 1111:
+        ret = 1031;
+        break;
+      case 1112:
+        ret = 1032;
+        break;
+      case 1113:
+        ret = 1033;
+        break;
+      case 1114:
+        ret = 1034;
+        break;
+      case 1115:
+        ret = 1035;
+        break;
+      case 1116:
+        ret = 1036;
+        break;
+      case 1118:
+        ret = 1038;
+        break;
+      case 1119:
+        ret = 1039;
+        break;
+      case 1121:
+        ret = 1120;
+        break;
+      case 1123:
+        ret = 1122;
+        break;
+      case 1125:
+        ret = 1124;
+        break;
+      case 1127:
+        ret = 1126;
+        break;
+      case 1129:
+        ret = 1128;
+        break;
+      case 1131:
+        ret = 1130;
+        break;
+      case 1133:
+        ret = 1132;
+        break;
+      case 1135:
+        ret = 1134;
+        break;
+      case 1137:
+        ret = 1136;
+        break;
+      case 1139:
+        ret = 1138;
+        break;
+      case 1141:
+        ret = 1140;
+        break;
+      case 1143:
+        ret = 1142;
+        break;
+      case 1145:
+        ret = 1144;
+        break;
+      case 1147:
+        ret = 1146;
+        break;
+      case 1149:
+        ret = 1148;
+        break;
+      case 1151:
+        ret = 1150;
+        break;
+      case 1153:
+        ret = 1152;
+        break;
+      case 1169:
+        ret = 1168;
+        break;
+      case 1171:
+        ret = 1170;
+        break;
+      case 1173:
+        ret = 1172;
+        break;
+      case 1175:
+        ret = 1174;
+        break;
+      case 1177:
+        ret = 1176;
+        break;
+      case 1179:
+        ret = 1178;
+        break;
+      case 1181:
+        ret = 1180;
+        break;
+      case 1183:
+        ret = 1182;
+        break;
+      case 1185:
+        ret = 1184;
+        break;
+      case 1187:
+        ret = 1186;
+        break;
+      case 1189:
+        ret = 1188;
+        break;
+      case 1191:
+        ret = 1190;
+        break;
+      case 1193:
+        ret = 1192;
+        break;
+      case 1195:
+        ret = 1194;
+        break;
+      case 1197:
+        ret = 1196;
+        break;
+      case 1199:
+        ret = 1198;
+        break;
+      case 1201:
+        ret = 1200;
+        break;
+      case 1203:
+        ret = 1202;
+        break;
+      case 1205:
+        ret = 1204;
+        break;
+      case 1207:
+        ret = 1206;
+        break;
+      case 1209:
+        ret = 1208;
+        break;
+      case 1211:
+        ret = 1210;
+        break;
+      case 1213:
+        ret = 1212;
+        break;
+      case 1215:
+        ret = 1214;
+        break;
+      case 1218:
+        ret = 1217;
+        break;
+      case 1220:
+        ret = 1219;
+        break;
+      case 1224:
+        ret = 1223;
+        break;
+      case 1228:
+        ret = 1227;
+        break;
+      case 1233:
+        ret = 1232;
+        break;
+      case 1235:
+        ret = 1234;
+        break;
+      case 1237:
+        ret = 1236;
+        break;
+      case 1239:
+        ret = 1238;
+        break;
+      case 1241:
+        ret = 1240;
+        break;
+      case 1243:
+        ret = 1242;
+        break;
+      case 1245:
+        ret = 1244;
+        break;
+      case 1247:
+        ret = 1246;
+        break;
+      case 1249:
+        ret = 1248;
+        break;
+      case 1251:
+        ret = 1250;
+        break;
+      case 1253:
+        ret = 1252;
+        break;
+      case 1255:
+        ret = 1254;
+        break;
+      case 1257:
+        ret = 1256;
+        break;
+      case 1259:
+        ret = 1258;
+        break;
+      case 1263:
+        ret = 1262;
+        break;
+      case 1265:
+        ret = 1264;
+        break;
+      case 1267:
+        ret = 1266;
+        break;
+      case 1269:
+        ret = 1268;
+        break;
+      case 1273:
+        ret = 1272;
+        break;
+      case 1377:
+        ret = 1329;
+        break;
+      case 1378:
+        ret = 1330;
+        break;
+      case 1379:
+        ret = 1331;
+        break;
+      case 1380:
+        ret = 1332;
+        break;
+      case 1381:
+        ret = 1333;
+        break;
+      case 1382:
+        ret = 1334;
+        break;
+      case 1383:
+        ret = 1335;
+        break;
+      case 1384:
+        ret = 1336;
+        break;
+      case 1385:
+        ret = 1337;
+        break;
+      case 1386:
+        ret = 1338;
+        break;
+      case 1387:
+        ret = 1339;
+        break;
+      case 1388:
+        ret = 1340;
+        break;
+      case 1389:
+        ret = 1341;
+        break;
+      case 1390:
+        ret = 1342;
+        break;
+      case 1391:
+        ret = 1343;
+        break;
+      case 1392:
+        ret = 1344;
+        break;
+      case 1393:
+        ret = 1345;
+        break;
+      case 1394:
+        ret = 1346;
+        break;
+      case 1395:
+        ret = 1347;
+        break;
+      case 1396:
+        ret = 1348;
+        break;
+      case 1397:
+        ret = 1349;
+        break;
+      case 1398:
+        ret = 1350;
+        break;
+      case 1399:
+        ret = 1351;
+        break;
+      case 1400:
+        ret = 1352;
+        break;
+      case 1401:
+        ret = 1353;
+        break;
+      case 1402:
+        ret = 1354;
+        break;
+      case 1403:
+        ret = 1355;
+        break;
+      case 1404:
+        ret = 1356;
+        break;
+      case 1405:
+        ret = 1357;
+        break;
+      case 1406:
+        ret = 1358;
+        break;
+      case 1407:
+        ret = 1359;
+        break;
+      case 1408:
+        ret = 1360;
+        break;
+      case 1409:
+        ret = 1361;
+        break;
+      case 1410:
+        ret = 1362;
+        break;
+      case 1411:
+        ret = 1363;
+        break;
+      case 1412:
+        ret = 1364;
+        break;
+      case 1413:
+        ret = 1365;
+        break;
+      case 1414:
+        ret = 1366;
+        break;
+      case 7681:
+        ret = 7680;
+        break;
+      case 7683:
+        ret = 7682;
+        break;
+      case 7685:
+        ret = 7684;
+        break;
+      case 7687:
+        ret = 7686;
+        break;
+      case 7689:
+        ret = 7688;
+        break;
+      case 7691:
+        ret = 7690;
+        break;
+      case 7693:
+        ret = 7692;
+        break;
+      case 7695:
+        ret = 7694;
+        break;
+      case 7697:
+        ret = 7696;
+        break;
+      case 7699:
+        ret = 7698;
+        break;
+      case 7701:
+        ret = 7700;
+        break;
+      case 7703:
+        ret = 7702;
+        break;
+      case 7705:
+        ret = 7704;
+        break;
+      case 7707:
+        ret = 7706;
+        break;
+      case 7709:
+        ret = 7708;
+        break;
+      case 7711:
+        ret = 7710;
+        break;
+      case 7713:
+        ret = 7712;
+        break;
+      case 7715:
+        ret = 7714;
+        break;
+      case 7717:
+        ret = 7716;
+        break;
+      case 7719:
+        ret = 7718;
+        break;
+      case 7721:
+        ret = 7720;
+        break;
+      case 7723:
+        ret = 7722;
+        break;
+      case 7725:
+        ret = 7724;
+        break;
+      case 7727:
+        ret = 7726;
+        break;
+      case 7729:
+        ret = 7728;
+        break;
+      case 7731:
+        ret = 7730;
+        break;
+      case 7733:
+        ret = 7732;
+        break;
+      case 7735:
+        ret = 7734;
+        break;
+      case 7737:
+        ret = 7736;
+        break;
+      case 7739:
+        ret = 7738;
+        break;
+      case 7741:
+        ret = 7740;
+        break;
+      case 7743:
+        ret = 7742;
+        break;
+      case 7745:
+        ret = 7744;
+        break;
+      case 7747:
+        ret = 7746;
+        break;
+      case 7749:
+        ret = 7748;
+        break;
+      case 7751:
+        ret = 7750;
+        break;
+      case 7753:
+        ret = 7752;
+        break;
+      case 7755:
+        ret = 7754;
+        break;
+      case 7757:
+        ret = 7756;
+        break;
+      case 7759:
+        ret = 7758;
+        break;
+      case 7761:
+        ret = 7760;
+        break;
+      case 7763:
+        ret = 7762;
+        break;
+      case 7765:
+        ret = 7764;
+        break;
+      case 7767:
+        ret = 7766;
+        break;
+      case 7769:
+        ret = 7768;
+        break;
+      case 7771:
+        ret = 7770;
+        break;
+      case 7773:
+        ret = 7772;
+        break;
+      case 7775:
+        ret = 7774;
+        break;
+      case 7777:
+        ret = 7776;
+        break;
+      case 7779:
+        ret = 7778;
+        break;
+      case 7781:
+        ret = 7780;
+        break;
+      case 7783:
+        ret = 7782;
+        break;
+      case 7785:
+        ret = 7784;
+        break;
+      case 7787:
+        ret = 7786;
+        break;
+      case 7789:
+        ret = 7788;
+        break;
+      case 7791:
+        ret = 7790;
+        break;
+      case 7793:
+        ret = 7792;
+        break;
+      case 7795:
+        ret = 7794;
+        break;
+      case 7797:
+        ret = 7796;
+        break;
+      case 7799:
+        ret = 7798;
+        break;
+      case 7801:
+        ret = 7800;
+        break;
+      case 7803:
+        ret = 7802;
+        break;
+      case 7805:
+        ret = 7804;
+        break;
+      case 7807:
+        ret = 7806;
+        break;
+      case 7809:
+        ret = 7808;
+        break;
+      case 7811:
+        ret = 7810;
+        break;
+      case 7813:
+        ret = 7812;
+        break;
+      case 7815:
+        ret = 7814;
+        break;
+      case 7817:
+        ret = 7816;
+        break;
+      case 7819:
+        ret = 7818;
+        break;
+      case 7821:
+        ret = 7820;
+        break;
+      case 7823:
+        ret = 7822;
+        break;
+      case 7825:
+        ret = 7824;
+        break;
+      case 7827:
+        ret = 7826;
+        break;
+      case 7829:
+        ret = 7828;
+        break;
+      case 7841:
+        ret = 7840;
+        break;
+      case 7843:
+        ret = 7842;
+        break;
+      case 7845:
+        ret = 7844;
+        break;
+      case 7847:
+        ret = 7846;
+        break;
+      case 7849:
+        ret = 7848;
+        break;
+      case 7851:
+        ret = 7850;
+        break;
+      case 7853:
+        ret = 7852;
+        break;
+      case 7855:
+        ret = 7854;
+        break;
+      case 7857:
+        ret = 7856;
+        break;
+      case 7859:
+        ret = 7858;
+        break;
+      case 7861:
+        ret = 7860;
+        break;
+      case 7863:
+        ret = 7862;
+        break;
+      case 7865:
+        ret = 7864;
+        break;
+      case 7867:
+        ret = 7866;
+        break;
+      case 7869:
+        ret = 7868;
+        break;
+      case 7871:
+        ret = 7870;
+        break;
+      case 7873:
+        ret = 7872;
+        break;
+      case 7875:
+        ret = 7874;
+        break;
+      case 7877:
+        ret = 7876;
+        break;
+      case 7879:
+        ret = 7878;
+        break;
+      case 7881:
+        ret = 7880;
+        break;
+      case 7883:
+        ret = 7882;
+        break;
+      case 7885:
+        ret = 7884;
+        break;
+      case 7887:
+        ret = 7886;
+        break;
+      case 7889:
+        ret = 7888;
+        break;
+      case 7891:
+        ret = 7890;
+        break;
+      case 7893:
+        ret = 7892;
+        break;
+      case 7895:
+        ret = 7894;
+        break;
+      case 7897:
+        ret = 7896;
+        break;
+      case 7899:
+        ret = 7898;
+        break;
+      case 7901:
+        ret = 7900;
+        break;
+      case 7903:
+        ret = 7902;
+        break;
+      case 7905:
+        ret = 7904;
+        break;
+      case 7907:
+        ret = 7906;
+        break;
+      case 7909:
+        ret = 7908;
+        break;
+      case 7911:
+        ret = 7910;
+        break;
+      case 7913:
+        ret = 7912;
+        break;
+      case 7915:
+        ret = 7914;
+        break;
+      case 7917:
+        ret = 7916;
+        break;
+      case 7919:
+        ret = 7918;
+        break;
+      case 7921:
+        ret = 7920;
+        break;
+      case 7923:
+        ret = 7922;
+        break;
+      case 7925:
+        ret = 7924;
+        break;
+      case 7927:
+        ret = 7926;
+        break;
+      case 7929:
+        ret = 7928;
+        break;
+      case 7936:
+        ret = 7944;
+        break;
+      case 7937:
+        ret = 7945;
+        break;
+      case 7938:
+        ret = 7946;
+        break;
+      case 7939:
+        ret = 7947;
+        break;
+      case 7940:
+        ret = 7948;
+        break;
+      case 7941:
+        ret = 7949;
+        break;
+      case 7942:
+        ret = 7950;
+        break;
+      case 7943:
+        ret = 7951;
+        break;
+      case 7952:
+        ret = 7960;
+        break;
+      case 7953:
+        ret = 7961;
+        break;
+      case 7954:
+        ret = 7962;
+        break;
+      case 7955:
+        ret = 7963;
+        break;
+      case 7956:
+        ret = 7964;
+        break;
+      case 7957:
+        ret = 7965;
+        break;
+      case 7968:
+        ret = 7976;
+        break;
+      case 7969:
+        ret = 7977;
+        break;
+      case 7970:
+        ret = 7978;
+        break;
+      case 7971:
+        ret = 7979;
+        break;
+      case 7972:
+        ret = 7980;
+        break;
+      case 7973:
+        ret = 7981;
+        break;
+      case 7974:
+        ret = 7982;
+        break;
+      case 7975:
+        ret = 7983;
+        break;
+      case 7984:
+        ret = 7992;
+        break;
+      case 7985:
+        ret = 7993;
+        break;
+      case 7986:
+        ret = 7994;
+        break;
+      case 7987:
+        ret = 7995;
+        break;
+      case 7988:
+        ret = 7996;
+        break;
+      case 7989:
+        ret = 7997;
+        break;
+      case 7990:
+        ret = 7998;
+        break;
+      case 7991:
+        ret = 7999;
+        break;
+      case 8000:
+        ret = 8008;
+        break;
+      case 8001:
+        ret = 8009;
+        break;
+      case 8002:
+        ret = 8010;
+        break;
+      case 8003:
+        ret = 8011;
+        break;
+      case 8004:
+        ret = 8012;
+        break;
+      case 8005:
+        ret = 8013;
+        break;
+      case 8017:
+        ret = 8025;
+        break;
+      case 8019:
+        ret = 8027;
+        break;
+      case 8021:
+        ret = 8029;
+        break;
+      case 8023:
+        ret = 8031;
+        break;
+      case 8032:
+        ret = 8040;
+        break;
+      case 8033:
+        ret = 8041;
+        break;
+      case 8034:
+        ret = 8042;
+        break;
+      case 8035:
+        ret = 8043;
+        break;
+      case 8036:
+        ret = 8044;
+        break;
+      case 8037:
+        ret = 8045;
+        break;
+      case 8038:
+        ret = 8046;
+        break;
+      case 8039:
+        ret = 8047;
+        break;
+      case 8048:
+        ret = 8122;
+        break;
+      case 8049:
+        ret = 8123;
+        break;
+      case 8050:
+        ret = 8136;
+        break;
+      case 8051:
+        ret = 8137;
+        break;
+      case 8052:
+        ret = 8138;
+        break;
+      case 8053:
+        ret = 8139;
+        break;
+      case 8054:
+        ret = 8154;
+        break;
+      case 8055:
+        ret = 8155;
+        break;
+      case 8056:
+        ret = 8184;
+        break;
+      case 8057:
+        ret = 8185;
+        break;
+      case 8058:
+        ret = 8170;
+        break;
+      case 8059:
+        ret = 8171;
+        break;
+      case 8060:
+        ret = 8186;
+        break;
+      case 8061:
+        ret = 8187;
+        break;
+      case 8064:
+        ret = 8072;
+        break;
+      case 8065:
+        ret = 8073;
+        break;
+      case 8066:
+        ret = 8074;
+        break;
+      case 8067:
+        ret = 8075;
+        break;
+      case 8068:
+        ret = 8076;
+        break;
+      case 8069:
+        ret = 8077;
+        break;
+      case 8070:
+        ret = 8078;
+        break;
+      case 8071:
+        ret = 8079;
+        break;
+      case 8080:
+        ret = 8088;
+        break;
+      case 8081:
+        ret = 8089;
+        break;
+      case 8082:
+        ret = 8090;
+        break;
+      case 8083:
+        ret = 8091;
+        break;
+      case 8084:
+        ret = 8092;
+        break;
+      case 8085:
+        ret = 8093;
+        break;
+      case 8086:
+        ret = 8094;
+        break;
+      case 8087:
+        ret = 8095;
+        break;
+      case 8096:
+        ret = 8104;
+        break;
+      case 8097:
+        ret = 8105;
+        break;
+      case 8098:
+        ret = 8106;
+        break;
+      case 8099:
+        ret = 8107;
+        break;
+      case 8100:
+        ret = 8108;
+        break;
+      case 8101:
+        ret = 8109;
+        break;
+      case 8102:
+        ret = 8110;
+        break;
+      case 8103:
+        ret = 8111;
+        break;
+      case 8112:
+        ret = 8120;
+        break;
+      case 8113:
+        ret = 8121;
+        break;
+      case 8115:
+        ret = 8124;
+        break;
+      case 8131:
+        ret = 8140;
+        break;
+      case 8144:
+        ret = 8152;
+        break;
+      case 8145:
+        ret = 8153;
+        break;
+      case 8160:
+        ret = 8168;
+        break;
+      case 8161:
+        ret = 8169;
+        break;
+      case 8165:
+        ret = 8172;
+        break;
+      case 8179:
+        ret = 8188;
+        break;
+      case 8560:
+        ret = 8544;
+        break;
+      case 8561:
+        ret = 8545;
+        break;
+      case 8562:
+        ret = 8546;
+        break;
+      case 8563:
+        ret = 8547;
+        break;
+      case 8564:
+        ret = 8548;
+        break;
+      case 8565:
+        ret = 8549;
+        break;
+      case 8566:
+        ret = 8550;
+        break;
+      case 8567:
+        ret = 8551;
+        break;
+      case 8568:
+        ret = 8552;
+        break;
+      case 8569:
+        ret = 8553;
+        break;
+      case 8570:
+        ret = 8554;
+        break;
+      case 8571:
+        ret = 8555;
+        break;
+      case 8572:
+        ret = 8556;
+        break;
+      case 8573:
+        ret = 8557;
+        break;
+      case 8574:
+        ret = 8558;
+        break;
+      case 8575:
+        ret = 8559;
+        break;
+      case 9424:
+        ret = 9398;
+        break;
+      case 9425:
+        ret = 9399;
+        break;
+      case 9426:
+        ret = 9400;
+        break;
+      case 9427:
+        ret = 9401;
+        break;
+      case 9428:
+        ret = 9402;
+        break;
+      case 9429:
+        ret = 9403;
+        break;
+      case 9430:
+        ret = 9404;
+        break;
+      case 9431:
+        ret = 9405;
+        break;
+      case 9432:
+        ret = 9406;
+        break;
+      case 9433:
+        ret = 9407;
+        break;
+      case 9434:
+        ret = 9408;
+        break;
+      case 9435:
+        ret = 9409;
+        break;
+      case 9436:
+        ret = 9410;
+        break;
+      case 9437:
+        ret = 9411;
+        break;
+      case 9438:
+        ret = 9412;
+        break;
+      case 9439:
+        ret = 9413;
+        break;
+      case 9440:
+        ret = 9414;
+        break;
+      case 9441:
+        ret = 9415;
+        break;
+      case 9442:
+        ret = 9416;
+        break;
+      case 9443:
+        ret = 9417;
+        break;
+      case 9444:
+        ret = 9418;
+        break;
+      case 9445:
+        ret = 9419;
+        break;
+      case 9446:
+        ret = 9420;
+        break;
+      case 9447:
+        ret = 9421;
+        break;
+      case 9448:
+        ret = 9422;
+        break;
+      case 9449:
+        ret = 9423;
+        break;
+      case 65345:
+        ret = 65313;
+        break;
+      case 65346:
+        ret = 65314;
+        break;
+      case 65347:
+        ret = 65315;
+        break;
+      case 65348:
+        ret = 65316;
+        break;
+      case 65349:
+        ret = 65317;
+        break;
+      case 65350:
+        ret = 65318;
+        break;
+      case 65351:
+        ret = 65319;
+        break;
+      case 65352:
+        ret = 65320;
+        break;
+      case 65353:
+        ret = 65321;
+        break;
+      case 65354:
+        ret = 65322;
+        break;
+      case 65355:
+        ret = 65323;
+        break;
+      case 65356:
+        ret = 65324;
+        break;
+      case 65357:
+        ret = 65325;
+        break;
+      case 65358:
+        ret = 65326;
+        break;
+      case 65359:
+        ret = 65327;
+        break;
+      case 65360:
+        ret = 65328;
+        break;
+      case 65361:
+        ret = 65329;
+        break;
+      case 65362:
+        ret = 65330;
+        break;
+      case 65363:
+        ret = 65331;
+        break;
+      case 65364:
+        ret = 65332;
+        break;
+      case 65365:
+        ret = 65333;
+        break;
+      case 65366:
+        ret = 65334;
+        break;
+      case 65367:
+        ret = 65335;
+        break;
+      case 65368:
+        ret = 65336;
+        break;
+      case 65369:
+        ret = 65337;
+        break;
+      case 65370:
+        ret = 65338;
+        break;
+      }
+      return (char) ret;
+    }
+    return Character.toUpperCase(c);
+  }
+
+  /** Convert a character to lower case. */
+  public static char toLowerCase(char c)
+  {
+    if (java_1_0)
+    {
+      int ret = (int) c;
+      switch (c)
+      {
+      case 65:
+        ret = 97;
+        break;
+      case 66:
+        ret = 98;
+        break;
+      case 67:
+        ret = 99;
+        break;
+      case 68:
+        ret = 100;
+        break;
+      case 69:
+        ret = 101;
+        break;
+      case 70:
+        ret = 102;
+        break;
+      case 71:
+        ret = 103;
+        break;
+      case 72:
+        ret = 104;
+        break;
+      case 73:
+        ret = 105;
+        break;
+      case 74:
+        ret = 106;
+        break;
+      case 75:
+        ret = 107;
+        break;
+      case 76:
+        ret = 108;
+        break;
+      case 77:
+        ret = 109;
+        break;
+      case 78:
+        ret = 110;
+        break;
+      case 79:
+        ret = 111;
+        break;
+      case 80:
+        ret = 112;
+        break;
+      case 81:
+        ret = 113;
+        break;
+      case 82:
+        ret = 114;
+        break;
+      case 83:
+        ret = 115;
+        break;
+      case 84:
+        ret = 116;
+        break;
+      case 85:
+        ret = 117;
+        break;
+      case 86:
+        ret = 118;
+        break;
+      case 87:
+        ret = 119;
+        break;
+      case 88:
+        ret = 120;
+        break;
+      case 89:
+        ret = 121;
+        break;
+      case 90:
+        ret = 122;
+        break;
+      case 192:
+        ret = 224;
+        break;
+      case 193:
+        ret = 225;
+        break;
+      case 194:
+        ret = 226;
+        break;
+      case 195:
+        ret = 227;
+        break;
+      case 196:
+        ret = 228;
+        break;
+      case 197:
+        ret = 229;
+        break;
+      case 198:
+        ret = 230;
+        break;
+      case 199:
+        ret = 231;
+        break;
+      case 200:
+        ret = 232;
+        break;
+      case 201:
+        ret = 233;
+        break;
+      case 202:
+        ret = 234;
+        break;
+      case 203:
+        ret = 235;
+        break;
+      case 204:
+        ret = 236;
+        break;
+      case 205:
+        ret = 237;
+        break;
+      case 206:
+        ret = 238;
+        break;
+      case 207:
+        ret = 239;
+        break;
+      case 208:
+        ret = 240;
+        break;
+      case 209:
+        ret = 241;
+        break;
+      case 210:
+        ret = 242;
+        break;
+      case 211:
+        ret = 243;
+        break;
+      case 212:
+        ret = 244;
+        break;
+      case 213:
+        ret = 245;
+        break;
+      case 214:
+        ret = 246;
+        break;
+      case 216:
+        ret = 248;
+        break;
+      case 217:
+        ret = 249;
+        break;
+      case 218:
+        ret = 250;
+        break;
+      case 219:
+        ret = 251;
+        break;
+      case 220:
+        ret = 252;
+        break;
+      case 221:
+        ret = 253;
+        break;
+      case 222:
+        ret = 254;
+        break;
+      case 256:
+        ret = 257;
+        break;
+      case 258:
+        ret = 259;
+        break;
+      case 260:
+        ret = 261;
+        break;
+      case 262:
+        ret = 263;
+        break;
+      case 264:
+        ret = 265;
+        break;
+      case 266:
+        ret = 267;
+        break;
+      case 268:
+        ret = 269;
+        break;
+      case 270:
+        ret = 271;
+        break;
+      case 272:
+        ret = 273;
+        break;
+      case 274:
+        ret = 275;
+        break;
+      case 276:
+        ret = 277;
+        break;
+      case 278:
+        ret = 279;
+        break;
+      case 280:
+        ret = 281;
+        break;
+      case 282:
+        ret = 283;
+        break;
+      case 284:
+        ret = 285;
+        break;
+      case 286:
+        ret = 287;
+        break;
+      case 288:
+        ret = 289;
+        break;
+      case 290:
+        ret = 291;
+        break;
+      case 292:
+        ret = 293;
+        break;
+      case 294:
+        ret = 295;
+        break;
+      case 296:
+        ret = 297;
+        break;
+      case 298:
+        ret = 299;
+        break;
+      case 300:
+        ret = 301;
+        break;
+      case 302:
+        ret = 303;
+        break;
+      case 304:
+        ret = 105;
+        break;
+      case 306:
+        ret = 307;
+        break;
+      case 308:
+        ret = 309;
+        break;
+      case 310:
+        ret = 311;
+        break;
+      case 313:
+        ret = 314;
+        break;
+      case 315:
+        ret = 316;
+        break;
+      case 317:
+        ret = 318;
+        break;
+      case 319:
+        ret = 320;
+        break;
+      case 321:
+        ret = 322;
+        break;
+      case 323:
+        ret = 324;
+        break;
+      case 325:
+        ret = 326;
+        break;
+      case 327:
+        ret = 328;
+        break;
+      case 330:
+        ret = 331;
+        break;
+      case 332:
+        ret = 333;
+        break;
+      case 334:
+        ret = 335;
+        break;
+      case 336:
+        ret = 337;
+        break;
+      case 338:
+        ret = 339;
+        break;
+      case 340:
+        ret = 341;
+        break;
+      case 342:
+        ret = 343;
+        break;
+      case 344:
+        ret = 345;
+        break;
+      case 346:
+        ret = 347;
+        break;
+      case 348:
+        ret = 349;
+        break;
+      case 350:
+        ret = 351;
+        break;
+      case 352:
+        ret = 353;
+        break;
+      case 354:
+        ret = 355;
+        break;
+      case 356:
+        ret = 357;
+        break;
+      case 358:
+        ret = 359;
+        break;
+      case 360:
+        ret = 361;
+        break;
+      case 362:
+        ret = 363;
+        break;
+      case 364:
+        ret = 365;
+        break;
+      case 366:
+        ret = 367;
+        break;
+      case 368:
+        ret = 369;
+        break;
+      case 370:
+        ret = 371;
+        break;
+      case 372:
+        ret = 373;
+        break;
+      case 374:
+        ret = 375;
+        break;
+      case 376:
+        ret = 255;
+        break;
+      case 377:
+        ret = 378;
+        break;
+      case 379:
+        ret = 380;
+        break;
+      case 381:
+        ret = 382;
+        break;
+      case 385:
+        ret = 595;
+        break;
+      case 386:
+        ret = 387;
+        break;
+      case 388:
+        ret = 389;
+        break;
+      case 390:
+        ret = 596;
+        break;
+      case 391:
+        ret = 392;
+        break;
+      case 393:
+        ret = 598;
+        break;
+      case 394:
+        ret = 599;
+        break;
+      case 395:
+        ret = 396;
+        break;
+      case 398:
+        ret = 600;
+        break;
+      case 399:
+        ret = 601;
+        break;
+      case 400:
+        ret = 603;
+        break;
+      case 401:
+        ret = 402;
+        break;
+      case 403:
+        ret = 608;
+        break;
+      case 404:
+        ret = 611;
+        break;
+      case 406:
+        ret = 617;
+        break;
+      case 407:
+        ret = 616;
+        break;
+      case 408:
+        ret = 409;
+        break;
+      case 412:
+        ret = 623;
+        break;
+      case 413:
+        ret = 626;
+        break;
+      case 416:
+        ret = 417;
+        break;
+      case 418:
+        ret = 419;
+        break;
+      case 420:
+        ret = 421;
+        break;
+      case 423:
+        ret = 424;
+        break;
+      case 425:
+        ret = 643;
+        break;
+      case 428:
+        ret = 429;
+        break;
+      case 430:
+        ret = 648;
+        break;
+      case 431:
+        ret = 432;
+        break;
+      case 433:
+        ret = 650;
+        break;
+      case 434:
+        ret = 651;
+        break;
+      case 435:
+        ret = 436;
+        break;
+      case 437:
+        ret = 438;
+        break;
+      case 439:
+        ret = 658;
+        break;
+      case 440:
+        ret = 441;
+        break;
+      case 444:
+        ret = 445;
+        break;
+      case 452:
+        ret = 454;
+        break;
+      case 453:
+        ret = 454;
+        break;
+      case 455:
+        ret = 457;
+        break;
+      case 456:
+        ret = 457;
+        break;
+      case 458:
+        ret = 460;
+        break;
+      case 459:
+        ret = 460;
+        break;
+      case 461:
+        ret = 462;
+        break;
+      case 463:
+        ret = 464;
+        break;
+      case 465:
+        ret = 466;
+        break;
+      case 467:
+        ret = 468;
+        break;
+      case 469:
+        ret = 470;
+        break;
+      case 471:
+        ret = 472;
+        break;
+      case 473:
+        ret = 474;
+        break;
+      case 475:
+        ret = 476;
+        break;
+      case 478:
+        ret = 479;
+        break;
+      case 480:
+        ret = 481;
+        break;
+      case 482:
+        ret = 483;
+        break;
+      case 484:
+        ret = 485;
+        break;
+      case 486:
+        ret = 487;
+        break;
+      case 488:
+        ret = 489;
+        break;
+      case 490:
+        ret = 491;
+        break;
+      case 492:
+        ret = 493;
+        break;
+      case 494:
+        ret = 495;
+        break;
+      case 497:
+        ret = 499;
+        break;
+      case 498:
+        ret = 499;
+        break;
+      case 500:
+        ret = 501;
+        break;
+      case 506:
+        ret = 507;
+        break;
+      case 508:
+        ret = 509;
+        break;
+      case 510:
+        ret = 511;
+        break;
+      case 512:
+        ret = 513;
+        break;
+      case 514:
+        ret = 515;
+        break;
+      case 516:
+        ret = 517;
+        break;
+      case 518:
+        ret = 519;
+        break;
+      case 520:
+        ret = 521;
+        break;
+      case 522:
+        ret = 523;
+        break;
+      case 524:
+        ret = 525;
+        break;
+      case 526:
+        ret = 527;
+        break;
+      case 528:
+        ret = 529;
+        break;
+      case 530:
+        ret = 531;
+        break;
+      case 532:
+        ret = 533;
+        break;
+      case 534:
+        ret = 535;
+        break;
+      case 902:
+        ret = 940;
+        break;
+      case 904:
+        ret = 941;
+        break;
+      case 905:
+        ret = 942;
+        break;
+      case 906:
+        ret = 943;
+        break;
+      case 908:
+        ret = 972;
+        break;
+      case 910:
+        ret = 973;
+        break;
+      case 911:
+        ret = 974;
+        break;
+      case 913:
+        ret = 945;
+        break;
+      case 914:
+        ret = 946;
+        break;
+      case 915:
+        ret = 947;
+        break;
+      case 916:
+        ret = 948;
+        break;
+      case 917:
+        ret = 949;
+        break;
+      case 918:
+        ret = 950;
+        break;
+      case 919:
+        ret = 951;
+        break;
+      case 920:
+        ret = 952;
+        break;
+      case 921:
+        ret = 953;
+        break;
+      case 922:
+        ret = 954;
+        break;
+      case 923:
+        ret = 955;
+        break;
+      case 924:
+        ret = 956;
+        break;
+      case 925:
+        ret = 957;
+        break;
+      case 926:
+        ret = 958;
+        break;
+      case 927:
+        ret = 959;
+        break;
+      case 928:
+        ret = 960;
+        break;
+      case 929:
+        ret = 961;
+        break;
+      case 931:
+        ret = 963;
+        break;
+      case 932:
+        ret = 964;
+        break;
+      case 933:
+        ret = 965;
+        break;
+      case 934:
+        ret = 966;
+        break;
+      case 935:
+        ret = 967;
+        break;
+      case 936:
+        ret = 968;
+        break;
+      case 937:
+        ret = 969;
+        break;
+      case 938:
+        ret = 970;
+        break;
+      case 939:
+        ret = 971;
+        break;
+      case 994:
+        ret = 995;
+        break;
+      case 996:
+        ret = 997;
+        break;
+      case 998:
+        ret = 999;
+        break;
+      case 1000:
+        ret = 1001;
+        break;
+      case 1002:
+        ret = 1003;
+        break;
+      case 1004:
+        ret = 1005;
+        break;
+      case 1006:
+        ret = 1007;
+        break;
+      case 1025:
+        ret = 1105;
+        break;
+      case 1026:
+        ret = 1106;
+        break;
+      case 1027:
+        ret = 1107;
+        break;
+      case 1028:
+        ret = 1108;
+        break;
+      case 1029:
+        ret = 1109;
+        break;
+      case 1030:
+        ret = 1110;
+        break;
+      case 1031:
+        ret = 1111;
+        break;
+      case 1032:
+        ret = 1112;
+        break;
+      case 1033:
+        ret = 1113;
+        break;
+      case 1034:
+        ret = 1114;
+        break;
+      case 1035:
+        ret = 1115;
+        break;
+      case 1036:
+        ret = 1116;
+        break;
+      case 1038:
+        ret = 1118;
+        break;
+      case 1039:
+        ret = 1119;
+        break;
+      case 1040:
+        ret = 1072;
+        break;
+      case 1041:
+        ret = 1073;
+        break;
+      case 1042:
+        ret = 1074;
+        break;
+      case 1043:
+        ret = 1075;
+        break;
+      case 1044:
+        ret = 1076;
+        break;
+      case 1045:
+        ret = 1077;
+        break;
+      case 1046:
+        ret = 1078;
+        break;
+      case 1047:
+        ret = 1079;
+        break;
+      case 1048:
+        ret = 1080;
+        break;
+      case 1049:
+        ret = 1081;
+        break;
+      case 1050:
+        ret = 1082;
+        break;
+      case 1051:
+        ret = 1083;
+        break;
+      case 1052:
+        ret = 1084;
+        break;
+      case 1053:
+        ret = 1085;
+        break;
+      case 1054:
+        ret = 1086;
+        break;
+      case 1055:
+        ret = 1087;
+        break;
+      case 1056:
+        ret = 1088;
+        break;
+      case 1057:
+        ret = 1089;
+        break;
+      case 1058:
+        ret = 1090;
+        break;
+      case 1059:
+        ret = 1091;
+        break;
+      case 1060:
+        ret = 1092;
+        break;
+      case 1061:
+        ret = 1093;
+        break;
+      case 1062:
+        ret = 1094;
+        break;
+      case 1063:
+        ret = 1095;
+        break;
+      case 1064:
+        ret = 1096;
+        break;
+      case 1065:
+        ret = 1097;
+        break;
+      case 1066:
+        ret = 1098;
+        break;
+      case 1067:
+        ret = 1099;
+        break;
+      case 1068:
+        ret = 1100;
+        break;
+      case 1069:
+        ret = 1101;
+        break;
+      case 1070:
+        ret = 1102;
+        break;
+      case 1071:
+        ret = 1103;
+        break;
+      case 1120:
+        ret = 1121;
+        break;
+      case 1122:
+        ret = 1123;
+        break;
+      case 1124:
+        ret = 1125;
+        break;
+      case 1126:
+        ret = 1127;
+        break;
+      case 1128:
+        ret = 1129;
+        break;
+      case 1130:
+        ret = 1131;
+        break;
+      case 1132:
+        ret = 1133;
+        break;
+      case 1134:
+        ret = 1135;
+        break;
+      case 1136:
+        ret = 1137;
+        break;
+      case 1138:
+        ret = 1139;
+        break;
+      case 1140:
+        ret = 1141;
+        break;
+      case 1142:
+        ret = 1143;
+        break;
+      case 1144:
+        ret = 1145;
+        break;
+      case 1146:
+        ret = 1147;
+        break;
+      case 1148:
+        ret = 1149;
+        break;
+      case 1150:
+        ret = 1151;
+        break;
+      case 1152:
+        ret = 1153;
+        break;
+      case 1168:
+        ret = 1169;
+        break;
+      case 1170:
+        ret = 1171;
+        break;
+      case 1172:
+        ret = 1173;
+        break;
+      case 1174:
+        ret = 1175;
+        break;
+      case 1176:
+        ret = 1177;
+        break;
+      case 1178:
+        ret = 1179;
+        break;
+      case 1180:
+        ret = 1181;
+        break;
+      case 1182:
+        ret = 1183;
+        break;
+      case 1184:
+        ret = 1185;
+        break;
+      case 1186:
+        ret = 1187;
+        break;
+      case 1188:
+        ret = 1189;
+        break;
+      case 1190:
+        ret = 1191;
+        break;
+      case 1192:
+        ret = 1193;
+        break;
+      case 1194:
+        ret = 1195;
+        break;
+      case 1196:
+        ret = 1197;
+        break;
+      case 1198:
+        ret = 1199;
+        break;
+      case 1200:
+        ret = 1201;
+        break;
+      case 1202:
+        ret = 1203;
+        break;
+      case 1204:
+        ret = 1205;
+        break;
+      case 1206:
+        ret = 1207;
+        break;
+      case 1208:
+        ret = 1209;
+        break;
+      case 1210:
+        ret = 1211;
+        break;
+      case 1212:
+        ret = 1213;
+        break;
+      case 1214:
+        ret = 1215;
+        break;
+      case 1217:
+        ret = 1218;
+        break;
+      case 1219:
+        ret = 1220;
+        break;
+      case 1223:
+        ret = 1224;
+        break;
+      case 1227:
+        ret = 1228;
+        break;
+      case 1232:
+        ret = 1233;
+        break;
+      case 1234:
+        ret = 1235;
+        break;
+      case 1236:
+        ret = 1237;
+        break;
+      case 1238:
+        ret = 1239;
+        break;
+      case 1240:
+        ret = 1241;
+        break;
+      case 1242:
+        ret = 1243;
+        break;
+      case 1244:
+        ret = 1245;
+        break;
+      case 1246:
+        ret = 1247;
+        break;
+      case 1248:
+        ret = 1249;
+        break;
+      case 1250:
+        ret = 1251;
+        break;
+      case 1252:
+        ret = 1253;
+        break;
+      case 1254:
+        ret = 1255;
+        break;
+      case 1256:
+        ret = 1257;
+        break;
+      case 1258:
+        ret = 1259;
+        break;
+      case 1262:
+        ret = 1263;
+        break;
+      case 1264:
+        ret = 1265;
+        break;
+      case 1266:
+        ret = 1267;
+        break;
+      case 1268:
+        ret = 1269;
+        break;
+      case 1272:
+        ret = 1273;
+        break;
+      case 1329:
+        ret = 1377;
+        break;
+      case 1330:
+        ret = 1378;
+        break;
+      case 1331:
+        ret = 1379;
+        break;
+      case 1332:
+        ret = 1380;
+        break;
+      case 1333:
+        ret = 1381;
+        break;
+      case 1334:
+        ret = 1382;
+        break;
+      case 1335:
+        ret = 1383;
+        break;
+      case 1336:
+        ret = 1384;
+        break;
+      case 1337:
+        ret = 1385;
+        break;
+      case 1338:
+        ret = 1386;
+        break;
+      case 1339:
+        ret = 1387;
+        break;
+      case 1340:
+        ret = 1388;
+        break;
+      case 1341:
+        ret = 1389;
+        break;
+      case 1342:
+        ret = 1390;
+        break;
+      case 1343:
+        ret = 1391;
+        break;
+      case 1344:
+        ret = 1392;
+        break;
+      case 1345:
+        ret = 1393;
+        break;
+      case 1346:
+        ret = 1394;
+        break;
+      case 1347:
+        ret = 1395;
+        break;
+      case 1348:
+        ret = 1396;
+        break;
+      case 1349:
+        ret = 1397;
+        break;
+      case 1350:
+        ret = 1398;
+        break;
+      case 1351:
+        ret = 1399;
+        break;
+      case 1352:
+        ret = 1400;
+        break;
+      case 1353:
+        ret = 1401;
+        break;
+      case 1354:
+        ret = 1402;
+        break;
+      case 1355:
+        ret = 1403;
+        break;
+      case 1356:
+        ret = 1404;
+        break;
+      case 1357:
+        ret = 1405;
+        break;
+      case 1358:
+        ret = 1406;
+        break;
+      case 1359:
+        ret = 1407;
+        break;
+      case 1360:
+        ret = 1408;
+        break;
+      case 1361:
+        ret = 1409;
+        break;
+      case 1362:
+        ret = 1410;
+        break;
+      case 1363:
+        ret = 1411;
+        break;
+      case 1364:
+        ret = 1412;
+        break;
+      case 1365:
+        ret = 1413;
+        break;
+      case 1366:
+        ret = 1414;
+        break;
+      case 4256:
+        ret = 4304;
+        break;
+      case 4257:
+        ret = 4305;
+        break;
+      case 4258:
+        ret = 4306;
+        break;
+      case 4259:
+        ret = 4307;
+        break;
+      case 4260:
+        ret = 4308;
+        break;
+      case 4261:
+        ret = 4309;
+        break;
+      case 4262:
+        ret = 4310;
+        break;
+      case 4263:
+        ret = 4311;
+        break;
+      case 4264:
+        ret = 4312;
+        break;
+      case 4265:
+        ret = 4313;
+        break;
+      case 4266:
+        ret = 4314;
+        break;
+      case 4267:
+        ret = 4315;
+        break;
+      case 4268:
+        ret = 4316;
+        break;
+      case 4269:
+        ret = 4317;
+        break;
+      case 4270:
+        ret = 4318;
+        break;
+      case 4271:
+        ret = 4319;
+        break;
+      case 4272:
+        ret = 4320;
+        break;
+      case 4273:
+        ret = 4321;
+        break;
+      case 4274:
+        ret = 4322;
+        break;
+      case 4275:
+        ret = 4323;
+        break;
+      case 4276:
+        ret = 4324;
+        break;
+      case 4277:
+        ret = 4325;
+        break;
+      case 4278:
+        ret = 4326;
+        break;
+      case 4279:
+        ret = 4327;
+        break;
+      case 4280:
+        ret = 4328;
+        break;
+      case 4281:
+        ret = 4329;
+        break;
+      case 4282:
+        ret = 4330;
+        break;
+      case 4283:
+        ret = 4331;
+        break;
+      case 4284:
+        ret = 4332;
+        break;
+      case 4285:
+        ret = 4333;
+        break;
+      case 4286:
+        ret = 4334;
+        break;
+      case 4287:
+        ret = 4335;
+        break;
+      case 4288:
+        ret = 4336;
+        break;
+      case 4289:
+        ret = 4337;
+        break;
+      case 4290:
+        ret = 4338;
+        break;
+      case 4291:
+        ret = 4339;
+        break;
+      case 4292:
+        ret = 4340;
+        break;
+      case 4293:
+        ret = 4341;
+        break;
+      case 7680:
+        ret = 7681;
+        break;
+      case 7682:
+        ret = 7683;
+        break;
+      case 7684:
+        ret = 7685;
+        break;
+      case 7686:
+        ret = 7687;
+        break;
+      case 7688:
+        ret = 7689;
+        break;
+      case 7690:
+        ret = 7691;
+        break;
+      case 7692:
+        ret = 7693;
+        break;
+      case 7694:
+        ret = 7695;
+        break;
+      case 7696:
+        ret = 7697;
+        break;
+      case 7698:
+        ret = 7699;
+        break;
+      case 7700:
+        ret = 7701;
+        break;
+      case 7702:
+        ret = 7703;
+        break;
+      case 7704:
+        ret = 7705;
+        break;
+      case 7706:
+        ret = 7707;
+        break;
+      case 7708:
+        ret = 7709;
+        break;
+      case 7710:
+        ret = 7711;
+        break;
+      case 7712:
+        ret = 7713;
+        break;
+      case 7714:
+        ret = 7715;
+        break;
+      case 7716:
+        ret = 7717;
+        break;
+      case 7718:
+        ret = 7719;
+        break;
+      case 7720:
+        ret = 7721;
+        break;
+      case 7722:
+        ret = 7723;
+        break;
+      case 7724:
+        ret = 7725;
+        break;
+      case 7726:
+        ret = 7727;
+        break;
+      case 7728:
+        ret = 7729;
+        break;
+      case 7730:
+        ret = 7731;
+        break;
+      case 7732:
+        ret = 7733;
+        break;
+      case 7734:
+        ret = 7735;
+        break;
+      case 7736:
+        ret = 7737;
+        break;
+      case 7738:
+        ret = 7739;
+        break;
+      case 7740:
+        ret = 7741;
+        break;
+      case 7742:
+        ret = 7743;
+        break;
+      case 7744:
+        ret = 7745;
+        break;
+      case 7746:
+        ret = 7747;
+        break;
+      case 7748:
+        ret = 7749;
+        break;
+      case 7750:
+        ret = 7751;
+        break;
+      case 7752:
+        ret = 7753;
+        break;
+      case 7754:
+        ret = 7755;
+        break;
+      case 7756:
+        ret = 7757;
+        break;
+      case 7758:
+        ret = 7759;
+        break;
+      case 7760:
+        ret = 7761;
+        break;
+      case 7762:
+        ret = 7763;
+        break;
+      case 7764:
+        ret = 7765;
+        break;
+      case 7766:
+        ret = 7767;
+        break;
+      case 7768:
+        ret = 7769;
+        break;
+      case 7770:
+        ret = 7771;
+        break;
+      case 7772:
+        ret = 7773;
+        break;
+      case 7774:
+        ret = 7775;
+        break;
+      case 7776:
+        ret = 7777;
+        break;
+      case 7778:
+        ret = 7779;
+        break;
+      case 7780:
+        ret = 7781;
+        break;
+      case 7782:
+        ret = 7783;
+        break;
+      case 7784:
+        ret = 7785;
+        break;
+      case 7786:
+        ret = 7787;
+        break;
+      case 7788:
+        ret = 7789;
+        break;
+      case 7790:
+        ret = 7791;
+        break;
+      case 7792:
+        ret = 7793;
+        break;
+      case 7794:
+        ret = 7795;
+        break;
+      case 7796:
+        ret = 7797;
+        break;
+      case 7798:
+        ret = 7799;
+        break;
+      case 7800:
+        ret = 7801;
+        break;
+      case 7802:
+        ret = 7803;
+        break;
+      case 7804:
+        ret = 7805;
+        break;
+      case 7806:
+        ret = 7807;
+        break;
+      case 7808:
+        ret = 7809;
+        break;
+      case 7810:
+        ret = 7811;
+        break;
+      case 7812:
+        ret = 7813;
+        break;
+      case 7814:
+        ret = 7815;
+        break;
+      case 7816:
+        ret = 7817;
+        break;
+      case 7818:
+        ret = 7819;
+        break;
+      case 7820:
+        ret = 7821;
+        break;
+      case 7822:
+        ret = 7823;
+        break;
+      case 7824:
+        ret = 7825;
+        break;
+      case 7826:
+        ret = 7827;
+        break;
+      case 7828:
+        ret = 7829;
+        break;
+      case 7840:
+        ret = 7841;
+        break;
+      case 7842:
+        ret = 7843;
+        break;
+      case 7844:
+        ret = 7845;
+        break;
+      case 7846:
+        ret = 7847;
+        break;
+      case 7848:
+        ret = 7849;
+        break;
+      case 7850:
+        ret = 7851;
+        break;
+      case 7852:
+        ret = 7853;
+        break;
+      case 7854:
+        ret = 7855;
+        break;
+      case 7856:
+        ret = 7857;
+        break;
+      case 7858:
+        ret = 7859;
+        break;
+      case 7860:
+        ret = 7861;
+        break;
+      case 7862:
+        ret = 7863;
+        break;
+      case 7864:
+        ret = 7865;
+        break;
+      case 7866:
+        ret = 7867;
+        break;
+      case 7868:
+        ret = 7869;
+        break;
+      case 7870:
+        ret = 7871;
+        break;
+      case 7872:
+        ret = 7873;
+        break;
+      case 7874:
+        ret = 7875;
+        break;
+      case 7876:
+        ret = 7877;
+        break;
+      case 7878:
+        ret = 7879;
+        break;
+      case 7880:
+        ret = 7881;
+        break;
+      case 7882:
+        ret = 7883;
+        break;
+      case 7884:
+        ret = 7885;
+        break;
+      case 7886:
+        ret = 7887;
+        break;
+      case 7888:
+        ret = 7889;
+        break;
+      case 7890:
+        ret = 7891;
+        break;
+      case 7892:
+        ret = 7893;
+        break;
+      case 7894:
+        ret = 7895;
+        break;
+      case 7896:
+        ret = 7897;
+        break;
+      case 7898:
+        ret = 7899;
+        break;
+      case 7900:
+        ret = 7901;
+        break;
+      case 7902:
+        ret = 7903;
+        break;
+      case 7904:
+        ret = 7905;
+        break;
+      case 7906:
+        ret = 7907;
+        break;
+      case 7908:
+        ret = 7909;
+        break;
+      case 7910:
+        ret = 7911;
+        break;
+      case 7912:
+        ret = 7913;
+        break;
+      case 7914:
+        ret = 7915;
+        break;
+      case 7916:
+        ret = 7917;
+        break;
+      case 7918:
+        ret = 7919;
+        break;
+      case 7920:
+        ret = 7921;
+        break;
+      case 7922:
+        ret = 7923;
+        break;
+      case 7924:
+        ret = 7925;
+        break;
+      case 7926:
+        ret = 7927;
+        break;
+      case 7928:
+        ret = 7929;
+        break;
+      case 7944:
+        ret = 7936;
+        break;
+      case 7945:
+        ret = 7937;
+        break;
+      case 7946:
+        ret = 7938;
+        break;
+      case 7947:
+        ret = 7939;
+        break;
+      case 7948:
+        ret = 7940;
+        break;
+      case 7949:
+        ret = 7941;
+        break;
+      case 7950:
+        ret = 7942;
+        break;
+      case 7951:
+        ret = 7943;
+        break;
+      case 7960:
+        ret = 7952;
+        break;
+      case 7961:
+        ret = 7953;
+        break;
+      case 7962:
+        ret = 7954;
+        break;
+      case 7963:
+        ret = 7955;
+        break;
+      case 7964:
+        ret = 7956;
+        break;
+      case 7965:
+        ret = 7957;
+        break;
+      case 7976:
+        ret = 7968;
+        break;
+      case 7977:
+        ret = 7969;
+        break;
+      case 7978:
+        ret = 7970;
+        break;
+      case 7979:
+        ret = 7971;
+        break;
+      case 7980:
+        ret = 7972;
+        break;
+      case 7981:
+        ret = 7973;
+        break;
+      case 7982:
+        ret = 7974;
+        break;
+      case 7983:
+        ret = 7975;
+        break;
+      case 7992:
+        ret = 7984;
+        break;
+      case 7993:
+        ret = 7985;
+        break;
+      case 7994:
+        ret = 7986;
+        break;
+      case 7995:
+        ret = 7987;
+        break;
+      case 7996:
+        ret = 7988;
+        break;
+      case 7997:
+        ret = 7989;
+        break;
+      case 7998:
+        ret = 7990;
+        break;
+      case 7999:
+        ret = 7991;
+        break;
+      case 8008:
+        ret = 8000;
+        break;
+      case 8009:
+        ret = 8001;
+        break;
+      case 8010:
+        ret = 8002;
+        break;
+      case 8011:
+        ret = 8003;
+        break;
+      case 8012:
+        ret = 8004;
+        break;
+      case 8013:
+        ret = 8005;
+        break;
+      case 8025:
+        ret = 8017;
+        break;
+      case 8027:
+        ret = 8019;
+        break;
+      case 8029:
+        ret = 8021;
+        break;
+      case 8031:
+        ret = 8023;
+        break;
+      case 8040:
+        ret = 8032;
+        break;
+      case 8041:
+        ret = 8033;
+        break;
+      case 8042:
+        ret = 8034;
+        break;
+      case 8043:
+        ret = 8035;
+        break;
+      case 8044:
+        ret = 8036;
+        break;
+      case 8045:
+        ret = 8037;
+        break;
+      case 8046:
+        ret = 8038;
+        break;
+      case 8047:
+        ret = 8039;
+        break;
+      case 8072:
+        ret = 8064;
+        break;
+      case 8073:
+        ret = 8065;
+        break;
+      case 8074:
+        ret = 8066;
+        break;
+      case 8075:
+        ret = 8067;
+        break;
+      case 8076:
+        ret = 8068;
+        break;
+      case 8077:
+        ret = 8069;
+        break;
+      case 8078:
+        ret = 8070;
+        break;
+      case 8079:
+        ret = 8071;
+        break;
+      case 8088:
+        ret = 8080;
+        break;
+      case 8089:
+        ret = 8081;
+        break;
+      case 8090:
+        ret = 8082;
+        break;
+      case 8091:
+        ret = 8083;
+        break;
+      case 8092:
+        ret = 8084;
+        break;
+      case 8093:
+        ret = 8085;
+        break;
+      case 8094:
+        ret = 8086;
+        break;
+      case 8095:
+        ret = 8087;
+        break;
+      case 8104:
+        ret = 8096;
+        break;
+      case 8105:
+        ret = 8097;
+        break;
+      case 8106:
+        ret = 8098;
+        break;
+      case 8107:
+        ret = 8099;
+        break;
+      case 8108:
+        ret = 8100;
+        break;
+      case 8109:
+        ret = 8101;
+        break;
+      case 8110:
+        ret = 8102;
+        break;
+      case 8111:
+        ret = 8103;
+        break;
+      case 8120:
+        ret = 8112;
+        break;
+      case 8121:
+        ret = 8113;
+        break;
+      case 8122:
+        ret = 8048;
+        break;
+      case 8123:
+        ret = 8049;
+        break;
+      case 8124:
+        ret = 8115;
+        break;
+      case 8136:
+        ret = 8050;
+        break;
+      case 8137:
+        ret = 8051;
+        break;
+      case 8138:
+        ret = 8052;
+        break;
+      case 8139:
+        ret = 8053;
+        break;
+      case 8140:
+        ret = 8131;
+        break;
+      case 8152:
+        ret = 8144;
+        break;
+      case 8153:
+        ret = 8145;
+        break;
+      case 8154:
+        ret = 8054;
+        break;
+      case 8155:
+        ret = 8055;
+        break;
+      case 8168:
+        ret = 8160;
+        break;
+      case 8169:
+        ret = 8161;
+        break;
+      case 8170:
+        ret = 8058;
+        break;
+      case 8171:
+        ret = 8059;
+        break;
+      case 8172:
+        ret = 8165;
+        break;
+      case 8184:
+        ret = 8056;
+        break;
+      case 8185:
+        ret = 8057;
+        break;
+      case 8186:
+        ret = 8060;
+        break;
+      case 8187:
+        ret = 8061;
+        break;
+      case 8188:
+        ret = 8179;
+        break;
+      case 8544:
+        ret = 8560;
+        break;
+      case 8545:
+        ret = 8561;
+        break;
+      case 8546:
+        ret = 8562;
+        break;
+      case 8547:
+        ret = 8563;
+        break;
+      case 8548:
+        ret = 8564;
+        break;
+      case 8549:
+        ret = 8565;
+        break;
+      case 8550:
+        ret = 8566;
+        break;
+      case 8551:
+        ret = 8567;
+        break;
+      case 8552:
+        ret = 8568;
+        break;
+      case 8553:
+        ret = 8569;
+        break;
+      case 8554:
+        ret = 8570;
+        break;
+      case 8555:
+        ret = 8571;
+        break;
+      case 8556:
+        ret = 8572;
+        break;
+      case 8557:
+        ret = 8573;
+        break;
+      case 8558:
+        ret = 8574;
+        break;
+      case 8559:
+        ret = 8575;
+        break;
+      case 9398:
+        ret = 9424;
+        break;
+      case 9399:
+        ret = 9425;
+        break;
+      case 9400:
+        ret = 9426;
+        break;
+      case 9401:
+        ret = 9427;
+        break;
+      case 9402:
+        ret = 9428;
+        break;
+      case 9403:
+        ret = 9429;
+        break;
+      case 9404:
+        ret = 9430;
+        break;
+      case 9405:
+        ret = 9431;
+        break;
+      case 9406:
+        ret = 9432;
+        break;
+      case 9407:
+        ret = 9433;
+        break;
+      case 9408:
+        ret = 9434;
+        break;
+      case 9409:
+        ret = 9435;
+        break;
+      case 9410:
+        ret = 9436;
+        break;
+      case 9411:
+        ret = 9437;
+        break;
+      case 9412:
+        ret = 9438;
+        break;
+      case 9413:
+        ret = 9439;
+        break;
+      case 9414:
+        ret = 9440;
+        break;
+      case 9415:
+        ret = 9441;
+        break;
+      case 9416:
+        ret = 9442;
+        break;
+      case 9417:
+        ret = 9443;
+        break;
+      case 9418:
+        ret = 9444;
+        break;
+      case 9419:
+        ret = 9445;
+        break;
+      case 9420:
+        ret = 9446;
+        break;
+      case 9421:
+        ret = 9447;
+        break;
+      case 9422:
+        ret = 9448;
+        break;
+      case 9423:
+        ret = 9449;
+        break;
+      case 65313:
+        ret = 65345;
+        break;
+      case 65314:
+        ret = 65346;
+        break;
+      case 65315:
+        ret = 65347;
+        break;
+      case 65316:
+        ret = 65348;
+        break;
+      case 65317:
+        ret = 65349;
+        break;
+      case 65318:
+        ret = 65350;
+        break;
+      case 65319:
+        ret = 65351;
+        break;
+      case 65320:
+        ret = 65352;
+        break;
+      case 65321:
+        ret = 65353;
+        break;
+      case 65322:
+        ret = 65354;
+        break;
+      case 65323:
+        ret = 65355;
+        break;
+      case 65324:
+        ret = 65356;
+        break;
+      case 65325:
+        ret = 65357;
+        break;
+      case 65326:
+        ret = 65358;
+        break;
+      case 65327:
+        ret = 65359;
+        break;
+      case 65328:
+        ret = 65360;
+        break;
+      case 65329:
+        ret = 65361;
+        break;
+      case 65330:
+        ret = 65362;
+        break;
+      case 65331:
+        ret = 65363;
+        break;
+      case 65332:
+        ret = 65364;
+        break;
+      case 65333:
+        ret = 65365;
+        break;
+      case 65334:
+        ret = 65366;
+        break;
+      case 65335:
+        ret = 65367;
+        break;
+      case 65336:
+        ret = 65368;
+        break;
+      case 65337:
+        ret = 65369;
+        break;
+      case 65338:
+        ret = 65370;
+        break;
+      }
+      return (char) ret;
+    }
+    return Character.toLowerCase(c);
+  }
+
+  /** Convert a String to title case. */
+  public static String toTitleCase(String s)
+  {
+    StringBuffer sb = new StringBuffer();
+    for (int i = 0; i < s.length(); i++)
+    {
+      sb.append(CaseMgr.toTitleCase(s.charAt(i)));
+    }
+    return sb.toString();
+  }
+
+  /** Convert a String to upper case. */
+  public static String toUpperCase(String s)
+  {
+    StringBuffer sb = new StringBuffer();
+    for (int i = 0; i < s.length(); i++)
+    {
+      sb.append(CaseMgr.toUpperCase(s.charAt(i)));
+    }
+    return sb.toString();
+  }
+
+  /** Convert a String to lower case. */
+  public static String toLowerCase(String s)
+  {
+    StringBuffer sb = new StringBuffer();
+    for (int i = 0; i < s.length(); i++)
+    {
+      sb.append(CaseMgr.toLowerCase(s.charAt(i)));
+    }
+    return sb.toString();
+  }
+
+  /** Convert a character to title case. */
+  public static char toTitleCase(char c)
+  {
+    if (java_1_0)
+    {
+      int ret = (int) toUpperCase(c);
+      switch (c)
+      {
+      case 452:
+        ret = 453;
+        break;
+      case 453:
+        ret = 453;
+        break;
+      case 454:
+        ret = 453;
+        break;
+      case 455:
+        ret = 456;
+        break;
+      case 456:
+        ret = 456;
+        break;
+      case 457:
+        ret = 456;
+        break;
+      case 458:
+        ret = 459;
+        break;
+      case 459:
+        ret = 459;
+        break;
+      case 460:
+        ret = 459;
+        break;
+      case 497:
+        ret = 498;
+        break;
+      case 498:
+        ret = 498;
+        break;
+      case 499:
+        ret = 498;
+        break;
+      }
+      return (char) ret;
+    }
+    return Character.toTitleCase(c);
+  }
+
+  /**
+   * Duplicates the regionMatches routine of String -- but makes use of the
+   * definitions of upper, lower, and title case in this class when ignoreCase
+   * is set.
+   */
+  public static boolean regionMatches(StringLike s1, boolean ign, int i1,
+          StringLike s2, int i2, int i3)
+  {
+    int itot = i2 + i3;
+    if (itot > s2.length() || i1 + i3 > s1.length())
+    {
+      return false;
+    }
+    if (!ign)
+    {
+      for (int i = i2; i < itot; i++)
+      {
+        if (s2.charAt(i) != s1.charAt(i1++))
+        {
+          return false;
+        }
+      }
+    }
+    else
+    {
+      for (int i = i2; i < itot; i++)
+      {
+        if (toLowerCase(s2.charAt(i)) != toLowerCase(s1.charAt(i1++)))
+        {
+          return false;
+        }
+      }
+    }
+    return true;
+  }
+
+  /**
+   * Duplicates the regionMatches routine of String -- but makes use of the
+   * definitions of upper, lower, and title case in this class when ignoreCase
+   * is set.
+   */
+  public static boolean regionMatches(String s1, boolean ign, int i1,
+          StringLike s2, int i2, int i3)
+  {
+    int itot = i2 + i3;
+    if (itot > s2.length() || i1 + i3 > s1.length())
+    {
+      return false;
+    }
+    if (!ign)
+    {
+      for (int i = i2; i < itot; i++)
+      {
+        if (s2.charAt(i) != s1.charAt(i1++))
+        {
+          return false;
+        }
+      }
+    }
+    else
+    {
+      for (int i = i2; i < itot; i++)
+      {
+        if (toLowerCase(s2.charAt(i)) != toLowerCase(s1.charAt(i1++)))
+        {
+          return false;
+        }
+      }
+    }
+    return true;
+  }
+
+  /**
+   * Duplicates the regionMatches routine of String -- but makes use of the
+   * definitions of upper, lower, and title case in this class when ignoreCase
+   * is set.
+   */
+  public static boolean regionMatches(StringLike s1, boolean ign, int i1,
+          String s2, int i2, int i3)
+  {
+    int itot = i2 + i3;
+    if (itot > s2.length() || i1 + i3 > s1.length())
+    {
+      return false;
+    }
+    if (!ign)
+    {
+      for (int i = i2; i < itot; i++)
+      {
+        if (s2.charAt(i) != s1.charAt(i1++))
+        {
+          return false;
+        }
+      }
+    }
+    else
+    {
+      for (int i = i2; i < itot; i++)
+      {
+        if (toLowerCase(s2.charAt(i)) != toLowerCase(s1.charAt(i1++)))
+        {
+          return false;
+        }
+      }
+    }
+    return true;
+  }
+
+  /**
+   * Duplicates the regionMatches routine of String -- but makes use of the
+   * definitions of upper, lower, and title case in this class when ignoreCase
+   * is set.
+   */
+  public static boolean regionMatches(String s1, boolean ign, int i1,
+          String s2, int i2, int i3)
+  {
+    int itot = i2 + i3;
+    if (itot > s2.length() || i1 + i3 > s1.length())
+    {
+      return false;
+    }
+    if (!ign)
+    {
+      for (int i = i2; i < itot; i++)
+      {
+        if (s2.charAt(i) != s1.charAt(i1++))
+        {
+          return false;
+        }
+      }
+    }
+    else
+    {
+      for (int i = i2; i < itot; i++)
+      {
+        if (toLowerCase(s2.charAt(i)) != toLowerCase(s1.charAt(i1++)))
+        {
+          return false;
+        }
+      }
+    }
+    return true;
+  }
+}
diff --git a/src/com/stevesoft/pat/ChangeRule.java b/src/com/stevesoft/pat/ChangeRule.java
index 31046ee..e8ef5df 100755
--- a/src/com/stevesoft/pat/ChangeRule.java
+++ b/src/com/stevesoft/pat/ChangeRule.java
@@ -1,47 +1,50 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-/** This class implements user defined special replacement rules
- * of the form ${=name}. See <a href="http://javaregex.com/code/trans2.java.html">trans2.java</a>
- * and <a href="http://javaregex.com/code/trans2a.java.html">trans2a.java</a>.
- */
-public class ChangeRule
-    extends SpecialRule
-{
-  Regex NewRule;
-  public ChangeRule(ChangeRule c)
-  {
-    NewRule = c.NewRule;
-  }
-
-  public ChangeRule(String nm, Regex rr)
-  {
-    name = nm;
-    NewRule = rr;
-  }
-
-  public ChangeRule(String nm, Transformer tr)
-  {
-    name = nm;
-    NewRule = tr.rp;
-  }
-
-  public Object clone1()
-  {
-    return new ChangeRule(this);
-  }
-
-  public String toString1()
-  {
-    return "${=" + name + "}";
-  }
-
-  public void apply(StringBufferLike sb, RegRes rr)
-  {}
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+/**
+ * This class implements user defined special replacement rules of the form
+ * ${=name}. See <a
+ * href="http://javaregex.com/code/trans2.java.html">trans2.java</a> and <a
+ * href="http://javaregex.com/code/trans2a.java.html">trans2a.java</a>.
+ */
+public class ChangeRule extends SpecialRule
+{
+  Regex NewRule;
+
+  public ChangeRule(ChangeRule c)
+  {
+    NewRule = c.NewRule;
+  }
+
+  public ChangeRule(String nm, Regex rr)
+  {
+    name = nm;
+    NewRule = rr;
+  }
+
+  public ChangeRule(String nm, Transformer tr)
+  {
+    name = nm;
+    NewRule = tr.rp;
+  }
+
+  public Object clone1()
+  {
+    return new ChangeRule(this);
+  }
+
+  public String toString1()
+  {
+    return "${=" + name + "}";
+  }
+
+  public void apply(StringBufferLike sb, RegRes rr)
+  {
+  }
+}
diff --git a/src/com/stevesoft/pat/CodeRule.java b/src/com/stevesoft/pat/CodeRule.java
index 763bf3e..aa9c4dc 100755
--- a/src/com/stevesoft/pat/CodeRule.java
+++ b/src/com/stevesoft/pat/CodeRule.java
@@ -1,32 +1,33 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-/** Implements the rules for \U, \L, \E, \Q in substitutions. */
-public final class CodeRule
-    extends SpecialRule
-{
-  char c = 'E';
-  public CodeRule()
-  {}
-
-  public CodeRule(char c)
-  {
-    this.c = c;
-  }
-
-  public void apply(StringBufferLike sb, RegRes res)
-  {
-    sb.setMode(c);
-  }
-
-  public String toString1()
-  {
-    return "\\" + c;
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+/** Implements the rules for \U, \L, \E, \Q in substitutions. */
+public final class CodeRule extends SpecialRule
+{
+  char c = 'E';
+
+  public CodeRule()
+  {
+  }
+
+  public CodeRule(char c)
+  {
+    this.c = c;
+  }
+
+  public void apply(StringBufferLike sb, RegRes res)
+  {
+    sb.setMode(c);
+  }
+
+  public String toString1()
+  {
+    return "\\" + c;
+  }
+}
diff --git a/src/com/stevesoft/pat/Ctrl.java b/src/com/stevesoft/pat/Ctrl.java
index 6fee70f..5d40098 100755
--- a/src/com/stevesoft/pat/Ctrl.java
+++ b/src/com/stevesoft/pat/Ctrl.java
@@ -1,271 +1,61 @@
-package //
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-    com.stevesoft.pat;
-
-public class Ctrl
-{
-  public final static char[] cmap =
-      {
-      (char) 64,
-      (char) 65,
-      (char) 66,
-      (char) 67,
-      (char) 68,
-      (char) 69,
-      (char) 70,
-      (char) 71,
-      (char) 72,
-      (char) 73,
-      (char) 74,
-      (char) 75,
-      (char) 76,
-      (char) 77,
-      (char) 78,
-      (char) 79,
-      (char) 80,
-      (char) 81,
-      (char) 82,
-      (char) 83,
-      (char) 84,
-      (char) 85,
-      (char) 86,
-      (char) 87,
-      (char) 88,
-      (char) 89,
-      (char) 90,
-      (char) 91,
-      (char) 92,
-      (char) 93,
-      (char) 94,
-      (char) 95,
-      (char) 96,
-      (char) 97,
-      (char) 97,
-      (char) 99,
-      (char) 100,
-      (char) 101,
-      (char) 102,
-      (char) 103,
-      (char) 104,
-      (char) 105,
-      (char) 106,
-      (char) 107,
-      (char) 108,
-      (char) 109,
-      (char) 110,
-      (char) 111,
-      (char) 112,
-      (char) 113,
-      (char) 114,
-      (char) 115,
-      (char) 116,
-      (char) 117,
-      (char) 118,
-      (char) 119,
-      (char) 120,
-      (char) 121,
-      (char) 122,
-      (char) 123,
-      (char) 124,
-      (char) 125,
-      (char) 126,
-      (char) 127,
-      (char) 0,
-      (char) 1,
-      (char) 2,
-      (char) 3,
-      (char) 4,
-      (char) 5,
-      (char) 6,
-      (char) 7,
-      (char) 8,
-      (char) 9,
-      (char) 10,
-      (char) 11,
-      (char) 12,
-      (char) 13,
-      (char) 14,
-      (char) 15,
-      (char) 16,
-      (char) 17,
-      (char) 18,
-      (char) 19,
-      (char) 20,
-      (char) 21,
-      (char) 22,
-      (char) 23,
-      (char) 24,
-      (char) 25,
-      (char) 26,
-      (char) 27,
-      (char) 27,
-      (char) 29,
-      (char) 30,
-      (char) 31,
-      (char) 32,
-      (char) 1,
-      (char) 2,
-      (char) 3,
-      (char) 4,
-      (char) 5,
-      (char) 6,
-      (char) 7,
-      (char) 8,
-      (char) 9,
-      (char) 10,
-      (char) 11,
-      (char) 12,
-      (char) 13,
-      (char) 14,
-      (char) 15,
-      (char) 16,
-      (char) 17,
-      (char) 18,
-      (char) 19,
-      (char) 20,
-      (char) 21,
-      (char) 22,
-      (char) 23,
-      (char) 24,
-      (char) 25,
-      (char) 26,
-      (char) 59,
-      (char) 60,
-      (char) 61,
-      (char) 62,
-      (char) 63,
-      (char) 192,
-      (char) 193,
-      (char) 194,
-      (char) 195,
-      (char) 196,
-      (char) 197,
-      (char) 198,
-      (char) 199,
-      (char) 200,
-      (char) 201,
-      (char) 202,
-      (char) 203,
-      (char) 204,
-      (char) 205,
-      (char) 206,
-      (char) 207,
-      (char) 208,
-      (char) 209,
-      (char) 210,
-      (char) 211,
-      (char) 212,
-      (char) 213,
-      (char) 214,
-      (char) 215,
-      (char) 216,
-      (char) 217,
-      (char) 218,
-      (char) 219,
-      (char) 220,
-      (char) 221,
-      (char) 222,
-      (char) 223,
-      (char) 224,
-      (char) 225,
-      (char) 226,
-      (char) 227,
-      (char) 228,
-      (char) 229,
-      (char) 230,
-      (char) 231,
-      (char) 232,
-      (char) 233,
-      (char) 234,
-      (char) 235,
-      (char) 236,
-      (char) 237,
-      (char) 238,
-      (char) 239,
-      (char) 240,
-      (char) 241,
-      (char) 242,
-      (char) 243,
-      (char) 244,
-      (char) 245,
-      (char) 246,
-      (char) 247,
-      (char) 248,
-      (char) 249,
-      (char) 250,
-      (char) 251,
-      (char) 252,
-      (char) 253,
-      (char) 254,
-      (char) 255,
-      (char) 128,
-      (char) 129,
-      (char) 130,
-      (char) 131,
-      (char) 132,
-      (char) 133,
-      (char) 134,
-      (char) 135,
-      (char) 136,
-      (char) 137,
-      (char) 138,
-      (char) 139,
-      (char) 140,
-      (char) 141,
-      (char) 142,
-      (char) 143,
-      (char) 144,
-      (char) 145,
-      (char) 146,
-      (char) 147,
-      (char) 148,
-      (char) 149,
-      (char) 150,
-      (char) 151,
-      (char) 152,
-      (char) 153,
-      (char) 154,
-      (char) 155,
-      (char) 156,
-      (char) 157,
-      (char) 158,
-      (char) 159,
-      (char) 160,
-      (char) 161,
-      (char) 162,
-      (char) 163,
-      (char) 164,
-      (char) 165,
-      (char) 166,
-      (char) 167,
-      (char) 168,
-      (char) 169,
-      (char) 170,
-      (char) 171,
-      (char) 172,
-      (char) 173,
-      (char) 174,
-      (char) 175,
-      (char) 176,
-      (char) 177,
-      (char) 178,
-      (char) 179,
-      (char) 180,
-      (char) 181,
-      (char) 182,
-      (char) 183,
-      (char) 184,
-      (char) 185,
-      (char) 186,
-      (char) 187,
-      (char) 188,
-      (char) 189,
-      (char) 190,
-      (char) 191
-  };
-}
+package //
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+com.stevesoft.pat;
+
+public class Ctrl
+{
+  public final static char[] cmap =
+  { (char) 64, (char) 65, (char) 66, (char) 67, (char) 68, (char) 69,
+      (char) 70, (char) 71, (char) 72, (char) 73, (char) 74, (char) 75,
+      (char) 76, (char) 77, (char) 78, (char) 79, (char) 80, (char) 81,
+      (char) 82, (char) 83, (char) 84, (char) 85, (char) 86, (char) 87,
+      (char) 88, (char) 89, (char) 90, (char) 91, (char) 92, (char) 93,
+      (char) 94, (char) 95, (char) 96, (char) 97, (char) 97, (char) 99,
+      (char) 100, (char) 101, (char) 102, (char) 103, (char) 104,
+      (char) 105, (char) 106, (char) 107, (char) 108, (char) 109,
+      (char) 110, (char) 111, (char) 112, (char) 113, (char) 114,
+      (char) 115, (char) 116, (char) 117, (char) 118, (char) 119,
+      (char) 120, (char) 121, (char) 122, (char) 123, (char) 124,
+      (char) 125, (char) 126, (char) 127, (char) 0, (char) 1, (char) 2,
+      (char) 3, (char) 4, (char) 5, (char) 6, (char) 7, (char) 8, (char) 9,
+      (char) 10, (char) 11, (char) 12, (char) 13, (char) 14, (char) 15,
+      (char) 16, (char) 17, (char) 18, (char) 19, (char) 20, (char) 21,
+      (char) 22, (char) 23, (char) 24, (char) 25, (char) 26, (char) 27,
+      (char) 27, (char) 29, (char) 30, (char) 31, (char) 32, (char) 1,
+      (char) 2, (char) 3, (char) 4, (char) 5, (char) 6, (char) 7, (char) 8,
+      (char) 9, (char) 10, (char) 11, (char) 12, (char) 13, (char) 14,
+      (char) 15, (char) 16, (char) 17, (char) 18, (char) 19, (char) 20,
+      (char) 21, (char) 22, (char) 23, (char) 24, (char) 25, (char) 26,
+      (char) 59, (char) 60, (char) 61, (char) 62, (char) 63, (char) 192,
+      (char) 193, (char) 194, (char) 195, (char) 196, (char) 197,
+      (char) 198, (char) 199, (char) 200, (char) 201, (char) 202,
+      (char) 203, (char) 204, (char) 205, (char) 206, (char) 207,
+      (char) 208, (char) 209, (char) 210, (char) 211, (char) 212,
+      (char) 213, (char) 214, (char) 215, (char) 216, (char) 217,
+      (char) 218, (char) 219, (char) 220, (char) 221, (char) 222,
+      (char) 223, (char) 224, (char) 225, (char) 226, (char) 227,
+      (char) 228, (char) 229, (char) 230, (char) 231, (char) 232,
+      (char) 233, (char) 234, (char) 235, (char) 236, (char) 237,
+      (char) 238, (char) 239, (char) 240, (char) 241, (char) 242,
+      (char) 243, (char) 244, (char) 245, (char) 246, (char) 247,
+      (char) 248, (char) 249, (char) 250, (char) 251, (char) 252,
+      (char) 253, (char) 254, (char) 255, (char) 128, (char) 129,
+      (char) 130, (char) 131, (char) 132, (char) 133, (char) 134,
+      (char) 135, (char) 136, (char) 137, (char) 138, (char) 139,
+      (char) 140, (char) 141, (char) 142, (char) 143, (char) 144,
+      (char) 145, (char) 146, (char) 147, (char) 148, (char) 149,
+      (char) 150, (char) 151, (char) 152, (char) 153, (char) 154,
+      (char) 155, (char) 156, (char) 157, (char) 158, (char) 159,
+      (char) 160, (char) 161, (char) 162, (char) 163, (char) 164,
+      (char) 165, (char) 166, (char) 167, (char) 168, (char) 169,
+      (char) 170, (char) 171, (char) 172, (char) 173, (char) 174,
+      (char) 175, (char) 176, (char) 177, (char) 178, (char) 179,
+      (char) 180, (char) 181, (char) 182, (char) 183, (char) 184,
+      (char) 185, (char) 186, (char) 187, (char) 188, (char) 189,
+      (char) 190, (char) 191 };
+}
diff --git a/src/com/stevesoft/pat/Custom.java b/src/com/stevesoft/pat/Custom.java
index 72aebc7..61879ac 100755
--- a/src/com/stevesoft/pat/Custom.java
+++ b/src/com/stevesoft/pat/Custom.java
@@ -1,60 +1,64 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-import java.util.*;
-
-/** Simple custom patterns.  See
-    <a href="http://javaregex.com/code/deriv2.java.html">deriv2.java</a>
-    and <a href="http://javaregex.com/code/deriv3.java.html">deriv3.java</a>
-    in the test directory.
-    @see com.stevesoft.pat.CustomEndpoint
- */
-class Custom
-    extends PatternSub
-{
-  String select;
-  Validator v;
-  int start;
-  Custom(String s)
-  {
-    select = s;
-    v = (Validator) Regex.validators.get(s);
-  }
-
-  public int matchInternal(int pos, Pthings pt)
-  {
-    start = pos;
-    return sub.matchInternal(pos, pt);
-  }
-
-  public String toString()
-  {
-    String a = v.argsave == null ? "" : ":" + v.argsave;
-    return "(??" + select + a + ")" + nextString();
-  }
-
-  public patInt minChars()
-  {
-    return v.minChars();
-  }
-
-  public patInt maxChars()
-  {
-    return v.maxChars();
-  }
-
-  Pattern clone1(Hashtable h)
-  {
-    Custom c = new Custom(select);
-    h.put(c, c);
-    h.put(this, c);
-    c.sub = sub.clone(h);
-    return c;
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+import java.util.*;
+
+/**
+ * Simple custom patterns. See <a
+ * href="http://javaregex.com/code/deriv2.java.html">deriv2.java</a> and <a
+ * href="http://javaregex.com/code/deriv3.java.html">deriv3.java</a> in the
+ * test directory.
+ * 
+ * @see com.stevesoft.pat.CustomEndpoint
+ */
+class Custom extends PatternSub
+{
+  String select;
+
+  Validator v;
+
+  int start;
+
+  Custom(String s)
+  {
+    select = s;
+    v = (Validator) Regex.validators.get(s);
+  }
+
+  public int matchInternal(int pos, Pthings pt)
+  {
+    start = pos;
+    return sub.matchInternal(pos, pt);
+  }
+
+  public String toString()
+  {
+    String a = v.argsave == null ? "" : ":" + v.argsave;
+    return "(??" + select + a + ")" + nextString();
+  }
+
+  public patInt minChars()
+  {
+    return v.minChars();
+  }
+
+  public patInt maxChars()
+  {
+    return v.maxChars();
+  }
+
+  Pattern clone1(Hashtable h)
+  {
+    Custom c = new Custom(select);
+    h.put(c, c);
+    h.put(this, c);
+    c.sub = sub.clone(h);
+    return c;
+  }
+}
diff --git a/src/com/stevesoft/pat/CustomEndpoint.java b/src/com/stevesoft/pat/CustomEndpoint.java
index ac6c4ba..9608f7e 100755
--- a/src/com/stevesoft/pat/CustomEndpoint.java
+++ b/src/com/stevesoft/pat/CustomEndpoint.java
@@ -1,43 +1,44 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-import java.util.*;
-
-/** This class is needed internally to make backtracking work
- * correctly in user-defined patterns.
- */
-class CustomEndpoint
-    extends Pattern
-{
-  Custom c;
-  CustomEndpoint(Custom cm)
-  {
-    c = cm;
-  }
-
-  public int matchInternal(int pos, Pthings pt)
-  {
-    int npos = c.v.validate(pt.src, c.start, pos);
-    if (npos >= 0)
-    {
-      return nextMatch(npos, pt);
-    }
-    return -1;
-  }
-
-  public String toString()
-  {
-    return "";
-  }
-
-  Pattern clone1(Hashtable h)
-  {
-    return new CustomEndpoint( (Custom) c.clone(h));
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+import java.util.*;
+
+/**
+ * This class is needed internally to make backtracking work correctly in
+ * user-defined patterns.
+ */
+class CustomEndpoint extends Pattern
+{
+  Custom c;
+
+  CustomEndpoint(Custom cm)
+  {
+    c = cm;
+  }
+
+  public int matchInternal(int pos, Pthings pt)
+  {
+    int npos = c.v.validate(pt.src, c.start, pos);
+    if (npos >= 0)
+    {
+      return nextMatch(npos, pt);
+    }
+    return -1;
+  }
+
+  public String toString()
+  {
+    return "";
+  }
+
+  Pattern clone1(Hashtable h)
+  {
+    return new CustomEndpoint((Custom) c.clone(h));
+  }
+}
diff --git a/src/com/stevesoft/pat/DirFileRegex.java b/src/com/stevesoft/pat/DirFileRegex.java
index 24c0cf6..bc62910 100755
--- a/src/com/stevesoft/pat/DirFileRegex.java
+++ b/src/com/stevesoft/pat/DirFileRegex.java
@@ -1,30 +1,31 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-/** This class is just like FileRegex, except that its accept method
- only returns true if the file matching the pattern is a directory.*/
-public class DirFileRegex
-    extends FileRegex
-{
-  public DirFileRegex()
-  {
-    dirflag = DIR;
-  }
-
-  public DirFileRegex(String fp)
-  {
-    super(fp);
-    dirflag = DIR;
-  }
-
-  public static String[] list(String f)
-  {
-    return list(f, DIR);
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+/**
+ * This class is just like FileRegex, except that its accept method only returns
+ * true if the file matching the pattern is a directory.
+ */
+public class DirFileRegex extends FileRegex
+{
+  public DirFileRegex()
+  {
+    dirflag = DIR;
+  }
+
+  public DirFileRegex(String fp)
+  {
+    super(fp);
+    dirflag = DIR;
+  }
+
+  public static String[] list(String f)
+  {
+    return list(f, DIR);
+  }
+}
diff --git a/src/com/stevesoft/pat/DotMulti.java b/src/com/stevesoft/pat/DotMulti.java
index 4691728..cc5f094 100755
--- a/src/com/stevesoft/pat/DotMulti.java
+++ b/src/com/stevesoft/pat/DotMulti.java
@@ -1,205 +1,209 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-import java.util.*;
-
-/** A special optimization of multi that is used when the
- * common subpattern ".*" is encountered.
- */
-class DotMulti
-    extends PatternSub
-{
-  patInt fewestMatches, mostMatches;
-  public patInt minChars()
-  {
-    return fewestMatches;
-  }
-
-  public patInt maxChars()
-  {
-    return mostMatches;
-  }
-
-  public boolean matchFewest = false;
-
-  StringLike src = null;
-  int srclength = 0;
-  boolean dotDoesntMatchCR = true;
-  DotMulti(patInt a, patInt b)
-  {
-    fewestMatches = a;
-    mostMatches = b;
-  }
-
-  public String toString()
-  {
-    return ".{"
-        + fewestMatches + "," + mostMatches + "}" +
-        (matchFewest ? "?" : "") + "(?# <= dot multi)" +
-        nextString();
-  }
-
-  final int submatchInternal(int pos, Pthings pt)
-  {
-    if (pos < srclength)
-    {
-      if (dotDoesntMatchCR)
-      {
-        if (src.charAt(pos) != '\n')
-        {
-          return 1 + pos;
-        }
-      }
-      else
-      {
-        return 1 + pos;
-      }
-    }
-    return -1;
-  }
-
-  final static int step = 1;
-  static int idcount = 1;
-  public int matchInternal(int pos, Pthings pt)
-  {
-    int m = -1;
-    int i = pos;
-    src = pt.src;
-    srclength = src.length();
-    dotDoesntMatchCR = pt.dotDoesntMatchCR;
-    if (matchFewest)
-    {
-      int nMatches = 0;
-      while (fewestMatches.intValue() > nMatches)
-      {
-        i = submatchInternal(i, pt);
-        if (i < 0)
-        {
-          return -1;
-        }
-        nMatches++;
-      }
-      if (i < 0)
-      {
-        return -1;
-      }
-      int ii = nextMatch(i, pt);
-      if (ii >= 0)
-      {
-        return ii;
-      }
-      if (!mostMatches.finite())
-      {
-        while (i >= 0)
-        {
-          i = submatchInternal(i, pt);
-          if (i < 0)
-          {
-            return -1;
-          }
-          ii = nextMatch(i, pt);
-          if (ii >= 0)
-          {
-            return ii;
-          }
-        }
-      }
-      else
-      {
-        while (i > 0)
-        {
-          i = submatchInternal(i, pt);
-          if (i < 0)
-          {
-            return -1;
-          }
-          nMatches++;
-          if (nMatches > mostMatches.intValue())
-          {
-            return -1;
-          }
-          ii = nextMatch(i, pt);
-          if (ii >= 0)
-          {
-            return ii;
-          }
-        }
-      }
-      return -1;
-    }
-    int nMatches = 0;
-    while (fewestMatches.intValue() > nMatches)
-    {
-      i = submatchInternal(i, pt);
-      if (i >= 0)
-      {
-        nMatches++;
-      }
-      else
-      {
-        return -1;
-      }
-    }
-    m = i;
-    if (mostMatches.finite())
-    {
-      while (nMatches < mostMatches.intValue())
-      {
-        i = submatchInternal(i, pt);
-        if (i >= 0)
-        {
-          m = i;
-          nMatches++;
-        }
-        else
-        {
-          break;
-        }
-      }
-    }
-    else
-    {
-      while (true)
-      {
-        i = submatchInternal(i, pt);
-        if (i >= 0)
-        {
-          m = i;
-          nMatches++;
-        }
-        else
-        {
-          break;
-        }
-      }
-    }
-    while (m >= pos)
-    {
-      int r = nextMatch(m, pt);
-      if (r >= 0)
-      {
-        return r;
-      }
-      m -= step;
-      nMatches--;
-      if (nMatches < fewestMatches.intValue())
-      {
-        return -1;
-      }
-    }
-    return -1;
-  }
-
-  Pattern clone1(Hashtable h)
-  {
-    DotMulti dm = new DotMulti(fewestMatches, mostMatches);
-    dm.matchFewest = matchFewest;
-    return dm;
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+import java.util.*;
+
+/**
+ * A special optimization of multi that is used when the common subpattern ".*"
+ * is encountered.
+ */
+class DotMulti extends PatternSub
+{
+  patInt fewestMatches, mostMatches;
+
+  public patInt minChars()
+  {
+    return fewestMatches;
+  }
+
+  public patInt maxChars()
+  {
+    return mostMatches;
+  }
+
+  public boolean matchFewest = false;
+
+  StringLike src = null;
+
+  int srclength = 0;
+
+  boolean dotDoesntMatchCR = true;
+
+  DotMulti(patInt a, patInt b)
+  {
+    fewestMatches = a;
+    mostMatches = b;
+  }
+
+  public String toString()
+  {
+    return ".{" + fewestMatches + "," + mostMatches + "}"
+            + (matchFewest ? "?" : "") + "(?# <= dot multi)" + nextString();
+  }
+
+  final int submatchInternal(int pos, Pthings pt)
+  {
+    if (pos < srclength)
+    {
+      if (dotDoesntMatchCR)
+      {
+        if (src.charAt(pos) != '\n')
+        {
+          return 1 + pos;
+        }
+      }
+      else
+      {
+        return 1 + pos;
+      }
+    }
+    return -1;
+  }
+
+  final static int step = 1;
+
+  static int idcount = 1;
+
+  public int matchInternal(int pos, Pthings pt)
+  {
+    int m = -1;
+    int i = pos;
+    src = pt.src;
+    srclength = src.length();
+    dotDoesntMatchCR = pt.dotDoesntMatchCR;
+    if (matchFewest)
+    {
+      int nMatches = 0;
+      while (fewestMatches.intValue() > nMatches)
+      {
+        i = submatchInternal(i, pt);
+        if (i < 0)
+        {
+          return -1;
+        }
+        nMatches++;
+      }
+      if (i < 0)
+      {
+        return -1;
+      }
+      int ii = nextMatch(i, pt);
+      if (ii >= 0)
+      {
+        return ii;
+      }
+      if (!mostMatches.finite())
+      {
+        while (i >= 0)
+        {
+          i = submatchInternal(i, pt);
+          if (i < 0)
+          {
+            return -1;
+          }
+          ii = nextMatch(i, pt);
+          if (ii >= 0)
+          {
+            return ii;
+          }
+        }
+      }
+      else
+      {
+        while (i > 0)
+        {
+          i = submatchInternal(i, pt);
+          if (i < 0)
+          {
+            return -1;
+          }
+          nMatches++;
+          if (nMatches > mostMatches.intValue())
+          {
+            return -1;
+          }
+          ii = nextMatch(i, pt);
+          if (ii >= 0)
+          {
+            return ii;
+          }
+        }
+      }
+      return -1;
+    }
+    int nMatches = 0;
+    while (fewestMatches.intValue() > nMatches)
+    {
+      i = submatchInternal(i, pt);
+      if (i >= 0)
+      {
+        nMatches++;
+      }
+      else
+      {
+        return -1;
+      }
+    }
+    m = i;
+    if (mostMatches.finite())
+    {
+      while (nMatches < mostMatches.intValue())
+      {
+        i = submatchInternal(i, pt);
+        if (i >= 0)
+        {
+          m = i;
+          nMatches++;
+        }
+        else
+        {
+          break;
+        }
+      }
+    }
+    else
+    {
+      while (true)
+      {
+        i = submatchInternal(i, pt);
+        if (i >= 0)
+        {
+          m = i;
+          nMatches++;
+        }
+        else
+        {
+          break;
+        }
+      }
+    }
+    while (m >= pos)
+    {
+      int r = nextMatch(m, pt);
+      if (r >= 0)
+      {
+        return r;
+      }
+      m -= step;
+      nMatches--;
+      if (nMatches < fewestMatches.intValue())
+      {
+        return -1;
+      }
+    }
+    return -1;
+  }
+
+  Pattern clone1(Hashtable h)
+  {
+    DotMulti dm = new DotMulti(fewestMatches, mostMatches);
+    dm.matchFewest = matchFewest;
+    return dm;
+  }
+}
diff --git a/src/com/stevesoft/pat/End.java b/src/com/stevesoft/pat/End.java
index 42894b3..547f3d6 100755
--- a/src/com/stevesoft/pat/End.java
+++ b/src/com/stevesoft/pat/End.java
@@ -1,70 +1,71 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-import java.util.*;
-
-//class AddToEnd extends RegSyntax {};
-
-/** Compiles the '$' or the '\Z' Pattern.  It is
- an error to have further Pattern elements after
- '\Z'.  It is the end of the String. */
-class End
-    extends Pattern
-{
-  boolean retIsEnd;
-  End(boolean b)
-  {
-    retIsEnd = b;
-  }
-
-  public int matchInternal(int pos, Pthings pt)
-  {
-    if (retIsEnd && pt.mFlag && pos < pt.src.length())
-    {
-      if (pt.src.charAt(pos) == '\n')
-      {
-        return nextMatch(pos, pt);
-      }
-    }
-    if (pt.src.length() == pos)
-    {
-      return nextMatch(pos, pt);
-    }
-    else if (pos < pt.src.length())
-    {
-      // Access the next character...
-      // this is crucial to making
-      // RegexReader work.
-      pt.src.charAt(pos);
-    }
-    return -1;
-  }
-
-  public String toString()
-  {
-    if (retIsEnd)
-    {
-      return "$";
-    }
-    else
-    {
-      return "\\Z";
-    }
-  }
-
-  public patInt maxChars()
-  {
-    return new patInt(1);
-  }
-
-  public Pattern clone1(Hashtable h)
-  {
-    return new End(retIsEnd);
-  }
-};
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+import java.util.*;
+
+//class AddToEnd extends RegSyntax {};
+
+/**
+ * Compiles the '$' or the '\Z' Pattern. It is an error to have further Pattern
+ * elements after '\Z'. It is the end of the String.
+ */
+class End extends Pattern
+{
+  boolean retIsEnd;
+
+  End(boolean b)
+  {
+    retIsEnd = b;
+  }
+
+  public int matchInternal(int pos, Pthings pt)
+  {
+    if (retIsEnd && pt.mFlag && pos < pt.src.length())
+    {
+      if (pt.src.charAt(pos) == '\n')
+      {
+        return nextMatch(pos, pt);
+      }
+    }
+    if (pt.src.length() == pos)
+    {
+      return nextMatch(pos, pt);
+    }
+    else if (pos < pt.src.length())
+    {
+      // Access the next character...
+      // this is crucial to making
+      // RegexReader work.
+      pt.src.charAt(pos);
+    }
+    return -1;
+  }
+
+  public String toString()
+  {
+    if (retIsEnd)
+    {
+      return "$";
+    }
+    else
+    {
+      return "\\Z";
+    }
+  }
+
+  public patInt maxChars()
+  {
+    return new patInt(1);
+  }
+
+  public Pattern clone1(Hashtable h)
+  {
+    return new End(retIsEnd);
+  }
+};
diff --git a/src/com/stevesoft/pat/FastBracket.java b/src/com/stevesoft/pat/FastBracket.java
index 5f5fff0..a10ec2b 100755
--- a/src/com/stevesoft/pat/FastBracket.java
+++ b/src/com/stevesoft/pat/FastBracket.java
@@ -1,256 +1,256 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-import java.util.*;
-
-/** Uses table lookup to match [] type constructs, but
-    only if it can use a lookup table 256 bits in size.
-    It is impractical to make a table if it is too large.
- */
-public class FastBracket
-    extends Bracket
-{
-  int min, max;
-  BitSet bs;
-  FastBracket(boolean n)
-  {
-    super(n);
-  }
-
-  // This routine can optimize a bracket, possibly
-  // it will replace it with a FastBracket.
-  static Bracket process(Bracket b, boolean ignc)
-  {
-    Vector v = b.v;
-    b.pv = null;
-    try
-    {
-
-      // Expand out the vector to make separate
-      // entries for other cases if ignoreCase is
-      // turned on.
-      Vector nv = v;
-      if (ignc)
-      {
-        nv = new Vector();
-        for (int i = 0; i < v.size(); i++)
-        {
-          Pattern p = (Pattern) v.elementAt(i);
-          nv.addElement(p);
-          if (p instanceof oneChar)
-          {
-            oneChar oc = (oneChar) p;
-            nv.addElement(new oneChar(oc.altc));
-          }
-          else if (p instanceof Range)
-          {
-            Range ra = (Range) p;
-            nv.addElement(new Range(ra.altlo, ra.althi));
-          }
-        }
-      }
-      v = nv;
-
-      // Bubble sort, make sure elements
-      // are in order.  This will allow us
-      // to merge them.
-      for (int i = 0; i < v.size() - 1; i++)
-      {
-        for (int j = 0; j < v.size() - 1; j++)
-        {
-          char c1 = getl(v.elementAt(j));
-          char c2 = getl(v.elementAt(j + 1));
-          if (c2 < c1)
-          {
-            Object o = v.elementAt(j);
-            v.setElementAt(v.elementAt(j + 1), j);
-            v.setElementAt(o, j + 1);
-          }
-        }
-      }
-
-      nv = new Vector();
-      // merge -- remove overlaps
-      Pattern p = (Pattern) v.elementAt(0);
-      nv.addElement(p);
-      for (int i = 1; i < v.size(); i++)
-      {
-        if (geth(p) + 1 >= getl(v.elementAt(i)))
-        {
-          Pattern p2 = (Pattern) v.elementAt(i);
-          char lo = min(getl(p), getl(p2));
-          char hi = max(geth(p), geth(p2));
-          nv.setElementAt(p = mkelem(lo, hi), nv.size() - 1);
-        }
-        else
-        {
-          p = (Pattern) v.elementAt(i);
-          nv.addElement(p);
-        }
-      }
-
-      b.v = v = nv;
-    }
-    catch (RegSyntax e)
-    {
-      e.printStackTrace();
-    }
-
-    // We don't want these things to be empty.
-    Vector negv = neg(v);
-    if (v.size() == 1)
-    {
-      return b;
-    }
-    if (negv.size() == 1)
-    {
-      b.v = negv;
-      b.neg = !b.neg;
-      return b;
-    }
-
-    // Now consider if we can make a FastBracket.
-    // Uses a BitSet to do a lookup.
-    FastBracket fb = newbrack(v, b.neg);
-    if (fb == null)
-    {
-      fb = newbrack(negv, !b.neg);
-    }
-    if (fb != null)
-    {
-      fb.parent = b.parent;
-      fb.next = b.next;
-      return fb;
-    }
-
-    // return the normal Bracket.
-    return b;
-  }
-
-  // Build a FastBracket and set bits.  If this can't
-  // be done, return null.
-  final static FastBracket newbrack(Vector v, boolean neg)
-  {
-    FastBracket fb = new FastBracket(neg);
-    fb.v = v;
-    if (v.size() == 0)
-    {
-      return null;
-    }
-    fb.min = getl(v.elementAt(0));
-    fb.max = geth(v.elementAt(v.size() - 1));
-    if (fb.max - fb.min <= 256)
-    {
-      fb.bs = new BitSet(fb.max - fb.min + 1);
-      for (int i = 0; i < v.size(); i++)
-      {
-        Object o = v.elementAt(i);
-        int min0 = getl(o) - fb.min;
-        int max0 = geth(o) - fb.min;
-        for (int j = min0; j <= max0; j++)
-        {
-          fb.bs.set(j);
-        }
-      }
-      return fb;
-    }
-    return null;
-  }
-
-  // Negate a sorted Vector.  Applying this
-  // operation twice should yield the same Vector
-  // back.
-  final static Vector neg(Vector v)
-  {
-    try
-    {
-      Vector nv = new Vector();
-      if (v.size() == 0)
-      {
-        nv.addElement(new Range( (char) 0, (char) 65535));
-        return nv;
-      }
-      int p0 = getl(v.elementAt(0));
-      if (p0 != 0)
-      {
-        nv.addElement(mkelem( (char) 0, (char) (p0 - 1)));
-      }
-      for (int i = 0; i < v.size() - 1; i++)
-      {
-        int hi = getl(v.elementAt(i + 1)) - 1;
-        int lo = geth(v.elementAt(i)) + 1;
-        nv.addElement(mkelem( (char) lo, (char) hi));
-      }
-      int pN = geth(v.lastElement());
-      if (pN != 65535)
-      {
-        nv.addElement(mkelem( (char) (pN + 1), (char) 65535));
-      }
-      return nv;
-    }
-    catch (RegSyntax rs)
-    {
-      return null;
-    }
-  }
-
-  // Make either a Range or oneChar Object, depending on which
-  // is appropriate.
-  final static Pattern mkelem(char lo, char hi)
-      throws RegSyntax
-  {
-    return lo == hi ? (Pattern) (new oneChar(lo)) : (Pattern) (new Range(lo, hi));
-  }
-
-  static final char min(char a, char b)
-  {
-    return a < b ? a : b;
-  }
-
-  static final char max(char a, char b)
-  {
-    return a > b ? a : b;
-  }
-
-  // getl -- get lower value of Range object,
-  // or get value of oneChar object.
-  final static char getl(Object o)
-  {
-    Pattern p = (Pattern) o;
-    if (p instanceof Range)
-    {
-      return ( (Range) p).lo;
-    }
-    return ( (oneChar) p).c;
-  }
-
-  // geth -- get higher value of Range object,
-  // or get value of oneChar object.
-  final static char geth(Object o)
-  {
-    Pattern p = (Pattern) o;
-    if (p instanceof Range)
-    {
-      return ( (Range) p).hi;
-    }
-    return ( (oneChar) p).c;
-  }
-
-  // This is the easy part!
-  public int matchInternal(int pos, Pthings pt)
-  {
-    if (pos >= pt.src.length() || Masked(pos, pt))
-    {
-      return -1;
-    }
-    char c = pt.src.charAt(pos);
-    return (neg ^ (c >= min && c <= max && bs.get(c - min))) ?
-        nextMatch(pos + 1, pt) : -1;
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+import java.util.*;
+
+/**
+ * Uses table lookup to match [] type constructs, but only if it can use a
+ * lookup table 256 bits in size. It is impractical to make a table if it is too
+ * large.
+ */
+public class FastBracket extends Bracket
+{
+  int min, max;
+
+  BitSet bs;
+
+  FastBracket(boolean n)
+  {
+    super(n);
+  }
+
+  // This routine can optimize a bracket, possibly
+  // it will replace it with a FastBracket.
+  static Bracket process(Bracket b, boolean ignc)
+  {
+    Vector v = b.v;
+    b.pv = null;
+    try
+    {
+
+      // Expand out the vector to make separate
+      // entries for other cases if ignoreCase is
+      // turned on.
+      Vector nv = v;
+      if (ignc)
+      {
+        nv = new Vector();
+        for (int i = 0; i < v.size(); i++)
+        {
+          Pattern p = (Pattern) v.elementAt(i);
+          nv.addElement(p);
+          if (p instanceof oneChar)
+          {
+            oneChar oc = (oneChar) p;
+            nv.addElement(new oneChar(oc.altc));
+          }
+          else if (p instanceof Range)
+          {
+            Range ra = (Range) p;
+            nv.addElement(new Range(ra.altlo, ra.althi));
+          }
+        }
+      }
+      v = nv;
+
+      // Bubble sort, make sure elements
+      // are in order. This will allow us
+      // to merge them.
+      for (int i = 0; i < v.size() - 1; i++)
+      {
+        for (int j = 0; j < v.size() - 1; j++)
+        {
+          char c1 = getl(v.elementAt(j));
+          char c2 = getl(v.elementAt(j + 1));
+          if (c2 < c1)
+          {
+            Object o = v.elementAt(j);
+            v.setElementAt(v.elementAt(j + 1), j);
+            v.setElementAt(o, j + 1);
+          }
+        }
+      }
+
+      nv = new Vector();
+      // merge -- remove overlaps
+      Pattern p = (Pattern) v.elementAt(0);
+      nv.addElement(p);
+      for (int i = 1; i < v.size(); i++)
+      {
+        if (geth(p) + 1 >= getl(v.elementAt(i)))
+        {
+          Pattern p2 = (Pattern) v.elementAt(i);
+          char lo = min(getl(p), getl(p2));
+          char hi = max(geth(p), geth(p2));
+          nv.setElementAt(p = mkelem(lo, hi), nv.size() - 1);
+        }
+        else
+        {
+          p = (Pattern) v.elementAt(i);
+          nv.addElement(p);
+        }
+      }
+
+      b.v = v = nv;
+    } catch (RegSyntax e)
+    {
+      e.printStackTrace();
+    }
+
+    // We don't want these things to be empty.
+    Vector negv = neg(v);
+    if (v.size() == 1)
+    {
+      return b;
+    }
+    if (negv.size() == 1)
+    {
+      b.v = negv;
+      b.neg = !b.neg;
+      return b;
+    }
+
+    // Now consider if we can make a FastBracket.
+    // Uses a BitSet to do a lookup.
+    FastBracket fb = newbrack(v, b.neg);
+    if (fb == null)
+    {
+      fb = newbrack(negv, !b.neg);
+    }
+    if (fb != null)
+    {
+      fb.parent = b.parent;
+      fb.next = b.next;
+      return fb;
+    }
+
+    // return the normal Bracket.
+    return b;
+  }
+
+  // Build a FastBracket and set bits. If this can't
+  // be done, return null.
+  final static FastBracket newbrack(Vector v, boolean neg)
+  {
+    FastBracket fb = new FastBracket(neg);
+    fb.v = v;
+    if (v.size() == 0)
+    {
+      return null;
+    }
+    fb.min = getl(v.elementAt(0));
+    fb.max = geth(v.elementAt(v.size() - 1));
+    if (fb.max - fb.min <= 256)
+    {
+      fb.bs = new BitSet(fb.max - fb.min + 1);
+      for (int i = 0; i < v.size(); i++)
+      {
+        Object o = v.elementAt(i);
+        int min0 = getl(o) - fb.min;
+        int max0 = geth(o) - fb.min;
+        for (int j = min0; j <= max0; j++)
+        {
+          fb.bs.set(j);
+        }
+      }
+      return fb;
+    }
+    return null;
+  }
+
+  // Negate a sorted Vector. Applying this
+  // operation twice should yield the same Vector
+  // back.
+  final static Vector neg(Vector v)
+  {
+    try
+    {
+      Vector nv = new Vector();
+      if (v.size() == 0)
+      {
+        nv.addElement(new Range((char) 0, (char) 65535));
+        return nv;
+      }
+      int p0 = getl(v.elementAt(0));
+      if (p0 != 0)
+      {
+        nv.addElement(mkelem((char) 0, (char) (p0 - 1)));
+      }
+      for (int i = 0; i < v.size() - 1; i++)
+      {
+        int hi = getl(v.elementAt(i + 1)) - 1;
+        int lo = geth(v.elementAt(i)) + 1;
+        nv.addElement(mkelem((char) lo, (char) hi));
+      }
+      int pN = geth(v.lastElement());
+      if (pN != 65535)
+      {
+        nv.addElement(mkelem((char) (pN + 1), (char) 65535));
+      }
+      return nv;
+    } catch (RegSyntax rs)
+    {
+      return null;
+    }
+  }
+
+  // Make either a Range or oneChar Object, depending on which
+  // is appropriate.
+  final static Pattern mkelem(char lo, char hi) throws RegSyntax
+  {
+    return lo == hi ? (Pattern) (new oneChar(lo)) : (Pattern) (new Range(
+            lo, hi));
+  }
+
+  static final char min(char a, char b)
+  {
+    return a < b ? a : b;
+  }
+
+  static final char max(char a, char b)
+  {
+    return a > b ? a : b;
+  }
+
+  // getl -- get lower value of Range object,
+  // or get value of oneChar object.
+  final static char getl(Object o)
+  {
+    Pattern p = (Pattern) o;
+    if (p instanceof Range)
+    {
+      return ((Range) p).lo;
+    }
+    return ((oneChar) p).c;
+  }
+
+  // geth -- get higher value of Range object,
+  // or get value of oneChar object.
+  final static char geth(Object o)
+  {
+    Pattern p = (Pattern) o;
+    if (p instanceof Range)
+    {
+      return ((Range) p).hi;
+    }
+    return ((oneChar) p).c;
+  }
+
+  // This is the easy part!
+  public int matchInternal(int pos, Pthings pt)
+  {
+    if (pos >= pt.src.length() || Masked(pos, pt))
+    {
+      return -1;
+    }
+    char c = pt.src.charAt(pos);
+    return (neg ^ (c >= min && c <= max && bs.get(c - min))) ? nextMatch(
+            pos + 1, pt) : -1;
+  }
+}
diff --git a/src/com/stevesoft/pat/FastMulti.java b/src/com/stevesoft/pat/FastMulti.java
index 53130fa..a8387b4 100755
--- a/src/com/stevesoft/pat/FastMulti.java
+++ b/src/com/stevesoft/pat/FastMulti.java
@@ -1,171 +1,169 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-import java.util.*;
-
-/** A special case of Multi, implemented when minChars().equals(maxChars()),
- * and some other conditions spelled out in RegOpt.safe4fm "Safe for
- * FastMulti."  It avoids stack growth problems as well as being slightly
- * faster.
- */
-class FastMulti
-    extends PatternSub
-{
-  patInt fewestMatches, mostMatches;
-  public patInt minChars()
-  {
-    return sub.countMinChars().mul(fewestMatches);
-  }
-
-  public patInt maxChars()
-  {
-    return sub.countMaxChars().mul(mostMatches);
-  }
-
-  public boolean matchFewest = false;
-
-  FastMulti(patInt a, patInt b, Pattern p)
-      throws RegSyntax
-  {
-    if (p == null)
-    {
-      RegSyntaxError.endItAll("Null length pattern " +
-                              "followed by *, +, or other Multi.");
-    }
-    fewestMatches = a;
-    mostMatches = b;
-    sub = p;
-    step = p.countMinChars().intValue();
-    sub.setParent(null);
-  }
-
-  public String toString()
-  {
-    return sub.toString() + "{"
-        + fewestMatches + "," + mostMatches + "}" +
-        (matchFewest ? "?" : "") + "(?# <= fast multi)" +
-        nextString();
-  }
-
-  int step = -1;
-  public int matchInternal(int pos, Pthings pt)
-  {
-    int m = -1;
-    int i = pos;
-    int endstr = pt.src.length() - step;
-    patInt matches = new patInt(0);
-    if (matchFewest)
-    {
-      if (fewestMatches.lessEq(matches))
-      {
-        int ii = nextMatch(i, pt);
-        if (ii >= 0)
-        {
-          return ii;
-        }
-      }
-      while (i >= 0 && i <= endstr)
-      {
-        i = sub.matchInternal(i, pt);
-        if (i >= 0)
-        {
-          matches.inc();
-          if (fewestMatches.lessEq(matches))
-          {
-            int ii = nextMatch(i, pt);
-            if (ii >= 0)
-            {
-              return ii;
-            }
-          }
-          if (matches.equals(mostMatches))
-          {
-            return -1;
-          }
-        }
-      }
-      return -1;
-    }
-    int nMatches = 0;
-    while (fewestMatches.intValue() > nMatches)
-    {
-      i = sub.matchInternal(i, pt);
-      if (i >= 0)
-      {
-        nMatches++;
-      }
-      else
-      {
-        return -1;
-      }
-    }
-    m = i;
-    if (mostMatches.finite())
-    {
-      while (nMatches < mostMatches.intValue())
-      {
-        i = sub.matchInternal(i, pt);
-        if (i >= 0)
-        {
-          m = i;
-          nMatches++;
-        }
-        else
-        {
-          break;
-        }
-      }
-    }
-    else
-    {
-      while (true)
-      {
-        i = sub.matchInternal(i, pt);
-        if (i >= 0)
-        {
-          m = i;
-          nMatches++;
-        }
-        else
-        {
-          break;
-        }
-      }
-    }
-    while (m >= pos)
-    {
-      int r = nextMatch(m, pt);
-      if (r >= 0)
-      {
-        return r;
-      }
-      m -= step;
-      nMatches--;
-      if (nMatches < fewestMatches.intValue())
-      {
-        return -1;
-      }
-    }
-    return -1;
-  }
-
-  public Pattern clone1(Hashtable h)
-  {
-    try
-    {
-      FastMulti fm = new FastMulti(fewestMatches, mostMatches, sub.clone(h));
-      fm.matchFewest = matchFewest;
-      return fm;
-    }
-    catch (RegSyntax rs)
-    {
-      return null;
-    }
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+import java.util.*;
+
+/**
+ * A special case of Multi, implemented when minChars().equals(maxChars()), and
+ * some other conditions spelled out in RegOpt.safe4fm "Safe for FastMulti." It
+ * avoids stack growth problems as well as being slightly faster.
+ */
+class FastMulti extends PatternSub
+{
+  patInt fewestMatches, mostMatches;
+
+  public patInt minChars()
+  {
+    return sub.countMinChars().mul(fewestMatches);
+  }
+
+  public patInt maxChars()
+  {
+    return sub.countMaxChars().mul(mostMatches);
+  }
+
+  public boolean matchFewest = false;
+
+  FastMulti(patInt a, patInt b, Pattern p) throws RegSyntax
+  {
+    if (p == null)
+    {
+      RegSyntaxError.endItAll("Null length pattern "
+              + "followed by *, +, or other Multi.");
+    }
+    fewestMatches = a;
+    mostMatches = b;
+    sub = p;
+    step = p.countMinChars().intValue();
+    sub.setParent(null);
+  }
+
+  public String toString()
+  {
+    return sub.toString() + "{" + fewestMatches + "," + mostMatches + "}"
+            + (matchFewest ? "?" : "") + "(?# <= fast multi)"
+            + nextString();
+  }
+
+  int step = -1;
+
+  public int matchInternal(int pos, Pthings pt)
+  {
+    int m = -1;
+    int i = pos;
+    int endstr = pt.src.length() - step;
+    patInt matches = new patInt(0);
+    if (matchFewest)
+    {
+      if (fewestMatches.lessEq(matches))
+      {
+        int ii = nextMatch(i, pt);
+        if (ii >= 0)
+        {
+          return ii;
+        }
+      }
+      while (i >= 0 && i <= endstr)
+      {
+        i = sub.matchInternal(i, pt);
+        if (i >= 0)
+        {
+          matches.inc();
+          if (fewestMatches.lessEq(matches))
+          {
+            int ii = nextMatch(i, pt);
+            if (ii >= 0)
+            {
+              return ii;
+            }
+          }
+          if (matches.equals(mostMatches))
+          {
+            return -1;
+          }
+        }
+      }
+      return -1;
+    }
+    int nMatches = 0;
+    while (fewestMatches.intValue() > nMatches)
+    {
+      i = sub.matchInternal(i, pt);
+      if (i >= 0)
+      {
+        nMatches++;
+      }
+      else
+      {
+        return -1;
+      }
+    }
+    m = i;
+    if (mostMatches.finite())
+    {
+      while (nMatches < mostMatches.intValue())
+      {
+        i = sub.matchInternal(i, pt);
+        if (i >= 0)
+        {
+          m = i;
+          nMatches++;
+        }
+        else
+        {
+          break;
+        }
+      }
+    }
+    else
+    {
+      while (true)
+      {
+        i = sub.matchInternal(i, pt);
+        if (i >= 0)
+        {
+          m = i;
+          nMatches++;
+        }
+        else
+        {
+          break;
+        }
+      }
+    }
+    while (m >= pos)
+    {
+      int r = nextMatch(m, pt);
+      if (r >= 0)
+      {
+        return r;
+      }
+      m -= step;
+      nMatches--;
+      if (nMatches < fewestMatches.intValue())
+      {
+        return -1;
+      }
+    }
+    return -1;
+  }
+
+  public Pattern clone1(Hashtable h)
+  {
+    try
+    {
+      FastMulti fm = new FastMulti(fewestMatches, mostMatches, sub.clone(h));
+      fm.matchFewest = matchFewest;
+      return fm;
+    } catch (RegSyntax rs)
+    {
+      return null;
+    }
+  }
+}
diff --git a/src/com/stevesoft/pat/FileRegex.java b/src/com/stevesoft/pat/FileRegex.java
index 37729eb..342d41c 100755
--- a/src/com/stevesoft/pat/FileRegex.java
+++ b/src/com/stevesoft/pat/FileRegex.java
@@ -1,293 +1,323 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-import java.io.*;
-import java.util.*;
-
-/** This class is a different form of Regex designed to work more
- like the file matching utility of a Unix shell.  It is implemented
- by some simple string transformations:
- <center>
- <table border=1>
- <tr> <td> FileRegex </td> <td> Regex </td>
- <tr> <td> * </td><td> .* </td>
- <tr> <td> . </td><td> \. </td>
- <tr> <td> { </td><td> (?: </td>
- <tr> <td> {?! </td><td> (?! </td>
- <tr> <td> {?= </td><td> (?= </td>
- <tr> <td> {?? </td><td> (?? </td>
- <tr> <td> } </td><td> ) </td>
- <tr> <td> ? </td><td> . </td>
- <tr> <td> {,} </td><td> (|) </td>
- </table>
- </center>
- Note that a FileRegex pattern always ends with the Regex
- pattern element "$".  If you like to experiment, try making
- FileRegex's and then printing them out.  The toString() method
- does a decompile of the pattern to a standard Regex.  Here are
- some more complete examples:
- <center>
- <table border=3>
- <tr> <td> FileRegex </td><td> Regex </td>
- <tr> <td>*.java </td><td> .*\.java$ </td>
- <tr> <td>*.{java,html} </td><td> .*\.(java|html)$ </td>
- <tr> <td> foo.[chC] </td><td> foo.[chC]$ </td>
- </table>
- </center>
- */
-public class FileRegex
-    extends Regex
-{
-  /** Build an unitialized FileRegex. */
-  public FileRegex()
-  {
-    dirflag = EITHER;
-  }
-
-  /** Build a FileRegex form String s. */
-  public FileRegex(String s)
-  {
-    super(s);
-    dirflag = EITHER;
-  }
-
-  /** Compile a new pattern.
-      Throws @exception com.stevesoft.pat.RegSyntax for
-      nonsensical patterns like "[9-0]+" just as Regex does.
-      @see com.stevesoft.pat#compile(java.lang.String)
-   */
-  public void compile(String s)
-      throws RegSyntax
-  {
-    String npat = toFileRegex(s);
-    super.compile(npat);
-    if (File.separatorChar == '\\') // MS-DOS
-    {
-      ignoreCase = true;
-    }
-  }
-
-  /** This is the method required by FileNameFilter.
-     To get a listing of files in the current directory
-       ending in .java, do this:
-      <pre>
-      File dot = new File(".");
-      FileRegex java_files = new FileRegex("*.java");
-      String[] file_list = dot.list(java_files);
-      </pre>
-   */
-  public boolean accept(File dir, String s)
-  {
-    if (dirflag != EITHER)
-    {
-      File f = new File(s);
-      if (f.isDirectory() && dirflag == NONDIR)
-      {
-        return false;
-      }
-      if (!f.isDirectory() && dirflag == DIR)
-      {
-        return false;
-      }
-    }
-    return matchAt(s, 0);
-  }
-
-  int dirflag = 0;
-  final static int EITHER = 0, DIR = 1, NONDIR = 2;
-
-  /** Provides an alternative to File.list -- this
-      separates its argument according to File.pathSeparator.
-      To each path, it splits off a directory -- all characters
-      up to and including the first instance of File.separator --
-      and a file pattern -- the part that comes after the directory.
-      It then produces a list of all the pattern matches on all
-      the paths.  Thus "*.java:../*.java" would produce a list of
-       all the java files in this directory and in the ".." directory
-       on a Unix machine.  "*.java;..\\*.java" would do the same thing
-       on a Dos machine. */
-   public static String[] list(String f)
-   {
-     return list(f, EITHER);
-   }
-
-  static String[] list(String f, int df)
-  {
-    //return list_(f,new FileRegex());
-    StringTokenizer st = new StringTokenizer(f, File.pathSeparator);
-    Vector v = new Vector();
-    while (st.hasMoreTokens())
-    {
-      String path = st.nextToken();
-      list1(path, v, df, true);
-    }
-    String[] sa = new String[v.size()];
-    v.copyInto(sa);
-    return sa;
-  }
-
-  final static Regex root = new Regex(File.separatorChar == '/' ?
-                                      "/$" : "(?:.:|)\\\\$");
-  static void list1(String path, Vector v, int df, boolean rec)
-  {
-    // if path looks like a/b/c/ or d:\ then add .
-    if (root.matchAt(path, 0))
-    {
-      v.addElement(path + ".");
-      return;
-    }
-    File f = new File(path);
-    if (f.getParent() != null && rec)
-    {
-      Vector v2 = new Vector();
-      list1(f.getParent(), v2, DIR, true);
-      for (int i = 0; i < v2.size(); i++)
-      {
-        String path2 = ( (String) v2.elementAt(i)) +
-            File.separator + f.getName();
-        list1(path2, v, df, false);
-      }
-    }
-    else
-    {
-      File base = new File(path);
-
-      String dir_s = base.getParent();
-      if (dir_s == null)
-      {
-        dir_s = ".";
-      }
-      File dir = new File(dir_s);
-
-      FileRegex fr = new FileRegex(base.getName());
-      if (fr.isLiteral())
-      {
-        v.addElement(dir_s + File.separator + base.getName());
-        return;
-      }
-      fr.dirflag = df;
-      String[] sa = dir.list(fr);
-      if (sa == null)
-      {
-        return;
-      }
-      for (int i = 0; i < sa.length; i++)
-      {
-        v.addElement(dir_s + File.separator + sa[i]);
-      }
-    }
-  }
-
-  /** This method takes a file regular expression, and translates it
-          into the type of pattern used by a normal Regex. */
-  public static String toFileRegex(String s)
-  {
-    StrPos sp = new StrPos(s, 0);
-    StringBuffer sb = new StringBuffer();
-    if (sp.incMatch("{?e="))
-    {
-      char e = sp.thisChar();
-      sp.inc();
-      if (sp.incMatch("}"))
-      {
-        sb.append("(?e=" + e + ")^");
-      }
-      else
-      {
-        sb.append("^(?e=");
-      }
-      sp.esc = e;
-    }
-    int ParenLvl = 0;
-    while (!sp.eos())
-    {
-      if (File.separatorChar == '\\')
-      {
-        if (sp.escaped())
-        {
-          sb.append("\\\\");
-        }
-        sp.dontMatch = false;
-      }
-      if (sp.incMatch("?"))
-      {
-        sb.append(".");
-      }
-      else if (sp.incMatch("."))
-      {
-        sb.append(sp.esc);
-        sb.append('.');
-      }
-      else if (sp.incMatch("{??"))
-      {
-        sb.append("(??");
-        ParenLvl++;
-        // allow negative lookahead to work
-      }
-      else if (sp.incMatch("{?!"))
-      {
-        sb.append("(?!");
-        ParenLvl++;
-        // allow positive lookahead to work
-      }
-      else if (sp.incMatch("{?="))
-      {
-        sb.append("(?=");
-        ParenLvl++;
-      }
-      else if (sp.incMatch("{"))
-      {
-        sb.append("(?:");
-        ParenLvl++;
-      }
-      else if (sp.incMatch("}"))
-      {
-        sb.append(')');
-        ParenLvl--;
-      }
-      else if (ParenLvl != 0 && sp.incMatch(","))
-      {
-        sb.append('|');
-      }
-      else if (sp.incMatch("*"))
-      {
-        sb.append(".*");
-      }
-      else
-      {
-        sb.append(sp.thisChar());
-        sp.inc();
-      }
-    }
-    sb.append("$");
-    return sb.toString();
-  }
-
-  public boolean isLiteral()
-  {
-    Pattern x = thePattern;
-    while (x != null && ! (x instanceof End))
-    {
-      if (x instanceof oneChar)
-      {
-        ;
-      }
-      else if (x instanceof Skipped)
-      {
-        ;
-      }
-      else
-      {
-        return false;
-      }
-      x = x.next;
-    }
-    return true;
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+import java.io.*;
+import java.util.*;
+
+/**
+ * This class is a different form of Regex designed to work more like the file
+ * matching utility of a Unix shell. It is implemented by some simple string
+ * transformations: <center> <table border=1>
+ * <tr>
+ * <td> FileRegex </td>
+ * <td> Regex </td>
+ * <tr>
+ * <td> * </td>
+ * <td> .* </td>
+ * <tr>
+ * <td> . </td>
+ * <td> \. </td>
+ * <tr>
+ * <td> { </td>
+ * <td> (?: </td>
+ * <tr>
+ * <td> {?! </td>
+ * <td> (?! </td>
+ * <tr>
+ * <td> {?= </td>
+ * <td> (?= </td>
+ * <tr>
+ * <td> {?? </td>
+ * <td> (?? </td>
+ * <tr>
+ * <td> } </td>
+ * <td> ) </td>
+ * <tr>
+ * <td> ? </td>
+ * <td> . </td>
+ * <tr>
+ * <td> {,} </td>
+ * <td> (|) </td>
+ * </table> </center> Note that a FileRegex pattern always ends with the Regex
+ * pattern element "$". If you like to experiment, try making FileRegex's and
+ * then printing them out. The toString() method does a decompile of the pattern
+ * to a standard Regex. Here are some more complete examples: <center> <table
+ * border=3>
+ * <tr>
+ * <td> FileRegex </td>
+ * <td> Regex </td>
+ * <tr>
+ * <td>*.java </td>
+ * <td> .*\.java$ </td>
+ * <tr>
+ * <td>*.{java,html} </td>
+ * <td> .*\.(java|html)$ </td>
+ * <tr>
+ * <td> foo.[chC] </td>
+ * <td> foo.[chC]$ </td>
+ * </table> </center>
+ */
+public class FileRegex extends Regex
+{
+  /** Build an unitialized FileRegex. */
+  public FileRegex()
+  {
+    dirflag = EITHER;
+  }
+
+  /** Build a FileRegex form String s. */
+  public FileRegex(String s)
+  {
+    super(s);
+    dirflag = EITHER;
+  }
+
+  /**
+   * Compile a new pattern. Throws
+   * 
+   * @exception com.stevesoft.pat.RegSyntax
+   *                    for nonsensical patterns like "[9-0]+" just as Regex
+   *                    does.
+   * @see com.stevesoft.pat#compile(java.lang.String)
+   */
+  public void compile(String s) throws RegSyntax
+  {
+    String npat = toFileRegex(s);
+    super.compile(npat);
+    if (File.separatorChar == '\\') // MS-DOS
+    {
+      ignoreCase = true;
+    }
+  }
+
+  /**
+   * This is the method required by FileNameFilter. To get a listing of files in
+   * the current directory ending in .java, do this:
+   * 
+   * <pre>
+   * File dot = new File(&quot;.&quot;);
+   * 
+   * FileRegex java_files = new FileRegex(&quot;*.java&quot;);
+   * 
+   * String[] file_list = dot.list(java_files);
+   * </pre>
+   */
+  public boolean accept(File dir, String s)
+  {
+    if (dirflag != EITHER)
+    {
+      File f = new File(s);
+      if (f.isDirectory() && dirflag == NONDIR)
+      {
+        return false;
+      }
+      if (!f.isDirectory() && dirflag == DIR)
+      {
+        return false;
+      }
+    }
+    return matchAt(s, 0);
+  }
+
+  int dirflag = 0;
+
+  final static int EITHER = 0, DIR = 1, NONDIR = 2;
+
+  /**
+   * Provides an alternative to File.list -- this separates its argument
+   * according to File.pathSeparator. To each path, it splits off a directory --
+   * all characters up to and including the first instance of File.separator --
+   * and a file pattern -- the part that comes after the directory. It then
+   * produces a list of all the pattern matches on all the paths. Thus
+   * "*.java:../*.java" would produce a list of all the java files in this
+   * directory and in the ".." directory on a Unix machine. "*.java;..\\*.java"
+   * would do the same thing on a Dos machine.
+   */
+  public static String[] list(String f)
+  {
+    return list(f, EITHER);
+  }
+
+  static String[] list(String f, int df)
+  {
+    // return list_(f,new FileRegex());
+    StringTokenizer st = new StringTokenizer(f, File.pathSeparator);
+    Vector v = new Vector();
+    while (st.hasMoreTokens())
+    {
+      String path = st.nextToken();
+      list1(path, v, df, true);
+    }
+    String[] sa = new String[v.size()];
+    v.copyInto(sa);
+    return sa;
+  }
+
+  final static Regex root = new Regex(File.separatorChar == '/' ? "/$"
+          : "(?:.:|)\\\\$");
+
+  static void list1(String path, Vector v, int df, boolean rec)
+  {
+    // if path looks like a/b/c/ or d:\ then add .
+    if (root.matchAt(path, 0))
+    {
+      v.addElement(path + ".");
+      return;
+    }
+    File f = new File(path);
+    if (f.getParent() != null && rec)
+    {
+      Vector v2 = new Vector();
+      list1(f.getParent(), v2, DIR, true);
+      for (int i = 0; i < v2.size(); i++)
+      {
+        String path2 = ((String) v2.elementAt(i)) + File.separator
+                + f.getName();
+        list1(path2, v, df, false);
+      }
+    }
+    else
+    {
+      File base = new File(path);
+
+      String dir_s = base.getParent();
+      if (dir_s == null)
+      {
+        dir_s = ".";
+      }
+      File dir = new File(dir_s);
+
+      FileRegex fr = new FileRegex(base.getName());
+      if (fr.isLiteral())
+      {
+        v.addElement(dir_s + File.separator + base.getName());
+        return;
+      }
+      fr.dirflag = df;
+      String[] sa = dir.list(fr);
+      if (sa == null)
+      {
+        return;
+      }
+      for (int i = 0; i < sa.length; i++)
+      {
+        v.addElement(dir_s + File.separator + sa[i]);
+      }
+    }
+  }
+
+  /**
+   * This method takes a file regular expression, and translates it into the
+   * type of pattern used by a normal Regex.
+   */
+  public static String toFileRegex(String s)
+  {
+    StrPos sp = new StrPos(s, 0);
+    StringBuffer sb = new StringBuffer();
+    if (sp.incMatch("{?e="))
+    {
+      char e = sp.thisChar();
+      sp.inc();
+      if (sp.incMatch("}"))
+      {
+        sb.append("(?e=" + e + ")^");
+      }
+      else
+      {
+        sb.append("^(?e=");
+      }
+      sp.esc = e;
+    }
+    int ParenLvl = 0;
+    while (!sp.eos())
+    {
+      if (File.separatorChar == '\\')
+      {
+        if (sp.escaped())
+        {
+          sb.append("\\\\");
+        }
+        sp.dontMatch = false;
+      }
+      if (sp.incMatch("?"))
+      {
+        sb.append(".");
+      }
+      else if (sp.incMatch("."))
+      {
+        sb.append(sp.esc);
+        sb.append('.');
+      }
+      else if (sp.incMatch("{??"))
+      {
+        sb.append("(??");
+        ParenLvl++;
+        // allow negative lookahead to work
+      }
+      else if (sp.incMatch("{?!"))
+      {
+        sb.append("(?!");
+        ParenLvl++;
+        // allow positive lookahead to work
+      }
+      else if (sp.incMatch("{?="))
+      {
+        sb.append("(?=");
+        ParenLvl++;
+      }
+      else if (sp.incMatch("{"))
+      {
+        sb.append("(?:");
+        ParenLvl++;
+      }
+      else if (sp.incMatch("}"))
+      {
+        sb.append(')');
+        ParenLvl--;
+      }
+      else if (ParenLvl != 0 && sp.incMatch(","))
+      {
+        sb.append('|');
+      }
+      else if (sp.incMatch("*"))
+      {
+        sb.append(".*");
+      }
+      else
+      {
+        sb.append(sp.thisChar());
+        sp.inc();
+      }
+    }
+    sb.append("$");
+    return sb.toString();
+  }
+
+  public boolean isLiteral()
+  {
+    Pattern x = thePattern;
+    while (x != null && !(x instanceof End))
+    {
+      if (x instanceof oneChar)
+      {
+        ;
+      }
+      else if (x instanceof Skipped)
+      {
+        ;
+      }
+      else
+      {
+        return false;
+      }
+      x = x.next;
+    }
+    return true;
+  }
+}
diff --git a/src/com/stevesoft/pat/Group.java b/src/com/stevesoft/pat/Group.java
index 4f538b5..e6f734c 100755
--- a/src/com/stevesoft/pat/Group.java
+++ b/src/com/stevesoft/pat/Group.java
@@ -1,75 +1,77 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-import java.util.*;
-
-/** This class implements the (?@<>) syntax that matches
- a balanced parenthesis.  Not in perl 5. */
-class Group
-    extends Pattern
-{
-  char op, cl;
-  Group(char opi, char cli)
-  {
-    op = opi;
-    cl = cli;
-  }
-
-  public int matchInternal(int pos, Pthings pt)
-  {
-    int i, count = 1;
-    if (pos < pt.src.length())
-    {
-      if (!Masked(pos, pt) && pt.src.charAt(pos) != op)
-      {
-        return -1;
-      }
-    }
-    for (i = pos + 1; i < pt.src.length(); i++)
-    {
-      char c = pt.src.charAt(i);
-      boolean b = !Masked(i, pt);
-      if (b && c == ESC)
-      {
-        i++;
-      }
-      else
-      {
-        if (b && c == cl)
-        {
-          count--;
-        }
-        if (count == 0)
-        {
-          return nextMatch(i + 1, pt);
-        }
-        if (b && c == op)
-        {
-          count++;
-        }
-      }
-    }
-    return -1;
-  }
-
-  public String toString()
-  {
-    return "(?@" + op + cl + ")" + nextString();
-  }
-
-  public patInt minChars()
-  {
-    return new patInt(2);
-  }
-
-  Pattern clone1(Hashtable h)
-  {
-    return new Group(op, cl);
-  }
-};
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+import java.util.*;
+
+/**
+ * This class implements the (?@<>) syntax that matches a balanced parenthesis.
+ * Not in perl 5.
+ */
+class Group extends Pattern
+{
+  char op, cl;
+
+  Group(char opi, char cli)
+  {
+    op = opi;
+    cl = cli;
+  }
+
+  public int matchInternal(int pos, Pthings pt)
+  {
+    int i, count = 1;
+    if (pos < pt.src.length())
+    {
+      if (!Masked(pos, pt) && pt.src.charAt(pos) != op)
+      {
+        return -1;
+      }
+    }
+    for (i = pos + 1; i < pt.src.length(); i++)
+    {
+      char c = pt.src.charAt(i);
+      boolean b = !Masked(i, pt);
+      if (b && c == ESC)
+      {
+        i++;
+      }
+      else
+      {
+        if (b && c == cl)
+        {
+          count--;
+        }
+        if (count == 0)
+        {
+          return nextMatch(i + 1, pt);
+        }
+        if (b && c == op)
+        {
+          count++;
+        }
+      }
+    }
+    return -1;
+  }
+
+  public String toString()
+  {
+    return "(?@" + op + cl + ")" + nextString();
+  }
+
+  public patInt minChars()
+  {
+    return new patInt(2);
+  }
+
+  Pattern clone1(Hashtable h)
+  {
+    return new Group(op, cl);
+  }
+};
diff --git a/src/com/stevesoft/pat/LeftRule.java b/src/com/stevesoft/pat/LeftRule.java
index 0b9bae3..c75a0a5 100755
--- a/src/com/stevesoft/pat/LeftRule.java
+++ b/src/com/stevesoft/pat/LeftRule.java
@@ -1,30 +1,31 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-/** The apply(StringBufferLike sb,RegRes res) method of this derivation
-    of ReplaceRule appends the contents of res.left() to the StringBuffer
-    sb.
-    @see com.stevesoft.pat.ReplaceRule
- */
-public class LeftRule
-    extends ReplaceRule
-{
-  public LeftRule()
-  {}
-
-  public void apply(StringBufferLike sb, RegRes res)
-  {
-    sb.append(res.left());
-  }
-
-  public String toString1()
-  {
-    return "$`";
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+/**
+ * The apply(StringBufferLike sb,RegRes res) method of this derivation of
+ * ReplaceRule appends the contents of res.left() to the StringBuffer sb.
+ * 
+ * @see com.stevesoft.pat.ReplaceRule
+ */
+public class LeftRule extends ReplaceRule
+{
+  public LeftRule()
+  {
+  }
+
+  public void apply(StringBufferLike sb, RegRes res)
+  {
+    sb.append(res.left());
+  }
+
+  public String toString1()
+  {
+    return "$`";
+  }
+}
diff --git a/src/com/stevesoft/pat/Multi.java b/src/com/stevesoft/pat/Multi.java
index 14b3a06..1fe197d 100755
--- a/src/com/stevesoft/pat/Multi.java
+++ b/src/com/stevesoft/pat/Multi.java
@@ -1,85 +1,90 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-import java.util.*;
-
-/** Matches any number of instances of sub Pattern
- this was the hardest method to write.  It implements
- '+', '*', '?', "{0,10}", "{5,}", "{5}", etc.
- @see pat.Multi_stage2
- @see pat.MultiMin
- */
-class Multi
-    extends PatternSub
-{
-  patInt a, b;
-  public patInt minChars()
-  {
-    return a.mul(p.countMinChars());
-  }
-
-  public patInt maxChars()
-  {
-    return b.mul(p.countMaxChars());
-  }
-
-  Pattern p;
-  Multi_stage2 st2;
-  public boolean matchFewest = false;
-  /**
-      @param a The fewest number of times the sub pattern can match.
-      @param b The maximum number of times the sub pattern can match.
-      @param p The sub pattern.
-      @see Multi_stage2
-      @see MultiMin
-   */
-  public Multi(patInt a, patInt b, Pattern p)
-      throws RegSyntax
-  {
-    this.a = a;
-    this.b = b;
-    this.p = p;
-    st2 = new Multi_stage2(a, b, p);
-    st2.parent = this;
-    sub = st2.sub;
-  }
-
-  public String toString()
-  {
-    st2.matchFewest = matchFewest;
-    return st2.toString();
-  }
-
-  public int matchInternal(int pos, Pthings pt)
-  {
-    try
-    {
-      st2 = new Multi_stage2(a, b, p);
-    }
-    catch (RegSyntax r__)
-    {}
-    st2.matchFewest = matchFewest;
-    st2.parent = this;
-    return st2.matchInternal(pos, pt);
-  }
-
-  public Pattern clone1(Hashtable h)
-  {
-    try
-    {
-      Multi m = new Multi(a, b, ( (Pattern) p).clone(h));
-      m.matchFewest = matchFewest;
-      return m;
-    }
-    catch (RegSyntax rs)
-    {
-      return null;
-    }
-  }
-};
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+import java.util.*;
+
+/**
+ * Matches any number of instances of sub Pattern this was the hardest method to
+ * write. It implements '+', '*', '?', "{0,10}", "{5,}", "{5}", etc.
+ * 
+ * @see pat.Multi_stage2
+ * @see pat.MultiMin
+ */
+class Multi extends PatternSub
+{
+  patInt a, b;
+
+  public patInt minChars()
+  {
+    return a.mul(p.countMinChars());
+  }
+
+  public patInt maxChars()
+  {
+    return b.mul(p.countMaxChars());
+  }
+
+  Pattern p;
+
+  Multi_stage2 st2;
+
+  public boolean matchFewest = false;
+
+  /**
+   * @param a
+   *                The fewest number of times the sub pattern can match.
+   * @param b
+   *                The maximum number of times the sub pattern can match.
+   * @param p
+   *                The sub pattern.
+   * @see Multi_stage2
+   * @see MultiMin
+   */
+  public Multi(patInt a, patInt b, Pattern p) throws RegSyntax
+  {
+    this.a = a;
+    this.b = b;
+    this.p = p;
+    st2 = new Multi_stage2(a, b, p);
+    st2.parent = this;
+    sub = st2.sub;
+  }
+
+  public String toString()
+  {
+    st2.matchFewest = matchFewest;
+    return st2.toString();
+  }
+
+  public int matchInternal(int pos, Pthings pt)
+  {
+    try
+    {
+      st2 = new Multi_stage2(a, b, p);
+    } catch (RegSyntax r__)
+    {
+    }
+    st2.matchFewest = matchFewest;
+    st2.parent = this;
+    return st2.matchInternal(pos, pt);
+  }
+
+  public Pattern clone1(Hashtable h)
+  {
+    try
+    {
+      Multi m = new Multi(a, b, ((Pattern) p).clone(h));
+      m.matchFewest = matchFewest;
+      return m;
+    } catch (RegSyntax rs)
+    {
+      return null;
+    }
+  }
+};
diff --git a/src/com/stevesoft/pat/MultiMin.java b/src/com/stevesoft/pat/MultiMin.java
index f741e99..6054e06 100755
--- a/src/com/stevesoft/pat/MultiMin.java
+++ b/src/com/stevesoft/pat/MultiMin.java
@@ -1,22 +1,21 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-/** This extension of multi is the version of multi
- which wants to match the fewest number of characters.
- It implements the *? type of syntax. */
-class MultiMin
-    extends Multi
-{
-  MultiMin(patInt i1, patInt i2, Pattern p)
-      throws RegSyntax
-  {
-    super(i1, i2, p);
-    matchFewest = true;
-  }
-};
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+/**
+ * This extension of multi is the version of multi which wants to match the
+ * fewest number of characters. It implements the *? type of syntax.
+ */
+class MultiMin extends Multi
+{
+  MultiMin(patInt i1, patInt i2, Pattern p) throws RegSyntax
+  {
+    super(i1, i2, p);
+    matchFewest = true;
+  }
+};
diff --git a/src/com/stevesoft/pat/Multi_stage2.java b/src/com/stevesoft/pat/Multi_stage2.java
index 990b0e6..b18ad1c 100755
--- a/src/com/stevesoft/pat/Multi_stage2.java
+++ b/src/com/stevesoft/pat/Multi_stage2.java
@@ -1,156 +1,157 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-import java.util.*;
-
-/** If Multi were not split into a second stage, then
- a nested Multi would try to re-use the same count
- variable and the whole thing would break. */
-class Multi_stage2
-    extends PatternSub
-{
-  Pattern nextRet;
-  patInt count;
-  patInt matchMin, matchMax;
-  public boolean matchFewest = false;
-  public String toString()
-  {
-    String ret = "";
-    ret += sub.toString();
-    ret += "{" + matchMin + "," + matchMax + "}";
-    if (matchFewest)
-    {
-      ret += "?";
-    }
-    ret += parent.nextString();
-    return ret;
-  }
-
-  Multi_stage2(patInt a, patInt b, Pattern p)
-      throws RegSyntax
-  {
-    if (p == null)
-    {
-      RegSyntaxError.endItAll(
-          "Multiple match of Null pattern requested.");
-    }
-    sub = p;
-    nextRet = this;
-    sub.setParent(this);
-    matchMin = a;
-    matchMax = b;
-    count = new patInt(0);
-    // we must have b > a > -1 for this
-    // to make sense.
-    if (!a.lessEq(b))
-    {
-      //throw new BadMultiArgs();
-      RegSyntaxError.endItAll("Bad Multi Args: " + a + ">" + b);
-    }
-    patInt i = new patInt( -1);
-    if (a.lessEq(i))
-    {
-      //throw new BadMultiArgs();
-      RegSyntaxError.endItAll("Bad Multi Args: " + a + "< 0");
-    }
-  }
-
-  public Pattern getNext()
-  {
-    return nextRet;
-  }
-
-  int pos_old = -1;
-  public int matchInternal(int pos, Pthings pt)
-  {
-    sub.setParent(this);
-
-    int canUse = -1;
-
-    // check for some forms of infinite recursion...
-    if (pos_old >= 0 && pos == pos_old)
-    {
-      return -1;
-    }
-    pos_old = pos;
-
-    if (matchMin.lessEq(count))
-    {
-      canUse = pos;
-    }
-    if (!count.lessEq(matchMax) || pos > pt.src.length())
-    {
-      return -1;
-    }
-
-    if ( (matchFewest || count.equals(matchMax)) && canUse >= 0)
-    {
-      Pattern n = super.getNext();
-      if (n == null)
-      {
-        return canUse;
-      }
-      int ret = testMatch(n, pos, pt);
-      if (ret >= 0)
-      {
-        return ret;
-      }
-      else
-      {
-        canUse = -1;
-      }
-    }
-
-    count.inc();
-    try
-    {
-      if (count.lessEq(matchMax))
-      {
-        int r = testMatch(sub, pos, pt);
-        if (r >= 0)
-        {
-          return r;
-        }
-      }
-    }
-    finally
-    {
-      count.dec();
-    }
-
-    if (!matchFewest && canUse >= 0)
-    {
-      Pattern n = super.getNext();
-      if (n == null)
-      {
-        return canUse;
-      }
-      int ret = testMatch(n, pos, pt);
-      return ret;
-    }
-    else
-    {
-      return canUse;
-    }
-  }
-
-  public Pattern clone1(Hashtable h)
-  {
-    try
-    {
-      Multi_stage2 m = new Multi_stage2(matchMin, matchMax, sub.clone(h));
-      m.matchFewest = matchFewest;
-      return m;
-    }
-    catch (RegSyntax rs)
-    {
-      return null;
-    }
-  }
-};
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+import java.util.*;
+
+/**
+ * If Multi were not split into a second stage, then a nested Multi would try to
+ * re-use the same count variable and the whole thing would break.
+ */
+class Multi_stage2 extends PatternSub
+{
+  Pattern nextRet;
+
+  patInt count;
+
+  patInt matchMin, matchMax;
+
+  public boolean matchFewest = false;
+
+  public String toString()
+  {
+    String ret = "";
+    ret += sub.toString();
+    ret += "{" + matchMin + "," + matchMax + "}";
+    if (matchFewest)
+    {
+      ret += "?";
+    }
+    ret += parent.nextString();
+    return ret;
+  }
+
+  Multi_stage2(patInt a, patInt b, Pattern p) throws RegSyntax
+  {
+    if (p == null)
+    {
+      RegSyntaxError.endItAll("Multiple match of Null pattern requested.");
+    }
+    sub = p;
+    nextRet = this;
+    sub.setParent(this);
+    matchMin = a;
+    matchMax = b;
+    count = new patInt(0);
+    // we must have b > a > -1 for this
+    // to make sense.
+    if (!a.lessEq(b))
+    {
+      // throw new BadMultiArgs();
+      RegSyntaxError.endItAll("Bad Multi Args: " + a + ">" + b);
+    }
+    patInt i = new patInt(-1);
+    if (a.lessEq(i))
+    {
+      // throw new BadMultiArgs();
+      RegSyntaxError.endItAll("Bad Multi Args: " + a + "< 0");
+    }
+  }
+
+  public Pattern getNext()
+  {
+    return nextRet;
+  }
+
+  int pos_old = -1;
+
+  public int matchInternal(int pos, Pthings pt)
+  {
+    sub.setParent(this);
+
+    int canUse = -1;
+
+    // check for some forms of infinite recursion...
+    if (pos_old >= 0 && pos == pos_old)
+    {
+      return -1;
+    }
+    pos_old = pos;
+
+    if (matchMin.lessEq(count))
+    {
+      canUse = pos;
+    }
+    if (!count.lessEq(matchMax) || pos > pt.src.length())
+    {
+      return -1;
+    }
+
+    if ((matchFewest || count.equals(matchMax)) && canUse >= 0)
+    {
+      Pattern n = super.getNext();
+      if (n == null)
+      {
+        return canUse;
+      }
+      int ret = testMatch(n, pos, pt);
+      if (ret >= 0)
+      {
+        return ret;
+      }
+      else
+      {
+        canUse = -1;
+      }
+    }
+
+    count.inc();
+    try
+    {
+      if (count.lessEq(matchMax))
+      {
+        int r = testMatch(sub, pos, pt);
+        if (r >= 0)
+        {
+          return r;
+        }
+      }
+    } finally
+    {
+      count.dec();
+    }
+
+    if (!matchFewest && canUse >= 0)
+    {
+      Pattern n = super.getNext();
+      if (n == null)
+      {
+        return canUse;
+      }
+      int ret = testMatch(n, pos, pt);
+      return ret;
+    }
+    else
+    {
+      return canUse;
+    }
+  }
+
+  public Pattern clone1(Hashtable h)
+  {
+    try
+    {
+      Multi_stage2 m = new Multi_stage2(matchMin, matchMax, sub.clone(h));
+      m.matchFewest = matchFewest;
+      return m;
+    } catch (RegSyntax rs)
+    {
+      return null;
+    }
+  }
+};
diff --git a/src/com/stevesoft/pat/NoPattern.java b/src/com/stevesoft/pat/NoPattern.java
index c5eba3c..444d094 100755
--- a/src/com/stevesoft/pat/NoPattern.java
+++ b/src/com/stevesoft/pat/NoPattern.java
@@ -1,33 +1,33 @@
-package //
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-    com.stevesoft.pat;
-
-import java.util.*;
-
-/** The idea behind this class is simply to eliminate the need for
- * testing to see if Regex.thePattern is null.  Every instruction
- * we can eliminate from _search will help.
- */
-public class NoPattern
-    extends Pattern
-{
-  public String toString()
-  {
-    return "(?e=#)[^#d#D]";
-  }
-
-  public int matchInternal(int i, Pthings p)
-  {
-    return -1;
-  }
-
-  Pattern clone1(Hashtable h)
-  {
-    return new NoPattern();
-  }
-}
+package //
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+com.stevesoft.pat;
+
+import java.util.*;
+
+/**
+ * The idea behind this class is simply to eliminate the need for testing to see
+ * if Regex.thePattern is null. Every instruction we can eliminate from _search
+ * will help.
+ */
+public class NoPattern extends Pattern
+{
+  public String toString()
+  {
+    return "(?e=#)[^#d#D]";
+  }
+
+  public int matchInternal(int i, Pthings p)
+  {
+    return -1;
+  }
+
+  Pattern clone1(Hashtable h)
+  {
+    return new NoPattern();
+  }
+}
diff --git a/src/com/stevesoft/pat/NonDirFileRegex.java b/src/com/stevesoft/pat/NonDirFileRegex.java
index cb7b69d..864243c 100755
--- a/src/com/stevesoft/pat/NonDirFileRegex.java
+++ b/src/com/stevesoft/pat/NonDirFileRegex.java
@@ -1,30 +1,31 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-/** This class is just like FileRegex, except that its accept method
- only returns true if the file matching the pattern is not a directory.*/
-public class NonDirFileRegex
-    extends FileRegex
-{
-  public NonDirFileRegex()
-  {
-    dirflag = NONDIR;
-  }
-
-  public NonDirFileRegex(String fp)
-  {
-    super(fp);
-    dirflag = NONDIR;
-  }
-
-  public static String[] list(String f)
-  {
-    return list(f, NONDIR);
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+/**
+ * This class is just like FileRegex, except that its accept method only returns
+ * true if the file matching the pattern is not a directory.
+ */
+public class NonDirFileRegex extends FileRegex
+{
+  public NonDirFileRegex()
+  {
+    dirflag = NONDIR;
+  }
+
+  public NonDirFileRegex(String fp)
+  {
+    super(fp);
+    dirflag = NONDIR;
+  }
+
+  public static String[] list(String f)
+  {
+    return list(f, NONDIR);
+  }
+}
diff --git a/src/com/stevesoft/pat/NotImplementedError.java b/src/com/stevesoft/pat/NotImplementedError.java
index 246ecad..11ce9eb 100755
--- a/src/com/stevesoft/pat/NotImplementedError.java
+++ b/src/com/stevesoft/pat/NotImplementedError.java
@@ -1,17 +1,16 @@
-package //
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-    com.stevesoft.pat;
-
-public class NotImplementedError
-    extends Error
-{
-  public NotImplementedError(String s)
-  {
-    super(s);
-  }
-}
+package //
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+com.stevesoft.pat;
+
+public class NotImplementedError extends Error
+{
+  public NotImplementedError(String s)
+  {
+    super(s);
+  }
+}
diff --git a/src/com/stevesoft/pat/NullPattern.java b/src/com/stevesoft/pat/NullPattern.java
index abdc5fa..09460de 100755
--- a/src/com/stevesoft/pat/NullPattern.java
+++ b/src/com/stevesoft/pat/NullPattern.java
@@ -1,37 +1,37 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-import java.util.*;
-
-/** This pattern matches nothing -- it is found in patterns
- * like (hello|world|) where a zero-length subelement occurs.
- */
-class NullPattern
-    extends Pattern
-{
-  public String toString()
-  {
-    return nextString();
-  }
-
-  public int matchInternal(int p, Pthings pt)
-  {
-    return nextMatch(p, pt);
-  }
-
-  public patInt maxChars()
-  {
-    return new patInt(0);
-  }
-
-  Pattern clone1(Hashtable h)
-  {
-    return new NullPattern();
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+import java.util.*;
+
+/**
+ * This pattern matches nothing -- it is found in patterns like (hello|world|)
+ * where a zero-length subelement occurs.
+ */
+class NullPattern extends Pattern
+{
+  public String toString()
+  {
+    return nextString();
+  }
+
+  public int matchInternal(int p, Pthings pt)
+  {
+    return nextMatch(p, pt);
+  }
+
+  public patInt maxChars()
+  {
+    return new patInt(0);
+  }
+
+  Pattern clone1(Hashtable h)
+  {
+    return new NullPattern();
+  }
+}
diff --git a/src/com/stevesoft/pat/NullRule.java b/src/com/stevesoft/pat/NullRule.java
index fe4e837..7c780e1 100755
--- a/src/com/stevesoft/pat/NullRule.java
+++ b/src/com/stevesoft/pat/NullRule.java
@@ -1,28 +1,30 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-/** The apply(StringBufferLike sb,RegRes res) method of this derivation
-    of ReplaceRule appends nothing to the contents of the StringBuffer sb.
-    @see com.stevesoft.pat.ReplaceRule
- */
-public class NullRule
-    extends ReplaceRule
-{
-  public NullRule()
-  {}
-
-  public void apply(StringBufferLike sb, RegRes res)
-  {
-  }
-
-  public String toString1()
-  {
-    return "";
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+/**
+ * The apply(StringBufferLike sb,RegRes res) method of this derivation of
+ * ReplaceRule appends nothing to the contents of the StringBuffer sb.
+ * 
+ * @see com.stevesoft.pat.ReplaceRule
+ */
+public class NullRule extends ReplaceRule
+{
+  public NullRule()
+  {
+  }
+
+  public void apply(StringBufferLike sb, RegRes res)
+  {
+  }
+
+  public String toString1()
+  {
+    return "";
+  }
+}
diff --git a/src/com/stevesoft/pat/Or.java b/src/com/stevesoft/pat/Or.java
index 05981aa..8d405e5 100755
--- a/src/com/stevesoft/pat/Or.java
+++ b/src/com/stevesoft/pat/Or.java
@@ -1,127 +1,130 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-import java.util.*;
-
-/** This class implements the (?: ... ) extended Pattern.
- It provides a base class from which we derive the
- [ ... ], ( ... ), (?! ... ), and (?= ... ) patterns. */
-class Or
-    extends Pattern
-{
-  Vector v;
-  Pattern[] pv = null;
-  Or()
-  {
-    v = new Vector();
-  }
-
-  String leftForm()
-  {
-    return "(?:";
-  }
-
-  String rightForm()
-  {
-    return ")";
-  }
-
-  String sepForm()
-  {
-    return "|";
-  }
-
-  public Or addOr(Pattern p)
-  {
-    pv = null;
-    v.addElement(p);
-    p.setParent(this);
-    return this;
-  }
-
-  public String toString()
-  {
-    int i;
-    StringBuffer sb = new StringBuffer();
-    sb.append(leftForm());
-    if (v.size() > 0)
-    {
-      sb.append( ( (Pattern) v.elementAt(0)).toString());
-    }
-    for (i = 1; i < v.size(); i++)
-    {
-      sb.append(sepForm());
-      sb.append( ( (Pattern) v.elementAt(i)).toString());
-    }
-    sb.append(rightForm());
-    sb.append(nextString());
-    return sb.toString();
-  }
-
-  public int matchInternal(int pos, Pthings pt)
-  {
-    if (pv == null)
-    {
-      pv = new Pattern[v.size()];
-      v.copyInto(pv);
-    }
-    for (int i = 0; i < v.size(); i++)
-    {
-      Pattern p = pv[i]; //(Pattern)v.elementAt(i);
-      int r = p.matchInternal(pos, pt);
-      if (r >= 0)
-      {
-        return r;
-      }
-    }
-    return -1;
-  }
-
-  public patInt minChars()
-  {
-    if (v.size() == 0)
-    {
-      return new patInt(0);
-    }
-    patInt m = ( (Pattern) v.elementAt(0)).countMinChars();
-    for (int i = 1; i < v.size(); i++)
-    {
-      Pattern p = (Pattern) v.elementAt(i);
-      m.mineq(p.countMinChars());
-    }
-    return m;
-  }
-
-  public patInt maxChars()
-  {
-    if (v.size() == 0)
-    {
-      return new patInt(0);
-    }
-    patInt m = ( (Pattern) v.elementAt(0)).countMaxChars();
-    for (int i = 1; i < v.size(); i++)
-    {
-      Pattern p = (Pattern) v.elementAt(i);
-      m.maxeq(p.countMaxChars());
-    }
-    return m;
-  }
-
-  Pattern clone1(Hashtable h)
-  {
-    Or o = new Or();
-    h.put(this, o);
-    h.put(o, o);
-    for (int i = 0; i < v.size(); i++)
-    {
-      o.v.addElement( ( (Pattern) v.elementAt(i)).clone(h));
-    }
-    return o;
-  }
-};
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+import java.util.*;
+
+/**
+ * This class implements the (?: ... ) extended Pattern. It provides a base
+ * class from which we derive the [ ... ], ( ... ), (?! ... ), and (?= ... )
+ * patterns.
+ */
+class Or extends Pattern
+{
+  Vector v;
+
+  Pattern[] pv = null;
+
+  Or()
+  {
+    v = new Vector();
+  }
+
+  String leftForm()
+  {
+    return "(?:";
+  }
+
+  String rightForm()
+  {
+    return ")";
+  }
+
+  String sepForm()
+  {
+    return "|";
+  }
+
+  public Or addOr(Pattern p)
+  {
+    pv = null;
+    v.addElement(p);
+    p.setParent(this);
+    return this;
+  }
+
+  public String toString()
+  {
+    int i;
+    StringBuffer sb = new StringBuffer();
+    sb.append(leftForm());
+    if (v.size() > 0)
+    {
+      sb.append(((Pattern) v.elementAt(0)).toString());
+    }
+    for (i = 1; i < v.size(); i++)
+    {
+      sb.append(sepForm());
+      sb.append(((Pattern) v.elementAt(i)).toString());
+    }
+    sb.append(rightForm());
+    sb.append(nextString());
+    return sb.toString();
+  }
+
+  public int matchInternal(int pos, Pthings pt)
+  {
+    if (pv == null)
+    {
+      pv = new Pattern[v.size()];
+      v.copyInto(pv);
+    }
+    for (int i = 0; i < v.size(); i++)
+    {
+      Pattern p = pv[i]; // (Pattern)v.elementAt(i);
+      int r = p.matchInternal(pos, pt);
+      if (r >= 0)
+      {
+        return r;
+      }
+    }
+    return -1;
+  }
+
+  public patInt minChars()
+  {
+    if (v.size() == 0)
+    {
+      return new patInt(0);
+    }
+    patInt m = ((Pattern) v.elementAt(0)).countMinChars();
+    for (int i = 1; i < v.size(); i++)
+    {
+      Pattern p = (Pattern) v.elementAt(i);
+      m.mineq(p.countMinChars());
+    }
+    return m;
+  }
+
+  public patInt maxChars()
+  {
+    if (v.size() == 0)
+    {
+      return new patInt(0);
+    }
+    patInt m = ((Pattern) v.elementAt(0)).countMaxChars();
+    for (int i = 1; i < v.size(); i++)
+    {
+      Pattern p = (Pattern) v.elementAt(i);
+      m.maxeq(p.countMaxChars());
+    }
+    return m;
+  }
+
+  Pattern clone1(Hashtable h)
+  {
+    Or o = new Or();
+    h.put(this, o);
+    h.put(o, o);
+    for (int i = 0; i < v.size(); i++)
+    {
+      o.v.addElement(((Pattern) v.elementAt(i)).clone(h));
+    }
+    return o;
+  }
+};
diff --git a/src/com/stevesoft/pat/OrMark.java b/src/com/stevesoft/pat/OrMark.java
index 77aac0f..89b8869 100755
--- a/src/com/stevesoft/pat/OrMark.java
+++ b/src/com/stevesoft/pat/OrMark.java
@@ -1,72 +1,73 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-import java.util.*;
-
-/** Implements the parenthesis pattern subelement.*/
-class OrMark
-    extends Or
-{
-  SubMark sm = new SubMark();
-  int id;
-  OrMark(int i)
-  {
-    sm.om = this;
-    id = i;
-  }
-
-  String leftForm()
-  {
-    return "(";
-  }
-
-  public Pattern getNext()
-  {
-    return sm;
-  }
-
-  public int matchInternal(int pos, Pthings pt)
-  {
-    sm.next = super.getNext();
-    if (pt.marks == null)
-    {
-      int n2 = 2 * pt.nMarks + 2;
-      pt.marks = new int[n2];
-      for (int i = 0; i < n2; i++)
-      {
-        pt.marks[i] = -1;
-      }
-    }
-    pt.marks[id] = pos;
-    int ret = super.matchInternal(pos, pt);
-    if (ret < 0)
-    {
-      pt.marks[id] = -1;
-    }
-    else if (pt.marks[id] > pt.marks[id + pt.nMarks])
-    {
-      int swap = pt.marks[id];
-      pt.marks[id] = pt.marks[id + pt.nMarks] + 1;
-      pt.marks[id + pt.nMarks] = swap + 1;
-    }
-    return ret;
-  }
-
-  public Pattern clone1(Hashtable h)
-  {
-    OrMark om = new OrMark(id);
-    h.put(om, om);
-    h.put(this, om);
-    for (int i = 0; i < v.size(); i++)
-    {
-      om.v.addElement( ( (Pattern) v.elementAt(i)).clone(h));
-    }
-    return om;
-  }
-};
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+import java.util.*;
+
+/** Implements the parenthesis pattern subelement. */
+class OrMark extends Or
+{
+  SubMark sm = new SubMark();
+
+  int id;
+
+  OrMark(int i)
+  {
+    sm.om = this;
+    id = i;
+  }
+
+  String leftForm()
+  {
+    return "(";
+  }
+
+  public Pattern getNext()
+  {
+    return sm;
+  }
+
+  public int matchInternal(int pos, Pthings pt)
+  {
+    sm.next = super.getNext();
+    if (pt.marks == null)
+    {
+      int n2 = 2 * pt.nMarks + 2;
+      pt.marks = new int[n2];
+      for (int i = 0; i < n2; i++)
+      {
+        pt.marks[i] = -1;
+      }
+    }
+    pt.marks[id] = pos;
+    int ret = super.matchInternal(pos, pt);
+    if (ret < 0)
+    {
+      pt.marks[id] = -1;
+    }
+    else if (pt.marks[id] > pt.marks[id + pt.nMarks])
+    {
+      int swap = pt.marks[id];
+      pt.marks[id] = pt.marks[id + pt.nMarks] + 1;
+      pt.marks[id + pt.nMarks] = swap + 1;
+    }
+    return ret;
+  }
+
+  public Pattern clone1(Hashtable h)
+  {
+    OrMark om = new OrMark(id);
+    h.put(om, om);
+    h.put(this, om);
+    for (int i = 0; i < v.size(); i++)
+    {
+      om.v.addElement(((Pattern) v.elementAt(i)).clone(h));
+    }
+    return om;
+  }
+};
diff --git a/src/com/stevesoft/pat/PartialBuffer.java b/src/com/stevesoft/pat/PartialBuffer.java
index 121dd32..c53d6df 100755
--- a/src/com/stevesoft/pat/PartialBuffer.java
+++ b/src/com/stevesoft/pat/PartialBuffer.java
@@ -1,106 +1,109 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-/** This class allows you to match on a partial string.
-    If the allowOverRun flag is true, then the
-    length() method returns a number 1 larger than
-    is actually contained by the class.
-    <p>
-    If one attempts to access the last character as
-    follows:
-    <pre>
-    StringBuffer sb = ...;
-    ...
-    PartialBuffer pb = new PartialBuffer(sb);
-    char c = pb.charAt(pb.length()-1);
-    </pre>
-    then two things happen.  First, a zero is returned
-    into the variable c.  Second, the overRun flag is
-    set to "true."  Accessing data beyond the end of
-    the buffer is considered an "overRun" of the data.
-    <p>
-    This can be helpful in determining whether more
-    characters are required for a match to occur, as
-    the pseudo-code below illustrates.
-    <pre>
-    int i = ...;
-    Regex r = new Regex("some pattern");
-    pb.allowOverRun = true;
-    pb.overRun = true;
-    boolean result = r.matchAt(pb,i);
-    if(pb.overRun) {
-      // The result of the match is not relevant, regardless
-      // of whether result is true or false.  We need to
-      // append more data to the buffer and try again.
-      ....
-      sb.append(more data);
-    }
-    </pre>
- */
-class PartialBuffer
-    implements StringLike
-{
-  int off;
-  public boolean allowOverRun = true;
-  public boolean overRun = false;
-  StringBuffer sb;
-  PartialBuffer(StringBuffer sb)
-  {
-    this.sb = sb;
-  }
-
-  public char charAt(int n)
-  {
-    n += off;
-    if (n == sb.length())
-    {
-      overRun = true;
-      return 0;
-    }
-    return sb.charAt(n);
-  }
-
-  public int length()
-  {
-    return allowOverRun ? sb.length() + 1 : sb.length();
-  }
-
-  public int indexOf(char c)
-  {
-    for (int i = 0; i < sb.length(); i++)
-    {
-      if (sb.charAt(i) == c)
-      {
-        return i;
-      }
-    }
-    return -1;
-  }
-
-  public Object unwrap()
-  {
-    return sb;
-  }
-
-  public String substring(int i1, int i2)
-  {
-    StringBuffer sb = new StringBuffer(i2 - i1);
-    for (int i = i1; i < i2; i++)
-    {
-      sb.append(charAt(i));
-    }
-    return sb.toString();
-  }
-
-  /** Just returns null. */
-  public BasicStringBufferLike newStringBufferLike()
-  {
-    return null;
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+/**
+ * This class allows you to match on a partial string. If the allowOverRun flag
+ * is true, then the length() method returns a number 1 larger than is actually
+ * contained by the class.
+ * <p>
+ * If one attempts to access the last character as follows:
+ * 
+ * <pre>
+ *  StringBuffer sb = ...;
+ *  ...
+ *  PartialBuffer pb = new PartialBuffer(sb);
+ *  char c = pb.charAt(pb.length()-1);
+ * </pre>
+ * 
+ * then two things happen. First, a zero is returned into the variable c.
+ * Second, the overRun flag is set to "true." Accessing data beyond the end of
+ * the buffer is considered an "overRun" of the data.
+ * <p>
+ * This can be helpful in determining whether more characters are required for a
+ * match to occur, as the pseudo-code below illustrates.
+ * 
+ * <pre>
+ *  int i = ...;
+ *  Regex r = new Regex(&quot;some pattern&quot;);
+ *  pb.allowOverRun = true;
+ *  pb.overRun = true;
+ *  boolean result = r.matchAt(pb,i);
+ *  if(pb.overRun) {
+ *  // The result of the match is not relevant, regardless
+ *  // of whether result is true or false.  We need to
+ *  // append more data to the buffer and try again.
+ *  ....
+ *  sb.append(more data);
+ *  }
+ * </pre>
+ */
+class PartialBuffer implements StringLike
+{
+  int off;
+
+  public boolean allowOverRun = true;
+
+  public boolean overRun = false;
+
+  StringBuffer sb;
+
+  PartialBuffer(StringBuffer sb)
+  {
+    this.sb = sb;
+  }
+
+  public char charAt(int n)
+  {
+    n += off;
+    if (n == sb.length())
+    {
+      overRun = true;
+      return 0;
+    }
+    return sb.charAt(n);
+  }
+
+  public int length()
+  {
+    return allowOverRun ? sb.length() + 1 : sb.length();
+  }
+
+  public int indexOf(char c)
+  {
+    for (int i = 0; i < sb.length(); i++)
+    {
+      if (sb.charAt(i) == c)
+      {
+        return i;
+      }
+    }
+    return -1;
+  }
+
+  public Object unwrap()
+  {
+    return sb;
+  }
+
+  public String substring(int i1, int i2)
+  {
+    StringBuffer sb = new StringBuffer(i2 - i1);
+    for (int i = i1; i < i2; i++)
+    {
+      sb.append(charAt(i));
+    }
+    return sb.toString();
+  }
+
+  /** Just returns null. */
+  public BasicStringBufferLike newStringBufferLike()
+  {
+    return null;
+  }
+}
diff --git a/src/com/stevesoft/pat/Pattern.java b/src/com/stevesoft/pat/Pattern.java
index a441b37..543391e 100755
--- a/src/com/stevesoft/pat/Pattern.java
+++ b/src/com/stevesoft/pat/Pattern.java
@@ -1,280 +1,294 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-import java.util.*;
-
-/**
-        Shareware: package pat
-   <a href="copyright.html">Copyright 2001, Steven R. Brandt</a>
- */
-/**
- Class Pattern is the base class on which all the other pattern
- elements are built. */
-
-public abstract class Pattern
-{
-  /** The ESC character, the user can provide his own value
-          for the escape character through regex.esc */
-  public final static char ESC = '\\';
-  final static String PROTECT_THESE = "[]{}(),$,-\"^.";
-
-  /** The interal match function, it must be provided by any
-      class which wishes to extend Pattern. */
-  public abstract int matchInternal(int i, Pthings p);
-
-  public abstract String toString();
-
-  // Class Pattern is a singly linked list
-  // chained together by member next.  The member
-  // parent is used so that sub patterns can access
-  // the chain they are branching from.
-  Pattern next = null, parent = null;
-
-  /** This gets the next element of a Pattern that
-          we wish to match.  If we are at the end of a
-          subchain of patterns, it will return us to the
-          parent chain. */
-  public Pattern getNext()
-  {
-    return next != null ? next :
-        (parent == null ? null : parent.getNext());
-  }
-
-  /** Call this method if you have a pattern element that
-          takes a sub pattern (such as Or), and
-          after you have added a sub pattern to the current
-          pattern element. */
-  public void setParent(Pattern p)
-  {
-    if (next != null)
-    {
-      next.setParent(p);
-    }
-    else
-    {
-      parent = p;
-    }
-  }
-
-  /** This determines if the remainder of a Pattern
-          matches.  Type "return nextMatch" from within
-          matchInternal if the current
-          Pattern matches.  Otherwise, return a -1.*/
-  public int nextMatch(int i, Pthings pt)
-  {
-    Pattern p = getNext();
-    /*if(p == null) return i;
-            return p.matchInternal(i,pt);*/
-    return p == null ? i : p.matchInternal(i, pt);
-  }
-
-  /** This is a toString() for the remainder
-          of the Pattern elements after this one.
-          use this when overriding toString(). Called from
-          within toString(). */
-  public String nextString()
-  {
-    if (next == null)
-    {
-      return "";
-    }
-    return next.toString();
-  }
-
-  /** a method to detect whether char c is in String s */
-  final static boolean inString(char c, String s)
-  {
-    int i;
-    for (i = 0; i < s.length(); i++)
-    {
-      if (s.charAt(i) == c)
-      {
-        return true;
-      }
-    }
-    return false;
-  }
-
-  /** A method to create a string that protects the characters
-          listed in PROTECT_THESE by prepending the esc character.
-          The esc character itself is automatically protected. */
-  final static
-      String protect(String s, String PROTECT_THESE, char esc)
-  {
-    int i;
-    StringBuffer sb = new StringBuffer();
-    String p = PROTECT_THESE + esc;
-    for (i = 0; i < s.length(); i++)
-    {
-      char c = s.charAt(i);
-      if (inString(c, p))
-      {
-        sb.append(esc);
-      }
-      sb.append(c);
-    }
-    return sb.toString();
-  }
-
-  /** This can be used to perform a match test from
-          within class Pattern. */
-  public int match(StringLike s, Pthings pt)
-  {
-    return matchAt(s, 0, pt);
-  }
-
-  /** This can be used to perform a match test from
-          within class Pattern. */
-  public int matchAt(StringLike s, int i, Pthings pt)
-  {
-    pt.src = s;
-    int r = matchInternal(i, pt);
-    if (r < 0)
-    {
-      return -1;
-    }
-    mfrom = r < i ? r + 1 : i;
-    return r < i ? i - r - 1 : r - i;
-  }
-
-  int mfrom = 0;
-
-  // Detect masked characters
-  final boolean Masked(int i, Pthings pt)
-  {
-    return pt.cbits == null ? false : pt.cbits.get(i);
-  }
-
-  /** add a Pattern to the singly-linked Pattern chain. */
-  public Pattern add(Pattern p)
-  {
-    if (next == null)
-    {
-      if (p == null)
-      {
-        return this;
-      }
-      next = p;
-      p.parent = parent;
-      parent = null;
-    }
-    else
-    {
-      next.add(p);
-    }
-    return this;
-  }
-
-  /** The minimum number of characters which
-      this pattern element can match. */
-  public patInt minChars()
-  {
-    return new patInt(0);
-  }
-
-  /** The maximum number of characters which
-      this pattern element can match. */
-  public patInt maxChars()
-  {
-    return new patInf();
-  }
-
-  /** return minimum number of characters in pattern */
-  public final patInt countMinChars()
-  {
-    Pattern p = this;
-    patInt sum = new patInt(0);
-    while (p != null)
-    {
-      sum.pluseq(p.minChars());
-      p = p.next;
-    }
-    return sum;
-  }
-
-  /** return maximum number of characters in pattern */
-  public final patInt countMaxChars()
-  {
-    Pattern p = this;
-    patInt sum = new patInt(0);
-    while (p != null)
-    {
-      sum.pluseq(p.maxChars());
-      p = p.next;
-    }
-    return sum;
-  }
-
-  // This method is only needed by Multi_stage2 so far...
-  // the reason is that it may try something else after a
-  // match succeeds.  OrMark will only record the last thing
-  // tried in marks, so we need to backup the result of the
-  // last successful match and restore it if the next one
-  // does not succeed.
-  final int testMatch(Pattern p, int pos, Pthings pt)
-  {
-    int[] tab = null;
-    if (pt.marks != null)
-    {
-      try
-      {
-        tab = new int[pt.marks.length];
-        for (int i = 0; i < tab.length; i++)
-        {
-          tab[i] = pt.marks[i];
-        }
-      }
-      catch (Throwable t)
-      {}
-    }
-    int ret = p.matchInternal(pos, pt);
-    if (ret < 0)
-    {
-      pt.marks = tab;
-    }
-    return ret;
-  }
-
-  /** Clones this pattern elements without cloning others in the
-      linked list. */
-  Pattern clone1(Hashtable h)
-  {
-    throw new Error("No such method as clone1 for " + getClass().getName());
-  }
-
-  Pattern clone(Hashtable h)
-  {
-    Pattern p = (Pattern) h.get(this);
-    if (p != null)
-    {
-      return p;
-    }
-    p = clone1(h);
-    if (p == null)
-    {
-      throw new Error("Null from clone1!");
-    }
-    h.put(this, p);
-    h.put(p, p);
-    if (next != null)
-    {
-      p.next = next.clone(h);
-    }
-    if (parent != null)
-    {
-      p.parent = parent.clone(h);
-    }
-    return p;
-  }
-
-  public boolean equals(Object o)
-  {
-    return o == this;
-  }
-};
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+import java.util.*;
+
+/**
+ Shareware: package pat
+ <a href="copyright.html">Copyright 2001, Steven R. Brandt</a>
+ */
+/**
+ * Class Pattern is the base class on which all the other pattern elements are
+ * built.
+ */
+
+public abstract class Pattern
+{
+  /**
+   * The ESC character, the user can provide his own value for the escape
+   * character through regex.esc
+   */
+  public final static char ESC = '\\';
+
+  final static String PROTECT_THESE = "[]{}(),$,-\"^.";
+
+  /**
+   * The interal match function, it must be provided by any class which wishes
+   * to extend Pattern.
+   */
+  public abstract int matchInternal(int i, Pthings p);
+
+  public abstract String toString();
+
+  // Class Pattern is a singly linked list
+  // chained together by member next. The member
+  // parent is used so that sub patterns can access
+  // the chain they are branching from.
+  Pattern next = null, parent = null;
+
+  /**
+   * This gets the next element of a Pattern that we wish to match. If we are at
+   * the end of a subchain of patterns, it will return us to the parent chain.
+   */
+  public Pattern getNext()
+  {
+    return next != null ? next : (parent == null ? null : parent.getNext());
+  }
+
+  /**
+   * Call this method if you have a pattern element that takes a sub pattern
+   * (such as Or), and after you have added a sub pattern to the current pattern
+   * element.
+   */
+  public void setParent(Pattern p)
+  {
+    if (next != null)
+    {
+      next.setParent(p);
+    }
+    else
+    {
+      parent = p;
+    }
+  }
+
+  /**
+   * This determines if the remainder of a Pattern matches. Type "return
+   * nextMatch" from within matchInternal if the current Pattern matches.
+   * Otherwise, return a -1.
+   */
+  public int nextMatch(int i, Pthings pt)
+  {
+    Pattern p = getNext();
+    /*
+     * if(p == null) return i; return p.matchInternal(i,pt);
+     */
+    return p == null ? i : p.matchInternal(i, pt);
+  }
+
+  /**
+   * This is a toString() for the remainder of the Pattern elements after this
+   * one. use this when overriding toString(). Called from within toString().
+   */
+  public String nextString()
+  {
+    if (next == null)
+    {
+      return "";
+    }
+    return next.toString();
+  }
+
+  /** a method to detect whether char c is in String s */
+  final static boolean inString(char c, String s)
+  {
+    int i;
+    for (i = 0; i < s.length(); i++)
+    {
+      if (s.charAt(i) == c)
+      {
+        return true;
+      }
+    }
+    return false;
+  }
+
+  /**
+   * A method to create a string that protects the characters listed in
+   * PROTECT_THESE by prepending the esc character. The esc character itself is
+   * automatically protected.
+   */
+  final static String protect(String s, String PROTECT_THESE, char esc)
+  {
+    int i;
+    StringBuffer sb = new StringBuffer();
+    String p = PROTECT_THESE + esc;
+    for (i = 0; i < s.length(); i++)
+    {
+      char c = s.charAt(i);
+      if (inString(c, p))
+      {
+        sb.append(esc);
+      }
+      sb.append(c);
+    }
+    return sb.toString();
+  }
+
+  /**
+   * This can be used to perform a match test from within class Pattern.
+   */
+  public int match(StringLike s, Pthings pt)
+  {
+    return matchAt(s, 0, pt);
+  }
+
+  /**
+   * This can be used to perform a match test from within class Pattern.
+   */
+  public int matchAt(StringLike s, int i, Pthings pt)
+  {
+    pt.src = s;
+    int r = matchInternal(i, pt);
+    if (r < 0)
+    {
+      return -1;
+    }
+    mfrom = r < i ? r + 1 : i;
+    return r < i ? i - r - 1 : r - i;
+  }
+
+  int mfrom = 0;
+
+  // Detect masked characters
+  final boolean Masked(int i, Pthings pt)
+  {
+    return pt.cbits == null ? false : pt.cbits.get(i);
+  }
+
+  /** add a Pattern to the singly-linked Pattern chain. */
+  public Pattern add(Pattern p)
+  {
+    if (next == null)
+    {
+      if (p == null)
+      {
+        return this;
+      }
+      next = p;
+      p.parent = parent;
+      parent = null;
+    }
+    else
+    {
+      next.add(p);
+    }
+    return this;
+  }
+
+  /**
+   * The minimum number of characters which this pattern element can match.
+   */
+  public patInt minChars()
+  {
+    return new patInt(0);
+  }
+
+  /**
+   * The maximum number of characters which this pattern element can match.
+   */
+  public patInt maxChars()
+  {
+    return new patInf();
+  }
+
+  /** return minimum number of characters in pattern */
+  public final patInt countMinChars()
+  {
+    Pattern p = this;
+    patInt sum = new patInt(0);
+    while (p != null)
+    {
+      sum.pluseq(p.minChars());
+      p = p.next;
+    }
+    return sum;
+  }
+
+  /** return maximum number of characters in pattern */
+  public final patInt countMaxChars()
+  {
+    Pattern p = this;
+    patInt sum = new patInt(0);
+    while (p != null)
+    {
+      sum.pluseq(p.maxChars());
+      p = p.next;
+    }
+    return sum;
+  }
+
+  // This method is only needed by Multi_stage2 so far...
+  // the reason is that it may try something else after a
+  // match succeeds. OrMark will only record the last thing
+  // tried in marks, so we need to backup the result of the
+  // last successful match and restore it if the next one
+  // does not succeed.
+  final int testMatch(Pattern p, int pos, Pthings pt)
+  {
+    int[] tab = null;
+    if (pt.marks != null)
+    {
+      try
+      {
+        tab = new int[pt.marks.length];
+        for (int i = 0; i < tab.length; i++)
+        {
+          tab[i] = pt.marks[i];
+        }
+      } catch (Throwable t)
+      {
+      }
+    }
+    int ret = p.matchInternal(pos, pt);
+    if (ret < 0)
+    {
+      pt.marks = tab;
+    }
+    return ret;
+  }
+
+  /**
+   * Clones this pattern elements without cloning others in the linked list.
+   */
+  Pattern clone1(Hashtable h)
+  {
+    throw new Error("No such method as clone1 for " + getClass().getName());
+  }
+
+  Pattern clone(Hashtable h)
+  {
+    Pattern p = (Pattern) h.get(this);
+    if (p != null)
+    {
+      return p;
+    }
+    p = clone1(h);
+    if (p == null)
+    {
+      throw new Error("Null from clone1!");
+    }
+    h.put(this, p);
+    h.put(p, p);
+    if (next != null)
+    {
+      p.next = next.clone(h);
+    }
+    if (parent != null)
+    {
+      p.parent = parent.clone(h);
+    }
+    return p;
+  }
+
+  public boolean equals(Object o)
+  {
+    return o == this;
+  }
+};
diff --git a/src/com/stevesoft/pat/PatternSub.java b/src/com/stevesoft/pat/PatternSub.java
index 57576e3..d790f4b 100755
--- a/src/com/stevesoft/pat/PatternSub.java
+++ b/src/com/stevesoft/pat/PatternSub.java
@@ -1,17 +1,16 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-/** This is simply a subclass of pattern that
- * contains a sub pattern.
- */
-abstract class PatternSub
-    extends Pattern
-{
-  Pattern sub;
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+/**
+ * This is simply a subclass of pattern that contains a sub pattern.
+ */
+abstract class PatternSub extends Pattern
+{
+  Pattern sub;
+}
diff --git a/src/com/stevesoft/pat/PopRule.java b/src/com/stevesoft/pat/PopRule.java
index c8622f3..4a17ab8 100755
--- a/src/com/stevesoft/pat/PopRule.java
+++ b/src/com/stevesoft/pat/PopRule.java
@@ -1,23 +1,24 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-/** Implements substitution rule $POP. See the example
- * file <a href="http://javaregex.com/code/trans3.java.html">trans3.html</a>.
- */
-public class PopRule
-    extends SpecialRule
-{
-  public PopRule()
-  {}
-
-  public String toString1()
-  {
-    return "${POP}";
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+/**
+ * Implements substitution rule $POP. See the example file <a
+ * href="http://javaregex.com/code/trans3.java.html">trans3.html</a>.
+ */
+public class PopRule extends SpecialRule
+{
+  public PopRule()
+  {
+  }
+
+  public String toString1()
+  {
+    return "${POP}";
+  }
+}
diff --git a/src/com/stevesoft/pat/Prop.java b/src/com/stevesoft/pat/Prop.java
index b6490a6..127e44a 100755
--- a/src/com/stevesoft/pat/Prop.java
+++ b/src/com/stevesoft/pat/Prop.java
@@ -1,73 +1,75 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-/** Get Unicode properties for a character.  See
- <a href="http://unicode.org">http://unicode.org</a>. */
-public class Prop
-{
-  /** Is this a "Decimal Digit" according to Unicode? */
-  public final static boolean isDecimalDigit(char c)
-  {
-    if (Bits.decimal_digit == null)
-    {
-      Bits.decimal_digit_f();
-    }
-    return Bits.decimal_digit.get(c);
-  }
-
-  /** Is this a "Alphabetic" according to Unicode? */
-  public final static boolean isAlphabetic(char c)
-  {
-    if (Bits.letter == null)
-    {
-      Bits.letter_f();
-    }
-    return Bits.letter.get(c);
-  }
-
-  /** Is this a "Math" according to Unicode? */
-  public final static boolean isMath(char c)
-  {
-    if (Bits.math == null)
-    {
-      Bits.math_f();
-    }
-    return Bits.math.get(c);
-  }
-
-  /** Is this a "Currency" according to Unicode? */
-  public final static boolean isCurrency(char c)
-  {
-    if (Bits.currency == null)
-    {
-      Bits.currency_f();
-    }
-    return Bits.currency.get(c);
-  }
-
-  /** Is c a white space character according to Unicode? */
-  public final static boolean isWhite(char c)
-  {
-    if (Bits.white == null)
-    {
-      Bits.white_f();
-    }
-    return Bits.white.get(c);
-  }
-
-  /** Is c a punctuation character according to Unicode? */
-  public final static boolean isPunct(char c)
-  {
-    if (Bits.punct == null)
-    {
-      Bits.punct_f();
-    }
-    return Bits.punct.get(c);
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+/**
+ * Get Unicode properties for a character. See <a
+ * href="http://unicode.org">http://unicode.org</a>.
+ */
+public class Prop
+{
+  /** Is this a "Decimal Digit" according to Unicode? */
+  public final static boolean isDecimalDigit(char c)
+  {
+    if (Bits.decimal_digit == null)
+    {
+      Bits.decimal_digit_f();
+    }
+    return Bits.decimal_digit.get(c);
+  }
+
+  /** Is this a "Alphabetic" according to Unicode? */
+  public final static boolean isAlphabetic(char c)
+  {
+    if (Bits.letter == null)
+    {
+      Bits.letter_f();
+    }
+    return Bits.letter.get(c);
+  }
+
+  /** Is this a "Math" according to Unicode? */
+  public final static boolean isMath(char c)
+  {
+    if (Bits.math == null)
+    {
+      Bits.math_f();
+    }
+    return Bits.math.get(c);
+  }
+
+  /** Is this a "Currency" according to Unicode? */
+  public final static boolean isCurrency(char c)
+  {
+    if (Bits.currency == null)
+    {
+      Bits.currency_f();
+    }
+    return Bits.currency.get(c);
+  }
+
+  /** Is c a white space character according to Unicode? */
+  public final static boolean isWhite(char c)
+  {
+    if (Bits.white == null)
+    {
+      Bits.white_f();
+    }
+    return Bits.white.get(c);
+  }
+
+  /** Is c a punctuation character according to Unicode? */
+  public final static boolean isPunct(char c)
+  {
+    if (Bits.punct == null)
+    {
+      Bits.punct_f();
+    }
+    return Bits.punct.get(c);
+  }
+}
diff --git a/src/com/stevesoft/pat/Pthings.java b/src/com/stevesoft/pat/Pthings.java
index 84e327b..69e8fed 100755
--- a/src/com/stevesoft/pat/Pthings.java
+++ b/src/com/stevesoft/pat/Pthings.java
@@ -1,35 +1,47 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-import java.util.*;
-
-/**
- Things that need to be kept track of during a
- match.  Passed along with Pattern.matchInternal. */
-public class Pthings
-{
-  /** The current text we are attempting to match. */
-  public StringLike src;
-  /** Whether we should ignore the case of letters in
-      this match. */
-  public boolean ignoreCase;
-  public boolean mFlag;
-  /** The mask to use when dontMatchInQuotes is set. */
-  public BitSet cbits;
-  /** Used to keep track of backreferences. */
-  //public Hashtable marks;
-  public int[] marks;
-  public int nMarks;
-  /** Used to set the behavior of "."  By default, it
-      now fails to match the '\n' character. */
-  public boolean dotDoesntMatchCR;
-  /** Determine if Skipped strings need to be checked. */
-  public boolean no_check;
-  int lastPos;
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+import java.util.*;
+
+/**
+ * Things that need to be kept track of during a match. Passed along with
+ * Pattern.matchInternal.
+ */
+public class Pthings
+{
+  /** The current text we are attempting to match. */
+  public StringLike src;
+
+  /**
+   * Whether we should ignore the case of letters in this match.
+   */
+  public boolean ignoreCase;
+
+  public boolean mFlag;
+
+  /** The mask to use when dontMatchInQuotes is set. */
+  public BitSet cbits;
+
+  /** Used to keep track of backreferences. */
+  // public Hashtable marks;
+  public int[] marks;
+
+  public int nMarks;
+
+  /**
+   * Used to set the behavior of "." By default, it now fails to match the '\n'
+   * character.
+   */
+  public boolean dotDoesntMatchCR;
+
+  /** Determine if Skipped strings need to be checked. */
+  public boolean no_check;
+
+  int lastPos;
+}
diff --git a/src/com/stevesoft/pat/PushRule.java b/src/com/stevesoft/pat/PushRule.java
index 3fbfe14..c9aee2b 100755
--- a/src/com/stevesoft/pat/PushRule.java
+++ b/src/com/stevesoft/pat/PushRule.java
@@ -1,47 +1,50 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-/** See the example file
-    <a href="http://javaregex.com/code/trans3.java.html">trans3.java</a> for
-    further examples of how this is used.  You will probably not
-    want to call it directly. */
-public class PushRule
-    extends SpecialRule
-{
-  Regex NewRule;
-  public PushRule(PushRule p)
-  {
-    NewRule = p.NewRule;
-  }
-
-  public PushRule(String nm, Regex rr)
-  {
-    name = nm;
-    NewRule = rr;
-  }
-
-  public PushRule(String nm, Transformer tr)
-  {
-    name = nm;
-    NewRule = tr.rp;
-  }
-
-  public Object clone1()
-  {
-    return new PushRule(this);
-  }
-
-  public String String1()
-  {
-    return "${+" + name + "}";
-  }
-
-  public void apply(StringBufferLike sbl, RegRes rr)
-  {}
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+/**
+ * See the example file <a
+ * href="http://javaregex.com/code/trans3.java.html">trans3.java</a> for
+ * further examples of how this is used. You will probably not want to call it
+ * directly.
+ */
+public class PushRule extends SpecialRule
+{
+  Regex NewRule;
+
+  public PushRule(PushRule p)
+  {
+    NewRule = p.NewRule;
+  }
+
+  public PushRule(String nm, Regex rr)
+  {
+    name = nm;
+    NewRule = rr;
+  }
+
+  public PushRule(String nm, Transformer tr)
+  {
+    name = nm;
+    NewRule = tr.rp;
+  }
+
+  public Object clone1()
+  {
+    return new PushRule(this);
+  }
+
+  public String String1()
+  {
+    return "${+" + name + "}";
+  }
+
+  public void apply(StringBufferLike sbl, RegRes rr)
+  {
+  }
+}
diff --git a/src/com/stevesoft/pat/RBuffer.java b/src/com/stevesoft/pat/RBuffer.java
index 44657af..7970a1a 100755
--- a/src/com/stevesoft/pat/RBuffer.java
+++ b/src/com/stevesoft/pat/RBuffer.java
@@ -1,47 +1,52 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-/** This class is used internally by RegexReader to
-    store blocks of data. */
-class RBuffer
-{
-  boolean done = false;
-  StringBuffer sb;
-  int pos, epos;
-  RBuffer next;
-  RBuffer()
-  {}
-
-  RBuffer(StringBuffer sb)
-  {
-    this.sb = sb;
-  }
-
-  public String toString()
-  {
-    return "sb=" + sb.toString().replace('\n', ' ') +
-        " pos=" + pos + " epos=" + epos +
-        " sb.length()=" + sb.length() +
-        "\n" + sp(pos + 3) + "^" + sp(epos - pos - 1) + "^";
-  }
-
-  String sp(int n)
-  {
-    if (n <= 0)
-    {
-      return "";
-    }
-    StringBuffer sb = new StringBuffer(n);
-    for (int i = 0; i < n; i++)
-    {
-      sb.append(' ');
-    }
-    return sb.toString();
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+/**
+ * This class is used internally by RegexReader to store blocks of data.
+ */
+class RBuffer
+{
+  boolean done = false;
+
+  StringBuffer sb;
+
+  int pos, epos;
+
+  RBuffer next;
+
+  RBuffer()
+  {
+  }
+
+  RBuffer(StringBuffer sb)
+  {
+    this.sb = sb;
+  }
+
+  public String toString()
+  {
+    return "sb=" + sb.toString().replace('\n', ' ') + " pos=" + pos
+            + " epos=" + epos + " sb.length()=" + sb.length() + "\n"
+            + sp(pos + 3) + "^" + sp(epos - pos - 1) + "^";
+  }
+
+  String sp(int n)
+  {
+    if (n <= 0)
+    {
+      return "";
+    }
+    StringBuffer sb = new StringBuffer(n);
+    for (int i = 0; i < n; i++)
+    {
+      sb.append(' ');
+    }
+    return sb.toString();
+  }
+}
diff --git a/src/com/stevesoft/pat/Range.java b/src/com/stevesoft/pat/Range.java
index 5b740cd..610a4d5 100755
--- a/src/com/stevesoft/pat/Range.java
+++ b/src/com/stevesoft/pat/Range.java
@@ -1,98 +1,97 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-import java.util.*;
-
-/** Thrown when one encounters things like [z-a] */
-class BadRangeArgs
-    extends RegSyntax
-{};
-
-/** Implments a subelement (ranges) of the [] pattern element.
- For example, [a-z023] is implemented using a range and tree oneChar
- classes.
- @see Bracket
- @see oneChar
- */
-class Range
-    extends Pattern
-{
-  char lo, hi, altlo, althi;
-  boolean printBrackets = false;
-  public String toString()
-  {
-    String s = protect("" + lo, PROTECT_THESE, ESC) + "-"
-        + protect("" + hi, PROTECT_THESE, ESC);
-    if (!printBrackets)
-    {
-      return s;
-    }
-    return "[" + s + "]";
-  }
-
-  Range(char loi, char hii)
-      throws RegSyntax
-  {
-    lo = loi;
-    hi = hii;
-    oneChar o = null;
-    if (lo >= hi)
-    {
-      //throw new BadRangeArgs();
-      RegSyntaxError.endItAll("Badly formed []'s : " + lo + " >= " + hi);
-    }
-    o = new oneChar(lo);
-    altlo = o.altc;
-    o = new oneChar(hi);
-    althi = o.altc;
-  }
-
-  public int matchInternal(int pos, Pthings pt)
-  {
-    if (pos >= pt.src.length())
-    {
-      return -1;
-    }
-    if (Masked(pos, pt))
-    {
-      return -1;
-    }
-    char c = pt.src.charAt(pos);
-    if (lo <= c && c <= hi ||
-        (pt.ignoreCase && (altlo <= c && c <= althi)))
-    {
-      return nextMatch(pos + 1, pt);
-    }
-    return -1;
-  }
-
-  public patInt minChars()
-  {
-    return new patInt(1);
-  }
-
-  public patInt maxChars()
-  {
-    return new patInt(1);
-  }
-
-  public Pattern clone1(Hashtable h)
-  {
-    try
-    {
-      Range r = new Range(lo, hi);
-      r.printBrackets = printBrackets;
-      return r;
-    }
-    catch (RegSyntax rs)
-    {
-      return null;
-    }
-  }
-};
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+import java.util.*;
+
+/** Thrown when one encounters things like [z-a] */
+class BadRangeArgs extends RegSyntax
+{
+};
+
+/**
+ * Implments a subelement (ranges) of the [] pattern element. For example,
+ * [a-z023] is implemented using a range and tree oneChar classes.
+ * 
+ * @see Bracket
+ * @see oneChar
+ */
+class Range extends Pattern
+{
+  char lo, hi, altlo, althi;
+
+  boolean printBrackets = false;
+
+  public String toString()
+  {
+    String s = protect("" + lo, PROTECT_THESE, ESC) + "-"
+            + protect("" + hi, PROTECT_THESE, ESC);
+    if (!printBrackets)
+    {
+      return s;
+    }
+    return "[" + s + "]";
+  }
+
+  Range(char loi, char hii) throws RegSyntax
+  {
+    lo = loi;
+    hi = hii;
+    oneChar o = null;
+    if (lo >= hi)
+    {
+      // throw new BadRangeArgs();
+      RegSyntaxError.endItAll("Badly formed []'s : " + lo + " >= " + hi);
+    }
+    o = new oneChar(lo);
+    altlo = o.altc;
+    o = new oneChar(hi);
+    althi = o.altc;
+  }
+
+  public int matchInternal(int pos, Pthings pt)
+  {
+    if (pos >= pt.src.length())
+    {
+      return -1;
+    }
+    if (Masked(pos, pt))
+    {
+      return -1;
+    }
+    char c = pt.src.charAt(pos);
+    if (lo <= c && c <= hi || (pt.ignoreCase && (altlo <= c && c <= althi)))
+    {
+      return nextMatch(pos + 1, pt);
+    }
+    return -1;
+  }
+
+  public patInt minChars()
+  {
+    return new patInt(1);
+  }
+
+  public patInt maxChars()
+  {
+    return new patInt(1);
+  }
+
+  public Pattern clone1(Hashtable h)
+  {
+    try
+    {
+      Range r = new Range(lo, hi);
+      r.printBrackets = printBrackets;
+      return r;
+    } catch (RegSyntax rs)
+    {
+      return null;
+    }
+  }
+};
diff --git a/src/com/stevesoft/pat/RegOpt.java b/src/com/stevesoft/pat/RegOpt.java
index f70df39..0d65139 100755
--- a/src/com/stevesoft/pat/RegOpt.java
+++ b/src/com/stevesoft/pat/RegOpt.java
@@ -1,469 +1,448 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-import java.util.*;
-
-/** This class is just like oneChar, but doesn't worry about case. */
-class FastChar
-    extends oneChar
-{
-  FastChar(char c)
-  {
-    super(c);
-  }
-
-  public int matchInternal(int p, Pthings pt)
-  {
-    return (p < pt.src.length()
-            && pt.src.charAt(p) == c) ?
-        nextMatch(p + 1, pt) : -1;
-  }
-
-  Pattern clone1(Hashtable h)
-  {
-    return new FastChar(c);
-  }
-}
-
-/** This class is a hashtable keyed by Character
- * Objects.  It is used to match things of the
- * form (?:a..|b..|c..|..) match with greater efficiency --
- * by using a Hashtable that indexes into the group
- * of patterns.
- */
-class Branch
-    extends Pattern
-{
-  Hashtable h = new Hashtable();
-  // We need to keep track of the order
-  // of the keys -- if we don't then
-  // recompiling the output of toString
-  // may produce errors by re-ordering
-  // ()'s and changing the id number of
-  // the backreference associated with
-  // a subpattern.
-  Vector keys = new Vector();
-  Branch()
-  {}
-
-  Pattern clone1(Hashtable x)
-  {
-    Branch b = new Branch();
-    b.keys = (Vector) keys.clone();
-    x.put(this, b);
-    x.put(b, b);
-
-    for (int i = 0; i < keys.size(); i++)
-    {
-      Pattern p = (Pattern) h.get(keys.elementAt(i));
-      b.h.put(keys.elementAt(i), p.clone(x));
-    }
-    return b;
-  }
-
-  // this function eliminates Branches with 0 or 1 elements.
-  final Pattern reduce(boolean ignoreCase, boolean dontMinQ)
-  {
-    if (h.size() == 1)
-    {
-      Enumeration e = h.keys();
-      Character c = (Character) e.nextElement();
-      Pattern oc;
-      if (ignoreCase || dontMinQ)
-      {
-        oc = new oneChar(c.charValue());
-      }
-      else
-      {
-        oc = new FastChar(c.charValue());
-      }
-      oc.next = (Pattern) h.get(c);
-      oc.add(next);
-      return oc;
-    }
-    else if (h.size() == 0)
-    {
-      return null;
-    }
-    return this;
-  }
-
-  public patInt maxChars()
-  {
-    Enumeration e = h.keys();
-    patInt count = new patInt(0);
-    while (e.hasMoreElements())
-    {
-      Object key = e.nextElement();
-      Pattern pa = (Pattern) h.get(key);
-      patInt pi = pa.maxChars();
-      pi.inc();
-      count.maxeq(pi);
-    }
-    return count;
-  }
-
-  public patInt minChars()
-  {
-    Enumeration e = h.keys();
-    patInt count = new patInt(0);
-    while (e.hasMoreElements())
-    {
-      Object key = e.nextElement();
-      Pattern pa = (Pattern) h.get(key);
-      patInt pi = pa.minChars();
-      pi.inc();
-      count.mineq(pi);
-    }
-    return count;
-  }
-
-  // adds a oneChar object to this Branch
-  void addc(oneChar o, boolean ignoreCase, boolean dontMinQ)
-  {
-    Pattern n = o.next;
-    if (n == null)
-    {
-      n = new NullPattern();
-    }
-    else
-    {
-      n = RegOpt.opt(n, ignoreCase, dontMinQ);
-    }
-    n.setParent(this);
-    set(new Character(o.c), n, ignoreCase, dontMinQ);
-    if (ignoreCase)
-    {
-      if (o.c != o.altc)
-      {
-        set(new Character(o.altc), n, ignoreCase, dontMinQ);
-      }
-      if (o.c != o.altc2 && o.altc != o.altc2)
-      {
-        set(new Character(o.altc2), n, ignoreCase, dontMinQ);
-      }
-    }
-  }
-
-  void set(Character c, Pattern n, boolean igc, boolean dontMinQ)
-  {
-    Pattern p = (Pattern) h.get(c);
-    next = null;
-    // This letter is not yet used in the Branch object.
-    // We need to add it.
-    if (p == null)
-    {
-      if (n instanceof Or)
-      {
-        // A NullPattern is prepended to an Or
-        // to prevent confusing this object.
-        // For example: (boo|bug) => (b(?:oo|ug))
-        // during this process.  However, we
-        // want (b(?:oo|ell)|bug)
-        NullPattern np = new NullPattern();
-        np.add(n);
-        h.put(c, np);
-      }
-      else
-      {
-        h.put(c, n);
-      }
-      // Make sure we remember the order things were
-      // added into the Branch object so that we can
-      // properly convert it to a String.
-      keys.addElement(c);
-    }
-    else if (p instanceof Or)
-    {
-      ( (Or) p).addOr(n);
-    }
-    else if (p instanceof oneChar && n instanceof oneChar
-             && ( (oneChar) p).c != ( (oneChar) n).c)
-    {
-      Branch b = new Branch();
-      b.addc( (oneChar) p, igc, dontMinQ);
-      b.addc( (oneChar) n, igc, dontMinQ);
-      h.put(c, b);
-      b.setParent(this);
-    }
-    else if (p instanceof Branch && n instanceof oneChar)
-    {
-      ( (Branch) p).addc( (oneChar) n, igc, dontMinQ);
-      n.setParent(p);
-    }
-    else
-    {
-      // Create an Or object to receive the variety
-      // of branches in the pattern if the current letter
-      // is matched.  We do not attempt to make these
-      // sub-branches into a Branch object yet.
-      Or o = new Or();
-      o.setParent(this);
-
-      // Remove NullPattern from p -- it's no longer needed.
-      if (p instanceof NullPattern
-          && p.parent == null && p.next != null)
-      {
-        o.addOr(p.next);
-      }
-      else
-      {
-        o.addOr(p);
-      }
-      o.addOr(n);
-
-      Pattern optpat = RegOpt.opt(o, igc, dontMinQ);
-      h.put(c, optpat);
-      optpat.setParent(this);
-    }
-  }
-
-  public String toString()
-  {
-    StringBuffer sb = new StringBuffer();
-    // should protect this...
-    sb.append("(?:(?#branch)"); // Hashtable)");
-    for (int i = 0; i < keys.size(); i++)
-    {
-      Character c = (Character) keys.elementAt(i);
-      sb.append(c);
-      sb.append(h.get(c));
-      if (i + 1 < keys.size())
-      {
-        sb.append("|");
-      }
-    }
-    sb.append(")");
-    sb.append(nextString());
-    return sb.toString();
-  }
-
-  public int matchInternal(int pos, Pthings pt)
-  {
-    if (pos >= pt.src.length())
-    {
-      return -1;
-    }
-    Pattern n = (Pattern) h.get(new Character(pt.src.charAt(pos)));
-    if (n == null)
-    {
-      return -1;
-    }
-    if (pt.cbits != null && pt.cbits.get(pos))
-    {
-      return -1;
-    }
-    return n.matchInternal(pos + 1, pt);
-  }
-}
-
-/** This is just a place to put the optimizing function.
-    It is never instantiated as an Object.  It just sorts
-    through the RegOpt looking for things it can change
-    and make faster. */
-public class RegOpt
-{
-  static Pattern opt(Pattern p, boolean ignoreCase,
-                     boolean dontMinQ)
-  {
-    if (p == null)
-    {
-      return p;
-    }
-    if (p instanceof Bracket)
-    {
-      Bracket b = (Bracket) p;
-      // FastBracket is the only special
-      // optimized class to have its own
-      // source file.
-      p = FastBracket.process(b, ignoreCase);
-      //if(!(p instanceof FastBracket)
-      //p = Switch.process(b,ignoreCase);
-      p.next = b.next;
-      p.parent = b.parent;
-    }
-    else if (p instanceof oneChar && !ignoreCase
-             && !dontMinQ)
-    {
-      oneChar o = (oneChar) p;
-      p = new FastChar(o.c);
-      p.next = o.next;
-      p.parent = o.parent;
-    }
-    else if (p instanceof Or
-             && ( (Or) p).leftForm().equals("(?:")
-             && ( (Or) p).v.size() == 1)
-    { // Eliminate this Or Object.
-      Or o = (Or) p;
-      p = (Pattern) o.v.elementAt(0);
-      p.setParent(null);
-      p = RegOpt.opt(p, ignoreCase, dontMinQ);
-      p.add(o.next);
-    }
-    else if (p instanceof Or)
-    {
-      Or o = (Or) p;
-      o.pv = null;
-      Vector v = o.v;
-      o.v = new Vector();
-      Branch b = new Branch();
-      b.parent = o.parent;
-      for (int i = 0; i < v.size(); i++)
-      {
-        Pattern pp = (Pattern) v.elementAt(i);
-        // We want to have at least two oneChar's in
-        // the Or Object to consider making a Branch.
-        if (pp instanceof oneChar && (b.h.size() >= 1 ||
-                                      (i + 1 < v.size() &&
-                                       v.elementAt(i + 1) instanceof oneChar)))
-        {
-          b.addc( (oneChar) pp, ignoreCase, dontMinQ);
-        }
-        else
-        {
-          if (b.keys.size() > 0)
-          {
-            Pattern p2 = (Pattern) b.reduce(ignoreCase, dontMinQ);
-            if (p2 != null)
-            {
-              o.addOr(p2);
-              b = new Branch();
-              b.parent = o.parent;
-            }
-          }
-          o.addOr(opt(pp, ignoreCase, dontMinQ));
-        }
-      }
-      if (b.keys.size() > 0)
-      {
-        Pattern p2 = (Pattern) b.reduce(ignoreCase, dontMinQ);
-        if (p2 != null)
-        {
-          o.addOr(p2);
-        }
-      }
-      if (o.v.size() == 1
-          && o.leftForm().equals("(?:"))
-      { // Eliminate Or Object
-        p = (Pattern) o.v.elementAt(0);
-        p.setParent(null);
-        p = RegOpt.opt(p, ignoreCase, dontMinQ);
-        p.add(o.next);
-      }
-    }
-    else if (p instanceof FastMulti)
-    {
-      PatternSub ps = (PatternSub) p;
-      ps.sub = RegOpt.opt(ps.sub, ignoreCase, dontMinQ);
-    }
-    else if (p instanceof Multi && safe4fm( ( (PatternSub) p).sub))
-    {
-      Multi m = (Multi) p;
-      FastMulti fm = null;
-      try
-      {
-        fm = new FastMulti(m.a, m.b,
-                           opt(m.sub, ignoreCase, dontMinQ));
-      }
-      catch (RegSyntax rs)
-      {}
-      fm.parent = m.parent;
-      fm.matchFewest = m.matchFewest;
-      fm.next = m.next;
-      p = fm;
-    }
-    if (p.next != null)
-    {
-      p.next = opt(p.next, ignoreCase, dontMinQ);
-    }
-    return p;
-  }
-
-  final static boolean safe4fm(Pattern x)
-  {
-    while (x != null)
-    {
-      if (x instanceof Bracket)
-      {
-        ;
-      }
-      else if (x instanceof Range)
-      {
-        ;
-      }
-      else if (x instanceof oneChar)
-      {
-        ;
-      }
-      else if (x instanceof Any)
-      {
-        ;
-      }
-      else if (x instanceof Custom
-               && ( (Custom) x).v instanceof UniValidator)
-      {
-        ;
-      }
-      else if (x instanceof Or)
-      {
-        Or o = (Or) x;
-        if (!o.leftForm().equals("(?:"))
-        {
-          return false;
-        }
-        patInt lo = o.countMinChars();
-        patInt hi = o.countMaxChars();
-        if (!lo.equals(hi))
-        {
-          return false;
-        }
-        for (int i = 0; i < o.v.size(); i++)
-        {
-          if (!safe4fm( (Pattern) o.v.elementAt(i)))
-          {
-            return false;
-          }
-        }
-      }
-      else
-      {
-        return false;
-      }
-      x = x.next;
-    }
-    return true;
-  }
-  /*
-       public static void setParents(Regex r) {
-    setParents(r.thePattern,null);
-       }
-       static void setParents(Pattern p,Pattern x) {
-    if(p instanceof PatternSub && !(p instanceof FastMulti)
-    && !(p instanceof DotMulti))
-      RegOpt.setParents( ((PatternSub)p).sub, p);
-    else if(p instanceof Or && !(p instanceof Bracket)) {
-      Or o = (Or)p;
-      for(int i=0;i<o.v.size();i++)
-        RegOpt.setParents((Pattern)o.v.elementAt(i),o);
-    } else if(p instanceof Branch) {
-      Branch b = (Branch)p;
-      Enumeration e = b.h.keys();
-      while(e.hasMoreElements()) {
-        Object o = e.nextElement();
-        RegOpt.setParents( (Pattern)b.h.get(o), b);
-      }
-    }
-    if(p.next == null)
-      p.parent = x;
-    else {
-      p.parent = null;
-      RegOpt.setParents(p.next,x);
-    }
-       }*/
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+import java.util.*;
+
+/** This class is just like oneChar, but doesn't worry about case. */
+class FastChar extends oneChar
+{
+  FastChar(char c)
+  {
+    super(c);
+  }
+
+  public int matchInternal(int p, Pthings pt)
+  {
+    return (p < pt.src.length() && pt.src.charAt(p) == c) ? nextMatch(
+            p + 1, pt) : -1;
+  }
+
+  Pattern clone1(Hashtable h)
+  {
+    return new FastChar(c);
+  }
+}
+
+/**
+ * This class is a hashtable keyed by Character Objects. It is used to match
+ * things of the form (?:a..|b..|c..|..) match with greater efficiency -- by
+ * using a Hashtable that indexes into the group of patterns.
+ */
+class Branch extends Pattern
+{
+  Hashtable h = new Hashtable();
+
+  // We need to keep track of the order
+  // of the keys -- if we don't then
+  // recompiling the output of toString
+  // may produce errors by re-ordering
+  // ()'s and changing the id number of
+  // the backreference associated with
+  // a subpattern.
+  Vector keys = new Vector();
+
+  Branch()
+  {
+  }
+
+  Pattern clone1(Hashtable x)
+  {
+    Branch b = new Branch();
+    b.keys = (Vector) keys.clone();
+    x.put(this, b);
+    x.put(b, b);
+
+    for (int i = 0; i < keys.size(); i++)
+    {
+      Pattern p = (Pattern) h.get(keys.elementAt(i));
+      b.h.put(keys.elementAt(i), p.clone(x));
+    }
+    return b;
+  }
+
+  // this function eliminates Branches with 0 or 1 elements.
+  final Pattern reduce(boolean ignoreCase, boolean dontMinQ)
+  {
+    if (h.size() == 1)
+    {
+      Enumeration e = h.keys();
+      Character c = (Character) e.nextElement();
+      Pattern oc;
+      if (ignoreCase || dontMinQ)
+      {
+        oc = new oneChar(c.charValue());
+      }
+      else
+      {
+        oc = new FastChar(c.charValue());
+      }
+      oc.next = (Pattern) h.get(c);
+      oc.add(next);
+      return oc;
+    }
+    else if (h.size() == 0)
+    {
+      return null;
+    }
+    return this;
+  }
+
+  public patInt maxChars()
+  {
+    Enumeration e = h.keys();
+    patInt count = new patInt(0);
+    while (e.hasMoreElements())
+    {
+      Object key = e.nextElement();
+      Pattern pa = (Pattern) h.get(key);
+      patInt pi = pa.maxChars();
+      pi.inc();
+      count.maxeq(pi);
+    }
+    return count;
+  }
+
+  public patInt minChars()
+  {
+    Enumeration e = h.keys();
+    patInt count = new patInt(0);
+    while (e.hasMoreElements())
+    {
+      Object key = e.nextElement();
+      Pattern pa = (Pattern) h.get(key);
+      patInt pi = pa.minChars();
+      pi.inc();
+      count.mineq(pi);
+    }
+    return count;
+  }
+
+  // adds a oneChar object to this Branch
+  void addc(oneChar o, boolean ignoreCase, boolean dontMinQ)
+  {
+    Pattern n = o.next;
+    if (n == null)
+    {
+      n = new NullPattern();
+    }
+    else
+    {
+      n = RegOpt.opt(n, ignoreCase, dontMinQ);
+    }
+    n.setParent(this);
+    set(new Character(o.c), n, ignoreCase, dontMinQ);
+    if (ignoreCase)
+    {
+      if (o.c != o.altc)
+      {
+        set(new Character(o.altc), n, ignoreCase, dontMinQ);
+      }
+      if (o.c != o.altc2 && o.altc != o.altc2)
+      {
+        set(new Character(o.altc2), n, ignoreCase, dontMinQ);
+      }
+    }
+  }
+
+  void set(Character c, Pattern n, boolean igc, boolean dontMinQ)
+  {
+    Pattern p = (Pattern) h.get(c);
+    next = null;
+    // This letter is not yet used in the Branch object.
+    // We need to add it.
+    if (p == null)
+    {
+      if (n instanceof Or)
+      {
+        // A NullPattern is prepended to an Or
+        // to prevent confusing this object.
+        // For example: (boo|bug) => (b(?:oo|ug))
+        // during this process. However, we
+        // want (b(?:oo|ell)|bug)
+        NullPattern np = new NullPattern();
+        np.add(n);
+        h.put(c, np);
+      }
+      else
+      {
+        h.put(c, n);
+      }
+      // Make sure we remember the order things were
+      // added into the Branch object so that we can
+      // properly convert it to a String.
+      keys.addElement(c);
+    }
+    else if (p instanceof Or)
+    {
+      ((Or) p).addOr(n);
+    }
+    else if (p instanceof oneChar && n instanceof oneChar
+            && ((oneChar) p).c != ((oneChar) n).c)
+    {
+      Branch b = new Branch();
+      b.addc((oneChar) p, igc, dontMinQ);
+      b.addc((oneChar) n, igc, dontMinQ);
+      h.put(c, b);
+      b.setParent(this);
+    }
+    else if (p instanceof Branch && n instanceof oneChar)
+    {
+      ((Branch) p).addc((oneChar) n, igc, dontMinQ);
+      n.setParent(p);
+    }
+    else
+    {
+      // Create an Or object to receive the variety
+      // of branches in the pattern if the current letter
+      // is matched. We do not attempt to make these
+      // sub-branches into a Branch object yet.
+      Or o = new Or();
+      o.setParent(this);
+
+      // Remove NullPattern from p -- it's no longer needed.
+      if (p instanceof NullPattern && p.parent == null && p.next != null)
+      {
+        o.addOr(p.next);
+      }
+      else
+      {
+        o.addOr(p);
+      }
+      o.addOr(n);
+
+      Pattern optpat = RegOpt.opt(o, igc, dontMinQ);
+      h.put(c, optpat);
+      optpat.setParent(this);
+    }
+  }
+
+  public String toString()
+  {
+    StringBuffer sb = new StringBuffer();
+    // should protect this...
+    sb.append("(?:(?#branch)"); // Hashtable)");
+    for (int i = 0; i < keys.size(); i++)
+    {
+      Character c = (Character) keys.elementAt(i);
+      sb.append(c);
+      sb.append(h.get(c));
+      if (i + 1 < keys.size())
+      {
+        sb.append("|");
+      }
+    }
+    sb.append(")");
+    sb.append(nextString());
+    return sb.toString();
+  }
+
+  public int matchInternal(int pos, Pthings pt)
+  {
+    if (pos >= pt.src.length())
+    {
+      return -1;
+    }
+    Pattern n = (Pattern) h.get(new Character(pt.src.charAt(pos)));
+    if (n == null)
+    {
+      return -1;
+    }
+    if (pt.cbits != null && pt.cbits.get(pos))
+    {
+      return -1;
+    }
+    return n.matchInternal(pos + 1, pt);
+  }
+}
+
+/**
+ * This is just a place to put the optimizing function. It is never instantiated
+ * as an Object. It just sorts through the RegOpt looking for things it can
+ * change and make faster.
+ */
+public class RegOpt
+{
+  static Pattern opt(Pattern p, boolean ignoreCase, boolean dontMinQ)
+  {
+    if (p == null)
+    {
+      return p;
+    }
+    if (p instanceof Bracket)
+    {
+      Bracket b = (Bracket) p;
+      // FastBracket is the only special
+      // optimized class to have its own
+      // source file.
+      p = FastBracket.process(b, ignoreCase);
+      // if(!(p instanceof FastBracket)
+      // p = Switch.process(b,ignoreCase);
+      p.next = b.next;
+      p.parent = b.parent;
+    }
+    else if (p instanceof oneChar && !ignoreCase && !dontMinQ)
+    {
+      oneChar o = (oneChar) p;
+      p = new FastChar(o.c);
+      p.next = o.next;
+      p.parent = o.parent;
+    }
+    else if (p instanceof Or && ((Or) p).leftForm().equals("(?:")
+            && ((Or) p).v.size() == 1)
+    { // Eliminate this Or Object.
+      Or o = (Or) p;
+      p = (Pattern) o.v.elementAt(0);
+      p.setParent(null);
+      p = RegOpt.opt(p, ignoreCase, dontMinQ);
+      p.add(o.next);
+    }
+    else if (p instanceof Or)
+    {
+      Or o = (Or) p;
+      o.pv = null;
+      Vector v = o.v;
+      o.v = new Vector();
+      Branch b = new Branch();
+      b.parent = o.parent;
+      for (int i = 0; i < v.size(); i++)
+      {
+        Pattern pp = (Pattern) v.elementAt(i);
+        // We want to have at least two oneChar's in
+        // the Or Object to consider making a Branch.
+        if (pp instanceof oneChar
+                && (b.h.size() >= 1 || (i + 1 < v.size() && v
+                        .elementAt(i + 1) instanceof oneChar)))
+        {
+          b.addc((oneChar) pp, ignoreCase, dontMinQ);
+        }
+        else
+        {
+          if (b.keys.size() > 0)
+          {
+            Pattern p2 = (Pattern) b.reduce(ignoreCase, dontMinQ);
+            if (p2 != null)
+            {
+              o.addOr(p2);
+              b = new Branch();
+              b.parent = o.parent;
+            }
+          }
+          o.addOr(opt(pp, ignoreCase, dontMinQ));
+        }
+      }
+      if (b.keys.size() > 0)
+      {
+        Pattern p2 = (Pattern) b.reduce(ignoreCase, dontMinQ);
+        if (p2 != null)
+        {
+          o.addOr(p2);
+        }
+      }
+      if (o.v.size() == 1 && o.leftForm().equals("(?:"))
+      { // Eliminate Or Object
+        p = (Pattern) o.v.elementAt(0);
+        p.setParent(null);
+        p = RegOpt.opt(p, ignoreCase, dontMinQ);
+        p.add(o.next);
+      }
+    }
+    else if (p instanceof FastMulti)
+    {
+      PatternSub ps = (PatternSub) p;
+      ps.sub = RegOpt.opt(ps.sub, ignoreCase, dontMinQ);
+    }
+    else if (p instanceof Multi && safe4fm(((PatternSub) p).sub))
+    {
+      Multi m = (Multi) p;
+      FastMulti fm = null;
+      try
+      {
+        fm = new FastMulti(m.a, m.b, opt(m.sub, ignoreCase, dontMinQ));
+      } catch (RegSyntax rs)
+      {
+      }
+      fm.parent = m.parent;
+      fm.matchFewest = m.matchFewest;
+      fm.next = m.next;
+      p = fm;
+    }
+    if (p.next != null)
+    {
+      p.next = opt(p.next, ignoreCase, dontMinQ);
+    }
+    return p;
+  }
+
+  final static boolean safe4fm(Pattern x)
+  {
+    while (x != null)
+    {
+      if (x instanceof Bracket)
+      {
+        ;
+      }
+      else if (x instanceof Range)
+      {
+        ;
+      }
+      else if (x instanceof oneChar)
+      {
+        ;
+      }
+      else if (x instanceof Any)
+      {
+        ;
+      }
+      else if (x instanceof Custom
+              && ((Custom) x).v instanceof UniValidator)
+      {
+        ;
+      }
+      else if (x instanceof Or)
+      {
+        Or o = (Or) x;
+        if (!o.leftForm().equals("(?:"))
+        {
+          return false;
+        }
+        patInt lo = o.countMinChars();
+        patInt hi = o.countMaxChars();
+        if (!lo.equals(hi))
+        {
+          return false;
+        }
+        for (int i = 0; i < o.v.size(); i++)
+        {
+          if (!safe4fm((Pattern) o.v.elementAt(i)))
+          {
+            return false;
+          }
+        }
+      }
+      else
+      {
+        return false;
+      }
+      x = x.next;
+    }
+    return true;
+  }
+  /*
+   * public static void setParents(Regex r) { setParents(r.thePattern,null); }
+   * static void setParents(Pattern p,Pattern x) { if(p instanceof PatternSub &&
+   * !(p instanceof FastMulti) && !(p instanceof DotMulti)) RegOpt.setParents(
+   * ((PatternSub)p).sub, p); else if(p instanceof Or && !(p instanceof
+   * Bracket)) { Or o = (Or)p; for(int i=0;i<o.v.size();i++)
+   * RegOpt.setParents((Pattern)o.v.elementAt(i),o); } else if(p instanceof
+   * Branch) { Branch b = (Branch)p; Enumeration e = b.h.keys();
+   * while(e.hasMoreElements()) { Object o = e.nextElement(); RegOpt.setParents(
+   * (Pattern)b.h.get(o), b); } } if(p.next == null) p.parent = x; else {
+   * p.parent = null; RegOpt.setParents(p.next,x); } }
+   */
+}
diff --git a/src/com/stevesoft/pat/RegRes.java b/src/com/stevesoft/pat/RegRes.java
index d644d0c..a204c47 100755
--- a/src/com/stevesoft/pat/RegRes.java
+++ b/src/com/stevesoft/pat/RegRes.java
@@ -1,276 +1,299 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-/**
-        Shareware: package pat
-   <a href="copyright.html">Copyright 2001, Steven R. Brandt</a>
- */
-/**
- This class is used to store a result from Regex */
-public class RegRes
-    implements Cloneable
-{
-  protected int[] marks = null;
-  protected boolean didMatch_ = false;
-  protected StringLike src = null;
-
-  /** Obtain the text String that was matched against. */
-  public String getString()
-  {
-    return src.toString();
-  }
-
-  /** Obtain the source StringLike object. */
-  public StringLike getStringLike()
-  {
-    return src;
-  }
-
-  protected int charsMatched_ = 0, matchFrom_ = 0, numSubs_ = 0;
-  public String toString()
-  {
-    StringBuffer sb = new StringBuffer();
-    sb.append("match=" + matchedFrom() + ":" + charsMatched());
-    if (!didMatch())
-    {
-      return sb.toString();
-    }
-    for (int i = 0; i < numSubs(); i++)
-    {
-      int n = i + 1;
-      sb.append(" sub(" + n + ")=" + matchedFrom(n) +
-                ":" + charsMatched(n));
-    }
-    return sb.toString();
-  }
-
-  public RegRes()
-  {}
-
-  public RegRes(RegRes r)
-  {
-    copyOutOf(r);
-  }
-
-  public void copyOutOf(RegRes r)
-  {
-    if (r.marks == null)
-    {
-      marks = null;
-    }
-    else
-    {
-      try
-      {
-        //marks = (Hashtable)r.marks.clone();
-        marks = new int[r.marks.length];
-        for (int i = 0; i < marks.length; i++)
-        {
-          marks[i] = r.marks[i];
-        }
-        //marks = (int[])r.marks.clone();
-      }
-      catch (Throwable t)
-      {}
-    }
-    didMatch_ = r.didMatch_;
-    src = r.src;
-    charsMatched_ = r.charsMatched_;
-    matchFrom_ = r.matchFrom_;
-    numSubs_ = r.numSubs_;
-  }
-
-  public Object clone()
-  {
-    return new RegRes(this);
-  }
-
-  public boolean equals(RegRes r)
-  {
-    if (charsMatched_ != r.charsMatched_
-        || matchFrom_ != r.matchFrom_
-        || didMatch_ != r.didMatch_
-        || numSubs_ != r.numSubs_
-        || !src.unwrap().equals(r.src.unwrap()))
-    {
-      return false;
-    }
-    if (marks == null && r.marks != null)
-    {
-      return false;
-    }
-    if (marks != null && r.marks == null)
-    {
-      return false;
-    }
-    for (int i = 1; i <= numSubs_; i++)
-    {
-      if (matchedFrom(i) != r.matchedFrom(i))
-      {
-        return false;
-      }
-      else if (charsMatched(i) != r.charsMatched(i))
-      {
-        return false;
-      }
-    }
-    return true;
-  }
-
-  /** Obtains the match if successful, null otherwise.*/
-  public String stringMatched()
-  {
-    int mf = matchedFrom(), cm = charsMatched();
-    return!didMatch_ || mf < 0 || cm < 0 ? null :
-        src.substring(mf, mf + cm);
-  }
-
-  /** Obtains the position backreference number i begins to match, or
-       -1 if backreference i was not matched. */
-  public int matchedFrom(int i)
-  {
-    if (marks == null || i > numSubs_)
-    {
-      return -1;
-    }
-    //Integer in=(Integer)marks.get("left"+i);
-    //return in == null ? -1 : in.intValue();
-    return marks[i];
-  }
-
-  /** Obtains the number of characters matched by backreference i, or
-       -1 if backreference i was not matched. */
-  public int charsMatched(int i)
-  {
-    if (marks == null || i > numSubs_ || !didMatch_)
-    {
-      return -1;
-    }
-    //Integer in = (Integer)marks.get("right"+i);
-    //int i2 = in==null ? -1 : in.intValue();
-    int mf = matchedFrom(i);
-    return mf < 0 ? -1 : marks[i + numSubs_] - matchedFrom(i);
-  }
-
-  /** This is either equal to matchedFrom(i)+charsMatched(i) if the match
-      was successful, or -1 if it was not. */
-  public int matchedTo(int i)
-  {
-    if (marks == null || i > numSubs_ || !didMatch_)
-    {
-      return -1;
-    }
-    return marks[i + numSubs_];
-  }
-
-  /** Obtains a substring matching the nth set
-              of parenthesis from the pattern. See
-              numSubs(void), or null if the nth backrefence did
-              not match. */
-  public String stringMatched(int i)
-  {
-    int mf = matchedFrom(i), cm = charsMatched(i);
-    return!didMatch_ || mf < 0 || cm < 0 ? null :
-        src.substring(mf, mf + cm);
-  }
-
-  /** This returns the part of the string that preceeds the match,
-       or null if the match failed.*/
-  public String left()
-  {
-    int mf = matchedFrom();
-    return!didMatch_ || (mf < 0) ? null : src.substring(0, mf);
-  }
-
-  /** This returns the part of the string that follows the ith
-              backreference, or null if the backreference did not match. */
-  public String left(int i)
-  {
-    int mf = matchedFrom(i);
-    return!didMatch_ || (mf < 0) ? null : src.substring(0, mf);
-  }
-
-  /** This returns the part of the string that follows the match,
-       or null if the backreference did not match.*/
-  public String right()
-  {
-    int mf = matchedFrom(), cm = charsMatched();
-    return!didMatch_ || mf < 0 || cm < 0 ? null : src.substring(mf +
-        cm, src.length());
-  }
-
-  /** This returns the string to the right of the ith backreference,
-       or null if the backreference did not match. */
-  public String right(int i)
-  {
-    int mf = matchedFrom(i), cm = charsMatched(i);
-    return!didMatch_ || mf < 0 || cm < 0 ? null :
-        src.substring(mf + cm, src.length());
-  }
-
-  /** After a successful match, this returns the location of
-              the first matching character, or -1 if the match failed.*/
-  public int matchedFrom()
-  {
-    return!didMatch_ ? -1 : matchFrom_;
-  }
-
-  /** After a successful match, this returns the number of
-              characters in the match, or -1 if the match failed. */
-  public int charsMatched()
-  {
-    return!didMatch_ || matchFrom_ < 0 ? -1 : charsMatched_;
-  }
-
-  /** This is matchedFrom()+charsMatched() after a successful match,
-      or -1 otherwise. */
-  public int matchedTo()
-  {
-    return!didMatch_ ? -1 : matchFrom_ + charsMatched_;
-  }
-
-  /** This returns the number of
-              backreferences (parenthesis) in the pattern,
-              i.e. the pattern "(ab)" has
-              one, the pattern "(a)(b)" has two, etc. */
-  public int numSubs()
-  {
-    return numSubs_;
-  }
-
-  /** Contains true if the last match was successful. */
-  public boolean didMatch()
-  {
-    return didMatch_;
-  }
-
-  /** An older name for matchedFrom. */
-  public int matchFrom()
-  {
-    return matchedFrom();
-  }
-
-  /** An older name for stringMatched(). */
-  public String substring()
-  {
-    return stringMatched();
-  }
-
-  /** An older name for matchedFrom. */
-  public int matchFrom(int i)
-  {
-    return matchedFrom(i);
-  }
-
-  /** An older name for stringMatched. */
-  public String substring(int i)
-  {
-    return stringMatched(i);
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+/**
+ Shareware: package pat
+ <a href="copyright.html">Copyright 2001, Steven R. Brandt</a>
+ */
+/**
+ * This class is used to store a result from Regex
+ */
+public class RegRes implements Cloneable
+{
+  protected int[] marks = null;
+
+  protected boolean didMatch_ = false;
+
+  protected StringLike src = null;
+
+  /** Obtain the text String that was matched against. */
+  public String getString()
+  {
+    return src.toString();
+  }
+
+  /** Obtain the source StringLike object. */
+  public StringLike getStringLike()
+  {
+    return src;
+  }
+
+  protected int charsMatched_ = 0, matchFrom_ = 0, numSubs_ = 0;
+
+  public String toString()
+  {
+    StringBuffer sb = new StringBuffer();
+    sb.append("match=" + matchedFrom() + ":" + charsMatched());
+    if (!didMatch())
+    {
+      return sb.toString();
+    }
+    for (int i = 0; i < numSubs(); i++)
+    {
+      int n = i + 1;
+      sb
+              .append(" sub(" + n + ")=" + matchedFrom(n) + ":"
+                      + charsMatched(n));
+    }
+    return sb.toString();
+  }
+
+  public RegRes()
+  {
+  }
+
+  public RegRes(RegRes r)
+  {
+    copyOutOf(r);
+  }
+
+  public void copyOutOf(RegRes r)
+  {
+    if (r.marks == null)
+    {
+      marks = null;
+    }
+    else
+    {
+      try
+      {
+        // marks = (Hashtable)r.marks.clone();
+        marks = new int[r.marks.length];
+        for (int i = 0; i < marks.length; i++)
+        {
+          marks[i] = r.marks[i];
+        }
+        // marks = (int[])r.marks.clone();
+      } catch (Throwable t)
+      {
+      }
+    }
+    didMatch_ = r.didMatch_;
+    src = r.src;
+    charsMatched_ = r.charsMatched_;
+    matchFrom_ = r.matchFrom_;
+    numSubs_ = r.numSubs_;
+  }
+
+  public Object clone()
+  {
+    return new RegRes(this);
+  }
+
+  public boolean equals(RegRes r)
+  {
+    if (charsMatched_ != r.charsMatched_ || matchFrom_ != r.matchFrom_
+            || didMatch_ != r.didMatch_ || numSubs_ != r.numSubs_
+            || !src.unwrap().equals(r.src.unwrap()))
+    {
+      return false;
+    }
+    if (marks == null && r.marks != null)
+    {
+      return false;
+    }
+    if (marks != null && r.marks == null)
+    {
+      return false;
+    }
+    for (int i = 1; i <= numSubs_; i++)
+    {
+      if (matchedFrom(i) != r.matchedFrom(i))
+      {
+        return false;
+      }
+      else if (charsMatched(i) != r.charsMatched(i))
+      {
+        return false;
+      }
+    }
+    return true;
+  }
+
+  /** Obtains the match if successful, null otherwise. */
+  public String stringMatched()
+  {
+    int mf = matchedFrom(), cm = charsMatched();
+    return !didMatch_ || mf < 0 || cm < 0 ? null : src.substring(mf, mf
+            + cm);
+  }
+
+  /**
+   * Obtains the position backreference number i begins to match, or -1 if
+   * backreference i was not matched.
+   */
+  public int matchedFrom(int i)
+  {
+    if (marks == null || i > numSubs_)
+    {
+      return -1;
+    }
+    // Integer in=(Integer)marks.get("left"+i);
+    // return in == null ? -1 : in.intValue();
+    return marks[i];
+  }
+
+  /**
+   * Obtains the number of characters matched by backreference i, or -1 if
+   * backreference i was not matched.
+   */
+  public int charsMatched(int i)
+  {
+    if (marks == null || i > numSubs_ || !didMatch_)
+    {
+      return -1;
+    }
+    // Integer in = (Integer)marks.get("right"+i);
+    // int i2 = in==null ? -1 : in.intValue();
+    int mf = matchedFrom(i);
+    return mf < 0 ? -1 : marks[i + numSubs_] - matchedFrom(i);
+  }
+
+  /**
+   * This is either equal to matchedFrom(i)+charsMatched(i) if the match was
+   * successful, or -1 if it was not.
+   */
+  public int matchedTo(int i)
+  {
+    if (marks == null || i > numSubs_ || !didMatch_)
+    {
+      return -1;
+    }
+    return marks[i + numSubs_];
+  }
+
+  /**
+   * Obtains a substring matching the nth set of parenthesis from the pattern.
+   * See numSubs(void), or null if the nth backrefence did not match.
+   */
+  public String stringMatched(int i)
+  {
+    int mf = matchedFrom(i), cm = charsMatched(i);
+    return !didMatch_ || mf < 0 || cm < 0 ? null : src.substring(mf, mf
+            + cm);
+  }
+
+  /**
+   * This returns the part of the string that preceeds the match, or null if the
+   * match failed.
+   */
+  public String left()
+  {
+    int mf = matchedFrom();
+    return !didMatch_ || (mf < 0) ? null : src.substring(0, mf);
+  }
+
+  /**
+   * This returns the part of the string that follows the ith backreference, or
+   * null if the backreference did not match.
+   */
+  public String left(int i)
+  {
+    int mf = matchedFrom(i);
+    return !didMatch_ || (mf < 0) ? null : src.substring(0, mf);
+  }
+
+  /**
+   * This returns the part of the string that follows the match, or null if the
+   * backreference did not match.
+   */
+  public String right()
+  {
+    int mf = matchedFrom(), cm = charsMatched();
+    return !didMatch_ || mf < 0 || cm < 0 ? null : src.substring(mf + cm,
+            src.length());
+  }
+
+  /**
+   * This returns the string to the right of the ith backreference, or null if
+   * the backreference did not match.
+   */
+  public String right(int i)
+  {
+    int mf = matchedFrom(i), cm = charsMatched(i);
+    return !didMatch_ || mf < 0 || cm < 0 ? null : src.substring(mf + cm,
+            src.length());
+  }
+
+  /**
+   * After a successful match, this returns the location of the first matching
+   * character, or -1 if the match failed.
+   */
+  public int matchedFrom()
+  {
+    return !didMatch_ ? -1 : matchFrom_;
+  }
+
+  /**
+   * After a successful match, this returns the number of characters in the
+   * match, or -1 if the match failed.
+   */
+  public int charsMatched()
+  {
+    return !didMatch_ || matchFrom_ < 0 ? -1 : charsMatched_;
+  }
+
+  /**
+   * This is matchedFrom()+charsMatched() after a successful match, or -1
+   * otherwise.
+   */
+  public int matchedTo()
+  {
+    return !didMatch_ ? -1 : matchFrom_ + charsMatched_;
+  }
+
+  /**
+   * This returns the number of backreferences (parenthesis) in the pattern,
+   * i.e. the pattern "(ab)" has one, the pattern "(a)(b)" has two, etc.
+   */
+  public int numSubs()
+  {
+    return numSubs_;
+  }
+
+  /** Contains true if the last match was successful. */
+  public boolean didMatch()
+  {
+    return didMatch_;
+  }
+
+  /** An older name for matchedFrom. */
+  public int matchFrom()
+  {
+    return matchedFrom();
+  }
+
+  /** An older name for stringMatched(). */
+  public String substring()
+  {
+    return stringMatched();
+  }
+
+  /** An older name for matchedFrom. */
+  public int matchFrom(int i)
+  {
+    return matchedFrom(i);
+  }
+
+  /** An older name for stringMatched. */
+  public String substring(int i)
+  {
+    return stringMatched(i);
+  }
+}
diff --git a/src/com/stevesoft/pat/RegSyntax.java b/src/com/stevesoft/pat/RegSyntax.java
index ac47c1a..635dc4c 100755
--- a/src/com/stevesoft/pat/RegSyntax.java
+++ b/src/com/stevesoft/pat/RegSyntax.java
@@ -1,29 +1,30 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-/*
-        Shareware: package pat
-   <a href="copyright.html">Copyright 2001, Steven R. Brandt</a>
- */
-/**
- This type of syntax error is thrown whenever a syntax error
- is encountered in the pattern. It may not be caught directly, as
- it is not in the throws clause of any method.  To detect it, catch
- Throwable, and use instanceof to see if it is a RegSyntax. */
-public class RegSyntax
-    extends Exception
-{
-  RegSyntax()
-  {}
-
-  RegSyntax(String msg)
-  {
-    super(msg);
-  }
-};
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+/*
+ Shareware: package pat
+ <a href="copyright.html">Copyright 2001, Steven R. Brandt</a>
+ */
+/**
+ * This type of syntax error is thrown whenever a syntax error is encountered in
+ * the pattern. It may not be caught directly, as it is not in the throws clause
+ * of any method. To detect it, catch Throwable, and use instanceof to see if it
+ * is a RegSyntax.
+ */
+public class RegSyntax extends Exception
+{
+  RegSyntax()
+  {
+  }
+
+  RegSyntax(String msg)
+  {
+    super(msg);
+  }
+};
diff --git a/src/com/stevesoft/pat/RegSyntaxError.java b/src/com/stevesoft/pat/RegSyntaxError.java
index 688c906..1e56122 100755
--- a/src/com/stevesoft/pat/RegSyntaxError.java
+++ b/src/com/stevesoft/pat/RegSyntaxError.java
@@ -1,42 +1,40 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-/** When enabled, this class is thrown instead of
-    the normal RegSyntax.  Thus, enabling of this
-    class will make your debugging easier -- but
-    if you leave it on and forget to catch RegSyntaxError
-    a user-supplied pattern could generate a
-    RegSyntaxError that will kill your application.
-
-    I strongly recommend turning this flag on, however,
-    as I think it is more likely to help than to hurt
-    your programming efforts.
- */
-public class RegSyntaxError
-    extends Error
-{
-  public static boolean RegSyntaxErrorEnabled = false;
-  public RegSyntaxError()
-  {}
-
-  public RegSyntaxError(String s)
-  {
-    super(s);
-  }
-
-  final static void endItAll(String s)
-      throws RegSyntax
-  {
-    if (RegSyntaxErrorEnabled)
-    {
-      throw new RegSyntaxError(s);
-    }
-    throw new RegSyntax(s);
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+/**
+ * When enabled, this class is thrown instead of the normal RegSyntax. Thus,
+ * enabling of this class will make your debugging easier -- but if you leave it
+ * on and forget to catch RegSyntaxError a user-supplied pattern could generate
+ * a RegSyntaxError that will kill your application.
+ * 
+ * I strongly recommend turning this flag on, however, as I think it is more
+ * likely to help than to hurt your programming efforts.
+ */
+public class RegSyntaxError extends Error
+{
+  public static boolean RegSyntaxErrorEnabled = false;
+
+  public RegSyntaxError()
+  {
+  }
+
+  public RegSyntaxError(String s)
+  {
+    super(s);
+  }
+
+  final static void endItAll(String s) throws RegSyntax
+  {
+    if (RegSyntaxErrorEnabled)
+    {
+      throw new RegSyntaxError(s);
+    }
+    throw new RegSyntax(s);
+  }
+}
diff --git a/src/com/stevesoft/pat/Regex.java b/src/com/stevesoft/pat/Regex.java
index 2b38ee7..04bb0da 100755
--- a/src/com/stevesoft/pat/Regex.java
+++ b/src/com/stevesoft/pat/Regex.java
@@ -1,2029 +1,2085 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-import java.io.*;
-import java.util.*;
-
-import com.stevesoft.pat.wrap.*;
-
-/** Matches a Unicode punctuation character. */
-class UnicodePunct
-    extends UniValidator
-{
-  public int validate(StringLike s, int from, int to)
-  {
-    return from < s.length() && Prop.isPunct(s.charAt(from)) ? to : -1;
-  }
-}
-
-/** Matches a Unicode white space character. */
-class UnicodeWhite
-    extends UniValidator
-{
-  public int validate(StringLike s, int from, int to)
-  {
-    return from < s.length() && Prop.isWhite(s.charAt(from)) ? to : -1;
-  }
-}
-
-/** Matches a character that is not a Unicode punctuation
- * character.
- */
-class NUnicodePunct
-    extends UniValidator
-{
-  public int validate(StringLike s, int from, int to)
-  {
-    return from < s.length() && !Prop.isPunct(s.charAt(from)) ? to : -1;
-  }
-}
-
-/** Matches a character that is not a
- * Unicode white space character.
- */
-class NUnicodeWhite
-    extends UniValidator
-{
-  public int validate(StringLike s, int from, int to)
-  {
-    return from < s.length() && !Prop.isWhite(s.charAt(from)) ? to : -1;
-  }
-}
-
-/** Matches a Unicode word character: an alphanumeric or underscore. */
-class UnicodeW
-    extends UniValidator
-{
-  public int validate(StringLike s, int from, int to)
-  {
-    if (from >= s.length())
-    {
-      return -1;
-    }
-    char c = s.charAt(from);
-    return (Prop.isAlphabetic(c) || Prop.isDecimalDigit(c) || c == '_') ? to :
-        -1;
-  }
-}
-
-/** Matches a character that is not a Unicode alphanumeric or underscore. */
-class NUnicodeW
-    extends UniValidator
-{
-  public int validate(StringLike s, int from, int to)
-  {
-    if (from >= s.length())
-    {
-      return -1;
-    }
-    char c = s.charAt(from);
-    return! (Prop.isAlphabetic(c) || Prop.isDecimalDigit(c) || c == '_') ? to :
-        -1;
-  }
-}
-
-/** Matches a Unicode decimal digit. */
-class UnicodeDigit
-    extends UniValidator
-{
-  public int validate(StringLike s, int from, int to)
-  {
-    return from < s.length() && Prop.isDecimalDigit(s.charAt(from)) ? to : -1;
-  }
-}
-
-/** Matches a character that is not a Unicode digit.*/
-class NUnicodeDigit
-    extends UniValidator
-{
-  public int validate(StringLike s, int from, int to)
-  {
-    return from < s.length() && !Prop.isDecimalDigit(s.charAt(from)) ? to : -1;
-  }
-}
-
-/** Matches a Unicode math character. */
-class UnicodeMath
-    extends UniValidator
-{
-  public int validate(StringLike s, int from, int to)
-  {
-    return from < s.length() && Prop.isMath(s.charAt(from)) ? to : -1;
-  }
-}
-
-/** Matches a non-math Unicode character. */
-class NUnicodeMath
-    extends UniValidator
-{
-  public int validate(StringLike s, int from, int to)
-  {
-    return from < s.length() && !Prop.isMath(s.charAt(from)) ? to : -1;
-  }
-}
-
-/** Matches a Unicode currency symbol. */
-class UnicodeCurrency
-    extends UniValidator
-{
-  public int validate(StringLike s, int from, int to)
-  {
-    return from < s.length() && Prop.isCurrency(s.charAt(from)) ? to : -1;
-  }
-}
-
-/** Matches a non-currency symbol Unicode character. */
-class NUnicodeCurrency
-    extends UniValidator
-{
-  public int validate(StringLike s, int from, int to)
-  {
-    return from < s.length() && !Prop.isCurrency(s.charAt(from)) ? to : -1;
-  }
-}
-
-/** Matches a Unicode alphabetic character. */
-class UnicodeAlpha
-    extends UniValidator
-{
-  public int validate(StringLike s, int from, int to)
-  {
-    return from < s.length() && Prop.isAlphabetic(s.charAt(from)) ? to : -1;
-  }
-}
-
-/** Matches a non-alphabetic Unicode character. */
-class NUnicodeAlpha
-    extends UniValidator
-{
-  public int validate(StringLike s, int from, int to)
-  {
-    return from < s.length() && !Prop.isAlphabetic(s.charAt(from)) ? to : -1;
-  }
-}
-
-/** Matches an upper case Unicode character. */
-class UnicodeUpper
-    extends UniValidator
-{
-  public int validate(StringLike s, int from, int to)
-  {
-    return from < s.length() && isUpper(s.charAt(from)) ? to : -1;
-  }
-
-  final boolean isUpper(char c)
-  {
-    return c == CaseMgr.toUpperCase(c) && c != CaseMgr.toLowerCase(c);
-  }
-}
-
-/** Matches an upper case Unicode character. */
-class UnicodeLower
-    extends UniValidator
-{
-  public int validate(StringLike s, int from, int to)
-  {
-    return from < s.length() && isLower(s.charAt(from)) ? to : -1;
-  }
-
-  final boolean isLower(char c)
-  {
-    return c != CaseMgr.toUpperCase(c) && c == CaseMgr.toLowerCase(c);
-  }
-}
-
-/**
- Regex provides the parser which constructs the linked list of
- Pattern classes from a String.
- <p>
- For the purpose of this documentation, the fact that java interprets the
- backslash will be ignored.  In practice, however, you will need a
- double backslash to obtain a string that contains a single backslash
- character.  Thus, the example pattern "\b" should really be typed
- as "\\b" inside java code.
- <p>
- Note that Regex is part of package "com.stevesoft.pat".
- To use it, simply import
- com.stevesoft.pat.Regex at the top of your file.
- <p>
- Regex is made with a constructor that takes a String that defines
- the regular expression.  Thus, for example
- <pre>
-      Regex r = new Regex("[a-c]*");
- </pre>
- matches any number of characters so long as the are 'a', 'b', or 'c').
- <p>
- To attempt to match the Pattern to a given string, you can use either
- the search(String) member function, or the matchAt(String,int position)
- member function.  These functions return a boolean which tells you
- whether or not the thing worked, and sets the methods "charsMatched()"
- and "matchedFrom()" in the Regex object appropriately.
- <p>
- The portion of the string before the match can be obtained by the
- left() member, and the portion after the match can be obtained
- by the right() member.
- <p>
- Essentially, this package implements a syntax that is very much
- like the perl 5 regular expression syntax.
-
- Longer example:
- <pre>
-        Regex r = new Regex("x(a|b)y");
-        r.matchAt("xay",0);
-        System.out.println("sub = "+r.stringMatched(1));
- </pre>
- The above would print "sub = a".
- <pre>
-        r.left() // would return "x"
-        r.right() // would return "y"
- </pre>
- <p>
- Differences between this package and perl5:<br>
- The extended Pattern for setting flags, is now supported,
- but the flags are different.  "(?i)" tells the pattern to
- ignore case, "(?Q)" sets the "dontMatchInQuotes" flag, and
- "(?iQ)" sets them both.  You can change the escape character.
- The pattern <pre>(?e=#)#d+</pre> is the same as <pre>\d+</pre>,
- but note that the sequence <pre>(?e=#)</pre> <b>must</b> occur
- at the very beginning of the pattern.  There may be other small
- differences as well.  I will either make my package conform
- or note them as I become aware of them.
- <p>
- This package supports additional patterns not in perl5:
- <center>
- <table border=1>
- <tr><td>(?@())</td><td>Group</td><td>This matches all characters between
- the '(' character and the balancing ')' character.  Thus, it will
- match "()" as well as "(())".  The balancing characters are
- arbitrary, thus (?@{}) matches on "{}" and "{{}}".</td>
- <tr><td>(?&lt1)</td><td>Backup</td><td>Moves the pointer backwards within the text.
- This allows you to make a "look behind."  It fails if it
- attempts to move to a position before the beginning of the string.
- "x(?&lt1)" is equivalent to "(?=x)".  The number, 1 in this example,
- is the number of characters to move backwards.</td>
- </table>
- </center>
- </dl>
- @author Steven R. Brandt
- @version package com.stevesoft.pat, release 1.5.3
- @see Pattern
- */
-public class Regex
-    extends RegRes implements FilenameFilter
-{
-  /** BackRefOffset gives the identity number of the first
-      pattern.  Version 1.0 used zero, version 1.1 uses 1 to be
-      more compatible with perl. */
-  static int BackRefOffset = 1;
-  private static Pattern none = new NoPattern();
-  Pattern thePattern = none;
-  patInt minMatch = new patInt(0);
-
-  static Hashtable validators = new Hashtable();
-  static
-  {
-    define("p", "(?>1)", new UnicodePunct());
-    define("P", "(?>1)", new NUnicodePunct());
-    define("s", "(?>1)", new UnicodeWhite());
-    define("S", "(?>1)", new NUnicodeWhite());
-    define("w", "(?>1)", new UnicodeW());
-    define("W", "(?>1)", new NUnicodeW());
-    define("d", "(?>1)", new UnicodeDigit());
-    define("D", "(?>1)", new NUnicodeDigit());
-    define("m", "(?>1)", new UnicodeMath());
-    define("M", "(?>1)", new NUnicodeMath());
-    define("c", "(?>1)", new UnicodeCurrency());
-    define("C", "(?>1)", new NUnicodeCurrency());
-    define("a", "(?>1)", new UnicodeAlpha());
-    define("A", "(?>1)", new NUnicodeAlpha());
-    define("uc", "(?>1)", new UnicodeUpper());
-    define("lc", "(?>1)", new UnicodeLower());
-  }
-
-  /** Set the dontMatch in quotes flag. */
-  public void setDontMatchInQuotes(boolean b)
-  {
-    dontMatchInQuotes = b;
-  }
-
-  /** Find out if the dontMatchInQuotes flag is enabled. */
-  public boolean getDontMatchInQuotes()
-  {
-    return dontMatchInQuotes;
-  }
-
-  boolean dontMatchInQuotes = false;
-
-  /** Set the state of the ignoreCase flag.  If set to true, then
-      the pattern matcher will ignore case when searching for a
-      match. */
-  public void setIgnoreCase(boolean b)
-  {
-    ignoreCase = b;
-  }
-
-  /** Get the state of the ignoreCase flag.  Returns true if we
-      are ignoring the case of the pattern, false otherwise. */
-  public boolean getIgnoreCase()
-  {
-    return ignoreCase;
-  }
-
-  boolean ignoreCase = false;
-
-  static boolean defaultMFlag = false;
-  /** Set the default value of the m flag.  If it
-      is set to true, then the MFlag will be on
-      for any regex search executed. */
-  public static void setDefaultMFlag(boolean mFlag)
-  {
-    defaultMFlag = mFlag;
-  }
-
-  /** Get the default value of the m flag.  If it
-      is set to true, then the MFlag will be on
-      for any regex search executed. */
-  public static boolean getDefaultMFlag()
-  {
-    return defaultMFlag;
-  }
-
-  /** Initializes the object without a Pattern. To supply a Pattern
-      use compile(String s).
-       @see com.stevesoft.pat.Regex#compile(java.lang.String)
-   */
-  public Regex()
-  {}
-
-  /** Create and compile a Regex, but do not throw any exceptions.
-      If you wish to have exceptions thrown for syntax errors,
-      you must use the Regex(void) constructor to create the
-      Regex object, and then call the compile method.  Therefore, you
-      should only call this method when you know your pattern is right.
-      I will probably become more like
-       @see com.stevesoft.pat.Regex#search(java.lang.String)
-       @see com.stevesoft.pat.Regex#compile(java.lang.String)
-   */
-  public Regex(String s)
-  {
-    try
-    {
-      compile(s);
-    }
-    catch (RegSyntax rs)
-    {}
-  }
-
-  ReplaceRule rep = null;
-  /** Create and compile both a Regex and a ReplaceRule.
-      @see com.stevesoft.pat.ReplaceRule
-      @see com.stevesoft.pat.Regex#compile(java.lang.String)
-   */
-  public Regex(String s, String rp)
-  {
-    this(s);
-    rep = ReplaceRule.perlCode(rp);
-  }
-
-  /** Create and compile a Regex, but give it the ReplaceRule
-      specified.  This allows the user finer control of the
-      Replacement process, if that is desired.
-      @see com.stevesoft.pat.ReplaceRule
-      @see com.stevesoft.pat.Regex#compile(java.lang.String)
-   */
-  public Regex(String s, ReplaceRule rp)
-  {
-    this(s);
-    rep = rp;
-  }
-
-  /** Change the ReplaceRule of this Regex by compiling
-      a new one using String rp. */
-  public void setReplaceRule(String rp)
-  {
-    rep = ReplaceRule.perlCode(rp);
-    repr = null; // Clear Replacer history
-  }
-
-  /** Change the ReplaceRule of this Regex to rp. */
-  public void setReplaceRule(ReplaceRule rp)
-  {
-    rep = rp;
-  }
-
-  /** Test to see if a custom defined rule exists.
-   @see com.stevesoft.pat#define(java.lang.String,java.lang.String,Validator)
-   */
-  public static boolean isDefined(String nm)
-  {
-    return validators.get(nm) != null;
-  }
-
-  /** Removes a custom defined rule.
-   @see com.stevesoft.pat#define(java.lang.String,java.lang.String,Validator)
-   */
-  public static void undefine(String nm)
-  {
-    validators.remove(nm);
-  }
-
-  /** Defines a method to create a new rule.  See test/deriv2.java
-      and test/deriv3.java for examples of how to use it. */
-  public static void define(String nm, String pat, Validator v)
-  {
-    v.pattern = pat;
-    validators.put(nm, v);
-  }
-
-  /** Defines a shorthand for a pattern.  The pattern will be
-      invoked by a string that has the form "(??"+nm+")".
-   */
-  public static void define(String nm, String pat)
-  {
-    validators.put(nm, pat);
-  }
-
-  /** Get the current ReplaceRule. */
-  public ReplaceRule getReplaceRule()
-  {
-    return rep;
-  }
-
-  Replacer repr = null;
-  final Replacer _getReplacer()
-  {
-    return repr == null ? repr = new Replacer() : repr;
-  }
-
-  public Replacer getReplacer()
-  {
-    if (repr == null)
-    {
-      repr = new Replacer();
-    }
-    repr.rh.me = this;
-    repr.rh.prev = null;
-    return repr;
-  }
-
-  /** Replace the first occurence of this pattern in String s
-      according to the ReplaceRule.
-      @see com.stevesoft.pat.ReplaceRule
-      @see com.stevesoft.pat.Regex#getReplaceRule()
-   */
-  public String replaceFirst(String s)
-  {
-    return _getReplacer().replaceFirstRegion(s, this, 0, s.length()).toString();
-  }
-
-  /** Replace the first occurence of this pattern in String s
-      beginning with position pos according to the ReplaceRule.
-      @see com.stevesoft.pat.ReplaceRule
-      @see com.stevesoft.pat.Regex#getReplaceRule()
-   */
-  public String replaceFirstFrom(String s, int pos)
-  {
-    return _getReplacer().replaceFirstRegion(s, this, pos, s.length()).toString();
-  }
-
-  /** Replace the first occurence of this pattern in String s
-      beginning with position start and ending with end
-      according to the ReplaceRule.
-      @see com.stevesoft.pat.ReplaceRule
-      @see com.stevesoft.pat.Regex#getReplaceRule()
-   */
-  public String replaceFirstRegion(String s, int start, int end)
-  {
-    return _getReplacer().replaceFirstRegion(s, this, start, end).toString();
-  }
-
-  /** Replace all occurences of this pattern in String s
-      according to the ReplaceRule.
-      @see com.stevesoft.pat.ReplaceRule
-      @see com.stevesoft.pat.Regex#getReplaceRule()
-   */
-  public String replaceAll(String s)
-  {
-    return _getReplacer().replaceAllRegion(s, this, 0, s.length()).toString();
-  }
-
-  public StringLike replaceAll(StringLike s)
-  {
-    return _getReplacer().replaceAllRegion(s, this, 0, s.length());
-  }
-
-  /** Replace all occurences of this pattern in String s
-      beginning with position pos according to the ReplaceRule.
-      @see com.stevesoft.pat.ReplaceRule
-      @see com.stevesoft.pat.Regex#getReplaceRule()
-   */
-  public String replaceAllFrom(String s, int pos)
-  {
-    return _getReplacer().replaceAllRegion(s, this, pos, s.length()).toString();
-  }
-
-  /** Replace all occurences of this pattern in String s
-      beginning with position start and ending with end
-      according to the ReplaceRule.
-      @see com.stevesoft.pat.ReplaceRule
-      @see com.stevesoft.pat.Regex#getReplaceRule()
-   */
-  public String replaceAllRegion(String s, int start, int end)
-  {
-    return _getReplacer().replaceAllRegion(s, this, start, end).toString();
-  }
-
-  /** Essentially clones the Regex object */
-  public Regex(Regex r)
-  {
-    super( (RegRes) r);
-    dontMatchInQuotes = r.dontMatchInQuotes;
-    esc = r.esc;
-    ignoreCase = r.ignoreCase;
-    gFlag = r.gFlag;
-    if (r.rep == null)
-    {
-      rep = null;
-    }
-    else
-    {
-      rep = (ReplaceRule) r.rep.clone();
-    }
-    /* try {
-        compile(r.toString());
-             } catch(RegSyntax r_) {} */
-    thePattern = r.thePattern.clone(new Hashtable());
-    minMatch = r.minMatch;
-    skipper = r.skipper;
-  }
-
-  /** By default,
-              the escape character is the backslash, but you can
-              make it anything you want by setting this variable. */
-  public char esc = Pattern.ESC;
-  /** This method compiles a regular expression, making it
-       possible to call the search or matchAt methods.
-              @exception com.stevesoft.pat.RegSyntax
-              is thrown if a syntax error is encountered
-              in the pattern.
-               For example, "x{3,1}" or "*a" are not valid
-               patterns.
-              @see com.stevesoft.pat.Regex#search
-              @see com.stevesoft.pat.Regex#matchAt
-   */
-  public void compile(String prepat)
-      throws RegSyntax
-  {
-    String postpat = parsePerl.codify(prepat, true);
-    String pat = postpat == null ? prepat : postpat;
-    minMatch = null;
-    ignoreCase = false;
-    dontMatchInQuotes = false;
-    Rthings mk = new Rthings(this);
-    int offset = mk.val;
-    String newpat = pat;
-    thePattern = none;
-    p = null;
-    or = null;
-    minMatch = new patInt(0);
-    StrPos sp = new StrPos(pat, 0);
-    if (sp.incMatch("(?e="))
-    {
-      char newEsc = sp.c;
-      sp.inc();
-      if (sp.match(')'))
-      {
-        newpat = reEscape(pat.substring(6),
-                          newEsc, Pattern.ESC);
-      }
-    }
-    else if (esc != Pattern.ESC)
-    {
-      newpat = reEscape(pat, esc, Pattern.ESC);
-    }
-    thePattern = _compile(newpat, mk);
-    numSubs_ = mk.val - offset;
-    mk.set(this);
-  }
-
-  /*  If a Regex is compared against a Regex, a check is
-      done to see that the patterns are equal as well as
-      the most recent match.  If a Regex is compare with
-      a RegRes, only the result of the most recent match
-      is compared. */
-  public boolean equals(Object o)
-  {
-    if (o instanceof Regex)
-    {
-      if (toString().equals(o.toString()))
-      {
-        return super.equals(o);
-      }
-      else
-      {
-        return false;
-      }
-    }
-    else
-    {
-      return super.equals(o);
-    }
-  }
-
-  /** A clone by any other name would smell as sweet. */
-  public Object clone()
-  {
-    return new Regex(this);
-  }
-
-  /** Return a clone of the underlying RegRes object. */
-  public RegRes result()
-  {
-    return (RegRes)super.clone();
-  }
-
-  // prep sets global variables of class
-  // Pattern so that it can access them
-  // during an attempt at a match
-  Pthings pt = new Pthings();
-  final Pthings prep(StringLike s)
-  {
-    //if(gFlag)
-    pt.lastPos = matchedTo();
-    if (pt.lastPos < 0)
-    {
-      pt.lastPos = 0;
-    }
-    if ( (s == null ? null : s.unwrap()) != (src == null ? null : s.unwrap()))
-    {
-      pt.lastPos = 0;
-    }
-    src = s;
-    pt.dotDoesntMatchCR = dotDoesntMatchCR && (!sFlag);
-    pt.mFlag = (mFlag | defaultMFlag);
-    pt.ignoreCase = ignoreCase;
-    pt.no_check = false;
-    if (pt.marks != null)
-    {
-      for (int i = 0; i < pt.marks.length; i++)
-      {
-        pt.marks[i] = -1;
-      }
-    }
-    pt.marks = null;
-    pt.nMarks = numSubs_;
-    pt.src = s;
-    if (dontMatchInQuotes)
-    {
-      setCbits(s, pt);
-    }
-    else
-    {
-      pt.cbits = null;
-    }
-    return pt;
-  }
-
-  /** Attempt to match a Pattern beginning
-      at a specified location within the string.
-      @see com.stevesoft.pat.Regex#search
-   */
-  public boolean matchAt(String s, int start_pos)
-  {
-    return _search(s, start_pos, start_pos);
-  }
-
-  /** Attempt to match a Pattern beginning
-      at a specified location within the StringLike.
-      @see com.stevesoft.pat.Regex#search
-   */
-  public boolean matchAt(StringLike s, int start_pos)
-  {
-    return _search(s, start_pos, start_pos);
-  }
-
-  /** Search through a String for the first
-      occurrence of a match.
-      @see com.stevesoft.pat.Regex#searchFrom
-      @see com.stevesoft.pat.Regex#matchAt
-   */
-  public boolean search(String s)
-  {
-    if (s == null)
-    {
-      throw new NullPointerException("Null String Given to Regex.search");
-    }
-    return _search(s, 0, s.length());
-  }
-
-  public boolean search(StringLike sl)
-  {
-    if (sl == null)
-    {
-      throw new NullPointerException("Null StringLike Given to Regex.search");
-    }
-    return _search(sl, 0, sl.length());
-  }
-
-  public boolean reverseSearch(String s)
-  {
-    if (s == null)
-    {
-      throw new NullPointerException("Null String Given to Regex.reverseSearch");
-    }
-    return _reverseSearch(s, 0, s.length());
-  }
-
-  public boolean reverseSearch(StringLike sl)
-  {
-    if (sl == null)
-    {
-      throw new NullPointerException(
-          "Null StringLike Given to Regex.reverseSearch");
-    }
-    return _reverseSearch(sl, 0, sl.length());
-  }
-
-  /** Search through a String for the first
-              occurence of a match, but start at position <pre>start</pre>*/
-  public boolean searchFrom(String s, int start)
-  {
-    if (s == null)
-    {
-      throw new NullPointerException("Null String Given to Regex.searchFrom");
-    }
-    return _search(s, start, s.length());
-  }
-
-  public boolean searchFrom(StringLike s, int start)
-  {
-    if (s == null)
-    {
-      throw new NullPointerException("Null String Given to Regex.searchFrom");
-    }
-    return _search(s, start, s.length());
-  }
-
-  /** Search through a region of a String
-      for the first occurence of a match. */
-  public boolean searchRegion(String s, int start, int end)
-  {
-    if (s == null)
-    {
-      throw new NullPointerException("Null String Given to Regex.searchRegion");
-    }
-    return _search(s, start, end);
-  }
-
-  /** Set this to change the default behavior of the "." pattern.
-              By default it now matches perl's behavior and fails to
-              match the '\n' character. */
-  public static boolean dotDoesntMatchCR = true;
-  StringLike gFlags;
-  int gFlagto = 0;
-  boolean gFlag = false;
-  /** Set the 'g' flag */
-  public void setGFlag(boolean b)
-  {
-    gFlag = b;
-  }
-
-  /** Get the state of the 'g' flag. */
-  public boolean getGFlag()
-  {
-    return gFlag;
-  }
-
-  boolean sFlag = false;
-  /** Get the state of the sFlag */
-  public boolean getSFlag()
-  {
-    return sFlag;
-  }
-
-  boolean mFlag = false;
-  /** Get the state of the sFlag */
-  public boolean getMFlag()
-  {
-    return mFlag;
-  }
-
-  final boolean _search(String s, int start, int end)
-  {
-    return _search(new StringWrap(s), start, end);
-  }
-
-  final boolean _search(StringLike s, int start, int end)
-  {
-    if (gFlag && gFlagto > 0 && gFlags != null && s.unwrap() == gFlags.unwrap())
-    {
-      start = gFlagto;
-    }
-    gFlags = null;
-
-    Pthings pt = prep(s);
-
-    int up = (minMatch == null ? end : end - minMatch.i);
-
-    if (up < start && end >= start)
-    {
-      up = start;
-    }
-
-    if (skipper == null)
-    {
-      for (int i = start; i <= up; i++)
-      {
-        charsMatched_ = thePattern.matchAt(s, i, pt);
-        if (charsMatched_ >= 0)
-        {
-          matchFrom_ = thePattern.mfrom;
-          marks = pt.marks;
-          gFlagto = matchFrom_ + charsMatched_;
-          gFlags = s;
-          return didMatch_ = true;
-        }
-      }
-    }
-    else
-    {
-      pt.no_check = true;
-      for (int i = start; i <= up; i++)
-      {
-        i = skipper.find(src, i, up);
-        if (i < 0)
-        {
-          charsMatched_ = matchFrom_ = -1;
-          return didMatch_ = false;
-        }
-        charsMatched_ = thePattern.matchAt(s, i, pt);
-        if (charsMatched_ >= 0)
-        {
-          matchFrom_ = thePattern.mfrom;
-          marks = pt.marks;
-          gFlagto = matchFrom_ + charsMatched_;
-          gFlags = s;
-          return didMatch_ = true;
-        }
-      }
-    }
-    return didMatch_ = false;
-  }
-
-  /*final boolean _search(LongStringLike s,long start,long end) {
-      if(gFlag && gFlagto > 0 && s==gFlags)
-          start = gFlagto;
-      gFlags = null;
-
-      Pthings pt=prep(s);
-
-      int up = end;//(minMatch == null ? end : end-minMatch.i);
-
-      if(up < start && end >= start) up = start;
-
-      if(skipper == null) {
-          for(long i=start;i<=up;i++) {
-              charsMatched_ = thePattern.matchAt(s,i,pt);
-              if(charsMatched_ >= 0) {
-                  matchFrom_ = thePattern.mfrom;
-                  marks = pt.marks;
-                  gFlagto = matchFrom_+charsMatched_;
-                  return didMatch_=true;
-              }
-          }
-      } else {
-          pt.no_check = true;
-          for(long i=start;i<=up;i++) {
-              i = skipper.find(src,i,up);
-              if(i<0) {
-                  charsMatched_ = matchFrom_ = -1;
-                  return didMatch_ = false;
-              }
-              charsMatched_ = thePattern.matchAt(s,i,pt);
-              if(charsMatched_ >= 0) {
-                  matchFrom_ = thePattern.mfrom;
-                  marks = pt.marks;
-                  gFlagto = matchFrom_+charsMatched_;
-                  gFlags = s;
-                  return didMatch_=true;
-              } else {
-                i = s.adjustIndex(i);
-                up = s.adjustEnd(i);
-              }
-          }
-      }
-      return didMatch_=false;
-       }*/
-
-  boolean _reverseSearch(String s, int start, int end)
-  {
-    return _reverseSearch(new StringWrap(s), start, end);
-  }
-
-  boolean _reverseSearch(StringLike s, int start, int end)
-  {
-    if (gFlag && gFlagto > 0 && s.unwrap() == gFlags.unwrap())
-    {
-      end = gFlagto;
-    }
-    gFlags = null;
-    Pthings pt = prep(s);
-    for (int i = end; i >= start; i--)
-    {
-      charsMatched_ = thePattern.matchAt(s, i, pt);
-      if (charsMatched_ >= 0)
-      {
-        matchFrom_ = thePattern.mfrom;
-        marks = pt.marks;
-        gFlagto = matchFrom_ - 1;
-        gFlags = s;
-        return didMatch_ = true;
-      }
-    }
-    return didMatch_ = false;
-  }
-
-  // This routine sets the cbits variable
-  // of class Pattern.  Cbits is true for
-  // the bit corresponding to a character inside
-  // a set of quotes.
-  static StringLike lasts = null;
-  static BitSet lastbs = null;
-  static void setCbits(StringLike s, Pthings pt)
-  {
-    if (s == lasts)
-    {
-      pt.cbits = lastbs;
-      return;
-    }
-    BitSet bs = new BitSet(s.length());
-    char qc = ' ';
-    boolean setBit = false;
-    for (int i = 0; i < s.length(); i++)
-    {
-      if (setBit)
-      {
-        bs.set(i);
-      }
-      char c = s.charAt(i);
-      if (!setBit && c == '"')
-      {
-        qc = c;
-        setBit = true;
-        bs.set(i);
-      }
-      else if (!setBit && c == '\'')
-      {
-        qc = c;
-        setBit = true;
-        bs.set(i);
-      }
-      else if (setBit && c == qc)
-      {
-        setBit = false;
-      }
-      else if (setBit && c == '\\' && i + 1 < s.length())
-      {
-        i++;
-        if (setBit)
-        {
-          bs.set(i);
-        }
-      }
-    }
-    pt.cbits = lastbs = bs;
-    lasts = s;
-  }
-
-  // Wanted user to over-ride this in alpha version,
-  // but it wasn't really necessary because of this trick:
-  Regex newRegex()
-  {
-    try
-    {
-      return (Regex) getClass().newInstance();
-    }
-    catch (InstantiationException ie)
-    {
-      return null;
-    }
-    catch (IllegalAccessException iae)
-    {
-      return null;
-    }
-  }
-
-  /** Only needed for creating your own extensions of
-       Regex.  This method adds the next Pattern in the chain
-       of patterns or sets the Pattern if it is the first call. */
-  protected void add(Pattern p2)
-  {
-    if (p == null)
-    {
-      p = p2;
-    }
-    else
-    {
-      p.add(p2);
-      p2 = p;
-    }
-  }
-
-  /** You only need to use this method if you are creating
-      your own extentions to Regex.
-      compile1 compiles one Pattern element, it can be
-      over-ridden to allow the Regex compiler to understand
-      new syntax.  See deriv.java for an example.  This routine
-      is the heart of class Regex. Rthings has one integer
-      member called intValue, it is used to keep track of the number
-      of ()'s in the Pattern.
-      @exception com.stevesoft.pat.RegSyntax is thrown when a nonsensensical
-      pattern is supplied.  For example, a pattern beginning
-      with *. */
-  protected void compile1(StrPos sp, Rthings mk)
-      throws RegSyntax
-  {
-    if (sp.match('['))
-    {
-      sp.inc();
-      add(matchBracket(sp));
-    }
-    else if (sp.match('|'))
-    {
-      if (or == null)
-      {
-        or = new Or();
-      }
-      if (p == null)
-      {
-        p = new NullPattern();
-      }
-      or.addOr(p);
-      p = null;
-    }
-    else if (sp.incMatch("(?<"))
-    {
-      patInt i = sp.getPatInt();
-      if (i == null)
-      {
-        RegSyntaxError.endItAll("No int after (?<");
-      }
-      add(new Backup(i.intValue()));
-      if (!sp.match(')'))
-      {
-        RegSyntaxError.endItAll("No ) after (?<");
-      }
-    }
-    else if (sp.incMatch("(?>"))
-    {
-      patInt i = sp.getPatInt();
-      if (i == null)
-      {
-        RegSyntaxError.endItAll("No int after (?>");
-      }
-      add(new Backup( -i.intValue()));
-      if (!sp.match(')'))
-      {
-        RegSyntaxError.endItAll("No ) after (?<");
-      }
-    }
-    else if (sp.incMatch("(?@"))
-    {
-      char op = sp.c;
-      sp.inc();
-      char cl = sp.c;
-      sp.inc();
-      if (!sp.match(')'))
-      {
-        RegSyntaxError.endItAll(
-            "(?@ does not have closing paren");
-      }
-      add(new Group(op, cl));
-    }
-    else if (sp.incMatch("(?#"))
-    {
-      while (!sp.match(')'))
-      {
-        sp.inc();
-      }
-    }
-    else if (sp.dontMatch && sp.c == 'w')
-    {
-      //Regex r = new Regex();
-      //r._compile("[a-zA-Z0-9_]",mk);
-      //add(new Goop("\\w",r.thePattern));
-      Bracket b = new Bracket(false);
-      b.addOr(new Range('a', 'z'));
-      b.addOr(new Range('A', 'Z'));
-      b.addOr(new Range('0', '9'));
-      b.addOr(new oneChar('_'));
-      add(b);
-    }
-    else if (sp.dontMatch && sp.c == 'G')
-    {
-      add(new BackG());
-    }
-    else if (sp.dontMatch && sp.c == 's')
-    {
-      //Regex r = new Regex();
-      //r._compile("[ \t\n\r\b]",mk);
-      //add(new Goop("\\s",r.thePattern));
-      Bracket b = new Bracket(false);
-      b.addOr(new oneChar( (char) 32));
-      b.addOr(new Range( (char) 8, (char) 10));
-      b.addOr(new oneChar( (char) 13));
-      add(b);
-    }
-    else if (sp.dontMatch && sp.c == 'd')
-    {
-      //Regex r = new Regex();
-      //r._compile("[0-9]",mk);
-      //add(new Goop("\\d",r.thePattern));
-      Range digit = new Range('0', '9');
-      digit.printBrackets = true;
-      add(digit);
-    }
-    else if (sp.dontMatch && sp.c == 'W')
-    {
-      //Regex r = new Regex();
-      //r._compile("[^a-zA-Z0-9_]",mk);
-      //add(new Goop("\\W",r.thePattern));
-      Bracket b = new Bracket(true);
-      b.addOr(new Range('a', 'z'));
-      b.addOr(new Range('A', 'Z'));
-      b.addOr(new Range('0', '9'));
-      b.addOr(new oneChar('_'));
-      add(b);
-    }
-    else if (sp.dontMatch && sp.c == 'S')
-    {
-      //Regex r = new Regex();
-      //r._compile("[^ \t\n\r\b]",mk);
-      //add(new Goop("\\S",r.thePattern));
-      Bracket b = new Bracket(true);
-      b.addOr(new oneChar( (char) 32));
-      b.addOr(new Range( (char) 8, (char) 10));
-      b.addOr(new oneChar( (char) 13));
-      add(b);
-    }
-    else if (sp.dontMatch && sp.c == 'D')
-    {
-      //Regex r = new Regex();
-      //r._compile("[^0-9]",mk);
-      //add(new Goop("\\D",r.thePattern));
-      Bracket b = new Bracket(true);
-      b.addOr(new Range('0', '9'));
-      add(b);
-    }
-    else if (sp.dontMatch && sp.c == 'B')
-    {
-      Regex r = new Regex();
-      r._compile("(?!" + back_slash + "b)", mk);
-      add(r.thePattern);
-    }
-    else if (isOctalString(sp))
-    {
-      int d = sp.c - '0';
-      sp.inc();
-      d = 8 * d + sp.c - '0';
-      StrPos sp2 = new StrPos(sp);
-      sp2.inc();
-      if (isOctalDigit(sp2, false))
-      {
-        sp.inc();
-        d = 8 * d + sp.c - '0';
-      }
-      add(new oneChar( (char) d));
-    }
-    else if (sp.dontMatch && sp.c >= '1' && sp.c <= '9')
-    {
-      int iv = sp.c - '0';
-      StrPos s2 = new StrPos(sp);
-      s2.inc();
-      if (!s2.dontMatch && s2.c >= '0' && s2.c <= '9')
-      {
-        iv = 10 * iv + (s2.c - '0');
-        sp.inc();
-      }
-      add(new BackMatch(iv));
-    }
-    else if (sp.dontMatch && sp.c == 'b')
-    {
-      add(new Boundary());
-    }
-    else if (sp.match('\b'))
-    {
-      add(new Boundary());
-    }
-    else if (sp.match('$'))
-    {
-      add(new End(true));
-    }
-    else if (sp.dontMatch && sp.c == 'Z')
-    {
-      add(new End(false));
-    }
-    else if (sp.match('.'))
-    {
-      add(new Any());
-    }
-    else if (sp.incMatch("(??"))
-    {
-      StringBuffer sb = new StringBuffer();
-      StringBuffer sb2 = new StringBuffer();
-      while (!sp.match(')') && !sp.match(':'))
-      {
-        sb.append(sp.c);
-        sp.inc();
-      }
-      if (sp.incMatch(":"))
-      {
-        while (!sp.match(')'))
-        {
-          sb2.append(sp.c);
-          sp.inc();
-        }
-      }
-      String sbs = sb.toString();
-      if (validators.get(sbs) instanceof String)
-      {
-        String pat = (String) validators.get(sbs);
-        Regex r = newRegex();
-        Rthings rth = new Rthings(this);
-        rth.noBackRefs = true;
-        r._compile(pat, rth);
-        add(r.thePattern);
-      }
-      else
-      {
-        Custom cm = new Custom(sb.toString());
-        if (cm.v != null)
-        {
-          Validator v2 = cm.v.arg(sb2.toString());
-          if (v2 != null)
-          {
-            v2.argsave = sb2.toString();
-            String p = cm.v.pattern;
-            cm.v = v2;
-            v2.pattern = p;
-          }
-          Regex r = newRegex();
-          Rthings rth = new Rthings(this);
-          rth.noBackRefs = true;
-          r._compile(cm.v.pattern, rth);
-          cm.sub = r.thePattern;
-          cm.sub.add(new CustomEndpoint(cm));
-          cm.sub.setParent(cm);
-          add(cm);
-        }
-      }
-    }
-    else if (sp.match('('))
-    {
-      mk.parenLevel++;
-      Regex r = newRegex();
-      // r.or = new Or();
-      sp.inc();
-      if (sp.incMatch("?:"))
-      {
-        r.or = new Or();
-      }
-      else if (sp.incMatch("?="))
-      {
-        r.or = new lookAhead(false);
-      }
-      else if (sp.incMatch("?!"))
-      {
-        r.or = new lookAhead(true);
-      }
-      else if (sp.match('?'))
-      {
-        sp.inc();
-        do
-        {
-          if (sp.c == 'i')
-          {
-            mk.ignoreCase = true;
-          }
-          if (sp.c == 'Q')
-          {
-            mk.dontMatchInQuotes = true;
-          }
-          if (sp.c == 'o')
-          {
-            mk.optimizeMe = true;
-          }
-          if (sp.c == 'g')
-          {
-            mk.gFlag = true;
-          }
-          if (sp.c == 's')
-          {
-            mk.sFlag = true;
-          }
-          if (sp.c == 'm')
-          {
-            mk.mFlag = true;
-          }
-          sp.inc();
-        }
-        while (!sp.match(')') && !sp.eos);
-        r = null;
-        mk.parenLevel--;
-        if (sp.eos) //throw new RegSyntax
-        {
-          RegSyntaxError.endItAll("Unclosed ()");
-        }
-      }
-      else
-      { // just ordinary parenthesis
-        r.or = mk.noBackRefs ? new Or() : new OrMark(mk.val++);
-      }
-      if (r != null)
-      {
-        add(r._compile(sp, mk));
-      }
-    }
-    else if (sp.match('^'))
-    {
-      add(new Start(true));
-    }
-    else if (sp.dontMatch && sp.c == 'A')
-    {
-      add(new Start(false));
-    }
-    else if (sp.match('*'))
-    {
-      addMulti(new patInt(0), new patInf());
-    }
-    else if (sp.match('+'))
-    {
-      addMulti(new patInt(1), new patInf());
-    }
-    else if (sp.match('?'))
-    {
-      addMulti(new patInt(0), new patInt(1));
-    }
-    else if (sp.match('{'))
-    {
-      boolean bad = false;
-      StrPos sp2 = new StrPos(sp);
-      //StringBuffer sb = new StringBuffer();
-      sp.inc();
-      patInt i1 = sp.getPatInt();
-      patInt i2 = null;
-      if (sp.match('}'))
-      {
-        i2 = i1;
-      }
-      else
-      {
-        if (!sp.match(','))
-        {
-          /*
-            RegSyntaxError.endItAll(
-               "String \"{"+i2+
-               "\" should be followed with , or }");
-           */
-          bad = true;
-        }
-        sp.inc();
-        if (sp.match('}'))
-        {
-          i2 = new patInf();
-        }
-        else
-        {
-          i2 = sp.getPatInt();
-        }
-      }
-      if (i1 == null || i2 == null)
-      {
-        /*
-                          throw new RegSyntax("Badly formatted Multi: "
-                          +"{"+i1+","+i2+"}"); */
-        bad = true;
-      }
-      if (bad)
-      {
-        sp.dup(sp2);
-        add(new oneChar(sp.c));
-      }
-      else
-      {
-        addMulti(i1, i2);
-      }
-    }
-    else if (sp.escMatch('x') && next2Hex(sp))
-    {
-      sp.inc();
-      int d = getHexDigit(sp);
-      sp.inc();
-      d = 16 * d + getHexDigit(sp);
-      add(new oneChar( (char) d));
-    }
-    else if (sp.escMatch('c'))
-    {
-      sp.inc();
-      if (sp.c < Ctrl.cmap.length)
-      {
-        add(new oneChar(Ctrl.cmap[sp.c]));
-      }
-      else
-      {
-        add(new oneChar(sp.c));
-      }
-    }
-    else if (sp.escMatch('f'))
-    {
-      add(new oneChar( (char) 12));
-    }
-    else if (sp.escMatch('a'))
-    {
-      add(new oneChar( (char) 7));
-    }
-    else if (sp.escMatch('t'))
-    {
-      add(new oneChar('\t'));
-    }
-    else if (sp.escMatch('n'))
-    {
-      add(new oneChar('\n'));
-    }
-    else if (sp.escMatch('r'))
-    {
-      add(new oneChar('\r'));
-    }
-    else if (sp.escMatch('b'))
-    {
-      add(new oneChar('\b'));
-    }
-    else if (sp.escMatch('e'))
-    {
-      add(new oneChar( (char) 27));
-    }
-    else
-    {
-      add(new oneChar(sp.c));
-      if (sp.match(')'))
-      {
-        RegSyntaxError.endItAll("Unmatched right paren in pattern");
-      }
-    }
-  }
-
-  // compiles all Pattern elements, internal method
-  private Pattern _compile(String pat, Rthings mk)
-      throws RegSyntax
-  {
-    minMatch = null;
-    sFlag = mFlag = ignoreCase = gFlag = false;
-    StrPos sp = new StrPos(pat, 0);
-    thePattern = _compile(sp, mk);
-    pt.marks = null;
-    return thePattern;
-  }
-
-  Pattern p = null;
-  Or or = null;
-  Pattern _compile(StrPos sp, Rthings mk)
-      throws RegSyntax
-  {
-    while (! (sp.eos || (or != null && sp.match(')'))))
-    {
-      compile1(sp, mk);
-      sp.inc();
-    }
-    if (sp.match(')'))
-    {
-      mk.parenLevel--;
-    }
-    else if (sp.eos && mk.parenLevel != 0)
-    {
-      RegSyntaxError.endItAll("Unclosed Parenthesis! lvl=" + mk.parenLevel);
-    }
-    if (or != null)
-    {
-      if (p == null)
-      {
-        p = new NullPattern();
-      }
-      or.addOr(p);
-      return or;
-    }
-    return p == null ? new NullPattern() : p;
-  }
-
-  // add a multi object to the end of the chain
-  // which applies to the last object
-  void addMulti(patInt i1, patInt i2)
-      throws RegSyntax
-  {
-    Pattern last, last2;
-    for (last = p; last != null && last.next != null; last = last.next)
-    {
-      ;
-    }
-    if (last == null || last == p)
-    {
-      last2 = null;
-    }
-    else
-    {
-      for (last2 = p; last2.next != last; last2 = last2.next)
-      {
-        ;
-      }
-    }
-    if (last instanceof Multi && i1.intValue() == 0 &&
-        i2.intValue() == 1)
-    {
-      ( (Multi) last).matchFewest = true;
-    }
-    else if (last instanceof FastMulti && i1.intValue() == 0 &&
-             i2.intValue() == 1)
-    {
-      ( (FastMulti) last).matchFewest = true;
-    }
-    else if (last instanceof DotMulti && i1.intValue() == 0 &&
-             i2.intValue() == 1)
-    {
-      ( (DotMulti) last).matchFewest = true;
-    }
-    else if (last instanceof Multi
-             || last instanceof DotMulti
-             || last instanceof FastMulti)
-    {
-      throw new RegSyntax("Syntax error.");
-    }
-    else if (last2 == null)
-    {
-      p = mkMulti(i1, i2, p);
-    }
-    else
-    {
-      last2.next = mkMulti(i1, i2, last);
-    }
-  }
-
-  final static Pattern mkMulti(patInt lo, patInt hi, Pattern p)
-      throws RegSyntax
-  {
-    if (p instanceof Any && p.next == null)
-    {
-      return (Pattern)new DotMulti(lo, hi);
-    }
-    return RegOpt.safe4fm(p) ? (Pattern)new FastMulti(lo, hi, p) :
-        (Pattern)new Multi(lo, hi, p);
-  }
-
-  // process the bracket operator
-  Pattern matchBracket(StrPos sp)
-      throws RegSyntax
-  {
-    Bracket ret;
-    if (sp.match('^'))
-    {
-      ret = new Bracket(true);
-      sp.inc();
-    }
-    else
-    {
-      ret = new Bracket(false);
-    }
-    if (sp.match(']'))
-    {
-      //throw new RegSyntax
-      RegSyntaxError.endItAll("Unmatched []");
-    }
-
-    while (!sp.eos && !sp.match(']'))
-    {
-      StrPos s1 = new StrPos(sp);
-      s1.inc();
-      StrPos s1_ = new StrPos(s1);
-      s1_.inc();
-      if (s1.match('-') && !s1_.match(']'))
-      {
-        StrPos s2 = new StrPos(s1);
-        s2.inc();
-        if (!s2.eos)
-        {
-          ret.addOr(new Range(sp.c, s2.c));
-        }
-        sp.inc();
-        sp.inc();
-      }
-      else if (sp.escMatch('Q'))
-      {
-        sp.inc();
-        while (!sp.escMatch('E'))
-        {
-          ret.addOr(new oneChar(sp.c));
-          sp.inc();
-        }
-      }
-      else if (sp.escMatch('d'))
-      {
-        ret.addOr(new Range('0', '9'));
-      }
-      else if (sp.escMatch('s'))
-      {
-        ret.addOr(new oneChar( (char) 32));
-        ret.addOr(new Range( (char) 8, (char) 10));
-        ret.addOr(new oneChar( (char) 13));
-      }
-      else if (sp.escMatch('w'))
-      {
-        ret.addOr(new Range('a', 'z'));
-        ret.addOr(new Range('A', 'Z'));
-        ret.addOr(new Range('0', '9'));
-        ret.addOr(new oneChar('_'));
-      }
-      else if (sp.escMatch('D'))
-      {
-        ret.addOr(new Range( (char) 0, (char) 47));
-        ret.addOr(new Range( (char) 58, (char) 65535));
-      }
-      else if (sp.escMatch('S'))
-      {
-        ret.addOr(new Range( (char) 0, (char) 7));
-        ret.addOr(new Range( (char) 11, (char) 12));
-        ret.addOr(new Range( (char) 14, (char) 31));
-        ret.addOr(new Range( (char) 33, (char) 65535));
-      }
-      else if (sp.escMatch('W'))
-      {
-        ret.addOr(new Range( (char) 0, (char) 64));
-        ret.addOr(new Range( (char) 91, (char) 94));
-        ret.addOr(new oneChar( (char) 96));
-        ret.addOr(new Range( (char) 123, (char) 65535));
-      }
-      else if (sp.escMatch('x') && next2Hex(sp))
-      {
-        sp.inc();
-        int d = getHexDigit(sp);
-        sp.inc();
-        d = 16 * d + getHexDigit(sp);
-        ret.addOr(new oneChar( (char) d));
-      }
-      else if (sp.escMatch('a'))
-      {
-        ret.addOr(new oneChar( (char) 7));
-      }
-      else if (sp.escMatch('f'))
-      {
-        ret.addOr(new oneChar( (char) 12));
-      }
-      else if (sp.escMatch('e'))
-      {
-        ret.addOr(new oneChar( (char) 27));
-      }
-      else if (sp.escMatch('n'))
-      {
-        ret.addOr(new oneChar('\n'));
-      }
-      else if (sp.escMatch('t'))
-      {
-        ret.addOr(new oneChar('\t'));
-      }
-      else if (sp.escMatch('r'))
-      {
-        ret.addOr(new oneChar('\r'));
-      }
-      else if (sp.escMatch('c'))
-      {
-        sp.inc();
-        if (sp.c < Ctrl.cmap.length)
-        {
-          ret.addOr(new oneChar(Ctrl.cmap[sp.c]));
-        }
-        else
-        {
-          ret.addOr(new oneChar(sp.c));
-        }
-      }
-      else if (isOctalString(sp))
-      {
-        int d = sp.c - '0';
-        sp.inc();
-        d = 8 * d + sp.c - '0';
-        StrPos sp2 = new StrPos(sp);
-        sp2.inc();
-        if (isOctalDigit(sp2, false))
-        {
-          sp.inc();
-          d = 8 * d + sp.c - '0';
-        }
-        ret.addOr(new oneChar( (char) d));
-      }
-      else
-      {
-        ret.addOr(new oneChar(sp.c));
-      }
-      sp.inc();
-    }
-    return ret;
-  }
-
-  /** Converts the stored Pattern to a String -- this is a
-        decompile.  Note that \t and \n will really print out here,
-        Not just the two character representations.
-        Also be prepared to see some strange output if your characters
-        are not printable. */
-  public String toString()
-  {
-    if (false && thePattern == null)
-    {
-      return "";
-    }
-    else
-    {
-      StringBuffer sb = new StringBuffer();
-      if (esc != Pattern.ESC)
-      {
-        sb.append("(?e=");
-        sb.append(esc);
-        sb.append(")");
-      }
-      if (gFlag
-          || mFlag
-          || !dotDoesntMatchCR
-          || sFlag
-          || ignoreCase
-          || dontMatchInQuotes
-          || optimized())
-      {
-        sb.append("(?");
-        if (ignoreCase)
-        {
-          sb.append("i");
-        }
-        if (mFlag)
-        {
-          sb.append("m");
-        }
-        if (sFlag || !dotDoesntMatchCR)
-        {
-          sb.append("s");
-        }
-        if (dontMatchInQuotes)
-        {
-          sb.append("Q");
-        }
-        if (optimized())
-        {
-          sb.append("o");
-        }
-        if (gFlag)
-        {
-          sb.append("g");
-        }
-        sb.append(")");
-      }
-      String patstr = thePattern.toString();
-      if (esc != Pattern.ESC)
-      {
-        patstr = reEscape(patstr, Pattern.ESC, esc);
-      }
-      sb.append(patstr);
-      return sb.toString();
-    }
-  }
-
-  // Re-escape Pattern, allows us to use a different escape
-  // character.
-  static String reEscape(String s, char oldEsc, char newEsc)
-  {
-    if (oldEsc == newEsc)
-    {
-      return s;
-    }
-    int i;
-    StringBuffer sb = new StringBuffer();
-    for (i = 0; i < s.length(); i++)
-    {
-      if (s.charAt(i) == oldEsc && i + 1 < s.length())
-      {
-        if (s.charAt(i + 1) == oldEsc)
-        {
-          sb.append(oldEsc);
-        }
-        else
-        {
-          sb.append(newEsc);
-          sb.append(s.charAt(i + 1));
-        }
-        i++;
-      }
-      else if (s.charAt(i) == newEsc)
-      {
-        sb.append(newEsc);
-        sb.append(newEsc);
-      }
-      else
-      {
-        sb.append(s.charAt(i));
-      }
-    }
-    return sb.toString();
-  }
-
-  /** This method implements FilenameFilter, allowing one
-       to use a Regex to search through a directory using File.list.
-       There is a FileRegex now that does this better.
-       @see com.stevesoft.pat.FileRegex
-   */
-  public boolean accept(File dir, String s)
-  {
-    return search(s);
-  }
-
-  /** The version of this package */
-  final static public String version()
-  {
-    return "lgpl release 1.5.3";
-  }
-
-  /** Once this method is called, the state of variables
-      ignoreCase and dontMatchInQuotes should not be changed as the
-      results will be unpredictable.  However,
-      search and matchAt will run more quickly.  Note that you
-      can check to see if the pattern has been optimized by calling
-      the optimized() method.<p>This method will attempt to rewrite
-      your pattern in a way that makes it faster (not all patterns
-      execute at the same speed).  In general, "(?: ... )" will be
-      faster than "( ... )" so if you don't need the backreference,
-      you should group using the former pattern.<p>It will also
-      introduce new pattern elements that you can't get to otherwise,
-      for example if you have a large table of strings, i.e. the
-      months of the year "(January|February|...)" optimize() will make
-      a Hashtable that takes it to the next appropriate pattern
-      element -- eliminating the need for a linear search.
-      @see com.stevesoft.pat.Regex#optimized
-      @see com.stevesoft.pat.Regex#ignoreCase
-      @see com.stevesoft.pat.Regex#dontMatchInQuotes
-      @see com.stevesoft.pat.Regex#matchAt
-      @see com.stevesoft.pat.Regex#search
-   */
-  public void optimize()
-  {
-    if (optimized() || thePattern == null)
-    {
-      return;
-    }
-    minMatch = new patInt(0); //thePattern.countMinChars();
-    thePattern = RegOpt.opt(thePattern, ignoreCase,
-                            dontMatchInQuotes);
-    skipper = Skip.findSkip(this);
-    //RegOpt.setParents(this);
-    return;
-  }
-
-  Skip skipper;
-  /** This function returns true if the optimize method has
-       been called. */
-  public boolean optimized()
-  {
-    return minMatch != null;
-  }
-
-  /** A bit of syntactic surgar for those who want to make
-      their code look more perl-like.  To use this initialize
-      your Regex object by saying:
-      <pre>
-      Regex r1 = Regex.perlCode("s/hello/goodbye/");
-      Regex r2 = Regex.perlCode("s'fish'frog'i");
-      Regex r3 = Regex.perlCode("m'hello');
-      </pre>
-      The i for ignoreCase is supported in
-      this syntax, as well as m, s, and x.  The g flat
-      is a bit of a special case.<p>
-      If you wish to replace all occurences of a pattern, you
-      do not put a 'g' in the perlCode, but call Regex's
-      replaceAll method.<p>
-      If you wish to simply
-      and only do a search for r2's pattern, you can do this
-      by calling the searchFrom method method repeatedly, or
-      by calling search repeatedly if the g flag is set.
-      <p>
-      Note: Currently perlCode does <em>not</em>
-      support the (?e=#) syntax for
-      changing the escape character.
-   */
-
-  public static Regex perlCode(String s)
-  {
-    // this file is big enough, see parsePerl.java
-    // for this function.
-    return parsePerl.parse(s);
-  }
-
-  static final char back_slash = '\\';
-
-  /** Checks to see if there are only literal and no special
-      pattern elements in this Regex. */
-  public boolean isLiteral()
-  {
-    Pattern x = thePattern;
-    while (x != null)
-    {
-      if (x instanceof oneChar)
-      {
-        ;
-      }
-      else if (x instanceof Skipped)
-      {
-        ;
-      }
-      else
-      {
-        return false;
-      }
-      x = x.next;
-    }
-    return true;
-  }
-
-  /** You only need to know about this if you are inventing
-      your own pattern elements. */
-  public patInt countMinChars()
-  {
-    return thePattern.countMinChars();
-  }
-
-  /** You only need to know about this if you are inventing
-      your own pattern elements. */
-  public patInt countMaxChars()
-  {
-    return thePattern.countMaxChars();
-  }
-
-  boolean isHexDigit(StrPos sp)
-  {
-    boolean r =
-        !sp.eos && !sp.dontMatch
-        && ( (sp.c >= '0' && sp.c <= '9')
-            || (sp.c >= 'a' && sp.c <= 'f')
-            || (sp.c >= 'A' && sp.c <= 'F'));
-    return r;
-  }
-
-  boolean isOctalDigit(StrPos sp, boolean first)
-  {
-    boolean r =
-        !sp.eos && ! (first ^ sp.dontMatch)
-        && sp.c >= '0' && sp.c <= '7';
-    return r;
-  }
-
-  int getHexDigit(StrPos sp)
-  {
-    if (sp.c >= '0' && sp.c <= '9')
-    {
-      return sp.c - '0';
-    }
-    if (sp.c >= 'a' && sp.c <= 'f')
-    {
-      return sp.c - 'a' + 10;
-    }
-    return sp.c - 'A' + 10;
-  }
-
-  boolean next2Hex(StrPos sp)
-  {
-    StrPos sp2 = new StrPos(sp);
-    sp2.inc();
-    if (!isHexDigit(sp2))
-    {
-      return false;
-    }
-    sp2.inc();
-    if (!isHexDigit(sp2))
-    {
-      return false;
-    }
-    return true;
-  }
-
-  boolean isOctalString(StrPos sp)
-  {
-    if (!isOctalDigit(sp, true))
-    {
-      return false;
-    }
-    StrPos sp2 = new StrPos(sp);
-    sp2.inc();
-    if (!isOctalDigit(sp2, false))
-    {
-      return false;
-    }
-    return true;
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+import java.io.*;
+import java.util.*;
+
+import com.stevesoft.pat.wrap.*;
+
+/** Matches a Unicode punctuation character. */
+class UnicodePunct extends UniValidator
+{
+  public int validate(StringLike s, int from, int to)
+  {
+    return from < s.length() && Prop.isPunct(s.charAt(from)) ? to : -1;
+  }
+}
+
+/** Matches a Unicode white space character. */
+class UnicodeWhite extends UniValidator
+{
+  public int validate(StringLike s, int from, int to)
+  {
+    return from < s.length() && Prop.isWhite(s.charAt(from)) ? to : -1;
+  }
+}
+
+/**
+ * Matches a character that is not a Unicode punctuation character.
+ */
+class NUnicodePunct extends UniValidator
+{
+  public int validate(StringLike s, int from, int to)
+  {
+    return from < s.length() && !Prop.isPunct(s.charAt(from)) ? to : -1;
+  }
+}
+
+/**
+ * Matches a character that is not a Unicode white space character.
+ */
+class NUnicodeWhite extends UniValidator
+{
+  public int validate(StringLike s, int from, int to)
+  {
+    return from < s.length() && !Prop.isWhite(s.charAt(from)) ? to : -1;
+  }
+}
+
+/** Matches a Unicode word character: an alphanumeric or underscore. */
+class UnicodeW extends UniValidator
+{
+  public int validate(StringLike s, int from, int to)
+  {
+    if (from >= s.length())
+    {
+      return -1;
+    }
+    char c = s.charAt(from);
+    return (Prop.isAlphabetic(c) || Prop.isDecimalDigit(c) || c == '_') ? to
+            : -1;
+  }
+}
+
+/** Matches a character that is not a Unicode alphanumeric or underscore. */
+class NUnicodeW extends UniValidator
+{
+  public int validate(StringLike s, int from, int to)
+  {
+    if (from >= s.length())
+    {
+      return -1;
+    }
+    char c = s.charAt(from);
+    return !(Prop.isAlphabetic(c) || Prop.isDecimalDigit(c) || c == '_') ? to
+            : -1;
+  }
+}
+
+/** Matches a Unicode decimal digit. */
+class UnicodeDigit extends UniValidator
+{
+  public int validate(StringLike s, int from, int to)
+  {
+    return from < s.length() && Prop.isDecimalDigit(s.charAt(from)) ? to
+            : -1;
+  }
+}
+
+/** Matches a character that is not a Unicode digit. */
+class NUnicodeDigit extends UniValidator
+{
+  public int validate(StringLike s, int from, int to)
+  {
+    return from < s.length() && !Prop.isDecimalDigit(s.charAt(from)) ? to
+            : -1;
+  }
+}
+
+/** Matches a Unicode math character. */
+class UnicodeMath extends UniValidator
+{
+  public int validate(StringLike s, int from, int to)
+  {
+    return from < s.length() && Prop.isMath(s.charAt(from)) ? to : -1;
+  }
+}
+
+/** Matches a non-math Unicode character. */
+class NUnicodeMath extends UniValidator
+{
+  public int validate(StringLike s, int from, int to)
+  {
+    return from < s.length() && !Prop.isMath(s.charAt(from)) ? to : -1;
+  }
+}
+
+/** Matches a Unicode currency symbol. */
+class UnicodeCurrency extends UniValidator
+{
+  public int validate(StringLike s, int from, int to)
+  {
+    return from < s.length() && Prop.isCurrency(s.charAt(from)) ? to : -1;
+  }
+}
+
+/** Matches a non-currency symbol Unicode character. */
+class NUnicodeCurrency extends UniValidator
+{
+  public int validate(StringLike s, int from, int to)
+  {
+    return from < s.length() && !Prop.isCurrency(s.charAt(from)) ? to : -1;
+  }
+}
+
+/** Matches a Unicode alphabetic character. */
+class UnicodeAlpha extends UniValidator
+{
+  public int validate(StringLike s, int from, int to)
+  {
+    return from < s.length() && Prop.isAlphabetic(s.charAt(from)) ? to : -1;
+  }
+}
+
+/** Matches a non-alphabetic Unicode character. */
+class NUnicodeAlpha extends UniValidator
+{
+  public int validate(StringLike s, int from, int to)
+  {
+    return from < s.length() && !Prop.isAlphabetic(s.charAt(from)) ? to
+            : -1;
+  }
+}
+
+/** Matches an upper case Unicode character. */
+class UnicodeUpper extends UniValidator
+{
+  public int validate(StringLike s, int from, int to)
+  {
+    return from < s.length() && isUpper(s.charAt(from)) ? to : -1;
+  }
+
+  final boolean isUpper(char c)
+  {
+    return c == CaseMgr.toUpperCase(c) && c != CaseMgr.toLowerCase(c);
+  }
+}
+
+/** Matches an upper case Unicode character. */
+class UnicodeLower extends UniValidator
+{
+  public int validate(StringLike s, int from, int to)
+  {
+    return from < s.length() && isLower(s.charAt(from)) ? to : -1;
+  }
+
+  final boolean isLower(char c)
+  {
+    return c != CaseMgr.toUpperCase(c) && c == CaseMgr.toLowerCase(c);
+  }
+}
+
+/**
+ * Regex provides the parser which constructs the linked list of Pattern classes
+ * from a String.
+ * <p>
+ * For the purpose of this documentation, the fact that java interprets the
+ * backslash will be ignored. In practice, however, you will need a double
+ * backslash to obtain a string that contains a single backslash character.
+ * Thus, the example pattern "\b" should really be typed as "\\b" inside java
+ * code.
+ * <p>
+ * Note that Regex is part of package "com.stevesoft.pat". To use it, simply
+ * import com.stevesoft.pat.Regex at the top of your file.
+ * <p>
+ * Regex is made with a constructor that takes a String that defines the regular
+ * expression. Thus, for example
+ * 
+ * <pre>
+ * Regex r = new Regex(&quot;[a-c]*&quot;);
+ * </pre>
+ * 
+ * matches any number of characters so long as the are 'a', 'b', or 'c').
+ * <p>
+ * To attempt to match the Pattern to a given string, you can use either the
+ * search(String) member function, or the matchAt(String,int position) member
+ * function. These functions return a boolean which tells you whether or not the
+ * thing worked, and sets the methods "charsMatched()" and "matchedFrom()" in
+ * the Regex object appropriately.
+ * <p>
+ * The portion of the string before the match can be obtained by the left()
+ * member, and the portion after the match can be obtained by the right()
+ * member.
+ * <p>
+ * Essentially, this package implements a syntax that is very much like the perl
+ * 5 regular expression syntax.
+ * 
+ * Longer example:
+ * 
+ * <pre>
+ * Regex r = new Regex(&quot;x(a|b)y&quot;);
+ * r.matchAt(&quot;xay&quot;, 0);
+ * System.out.println(&quot;sub = &quot; + r.stringMatched(1));
+ * </pre>
+ * 
+ * The above would print "sub = a".
+ * 
+ * <pre>
+ *  r.left() // would return &quot;x&quot;
+ *  r.right() // would return &quot;y&quot;
+ * </pre>
+ * 
+ * <p>
+ * Differences between this package and perl5:<br>
+ * The extended Pattern for setting flags, is now supported, but the flags are
+ * different. "(?i)" tells the pattern to ignore case, "(?Q)" sets the
+ * "dontMatchInQuotes" flag, and "(?iQ)" sets them both. You can change the
+ * escape character. The pattern
+ * 
+ * <pre>
+ * (?e=#)#d+
+ * </pre>
+ * 
+ * is the same as
+ * 
+ * <pre>
+ * \d+
+ * </pre>, but note that the sequence
+ * 
+ * <pre>
+ * (?e=#)
+ * </pre>
+ * 
+ * <b>must</b> occur at the very beginning of the pattern. There may be other
+ * small differences as well. I will either make my package conform or note them
+ * as I become aware of them.
+ * <p>
+ * This package supports additional patterns not in perl5: <center> <table
+ * border=1>
+ * <tr>
+ * <td>(?@())</td>
+ * <td>Group</td>
+ * <td>This matches all characters between the '(' character and the balancing
+ * ')' character. Thus, it will match "()" as well as "(())". The balancing
+ * characters are arbitrary, thus (?@{}) matches on "{}" and "{{}}".</td>
+ * <tr>
+ * <td>(?&lt1)</td>
+ * <td>Backup</td>
+ * <td>Moves the pointer backwards within the text. This allows you to make a
+ * "look behind." It fails if it attempts to move to a position before the
+ * beginning of the string. "x(?&lt1)" is equivalent to "(?=x)". The number, 1
+ * in this example, is the number of characters to move backwards.</td>
+ * </table> </center>
+ * </dl>
+ * 
+ * @author Steven R. Brandt
+ * @version package com.stevesoft.pat, release 1.5.3
+ * @see Pattern
+ */
+public class Regex extends RegRes implements FilenameFilter
+{
+  /**
+   * BackRefOffset gives the identity number of the first pattern. Version 1.0
+   * used zero, version 1.1 uses 1 to be more compatible with perl.
+   */
+  static int BackRefOffset = 1;
+
+  private static Pattern none = new NoPattern();
+
+  Pattern thePattern = none;
+
+  patInt minMatch = new patInt(0);
+
+  static Hashtable validators = new Hashtable();
+  static
+  {
+    define("p", "(?>1)", new UnicodePunct());
+    define("P", "(?>1)", new NUnicodePunct());
+    define("s", "(?>1)", new UnicodeWhite());
+    define("S", "(?>1)", new NUnicodeWhite());
+    define("w", "(?>1)", new UnicodeW());
+    define("W", "(?>1)", new NUnicodeW());
+    define("d", "(?>1)", new UnicodeDigit());
+    define("D", "(?>1)", new NUnicodeDigit());
+    define("m", "(?>1)", new UnicodeMath());
+    define("M", "(?>1)", new NUnicodeMath());
+    define("c", "(?>1)", new UnicodeCurrency());
+    define("C", "(?>1)", new NUnicodeCurrency());
+    define("a", "(?>1)", new UnicodeAlpha());
+    define("A", "(?>1)", new NUnicodeAlpha());
+    define("uc", "(?>1)", new UnicodeUpper());
+    define("lc", "(?>1)", new UnicodeLower());
+  }
+
+  /** Set the dontMatch in quotes flag. */
+  public void setDontMatchInQuotes(boolean b)
+  {
+    dontMatchInQuotes = b;
+  }
+
+  /** Find out if the dontMatchInQuotes flag is enabled. */
+  public boolean getDontMatchInQuotes()
+  {
+    return dontMatchInQuotes;
+  }
+
+  boolean dontMatchInQuotes = false;
+
+  /**
+   * Set the state of the ignoreCase flag. If set to true, then the pattern
+   * matcher will ignore case when searching for a match.
+   */
+  public void setIgnoreCase(boolean b)
+  {
+    ignoreCase = b;
+  }
+
+  /**
+   * Get the state of the ignoreCase flag. Returns true if we are ignoring the
+   * case of the pattern, false otherwise.
+   */
+  public boolean getIgnoreCase()
+  {
+    return ignoreCase;
+  }
+
+  boolean ignoreCase = false;
+
+  static boolean defaultMFlag = false;
+
+  /**
+   * Set the default value of the m flag. If it is set to true, then the MFlag
+   * will be on for any regex search executed.
+   */
+  public static void setDefaultMFlag(boolean mFlag)
+  {
+    defaultMFlag = mFlag;
+  }
+
+  /**
+   * Get the default value of the m flag. If it is set to true, then the MFlag
+   * will be on for any regex search executed.
+   */
+  public static boolean getDefaultMFlag()
+  {
+    return defaultMFlag;
+  }
+
+  /**
+   * Initializes the object without a Pattern. To supply a Pattern use
+   * compile(String s).
+   * 
+   * @see com.stevesoft.pat.Regex#compile(java.lang.String)
+   */
+  public Regex()
+  {
+  }
+
+  /**
+   * Create and compile a Regex, but do not throw any exceptions. If you wish to
+   * have exceptions thrown for syntax errors, you must use the Regex(void)
+   * constructor to create the Regex object, and then call the compile method.
+   * Therefore, you should only call this method when you know your pattern is
+   * right. I will probably become more like
+   * 
+   * @see com.stevesoft.pat.Regex#search(java.lang.String)
+   * @see com.stevesoft.pat.Regex#compile(java.lang.String)
+   */
+  public Regex(String s)
+  {
+    try
+    {
+      compile(s);
+    } catch (RegSyntax rs)
+    {
+    }
+  }
+
+  ReplaceRule rep = null;
+
+  /**
+   * Create and compile both a Regex and a ReplaceRule.
+   * 
+   * @see com.stevesoft.pat.ReplaceRule
+   * @see com.stevesoft.pat.Regex#compile(java.lang.String)
+   */
+  public Regex(String s, String rp)
+  {
+    this(s);
+    rep = ReplaceRule.perlCode(rp);
+  }
+
+  /**
+   * Create and compile a Regex, but give it the ReplaceRule specified. This
+   * allows the user finer control of the Replacement process, if that is
+   * desired.
+   * 
+   * @see com.stevesoft.pat.ReplaceRule
+   * @see com.stevesoft.pat.Regex#compile(java.lang.String)
+   */
+  public Regex(String s, ReplaceRule rp)
+  {
+    this(s);
+    rep = rp;
+  }
+
+  /**
+   * Change the ReplaceRule of this Regex by compiling a new one using String
+   * rp.
+   */
+  public void setReplaceRule(String rp)
+  {
+    rep = ReplaceRule.perlCode(rp);
+    repr = null; // Clear Replacer history
+  }
+
+  /** Change the ReplaceRule of this Regex to rp. */
+  public void setReplaceRule(ReplaceRule rp)
+  {
+    rep = rp;
+  }
+
+  /**
+   * Test to see if a custom defined rule exists.
+   * 
+   * @see com.stevesoft.pat#define(java.lang.String,java.lang.String,Validator)
+   */
+  public static boolean isDefined(String nm)
+  {
+    return validators.get(nm) != null;
+  }
+
+  /**
+   * Removes a custom defined rule.
+   * 
+   * @see com.stevesoft.pat#define(java.lang.String,java.lang.String,Validator)
+   */
+  public static void undefine(String nm)
+  {
+    validators.remove(nm);
+  }
+
+  /**
+   * Defines a method to create a new rule. See test/deriv2.java and
+   * test/deriv3.java for examples of how to use it.
+   */
+  public static void define(String nm, String pat, Validator v)
+  {
+    v.pattern = pat;
+    validators.put(nm, v);
+  }
+
+  /**
+   * Defines a shorthand for a pattern. The pattern will be invoked by a string
+   * that has the form "(??"+nm+")".
+   */
+  public static void define(String nm, String pat)
+  {
+    validators.put(nm, pat);
+  }
+
+  /** Get the current ReplaceRule. */
+  public ReplaceRule getReplaceRule()
+  {
+    return rep;
+  }
+
+  Replacer repr = null;
+
+  final Replacer _getReplacer()
+  {
+    return repr == null ? repr = new Replacer() : repr;
+  }
+
+  public Replacer getReplacer()
+  {
+    if (repr == null)
+    {
+      repr = new Replacer();
+    }
+    repr.rh.me = this;
+    repr.rh.prev = null;
+    return repr;
+  }
+
+  /**
+   * Replace the first occurence of this pattern in String s according to the
+   * ReplaceRule.
+   * 
+   * @see com.stevesoft.pat.ReplaceRule
+   * @see com.stevesoft.pat.Regex#getReplaceRule()
+   */
+  public String replaceFirst(String s)
+  {
+    return _getReplacer().replaceFirstRegion(s, this, 0, s.length())
+            .toString();
+  }
+
+  /**
+   * Replace the first occurence of this pattern in String s beginning with
+   * position pos according to the ReplaceRule.
+   * 
+   * @see com.stevesoft.pat.ReplaceRule
+   * @see com.stevesoft.pat.Regex#getReplaceRule()
+   */
+  public String replaceFirstFrom(String s, int pos)
+  {
+    return _getReplacer().replaceFirstRegion(s, this, pos, s.length())
+            .toString();
+  }
+
+  /**
+   * Replace the first occurence of this pattern in String s beginning with
+   * position start and ending with end according to the ReplaceRule.
+   * 
+   * @see com.stevesoft.pat.ReplaceRule
+   * @see com.stevesoft.pat.Regex#getReplaceRule()
+   */
+  public String replaceFirstRegion(String s, int start, int end)
+  {
+    return _getReplacer().replaceFirstRegion(s, this, start, end)
+            .toString();
+  }
+
+  /**
+   * Replace all occurences of this pattern in String s according to the
+   * ReplaceRule.
+   * 
+   * @see com.stevesoft.pat.ReplaceRule
+   * @see com.stevesoft.pat.Regex#getReplaceRule()
+   */
+  public String replaceAll(String s)
+  {
+    return _getReplacer().replaceAllRegion(s, this, 0, s.length())
+            .toString();
+  }
+
+  public StringLike replaceAll(StringLike s)
+  {
+    return _getReplacer().replaceAllRegion(s, this, 0, s.length());
+  }
+
+  /**
+   * Replace all occurences of this pattern in String s beginning with position
+   * pos according to the ReplaceRule.
+   * 
+   * @see com.stevesoft.pat.ReplaceRule
+   * @see com.stevesoft.pat.Regex#getReplaceRule()
+   */
+  public String replaceAllFrom(String s, int pos)
+  {
+    return _getReplacer().replaceAllRegion(s, this, pos, s.length())
+            .toString();
+  }
+
+  /**
+   * Replace all occurences of this pattern in String s beginning with position
+   * start and ending with end according to the ReplaceRule.
+   * 
+   * @see com.stevesoft.pat.ReplaceRule
+   * @see com.stevesoft.pat.Regex#getReplaceRule()
+   */
+  public String replaceAllRegion(String s, int start, int end)
+  {
+    return _getReplacer().replaceAllRegion(s, this, start, end).toString();
+  }
+
+  /** Essentially clones the Regex object */
+  public Regex(Regex r)
+  {
+    super((RegRes) r);
+    dontMatchInQuotes = r.dontMatchInQuotes;
+    esc = r.esc;
+    ignoreCase = r.ignoreCase;
+    gFlag = r.gFlag;
+    if (r.rep == null)
+    {
+      rep = null;
+    }
+    else
+    {
+      rep = (ReplaceRule) r.rep.clone();
+    }
+    /*
+     * try { compile(r.toString()); } catch(RegSyntax r_) {}
+     */
+    thePattern = r.thePattern.clone(new Hashtable());
+    minMatch = r.minMatch;
+    skipper = r.skipper;
+  }
+
+  /**
+   * By default, the escape character is the backslash, but you can make it
+   * anything you want by setting this variable.
+   */
+  public char esc = Pattern.ESC;
+
+  /**
+   * This method compiles a regular expression, making it possible to call the
+   * search or matchAt methods.
+   * 
+   * @exception com.stevesoft.pat.RegSyntax
+   *                    is thrown if a syntax error is encountered in the
+   *                    pattern. For example, "x{3,1}" or "*a" are not valid
+   *                    patterns.
+   * @see com.stevesoft.pat.Regex#search
+   * @see com.stevesoft.pat.Regex#matchAt
+   */
+  public void compile(String prepat) throws RegSyntax
+  {
+    String postpat = parsePerl.codify(prepat, true);
+    String pat = postpat == null ? prepat : postpat;
+    minMatch = null;
+    ignoreCase = false;
+    dontMatchInQuotes = false;
+    Rthings mk = new Rthings(this);
+    int offset = mk.val;
+    String newpat = pat;
+    thePattern = none;
+    p = null;
+    or = null;
+    minMatch = new patInt(0);
+    StrPos sp = new StrPos(pat, 0);
+    if (sp.incMatch("(?e="))
+    {
+      char newEsc = sp.c;
+      sp.inc();
+      if (sp.match(')'))
+      {
+        newpat = reEscape(pat.substring(6), newEsc, Pattern.ESC);
+      }
+    }
+    else if (esc != Pattern.ESC)
+    {
+      newpat = reEscape(pat, esc, Pattern.ESC);
+    }
+    thePattern = _compile(newpat, mk);
+    numSubs_ = mk.val - offset;
+    mk.set(this);
+  }
+
+  /*
+   * If a Regex is compared against a Regex, a check is done to see that the
+   * patterns are equal as well as the most recent match. If a Regex is compare
+   * with a RegRes, only the result of the most recent match is compared.
+   */
+  public boolean equals(Object o)
+  {
+    if (o instanceof Regex)
+    {
+      if (toString().equals(o.toString()))
+      {
+        return super.equals(o);
+      }
+      else
+      {
+        return false;
+      }
+    }
+    else
+    {
+      return super.equals(o);
+    }
+  }
+
+  /** A clone by any other name would smell as sweet. */
+  public Object clone()
+  {
+    return new Regex(this);
+  }
+
+  /** Return a clone of the underlying RegRes object. */
+  public RegRes result()
+  {
+    return (RegRes) super.clone();
+  }
+
+  // prep sets global variables of class
+  // Pattern so that it can access them
+  // during an attempt at a match
+  Pthings pt = new Pthings();
+
+  final Pthings prep(StringLike s)
+  {
+    // if(gFlag)
+    pt.lastPos = matchedTo();
+    if (pt.lastPos < 0)
+    {
+      pt.lastPos = 0;
+    }
+    if ((s == null ? null : s.unwrap()) != (src == null ? null : s.unwrap()))
+    {
+      pt.lastPos = 0;
+    }
+    src = s;
+    pt.dotDoesntMatchCR = dotDoesntMatchCR && (!sFlag);
+    pt.mFlag = (mFlag | defaultMFlag);
+    pt.ignoreCase = ignoreCase;
+    pt.no_check = false;
+    if (pt.marks != null)
+    {
+      for (int i = 0; i < pt.marks.length; i++)
+      {
+        pt.marks[i] = -1;
+      }
+    }
+    pt.marks = null;
+    pt.nMarks = numSubs_;
+    pt.src = s;
+    if (dontMatchInQuotes)
+    {
+      setCbits(s, pt);
+    }
+    else
+    {
+      pt.cbits = null;
+    }
+    return pt;
+  }
+
+  /**
+   * Attempt to match a Pattern beginning at a specified location within the
+   * string.
+   * 
+   * @see com.stevesoft.pat.Regex#search
+   */
+  public boolean matchAt(String s, int start_pos)
+  {
+    return _search(s, start_pos, start_pos);
+  }
+
+  /**
+   * Attempt to match a Pattern beginning at a specified location within the
+   * StringLike.
+   * 
+   * @see com.stevesoft.pat.Regex#search
+   */
+  public boolean matchAt(StringLike s, int start_pos)
+  {
+    return _search(s, start_pos, start_pos);
+  }
+
+  /**
+   * Search through a String for the first occurrence of a match.
+   * 
+   * @see com.stevesoft.pat.Regex#searchFrom
+   * @see com.stevesoft.pat.Regex#matchAt
+   */
+  public boolean search(String s)
+  {
+    if (s == null)
+    {
+      throw new NullPointerException("Null String Given to Regex.search");
+    }
+    return _search(s, 0, s.length());
+  }
+
+  public boolean search(StringLike sl)
+  {
+    if (sl == null)
+    {
+      throw new NullPointerException(
+              "Null StringLike Given to Regex.search");
+    }
+    return _search(sl, 0, sl.length());
+  }
+
+  public boolean reverseSearch(String s)
+  {
+    if (s == null)
+    {
+      throw new NullPointerException(
+              "Null String Given to Regex.reverseSearch");
+    }
+    return _reverseSearch(s, 0, s.length());
+  }
+
+  public boolean reverseSearch(StringLike sl)
+  {
+    if (sl == null)
+    {
+      throw new NullPointerException(
+              "Null StringLike Given to Regex.reverseSearch");
+    }
+    return _reverseSearch(sl, 0, sl.length());
+  }
+
+  /**
+   * Search through a String for the first occurence of a match, but start at
+   * position
+   * 
+   * <pre>
+   * start
+   * </pre>
+   */
+  public boolean searchFrom(String s, int start)
+  {
+    if (s == null)
+    {
+      throw new NullPointerException(
+              "Null String Given to Regex.searchFrom");
+    }
+    return _search(s, start, s.length());
+  }
+
+  public boolean searchFrom(StringLike s, int start)
+  {
+    if (s == null)
+    {
+      throw new NullPointerException(
+              "Null String Given to Regex.searchFrom");
+    }
+    return _search(s, start, s.length());
+  }
+
+  /**
+   * Search through a region of a String for the first occurence of a match.
+   */
+  public boolean searchRegion(String s, int start, int end)
+  {
+    if (s == null)
+    {
+      throw new NullPointerException(
+              "Null String Given to Regex.searchRegion");
+    }
+    return _search(s, start, end);
+  }
+
+  /**
+   * Set this to change the default behavior of the "." pattern. By default it
+   * now matches perl's behavior and fails to match the '\n' character.
+   */
+  public static boolean dotDoesntMatchCR = true;
+
+  StringLike gFlags;
+
+  int gFlagto = 0;
+
+  boolean gFlag = false;
+
+  /** Set the 'g' flag */
+  public void setGFlag(boolean b)
+  {
+    gFlag = b;
+  }
+
+  /** Get the state of the 'g' flag. */
+  public boolean getGFlag()
+  {
+    return gFlag;
+  }
+
+  boolean sFlag = false;
+
+  /** Get the state of the sFlag */
+  public boolean getSFlag()
+  {
+    return sFlag;
+  }
+
+  boolean mFlag = false;
+
+  /** Get the state of the sFlag */
+  public boolean getMFlag()
+  {
+    return mFlag;
+  }
+
+  final boolean _search(String s, int start, int end)
+  {
+    return _search(new StringWrap(s), start, end);
+  }
+
+  final boolean _search(StringLike s, int start, int end)
+  {
+    if (gFlag && gFlagto > 0 && gFlags != null
+            && s.unwrap() == gFlags.unwrap())
+    {
+      start = gFlagto;
+    }
+    gFlags = null;
+
+    Pthings pt = prep(s);
+
+    int up = (minMatch == null ? end : end - minMatch.i);
+
+    if (up < start && end >= start)
+    {
+      up = start;
+    }
+
+    if (skipper == null)
+    {
+      for (int i = start; i <= up; i++)
+      {
+        charsMatched_ = thePattern.matchAt(s, i, pt);
+        if (charsMatched_ >= 0)
+        {
+          matchFrom_ = thePattern.mfrom;
+          marks = pt.marks;
+          gFlagto = matchFrom_ + charsMatched_;
+          gFlags = s;
+          return didMatch_ = true;
+        }
+      }
+    }
+    else
+    {
+      pt.no_check = true;
+      for (int i = start; i <= up; i++)
+      {
+        i = skipper.find(src, i, up);
+        if (i < 0)
+        {
+          charsMatched_ = matchFrom_ = -1;
+          return didMatch_ = false;
+        }
+        charsMatched_ = thePattern.matchAt(s, i, pt);
+        if (charsMatched_ >= 0)
+        {
+          matchFrom_ = thePattern.mfrom;
+          marks = pt.marks;
+          gFlagto = matchFrom_ + charsMatched_;
+          gFlags = s;
+          return didMatch_ = true;
+        }
+      }
+    }
+    return didMatch_ = false;
+  }
+
+  /*
+   * final boolean _search(LongStringLike s,long start,long end) { if(gFlag &&
+   * gFlagto > 0 && s==gFlags) start = gFlagto; gFlags = null;
+   * 
+   * Pthings pt=prep(s);
+   * 
+   * int up = end;//(minMatch == null ? end : end-minMatch.i);
+   * 
+   * if(up < start && end >= start) up = start;
+   * 
+   * if(skipper == null) { for(long i=start;i<=up;i++) { charsMatched_ =
+   * thePattern.matchAt(s,i,pt); if(charsMatched_ >= 0) { matchFrom_ =
+   * thePattern.mfrom; marks = pt.marks; gFlagto = matchFrom_+charsMatched_;
+   * return didMatch_=true; } } } else { pt.no_check = true; for(long i=start;i<=up;i++) {
+   * i = skipper.find(src,i,up); if(i<0) { charsMatched_ = matchFrom_ = -1;
+   * return didMatch_ = false; } charsMatched_ = thePattern.matchAt(s,i,pt);
+   * if(charsMatched_ >= 0) { matchFrom_ = thePattern.mfrom; marks = pt.marks;
+   * gFlagto = matchFrom_+charsMatched_; gFlags = s; return didMatch_=true; }
+   * else { i = s.adjustIndex(i); up = s.adjustEnd(i); } } } return
+   * didMatch_=false; }
+   */
+
+  boolean _reverseSearch(String s, int start, int end)
+  {
+    return _reverseSearch(new StringWrap(s), start, end);
+  }
+
+  boolean _reverseSearch(StringLike s, int start, int end)
+  {
+    if (gFlag && gFlagto > 0 && s.unwrap() == gFlags.unwrap())
+    {
+      end = gFlagto;
+    }
+    gFlags = null;
+    Pthings pt = prep(s);
+    for (int i = end; i >= start; i--)
+    {
+      charsMatched_ = thePattern.matchAt(s, i, pt);
+      if (charsMatched_ >= 0)
+      {
+        matchFrom_ = thePattern.mfrom;
+        marks = pt.marks;
+        gFlagto = matchFrom_ - 1;
+        gFlags = s;
+        return didMatch_ = true;
+      }
+    }
+    return didMatch_ = false;
+  }
+
+  // This routine sets the cbits variable
+  // of class Pattern. Cbits is true for
+  // the bit corresponding to a character inside
+  // a set of quotes.
+  static StringLike lasts = null;
+
+  static BitSet lastbs = null;
+
+  static void setCbits(StringLike s, Pthings pt)
+  {
+    if (s == lasts)
+    {
+      pt.cbits = lastbs;
+      return;
+    }
+    BitSet bs = new BitSet(s.length());
+    char qc = ' ';
+    boolean setBit = false;
+    for (int i = 0; i < s.length(); i++)
+    {
+      if (setBit)
+      {
+        bs.set(i);
+      }
+      char c = s.charAt(i);
+      if (!setBit && c == '"')
+      {
+        qc = c;
+        setBit = true;
+        bs.set(i);
+      }
+      else if (!setBit && c == '\'')
+      {
+        qc = c;
+        setBit = true;
+        bs.set(i);
+      }
+      else if (setBit && c == qc)
+      {
+        setBit = false;
+      }
+      else if (setBit && c == '\\' && i + 1 < s.length())
+      {
+        i++;
+        if (setBit)
+        {
+          bs.set(i);
+        }
+      }
+    }
+    pt.cbits = lastbs = bs;
+    lasts = s;
+  }
+
+  // Wanted user to over-ride this in alpha version,
+  // but it wasn't really necessary because of this trick:
+  Regex newRegex()
+  {
+    try
+    {
+      return (Regex) getClass().newInstance();
+    } catch (InstantiationException ie)
+    {
+      return null;
+    } catch (IllegalAccessException iae)
+    {
+      return null;
+    }
+  }
+
+  /**
+   * Only needed for creating your own extensions of Regex. This method adds the
+   * next Pattern in the chain of patterns or sets the Pattern if it is the
+   * first call.
+   */
+  protected void add(Pattern p2)
+  {
+    if (p == null)
+    {
+      p = p2;
+    }
+    else
+    {
+      p.add(p2);
+      p2 = p;
+    }
+  }
+
+  /**
+   * You only need to use this method if you are creating your own extentions to
+   * Regex. compile1 compiles one Pattern element, it can be over-ridden to
+   * allow the Regex compiler to understand new syntax. See deriv.java for an
+   * example. This routine is the heart of class Regex. Rthings has one integer
+   * member called intValue, it is used to keep track of the number of ()'s in
+   * the Pattern.
+   * 
+   * @exception com.stevesoft.pat.RegSyntax
+   *                    is thrown when a nonsensensical pattern is supplied. For
+   *                    example, a pattern beginning with *.
+   */
+  protected void compile1(StrPos sp, Rthings mk) throws RegSyntax
+  {
+    if (sp.match('['))
+    {
+      sp.inc();
+      add(matchBracket(sp));
+    }
+    else if (sp.match('|'))
+    {
+      if (or == null)
+      {
+        or = new Or();
+      }
+      if (p == null)
+      {
+        p = new NullPattern();
+      }
+      or.addOr(p);
+      p = null;
+    }
+    else if (sp.incMatch("(?<"))
+    {
+      patInt i = sp.getPatInt();
+      if (i == null)
+      {
+        RegSyntaxError.endItAll("No int after (?<");
+      }
+      add(new Backup(i.intValue()));
+      if (!sp.match(')'))
+      {
+        RegSyntaxError.endItAll("No ) after (?<");
+      }
+    }
+    else if (sp.incMatch("(?>"))
+    {
+      patInt i = sp.getPatInt();
+      if (i == null)
+      {
+        RegSyntaxError.endItAll("No int after (?>");
+      }
+      add(new Backup(-i.intValue()));
+      if (!sp.match(')'))
+      {
+        RegSyntaxError.endItAll("No ) after (?<");
+      }
+    }
+    else if (sp.incMatch("(?@"))
+    {
+      char op = sp.c;
+      sp.inc();
+      char cl = sp.c;
+      sp.inc();
+      if (!sp.match(')'))
+      {
+        RegSyntaxError.endItAll("(?@ does not have closing paren");
+      }
+      add(new Group(op, cl));
+    }
+    else if (sp.incMatch("(?#"))
+    {
+      while (!sp.match(')'))
+      {
+        sp.inc();
+      }
+    }
+    else if (sp.dontMatch && sp.c == 'w')
+    {
+      // Regex r = new Regex();
+      // r._compile("[a-zA-Z0-9_]",mk);
+      // add(new Goop("\\w",r.thePattern));
+      Bracket b = new Bracket(false);
+      b.addOr(new Range('a', 'z'));
+      b.addOr(new Range('A', 'Z'));
+      b.addOr(new Range('0', '9'));
+      b.addOr(new oneChar('_'));
+      add(b);
+    }
+    else if (sp.dontMatch && sp.c == 'G')
+    {
+      add(new BackG());
+    }
+    else if (sp.dontMatch && sp.c == 's')
+    {
+      // Regex r = new Regex();
+      // r._compile("[ \t\n\r\b]",mk);
+      // add(new Goop("\\s",r.thePattern));
+      Bracket b = new Bracket(false);
+      b.addOr(new oneChar((char) 32));
+      b.addOr(new Range((char) 8, (char) 10));
+      b.addOr(new oneChar((char) 13));
+      add(b);
+    }
+    else if (sp.dontMatch && sp.c == 'd')
+    {
+      // Regex r = new Regex();
+      // r._compile("[0-9]",mk);
+      // add(new Goop("\\d",r.thePattern));
+      Range digit = new Range('0', '9');
+      digit.printBrackets = true;
+      add(digit);
+    }
+    else if (sp.dontMatch && sp.c == 'W')
+    {
+      // Regex r = new Regex();
+      // r._compile("[^a-zA-Z0-9_]",mk);
+      // add(new Goop("\\W",r.thePattern));
+      Bracket b = new Bracket(true);
+      b.addOr(new Range('a', 'z'));
+      b.addOr(new Range('A', 'Z'));
+      b.addOr(new Range('0', '9'));
+      b.addOr(new oneChar('_'));
+      add(b);
+    }
+    else if (sp.dontMatch && sp.c == 'S')
+    {
+      // Regex r = new Regex();
+      // r._compile("[^ \t\n\r\b]",mk);
+      // add(new Goop("\\S",r.thePattern));
+      Bracket b = new Bracket(true);
+      b.addOr(new oneChar((char) 32));
+      b.addOr(new Range((char) 8, (char) 10));
+      b.addOr(new oneChar((char) 13));
+      add(b);
+    }
+    else if (sp.dontMatch && sp.c == 'D')
+    {
+      // Regex r = new Regex();
+      // r._compile("[^0-9]",mk);
+      // add(new Goop("\\D",r.thePattern));
+      Bracket b = new Bracket(true);
+      b.addOr(new Range('0', '9'));
+      add(b);
+    }
+    else if (sp.dontMatch && sp.c == 'B')
+    {
+      Regex r = new Regex();
+      r._compile("(?!" + back_slash + "b)", mk);
+      add(r.thePattern);
+    }
+    else if (isOctalString(sp))
+    {
+      int d = sp.c - '0';
+      sp.inc();
+      d = 8 * d + sp.c - '0';
+      StrPos sp2 = new StrPos(sp);
+      sp2.inc();
+      if (isOctalDigit(sp2, false))
+      {
+        sp.inc();
+        d = 8 * d + sp.c - '0';
+      }
+      add(new oneChar((char) d));
+    }
+    else if (sp.dontMatch && sp.c >= '1' && sp.c <= '9')
+    {
+      int iv = sp.c - '0';
+      StrPos s2 = new StrPos(sp);
+      s2.inc();
+      if (!s2.dontMatch && s2.c >= '0' && s2.c <= '9')
+      {
+        iv = 10 * iv + (s2.c - '0');
+        sp.inc();
+      }
+      add(new BackMatch(iv));
+    }
+    else if (sp.dontMatch && sp.c == 'b')
+    {
+      add(new Boundary());
+    }
+    else if (sp.match('\b'))
+    {
+      add(new Boundary());
+    }
+    else if (sp.match('$'))
+    {
+      add(new End(true));
+    }
+    else if (sp.dontMatch && sp.c == 'Z')
+    {
+      add(new End(false));
+    }
+    else if (sp.match('.'))
+    {
+      add(new Any());
+    }
+    else if (sp.incMatch("(??"))
+    {
+      StringBuffer sb = new StringBuffer();
+      StringBuffer sb2 = new StringBuffer();
+      while (!sp.match(')') && !sp.match(':'))
+      {
+        sb.append(sp.c);
+        sp.inc();
+      }
+      if (sp.incMatch(":"))
+      {
+        while (!sp.match(')'))
+        {
+          sb2.append(sp.c);
+          sp.inc();
+        }
+      }
+      String sbs = sb.toString();
+      if (validators.get(sbs) instanceof String)
+      {
+        String pat = (String) validators.get(sbs);
+        Regex r = newRegex();
+        Rthings rth = new Rthings(this);
+        rth.noBackRefs = true;
+        r._compile(pat, rth);
+        add(r.thePattern);
+      }
+      else
+      {
+        Custom cm = new Custom(sb.toString());
+        if (cm.v != null)
+        {
+          Validator v2 = cm.v.arg(sb2.toString());
+          if (v2 != null)
+          {
+            v2.argsave = sb2.toString();
+            String p = cm.v.pattern;
+            cm.v = v2;
+            v2.pattern = p;
+          }
+          Regex r = newRegex();
+          Rthings rth = new Rthings(this);
+          rth.noBackRefs = true;
+          r._compile(cm.v.pattern, rth);
+          cm.sub = r.thePattern;
+          cm.sub.add(new CustomEndpoint(cm));
+          cm.sub.setParent(cm);
+          add(cm);
+        }
+      }
+    }
+    else if (sp.match('('))
+    {
+      mk.parenLevel++;
+      Regex r = newRegex();
+      // r.or = new Or();
+      sp.inc();
+      if (sp.incMatch("?:"))
+      {
+        r.or = new Or();
+      }
+      else if (sp.incMatch("?="))
+      {
+        r.or = new lookAhead(false);
+      }
+      else if (sp.incMatch("?!"))
+      {
+        r.or = new lookAhead(true);
+      }
+      else if (sp.match('?'))
+      {
+        sp.inc();
+        do
+        {
+          if (sp.c == 'i')
+          {
+            mk.ignoreCase = true;
+          }
+          if (sp.c == 'Q')
+          {
+            mk.dontMatchInQuotes = true;
+          }
+          if (sp.c == 'o')
+          {
+            mk.optimizeMe = true;
+          }
+          if (sp.c == 'g')
+          {
+            mk.gFlag = true;
+          }
+          if (sp.c == 's')
+          {
+            mk.sFlag = true;
+          }
+          if (sp.c == 'm')
+          {
+            mk.mFlag = true;
+          }
+          sp.inc();
+        } while (!sp.match(')') && !sp.eos);
+        r = null;
+        mk.parenLevel--;
+        if (sp.eos) // throw new RegSyntax
+        {
+          RegSyntaxError.endItAll("Unclosed ()");
+        }
+      }
+      else
+      { // just ordinary parenthesis
+        r.or = mk.noBackRefs ? new Or() : new OrMark(mk.val++);
+      }
+      if (r != null)
+      {
+        add(r._compile(sp, mk));
+      }
+    }
+    else if (sp.match('^'))
+    {
+      add(new Start(true));
+    }
+    else if (sp.dontMatch && sp.c == 'A')
+    {
+      add(new Start(false));
+    }
+    else if (sp.match('*'))
+    {
+      addMulti(new patInt(0), new patInf());
+    }
+    else if (sp.match('+'))
+    {
+      addMulti(new patInt(1), new patInf());
+    }
+    else if (sp.match('?'))
+    {
+      addMulti(new patInt(0), new patInt(1));
+    }
+    else if (sp.match('{'))
+    {
+      boolean bad = false;
+      StrPos sp2 = new StrPos(sp);
+      // StringBuffer sb = new StringBuffer();
+      sp.inc();
+      patInt i1 = sp.getPatInt();
+      patInt i2 = null;
+      if (sp.match('}'))
+      {
+        i2 = i1;
+      }
+      else
+      {
+        if (!sp.match(','))
+        {
+          /*
+           * RegSyntaxError.endItAll( "String \"{"+i2+ "\" should be followed
+           * with , or }");
+           */
+          bad = true;
+        }
+        sp.inc();
+        if (sp.match('}'))
+        {
+          i2 = new patInf();
+        }
+        else
+        {
+          i2 = sp.getPatInt();
+        }
+      }
+      if (i1 == null || i2 == null)
+      {
+        /*
+         * throw new RegSyntax("Badly formatted Multi: " +"{"+i1+","+i2+"}");
+         */
+        bad = true;
+      }
+      if (bad)
+      {
+        sp.dup(sp2);
+        add(new oneChar(sp.c));
+      }
+      else
+      {
+        addMulti(i1, i2);
+      }
+    }
+    else if (sp.escMatch('x') && next2Hex(sp))
+    {
+      sp.inc();
+      int d = getHexDigit(sp);
+      sp.inc();
+      d = 16 * d + getHexDigit(sp);
+      add(new oneChar((char) d));
+    }
+    else if (sp.escMatch('c'))
+    {
+      sp.inc();
+      if (sp.c < Ctrl.cmap.length)
+      {
+        add(new oneChar(Ctrl.cmap[sp.c]));
+      }
+      else
+      {
+        add(new oneChar(sp.c));
+      }
+    }
+    else if (sp.escMatch('f'))
+    {
+      add(new oneChar((char) 12));
+    }
+    else if (sp.escMatch('a'))
+    {
+      add(new oneChar((char) 7));
+    }
+    else if (sp.escMatch('t'))
+    {
+      add(new oneChar('\t'));
+    }
+    else if (sp.escMatch('n'))
+    {
+      add(new oneChar('\n'));
+    }
+    else if (sp.escMatch('r'))
+    {
+      add(new oneChar('\r'));
+    }
+    else if (sp.escMatch('b'))
+    {
+      add(new oneChar('\b'));
+    }
+    else if (sp.escMatch('e'))
+    {
+      add(new oneChar((char) 27));
+    }
+    else
+    {
+      add(new oneChar(sp.c));
+      if (sp.match(')'))
+      {
+        RegSyntaxError.endItAll("Unmatched right paren in pattern");
+      }
+    }
+  }
+
+  // compiles all Pattern elements, internal method
+  private Pattern _compile(String pat, Rthings mk) throws RegSyntax
+  {
+    minMatch = null;
+    sFlag = mFlag = ignoreCase = gFlag = false;
+    StrPos sp = new StrPos(pat, 0);
+    thePattern = _compile(sp, mk);
+    pt.marks = null;
+    return thePattern;
+  }
+
+  Pattern p = null;
+
+  Or or = null;
+
+  Pattern _compile(StrPos sp, Rthings mk) throws RegSyntax
+  {
+    while (!(sp.eos || (or != null && sp.match(')'))))
+    {
+      compile1(sp, mk);
+      sp.inc();
+    }
+    if (sp.match(')'))
+    {
+      mk.parenLevel--;
+    }
+    else if (sp.eos && mk.parenLevel != 0)
+    {
+      RegSyntaxError.endItAll("Unclosed Parenthesis! lvl=" + mk.parenLevel);
+    }
+    if (or != null)
+    {
+      if (p == null)
+      {
+        p = new NullPattern();
+      }
+      or.addOr(p);
+      return or;
+    }
+    return p == null ? new NullPattern() : p;
+  }
+
+  // add a multi object to the end of the chain
+  // which applies to the last object
+  void addMulti(patInt i1, patInt i2) throws RegSyntax
+  {
+    Pattern last, last2;
+    for (last = p; last != null && last.next != null; last = last.next)
+    {
+      ;
+    }
+    if (last == null || last == p)
+    {
+      last2 = null;
+    }
+    else
+    {
+      for (last2 = p; last2.next != last; last2 = last2.next)
+      {
+        ;
+      }
+    }
+    if (last instanceof Multi && i1.intValue() == 0 && i2.intValue() == 1)
+    {
+      ((Multi) last).matchFewest = true;
+    }
+    else if (last instanceof FastMulti && i1.intValue() == 0
+            && i2.intValue() == 1)
+    {
+      ((FastMulti) last).matchFewest = true;
+    }
+    else if (last instanceof DotMulti && i1.intValue() == 0
+            && i2.intValue() == 1)
+    {
+      ((DotMulti) last).matchFewest = true;
+    }
+    else if (last instanceof Multi || last instanceof DotMulti
+            || last instanceof FastMulti)
+    {
+      throw new RegSyntax("Syntax error.");
+    }
+    else if (last2 == null)
+    {
+      p = mkMulti(i1, i2, p);
+    }
+    else
+    {
+      last2.next = mkMulti(i1, i2, last);
+    }
+  }
+
+  final static Pattern mkMulti(patInt lo, patInt hi, Pattern p)
+          throws RegSyntax
+  {
+    if (p instanceof Any && p.next == null)
+    {
+      return (Pattern) new DotMulti(lo, hi);
+    }
+    return RegOpt.safe4fm(p) ? (Pattern) new FastMulti(lo, hi, p)
+            : (Pattern) new Multi(lo, hi, p);
+  }
+
+  // process the bracket operator
+  Pattern matchBracket(StrPos sp) throws RegSyntax
+  {
+    Bracket ret;
+    if (sp.match('^'))
+    {
+      ret = new Bracket(true);
+      sp.inc();
+    }
+    else
+    {
+      ret = new Bracket(false);
+    }
+    if (sp.match(']'))
+    {
+      // throw new RegSyntax
+      RegSyntaxError.endItAll("Unmatched []");
+    }
+
+    while (!sp.eos && !sp.match(']'))
+    {
+      StrPos s1 = new StrPos(sp);
+      s1.inc();
+      StrPos s1_ = new StrPos(s1);
+      s1_.inc();
+      if (s1.match('-') && !s1_.match(']'))
+      {
+        StrPos s2 = new StrPos(s1);
+        s2.inc();
+        if (!s2.eos)
+        {
+          ret.addOr(new Range(sp.c, s2.c));
+        }
+        sp.inc();
+        sp.inc();
+      }
+      else if (sp.escMatch('Q'))
+      {
+        sp.inc();
+        while (!sp.escMatch('E'))
+        {
+          ret.addOr(new oneChar(sp.c));
+          sp.inc();
+        }
+      }
+      else if (sp.escMatch('d'))
+      {
+        ret.addOr(new Range('0', '9'));
+      }
+      else if (sp.escMatch('s'))
+      {
+        ret.addOr(new oneChar((char) 32));
+        ret.addOr(new Range((char) 8, (char) 10));
+        ret.addOr(new oneChar((char) 13));
+      }
+      else if (sp.escMatch('w'))
+      {
+        ret.addOr(new Range('a', 'z'));
+        ret.addOr(new Range('A', 'Z'));
+        ret.addOr(new Range('0', '9'));
+        ret.addOr(new oneChar('_'));
+      }
+      else if (sp.escMatch('D'))
+      {
+        ret.addOr(new Range((char) 0, (char) 47));
+        ret.addOr(new Range((char) 58, (char) 65535));
+      }
+      else if (sp.escMatch('S'))
+      {
+        ret.addOr(new Range((char) 0, (char) 7));
+        ret.addOr(new Range((char) 11, (char) 12));
+        ret.addOr(new Range((char) 14, (char) 31));
+        ret.addOr(new Range((char) 33, (char) 65535));
+      }
+      else if (sp.escMatch('W'))
+      {
+        ret.addOr(new Range((char) 0, (char) 64));
+        ret.addOr(new Range((char) 91, (char) 94));
+        ret.addOr(new oneChar((char) 96));
+        ret.addOr(new Range((char) 123, (char) 65535));
+      }
+      else if (sp.escMatch('x') && next2Hex(sp))
+      {
+        sp.inc();
+        int d = getHexDigit(sp);
+        sp.inc();
+        d = 16 * d + getHexDigit(sp);
+        ret.addOr(new oneChar((char) d));
+      }
+      else if (sp.escMatch('a'))
+      {
+        ret.addOr(new oneChar((char) 7));
+      }
+      else if (sp.escMatch('f'))
+      {
+        ret.addOr(new oneChar((char) 12));
+      }
+      else if (sp.escMatch('e'))
+      {
+        ret.addOr(new oneChar((char) 27));
+      }
+      else if (sp.escMatch('n'))
+      {
+        ret.addOr(new oneChar('\n'));
+      }
+      else if (sp.escMatch('t'))
+      {
+        ret.addOr(new oneChar('\t'));
+      }
+      else if (sp.escMatch('r'))
+      {
+        ret.addOr(new oneChar('\r'));
+      }
+      else if (sp.escMatch('c'))
+      {
+        sp.inc();
+        if (sp.c < Ctrl.cmap.length)
+        {
+          ret.addOr(new oneChar(Ctrl.cmap[sp.c]));
+        }
+        else
+        {
+          ret.addOr(new oneChar(sp.c));
+        }
+      }
+      else if (isOctalString(sp))
+      {
+        int d = sp.c - '0';
+        sp.inc();
+        d = 8 * d + sp.c - '0';
+        StrPos sp2 = new StrPos(sp);
+        sp2.inc();
+        if (isOctalDigit(sp2, false))
+        {
+          sp.inc();
+          d = 8 * d + sp.c - '0';
+        }
+        ret.addOr(new oneChar((char) d));
+      }
+      else
+      {
+        ret.addOr(new oneChar(sp.c));
+      }
+      sp.inc();
+    }
+    return ret;
+  }
+
+  /**
+   * Converts the stored Pattern to a String -- this is a decompile. Note that
+   * \t and \n will really print out here, Not just the two character
+   * representations. Also be prepared to see some strange output if your
+   * characters are not printable.
+   */
+  public String toString()
+  {
+    if (false && thePattern == null)
+    {
+      return "";
+    }
+    else
+    {
+      StringBuffer sb = new StringBuffer();
+      if (esc != Pattern.ESC)
+      {
+        sb.append("(?e=");
+        sb.append(esc);
+        sb.append(")");
+      }
+      if (gFlag || mFlag || !dotDoesntMatchCR || sFlag || ignoreCase
+              || dontMatchInQuotes || optimized())
+      {
+        sb.append("(?");
+        if (ignoreCase)
+        {
+          sb.append("i");
+        }
+        if (mFlag)
+        {
+          sb.append("m");
+        }
+        if (sFlag || !dotDoesntMatchCR)
+        {
+          sb.append("s");
+        }
+        if (dontMatchInQuotes)
+        {
+          sb.append("Q");
+        }
+        if (optimized())
+        {
+          sb.append("o");
+        }
+        if (gFlag)
+        {
+          sb.append("g");
+        }
+        sb.append(")");
+      }
+      String patstr = thePattern.toString();
+      if (esc != Pattern.ESC)
+      {
+        patstr = reEscape(patstr, Pattern.ESC, esc);
+      }
+      sb.append(patstr);
+      return sb.toString();
+    }
+  }
+
+  // Re-escape Pattern, allows us to use a different escape
+  // character.
+  static String reEscape(String s, char oldEsc, char newEsc)
+  {
+    if (oldEsc == newEsc)
+    {
+      return s;
+    }
+    int i;
+    StringBuffer sb = new StringBuffer();
+    for (i = 0; i < s.length(); i++)
+    {
+      if (s.charAt(i) == oldEsc && i + 1 < s.length())
+      {
+        if (s.charAt(i + 1) == oldEsc)
+        {
+          sb.append(oldEsc);
+        }
+        else
+        {
+          sb.append(newEsc);
+          sb.append(s.charAt(i + 1));
+        }
+        i++;
+      }
+      else if (s.charAt(i) == newEsc)
+      {
+        sb.append(newEsc);
+        sb.append(newEsc);
+      }
+      else
+      {
+        sb.append(s.charAt(i));
+      }
+    }
+    return sb.toString();
+  }
+
+  /**
+   * This method implements FilenameFilter, allowing one to use a Regex to
+   * search through a directory using File.list. There is a FileRegex now that
+   * does this better.
+   * 
+   * @see com.stevesoft.pat.FileRegex
+   */
+  public boolean accept(File dir, String s)
+  {
+    return search(s);
+  }
+
+  /** The version of this package */
+  final static public String version()
+  {
+    return "lgpl release 1.5.3";
+  }
+
+  /**
+   * Once this method is called, the state of variables ignoreCase and
+   * dontMatchInQuotes should not be changed as the results will be
+   * unpredictable. However, search and matchAt will run more quickly. Note that
+   * you can check to see if the pattern has been optimized by calling the
+   * optimized() method.
+   * <p>
+   * This method will attempt to rewrite your pattern in a way that makes it
+   * faster (not all patterns execute at the same speed). In general, "(?: ... )"
+   * will be faster than "( ... )" so if you don't need the backreference, you
+   * should group using the former pattern.
+   * <p>
+   * It will also introduce new pattern elements that you can't get to
+   * otherwise, for example if you have a large table of strings, i.e. the
+   * months of the year "(January|February|...)" optimize() will make a
+   * Hashtable that takes it to the next appropriate pattern element --
+   * eliminating the need for a linear search.
+   * 
+   * @see com.stevesoft.pat.Regex#optimized
+   * @see com.stevesoft.pat.Regex#ignoreCase
+   * @see com.stevesoft.pat.Regex#dontMatchInQuotes
+   * @see com.stevesoft.pat.Regex#matchAt
+   * @see com.stevesoft.pat.Regex#search
+   */
+  public void optimize()
+  {
+    if (optimized() || thePattern == null)
+    {
+      return;
+    }
+    minMatch = new patInt(0); // thePattern.countMinChars();
+    thePattern = RegOpt.opt(thePattern, ignoreCase, dontMatchInQuotes);
+    skipper = Skip.findSkip(this);
+    // RegOpt.setParents(this);
+    return;
+  }
+
+  Skip skipper;
+
+  /**
+   * This function returns true if the optimize method has been called.
+   */
+  public boolean optimized()
+  {
+    return minMatch != null;
+  }
+
+  /**
+   * A bit of syntactic surgar for those who want to make their code look more
+   * perl-like. To use this initialize your Regex object by saying:
+   * 
+   * <pre>
+   *       Regex r1 = Regex.perlCode(&quot;s/hello/goodbye/&quot;);
+   *       Regex r2 = Regex.perlCode(&quot;s'fish'frog'i&quot;);
+   *       Regex r3 = Regex.perlCode(&quot;m'hello');
+   * </pre>
+   * 
+   * The i for ignoreCase is supported in this syntax, as well as m, s, and x.
+   * The g flat is a bit of a special case.
+   * <p>
+   * If you wish to replace all occurences of a pattern, you do not put a 'g' in
+   * the perlCode, but call Regex's replaceAll method.
+   * <p>
+   * If you wish to simply and only do a search for r2's pattern, you can do
+   * this by calling the searchFrom method method repeatedly, or by calling
+   * search repeatedly if the g flag is set.
+   * <p>
+   * Note: Currently perlCode does <em>not</em> support the (?e=#) syntax for
+   * changing the escape character.
+   */
+
+  public static Regex perlCode(String s)
+  {
+    // this file is big enough, see parsePerl.java
+    // for this function.
+    return parsePerl.parse(s);
+  }
+
+  static final char back_slash = '\\';
+
+  /**
+   * Checks to see if there are only literal and no special pattern elements in
+   * this Regex.
+   */
+  public boolean isLiteral()
+  {
+    Pattern x = thePattern;
+    while (x != null)
+    {
+      if (x instanceof oneChar)
+      {
+        ;
+      }
+      else if (x instanceof Skipped)
+      {
+        ;
+      }
+      else
+      {
+        return false;
+      }
+      x = x.next;
+    }
+    return true;
+  }
+
+  /**
+   * You only need to know about this if you are inventing your own pattern
+   * elements.
+   */
+  public patInt countMinChars()
+  {
+    return thePattern.countMinChars();
+  }
+
+  /**
+   * You only need to know about this if you are inventing your own pattern
+   * elements.
+   */
+  public patInt countMaxChars()
+  {
+    return thePattern.countMaxChars();
+  }
+
+  boolean isHexDigit(StrPos sp)
+  {
+    boolean r = !sp.eos
+            && !sp.dontMatch
+            && ((sp.c >= '0' && sp.c <= '9')
+                    || (sp.c >= 'a' && sp.c <= 'f') || (sp.c >= 'A' && sp.c <= 'F'));
+    return r;
+  }
+
+  boolean isOctalDigit(StrPos sp, boolean first)
+  {
+    boolean r = !sp.eos && !(first ^ sp.dontMatch) && sp.c >= '0'
+            && sp.c <= '7';
+    return r;
+  }
+
+  int getHexDigit(StrPos sp)
+  {
+    if (sp.c >= '0' && sp.c <= '9')
+    {
+      return sp.c - '0';
+    }
+    if (sp.c >= 'a' && sp.c <= 'f')
+    {
+      return sp.c - 'a' + 10;
+    }
+    return sp.c - 'A' + 10;
+  }
+
+  boolean next2Hex(StrPos sp)
+  {
+    StrPos sp2 = new StrPos(sp);
+    sp2.inc();
+    if (!isHexDigit(sp2))
+    {
+      return false;
+    }
+    sp2.inc();
+    if (!isHexDigit(sp2))
+    {
+      return false;
+    }
+    return true;
+  }
+
+  boolean isOctalString(StrPos sp)
+  {
+    if (!isOctalDigit(sp, true))
+    {
+      return false;
+    }
+    StrPos sp2 = new StrPos(sp);
+    sp2.inc();
+    if (!isOctalDigit(sp2, false))
+    {
+      return false;
+    }
+    return true;
+  }
+}
diff --git a/src/com/stevesoft/pat/RegexReader.java b/src/com/stevesoft/pat/RegexReader.java
index 6475dfe..2e10f16 100755
--- a/src/com/stevesoft/pat/RegexReader.java
+++ b/src/com/stevesoft/pat/RegexReader.java
@@ -1,325 +1,309 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-import java.io.*;
-
-import com.stevesoft.pat.wrap.*;
-
-/** This class allows you to replace the text in strings
-    as you read them in.  Be careful what you do with
-    this freedom... using Regex.perlCode("s{.*}{x}s")
-    as your pattern will result in loading the entire
-    contents of the Reader into memory.
- */
-public class RegexReader
-    extends Reader
-{
-  RBuffer rb = new RBuffer(new StringBuffer());
-  PartialBuffer wrap = new PartialBuffer(rb.sb);
-  boolean moreToRead = true;
-  Reader r;
-  Replacer rp;
-
-  // the buffer size
-  int nmax = 2 * 1024;
-
-  public RegexReader(Regex rex, Reader r)
-  {
-    this.r = r;
-    rp = rex.getReplacer();
-  }
-
-  public RegexReader(Transformer tex, Reader r)
-  {
-    this.r = r;
-    rp = tex.getReplacer();
-  }
-
-  public void reset()
-      throws IOException
-  {
-    r.reset();
-    rb = new RBuffer(new StringBuffer());
-    wrap = new PartialBuffer(rb.sb);
-    moreToRead = true;
-  }
-
-  void readData()
-      throws IOException
-  {
-    int c;
-    int n = 0;
-    while ( (c = r.read()) != -1)
-    {
-      rb.sb.append( (char) c);
-      if (n++ > nmax)
-      {
-        break;
-      }
-    }
-    if (c == -1 && n == 0)
-    {
-      moreToRead = false;
-      wrap.allowOverRun = false;
-    }
-  }
-
-  void getMoreData()
-      throws IOException
-  {
-    while (rb.pos >= rb.epos)
-    {
-      wrap.overRun = false;
-      if (rb.next != null)
-      {
-        rb = rb.next;
-      }
-      else if (rb.done)
-      {
-        break;
-      }
-      else if (rb.epos >= rb.sb.length()
-               && rb.epos > nmax)
-      {
-        rb.pos = 1;
-        rb.epos = 1;
-        rb.sb.setLength(1);
-        readData();
-      }
-      else if (rb.epos >= rb.sb.length()
-               && moreToRead)
-      {
-        readData();
-      }
-      else if (rp.getRegex().matchAt(wrap, rb.epos))
-      {
-        if (wrap.overRun)
-        {
-          readData();
-        }
-        else
-        {
-          StringBufferWrap sbw = new StringBufferWrap();
-          StringBufferLike sbl = new StringBufferLike(sbw);
-          /*
-                 ReplaceRule rr = rex.getReplaceRule();
-              while(rr != null) {
-            rr.apply(sbl,rex);
-            rr = rr.next;
-              }
-           */
-          Regex rex = rp.getRegex();
-          int npos = rex.matchedTo();
-          rp.setBuffer(sbl);
-          rp.setSource(wrap);
-          rp.setPos(npos);
-          rp.apply(rex, rex.getReplaceRule());
-          int opos = rb.epos;
-          RBuffer rb2 = new RBuffer( (StringBuffer) sbw.unwrap());
-          rb2.epos = rb2.sb.length();
-          RBuffer rb3 = new RBuffer(rb.sb);
-
-          rb.next = rb2;
-          rb2.next = rb3;
-
-          if (npos == opos)
-          {
-            rb3.epos = npos + 1;
-            if (rb3.epos > rb3.sb.length())
-            {
-              if (rb.pos >= rb.epos)
-              {
-                rb = rb.next;
-              }
-              rb3.pos = rb3.epos = 0;
-              rb3.done = true;
-              //break;
-            }
-            rb3.pos = npos;
-          }
-          else
-          {
-            rb3.pos = rb3.epos = npos;
-          }
-
-        }
-      }
-      else
-      {
-        if (wrap.overRun)
-        {
-          readData();
-        }
-        else if (rb.epos < rb.sb.length())
-        {
-          rb.epos++;
-        }
-        else
-        {
-          break;
-        }
-      }
-    }
-  }
-
-  public int read()
-      throws IOException
-  {
-    if (rb.pos >= rb.epos)
-    {
-      getMoreData();
-      if (rb.pos >= rb.epos)
-      {
-        return -1;
-      }
-    }
-    //System.out.println(rb);
-    return rb.sb.charAt(rb.pos++);
-  }
-
-  public int read(char[] buf, int off, int len)
-      throws IOException
-  {
-    int c = -1;
-    int end = off + len;
-    for (int i = off; i < end; i++)
-    {
-      c = read();
-      if (c < 0)
-      {
-        if (i == off)
-        {
-          return -1;
-        }
-        return i - off;
-      }
-      buf[i] = (char) c;
-    }
-    return len;
-  }
-
-  public void close()
-      throws IOException
-  {
-    r.close();
-  }
-
-  public boolean markSupported()
-  {
-    return false;
-  }
-
-  /** Get the size of the working buffer.
-      The current buffer may be larger if
-      the pattern demands it. */
-  public int getBufferSize()
-  {
-    return nmax;
-  }
-
-  /** Set the size of the working buffer.
-      The current buffer may be larger if
-      the pattern demands it. */
-  public void setBufferSize(int n)
-  {
-    nmax = n;
-  }
-
-  int max_lines = 2;
-  /** This function no longer serves any purpose.
-      @deprecated
-   */
-  public int getMaxLines()
-  {
-    return max_lines;
-  }
-
-  /** This function no longer serves any purpose.
-      @deprecated
-   */
-  public void setMaxLines(int ml)
-  {
-    max_lines = ml;
-  }
-
-  char EOLchar = '\n';
-  /** This function no longer serves any purpose.
-      @deprecated
-   */
-  public char getEOLchar()
-  {
-    return EOLchar;
-  }
-
-  /** This function no longer serves any purpose.
-      @deprecated
-   */
-  public void setEOLchar(char c)
-  {
-    EOLchar = c;
-  }
-
-  public long skip(long d)
-      throws IOException
-  {
-    // This is probably inefficient, I just did it
-    // this way to avoid possible bugs.
-    long n = 0;
-    while (n < d && read() != -1)
-    {
-      n++;
-    }
-    return n;
-  }
-
-  /*
-     static void test(String re,String inp,int n) throws Exception {
-    Reader r = new StringReader(inp);
-    r = new BufferedReader(r);
-    Regex rex = Regex.perlCode(re);
-    String res1 = rex.replaceAll(inp);
-    int c = -1;
-    StringBuffer sb = new StringBuffer();
-    RegexReader rr = new RegexReader(rex,r);
-    rr.setBufferSize(n);
-    while( (c = rr.read()) != -1)
-      sb.append((char)c);
-    String res2 = sb.toString();
-    if(!res1.equals(res2)) {
-      System.out.println("nmax="+n);
-      System.out.println("re="+re);
-      System.out.println("inp="+inp);
-      System.out.println("res1="+res1);
-      System.out.println("res2="+res2);
-      System.exit(255);
-    }
-     }
-     public static void main(String[] args) throws Exception {
-    for(int n=6;n<15;n++) {
-      test("s/x/y/","-----x123456789",n);
-      test("s/x/y/","x123456789",n);
-      test("s/x/y/","-----x",n);
-      test("s/x.*?x/y/",".xx..x..x...x...x....x....x",n);
-      test("s/x.*x/[$&]/","--x........x--xx",n);
-      test("s/x.*x/[$&]/","--x........x------",n);
-      test("s/.$/a/m","bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbbbbbbbbbbbb",n);
-      test("s/.$/a/","123",n);
-      test("s/.$/a/","bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbb",n);
-      test("s/^./a/","bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbb",n);
-      test("s/$/a/","bbb",n);
-      test("s/^/a/","bbb",n);
-      test("s/^/a/","",n);
-      test("s{.*}{N}","xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx",n);
-      test("s/.{0,7}/y/","AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA",n);
-      test("s/x/$&/","xxx",n);
-    }
-    System.out.println("Success!!!");
-     }
-   */
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+import java.io.*;
+
+import com.stevesoft.pat.wrap.*;
+
+/**
+ * This class allows you to replace the text in strings as you read them in. Be
+ * careful what you do with this freedom... using Regex.perlCode("s{.*}{x}s") as
+ * your pattern will result in loading the entire contents of the Reader into
+ * memory.
+ */
+public class RegexReader extends Reader
+{
+  RBuffer rb = new RBuffer(new StringBuffer());
+
+  PartialBuffer wrap = new PartialBuffer(rb.sb);
+
+  boolean moreToRead = true;
+
+  Reader r;
+
+  Replacer rp;
+
+  // the buffer size
+  int nmax = 2 * 1024;
+
+  public RegexReader(Regex rex, Reader r)
+  {
+    this.r = r;
+    rp = rex.getReplacer();
+  }
+
+  public RegexReader(Transformer tex, Reader r)
+  {
+    this.r = r;
+    rp = tex.getReplacer();
+  }
+
+  public void reset() throws IOException
+  {
+    r.reset();
+    rb = new RBuffer(new StringBuffer());
+    wrap = new PartialBuffer(rb.sb);
+    moreToRead = true;
+  }
+
+  void readData() throws IOException
+  {
+    int c;
+    int n = 0;
+    while ((c = r.read()) != -1)
+    {
+      rb.sb.append((char) c);
+      if (n++ > nmax)
+      {
+        break;
+      }
+    }
+    if (c == -1 && n == 0)
+    {
+      moreToRead = false;
+      wrap.allowOverRun = false;
+    }
+  }
+
+  void getMoreData() throws IOException
+  {
+    while (rb.pos >= rb.epos)
+    {
+      wrap.overRun = false;
+      if (rb.next != null)
+      {
+        rb = rb.next;
+      }
+      else if (rb.done)
+      {
+        break;
+      }
+      else if (rb.epos >= rb.sb.length() && rb.epos > nmax)
+      {
+        rb.pos = 1;
+        rb.epos = 1;
+        rb.sb.setLength(1);
+        readData();
+      }
+      else if (rb.epos >= rb.sb.length() && moreToRead)
+      {
+        readData();
+      }
+      else if (rp.getRegex().matchAt(wrap, rb.epos))
+      {
+        if (wrap.overRun)
+        {
+          readData();
+        }
+        else
+        {
+          StringBufferWrap sbw = new StringBufferWrap();
+          StringBufferLike sbl = new StringBufferLike(sbw);
+          /*
+           * ReplaceRule rr = rex.getReplaceRule(); while(rr != null) {
+           * rr.apply(sbl,rex); rr = rr.next; }
+           */
+          Regex rex = rp.getRegex();
+          int npos = rex.matchedTo();
+          rp.setBuffer(sbl);
+          rp.setSource(wrap);
+          rp.setPos(npos);
+          rp.apply(rex, rex.getReplaceRule());
+          int opos = rb.epos;
+          RBuffer rb2 = new RBuffer((StringBuffer) sbw.unwrap());
+          rb2.epos = rb2.sb.length();
+          RBuffer rb3 = new RBuffer(rb.sb);
+
+          rb.next = rb2;
+          rb2.next = rb3;
+
+          if (npos == opos)
+          {
+            rb3.epos = npos + 1;
+            if (rb3.epos > rb3.sb.length())
+            {
+              if (rb.pos >= rb.epos)
+              {
+                rb = rb.next;
+              }
+              rb3.pos = rb3.epos = 0;
+              rb3.done = true;
+              // break;
+            }
+            rb3.pos = npos;
+          }
+          else
+          {
+            rb3.pos = rb3.epos = npos;
+          }
+
+        }
+      }
+      else
+      {
+        if (wrap.overRun)
+        {
+          readData();
+        }
+        else if (rb.epos < rb.sb.length())
+        {
+          rb.epos++;
+        }
+        else
+        {
+          break;
+        }
+      }
+    }
+  }
+
+  public int read() throws IOException
+  {
+    if (rb.pos >= rb.epos)
+    {
+      getMoreData();
+      if (rb.pos >= rb.epos)
+      {
+        return -1;
+      }
+    }
+    // System.out.println(rb);
+    return rb.sb.charAt(rb.pos++);
+  }
+
+  public int read(char[] buf, int off, int len) throws IOException
+  {
+    int c = -1;
+    int end = off + len;
+    for (int i = off; i < end; i++)
+    {
+      c = read();
+      if (c < 0)
+      {
+        if (i == off)
+        {
+          return -1;
+        }
+        return i - off;
+      }
+      buf[i] = (char) c;
+    }
+    return len;
+  }
+
+  public void close() throws IOException
+  {
+    r.close();
+  }
+
+  public boolean markSupported()
+  {
+    return false;
+  }
+
+  /**
+   * Get the size of the working buffer. The current buffer may be larger if the
+   * pattern demands it.
+   */
+  public int getBufferSize()
+  {
+    return nmax;
+  }
+
+  /**
+   * Set the size of the working buffer. The current buffer may be larger if the
+   * pattern demands it.
+   */
+  public void setBufferSize(int n)
+  {
+    nmax = n;
+  }
+
+  int max_lines = 2;
+
+  /**
+   * This function no longer serves any purpose.
+   * 
+   * @deprecated
+   */
+  public int getMaxLines()
+  {
+    return max_lines;
+  }
+
+  /**
+   * This function no longer serves any purpose.
+   * 
+   * @deprecated
+   */
+  public void setMaxLines(int ml)
+  {
+    max_lines = ml;
+  }
+
+  char EOLchar = '\n';
+
+  /**
+   * This function no longer serves any purpose.
+   * 
+   * @deprecated
+   */
+  public char getEOLchar()
+  {
+    return EOLchar;
+  }
+
+  /**
+   * This function no longer serves any purpose.
+   * 
+   * @deprecated
+   */
+  public void setEOLchar(char c)
+  {
+    EOLchar = c;
+  }
+
+  public long skip(long d) throws IOException
+  {
+    // This is probably inefficient, I just did it
+    // this way to avoid possible bugs.
+    long n = 0;
+    while (n < d && read() != -1)
+    {
+      n++;
+    }
+    return n;
+  }
+
+  /*
+   * static void test(String re,String inp,int n) throws Exception { Reader r =
+   * new StringReader(inp); r = new BufferedReader(r); Regex rex =
+   * Regex.perlCode(re); String res1 = rex.replaceAll(inp); int c = -1;
+   * StringBuffer sb = new StringBuffer(); RegexReader rr = new
+   * RegexReader(rex,r); rr.setBufferSize(n); while( (c = rr.read()) != -1)
+   * sb.append((char)c); String res2 = sb.toString(); if(!res1.equals(res2)) {
+   * System.out.println("nmax="+n); System.out.println("re="+re);
+   * System.out.println("inp="+inp); System.out.println("res1="+res1);
+   * System.out.println("res2="+res2); System.exit(255); } } public static void
+   * main(String[] args) throws Exception { for(int n=6;n<15;n++) {
+   * test("s/x/y/","-----x123456789",n); test("s/x/y/","x123456789",n);
+   * test("s/x/y/","-----x",n);
+   * test("s/x.*?x/y/",".xx..x..x...x...x....x....x",n);
+   * test("s/x.*x/[$&]/","--x........x--xx",n);
+   * test("s/x.*x/[$&]/","--x........x------",n);
+   * test("s/.$/a/m","bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbbbbbbbbbbbb",n);
+   * test("s/.$/a/","123",n);
+   * test("s/.$/a/","bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbb",n);
+   * test("s/^./a/","bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbb",n);
+   * test("s/$/a/","bbb",n); test("s/^/a/","bbb",n); test("s/^/a/","",n);
+   * test("s{.*}{N}","xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx",n);
+   * test("s/.{0,7}/y/","AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA",n);
+   * test("s/x/$&/","xxx",n); } System.out.println("Success!!!"); }
+   */
+}
diff --git a/src/com/stevesoft/pat/RegexTokenizer.java b/src/com/stevesoft/pat/RegexTokenizer.java
index 76fa005..0378f3a 100755
--- a/src/com/stevesoft/pat/RegexTokenizer.java
+++ b/src/com/stevesoft/pat/RegexTokenizer.java
@@ -1,161 +1,171 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-import java.util.*;
-
-/**
-        Shareware: package pat
-   <a href="copyright.html">Copyright 2001, Steven R. Brandt</a>
- */
-/**
- The RegexTokenizer is similar to the StringTokenizer class
- provided with java, but allows one to tokenize using
- regular expressions, rather than a simple list of characters.
- Tokens are any strings between the supplied regular expression,
- as well as any backreferences (things in parenthesis)
- contained within the regular expression. */
-public class RegexTokenizer
-    implements Enumeration
-{
-  String toParse;
-  Regex r;
-  int count = 0;
-  Vector v = new Vector();
-  Vector vi = new Vector();
-  int pos = 0;
-
-  int offset = 1;
-  void getMore()
-  {
-    String s = r.right();
-    if (r.searchFrom(toParse, pos))
-    {
-      v.addElement(r.left().substring(pos));
-      vi.addElement(new Integer(r.matchFrom() +
-                                r.charsMatched()));
-      for (int i = 0; i < r.numSubs(); i++)
-      {
-        if (r.substring() != null)
-        {
-          v.addElement(r.substring(i + offset));
-          vi.addElement(
-              new Integer(r.matchFrom(i + offset) +
-                          r.charsMatched(i + offset)));
-        }
-      }
-      pos = r.matchFrom() + r.charsMatched();
-    }
-    else if (s != null)
-    {
-      v.addElement(s);
-    }
-  }
-
-  /** Initialize the tokenizer with a string of text and a pattern */
-  public RegexTokenizer(String txt, String ptrn)
-  {
-    toParse = txt;
-    r = new Regex(ptrn);
-    offset = Regex.BackRefOffset;
-    getMore();
-  }
-
-  /** Initialize the tokenizer with a Regex object. */
-  public RegexTokenizer(String txt, Regex r)
-  {
-    toParse = txt;
-    this.r = r;
-    offset = Regex.BackRefOffset;
-    getMore();
-  }
-
-  /** This should always be cast to a String, as in StringTokenizer,
-       and as in StringTokenizer one can do this by calling
-       nextString(). */
-  public Object nextElement()
-  {
-    if (count >= v.size())
-    {
-      getMore();
-    }
-    return v.elementAt(count++);
-  }
-
-  /** This is the equivalent (String)nextElement(). */
-  public String nextToken()
-  {
-    return (String) nextElement();
-  }
-
-  /** This asks for the next token, and changes the pattern
-       being used at the same time. */
-  public String nextToken(String newpat)
-  {
-    try
-    {
-      r.compile(newpat);
-    }
-    catch (RegSyntax r_)
-    {}
-    return nextToken(r);
-  }
-
-  /** This asks for the next token, and changes the pattern
-       being used at the same time. */
-  public String nextToken(Regex nr)
-  {
-    r = nr;
-    if (vi.size() > count)
-    {
-      pos = ( (Integer) vi.elementAt(count)).intValue();
-      v.setSize(count);
-      vi.setSize(count);
-    }
-    getMore();
-    return nextToken();
-  }
-
-  /** Tells whether there are more tokens in the pattern. */
-  public boolean hasMoreElements()
-  {
-    if (count >= v.size())
-    {
-      getMore();
-    }
-    return count < v.size();
-  }
-
-  /** Tells whether there are more tokens in the pattern, but
-       in the fashion of StringTokenizer. */
-  public boolean hasMoreTokens()
-  {
-    return hasMoreElements();
-  }
-
-  /** Determines the # of remaining tokens */
-  public int countTokens()
-  {
-    int _count = count;
-    while (hasMoreTokens())
-    {
-      nextToken();
-    }
-    count = _count;
-    return v.size() - count;
-  }
-
-  /** Returns all tokens in the String */
-  public String[] allTokens()
-  {
-    countTokens();
-    String[] ret = new String[v.size()];
-    v.copyInto(ret);
-    return ret;
-  }
-};
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+import java.util.*;
+
+/**
+ Shareware: package pat
+ <a href="copyright.html">Copyright 2001, Steven R. Brandt</a>
+ */
+/**
+ * The RegexTokenizer is similar to the StringTokenizer class provided with
+ * java, but allows one to tokenize using regular expressions, rather than a
+ * simple list of characters. Tokens are any strings between the supplied
+ * regular expression, as well as any backreferences (things in parenthesis)
+ * contained within the regular expression.
+ */
+public class RegexTokenizer implements Enumeration
+{
+  String toParse;
+
+  Regex r;
+
+  int count = 0;
+
+  Vector v = new Vector();
+
+  Vector vi = new Vector();
+
+  int pos = 0;
+
+  int offset = 1;
+
+  void getMore()
+  {
+    String s = r.right();
+    if (r.searchFrom(toParse, pos))
+    {
+      v.addElement(r.left().substring(pos));
+      vi.addElement(new Integer(r.matchFrom() + r.charsMatched()));
+      for (int i = 0; i < r.numSubs(); i++)
+      {
+        if (r.substring() != null)
+        {
+          v.addElement(r.substring(i + offset));
+          vi.addElement(new Integer(r.matchFrom(i + offset)
+                  + r.charsMatched(i + offset)));
+        }
+      }
+      pos = r.matchFrom() + r.charsMatched();
+    }
+    else if (s != null)
+    {
+      v.addElement(s);
+    }
+  }
+
+  /** Initialize the tokenizer with a string of text and a pattern */
+  public RegexTokenizer(String txt, String ptrn)
+  {
+    toParse = txt;
+    r = new Regex(ptrn);
+    offset = Regex.BackRefOffset;
+    getMore();
+  }
+
+  /** Initialize the tokenizer with a Regex object. */
+  public RegexTokenizer(String txt, Regex r)
+  {
+    toParse = txt;
+    this.r = r;
+    offset = Regex.BackRefOffset;
+    getMore();
+  }
+
+  /**
+   * This should always be cast to a String, as in StringTokenizer, and as in
+   * StringTokenizer one can do this by calling nextString().
+   */
+  public Object nextElement()
+  {
+    if (count >= v.size())
+    {
+      getMore();
+    }
+    return v.elementAt(count++);
+  }
+
+  /** This is the equivalent (String)nextElement(). */
+  public String nextToken()
+  {
+    return (String) nextElement();
+  }
+
+  /**
+   * This asks for the next token, and changes the pattern being used at the
+   * same time.
+   */
+  public String nextToken(String newpat)
+  {
+    try
+    {
+      r.compile(newpat);
+    } catch (RegSyntax r_)
+    {
+    }
+    return nextToken(r);
+  }
+
+  /**
+   * This asks for the next token, and changes the pattern being used at the
+   * same time.
+   */
+  public String nextToken(Regex nr)
+  {
+    r = nr;
+    if (vi.size() > count)
+    {
+      pos = ((Integer) vi.elementAt(count)).intValue();
+      v.setSize(count);
+      vi.setSize(count);
+    }
+    getMore();
+    return nextToken();
+  }
+
+  /** Tells whether there are more tokens in the pattern. */
+  public boolean hasMoreElements()
+  {
+    if (count >= v.size())
+    {
+      getMore();
+    }
+    return count < v.size();
+  }
+
+  /**
+   * Tells whether there are more tokens in the pattern, but in the fashion of
+   * StringTokenizer.
+   */
+  public boolean hasMoreTokens()
+  {
+    return hasMoreElements();
+  }
+
+  /** Determines the # of remaining tokens */
+  public int countTokens()
+  {
+    int _count = count;
+    while (hasMoreTokens())
+    {
+      nextToken();
+    }
+    count = _count;
+    return v.size() - count;
+  }
+
+  /** Returns all tokens in the String */
+  public String[] allTokens()
+  {
+    countTokens();
+    String[] ret = new String[v.size()];
+    v.copyInto(ret);
+    return ret;
+  }
+};
diff --git a/src/com/stevesoft/pat/RegexWriter.java b/src/com/stevesoft/pat/RegexWriter.java
index bcfbd5b..a8c3e50 100755
--- a/src/com/stevesoft/pat/RegexWriter.java
+++ b/src/com/stevesoft/pat/RegexWriter.java
@@ -1,267 +1,276 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-import java.io.*;
-
-import com.stevesoft.pat.wrap.*;
-
-/** A basic extension of FilterWriter that uses Transformer
- to make replacements in data as it is written out.  It attempts
- to transform a string whenever the End-of-Line (EOL) character
- is written (which is, by default, the carriage return '\n').
- Only the transformed portion of the line is written out, allowing
- the RegexWriter to wait until a complete pattern is present before
- attempting to write out info.  Until a pattern completes, data is
- stored in a StringBuffer -- which can be accessed through the
- length() and charAt() methods of this class.
- <p>
- Note a subtlety here -- while a Transformer normally matches
- at higher priority against the pattern added to it first, this
- will not necessarily be true when a multi-line match is in progress
- because one of the complete multi-line patterns may not be completely
- loaded in RegexWriter's buffer.  For this reason, the Transformer
- class is equipped with a way to add a pattern and replacement rule
- in three pieces -- a beginning (once this matches, nothing else in
- the Transformer can match until the whole pattern matches), an
- ending (the whole pattern is a String formed by adding the beginning
- and ending), and a ReplaceRule.
- <p>
- An illustration of this is given in the this
- <a href="../test/trans.java">example.</a>
- */
-public class RegexWriter
-    extends Writer
-{
-  Replacer repr;
-  Writer w;
-  WriterWrap ww;
-  StringBuffer sb = new StringBuffer();
-  PartialBuffer wrap = new PartialBuffer(sb);
-  int pos, epos;
-  int interval = 128;
-  int bufferSize = 2 * 1024;
-
-  public RegexWriter(Transformer t, Writer w)
-  {
-    this.w = w;
-    ww = new WriterWrap(w);
-    repr = t.getReplacer();
-    repr.setBuffer(new StringBufferLike(ww));
-    repr.setSource(wrap);
-  }
-
-  public RegexWriter(Regex r, Writer w)
-  {
-    this.w = w;
-    ww = new WriterWrap(w);
-    repr = r.getReplacer();
-    repr.setBuffer(new StringBufferLike(ww));
-    repr.setSource(wrap);
-  }
-
-  char EOLchar = '\n';
-  /** This method no longer serves any purpose.
-      @deprecated
-   */
-  public char getEOLchar()
-  {
-    return EOLchar;
-  }
-
-  /** This method no longer serves any purpose.
-   @deprecated
-   */
-  public void setEOLchar(char c)
-  {
-    EOLchar = c;
-  }
-
-  int max_lines = 2;
-  /** This method no longer serves any purpose.
-   @deprecated
-   */
-  public int getMaxLines()
-  {
-    return max_lines;
-  }
-
-  /** This method no longer serves any purpose.
-   @deprecated
-   */
-  public void setMaxLines(int ml)
-  {
-    max_lines = ml;
-  }
-
-  void write()
-      throws IOException
-  {
-    Regex rex = repr.getRegex();
-    int eposOld = epos;
-    if (rex.matchAt(wrap, epos) && !wrap.overRun)
-    {
-      while (pos < epos)
-      {
-        w.write(sb.charAt(pos++));
-      }
-      int to = rex.matchedTo();
-      repr.setPos(to);
-      repr.apply(rex, rex.getReplaceRule());
-      epos = pos = to;
-      if (epos == eposOld && epos < sb.length())
-      {
-        epos++;
-      }
-    }
-    else if (!wrap.overRun && epos < sb.length())
-    {
-      epos++;
-    }
-    while (pos < epos)
-    {
-      w.write(sb.charAt(pos++));
-    }
-    if (epos == sb.length())
-    {
-      sb.setLength(1);
-      pos = epos = 1;
-    }
-    else if (pos > bufferSize)
-    {
-      for (int i = bufferSize; i < sb.length(); i++)
-      {
-        sb.setCharAt(i - bufferSize, sb.charAt(i));
-      }
-      pos -= bufferSize;
-      epos -= bufferSize;
-      sb.setLength(sb.length() - bufferSize);
-    }
-  }
-
-  public void write(char[] ca, int b, int n)
-      throws IOException
-  {
-    int m = b + n;
-    for (int i = b; i < m; i++)
-    {
-      sb.append(ca[i]);
-      if (sb.length() % interval == interval - 1)
-      {
-        wrap.overRun = false;
-        while (epos + interval < sb.length() && !wrap.overRun)
-        {
-          write();
-        }
-      }
-    }
-  }
-
-  public void flush()
-      throws IOException
-  {
-  }
-
-  public void close()
-      throws IOException
-  {
-    wrap.allowOverRun = false;
-    wrap.overRun = false;
-    while (epos < sb.length())
-    {
-      write();
-    }
-    write();
-    w.close();
-  }
-
-  /** The current size of the StringBuffer in use by RegexWriter. */
-  public int length()
-  {
-    return sb.length();
-  }
-
-  /** The character at location i in the StringBuffer. */
-  public char charAt(int i)
-  {
-    return sb.charAt(i);
-  }
-
-  /** Set the interval at which regex patterns are checked. */
-  public void setInterval(int i)
-  {
-    interval = i;
-  }
-
-  /** Get the interval at which regex matches are checked. */
-  public int getInterval()
-  {
-    return interval;
-  }
-
-  /** Get the buffer size. */
-  public int getBufferSize()
-  {
-    return bufferSize;
-  }
-
-  /** Set the buffer size. */
-  public void setBufferSize(int i)
-  {
-    bufferSize = i;
-  }
-
-  static void test(String re, String inp, int n)
-      throws Exception
-  {
-    StringWriter sw = new StringWriter();
-    Regex rex = Regex.perlCode(re);
-    String res1 = rex.replaceAll(inp);
-    RegexWriter rw = new RegexWriter(rex, sw);
-    for (int i = 0; i < inp.length(); i++)
-    {
-      rw.write(inp.charAt(i));
-    }
-    rw.close();
-    String res2 = sw.toString();
-    if (!res1.equals(res2))
-    {
-      System.out.println("nmax=" + n);
-      System.out.println("re=" + re);
-      System.out.println("inp=" + inp);
-      System.out.println("res1=" + res1);
-      System.out.println("res2=" + res2);
-      System.exit(255);
-    }
-  }
-
-  public static void main(String[] args)
-      throws Exception
-  {
-    for (int n = 1; n <= 1; n++)
-    {
-      test("s/x/y/", "-----x123456789", n);
-      test("s/x/y/", "x123456789", n);
-      test("s/x/y/", "-----x", n);
-      test("s/x.*?x/y/", ".xx..x..x...x...x....x....x", n);
-      test("s/x.*x/[$&]/", "--x........x--xx", n);
-      test("s/x.*x/[$&]/", "--x........x------", n);
-      test("s/.$/a/m", "bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbbbbbbbbbbbb", n);
-      test("s/.$/a/", "123", n);
-      test("s/.$/a/", "bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbb", n);
-      test("s/^./a/", "bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbb", n);
-      test("s/$/a/", "bbb", n);
-      test("s/^/a/", "bbb", n);
-      test("s/^/a/", "", n);
-      test("s{.*}{N}", "xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx", n);
-      test("s/.{0,7}/y/", "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", n);
-      test("s/x/$&/", "xxx", n);
-    }
-    System.out.println("Success!!!");
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+import java.io.*;
+
+import com.stevesoft.pat.wrap.*;
+
+/**
+ * A basic extension of FilterWriter that uses Transformer to make replacements
+ * in data as it is written out. It attempts to transform a string whenever the
+ * End-of-Line (EOL) character is written (which is, by default, the carriage
+ * return '\n'). Only the transformed portion of the line is written out,
+ * allowing the RegexWriter to wait until a complete pattern is present before
+ * attempting to write out info. Until a pattern completes, data is stored in a
+ * StringBuffer -- which can be accessed through the length() and charAt()
+ * methods of this class.
+ * <p>
+ * Note a subtlety here -- while a Transformer normally matches at higher
+ * priority against the pattern added to it first, this will not necessarily be
+ * true when a multi-line match is in progress because one of the complete
+ * multi-line patterns may not be completely loaded in RegexWriter's buffer. For
+ * this reason, the Transformer class is equipped with a way to add a pattern
+ * and replacement rule in three pieces -- a beginning (once this matches,
+ * nothing else in the Transformer can match until the whole pattern matches),
+ * an ending (the whole pattern is a String formed by adding the beginning and
+ * ending), and a ReplaceRule.
+ * <p>
+ * An illustration of this is given in the this <a
+ * href="../test/trans.java">example.</a>
+ */
+public class RegexWriter extends Writer
+{
+  Replacer repr;
+
+  Writer w;
+
+  WriterWrap ww;
+
+  StringBuffer sb = new StringBuffer();
+
+  PartialBuffer wrap = new PartialBuffer(sb);
+
+  int pos, epos;
+
+  int interval = 128;
+
+  int bufferSize = 2 * 1024;
+
+  public RegexWriter(Transformer t, Writer w)
+  {
+    this.w = w;
+    ww = new WriterWrap(w);
+    repr = t.getReplacer();
+    repr.setBuffer(new StringBufferLike(ww));
+    repr.setSource(wrap);
+  }
+
+  public RegexWriter(Regex r, Writer w)
+  {
+    this.w = w;
+    ww = new WriterWrap(w);
+    repr = r.getReplacer();
+    repr.setBuffer(new StringBufferLike(ww));
+    repr.setSource(wrap);
+  }
+
+  char EOLchar = '\n';
+
+  /**
+   * This method no longer serves any purpose.
+   * 
+   * @deprecated
+   */
+  public char getEOLchar()
+  {
+    return EOLchar;
+  }
+
+  /**
+   * This method no longer serves any purpose.
+   * 
+   * @deprecated
+   */
+  public void setEOLchar(char c)
+  {
+    EOLchar = c;
+  }
+
+  int max_lines = 2;
+
+  /**
+   * This method no longer serves any purpose.
+   * 
+   * @deprecated
+   */
+  public int getMaxLines()
+  {
+    return max_lines;
+  }
+
+  /**
+   * This method no longer serves any purpose.
+   * 
+   * @deprecated
+   */
+  public void setMaxLines(int ml)
+  {
+    max_lines = ml;
+  }
+
+  void write() throws IOException
+  {
+    Regex rex = repr.getRegex();
+    int eposOld = epos;
+    if (rex.matchAt(wrap, epos) && !wrap.overRun)
+    {
+      while (pos < epos)
+      {
+        w.write(sb.charAt(pos++));
+      }
+      int to = rex.matchedTo();
+      repr.setPos(to);
+      repr.apply(rex, rex.getReplaceRule());
+      epos = pos = to;
+      if (epos == eposOld && epos < sb.length())
+      {
+        epos++;
+      }
+    }
+    else if (!wrap.overRun && epos < sb.length())
+    {
+      epos++;
+    }
+    while (pos < epos)
+    {
+      w.write(sb.charAt(pos++));
+    }
+    if (epos == sb.length())
+    {
+      sb.setLength(1);
+      pos = epos = 1;
+    }
+    else if (pos > bufferSize)
+    {
+      for (int i = bufferSize; i < sb.length(); i++)
+      {
+        sb.setCharAt(i - bufferSize, sb.charAt(i));
+      }
+      pos -= bufferSize;
+      epos -= bufferSize;
+      sb.setLength(sb.length() - bufferSize);
+    }
+  }
+
+  public void write(char[] ca, int b, int n) throws IOException
+  {
+    int m = b + n;
+    for (int i = b; i < m; i++)
+    {
+      sb.append(ca[i]);
+      if (sb.length() % interval == interval - 1)
+      {
+        wrap.overRun = false;
+        while (epos + interval < sb.length() && !wrap.overRun)
+        {
+          write();
+        }
+      }
+    }
+  }
+
+  public void flush() throws IOException
+  {
+  }
+
+  public void close() throws IOException
+  {
+    wrap.allowOverRun = false;
+    wrap.overRun = false;
+    while (epos < sb.length())
+    {
+      write();
+    }
+    write();
+    w.close();
+  }
+
+  /** The current size of the StringBuffer in use by RegexWriter. */
+  public int length()
+  {
+    return sb.length();
+  }
+
+  /** The character at location i in the StringBuffer. */
+  public char charAt(int i)
+  {
+    return sb.charAt(i);
+  }
+
+  /** Set the interval at which regex patterns are checked. */
+  public void setInterval(int i)
+  {
+    interval = i;
+  }
+
+  /** Get the interval at which regex matches are checked. */
+  public int getInterval()
+  {
+    return interval;
+  }
+
+  /** Get the buffer size. */
+  public int getBufferSize()
+  {
+    return bufferSize;
+  }
+
+  /** Set the buffer size. */
+  public void setBufferSize(int i)
+  {
+    bufferSize = i;
+  }
+
+  static void test(String re, String inp, int n) throws Exception
+  {
+    StringWriter sw = new StringWriter();
+    Regex rex = Regex.perlCode(re);
+    String res1 = rex.replaceAll(inp);
+    RegexWriter rw = new RegexWriter(rex, sw);
+    for (int i = 0; i < inp.length(); i++)
+    {
+      rw.write(inp.charAt(i));
+    }
+    rw.close();
+    String res2 = sw.toString();
+    if (!res1.equals(res2))
+    {
+      System.out.println("nmax=" + n);
+      System.out.println("re=" + re);
+      System.out.println("inp=" + inp);
+      System.out.println("res1=" + res1);
+      System.out.println("res2=" + res2);
+      System.exit(255);
+    }
+  }
+
+  public static void main(String[] args) throws Exception
+  {
+    for (int n = 1; n <= 1; n++)
+    {
+      test("s/x/y/", "-----x123456789", n);
+      test("s/x/y/", "x123456789", n);
+      test("s/x/y/", "-----x", n);
+      test("s/x.*?x/y/", ".xx..x..x...x...x....x....x", n);
+      test("s/x.*x/[$&]/", "--x........x--xx", n);
+      test("s/x.*x/[$&]/", "--x........x------", n);
+      test("s/.$/a/m", "bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbbbbbbbbbbbb", n);
+      test("s/.$/a/", "123", n);
+      test("s/.$/a/", "bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbb", n);
+      test("s/^./a/", "bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbb", n);
+      test("s/$/a/", "bbb", n);
+      test("s/^/a/", "bbb", n);
+      test("s/^/a/", "", n);
+      test("s{.*}{N}", "xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx", n);
+      test("s/.{0,7}/y/", "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", n);
+      test("s/x/$&/", "xxx", n);
+    }
+    System.out.println("Success!!!");
+  }
+}
diff --git a/src/com/stevesoft/pat/ReplaceRule.java b/src/com/stevesoft/pat/ReplaceRule.java
index d4f09bb..bf56143 100755
--- a/src/com/stevesoft/pat/ReplaceRule.java
+++ b/src/com/stevesoft/pat/ReplaceRule.java
@@ -1,398 +1,400 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-import java.util.*;
-
-/** ReplaceRule is a singly linked list of Objects which describe how
-    to replace the matched portion of a String.  The only member method
-    that you absolutely need to define to use this class is apply(StringBuffer,RegRes) --
-    although you may want define toString1() and clone1() (if you are
-    unhappy with the default methods) that are needed by
-    the clone() or toString() methods on this class.
-    During the replacement process, each ReplaceRule tells the replacer
-    what to add to StringBuffer and uses the contents of the Regular
-    expression result to get the information it needs to
-    do this.  Here is an <a href="http://javaregex.com/code/fancy.java.html">example</a>
-
-    @see com.stevesoft.pat.NullRule
-    @see com.stevesoft.pat.AmpersandRule
-    @see com.stevesoft.pat.BackRefRule
-    @see com.stevesoft.pat.LeftRule
-    @see com.stevesoft.pat.RightRule
-    @see com.stevesoft.pat.StringRule
- */
-public abstract class ReplaceRule
-{
-  /** points to the next ReplaceRule in the linked list. */
-  protected ReplaceRule next = null;
-  /** This function appends to the StringBufferLike the text you want
-      to replaced the portion of the String last matched. */
-  public abstract void apply(StringBufferLike sb, RegRes r);
-
-  /** A rule describing how to clone only the current ReplaceRule,
-      and none of the others in this linked list.  It is called by
-      clone() for each item in the list. */
-  public Object clone1()
-  {
-    return new RuleHolder(this);
-  }
-
-  public final Object clone()
-  {
-    ReplaceRule x = (ReplaceRule) clone1();
-    ReplaceRule xsav = x;
-    ReplaceRule y = this;
-    while (y.next != null)
-    {
-      x.next = (ReplaceRule) y.next.clone1();
-      x.name = y.name;
-      x = x.next;
-      y = y.next;
-    }
-    return xsav;
-  }
-
-  static ReplaceRule add(ReplaceRule head, ReplaceRule adding)
-  {
-    if (head == null)
-    {
-      return head = adding;
-    }
-    head.addRule(adding);
-    return head;
-  }
-
-  public ReplaceRule add(ReplaceRule adding)
-  {
-    return add(this, adding);
-  }
-
-  /** Add another ReplaceRule to the linked list. */
-  public void addRule(ReplaceRule r)
-  {
-    if (next == null)
-    {
-      next = r;
-    }
-    else
-    {
-      next.addRule(r);
-    }
-  }
-
-  static Regex getvar = null;
-  final static Regex getv()
-  {
-    // Thanks to Michael Jimenez for pointing out the need
-    // to clone getvar rather than simply returning it.
-    // Previously this was not thread safe.
-    //if(getvar != null) return getvar;
-    if (getvar != null)
-    {
-      return (Regex) getvar.clone();
-    }
-    getvar =
-        new Regex(
-            "(?:\\\\(\\d+)|" + // ref 1
-            "\\$(?:" +
-            "(\\d+)|" + // ref 2
-            "(\\w+)|" + // ref 3
-            "([&'`])|" + // ref 4
-            "\\{(?:(\\d+)|" + // ref 5
-            "([^\n}\\\\]+))}" + // ref 6
-            ")|" +
-            "\\\\([nrbtaef])|" + // ref 7
-            "\\\\c([\u0000-\uFFFF])|" + // ref 8
-            "\\\\x([A-Fa-f0-9]{2})|" + // ref 9
-            "\\\\([\u0000-\uFFFF])" + // ref 10
-            ")");
-    getvar.optimize();
-    return getvar;
-  }
-
-  /** Compile a ReplaceRule using the text that would go between
-      the second and third /'s in a typical substitution pattern
-      in Perl: s/ ... / <i>The argument to ReplaceRule.perlCode</i> /.
-   */
-  public static ReplaceRule perlCode(String s)
-  {
-    //String sav_backGs = Regex.backGs;
-    //int sav_backGto = Regex.backGto;
-    try
-    {
-      int mf = 0, mt = 0;
-      Regex gv = getv();
-      ReplaceRule head = null;
-      Object tmp = null;
-      while (gv.searchFrom(s, mt))
-      {
-        int off = Regex.BackRefOffset - 1;
-        mf = gv.matchedFrom();
-        if (mf > mt)
-        {
-          head = add(head,
-                     new StringRule(s.substring(mt, mf)));
-        }
-        String var = null;
-        if ( (var = gv.stringMatched(1 + off)) != null
-            || (var = gv.stringMatched(2 + off)) != null
-            || (var = gv.stringMatched(5 + off)) != null)
-        {
-          int d = 0;
-          for (int i = 0; i < var.length(); i++)
-          {
-            d = 8 * d + (var.charAt(i) - '0');
-          }
-          if (var.length() == 1)
-          {
-            head = add(head, new BackRefRule(d));
-          }
-          else
-          {
-            head = new StringRule("" + (char) d);
-          }
-        }
-        else if (
-            (var = gv.stringMatched(10 + off)) != null)
-        {
-          if ("QELlUu".indexOf(var) >= 0)
-          {
-            head = add(head, new CodeRule(var.charAt(0)));
-          }
-          else
-          {
-            head = add(head, new StringRule(var));
-          }
-        }
-        else if (
-            (var = gv.stringMatched(3 + off)) != null
-            || (var = gv.stringMatched(4 + off)) != null
-            || (var = gv.stringMatched(6 + off)) != null)
-        {
-          String arg = "";
-          int pc;
-          if ( (pc = var.indexOf(':')) > 0)
-          {
-            arg = var.substring(pc + 1);
-            var = var.substring(0, pc);
-          }
-          if (var.equals("&") || var.equals("MATCH"))
-          {
-            head = add(head, new AmpersandRule());
-          }
-          else if (var.equals("`") || var.equals("PREMATCH"))
-          {
-            head = add(head, new LeftRule());
-          }
-          else if (var.equals("'") || var.equals("POSTMATCH"))
-          {
-            head = add(head, new RightRule());
-          }
-          else if (var.equals("WANT_MORE_TEXT"))
-          {
-            head = add(head, new WantMoreTextReplaceRule());
-          }
-          else if (var.equals("POP"))
-          {
-            head = add(head, new PopRule());
-          }
-          else if (var.startsWith("+") && (tmp = defs.get(var.substring(1))) != null)
-          {
-            if (tmp instanceof Regex)
-            {
-              head = add(head, new PushRule(var.substring(1), (Regex) tmp));
-            }
-            else if (tmp instanceof Transformer)
-            {
-              head = add(head, new PushRule(var.substring(1), (Transformer) tmp));
-            }
-            else
-            {
-              head = add(head, new StringRule("${" + var + "}"));
-            }
-          }
-          else if (var.startsWith("=") && (tmp = defs.get(var.substring(1))) != null)
-          {
-            if (tmp instanceof Regex)
-            {
-              head = add(head, new ChangeRule(var.substring(1), (Regex) tmp));
-            }
-            else if (tmp instanceof Transformer)
-            {
-              head = add(head,
-                         new ChangeRule(var.substring(1), (Transformer) tmp));
-            }
-            else
-            {
-              head = add(head, new StringRule("${" + var + "}"));
-            }
-          }
-          else if ( (tmp = defs.get(var)) != null)
-          {
-            if (tmp instanceof ReplaceRule)
-            {
-              ReplaceRule alt = ( (ReplaceRule) tmp).arg(arg);
-              if (alt == null)
-              {
-                alt = ( (ReplaceRule) tmp);
-              }
-              head = add(head, (ReplaceRule) (alt.clone()));
-            }
-          }
-          else // can't figure out how to transform this thing...
-          {
-            head = add(head, new StringRule("${" + var + "}"));
-          }
-        }
-        else if (
-            (var = gv.stringMatched(7 + off)) != null)
-        {
-          char c = var.charAt(0);
-          if (c == 'n')
-          {
-            head = add(head, new StringRule("\n"));
-          }
-          else if (c == 't')
-          {
-            head = add(head, new StringRule("\t"));
-          }
-          else if (c == 'r')
-          {
-            head = add(head, new StringRule("\r"));
-          }
-          else if (c == 'b')
-          {
-            head = add(head, new StringRule("\r"));
-          }
-          else if (c == 'a')
-          {
-            head = add(head, new StringRule("" + (char) 7));
-          }
-          else if (c == 'e')
-          {
-            head = add(head, new StringRule("" + (char) 27));
-          }
-          else if (c == 'f')
-          {
-            head = add(head, new StringRule("" + (char) 12));
-          }
-        }
-        else if (
-            (var = gv.stringMatched(8 + off)) != null)
-        {
-          char c = var.charAt(0);
-          if (c < Ctrl.cmap.length)
-          {
-            c = Ctrl.cmap[c];
-          }
-          head = add(head, new StringRule("" + c));
-        }
-        else if (
-            (var = gv.stringMatched(9 + off)) != null)
-        {
-          int d =
-              16 * getHexDigit(var.charAt(0)) +
-              getHexDigit(var.charAt(1));
-          head = add(head, new StringRule("" + (char) d));
-        }
-        mt = gv.matchedTo();
-      }
-      if (mt <= s.length())
-      {
-        head = add(head, new StringRule(s.substring(mt)));
-      }
-      return head;
-    }
-    finally
-    {
-      //Regex.backGs = sav_backGs;
-      //Regex.backGto = sav_backGto;
-    }
-  }
-
-  static Hashtable defs = new Hashtable();
-  public static boolean isDefined(String s)
-  {
-    return defs.get(s) != null;
-  }
-
-  public static void define(String s, Regex r)
-  {
-    defs.put(s, r);
-  }
-
-  public static void define(String s, ReplaceRule r)
-  {
-    defs.put(s, r);
-    r.name = s;
-  }
-
-  String name = getClass().getName();
-
-  public static void define(String s, Transformer t)
-  {
-    defs.put(s, t);
-  }
-
-  public static void undefine(String s)
-  {
-    defs.remove(s);
-  }
-
-  /** This tells how to convert just the current element (and none
-      of the other items in the linked list) to a String. This
-      method is called by toString() for each item in the linked
-      list. */
-  public String toString1()
-  {
-    return "${" + name + "}";
-  }
-
-  /** Convert to a String. */
-  public final String toString()
-  {
-    StringBuffer sb = new StringBuffer();
-    sb.append(toString1());
-    ReplaceRule rr = this.next;
-    while (rr != null)
-    {
-      sb.append(rr.toString1());
-      rr = rr.next;
-    }
-    return sb.toString();
-  }
-
-  /** Modified the behavior of a ReplaceRule by supplying
-      an argument.  If a ReplaceRule named "foo" is defined
-      and the pattern "s/x/${foo:5}/" is given to Regex.perlCode,
-      then the "foo" the definition of "foo" will be retrieved
-      and arg("5") will be called.  If the result is non-null,
-      that is the ReplaceRule that will be used.  If the result
-      is null, then the pattern works just as if it were
-      "s/x/${foo}/".
-      @see com.stevesoft.pat.Validator#arg(java.lang.String)
-   */
-  public ReplaceRule arg(String s)
-  {
-    return null;
-  }
-
-  static int getHexDigit(char c)
-  {
-    if (c >= '0' && c <= '9')
-    {
-      return c - '0';
-    }
-    if (c >= 'a' && c <= 'f')
-    {
-      return c - 'a' + 10;
-    }
-    return c - 'A' + 10;
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+import java.util.*;
+
+/**
+ * ReplaceRule is a singly linked list of Objects which describe how to replace
+ * the matched portion of a String. The only member method that you absolutely
+ * need to define to use this class is apply(StringBuffer,RegRes) -- although
+ * you may want define toString1() and clone1() (if you are unhappy with the
+ * default methods) that are needed by the clone() or toString() methods on this
+ * class. During the replacement process, each ReplaceRule tells the replacer
+ * what to add to StringBuffer and uses the contents of the Regular expression
+ * result to get the information it needs to do this. Here is an <a
+ * href="http://javaregex.com/code/fancy.java.html">example</a>
+ * 
+ * @see com.stevesoft.pat.NullRule
+ * @see com.stevesoft.pat.AmpersandRule
+ * @see com.stevesoft.pat.BackRefRule
+ * @see com.stevesoft.pat.LeftRule
+ * @see com.stevesoft.pat.RightRule
+ * @see com.stevesoft.pat.StringRule
+ */
+public abstract class ReplaceRule
+{
+  /** points to the next ReplaceRule in the linked list. */
+  protected ReplaceRule next = null;
+
+  /**
+   * This function appends to the StringBufferLike the text you want to replaced
+   * the portion of the String last matched.
+   */
+  public abstract void apply(StringBufferLike sb, RegRes r);
+
+  /**
+   * A rule describing how to clone only the current ReplaceRule, and none of
+   * the others in this linked list. It is called by clone() for each item in
+   * the list.
+   */
+  public Object clone1()
+  {
+    return new RuleHolder(this);
+  }
+
+  public final Object clone()
+  {
+    ReplaceRule x = (ReplaceRule) clone1();
+    ReplaceRule xsav = x;
+    ReplaceRule y = this;
+    while (y.next != null)
+    {
+      x.next = (ReplaceRule) y.next.clone1();
+      x.name = y.name;
+      x = x.next;
+      y = y.next;
+    }
+    return xsav;
+  }
+
+  static ReplaceRule add(ReplaceRule head, ReplaceRule adding)
+  {
+    if (head == null)
+    {
+      return head = adding;
+    }
+    head.addRule(adding);
+    return head;
+  }
+
+  public ReplaceRule add(ReplaceRule adding)
+  {
+    return add(this, adding);
+  }
+
+  /** Add another ReplaceRule to the linked list. */
+  public void addRule(ReplaceRule r)
+  {
+    if (next == null)
+    {
+      next = r;
+    }
+    else
+    {
+      next.addRule(r);
+    }
+  }
+
+  static Regex getvar = null;
+
+  final static Regex getv()
+  {
+    // Thanks to Michael Jimenez for pointing out the need
+    // to clone getvar rather than simply returning it.
+    // Previously this was not thread safe.
+    // if(getvar != null) return getvar;
+    if (getvar != null)
+    {
+      return (Regex) getvar.clone();
+    }
+    getvar = new Regex("(?:\\\\(\\d+)|" + // ref 1
+            "\\$(?:" + "(\\d+)|" + // ref 2
+            "(\\w+)|" + // ref 3
+            "([&'`])|" + // ref 4
+            "\\{(?:(\\d+)|" + // ref 5
+            "([^\n}\\\\]+))}" + // ref 6
+            ")|" + "\\\\([nrbtaef])|" + // ref 7
+            "\\\\c([\u0000-\uFFFF])|" + // ref 8
+            "\\\\x([A-Fa-f0-9]{2})|" + // ref 9
+            "\\\\([\u0000-\uFFFF])" + // ref 10
+            ")");
+    getvar.optimize();
+    return getvar;
+  }
+
+  /**
+   * Compile a ReplaceRule using the text that would go between the second and
+   * third /'s in a typical substitution pattern in Perl: s/ ... / <i>The
+   * argument to ReplaceRule.perlCode</i> /.
+   */
+  public static ReplaceRule perlCode(String s)
+  {
+    // String sav_backGs = Regex.backGs;
+    // int sav_backGto = Regex.backGto;
+    try
+    {
+      int mf = 0, mt = 0;
+      Regex gv = getv();
+      ReplaceRule head = null;
+      Object tmp = null;
+      while (gv.searchFrom(s, mt))
+      {
+        int off = Regex.BackRefOffset - 1;
+        mf = gv.matchedFrom();
+        if (mf > mt)
+        {
+          head = add(head, new StringRule(s.substring(mt, mf)));
+        }
+        String var = null;
+        if ((var = gv.stringMatched(1 + off)) != null
+                || (var = gv.stringMatched(2 + off)) != null
+                || (var = gv.stringMatched(5 + off)) != null)
+        {
+          int d = 0;
+          for (int i = 0; i < var.length(); i++)
+          {
+            d = 8 * d + (var.charAt(i) - '0');
+          }
+          if (var.length() == 1)
+          {
+            head = add(head, new BackRefRule(d));
+          }
+          else
+          {
+            head = new StringRule("" + (char) d);
+          }
+        }
+        else if ((var = gv.stringMatched(10 + off)) != null)
+        {
+          if ("QELlUu".indexOf(var) >= 0)
+          {
+            head = add(head, new CodeRule(var.charAt(0)));
+          }
+          else
+          {
+            head = add(head, new StringRule(var));
+          }
+        }
+        else if ((var = gv.stringMatched(3 + off)) != null
+                || (var = gv.stringMatched(4 + off)) != null
+                || (var = gv.stringMatched(6 + off)) != null)
+        {
+          String arg = "";
+          int pc;
+          if ((pc = var.indexOf(':')) > 0)
+          {
+            arg = var.substring(pc + 1);
+            var = var.substring(0, pc);
+          }
+          if (var.equals("&") || var.equals("MATCH"))
+          {
+            head = add(head, new AmpersandRule());
+          }
+          else if (var.equals("`") || var.equals("PREMATCH"))
+          {
+            head = add(head, new LeftRule());
+          }
+          else if (var.equals("'") || var.equals("POSTMATCH"))
+          {
+            head = add(head, new RightRule());
+          }
+          else if (var.equals("WANT_MORE_TEXT"))
+          {
+            head = add(head, new WantMoreTextReplaceRule());
+          }
+          else if (var.equals("POP"))
+          {
+            head = add(head, new PopRule());
+          }
+          else if (var.startsWith("+")
+                  && (tmp = defs.get(var.substring(1))) != null)
+          {
+            if (tmp instanceof Regex)
+            {
+              head = add(head, new PushRule(var.substring(1), (Regex) tmp));
+            }
+            else if (tmp instanceof Transformer)
+            {
+              head = add(head, new PushRule(var.substring(1),
+                      (Transformer) tmp));
+            }
+            else
+            {
+              head = add(head, new StringRule("${" + var + "}"));
+            }
+          }
+          else if (var.startsWith("=")
+                  && (tmp = defs.get(var.substring(1))) != null)
+          {
+            if (tmp instanceof Regex)
+            {
+              head = add(head,
+                      new ChangeRule(var.substring(1), (Regex) tmp));
+            }
+            else if (tmp instanceof Transformer)
+            {
+              head = add(head, new ChangeRule(var.substring(1),
+                      (Transformer) tmp));
+            }
+            else
+            {
+              head = add(head, new StringRule("${" + var + "}"));
+            }
+          }
+          else if ((tmp = defs.get(var)) != null)
+          {
+            if (tmp instanceof ReplaceRule)
+            {
+              ReplaceRule alt = ((ReplaceRule) tmp).arg(arg);
+              if (alt == null)
+              {
+                alt = ((ReplaceRule) tmp);
+              }
+              head = add(head, (ReplaceRule) (alt.clone()));
+            }
+          }
+          else
+          // can't figure out how to transform this thing...
+          {
+            head = add(head, new StringRule("${" + var + "}"));
+          }
+        }
+        else if ((var = gv.stringMatched(7 + off)) != null)
+        {
+          char c = var.charAt(0);
+          if (c == 'n')
+          {
+            head = add(head, new StringRule("\n"));
+          }
+          else if (c == 't')
+          {
+            head = add(head, new StringRule("\t"));
+          }
+          else if (c == 'r')
+          {
+            head = add(head, new StringRule("\r"));
+          }
+          else if (c == 'b')
+          {
+            head = add(head, new StringRule("\r"));
+          }
+          else if (c == 'a')
+          {
+            head = add(head, new StringRule("" + (char) 7));
+          }
+          else if (c == 'e')
+          {
+            head = add(head, new StringRule("" + (char) 27));
+          }
+          else if (c == 'f')
+          {
+            head = add(head, new StringRule("" + (char) 12));
+          }
+        }
+        else if ((var = gv.stringMatched(8 + off)) != null)
+        {
+          char c = var.charAt(0);
+          if (c < Ctrl.cmap.length)
+          {
+            c = Ctrl.cmap[c];
+          }
+          head = add(head, new StringRule("" + c));
+        }
+        else if ((var = gv.stringMatched(9 + off)) != null)
+        {
+          int d = 16 * getHexDigit(var.charAt(0))
+                  + getHexDigit(var.charAt(1));
+          head = add(head, new StringRule("" + (char) d));
+        }
+        mt = gv.matchedTo();
+      }
+      if (mt <= s.length())
+      {
+        head = add(head, new StringRule(s.substring(mt)));
+      }
+      return head;
+    } finally
+    {
+      // Regex.backGs = sav_backGs;
+      // Regex.backGto = sav_backGto;
+    }
+  }
+
+  static Hashtable defs = new Hashtable();
+
+  public static boolean isDefined(String s)
+  {
+    return defs.get(s) != null;
+  }
+
+  public static void define(String s, Regex r)
+  {
+    defs.put(s, r);
+  }
+
+  public static void define(String s, ReplaceRule r)
+  {
+    defs.put(s, r);
+    r.name = s;
+  }
+
+  String name = getClass().getName();
+
+  public static void define(String s, Transformer t)
+  {
+    defs.put(s, t);
+  }
+
+  public static void undefine(String s)
+  {
+    defs.remove(s);
+  }
+
+  /**
+   * This tells how to convert just the current element (and none of the other
+   * items in the linked list) to a String. This method is called by toString()
+   * for each item in the linked list.
+   */
+  public String toString1()
+  {
+    return "${" + name + "}";
+  }
+
+  /** Convert to a String. */
+  public final String toString()
+  {
+    StringBuffer sb = new StringBuffer();
+    sb.append(toString1());
+    ReplaceRule rr = this.next;
+    while (rr != null)
+    {
+      sb.append(rr.toString1());
+      rr = rr.next;
+    }
+    return sb.toString();
+  }
+
+  /**
+   * Modified the behavior of a ReplaceRule by supplying an argument. If a
+   * ReplaceRule named "foo" is defined and the pattern "s/x/${foo:5}/" is given
+   * to Regex.perlCode, then the "foo" the definition of "foo" will be retrieved
+   * and arg("5") will be called. If the result is non-null, that is the
+   * ReplaceRule that will be used. If the result is null, then the pattern
+   * works just as if it were "s/x/${foo}/".
+   * 
+   * @see com.stevesoft.pat.Validator#arg(java.lang.String)
+   */
+  public ReplaceRule arg(String s)
+  {
+    return null;
+  }
+
+  static int getHexDigit(char c)
+  {
+    if (c >= '0' && c <= '9')
+    {
+      return c - '0';
+    }
+    if (c >= 'a' && c <= 'f')
+    {
+      return c - 'a' + 10;
+    }
+    return c - 'A' + 10;
+  }
+}
diff --git a/src/com/stevesoft/pat/Replacer.java b/src/com/stevesoft/pat/Replacer.java
index 77570f9..062a548 100755
--- a/src/com/stevesoft/pat/Replacer.java
+++ b/src/com/stevesoft/pat/Replacer.java
@@ -1,357 +1,367 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-import com.stevesoft.pat.wrap.*;
-
-/** Internally used class. */
-class RegHolder
-{
-  Regex me = null;
-  RegHolder prev = null;
-}
-
-/** Internally used class.
- * @see CodeRule
- */
-class CodeVal
-{
-  int pos;
-  char code;
-  CodeVal(int p, char c)
-  {
-    pos = p;
-    code = c;
-  }
-
-  public String toString()
-  {
-    return "(" + pos + "," + code + ")";
-  }
-}
-
-/**
-  To use this class, first use either the getReplacer() method from
-  Transformer or Regex.  You can then use replaceAll, replaceFirst,
-  etc. methods on the Replacer in the same way that you can from
-  either of those two classes.
-  <p>
-  The only potential difference between using the methods of
-  Replacer to do the replacing is that Replacer remembers changes
-  to the replacing object between calls to replaceAll, replaceFirst
-  etc.  For details, see the example file
-  <a href="http://javaregex.com/code/trans3.java.html">trans3.java</a>.
-  @see com.stevesoft.pat.Transformer
-  @see com.stevesoft.pat.Regex
- */
-public class Replacer
-{
-  boolean first;
-
-  /** Instantiate a new Replacer. */
-  public Replacer()
-  {}
-
-  public StringLike replaceFirstRegion(String s, Regex r,
-                                       int start, int end)
-  {
-    return replaceFirstRegion(new StringWrap(s), r, start, end);
-  }
-
-  /** This method replaces the first occurence of the Regex in the
-      String starting with position pos
-      according to the Replacer rule of this object. */
-  public StringLike replaceFirstRegion(StringLike s, Regex r,
-                                       int start, int end)
-  {
-    first = true;
-    rh.me = r;
-    rh.prev = null;
-    return dorep(s, start, end);
-  }
-
-  public StringLike replaceFirst(StringLike s)
-  {
-    return replaceFirstRegion(s, 0, s.length());
-  }
-
-  public StringLike replaceFirstFrom(StringLike s, int start)
-  {
-    return replaceFirstRegion(s, start, s.length());
-  }
-
-  public StringLike replaceFirstRegion(StringLike s, int start, int end)
-  {
-    first = true;
-    return dorep(s, start, end);
-  }
-
-  RegHolder rh = new RegHolder();
-
-  public StringLike replaceAllRegion(String s, Regex r,
-                                     int start, int end)
-  {
-    return replaceAllRegion(new StringWrap(s), r, start, end);
-  }
-
-  /** This method replaces all occurences of the Regex in the
-      String starting with postition pos
-      according to the Replacer rule of this object. */
-  public StringLike replaceAllRegion(StringLike s, Regex r,
-                                     int start, int end)
-  {
-    first = false;
-    // reset
-    rh.me = r;
-    rh.prev = null;
-    return dorep(s, start, end);
-  }
-
-  public StringLike replaceAll(StringLike s)
-  {
-    return replaceAllRegion(s, 0, s.length());
-  }
-
-  public StringLike replaceAllFrom(StringLike s, int start)
-  {
-    return replaceAllRegion(s, start, s.length());
-  }
-
-  public StringLike replaceAllRegion(StringLike s, int start, int end)
-  {
-    first = false;
-    return dorep(s, start, end);
-  }
-
-  public String replaceAll(String s)
-  {
-    return replaceAllRegion(new StringWrap(s), 0, s.length()).toString();
-  }
-
-  public String replaceAllFrom(String s, int start)
-  {
-    return replaceAllRegion(new StringWrap(s), start, s.length()).toString();
-  }
-
-  public String replaceAllRegion(String s, int start, int end)
-  {
-    first = false;
-    return dorep(new StringWrap(s), start, end).toString();
-  }
-
-  final public boolean isSpecial(ReplaceRule x)
-  {
-    while (x != null)
-    {
-      if (x instanceof SpecialRule
-          ||
-          (x instanceof RuleHolder && ( (RuleHolder) x).held instanceof SpecialRule))
-      {
-        return true;
-      }
-      x = x.next;
-    }
-    return false;
-  }
-
-  final public void apply1(RegRes rr)
-  {
-    rr.charsMatched_++;
-    apply(rr, null);
-    rr.charsMatched_--;
-  }
-
-  final StringLike dorep(StringLike s, int start, int end)
-  {
-    StringLike ret = s;
-    want_more_text = false;
-    lastMatchedTo = 0;
-    if (rh.me == null)
-    {
-      throw new NullPointerException("Replacer has null Regex pointer");
-    }
-    if (rh.me._search(s, start, end))
-    {
-      int rmn = rh.me.matchedTo();
-      if (rh.me.charsMatched() == 0 && !isSpecial(rh.me.getReplaceRule()))
-      {
-        apply1(rh.me);
-        rmn++;
-      }
-      apply(rh.me);
-      if (!first)
-      {
-        for (int i = rmn;
-             !want_more_text && rh.me._search(s, i, end); i = rmn)
-        {
-          rmn = rh.me.matchedTo();
-          if (rh.me.charsMatched() == 0)
-          {
-            if (!isSpecial(rh.me.getReplaceRule()))
-            {
-              apply1(rh.me);
-            }
-            rmn++;
-          }
-          apply(rh.me);
-        }
-      }
-      ret = finish();
-      ret = ret == null ? s : ret;
-    }
-    return ret;
-  }
-
-  StringBufferLike sb = null;
-  StringLike src = null;
-  int pos = 0;
-  /** This method allows you to apply the results of several
-      matches in a sequence to modify a String of text.  Each
-      call in the sequence must operate on the same piece of
-      text and the matchedFrom() of each RegRes given to this
-      method must be greater in value than the preceeding
-      RegRes's matchedTo() value.
-   */
-  public void apply(RegRes r, ReplaceRule rp)
-  {
-    if (rp == null || (rp.next == null && rp instanceof AmpersandRule))
-    {
-      return;
-    }
-    if (r.didMatch())
-    {
-      if (src == null)
-      {
-        src = r.getStringLike();
-      }
-      if (sb == null)
-      {
-        sb = new StringBufferLike(src.newStringBufferLike());
-      }
-      int rmf = r.matchedFrom();
-      for (int ii = pos; ii < rmf; ii++)
-      {
-        sb.append(src.charAt(ii));
-      }
-
-      for (ReplaceRule x = rp; x != null; x = x.next)
-      {
-        x.apply(sb, r);
-        if (x instanceof SpecialRule)
-        {
-          if (x instanceof WantMoreTextReplaceRule
-              && want_more_text_enable)
-          {
-            want_more_text = true;
-          }
-          else if (x instanceof PushRule)
-          {
-            RegHolder rh2 = new RegHolder();
-            rh2.me = ( (PushRule) x).NewRule;
-            rh2.prev = rh;
-            rh = rh2;
-          }
-          else if (x instanceof PopRule)
-          {
-            if (rh.prev != null)
-            {
-              rh = rh.prev;
-            }
-          }
-          else if (x instanceof ChangeRule)
-          {
-            rh.me = ( (ChangeRule) x).NewRule;
-          }
-        }
-      }
-      if (!want_more_text)
-      {
-        pos = r.matchedTo();
-      }
-    }
-  }
-
-  boolean want_more_text = false, want_more_text_enable = false;
-  public boolean WantMoreText()
-  {
-    return want_more_text;
-  }
-
-  /** Another form of apply, it is the same as
-      apply(r,r.getReplaceRule()). */
-  public void apply(Regex r)
-  {
-    apply(r, r.getReplaceRule());
-  }
-
-  /** This finishes the replacement, appending the right() part of
-      the last RegRes given to substitute(RegRes).  After this method
-      is called, the Replace object is reset to perform another
-      substitution. If no RegRes objects with a true didMatch are
-      applied, this returns null. */
-  public StringLike finish()
-  {
-    if (src == null)
-    {
-      return null;
-    }
-    //sb.append(src.substring(pos,src.length()));
-    int s_end = src.length();
-    for (int ii = pos; ii < s_end; ii++)
-    {
-      sb.append(src.charAt(ii));
-    }
-    src = null;
-    lastMatchedTo = pos;
-    pos = 0;
-    StringLike retstr = sb.toStringLike();
-    sb = null;
-    return retstr;
-  }
-
-  int lastMatchedTo = 0;
-  public Object clone()
-  {
-    Replacer r = new Replacer();
-    r.first = first;
-    r.src = src;
-    r.sb = sb;
-    r.pos = pos;
-    r.lastMatchedTo = lastMatchedTo;
-    r.want_more_text = want_more_text;
-    r.want_more_text_enable = want_more_text_enable;
-    r.rh.me = rh.me;
-    r.rh.prev = rh.prev;
-    return r;
-  }
-
-  public int lastMatchedTo()
-  {
-    return lastMatchedTo;
-  }
-
-  public Regex getRegex()
-  {
-    return rh.me;
-  }
-
-  public void setSource(StringLike sl)
-  {
-    src = sl;
-  }
-
-  public void setBuffer(StringBufferLike sbl)
-  {
-    sb = sbl;
-  }
-
-  public void setPos(int pos)
-  {
-    this.pos = pos;
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+import com.stevesoft.pat.wrap.*;
+
+/** Internally used class. */
+class RegHolder
+{
+  Regex me = null;
+
+  RegHolder prev = null;
+}
+
+/**
+ * Internally used class.
+ * 
+ * @see CodeRule
+ */
+class CodeVal
+{
+  int pos;
+
+  char code;
+
+  CodeVal(int p, char c)
+  {
+    pos = p;
+    code = c;
+  }
+
+  public String toString()
+  {
+    return "(" + pos + "," + code + ")";
+  }
+}
+
+/**
+ * To use this class, first use either the getReplacer() method from Transformer
+ * or Regex. You can then use replaceAll, replaceFirst, etc. methods on the
+ * Replacer in the same way that you can from either of those two classes.
+ * <p>
+ * The only potential difference between using the methods of Replacer to do the
+ * replacing is that Replacer remembers changes to the replacing object between
+ * calls to replaceAll, replaceFirst etc. For details, see the example file <a
+ * href="http://javaregex.com/code/trans3.java.html">trans3.java</a>.
+ * 
+ * @see com.stevesoft.pat.Transformer
+ * @see com.stevesoft.pat.Regex
+ */
+public class Replacer
+{
+  boolean first;
+
+  /** Instantiate a new Replacer. */
+  public Replacer()
+  {
+  }
+
+  public StringLike replaceFirstRegion(String s, Regex r, int start, int end)
+  {
+    return replaceFirstRegion(new StringWrap(s), r, start, end);
+  }
+
+  /**
+   * This method replaces the first occurence of the Regex in the String
+   * starting with position pos according to the Replacer rule of this object.
+   */
+  public StringLike replaceFirstRegion(StringLike s, Regex r, int start,
+          int end)
+  {
+    first = true;
+    rh.me = r;
+    rh.prev = null;
+    return dorep(s, start, end);
+  }
+
+  public StringLike replaceFirst(StringLike s)
+  {
+    return replaceFirstRegion(s, 0, s.length());
+  }
+
+  public StringLike replaceFirstFrom(StringLike s, int start)
+  {
+    return replaceFirstRegion(s, start, s.length());
+  }
+
+  public StringLike replaceFirstRegion(StringLike s, int start, int end)
+  {
+    first = true;
+    return dorep(s, start, end);
+  }
+
+  RegHolder rh = new RegHolder();
+
+  public StringLike replaceAllRegion(String s, Regex r, int start, int end)
+  {
+    return replaceAllRegion(new StringWrap(s), r, start, end);
+  }
+
+  /**
+   * This method replaces all occurences of the Regex in the String starting
+   * with postition pos according to the Replacer rule of this object.
+   */
+  public StringLike replaceAllRegion(StringLike s, Regex r, int start,
+          int end)
+  {
+    first = false;
+    // reset
+    rh.me = r;
+    rh.prev = null;
+    return dorep(s, start, end);
+  }
+
+  public StringLike replaceAll(StringLike s)
+  {
+    return replaceAllRegion(s, 0, s.length());
+  }
+
+  public StringLike replaceAllFrom(StringLike s, int start)
+  {
+    return replaceAllRegion(s, start, s.length());
+  }
+
+  public StringLike replaceAllRegion(StringLike s, int start, int end)
+  {
+    first = false;
+    return dorep(s, start, end);
+  }
+
+  public String replaceAll(String s)
+  {
+    return replaceAllRegion(new StringWrap(s), 0, s.length()).toString();
+  }
+
+  public String replaceAllFrom(String s, int start)
+  {
+    return replaceAllRegion(new StringWrap(s), start, s.length())
+            .toString();
+  }
+
+  public String replaceAllRegion(String s, int start, int end)
+  {
+    first = false;
+    return dorep(new StringWrap(s), start, end).toString();
+  }
+
+  final public boolean isSpecial(ReplaceRule x)
+  {
+    while (x != null)
+    {
+      if (x instanceof SpecialRule
+              || (x instanceof RuleHolder && ((RuleHolder) x).held instanceof SpecialRule))
+      {
+        return true;
+      }
+      x = x.next;
+    }
+    return false;
+  }
+
+  final public void apply1(RegRes rr)
+  {
+    rr.charsMatched_++;
+    apply(rr, null);
+    rr.charsMatched_--;
+  }
+
+  final StringLike dorep(StringLike s, int start, int end)
+  {
+    StringLike ret = s;
+    want_more_text = false;
+    lastMatchedTo = 0;
+    if (rh.me == null)
+    {
+      throw new NullPointerException("Replacer has null Regex pointer");
+    }
+    if (rh.me._search(s, start, end))
+    {
+      int rmn = rh.me.matchedTo();
+      if (rh.me.charsMatched() == 0 && !isSpecial(rh.me.getReplaceRule()))
+      {
+        apply1(rh.me);
+        rmn++;
+      }
+      apply(rh.me);
+      if (!first)
+      {
+        for (int i = rmn; !want_more_text && rh.me._search(s, i, end); i = rmn)
+        {
+          rmn = rh.me.matchedTo();
+          if (rh.me.charsMatched() == 0)
+          {
+            if (!isSpecial(rh.me.getReplaceRule()))
+            {
+              apply1(rh.me);
+            }
+            rmn++;
+          }
+          apply(rh.me);
+        }
+      }
+      ret = finish();
+      ret = ret == null ? s : ret;
+    }
+    return ret;
+  }
+
+  StringBufferLike sb = null;
+
+  StringLike src = null;
+
+  int pos = 0;
+
+  /**
+   * This method allows you to apply the results of several matches in a
+   * sequence to modify a String of text. Each call in the sequence must operate
+   * on the same piece of text and the matchedFrom() of each RegRes given to
+   * this method must be greater in value than the preceeding RegRes's
+   * matchedTo() value.
+   */
+  public void apply(RegRes r, ReplaceRule rp)
+  {
+    if (rp == null || (rp.next == null && rp instanceof AmpersandRule))
+    {
+      return;
+    }
+    if (r.didMatch())
+    {
+      if (src == null)
+      {
+        src = r.getStringLike();
+      }
+      if (sb == null)
+      {
+        sb = new StringBufferLike(src.newStringBufferLike());
+      }
+      int rmf = r.matchedFrom();
+      for (int ii = pos; ii < rmf; ii++)
+      {
+        sb.append(src.charAt(ii));
+      }
+
+      for (ReplaceRule x = rp; x != null; x = x.next)
+      {
+        x.apply(sb, r);
+        if (x instanceof SpecialRule)
+        {
+          if (x instanceof WantMoreTextReplaceRule && want_more_text_enable)
+          {
+            want_more_text = true;
+          }
+          else if (x instanceof PushRule)
+          {
+            RegHolder rh2 = new RegHolder();
+            rh2.me = ((PushRule) x).NewRule;
+            rh2.prev = rh;
+            rh = rh2;
+          }
+          else if (x instanceof PopRule)
+          {
+            if (rh.prev != null)
+            {
+              rh = rh.prev;
+            }
+          }
+          else if (x instanceof ChangeRule)
+          {
+            rh.me = ((ChangeRule) x).NewRule;
+          }
+        }
+      }
+      if (!want_more_text)
+      {
+        pos = r.matchedTo();
+      }
+    }
+  }
+
+  boolean want_more_text = false, want_more_text_enable = false;
+
+  public boolean WantMoreText()
+  {
+    return want_more_text;
+  }
+
+  /**
+   * Another form of apply, it is the same as apply(r,r.getReplaceRule()).
+   */
+  public void apply(Regex r)
+  {
+    apply(r, r.getReplaceRule());
+  }
+
+  /**
+   * This finishes the replacement, appending the right() part of the last
+   * RegRes given to substitute(RegRes). After this method is called, the
+   * Replace object is reset to perform another substitution. If no RegRes
+   * objects with a true didMatch are applied, this returns null.
+   */
+  public StringLike finish()
+  {
+    if (src == null)
+    {
+      return null;
+    }
+    // sb.append(src.substring(pos,src.length()));
+    int s_end = src.length();
+    for (int ii = pos; ii < s_end; ii++)
+    {
+      sb.append(src.charAt(ii));
+    }
+    src = null;
+    lastMatchedTo = pos;
+    pos = 0;
+    StringLike retstr = sb.toStringLike();
+    sb = null;
+    return retstr;
+  }
+
+  int lastMatchedTo = 0;
+
+  public Object clone()
+  {
+    Replacer r = new Replacer();
+    r.first = first;
+    r.src = src;
+    r.sb = sb;
+    r.pos = pos;
+    r.lastMatchedTo = lastMatchedTo;
+    r.want_more_text = want_more_text;
+    r.want_more_text_enable = want_more_text_enable;
+    r.rh.me = rh.me;
+    r.rh.prev = rh.prev;
+    return r;
+  }
+
+  public int lastMatchedTo()
+  {
+    return lastMatchedTo;
+  }
+
+  public Regex getRegex()
+  {
+    return rh.me;
+  }
+
+  public void setSource(StringLike sl)
+  {
+    src = sl;
+  }
+
+  public void setBuffer(StringBufferLike sbl)
+  {
+    sb = sbl;
+  }
+
+  public void setPos(int pos)
+  {
+    this.pos = pos;
+  }
+}
diff --git a/src/com/stevesoft/pat/RightRule.java b/src/com/stevesoft/pat/RightRule.java
index c27d2e4..cddcb4a 100755
--- a/src/com/stevesoft/pat/RightRule.java
+++ b/src/com/stevesoft/pat/RightRule.java
@@ -1,29 +1,31 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-/** The apply(StringBufferLike sb,RegRes res) method of this derivation
-    of ReplaceRule appends the contents of res.right() to the     StringBufferLike sb.
-    @see com.stevesoft.pat.ReplaceRule
- */
-public class RightRule
-    extends ReplaceRule
-{
-  public RightRule()
-  {}
-
-  public void apply(StringBufferLike sb, RegRes res)
-  {
-    sb.append(res.right());
-  }
-
-  public String toString1()
-  {
-    return "$'";
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+/**
+ * The apply(StringBufferLike sb,RegRes res) method of this derivation of
+ * ReplaceRule appends the contents of res.right() to the StringBufferLike sb.
+ * 
+ * @see com.stevesoft.pat.ReplaceRule
+ */
+public class RightRule extends ReplaceRule
+{
+  public RightRule()
+  {
+  }
+
+  public void apply(StringBufferLike sb, RegRes res)
+  {
+    sb.append(res.right());
+  }
+
+  public String toString1()
+  {
+    return "$'";
+  }
+}
diff --git a/src/com/stevesoft/pat/Rthings.java b/src/com/stevesoft/pat/Rthings.java
index 4c4db39..58afe8e 100755
--- a/src/com/stevesoft/pat/Rthings.java
+++ b/src/com/stevesoft/pat/Rthings.java
@@ -1,52 +1,68 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-/**
-        Shareware: package pat
-   <a href="copyright.html">Copyright 2001, Steven R. Brandt</a>
- */
-/**
- This class only exists to store data needed during the
- compilation of a regular expression. */
-public class Rthings
-{
-  /** The numeric identity of the next () to be encountered
-       while compiling the pattern. */
-  public int val = Regex.BackRefOffset;
-  /** Needed in case (?i) is encountered, to pass back the
-       message that ignoreCase should be set. */
-  public boolean ignoreCase;
-  /** Needed in case (?Q) is encountered, to pass back the
-       message that dontMatchInQuotes should be set. */
-  public boolean dontMatchInQuotes;
-  public boolean optimizeMe = false;
-  public boolean noBackRefs = false;
-  public int parenLevel = 0;
-  boolean gFlag = false, mFlag = false, sFlag = false;
-  Pattern p;
-  Or o;
-  Rthings(Regex r)
-  {
-    ignoreCase = r.ignoreCase;
-    dontMatchInQuotes = r.dontMatchInQuotes;
-  }
-
-  void set(Regex r)
-  {
-    r.gFlag = gFlag;
-    r.mFlag = mFlag;
-    r.sFlag = sFlag;
-    r.ignoreCase = ignoreCase;
-    r.dontMatchInQuotes = dontMatchInQuotes;
-    if (optimizeMe)
-    {
-      r.optimize();
-    }
-  }
-};
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+/**
+ Shareware: package pat
+ <a href="copyright.html">Copyright 2001, Steven R. Brandt</a>
+ */
+/**
+ * This class only exists to store data needed during the compilation of a
+ * regular expression.
+ */
+public class Rthings
+{
+  /**
+   * The numeric identity of the next () to be encountered while compiling the
+   * pattern.
+   */
+  public int val = Regex.BackRefOffset;
+
+  /**
+   * Needed in case (?i) is encountered, to pass back the message that
+   * ignoreCase should be set.
+   */
+  public boolean ignoreCase;
+
+  /**
+   * Needed in case (?Q) is encountered, to pass back the message that
+   * dontMatchInQuotes should be set.
+   */
+  public boolean dontMatchInQuotes;
+
+  public boolean optimizeMe = false;
+
+  public boolean noBackRefs = false;
+
+  public int parenLevel = 0;
+
+  boolean gFlag = false, mFlag = false, sFlag = false;
+
+  Pattern p;
+
+  Or o;
+
+  Rthings(Regex r)
+  {
+    ignoreCase = r.ignoreCase;
+    dontMatchInQuotes = r.dontMatchInQuotes;
+  }
+
+  void set(Regex r)
+  {
+    r.gFlag = gFlag;
+    r.mFlag = mFlag;
+    r.sFlag = sFlag;
+    r.ignoreCase = ignoreCase;
+    r.dontMatchInQuotes = dontMatchInQuotes;
+    if (optimizeMe)
+    {
+      r.optimize();
+    }
+  }
+};
diff --git a/src/com/stevesoft/pat/RuleHolder.java b/src/com/stevesoft/pat/RuleHolder.java
index 9b8017d..8b50149 100755
--- a/src/com/stevesoft/pat/RuleHolder.java
+++ b/src/com/stevesoft/pat/RuleHolder.java
@@ -1,42 +1,43 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-/** This class is used internally. */
-class RuleHolder
-    extends ReplaceRule
-{
-  ReplaceRule held = null;
-  RuleHolder()
-  {}
-
-  RuleHolder(ReplaceRule h)
-  {
-    held = h;
-  }
-
-  public Object clone1()
-  {
-    return new RuleHolder(held);
-  }
-
-  public String toString1()
-  {
-    return held.toString1();
-  }
-
-  public void apply(StringBufferLike sb, RegRes rr)
-  {
-    held.apply(sb, rr);
-  }
-
-  public ReplaceRule arg(String s)
-  {
-    return new RuleHolder(held.arg(s));
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+/** This class is used internally. */
+class RuleHolder extends ReplaceRule
+{
+  ReplaceRule held = null;
+
+  RuleHolder()
+  {
+  }
+
+  RuleHolder(ReplaceRule h)
+  {
+    held = h;
+  }
+
+  public Object clone1()
+  {
+    return new RuleHolder(held);
+  }
+
+  public String toString1()
+  {
+    return held.toString1();
+  }
+
+  public void apply(StringBufferLike sb, RegRes rr)
+  {
+    held.apply(sb, rr);
+  }
+
+  public ReplaceRule arg(String s)
+  {
+    return new RuleHolder(held.arg(s));
+  }
+}
diff --git a/src/com/stevesoft/pat/Skip.java b/src/com/stevesoft/pat/Skip.java
index 16aada1..d3f3822 100755
--- a/src/com/stevesoft/pat/Skip.java
+++ b/src/com/stevesoft/pat/Skip.java
@@ -1,186 +1,196 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-/** This class is used internally to search ahead for some
-    optimized Regex objects.  It searches within a String
-    for occrences of a given String -- like a more flexible
-    version of String.indexOf.
-    @see com.stevesoft.pat.Skip2
-    @see com.stevesoft.pat.SkipBMH
- */
-public class Skip
-{
-  static int mkmask(int c)
-  {
-    char x = (char) c;
-    return~ (CaseMgr.toUpperCase(x) |
-             CaseMgr.toLowerCase(x) |
-             CaseMgr.toTitleCase(x));
-  }
-
-  String src;
-  int c, mask;
-  int offset;
-  boolean ign, m1;
-  /** Examine a Regex to determine what String it will
-      attempt to skip to when searching for patterns.
-      Return -1 if we aren't doing this. */
-  public static String string(Regex r)
-  {
-    return r.skipper == null ? null : r.skipper.src;
-  }
-
-  /** Determine the offset of the String within the pattern
-      that we are skipping to. Return -1 if we aren't doing
-      this.  */
-  public static int offset(Regex r)
-  {
-    return r.skipper == null ? -1 : r.skipper.offset;
-  }
-
-  /** Initialize, give it a String to search for, tell it
-      whether or not to ignoreCase, and what the offset is
-      of the String within the String to be searched. */
-  public Skip(String s, boolean ign, int o)
-  {
-    src = s;
-    c = s.charAt(0);
-    if (ign)
-    {
-      mask = mkmask(c);
-    }
-    else
-    {
-      mask = 0;
-    }
-    offset = o;
-    this.ign = ign;
-    m1 = (s.length() == 1);
-  }
-
-  /** The same as find(s,0,s.length()) */
-  public final int find(StringLike s)
-  {
-    return find(s, 0, s.length());
-  }
-
-  static final int min(int a, int b)
-  {
-    return a < b ? a : b;
-  }
-
-  /** Searches a given region of text beginning at position start
-      and ending at position end for the skip object. */
-  public int find(StringLike s, int start, int end)
-  {
-    if (start > end)
-    {
-      return -1;
-    }
-    start += offset;
-    int vend = min(s.length() - 1, end + offset);
-    if (mask != c)
-    {
-      for (int i = start; i <= vend; i++)
-      {
-        if (0 == (s.charAt(i) & mask))
-        {
-          //if(m1||s.regionMatches(ign,i,src,0,src.length()) )
-          if (m1 || CaseMgr.regionMatches(s, ign, i, src, 0, src.length()))
-          {
-            return i - offset;
-          }
-        }
-      }
-    }
-    else
-    {
-      for (int i = start; i <= vend; i++)
-      {
-        if (c == s.charAt(i))
-        {
-          //if(m1||s.regionMatches(ign,i,src,0,src.length()) )
-          if (m1 || CaseMgr.regionMatches(s, ign, i, src, 0, src.length()))
-          {
-            return i - offset;
-          }
-        }
-      }
-    }
-    return -1;
-  }
-
-  static Skip findSkip(Regex r)
-  {
-    return findSkip(r.thePattern, r.ignoreCase, !r.dontMatchInQuotes);
-  }
-
-  // look for things that can be skipped
-  static Skip findSkip(Pattern p, boolean ignoreCase, boolean trnc)
-  {
-    StringBuffer sb = new StringBuffer();
-    Skip subsk = null;
-    int offset = 0;
-    int skipc = -1, skipoff = 0;
-    for (; p != null; p = p.next)
-    {
-      if (p instanceof oneChar)
-      {
-        skipc = ( (oneChar) p).c;
-        skipoff = offset;
-      }
-      if (p instanceof oneChar && p.next instanceof oneChar)
-      {
-        Pattern psav = p;
-        sb.append( ( (oneChar) p).c);
-        while (p.next instanceof oneChar)
-        {
-          sb.append( ( (oneChar) p.next).c);
-          p = p.next;
-        }
-        String st = sb.toString();
-        Skip sk = null;
-        if (st.length() > 2)
-        {
-          sk = new SkipBMH(st, ignoreCase, offset);
-        }
-        else
-        {
-          sk = new Skip2(st, ignoreCase, offset);
-        }
-        if (trnc && st.length() > 2)
-        { // chop out a whole string...
-          psav.next = new Skipped(st.substring(1));
-          psav.next.next = p.next;
-          psav.next.parent = p.parent;
-        }
-        return sk;
-      }
-      else if (p instanceof Or && ( (Or) p).v.size() == 1
-               && ! ( (Or) p).leftForm().equals("(?!")
-               && null != (subsk =
-                           findSkip( (Pattern) ( (Or) p).v.elementAt(0),
-                                    ignoreCase, trnc)))
-      {
-        subsk.offset += offset;
-        return subsk;
-      }
-      else if (p.minChars().equals(p.maxChars()))
-      {
-        offset += p.minChars().intValue();
-      }
-      else
-      {
-        return skipc < 0 ? null :
-            new Skip("" + (char) skipc, ignoreCase, skipoff);
-      }
-    }
-    return null;
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+/**
+ * This class is used internally to search ahead for some optimized Regex
+ * objects. It searches within a String for occrences of a given String -- like
+ * a more flexible version of String.indexOf.
+ * 
+ * @see com.stevesoft.pat.Skip2
+ * @see com.stevesoft.pat.SkipBMH
+ */
+public class Skip
+{
+  static int mkmask(int c)
+  {
+    char x = (char) c;
+    return ~(CaseMgr.toUpperCase(x) | CaseMgr.toLowerCase(x) | CaseMgr
+            .toTitleCase(x));
+  }
+
+  String src;
+
+  int c, mask;
+
+  int offset;
+
+  boolean ign, m1;
+
+  /**
+   * Examine a Regex to determine what String it will attempt to skip to when
+   * searching for patterns. Return -1 if we aren't doing this.
+   */
+  public static String string(Regex r)
+  {
+    return r.skipper == null ? null : r.skipper.src;
+  }
+
+  /**
+   * Determine the offset of the String within the pattern that we are skipping
+   * to. Return -1 if we aren't doing this.
+   */
+  public static int offset(Regex r)
+  {
+    return r.skipper == null ? -1 : r.skipper.offset;
+  }
+
+  /**
+   * Initialize, give it a String to search for, tell it whether or not to
+   * ignoreCase, and what the offset is of the String within the String to be
+   * searched.
+   */
+  public Skip(String s, boolean ign, int o)
+  {
+    src = s;
+    c = s.charAt(0);
+    if (ign)
+    {
+      mask = mkmask(c);
+    }
+    else
+    {
+      mask = 0;
+    }
+    offset = o;
+    this.ign = ign;
+    m1 = (s.length() == 1);
+  }
+
+  /** The same as find(s,0,s.length()) */
+  public final int find(StringLike s)
+  {
+    return find(s, 0, s.length());
+  }
+
+  static final int min(int a, int b)
+  {
+    return a < b ? a : b;
+  }
+
+  /**
+   * Searches a given region of text beginning at position start and ending at
+   * position end for the skip object.
+   */
+  public int find(StringLike s, int start, int end)
+  {
+    if (start > end)
+    {
+      return -1;
+    }
+    start += offset;
+    int vend = min(s.length() - 1, end + offset);
+    if (mask != c)
+    {
+      for (int i = start; i <= vend; i++)
+      {
+        if (0 == (s.charAt(i) & mask))
+        {
+          // if(m1||s.regionMatches(ign,i,src,0,src.length()) )
+          if (m1 || CaseMgr.regionMatches(s, ign, i, src, 0, src.length()))
+          {
+            return i - offset;
+          }
+        }
+      }
+    }
+    else
+    {
+      for (int i = start; i <= vend; i++)
+      {
+        if (c == s.charAt(i))
+        {
+          // if(m1||s.regionMatches(ign,i,src,0,src.length()) )
+          if (m1 || CaseMgr.regionMatches(s, ign, i, src, 0, src.length()))
+          {
+            return i - offset;
+          }
+        }
+      }
+    }
+    return -1;
+  }
+
+  static Skip findSkip(Regex r)
+  {
+    return findSkip(r.thePattern, r.ignoreCase, !r.dontMatchInQuotes);
+  }
+
+  // look for things that can be skipped
+  static Skip findSkip(Pattern p, boolean ignoreCase, boolean trnc)
+  {
+    StringBuffer sb = new StringBuffer();
+    Skip subsk = null;
+    int offset = 0;
+    int skipc = -1, skipoff = 0;
+    for (; p != null; p = p.next)
+    {
+      if (p instanceof oneChar)
+      {
+        skipc = ((oneChar) p).c;
+        skipoff = offset;
+      }
+      if (p instanceof oneChar && p.next instanceof oneChar)
+      {
+        Pattern psav = p;
+        sb.append(((oneChar) p).c);
+        while (p.next instanceof oneChar)
+        {
+          sb.append(((oneChar) p.next).c);
+          p = p.next;
+        }
+        String st = sb.toString();
+        Skip sk = null;
+        if (st.length() > 2)
+        {
+          sk = new SkipBMH(st, ignoreCase, offset);
+        }
+        else
+        {
+          sk = new Skip2(st, ignoreCase, offset);
+        }
+        if (trnc && st.length() > 2)
+        { // chop out a whole string...
+          psav.next = new Skipped(st.substring(1));
+          psav.next.next = p.next;
+          psav.next.parent = p.parent;
+        }
+        return sk;
+      }
+      else if (p instanceof Or
+              && ((Or) p).v.size() == 1
+              && !((Or) p).leftForm().equals("(?!")
+              && null != (subsk = findSkip((Pattern) ((Or) p).v
+                      .elementAt(0), ignoreCase, trnc)))
+      {
+        subsk.offset += offset;
+        return subsk;
+      }
+      else if (p.minChars().equals(p.maxChars()))
+      {
+        offset += p.minChars().intValue();
+      }
+      else
+      {
+        return skipc < 0 ? null : new Skip("" + (char) skipc, ignoreCase,
+                skipoff);
+      }
+    }
+    return null;
+  }
+}
diff --git a/src/com/stevesoft/pat/Skip2.java b/src/com/stevesoft/pat/Skip2.java
index ca1c5a8..5f6bb5a 100755
--- a/src/com/stevesoft/pat/Skip2.java
+++ b/src/com/stevesoft/pat/Skip2.java
@@ -1,55 +1,57 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-/** This is the same as Skip, except it needs a minimum
-    of two characters in the initializing String.
-    @see com.stevesoft.pat.Skip
-    @see com.stevesoft.pat.SkipBMH
- */
-public class Skip2
-    extends Skip
-{
-  int c1, mask1;
-  public Skip2(String s, boolean ign, int offset)
-  {
-    super(s, ign, offset);
-    c1 = s.charAt(1);
-    m1 = 2 == s.length();
-    if (ign)
-    {
-      mask1 = mkmask(c1);
-    }
-    else
-    {
-      mask1 = 0;
-    }
-  }
-
-  public int find(StringLike s, int start, int end)
-  {
-    if (start > end)
-    {
-      return -1;
-    }
-    start += offset;
-    int vend = min(s.length() - 2, end + offset);
-    for (int i = start; i <= vend; i++)
-    {
-      if (0 == (s.charAt(i) & mask) && 0 == (s.charAt(i + 1) & mask1))
-      {
-        //if(m1||s.regionMatches(ign,i,src,0,src.length()) )
-        if (m1 || CaseMgr.regionMatches(s, ign, i, src, 0, src.length()))
-        {
-          return i - offset;
-        }
-      }
-    }
-    return -1;
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+/**
+ * This is the same as Skip, except it needs a minimum of two characters in the
+ * initializing String.
+ * 
+ * @see com.stevesoft.pat.Skip
+ * @see com.stevesoft.pat.SkipBMH
+ */
+public class Skip2 extends Skip
+{
+  int c1, mask1;
+
+  public Skip2(String s, boolean ign, int offset)
+  {
+    super(s, ign, offset);
+    c1 = s.charAt(1);
+    m1 = 2 == s.length();
+    if (ign)
+    {
+      mask1 = mkmask(c1);
+    }
+    else
+    {
+      mask1 = 0;
+    }
+  }
+
+  public int find(StringLike s, int start, int end)
+  {
+    if (start > end)
+    {
+      return -1;
+    }
+    start += offset;
+    int vend = min(s.length() - 2, end + offset);
+    for (int i = start; i <= vend; i++)
+    {
+      if (0 == (s.charAt(i) & mask) && 0 == (s.charAt(i + 1) & mask1))
+      {
+        // if(m1||s.regionMatches(ign,i,src,0,src.length()) )
+        if (m1 || CaseMgr.regionMatches(s, ign, i, src, 0, src.length()))
+        {
+          return i - offset;
+        }
+      }
+    }
+    return -1;
+  }
+}
diff --git a/src/com/stevesoft/pat/SkipBMH.java b/src/com/stevesoft/pat/SkipBMH.java
index 632418e..1397b90 100755
--- a/src/com/stevesoft/pat/SkipBMH.java
+++ b/src/com/stevesoft/pat/SkipBMH.java
@@ -1,271 +1,279 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-import com.stevesoft.pat.wrap.*;
-
-/** Like Skip, but implements a
- <a href="http://www.dcc.uchile.cl/~rbaeza/handbook/algs/7/713b.srch.p.html">
-    Boyer-Moore-Horspool</a> type search
-    method that has been modified to be more like a "T-search" (see
-    the Michael Tamm''s article in <i>C'T, magazin fuer computer und technic</i>, August 97
-    p 292).  Yet another important source of information for me was
-    the <a href="http://www.go2net.com/people/paulp/deep/1997/05/14/">
-    Deep Magic</a> article on string searching.  As of this writing, I can
-    beat String's indexOf method in many cases.
-    @see com.stevesoft.pat.Skip
-    @see com.stevesoft.pat.Skip2
- */
-public class SkipBMH
-    extends Skip
-{
-  // This number could be 256, but I think it's
-  // big enough.  Note, it must be a power of 2.
-  final int MAX_CHAR = 64;
-  final char[] skip = new char[MAX_CHAR];
-  int sm1;
-  int jump_ahead = 0;
-  char uc, lc, tc, x;
-  final boolean exact(char c)
-  {
-    return (ign && anyc(c)) || c == x;
-  }
-
-  final boolean anyc(char c)
-  {
-    return c == uc || c == lc || c == tc;
-  }
-
-  public SkipBMH(String pt, boolean ign)
-  {
-    this(pt, ign, 0);
-  }
-
-  public SkipBMH(String pt)
-  {
-    this(pt, false, 0);
-  }
-
-  public SkipBMH(String pt, boolean ign, int offset)
-  {
-    super(pt, ign, offset);
-    for (int k = 0; k < MAX_CHAR; k++)
-    {
-      skip[k] = (char) src.length();
-    }
-
-    sm1 = src.length() - 1;
-    x = src.charAt(sm1);
-    uc = CaseMgr.toUpperCase(x);
-    lc = CaseMgr.toLowerCase(x);
-    tc = CaseMgr.toTitleCase(x);
-
-    // We don't really want 65536 long arrays in skip[],
-    // so we mask of the higher bits.  This can be combined
-    // with ignore case, so accounting for upper
-    // case costs us nothing extra.
-    for (int k = 0; k < src.length() - 1; k++)
-    {
-      char x_ = src.charAt(k);
-      if (ign)
-      {
-        char uc_ = CaseMgr.toUpperCase(x_);
-        char lc_ = CaseMgr.toLowerCase(x_);
-        char tc_ = CaseMgr.toTitleCase(x_);
-        skip[uc_ & (MAX_CHAR - 1)] = (char) (src.length() - k - 1);
-        skip[lc_ & (MAX_CHAR - 1)] = (char) (src.length() - k - 1);
-        skip[tc_ & (MAX_CHAR - 1)] = (char) (src.length() - k - 1);
-      }
-      else
-      {
-        skip[x_ & (MAX_CHAR - 1)] = (char) (src.length() - k - 1);
-      }
-    }
-
-    // This trick can be found in the July issue of
-    // C-T magazine.  This makes the method a type of
-    // "T-search."
-    jump_ahead = src.length() - 1;
-    for (int k = 0; k < src.length() - 1; k++)
-    {
-      char y = src.charAt(sm1 - k - 1);
-      if (exact(y))
-      {
-        jump_ahead = k;
-        break;
-      }
-    }
-  }
-
-  /** Set to true if you only want to compare two of the
-      characters in the String. */
-  final public int searchRegion(String s, int start, int end)
-  {
-    return find(s, start, end);
-  }
-
-  final public int searchFrom(String s, int start)
-  {
-    return find(s, start, s.length());
-  }
-
-  final public int search(String s)
-  {
-    return find(s, 0, s.length());
-  }
-
-  public int find(String s, int start, int end)
-  {
-    start += offset + sm1;
-    int vend = min(s.length() - 1, end + sm1 + offset), k;
-    int vend1 = vend - jump_ahead;
-    if (ign)
-    {
-      for (k = start; k <= vend1; k += skip[s.charAt(k) & (MAX_CHAR - 1)])
-      {
-        // table look-up is expensive, avoid it if possible
-        if (anyc(s.charAt(k)))
-        {
-          if (CaseMgr.regionMatches(src, ign, 0, s, k - sm1, sm1))
-          {
-            return k - sm1 - offset;
-          }
-          k += jump_ahead;
-        }
-      }
-      for (; k <= vend; k += skip[s.charAt(k) & (MAX_CHAR - 1)])
-      {
-        // table look-up is expensive, avoid it if possible
-        if (anyc(s.charAt(k)))
-        {
-          if (CaseMgr.regionMatches(src, ign, 0, s, k - sm1, sm1))
-          {
-            return k - sm1 - offset;
-          }
-          k += jump_ahead;
-          if (k > vend)
-          {
-            return -1;
-          }
-        }
-      }
-    }
-    else
-    {
-      for (k = start; k <= vend1; k += skip[s.charAt(k) & (MAX_CHAR - 1)])
-      {
-        // table look-up is expensive, avoid it if possible
-        if (x == s.charAt(k))
-        {
-          //if(src.regionMatches(0,s,k-sm1,sm1))
-          if (CaseMgr.regionMatches(src, false, 0, s, k - sm1, sm1))
-          {
-            return k - sm1 - offset;
-          }
-          k += jump_ahead;
-        }
-      }
-      for (; k <= vend; k += skip[s.charAt(k) & (MAX_CHAR - 1)])
-      {
-        // table look-up is expensive, avoid it if possible
-        if (x == s.charAt(k))
-        {
-          //if(src.regionMatches(0,s,k-sm1,sm1))
-          if (CaseMgr.regionMatches(src, false, 0, s, k - sm1, sm1))
-          {
-            return k - sm1 - offset;
-          }
-          k += jump_ahead;
-          if (k > vend)
-          {
-            return -1;
-          }
-        }
-      }
-    }
-
-    return -1;
-  }
-
-  public int find(StringLike s, int start, int end)
-  {
-    if (s instanceof StringWrap)
-    {
-      return find(s.toString(), start, end);
-    }
-    start += offset + sm1;
-    int vend = min(s.length() - 1, end + sm1 + offset), k;
-    int vend1 = vend - jump_ahead;
-    if (ign)
-    {
-      for (k = start; k <= vend1; k += skip[s.charAt(k) & (MAX_CHAR - 1)])
-      {
-        // table look-up is expensive, avoid it if possible
-        if (anyc(s.charAt(k)))
-        {
-          if (CaseMgr.regionMatches(src, ign, 0, s, k - sm1, sm1))
-          {
-            return k - sm1 - offset;
-          }
-          k += jump_ahead;
-        }
-      }
-      for (; k <= vend; k += skip[s.charAt(k) & (MAX_CHAR - 1)])
-      {
-        // table look-up is expensive, avoid it if possible
-        if (anyc(s.charAt(k)))
-        {
-          if (CaseMgr.regionMatches(src, ign, 0, s, k - sm1, sm1))
-          {
-            return k - sm1 - offset;
-          }
-          k += jump_ahead;
-          if (k > vend)
-          {
-            return -1;
-          }
-        }
-      }
-    }
-    else
-    {
-      for (k = start; k <= vend1; k += skip[s.charAt(k) & (MAX_CHAR - 1)])
-      {
-        // table look-up is expensive, avoid it if possible
-        if (x == s.charAt(k))
-        {
-          //if(src.regionMatches(0,s,k-sm1,sm1))
-          if (CaseMgr.regionMatches(src, false, 0, s, k - sm1, sm1))
-          {
-            return k - sm1 - offset;
-          }
-          k += jump_ahead;
-        }
-      }
-      for (; k <= vend; k += skip[s.charAt(k) & (MAX_CHAR - 1)])
-      {
-        // table look-up is expensive, avoid it if possible
-        if (x == s.charAt(k))
-        {
-          //if(src.regionMatches(0,s,k-sm1,sm1))
-          if (CaseMgr.regionMatches(src, false, 0, s, k - sm1, sm1))
-          {
-            return k - sm1 - offset;
-          }
-          k += jump_ahead;
-          if (k > vend)
-          {
-            return -1;
-          }
-        }
-      }
-    }
-
-    return -1;
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+import com.stevesoft.pat.wrap.*;
+
+/**
+ * Like Skip, but implements a <a
+ * href="http://www.dcc.uchile.cl/~rbaeza/handbook/algs/7/713b.srch.p.html">
+ * Boyer-Moore-Horspool</a> type search method that has been modified to be
+ * more like a "T-search" (see the Michael Tamm''s article in <i>C'T, magazin
+ * fuer computer und technic</i>, August 97 p 292). Yet another important
+ * source of information for me was the <a
+ * href="http://www.go2net.com/people/paulp/deep/1997/05/14/"> Deep Magic</a>
+ * article on string searching. As of this writing, I can beat String's indexOf
+ * method in many cases.
+ * 
+ * @see com.stevesoft.pat.Skip
+ * @see com.stevesoft.pat.Skip2
+ */
+public class SkipBMH extends Skip
+{
+  // This number could be 256, but I think it's
+  // big enough. Note, it must be a power of 2.
+  final int MAX_CHAR = 64;
+
+  final char[] skip = new char[MAX_CHAR];
+
+  int sm1;
+
+  int jump_ahead = 0;
+
+  char uc, lc, tc, x;
+
+  final boolean exact(char c)
+  {
+    return (ign && anyc(c)) || c == x;
+  }
+
+  final boolean anyc(char c)
+  {
+    return c == uc || c == lc || c == tc;
+  }
+
+  public SkipBMH(String pt, boolean ign)
+  {
+    this(pt, ign, 0);
+  }
+
+  public SkipBMH(String pt)
+  {
+    this(pt, false, 0);
+  }
+
+  public SkipBMH(String pt, boolean ign, int offset)
+  {
+    super(pt, ign, offset);
+    for (int k = 0; k < MAX_CHAR; k++)
+    {
+      skip[k] = (char) src.length();
+    }
+
+    sm1 = src.length() - 1;
+    x = src.charAt(sm1);
+    uc = CaseMgr.toUpperCase(x);
+    lc = CaseMgr.toLowerCase(x);
+    tc = CaseMgr.toTitleCase(x);
+
+    // We don't really want 65536 long arrays in skip[],
+    // so we mask of the higher bits. This can be combined
+    // with ignore case, so accounting for upper
+    // case costs us nothing extra.
+    for (int k = 0; k < src.length() - 1; k++)
+    {
+      char x_ = src.charAt(k);
+      if (ign)
+      {
+        char uc_ = CaseMgr.toUpperCase(x_);
+        char lc_ = CaseMgr.toLowerCase(x_);
+        char tc_ = CaseMgr.toTitleCase(x_);
+        skip[uc_ & (MAX_CHAR - 1)] = (char) (src.length() - k - 1);
+        skip[lc_ & (MAX_CHAR - 1)] = (char) (src.length() - k - 1);
+        skip[tc_ & (MAX_CHAR - 1)] = (char) (src.length() - k - 1);
+      }
+      else
+      {
+        skip[x_ & (MAX_CHAR - 1)] = (char) (src.length() - k - 1);
+      }
+    }
+
+    // This trick can be found in the July issue of
+    // C-T magazine. This makes the method a type of
+    // "T-search."
+    jump_ahead = src.length() - 1;
+    for (int k = 0; k < src.length() - 1; k++)
+    {
+      char y = src.charAt(sm1 - k - 1);
+      if (exact(y))
+      {
+        jump_ahead = k;
+        break;
+      }
+    }
+  }
+
+  /**
+   * Set to true if you only want to compare two of the characters in the
+   * String.
+   */
+  final public int searchRegion(String s, int start, int end)
+  {
+    return find(s, start, end);
+  }
+
+  final public int searchFrom(String s, int start)
+  {
+    return find(s, start, s.length());
+  }
+
+  final public int search(String s)
+  {
+    return find(s, 0, s.length());
+  }
+
+  public int find(String s, int start, int end)
+  {
+    start += offset + sm1;
+    int vend = min(s.length() - 1, end + sm1 + offset), k;
+    int vend1 = vend - jump_ahead;
+    if (ign)
+    {
+      for (k = start; k <= vend1; k += skip[s.charAt(k) & (MAX_CHAR - 1)])
+      {
+        // table look-up is expensive, avoid it if possible
+        if (anyc(s.charAt(k)))
+        {
+          if (CaseMgr.regionMatches(src, ign, 0, s, k - sm1, sm1))
+          {
+            return k - sm1 - offset;
+          }
+          k += jump_ahead;
+        }
+      }
+      for (; k <= vend; k += skip[s.charAt(k) & (MAX_CHAR - 1)])
+      {
+        // table look-up is expensive, avoid it if possible
+        if (anyc(s.charAt(k)))
+        {
+          if (CaseMgr.regionMatches(src, ign, 0, s, k - sm1, sm1))
+          {
+            return k - sm1 - offset;
+          }
+          k += jump_ahead;
+          if (k > vend)
+          {
+            return -1;
+          }
+        }
+      }
+    }
+    else
+    {
+      for (k = start; k <= vend1; k += skip[s.charAt(k) & (MAX_CHAR - 1)])
+      {
+        // table look-up is expensive, avoid it if possible
+        if (x == s.charAt(k))
+        {
+          // if(src.regionMatches(0,s,k-sm1,sm1))
+          if (CaseMgr.regionMatches(src, false, 0, s, k - sm1, sm1))
+          {
+            return k - sm1 - offset;
+          }
+          k += jump_ahead;
+        }
+      }
+      for (; k <= vend; k += skip[s.charAt(k) & (MAX_CHAR - 1)])
+      {
+        // table look-up is expensive, avoid it if possible
+        if (x == s.charAt(k))
+        {
+          // if(src.regionMatches(0,s,k-sm1,sm1))
+          if (CaseMgr.regionMatches(src, false, 0, s, k - sm1, sm1))
+          {
+            return k - sm1 - offset;
+          }
+          k += jump_ahead;
+          if (k > vend)
+          {
+            return -1;
+          }
+        }
+      }
+    }
+
+    return -1;
+  }
+
+  public int find(StringLike s, int start, int end)
+  {
+    if (s instanceof StringWrap)
+    {
+      return find(s.toString(), start, end);
+    }
+    start += offset + sm1;
+    int vend = min(s.length() - 1, end + sm1 + offset), k;
+    int vend1 = vend - jump_ahead;
+    if (ign)
+    {
+      for (k = start; k <= vend1; k += skip[s.charAt(k) & (MAX_CHAR - 1)])
+      {
+        // table look-up is expensive, avoid it if possible
+        if (anyc(s.charAt(k)))
+        {
+          if (CaseMgr.regionMatches(src, ign, 0, s, k - sm1, sm1))
+          {
+            return k - sm1 - offset;
+          }
+          k += jump_ahead;
+        }
+      }
+      for (; k <= vend; k += skip[s.charAt(k) & (MAX_CHAR - 1)])
+      {
+        // table look-up is expensive, avoid it if possible
+        if (anyc(s.charAt(k)))
+        {
+          if (CaseMgr.regionMatches(src, ign, 0, s, k - sm1, sm1))
+          {
+            return k - sm1 - offset;
+          }
+          k += jump_ahead;
+          if (k > vend)
+          {
+            return -1;
+          }
+        }
+      }
+    }
+    else
+    {
+      for (k = start; k <= vend1; k += skip[s.charAt(k) & (MAX_CHAR - 1)])
+      {
+        // table look-up is expensive, avoid it if possible
+        if (x == s.charAt(k))
+        {
+          // if(src.regionMatches(0,s,k-sm1,sm1))
+          if (CaseMgr.regionMatches(src, false, 0, s, k - sm1, sm1))
+          {
+            return k - sm1 - offset;
+          }
+          k += jump_ahead;
+        }
+      }
+      for (; k <= vend; k += skip[s.charAt(k) & (MAX_CHAR - 1)])
+      {
+        // table look-up is expensive, avoid it if possible
+        if (x == s.charAt(k))
+        {
+          // if(src.regionMatches(0,s,k-sm1,sm1))
+          if (CaseMgr.regionMatches(src, false, 0, s, k - sm1, sm1))
+          {
+            return k - sm1 - offset;
+          }
+          k += jump_ahead;
+          if (k > vend)
+          {
+            return -1;
+          }
+        }
+      }
+    }
+
+    return -1;
+  }
+}
diff --git a/src/com/stevesoft/pat/Skipped.java b/src/com/stevesoft/pat/Skipped.java
index 9bf2837..551166b 100755
--- a/src/com/stevesoft/pat/Skipped.java
+++ b/src/com/stevesoft/pat/Skipped.java
@@ -1,54 +1,56 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-import java.util.*;
-
-/** Implements the (?&lt;number) Pattern, where number is
- an integer telling us how far to back up in the Pattern.
- Not in perl 5. */
-class Skipped
-    extends Pattern
-{
-  String s;
-  Skipped(String s)
-  {
-    this.s = s;
-  }
-
-  public String toString()
-  {
-    return s + nextString();
-  }
-
-  public int matchInternal(int pos, Pthings pt)
-  {
-    //if(pt.no_check || s.regionMatches(pt.ignoreCase,0,pt.src,pos,s.length()))
-    if (pt.no_check ||
-        CaseMgr.regionMatches(s, pt.ignoreCase, 0, pt.src, pos, s.length()))
-    {
-      return nextMatch(pos + s.length(), pt);
-    }
-    return -1;
-  }
-
-  public patInt minChars()
-  {
-    return new patInt(s.length());
-  }
-
-  public patInt maxChars()
-  {
-    return new patInt(s.length());
-  }
-
-  Pattern clone1(Hashtable h)
-  {
-    return new Skipped(s);
-  }
-};
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+import java.util.*;
+
+/**
+ * Implements the (?&lt;number) Pattern, where number is an integer telling us
+ * how far to back up in the Pattern. Not in perl 5.
+ */
+class Skipped extends Pattern
+{
+  String s;
+
+  Skipped(String s)
+  {
+    this.s = s;
+  }
+
+  public String toString()
+  {
+    return s + nextString();
+  }
+
+  public int matchInternal(int pos, Pthings pt)
+  {
+    // if(pt.no_check || s.regionMatches(pt.ignoreCase,0,pt.src,pos,s.length()))
+    if (pt.no_check
+            || CaseMgr.regionMatches(s, pt.ignoreCase, 0, pt.src, pos, s
+                    .length()))
+    {
+      return nextMatch(pos + s.length(), pt);
+    }
+    return -1;
+  }
+
+  public patInt minChars()
+  {
+    return new patInt(s.length());
+  }
+
+  public patInt maxChars()
+  {
+    return new patInt(s.length());
+  }
+
+  Pattern clone1(Hashtable h)
+  {
+    return new Skipped(s);
+  }
+};
diff --git a/src/com/stevesoft/pat/SpecialRule.java b/src/com/stevesoft/pat/SpecialRule.java
index fbae452..2a249a2 100755
--- a/src/com/stevesoft/pat/SpecialRule.java
+++ b/src/com/stevesoft/pat/SpecialRule.java
@@ -1,18 +1,19 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-public class SpecialRule
-    extends ReplaceRule
-{
-  public SpecialRule()
-  {}
-
-  public void apply(StringBufferLike sb, RegRes rr)
-  {}
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+public class SpecialRule extends ReplaceRule
+{
+  public SpecialRule()
+  {
+  }
+
+  public void apply(StringBufferLike sb, RegRes rr)
+  {
+  }
+}
diff --git a/src/com/stevesoft/pat/Start.java b/src/com/stevesoft/pat/Start.java
index c47ee53..650e7a7 100755
--- a/src/com/stevesoft/pat/Start.java
+++ b/src/com/stevesoft/pat/Start.java
@@ -1,58 +1,56 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-import java.util.*;
-
-/** The '^' or the '\A' Pattern, matches the start of a string. */
-class Start
-    extends Pattern
-{
-  boolean retIsStart;
-  Start(boolean b)
-  {
-    retIsStart = b;
-  }
-
-  public int matchInternal(int pos, Pthings pt)
-  {
-    if (retIsStart
-        && pt.mFlag
-        && pos > 0 && pt.src.charAt(pos - 1) == '\n')
-    {
-      return nextMatch(pos, pt);
-    }
-    if (pos == 0)
-    {
-      return nextMatch(pos, pt);
-    }
-    return -1;
-  }
-
-  public String toString()
-  {
-    if (retIsStart)
-    {
-      return "^" + nextString();
-    }
-    else
-    {
-      return "\\A" + nextString();
-    }
-  }
-
-  public patInt maxChars()
-  {
-    return new patInt(0);
-  }
-
-  Pattern clone1(Hashtable h)
-  {
-    return new Start(retIsStart);
-  }
-};
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+import java.util.*;
+
+/** The '^' or the '\A' Pattern, matches the start of a string. */
+class Start extends Pattern
+{
+  boolean retIsStart;
+
+  Start(boolean b)
+  {
+    retIsStart = b;
+  }
+
+  public int matchInternal(int pos, Pthings pt)
+  {
+    if (retIsStart && pt.mFlag && pos > 0 && pt.src.charAt(pos - 1) == '\n')
+    {
+      return nextMatch(pos, pt);
+    }
+    if (pos == 0)
+    {
+      return nextMatch(pos, pt);
+    }
+    return -1;
+  }
+
+  public String toString()
+  {
+    if (retIsStart)
+    {
+      return "^" + nextString();
+    }
+    else
+    {
+      return "\\A" + nextString();
+    }
+  }
+
+  public patInt maxChars()
+  {
+    return new patInt(0);
+  }
+
+  Pattern clone1(Hashtable h)
+  {
+    return new Start(retIsStart);
+  }
+};
diff --git a/src/com/stevesoft/pat/StrPos.java b/src/com/stevesoft/pat/StrPos.java
index d9383dd..1f08e31 100755
--- a/src/com/stevesoft/pat/StrPos.java
+++ b/src/com/stevesoft/pat/StrPos.java
@@ -1,175 +1,192 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-/**
-        Shareware: package pat
-   <a href="copyright.html">Copyright 2001, Steven R. Brandt</a>
- */
-/**
- StrPos is used internally by regex to parse the regular expression. */
-public class StrPos
-{
-  String s;
-  int pos;
-  /** Return the position in the string pointed to */
-  public int pos()
-  {
-    return pos;
-  }
-
-  /** This contains the escape character, which is \ by default. */
-  public char esc = Pattern.ESC;
-  char c;
-  /** Returns the current, possibly escaped, character. */
-  public char thisChar()
-  {
-    return c;
-  }
-
-  boolean dontMatch, eos;
-
-  /** tell whether we are at end of string */
-  public boolean eos()
-  {
-    return eos;
-  }
-
-  /** initialize a StrPos from another StrPos. */
-  public StrPos(StrPos sp)
-  {
-    dup(sp);
-  }
-
-  /** copy a StrPos from sp to this. */
-  public void dup(StrPos sp)
-  {
-    s = sp.s;
-    pos = sp.pos;
-    c = sp.c;
-    dontMatch = sp.dontMatch;
-    eos = sp.eos;
-  }
-
-  /** Initialize a StrPos by giving it a String, and a
-       position within the String. */
-  public StrPos(String s, int pos)
-  {
-    this.s = s;
-    this.pos = pos - 1;
-    inc();
-  }
-
-  /** Advance the place where StrPos points within the String.
-       Counts a backslash as part of the next character. */
-  public StrPos inc()
-  {
-    pos++;
-    if (pos >= s.length())
-    {
-      eos = true;
-      return this;
-    }
-    eos = false;
-    c = s.charAt(pos);
-    if (c == esc && pos + 1 < s.length())
-    {
-      pos++;
-      c = s.charAt(pos);
-      if (c != esc)
-      {
-        dontMatch = true;
-      }
-      else
-      {
-        dontMatch = false;
-      }
-    }
-    else
-    {
-      dontMatch = false;
-    }
-    return this;
-  }
-
-  /** Compare the (possibly escaped) character
-       pointed to by StrPos.  Return true if they are the
-       same, but lways return if character pointed to is escaped. */
-  public boolean match(char ch)
-  {
-    if (dontMatch || eos)
-    {
-      return false;
-    }
-    return c == ch;
-  }
-
-  /** As match, but only matches if the character is escaped. */
-  public boolean escMatch(char ch)
-  {
-    if (!dontMatch || eos)
-    {
-      return false;
-    }
-    return c == ch;
-  }
-
-  /** Returns true if the current
-      character is escaped (preceeded by "\"). */
-  public boolean escaped()
-  {
-    return dontMatch;
-  }
-
-  /** Increment the string pointer by each character in
-       <pre>st</pre> that matches a non-escaped
-       character. */
-  public boolean incMatch(String st)
-  {
-    StrPos sp = new StrPos(this);
-    int i;
-    for (i = 0; i < st.length(); i++)
-    {
-      if (!sp.match(st.charAt(i)))
-      {
-        return false;
-      }
-      sp.inc();
-    }
-    dup(sp);
-    return true;
-  }
-
-  /** Read in an integer. */
-  public patInt getPatInt()
-  {
-    if (incMatch("inf"))
-    {
-      return new patInf();
-    }
-    int i, cnt = 0;
-    StrPos sp = new StrPos(this);
-    for (i = 0; !sp.eos && sp.c >= '0' && sp.c <= '9'; i++)
-    {
-      cnt = 10 * cnt + sp.c - '0';
-      sp.inc();
-    }
-    if (i == 0)
-    {
-      return null;
-    }
-    dup(sp);
-    return new patInt(cnt);
-  }
-
-  /** get the string that we are processing. */
-  public String getString()
-  {
-    return s;
-  }
-};
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+/**
+ Shareware: package pat
+ <a href="copyright.html">Copyright 2001, Steven R. Brandt</a>
+ */
+/**
+ * StrPos is used internally by regex to parse the regular expression.
+ */
+public class StrPos
+{
+  String s;
+
+  int pos;
+
+  /** Return the position in the string pointed to */
+  public int pos()
+  {
+    return pos;
+  }
+
+  /** This contains the escape character, which is \ by default. */
+  public char esc = Pattern.ESC;
+
+  char c;
+
+  /** Returns the current, possibly escaped, character. */
+  public char thisChar()
+  {
+    return c;
+  }
+
+  boolean dontMatch, eos;
+
+  /** tell whether we are at end of string */
+  public boolean eos()
+  {
+    return eos;
+  }
+
+  /** initialize a StrPos from another StrPos. */
+  public StrPos(StrPos sp)
+  {
+    dup(sp);
+  }
+
+  /** copy a StrPos from sp to this. */
+  public void dup(StrPos sp)
+  {
+    s = sp.s;
+    pos = sp.pos;
+    c = sp.c;
+    dontMatch = sp.dontMatch;
+    eos = sp.eos;
+  }
+
+  /**
+   * Initialize a StrPos by giving it a String, and a position within the
+   * String.
+   */
+  public StrPos(String s, int pos)
+  {
+    this.s = s;
+    this.pos = pos - 1;
+    inc();
+  }
+
+  /**
+   * Advance the place where StrPos points within the String. Counts a backslash
+   * as part of the next character.
+   */
+  public StrPos inc()
+  {
+    pos++;
+    if (pos >= s.length())
+    {
+      eos = true;
+      return this;
+    }
+    eos = false;
+    c = s.charAt(pos);
+    if (c == esc && pos + 1 < s.length())
+    {
+      pos++;
+      c = s.charAt(pos);
+      if (c != esc)
+      {
+        dontMatch = true;
+      }
+      else
+      {
+        dontMatch = false;
+      }
+    }
+    else
+    {
+      dontMatch = false;
+    }
+    return this;
+  }
+
+  /**
+   * Compare the (possibly escaped) character pointed to by StrPos. Return true
+   * if they are the same, but lways return if character pointed to is escaped.
+   */
+  public boolean match(char ch)
+  {
+    if (dontMatch || eos)
+    {
+      return false;
+    }
+    return c == ch;
+  }
+
+  /** As match, but only matches if the character is escaped. */
+  public boolean escMatch(char ch)
+  {
+    if (!dontMatch || eos)
+    {
+      return false;
+    }
+    return c == ch;
+  }
+
+  /**
+   * Returns true if the current character is escaped (preceeded by "\").
+   */
+  public boolean escaped()
+  {
+    return dontMatch;
+  }
+
+  /**
+   * Increment the string pointer by each character in
+   * 
+   * <pre>
+   * st
+   * </pre>
+   * 
+   * that matches a non-escaped character.
+   */
+  public boolean incMatch(String st)
+  {
+    StrPos sp = new StrPos(this);
+    int i;
+    for (i = 0; i < st.length(); i++)
+    {
+      if (!sp.match(st.charAt(i)))
+      {
+        return false;
+      }
+      sp.inc();
+    }
+    dup(sp);
+    return true;
+  }
+
+  /** Read in an integer. */
+  public patInt getPatInt()
+  {
+    if (incMatch("inf"))
+    {
+      return new patInf();
+    }
+    int i, cnt = 0;
+    StrPos sp = new StrPos(this);
+    for (i = 0; !sp.eos && sp.c >= '0' && sp.c <= '9'; i++)
+    {
+      cnt = 10 * cnt + sp.c - '0';
+      sp.inc();
+    }
+    if (i == 0)
+    {
+      return null;
+    }
+    dup(sp);
+    return new patInt(cnt);
+  }
+
+  /** get the string that we are processing. */
+  public String getString()
+  {
+    return s;
+  }
+};
diff --git a/src/com/stevesoft/pat/StringBufferLike.java b/src/com/stevesoft/pat/StringBufferLike.java
index 96d2178..d125758 100755
--- a/src/com/stevesoft/pat/StringBufferLike.java
+++ b/src/com/stevesoft/pat/StringBufferLike.java
@@ -1,90 +1,92 @@
-package //
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-    com.stevesoft.pat;
-
-/** A tool that is used to make the \E, \U, \L, and \Q
-    elements of a substitution. */
-public class StringBufferLike
-    implements BasicStringBufferLike
-{
-  BasicStringBufferLike sbl;
-  public StringBufferLike(BasicStringBufferLike sbl)
-  {
-    this.sbl = sbl;
-  }
-
-  char mode = 'E', altMode = ' ';
-  public StringLike toStringLike()
-  {
-    return sbl.toStringLike();
-  }
-
-  public String toString()
-  {
-    return sbl.toString();
-  }
-
-  public void append(char c)
-  {
-
-    switch (mode)
-    {
-      case 'u':
-        mode = altMode;
-        altMode = ' ';
-      case 'U':
-        sbl.append(CaseMgr.toUpperCase(c));
-        break;
-      case 'l':
-        mode = altMode;
-        altMode = ' ';
-      case 'L':
-        sbl.append(CaseMgr.toLowerCase(c));
-        break;
-      case 'Q':
-        if ( (c >= 'a' && c <= 'z')
-            || (c >= 'A' && c <= 'Z')
-            || (c >= '0' && c <= '9'))
-        {
-          ;
-        }
-        else
-        {
-          sbl.append('\\');
-        }
-      default:
-        sbl.append(c);
-        break;
-    }
-  }
-
-  public void append(String s)
-  {
-    for (int i = 0; i < s.length(); i++)
-    {
-      append(s.charAt(i));
-    }
-  }
-
-  public void setMode(char c)
-  {
-    if (c == 'u' || c == 'l')
-    {
-      if (altMode == ' ')
-      {
-        altMode = mode;
-      }
-    }
-    mode = c;
-  }
-
-  public Object unwrap()
-  {
-    return sbl.unwrap();
-  }
-}
+package //
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+com.stevesoft.pat;
+
+/**
+ * A tool that is used to make the \E, \U, \L, and \Q elements of a
+ * substitution.
+ */
+public class StringBufferLike implements BasicStringBufferLike
+{
+  BasicStringBufferLike sbl;
+
+  public StringBufferLike(BasicStringBufferLike sbl)
+  {
+    this.sbl = sbl;
+  }
+
+  char mode = 'E', altMode = ' ';
+
+  public StringLike toStringLike()
+  {
+    return sbl.toStringLike();
+  }
+
+  public String toString()
+  {
+    return sbl.toString();
+  }
+
+  public void append(char c)
+  {
+
+    switch (mode)
+    {
+    case 'u':
+      mode = altMode;
+      altMode = ' ';
+    case 'U':
+      sbl.append(CaseMgr.toUpperCase(c));
+      break;
+    case 'l':
+      mode = altMode;
+      altMode = ' ';
+    case 'L':
+      sbl.append(CaseMgr.toLowerCase(c));
+      break;
+    case 'Q':
+      if ((c >= 'a' && c <= 'z') || (c >= 'A' && c <= 'Z')
+              || (c >= '0' && c <= '9'))
+      {
+        ;
+      }
+      else
+      {
+        sbl.append('\\');
+      }
+    default:
+      sbl.append(c);
+      break;
+    }
+  }
+
+  public void append(String s)
+  {
+    for (int i = 0; i < s.length(); i++)
+    {
+      append(s.charAt(i));
+    }
+  }
+
+  public void setMode(char c)
+  {
+    if (c == 'u' || c == 'l')
+    {
+      if (altMode == ' ')
+      {
+        altMode = mode;
+      }
+    }
+    mode = c;
+  }
+
+  public Object unwrap()
+  {
+    return sbl.unwrap();
+  }
+}
diff --git a/src/com/stevesoft/pat/StringLike.java b/src/com/stevesoft/pat/StringLike.java
index 07bc441..be98ff3 100755
--- a/src/com/stevesoft/pat/StringLike.java
+++ b/src/com/stevesoft/pat/StringLike.java
@@ -1,44 +1,47 @@
-package //
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-    com.stevesoft.pat;
-
-/** Package pat can search anything that implements this
-    interface.  Package pat assumes the following:
-    <ul>
-    <li>The StringLike object will not change.  Calls to
-        charAt(int) will not vary with time.
-    <li>The length of the object being searched is known
-        before the search begins and does not vary with time.
-    </ul>
-    Note that searching String is probably faster than searching
-    other objects, so searching String is still preferred if
-    possible.
- */
-public interface StringLike
-{
-  public char charAt(int i);
-
-  public String toString();
-
-  public int length();
-
-  public String substring(int i1, int i2);
-
-  /** Obtain the underlying object, be it a String, char[],
-      RandomAccessFile, whatever. */
-  public Object unwrap();
-
-  /** By default, the result is put in a String or char[]
-      when a replace is done.  If you wish to save the result
-      in some other StringBufferLike then you can do this
-      by implementing this method, or over-riding it's behavior
-      from an existing class. */
-  public BasicStringBufferLike newStringBufferLike();
-
-  public int indexOf(char c);
-}
+package //
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+com.stevesoft.pat;
+
+/**
+ * Package pat can search anything that implements this interface. Package pat
+ * assumes the following:
+ * <ul>
+ * <li>The StringLike object will not change. Calls to charAt(int) will not
+ * vary with time.
+ * <li>The length of the object being searched is known before the search
+ * begins and does not vary with time.
+ * </ul>
+ * Note that searching String is probably faster than searching other objects,
+ * so searching String is still preferred if possible.
+ */
+public interface StringLike
+{
+  public char charAt(int i);
+
+  public String toString();
+
+  public int length();
+
+  public String substring(int i1, int i2);
+
+  /**
+   * Obtain the underlying object, be it a String, char[], RandomAccessFile,
+   * whatever.
+   */
+  public Object unwrap();
+
+  /**
+   * By default, the result is put in a String or char[] when a replace is done.
+   * If you wish to save the result in some other StringBufferLike then you can
+   * do this by implementing this method, or over-riding it's behavior from an
+   * existing class.
+   */
+  public BasicStringBufferLike newStringBufferLike();
+
+  public int indexOf(char c);
+}
diff --git a/src/com/stevesoft/pat/StringRule.java b/src/com/stevesoft/pat/StringRule.java
index e831a14..10557d8 100755
--- a/src/com/stevesoft/pat/StringRule.java
+++ b/src/com/stevesoft/pat/StringRule.java
@@ -1,37 +1,39 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-/** The apply method of this ReplaceRule simply appends the text
-    it was initialized with to the StringBufferLike.
-    @see com.stevesoft.pat.ReplaceRule
- */
-public class StringRule
-    extends ReplaceRule
-{
-  String s;
-  public StringRule(String s)
-  {
-    this.s = s;
-  }
-
-  public void apply(StringBufferLike sb, RegRes res)
-  {
-    sb.append(s);
-  }
-
-  public String toString1()
-  {
-    return s;
-  }
-
-  public Object clone1()
-  {
-    return new StringRule(s);
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+/**
+ * The apply method of this ReplaceRule simply appends the text it was
+ * initialized with to the StringBufferLike.
+ * 
+ * @see com.stevesoft.pat.ReplaceRule
+ */
+public class StringRule extends ReplaceRule
+{
+  String s;
+
+  public StringRule(String s)
+  {
+    this.s = s;
+  }
+
+  public void apply(StringBufferLike sb, RegRes res)
+  {
+    sb.append(s);
+  }
+
+  public String toString1()
+  {
+    return s;
+  }
+
+  public Object clone1()
+  {
+    return new StringRule(s);
+  }
+}
diff --git a/src/com/stevesoft/pat/SubMark.java b/src/com/stevesoft/pat/SubMark.java
index 16c3306..245fa6c 100755
--- a/src/com/stevesoft/pat/SubMark.java
+++ b/src/com/stevesoft/pat/SubMark.java
@@ -1,31 +1,32 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-/** OrMark and SubMark together implement ( ... ) */
-class SubMark
-    extends Pattern
-{
-  int end_pos, start_pos;
-  OrMark om;
-  public String toString()
-  {
-    return "";
-  }
-
-  public int matchInternal(int i, Pthings pt)
-  {
-    pt.marks[om.id + pt.nMarks] = i;
-    int ret = nextMatch(i, pt);
-    if (ret < 0)
-    {
-      pt.marks[om.id + pt.nMarks] = -1;
-    }
-    return ret;
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+/** OrMark and SubMark together implement ( ... ) */
+class SubMark extends Pattern
+{
+  int end_pos, start_pos;
+
+  OrMark om;
+
+  public String toString()
+  {
+    return "";
+  }
+
+  public int matchInternal(int i, Pthings pt)
+  {
+    pt.marks[om.id + pt.nMarks] = i;
+    int ret = nextMatch(i, pt);
+    if (ret < 0)
+    {
+      pt.marks[om.id + pt.nMarks] = -1;
+    }
+    return ret;
+  }
+}
diff --git a/src/com/stevesoft/pat/TransPat.java b/src/com/stevesoft/pat/TransPat.java
index 4c71c1f..b9a0989 100755
--- a/src/com/stevesoft/pat/TransPat.java
+++ b/src/com/stevesoft/pat/TransPat.java
@@ -1,45 +1,51 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-/** This class is used to implement the Transformer
-    @see com.stevesoft.pat.Transform
- */
-class TransPat
-    extends Pattern
-{
-  Regex[] ra = new Regex[10];
-  int ra_len = 0;
-  int pn = -1;
-  public String toString()
-  {
-    return "(?#TransPat)";
-  }
-
-  TransPat()
-  {}
-
-  int lastMatchedTo = -1;
-  public int matchInternal(int pos, Pthings pt)
-  {
-    for (int i = 0; i < ra_len; i++)
-    {
-      pt.ignoreCase = ra[i].ignoreCase;
-      pt.mFlag = ra[i].mFlag;
-      pt.dotDoesntMatchCR = Regex.dotDoesntMatchCR;
-      int r = ra[i].thePattern.matchInternal(pos, pt);
-      if (r >= 0)
-      {
-        pn = i;
-        return r;
-      }
-    }
-    pn = -1;
-    return -1;
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+/**
+ * This class is used to implement the Transformer
+ * 
+ * @see com.stevesoft.pat.Transform
+ */
+class TransPat extends Pattern
+{
+  Regex[] ra = new Regex[10];
+
+  int ra_len = 0;
+
+  int pn = -1;
+
+  public String toString()
+  {
+    return "(?#TransPat)";
+  }
+
+  TransPat()
+  {
+  }
+
+  int lastMatchedTo = -1;
+
+  public int matchInternal(int pos, Pthings pt)
+  {
+    for (int i = 0; i < ra_len; i++)
+    {
+      pt.ignoreCase = ra[i].ignoreCase;
+      pt.mFlag = ra[i].mFlag;
+      pt.dotDoesntMatchCR = Regex.dotDoesntMatchCR;
+      int r = ra[i].thePattern.matchInternal(pos, pt);
+      if (r >= 0)
+      {
+        pn = i;
+        return r;
+      }
+    }
+    pn = -1;
+    return -1;
+  }
+}
diff --git a/src/com/stevesoft/pat/Transformer.java b/src/com/stevesoft/pat/Transformer.java
index 843fbfa..d770f08 100755
--- a/src/com/stevesoft/pat/Transformer.java
+++ b/src/com/stevesoft/pat/Transformer.java
@@ -1,219 +1,233 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-import com.stevesoft.pat.wrap.*;
-
-/** Replacement rule used by the Transformer.
-    @see com.stevesoft.pat.Transformer
- */
-class TransRepRule
-    extends ReplaceRule
-{
-  Transformer t;
-  TransRepRule(Transformer t)
-  {
-    this.t = t;
-  }
-
-  public String toString1()
-  {
-    return "";
-  }
-
-  public Object clone1()
-  {
-    return new TransRepRule(t);
-  }
-
-  public void apply(StringBufferLike sb, RegRes rr)
-  {
-    // get the ReplaceRule of the Regex that matched.
-    next = t.tp.ra[t.tp.pn].getReplaceRule();
-  }
-}
-
-/** Sometimes you want to replace a whole bunch of things
-  that might occur within a single line of text.  One efficient
-  way to do this, both in terms of performance and programming
-  ease, is with Transformer. The Transformer contains an array
-  of Regex's and uses the Regex that matches earliest within the
-  text to do the replacing, if two Regex's match at the same
-  time it uses the one put in the Transformer first.
-  <p>
-  This feature can be used to prevent transformations from
-  occurring in certain regions. For example, if I add the rule
-  s'//.*'$&' and then add the
-  rule s/hello/goodbye/ the Transformer will replace "hello"
-  with "goodbye" except when it occurs inside a double-slash
-  style of comment.   The transformation on the comment goes first,
-  does nothing, and precludes transformation on the same region
-  of text as the s/hello/goodbye/ rule.
-  <p>
-  So far, at least, this class does not have the capability of
-  turning into a giant robot :-)
- */
-public class Transformer
-{
-  TransPat tp;
-  Regex rp = new Regex();
-  boolean auto_optimize;
-
-  /** Get a replacer to that works with the current Regex.
-   @see com.stevesoft.pat.Replacer
-   */
-  public Replacer getReplacer()
-  {
-    return rp.getReplacer();
-  }
-
-  /** Instantiate a new Transformer object. */
-  public Transformer(boolean auto)
-  {
-    auto_optimize = auto;
-    tp = new TransPat();
-    rp.setReplaceRule(new TransRepRule(this));
-    rp.thePattern = tp;
-  }
-
-  /** Add a new Regex to the set of Regex's. */
-  public void add(Regex r)
-  {
-    if (auto_optimize)
-    {
-      r.optimize();
-    }
-    tp.ra[tp.ra_len++] = r;
-    if (tp.ra.length == tp.ra_len)
-    {
-      Regex[] ra2 = new Regex[tp.ra_len + 10];
-      for (int i = 0; i < tp.ra_len; i++)
-      {
-        ra2[i] = tp.ra[i];
-      }
-      tp.ra = ra2;
-    }
-    rp.numSubs_ = r.numSubs_ > rp.numSubs_ ? r.numSubs_ : rp.numSubs_;
-  }
-
-  /** Returns the number of Regex's in this Transformer. */
-  public int patterns()
-  {
-    return tp.ra_len;
-  }
-
-  /** Get the Regex at position i in this Transformer. */
-  public Regex getRegexAt(int i)
-  {
-    if (i >= tp.ra_len)
-    {
-      throw new ArrayIndexOutOfBoundsException("i=" + i + ">=" + patterns());
-    }
-    if (i < 0)
-    {
-      throw new ArrayIndexOutOfBoundsException("i=" + i + "< 0");
-    }
-    return tp.ra[i];
-  }
-
-  /** Set the Regex at position i in this Transformer. */
-  public void setRegexAt(Regex rx, int i)
-  {
-    if (i >= tp.ra_len)
-    {
-      throw new ArrayIndexOutOfBoundsException("i=" + i + ">=" + patterns());
-    }
-    if (i < 0)
-    {
-      throw new ArrayIndexOutOfBoundsException("i=" + i + "< 0");
-    }
-    tp.ra[i] = rx;
-  }
-
-  /** Add a new Regex by calling Regex.perlCode
-      @see com.stevesoft.pat.Regex#perlCode(java.lang.String)
-   */
-  public void add(String rs)
-  {
-    Regex r = Regex.perlCode(rs);
-    if (r == null)
-    {
-      throw new NullPointerException("bad pattern to Regex.perlCode: " + rs);
-    }
-    add(r);
-  }
-
-  /** Add an array of Strings (which will be converted to
-      Regex's via the Regex.perlCode method.
-      @see com.stevesoft.pat.Regex#perlCode(java.lang.String)
-   */
-  public void add(String[] array)
-  {
-    for (int i = 0; i < array.length; i++)
-    {
-      add(array[i]);
-    }
-  }
-
-  /** Replace all matches in the current String. */
-  public String replaceAll(String s)
-  {
-    return dorep(s, 0, s.length());
-  }
-
-  public StringLike replaceAll(StringLike s)
-  {
-    return dorep(s, 0, s.length());
-  }
-
-  /** Replace all matching patterns beginning at position start. */
-  public String replaceAllFrom(String s, int start)
-  {
-    return dorep(s, start, s.length());
-  }
-
-  /** Replace all matching patterns beginning between the positions
-      start and end inclusive. */
-  public String replaceAllRegion(String s, int start, int end)
-  {
-    return dorep(s, start, end);
-  }
-
-  Replacer repr = new Replacer();
-  final StringLike dorep(StringLike s, int start, int end)
-  {
-    StringLike tfmd = repr.replaceAllRegion(s, rp, start, end);
-    tp.lastMatchedTo = repr.lastMatchedTo;
-    return tfmd;
-  }
-
-  final String dorep(String s, int start, int end)
-  {
-    return dorep(new StringWrap(s), start, end).toString();
-  }
-
-  /** Replace the first matching pattern in String s. */
-  public String replaceFirst(String s)
-  {
-    return dorep(s, 0, s.length());
-  }
-
-  /** Replace the first matching pattern after position start in
-      String s. */
-  public String replaceFirstFrom(String s, int start)
-  {
-    return dorep(s, start, s.length());
-  }
-
-  /** Replace the first matching pattern that begins between
-      start and end inclusive. */
-  public String replaceFirstRegion(String s, int start, int end)
-  {
-    return dorep(s, start, end);
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+import com.stevesoft.pat.wrap.*;
+
+/**
+ * Replacement rule used by the Transformer.
+ * 
+ * @see com.stevesoft.pat.Transformer
+ */
+class TransRepRule extends ReplaceRule
+{
+  Transformer t;
+
+  TransRepRule(Transformer t)
+  {
+    this.t = t;
+  }
+
+  public String toString1()
+  {
+    return "";
+  }
+
+  public Object clone1()
+  {
+    return new TransRepRule(t);
+  }
+
+  public void apply(StringBufferLike sb, RegRes rr)
+  {
+    // get the ReplaceRule of the Regex that matched.
+    next = t.tp.ra[t.tp.pn].getReplaceRule();
+  }
+}
+
+/**
+ * Sometimes you want to replace a whole bunch of things that might occur within
+ * a single line of text. One efficient way to do this, both in terms of
+ * performance and programming ease, is with Transformer. The Transformer
+ * contains an array of Regex's and uses the Regex that matches earliest within
+ * the text to do the replacing, if two Regex's match at the same time it uses
+ * the one put in the Transformer first.
+ * <p>
+ * This feature can be used to prevent transformations from occurring in certain
+ * regions. For example, if I add the rule s'//.*'$&' and then add the rule
+ * s/hello/goodbye/ the Transformer will replace "hello" with "goodbye" except
+ * when it occurs inside a double-slash style of comment. The transformation on
+ * the comment goes first, does nothing, and precludes transformation on the
+ * same region of text as the s/hello/goodbye/ rule.
+ * <p>
+ * So far, at least, this class does not have the capability of turning into a
+ * giant robot :-)
+ */
+public class Transformer
+{
+  TransPat tp;
+
+  Regex rp = new Regex();
+
+  boolean auto_optimize;
+
+  /**
+   * Get a replacer to that works with the current Regex.
+   * 
+   * @see com.stevesoft.pat.Replacer
+   */
+  public Replacer getReplacer()
+  {
+    return rp.getReplacer();
+  }
+
+  /** Instantiate a new Transformer object. */
+  public Transformer(boolean auto)
+  {
+    auto_optimize = auto;
+    tp = new TransPat();
+    rp.setReplaceRule(new TransRepRule(this));
+    rp.thePattern = tp;
+  }
+
+  /** Add a new Regex to the set of Regex's. */
+  public void add(Regex r)
+  {
+    if (auto_optimize)
+    {
+      r.optimize();
+    }
+    tp.ra[tp.ra_len++] = r;
+    if (tp.ra.length == tp.ra_len)
+    {
+      Regex[] ra2 = new Regex[tp.ra_len + 10];
+      for (int i = 0; i < tp.ra_len; i++)
+      {
+        ra2[i] = tp.ra[i];
+      }
+      tp.ra = ra2;
+    }
+    rp.numSubs_ = r.numSubs_ > rp.numSubs_ ? r.numSubs_ : rp.numSubs_;
+  }
+
+  /** Returns the number of Regex's in this Transformer. */
+  public int patterns()
+  {
+    return tp.ra_len;
+  }
+
+  /** Get the Regex at position i in this Transformer. */
+  public Regex getRegexAt(int i)
+  {
+    if (i >= tp.ra_len)
+    {
+      throw new ArrayIndexOutOfBoundsException("i=" + i + ">=" + patterns());
+    }
+    if (i < 0)
+    {
+      throw new ArrayIndexOutOfBoundsException("i=" + i + "< 0");
+    }
+    return tp.ra[i];
+  }
+
+  /** Set the Regex at position i in this Transformer. */
+  public void setRegexAt(Regex rx, int i)
+  {
+    if (i >= tp.ra_len)
+    {
+      throw new ArrayIndexOutOfBoundsException("i=" + i + ">=" + patterns());
+    }
+    if (i < 0)
+    {
+      throw new ArrayIndexOutOfBoundsException("i=" + i + "< 0");
+    }
+    tp.ra[i] = rx;
+  }
+
+  /**
+   * Add a new Regex by calling Regex.perlCode
+   * 
+   * @see com.stevesoft.pat.Regex#perlCode(java.lang.String)
+   */
+  public void add(String rs)
+  {
+    Regex r = Regex.perlCode(rs);
+    if (r == null)
+    {
+      throw new NullPointerException("bad pattern to Regex.perlCode: " + rs);
+    }
+    add(r);
+  }
+
+  /**
+   * Add an array of Strings (which will be converted to Regex's via the
+   * Regex.perlCode method.
+   * 
+   * @see com.stevesoft.pat.Regex#perlCode(java.lang.String)
+   */
+  public void add(String[] array)
+  {
+    for (int i = 0; i < array.length; i++)
+    {
+      add(array[i]);
+    }
+  }
+
+  /** Replace all matches in the current String. */
+  public String replaceAll(String s)
+  {
+    return dorep(s, 0, s.length());
+  }
+
+  public StringLike replaceAll(StringLike s)
+  {
+    return dorep(s, 0, s.length());
+  }
+
+  /** Replace all matching patterns beginning at position start. */
+  public String replaceAllFrom(String s, int start)
+  {
+    return dorep(s, start, s.length());
+  }
+
+  /**
+   * Replace all matching patterns beginning between the positions start and end
+   * inclusive.
+   */
+  public String replaceAllRegion(String s, int start, int end)
+  {
+    return dorep(s, start, end);
+  }
+
+  Replacer repr = new Replacer();
+
+  final StringLike dorep(StringLike s, int start, int end)
+  {
+    StringLike tfmd = repr.replaceAllRegion(s, rp, start, end);
+    tp.lastMatchedTo = repr.lastMatchedTo;
+    return tfmd;
+  }
+
+  final String dorep(String s, int start, int end)
+  {
+    return dorep(new StringWrap(s), start, end).toString();
+  }
+
+  /** Replace the first matching pattern in String s. */
+  public String replaceFirst(String s)
+  {
+    return dorep(s, 0, s.length());
+  }
+
+  /**
+   * Replace the first matching pattern after position start in String s.
+   */
+  public String replaceFirstFrom(String s, int start)
+  {
+    return dorep(s, start, s.length());
+  }
+
+  /**
+   * Replace the first matching pattern that begins between start and end
+   * inclusive.
+   */
+  public String replaceFirstRegion(String s, int start, int end)
+  {
+    return dorep(s, start, end);
+  }
+}
diff --git a/src/com/stevesoft/pat/UniValidator.java b/src/com/stevesoft/pat/UniValidator.java
index 4d86074..31ae272 100755
--- a/src/com/stevesoft/pat/UniValidator.java
+++ b/src/com/stevesoft/pat/UniValidator.java
@@ -1,25 +1,24 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-/** This provides a base class for all the Unicode character
- * matching rules.
- */
-class UniValidator
-    extends Validator
-{
-  public patInt minChars()
-  {
-    return new patInt(1);
-  }
-
-  public patInt maxChars()
-  {
-    return new patInt(1);
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+/**
+ * This provides a base class for all the Unicode character matching rules.
+ */
+class UniValidator extends Validator
+{
+  public patInt minChars()
+  {
+    return new patInt(1);
+  }
+
+  public patInt maxChars()
+  {
+    return new patInt(1);
+  }
+}
diff --git a/src/com/stevesoft/pat/Validator.java b/src/com/stevesoft/pat/Validator.java
index 34b07da..dbedca5 100755
--- a/src/com/stevesoft/pat/Validator.java
+++ b/src/com/stevesoft/pat/Validator.java
@@ -1,70 +1,75 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-/** This class makes it easy to create your own patterns
- and integrate them into Regex.  For more detail, see the
- example file <a href="http://javaregex.com/code/deriv2.java.html">deriv2.java</a> or
- <a href="http://javaregex.com/code/deriv3.java.html">deriv3.java</a>. */
-
-public class Validator
-{
-  String argsave = null;
-  String pattern = ".";
-  /**
-       This method does extra checking on a matched section of
-       a String beginning at position start and ending at end.
-       The idea is that you can do extra checking with this
-       that you don't know how to do with a standard Regex.
-
-       If this method is successful, it returns the location
-       of the end of this pattern element -- that may be the
-       value end provided or some other value.  A negative
-       value signifies that a match failure.
-
-       By default, this method just returns end and thus
-       does nothing.
-       @see com.stevesoft.pat.Regex#define(java.lang.String,java.lang.String,com.stevesoft.pat.Validator)
-   */
-  public int validate(StringLike src, int start, int end)
-  {
-    return end;
-  }
-
-  /* This method allows you to modify the behavior of this
-       validator by making a new Validator object.  If a Validator
-       named "foo" is defined, then the pattern "{??foo:bar}" will
-       cause Regex to first get the Validator given to Regex.define
-       and then to call its arg method with the string "bar".
-       If this method returns a null (the default) you get the same
-       behavior as the pattern "{??foo}" would supply. */
-  public Validator arg(String s)
-  {
-    return null;
-  }
-
-  /** For optimization it is helpful, but not necessary, that
-       you define the minimum number of characters this validator
-       will allow to match.  To do this
-       return new patInt(number) where number is the smallest
-       number of characters that can match. */
-  public patInt minChars()
-  {
-    return new patInt(0);
-  }
-
-  /** For optimization it is helpful, but not necessary, that
-       you define the maximum number of characters this validator
-       will allow to match.  To do this either
-       return new patInt(number), or new patInf() if an infinite
-       number of characters may match. */
-  public patInt maxChars()
-  {
-    return new patInf();
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+/**
+ * This class makes it easy to create your own patterns and integrate them into
+ * Regex. For more detail, see the example file <a
+ * href="http://javaregex.com/code/deriv2.java.html">deriv2.java</a> or <a
+ * href="http://javaregex.com/code/deriv3.java.html">deriv3.java</a>.
+ */
+
+public class Validator
+{
+  String argsave = null;
+
+  String pattern = ".";
+
+  /**
+   * This method does extra checking on a matched section of a String beginning
+   * at position start and ending at end. The idea is that you can do extra
+   * checking with this that you don't know how to do with a standard Regex.
+   * 
+   * If this method is successful, it returns the location of the end of this
+   * pattern element -- that may be the value end provided or some other value.
+   * A negative value signifies that a match failure.
+   * 
+   * By default, this method just returns end and thus does nothing.
+   * 
+   * @see com.stevesoft.pat.Regex#define(java.lang.String,java.lang.String,com.stevesoft.pat.Validator)
+   */
+  public int validate(StringLike src, int start, int end)
+  {
+    return end;
+  }
+
+  /*
+   * This method allows you to modify the behavior of this validator by making a
+   * new Validator object. If a Validator named "foo" is defined, then the
+   * pattern "{??foo:bar}" will cause Regex to first get the Validator given to
+   * Regex.define and then to call its arg method with the string "bar". If this
+   * method returns a null (the default) you get the same behavior as the
+   * pattern "{??foo}" would supply.
+   */
+  public Validator arg(String s)
+  {
+    return null;
+  }
+
+  /**
+   * For optimization it is helpful, but not necessary, that you define the
+   * minimum number of characters this validator will allow to match. To do this
+   * return new patInt(number) where number is the smallest number of characters
+   * that can match.
+   */
+  public patInt minChars()
+  {
+    return new patInt(0);
+  }
+
+  /**
+   * For optimization it is helpful, but not necessary, that you define the
+   * maximum number of characters this validator will allow to match. To do this
+   * either return new patInt(number), or new patInf() if an infinite number of
+   * characters may match.
+   */
+  public patInt maxChars()
+  {
+    return new patInf();
+  }
+}
diff --git a/src/com/stevesoft/pat/WantMoreTextReplaceRule.java b/src/com/stevesoft/pat/WantMoreTextReplaceRule.java
index 34b73e5..6c0ddeb 100755
--- a/src/com/stevesoft/pat/WantMoreTextReplaceRule.java
+++ b/src/com/stevesoft/pat/WantMoreTextReplaceRule.java
@@ -1,28 +1,29 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-/** Triggers the reading of another line of text, allowing a longer
-    pattern to match -- for details see
-    <a href="http://javaregex.com/code/WantMore.java.html">WantMore.java</a>.
- */
-public class WantMoreTextReplaceRule
-    extends SpecialRule
-{
-  public WantMoreTextReplaceRule()
-  {}
-
-  public void apply(StringBufferLike sb, RegRes res)
-  {
-  }
-
-  public String toString1()
-  {
-    return "${WANT_MORE_TEXT}";
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+/**
+ * Triggers the reading of another line of text, allowing a longer pattern to
+ * match -- for details see <a
+ * href="http://javaregex.com/code/WantMore.java.html">WantMore.java</a>.
+ */
+public class WantMoreTextReplaceRule extends SpecialRule
+{
+  public WantMoreTextReplaceRule()
+  {
+  }
+
+  public void apply(StringBufferLike sb, RegRes res)
+  {
+  }
+
+  public String toString1()
+  {
+    return "${WANT_MORE_TEXT}";
+  }
+}
diff --git a/src/com/stevesoft/pat/lookAhead.java b/src/com/stevesoft/pat/lookAhead.java
index 73be36a..d7d71c3 100755
--- a/src/com/stevesoft/pat/lookAhead.java
+++ b/src/com/stevesoft/pat/lookAhead.java
@@ -1,99 +1,99 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-import java.util.*;
-
-/** Implements "(?=  )" and "(?! )" */
-class lookAhead
-    extends Or
-{
-  boolean reverse;
-  lookAhead(boolean b)
-  {
-    reverse = b;
-  }
-
-  public Pattern getNext()
-  {
-    return null;
-  }
-
-  public int nextMatch(int pos, Pthings pt)
-  {
-    Pattern p = super.getNext();
-    if (p != null)
-    {
-      return p.matchInternal(pos, pt);
-    }
-    else
-    {
-      return pos;
-    }
-  }
-
-  public int matchInternal(int pos, Pthings pt)
-  {
-    if (super.matchInternal(pos, pt) >= 0)
-    {
-      if (reverse)
-      {
-        return -1;
-      }
-      else
-      {
-        return nextMatch(pos, pt);
-      }
-    }
-    else
-    {
-      if (reverse)
-      {
-        return nextMatch(pos, pt);
-      }
-      else
-      {
-        return -1;
-      }
-    }
-  }
-
-  String leftForm()
-  {
-    if (reverse)
-    {
-      return "(?!";
-    }
-    else
-    {
-      return "(?=";
-    }
-  }
-
-  public patInt minChars()
-  {
-    return new patInt(0);
-  }
-
-  public patInt maxChars()
-  {
-    return new patInt(0);
-  }
-
-  Pattern clone1(Hashtable h)
-  {
-    lookAhead la = new lookAhead(reverse);
-    h.put(this, la);
-    h.put(la, la);
-    for (int i = 0; i < v.size(); i++)
-    {
-      la.v.addElement( ( (Pattern) v.elementAt(i)).clone(h));
-    }
-    return la;
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+import java.util.*;
+
+/** Implements "(?= )" and "(?! )" */
+class lookAhead extends Or
+{
+  boolean reverse;
+
+  lookAhead(boolean b)
+  {
+    reverse = b;
+  }
+
+  public Pattern getNext()
+  {
+    return null;
+  }
+
+  public int nextMatch(int pos, Pthings pt)
+  {
+    Pattern p = super.getNext();
+    if (p != null)
+    {
+      return p.matchInternal(pos, pt);
+    }
+    else
+    {
+      return pos;
+    }
+  }
+
+  public int matchInternal(int pos, Pthings pt)
+  {
+    if (super.matchInternal(pos, pt) >= 0)
+    {
+      if (reverse)
+      {
+        return -1;
+      }
+      else
+      {
+        return nextMatch(pos, pt);
+      }
+    }
+    else
+    {
+      if (reverse)
+      {
+        return nextMatch(pos, pt);
+      }
+      else
+      {
+        return -1;
+      }
+    }
+  }
+
+  String leftForm()
+  {
+    if (reverse)
+    {
+      return "(?!";
+    }
+    else
+    {
+      return "(?=";
+    }
+  }
+
+  public patInt minChars()
+  {
+    return new patInt(0);
+  }
+
+  public patInt maxChars()
+  {
+    return new patInt(0);
+  }
+
+  Pattern clone1(Hashtable h)
+  {
+    lookAhead la = new lookAhead(reverse);
+    h.put(this, la);
+    h.put(la, la);
+    for (int i = 0; i < v.size(); i++)
+    {
+      la.v.addElement(((Pattern) v.elementAt(i)).clone(h));
+    }
+    return la;
+  }
+}
diff --git a/src/com/stevesoft/pat/oneChar.java b/src/com/stevesoft/pat/oneChar.java
index da7c6d0..ebbe991 100755
--- a/src/com/stevesoft/pat/oneChar.java
+++ b/src/com/stevesoft/pat/oneChar.java
@@ -1,75 +1,76 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-import java.util.*;
-
-/** This class matches a single character. */
-class oneChar
-    extends Pattern
-{
-  char c, altc, altc2;
-  int mask;
-  public oneChar(char ci)
-  {
-    c = ci;
-    char cu, cl, ct;
-    cu = CaseMgr.toUpperCase(c);
-    cl = CaseMgr.toLowerCase(c);
-    ct = CaseMgr.toTitleCase(c);
-    if (c == cu)
-    {
-      altc = cl;
-      altc2 = ct;
-    }
-    else if (c == cl)
-    {
-      altc = cu;
-      altc2 = ct;
-    }
-    else
-    {
-      altc = cl;
-      altc2 = cu;
-    }
-    mask = c & altc & altc2;
-  }
-
-  public int matchInternal(int pos, Pthings pt)
-  {
-    char p;
-    int ret = -1;
-    if (pos < pt.src.length() && !Masked(pos, pt)
-        && ( (p = pt.src.charAt(pos)) == c ||
-            (pt.ignoreCase && (p == altc || p == altc2))))
-    {
-      ret = nextMatch(pos + 1, pt);
-    }
-    return ret;
-  }
-
-  public String toString()
-  {
-    return protect("" + c, PROTECT_THESE, ESC) + nextString();
-  }
-
-  public patInt minChars()
-  {
-    return new patInt(1);
-  }
-
-  public patInt maxChars()
-  {
-    return new patInt(1);
-  }
-
-  Pattern clone1(Hashtable h)
-  {
-    return new oneChar(c);
-  }
-};
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+import java.util.*;
+
+/** This class matches a single character. */
+class oneChar extends Pattern
+{
+  char c, altc, altc2;
+
+  int mask;
+
+  public oneChar(char ci)
+  {
+    c = ci;
+    char cu, cl, ct;
+    cu = CaseMgr.toUpperCase(c);
+    cl = CaseMgr.toLowerCase(c);
+    ct = CaseMgr.toTitleCase(c);
+    if (c == cu)
+    {
+      altc = cl;
+      altc2 = ct;
+    }
+    else if (c == cl)
+    {
+      altc = cu;
+      altc2 = ct;
+    }
+    else
+    {
+      altc = cl;
+      altc2 = cu;
+    }
+    mask = c & altc & altc2;
+  }
+
+  public int matchInternal(int pos, Pthings pt)
+  {
+    char p;
+    int ret = -1;
+    if (pos < pt.src.length()
+            && !Masked(pos, pt)
+            && ((p = pt.src.charAt(pos)) == c || (pt.ignoreCase && (p == altc || p == altc2))))
+    {
+      ret = nextMatch(pos + 1, pt);
+    }
+    return ret;
+  }
+
+  public String toString()
+  {
+    return protect("" + c, PROTECT_THESE, ESC) + nextString();
+  }
+
+  public patInt minChars()
+  {
+    return new patInt(1);
+  }
+
+  public patInt maxChars()
+  {
+    return new patInt(1);
+  }
+
+  Pattern clone1(Hashtable h)
+  {
+    return new oneChar(c);
+  }
+};
diff --git a/src/com/stevesoft/pat/parsePerl.java b/src/com/stevesoft/pat/parsePerl.java
index 5de9f07..0d1f14e 100755
--- a/src/com/stevesoft/pat/parsePerl.java
+++ b/src/com/stevesoft/pat/parsePerl.java
@@ -1,379 +1,373 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-/** This class provides a method for parsing the "s/.../.../" constructs
- of Regex.perlCode.
- @see Regex#perlCode
- */
-class parsePerl
-{
-  final static char close(char c)
-  {
-    // This switch statement does not behave
-    // properly when compiled with jdk1.1.5
-    // and the -O flag.
-    /*
-             switch(c) {
-             case '[':
-      return ']';
-             case '(':
-      return ')';
-             case '{':
-      return '}';
-             }
-             return c;*/
-    if (c == '<')
-    {
-      return '>';
-    }
-    if (c == '[')
-    {
-      return ']';
-    }
-    if (c == '(')
-    {
-      return ')';
-    }
-    if (c == '{')
-    {
-      return '}';
-    }
-    return c;
-  }
-
-  final public static String codify(String s, boolean keepbs)
-  {
-    return codify(s, 0, s.length(), keepbs);
-  }
-
-  final public static String codify(String s, int i0, int iN, boolean keepbs)
-  {
-    StringBuffer sb = new StringBuffer();
-    boolean ucmode = false, lcmode = false, litmode = false;
-    boolean uc1 = false, lc1 = false;
-    boolean modified = false;
-    for (int i = i0; i < iN; i++)
-    {
-      char c = s.charAt(i);
-      boolean mf = true, app = true;
-      if (c == '\\')
-      {
-        app = false;
-        i++;
-        if (i < s.length())
-        {
-          char c2 = s.charAt(i);
-          switch (c2)
-          {
-            case 'Q':
-              litmode = true;
-              break;
-            case 'U':
-              ucmode = true;
-              break;
-            case 'L':
-              lcmode = true;
-              break;
-            case 'u':
-              uc1 = true;
-              break;
-            case 'l':
-              lc1 = true;
-              break;
-            case 'E':
-              uc1 = lc1 = ucmode = lcmode = litmode = false;
-              break;
-            default:
-              if (keepbs)
-              {
-                sb.append('\\');
-              }
-              c = c2;
-              if (keepbs)
-              {
-                mf = false;
-              }
-              app = true;
-              break;
-          }
-          modified |= mf;
-        }
-      }
-      if (app)
-      {
-        if (lc1)
-        {
-          c = lc(c);
-          lc1 = false;
-        }
-        else if (uc1)
-        {
-          c = uc(c);
-          uc1 = false;
-        }
-        else if (ucmode)
-        {
-          c = uc(c);
-        }
-        else if (lcmode)
-        {
-          c = lc(c);
-        }
-        if (litmode && needbs(c))
-        {
-          sb.append('\\');
-        }
-        sb.append(c);
-      }
-    }
-    return modified ? sb.toString() : s;
-  }
-
-  final static char uc(char c)
-  {
-    return CaseMgr.toUpperCase(c);
-  }
-
-  final static char lc(char c)
-  {
-    return CaseMgr.toLowerCase(c);
-  }
-
-  final static boolean needbs(char c)
-  {
-    if (c >= 'a' && c <= 'z')
-    {
-      return false;
-    }
-    if (c >= 'A' && c <= 'Z')
-    {
-      return false;
-    }
-    if (c >= '0' && c <= '9')
-    {
-      return false;
-    }
-    if (c == '_')
-    {
-      return false;
-    }
-    return true;
-  }
-
-  final static Regex parse(String s)
-  {
-    boolean igncase = false, optim = false, gFlag = false;
-    boolean sFlag = false, mFlag = false, xFlag = false;
-
-    StringBuffer s1 = new StringBuffer();
-    StringBuffer s2 = new StringBuffer();
-    int i = 0, count = 0;
-    char mode, delim = '/', cdelim = '/';
-    if (s.length() >= 3 && s.charAt(0) == 's')
-    {
-      mode = 's';
-      delim = s.charAt(1);
-      cdelim = close(delim);
-      i = 2;
-    }
-    else if (s.length() >= 2 && s.charAt(0) == 'm')
-    {
-      mode = 'm';
-      delim = s.charAt(1);
-      cdelim = close(delim);
-      i = 2;
-    }
-    else if (s.length() >= 1 && s.charAt(0) == '/')
-    {
-      mode = 'm';
-      i = 1;
-    }
-    else
-    {
-      try
-      {
-        RegSyntaxError.endItAll(
-            "Regex.perlCode should be of the " +
-            "form s/// or m// or //");
-      }
-      catch (RegSyntax rs)
-      {}
-      return null;
-    }
-    for (; i < s.length(); i++)
-    {
-      if (s.charAt(i) == '\\')
-      {
-        s1.append('\\');
-        i++;
-      }
-      else if (s.charAt(i) == cdelim && count == 0)
-      {
-        i++;
-        break;
-      }
-      else if (s.charAt(i) == delim && cdelim != delim)
-      {
-        count++;
-      }
-      else if (s.charAt(i) == cdelim && cdelim != delim)
-      {
-        count--;
-      }
-      s1.append(s.charAt(i));
-    }
-    if (mode == 's' && cdelim != delim)
-    {
-      while (i < s.length() && Prop.isWhite(s.charAt(i)))
-      {
-        i++;
-      }
-      if (i >= s.length())
-      {
-        try
-        {
-          RegSyntaxError.endItAll("" + mode + delim + " needs " + cdelim);
-        }
-        catch (RegSyntax rs)
-        {}
-        return null;
-      }
-      cdelim = close(delim = s.charAt(i));
-      i++;
-    }
-    count = 0;
-    if (mode == 's')
-    {
-      for (; i < s.length(); i++)
-      {
-        if (s.charAt(i) == '\\')
-        {
-          s2.append('\\');
-          i++;
-        }
-        else if (s.charAt(i) == cdelim && count == 0)
-        {
-          i++;
-          break;
-        }
-        else if (s.charAt(i) == delim && cdelim != delim)
-        {
-          count++;
-        }
-        else if (s.charAt(i) == cdelim && cdelim != delim)
-        {
-          count--;
-        }
-        s2.append(s.charAt(i));
-      }
-    }
-    for (; i < s.length(); i++)
-    {
-      char c = s.charAt(i);
-      switch (c)
-      {
-        case 'x':
-          xFlag = true;
-          break;
-        case 'i':
-          igncase = true;
-          break;
-        case 'o':
-          optim = true;
-          break;
-        case 's':
-          sFlag = true;
-          break;
-        case 'm':
-          mFlag = true;
-          break;
-        case 'g':
-          gFlag = true;
-          break;
-        default:
-
-          // syntax error!
-          try
-          {
-            RegSyntaxError.endItAll("Illegal flag to pattern: " + c);
-          }
-          catch (RegSyntax rs)
-          {}
-          return null;
-      }
-    }
-    Regex r = new Regex();
-    try
-    {
-      String pat = s1.toString(), reprul = s2.toString();
-      if (xFlag)
-      {
-        pat = strip(pat);
-        reprul = strip(reprul);
-      }
-      r.compile(pat);
-      r.ignoreCase |= igncase;
-      r.gFlag |= gFlag;
-      r.sFlag |= sFlag;
-      r.mFlag |= mFlag;
-      if (optim)
-      {
-        r.optimize();
-      }
-      if (delim == '\'')
-      {
-        r.setReplaceRule(new StringRule(reprul));
-      }
-      else
-      {
-        r.setReplaceRule(ReplaceRule.perlCode(reprul));
-      }
-    }
-    catch (RegSyntax rs)
-    {
-      r = null;
-    }
-    return r;
-  }
-
-  static String strip(String s)
-  {
-    StringBuffer sb = new StringBuffer();
-    for (int i = 0; i < s.length(); i++)
-    {
-      char c = s.charAt(i);
-      if (Prop.isWhite(c))
-      {
-        ;
-      }
-      else if (c == '#')
-      {
-        i++;
-        while (i < s.length())
-        {
-          if (s.charAt(i) == '\n')
-          {
-            break;
-          }
-          i++;
-        }
-      }
-      else if (c == '\\')
-      {
-        sb.append(c);
-        sb.append(s.charAt(++i));
-      }
-      else
-      {
-        sb.append(c);
-      }
-    }
-    return sb.toString();
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+/**
+ * This class provides a method for parsing the "s/.../.../" constructs of
+ * Regex.perlCode.
+ * 
+ * @see Regex#perlCode
+ */
+class parsePerl
+{
+  final static char close(char c)
+  {
+    // This switch statement does not behave
+    // properly when compiled with jdk1.1.5
+    // and the -O flag.
+    /*
+     * switch(c) { case '[': return ']'; case '(': return ')'; case '{': return
+     * '}'; } return c;
+     */
+    if (c == '<')
+    {
+      return '>';
+    }
+    if (c == '[')
+    {
+      return ']';
+    }
+    if (c == '(')
+    {
+      return ')';
+    }
+    if (c == '{')
+    {
+      return '}';
+    }
+    return c;
+  }
+
+  final public static String codify(String s, boolean keepbs)
+  {
+    return codify(s, 0, s.length(), keepbs);
+  }
+
+  final public static String codify(String s, int i0, int iN, boolean keepbs)
+  {
+    StringBuffer sb = new StringBuffer();
+    boolean ucmode = false, lcmode = false, litmode = false;
+    boolean uc1 = false, lc1 = false;
+    boolean modified = false;
+    for (int i = i0; i < iN; i++)
+    {
+      char c = s.charAt(i);
+      boolean mf = true, app = true;
+      if (c == '\\')
+      {
+        app = false;
+        i++;
+        if (i < s.length())
+        {
+          char c2 = s.charAt(i);
+          switch (c2)
+          {
+          case 'Q':
+            litmode = true;
+            break;
+          case 'U':
+            ucmode = true;
+            break;
+          case 'L':
+            lcmode = true;
+            break;
+          case 'u':
+            uc1 = true;
+            break;
+          case 'l':
+            lc1 = true;
+            break;
+          case 'E':
+            uc1 = lc1 = ucmode = lcmode = litmode = false;
+            break;
+          default:
+            if (keepbs)
+            {
+              sb.append('\\');
+            }
+            c = c2;
+            if (keepbs)
+            {
+              mf = false;
+            }
+            app = true;
+            break;
+          }
+          modified |= mf;
+        }
+      }
+      if (app)
+      {
+        if (lc1)
+        {
+          c = lc(c);
+          lc1 = false;
+        }
+        else if (uc1)
+        {
+          c = uc(c);
+          uc1 = false;
+        }
+        else if (ucmode)
+        {
+          c = uc(c);
+        }
+        else if (lcmode)
+        {
+          c = lc(c);
+        }
+        if (litmode && needbs(c))
+        {
+          sb.append('\\');
+        }
+        sb.append(c);
+      }
+    }
+    return modified ? sb.toString() : s;
+  }
+
+  final static char uc(char c)
+  {
+    return CaseMgr.toUpperCase(c);
+  }
+
+  final static char lc(char c)
+  {
+    return CaseMgr.toLowerCase(c);
+  }
+
+  final static boolean needbs(char c)
+  {
+    if (c >= 'a' && c <= 'z')
+    {
+      return false;
+    }
+    if (c >= 'A' && c <= 'Z')
+    {
+      return false;
+    }
+    if (c >= '0' && c <= '9')
+    {
+      return false;
+    }
+    if (c == '_')
+    {
+      return false;
+    }
+    return true;
+  }
+
+  final static Regex parse(String s)
+  {
+    boolean igncase = false, optim = false, gFlag = false;
+    boolean sFlag = false, mFlag = false, xFlag = false;
+
+    StringBuffer s1 = new StringBuffer();
+    StringBuffer s2 = new StringBuffer();
+    int i = 0, count = 0;
+    char mode, delim = '/', cdelim = '/';
+    if (s.length() >= 3 && s.charAt(0) == 's')
+    {
+      mode = 's';
+      delim = s.charAt(1);
+      cdelim = close(delim);
+      i = 2;
+    }
+    else if (s.length() >= 2 && s.charAt(0) == 'm')
+    {
+      mode = 'm';
+      delim = s.charAt(1);
+      cdelim = close(delim);
+      i = 2;
+    }
+    else if (s.length() >= 1 && s.charAt(0) == '/')
+    {
+      mode = 'm';
+      i = 1;
+    }
+    else
+    {
+      try
+      {
+        RegSyntaxError.endItAll("Regex.perlCode should be of the "
+                + "form s/// or m// or //");
+      } catch (RegSyntax rs)
+      {
+      }
+      return null;
+    }
+    for (; i < s.length(); i++)
+    {
+      if (s.charAt(i) == '\\')
+      {
+        s1.append('\\');
+        i++;
+      }
+      else if (s.charAt(i) == cdelim && count == 0)
+      {
+        i++;
+        break;
+      }
+      else if (s.charAt(i) == delim && cdelim != delim)
+      {
+        count++;
+      }
+      else if (s.charAt(i) == cdelim && cdelim != delim)
+      {
+        count--;
+      }
+      s1.append(s.charAt(i));
+    }
+    if (mode == 's' && cdelim != delim)
+    {
+      while (i < s.length() && Prop.isWhite(s.charAt(i)))
+      {
+        i++;
+      }
+      if (i >= s.length())
+      {
+        try
+        {
+          RegSyntaxError.endItAll("" + mode + delim + " needs " + cdelim);
+        } catch (RegSyntax rs)
+        {
+        }
+        return null;
+      }
+      cdelim = close(delim = s.charAt(i));
+      i++;
+    }
+    count = 0;
+    if (mode == 's')
+    {
+      for (; i < s.length(); i++)
+      {
+        if (s.charAt(i) == '\\')
+        {
+          s2.append('\\');
+          i++;
+        }
+        else if (s.charAt(i) == cdelim && count == 0)
+        {
+          i++;
+          break;
+        }
+        else if (s.charAt(i) == delim && cdelim != delim)
+        {
+          count++;
+        }
+        else if (s.charAt(i) == cdelim && cdelim != delim)
+        {
+          count--;
+        }
+        s2.append(s.charAt(i));
+      }
+    }
+    for (; i < s.length(); i++)
+    {
+      char c = s.charAt(i);
+      switch (c)
+      {
+      case 'x':
+        xFlag = true;
+        break;
+      case 'i':
+        igncase = true;
+        break;
+      case 'o':
+        optim = true;
+        break;
+      case 's':
+        sFlag = true;
+        break;
+      case 'm':
+        mFlag = true;
+        break;
+      case 'g':
+        gFlag = true;
+        break;
+      default:
+
+        // syntax error!
+        try
+        {
+          RegSyntaxError.endItAll("Illegal flag to pattern: " + c);
+        } catch (RegSyntax rs)
+        {
+        }
+        return null;
+      }
+    }
+    Regex r = new Regex();
+    try
+    {
+      String pat = s1.toString(), reprul = s2.toString();
+      if (xFlag)
+      {
+        pat = strip(pat);
+        reprul = strip(reprul);
+      }
+      r.compile(pat);
+      r.ignoreCase |= igncase;
+      r.gFlag |= gFlag;
+      r.sFlag |= sFlag;
+      r.mFlag |= mFlag;
+      if (optim)
+      {
+        r.optimize();
+      }
+      if (delim == '\'')
+      {
+        r.setReplaceRule(new StringRule(reprul));
+      }
+      else
+      {
+        r.setReplaceRule(ReplaceRule.perlCode(reprul));
+      }
+    } catch (RegSyntax rs)
+    {
+      r = null;
+    }
+    return r;
+  }
+
+  static String strip(String s)
+  {
+    StringBuffer sb = new StringBuffer();
+    for (int i = 0; i < s.length(); i++)
+    {
+      char c = s.charAt(i);
+      if (Prop.isWhite(c))
+      {
+        ;
+      }
+      else if (c == '#')
+      {
+        i++;
+        while (i < s.length())
+        {
+          if (s.charAt(i) == '\n')
+          {
+            break;
+          }
+          i++;
+        }
+      }
+      else if (c == '\\')
+      {
+        sb.append(c);
+        sb.append(s.charAt(++i));
+      }
+      else
+      {
+        sb.append(c);
+      }
+    }
+    return sb.toString();
+  }
+}
diff --git a/src/com/stevesoft/pat/patInf.java b/src/com/stevesoft/pat/patInf.java
index 28580e2..cbdbf9e 100755
--- a/src/com/stevesoft/pat/patInf.java
+++ b/src/com/stevesoft/pat/patInf.java
@@ -1,17 +1,16 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-final class patInf
-    extends patInt
-{
-  patInf()
-  {
-    inf = true;
-  }
-};
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+final class patInf extends patInt
+{
+  patInf()
+  {
+    inf = true;
+  }
+};
diff --git a/src/com/stevesoft/pat/patInt.java b/src/com/stevesoft/pat/patInt.java
index f997a52..df0d028 100755
--- a/src/com/stevesoft/pat/patInt.java
+++ b/src/com/stevesoft/pat/patInt.java
@@ -1,171 +1,180 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat;
-
-/** This is just an integer that can have infinite value.
-    It is used internally to implement the *, and + parts
-    of regular expressions.
- */
-public class patInt
-{
-  int i;
-  boolean inf;
-  /** Initialize to zero. */
-  public patInt()
-  {
-    i = 0;
-    inf = false;
-  }
-
-  /** Initialize to the value of init. */
-  public patInt(int init)
-  {
-    i = init;
-    inf = false;
-  }
-
-  /** Initialize to the value of p. */
-  public patInt(patInt p)
-  {
-    i = p.i;
-    inf = p.inf;
-  }
-
-  /** set this int to infinity. */
-  public void setInf(boolean b)
-  {
-    inf = b;
-    if (b)
-    {
-      i = Integer.MAX_VALUE;
-    }
-  }
-
-  /** Increment the value of this by 1. */
-  public final void inc()
-  {
-    if (!inf)
-    {
-      i++;
-    }
-  }
-
-  /** Decrement the value of this by 1. */
-  public final void dec()
-  {
-    if (!inf)
-    {
-      i--;
-    }
-  }
-
-  /** Test to see if this is less than or equal to j. */
-  public final boolean lessEq(patInt j)
-  { /*
-                     if(inf) return false;
-                     if(j.inf) return true;
-                     return i <= j.i; */
-    return!inf && (j.inf || i <= j.i);
-   }
-
-  /** Test to see if two patterns are equal. */
-  public final boolean equals(patInt j)
-  {
-    return!j.inf && !inf && i == j.i;
-  }
-
-  /** Formats the pattern as a String.  Contrary to
-       what you might expect, infinity is formatted as "" */
-  final public String toString()
-  {
-    if (inf)
-    {
-      return "";
-    }
-    else
-    {
-      return "" + i;
-    }
-  }
-
-  /** This would be operator+=(patInt) if I were programming
-       in C++. */
-  public final patInt pluseq(patInt p)
-  {
-    if (inf || p.inf)
-    {
-      setInf(true);
-    }
-    else
-    {
-      i += p.i;
-    }
-    return this;
-  }
-
-  /** Returns a patInt with value equal to the product
-       of the value of p and this. */
-  public final patInt mul(patInt p)
-  {
-    if (inf || p.inf)
-    {
-      return new patInf();
-    }
-    return new patInt(i * p.i);
-  }
-
-  /** If the argument p has a smaller value than this,
-       then set this Object equal to p. */
-  public final patInt mineq(patInt p)
-  {
-    if (p.inf)
-    {
-      return this;
-    }
-    if (inf)
-    {
-      i = p.i;
-    }
-    else if (p.i < i)
-    {
-      i = p.i;
-    }
-    setInf(false);
-    return this;
-  }
-
-  /** If the argument p has a greater than this,
-       then set this object equal to p. */
-  public final patInt maxeq(patInt p)
-  {
-    if (inf || p.inf)
-    {
-      setInf(true);
-      return this;
-    }
-    if (p.i > i)
-    {
-      i = p.i;
-    }
-    return this;
-  }
-
-  /** Tests to see if this represents an infinite quantity. */
-  public boolean finite()
-  {
-    return!inf;
-  }
-
-  /** Converts to a patInt to an int.  Infinity is
-       mapped Integer.MAX_VALUE;
-   */
-  public int intValue()
-  {
-    return inf ? Integer.MAX_VALUE : i;
-  }
-};
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat;
+
+/**
+ * This is just an integer that can have infinite value. It is used internally
+ * to implement the *, and + parts of regular expressions.
+ */
+public class patInt
+{
+  int i;
+
+  boolean inf;
+
+  /** Initialize to zero. */
+  public patInt()
+  {
+    i = 0;
+    inf = false;
+  }
+
+  /** Initialize to the value of init. */
+  public patInt(int init)
+  {
+    i = init;
+    inf = false;
+  }
+
+  /** Initialize to the value of p. */
+  public patInt(patInt p)
+  {
+    i = p.i;
+    inf = p.inf;
+  }
+
+  /** set this int to infinity. */
+  public void setInf(boolean b)
+  {
+    inf = b;
+    if (b)
+    {
+      i = Integer.MAX_VALUE;
+    }
+  }
+
+  /** Increment the value of this by 1. */
+  public final void inc()
+  {
+    if (!inf)
+    {
+      i++;
+    }
+  }
+
+  /** Decrement the value of this by 1. */
+  public final void dec()
+  {
+    if (!inf)
+    {
+      i--;
+    }
+  }
+
+  /** Test to see if this is less than or equal to j. */
+  public final boolean lessEq(patInt j)
+  { /*
+     * if(inf) return false; if(j.inf) return true; return i <= j.i;
+     */
+    return !inf && (j.inf || i <= j.i);
+  }
+
+  /** Test to see if two patterns are equal. */
+  public final boolean equals(patInt j)
+  {
+    return !j.inf && !inf && i == j.i;
+  }
+
+  /**
+   * Formats the pattern as a String. Contrary to what you might expect,
+   * infinity is formatted as ""
+   */
+  final public String toString()
+  {
+    if (inf)
+    {
+      return "";
+    }
+    else
+    {
+      return "" + i;
+    }
+  }
+
+  /**
+   * This would be operator+=(patInt) if I were programming in C++.
+   */
+  public final patInt pluseq(patInt p)
+  {
+    if (inf || p.inf)
+    {
+      setInf(true);
+    }
+    else
+    {
+      i += p.i;
+    }
+    return this;
+  }
+
+  /**
+   * Returns a patInt with value equal to the product of the value of p and
+   * this.
+   */
+  public final patInt mul(patInt p)
+  {
+    if (inf || p.inf)
+    {
+      return new patInf();
+    }
+    return new patInt(i * p.i);
+  }
+
+  /**
+   * If the argument p has a smaller value than this, then set this Object equal
+   * to p.
+   */
+  public final patInt mineq(patInt p)
+  {
+    if (p.inf)
+    {
+      return this;
+    }
+    if (inf)
+    {
+      i = p.i;
+    }
+    else if (p.i < i)
+    {
+      i = p.i;
+    }
+    setInf(false);
+    return this;
+  }
+
+  /**
+   * If the argument p has a greater than this, then set this object equal to p.
+   */
+  public final patInt maxeq(patInt p)
+  {
+    if (inf || p.inf)
+    {
+      setInf(true);
+      return this;
+    }
+    if (p.i > i)
+    {
+      i = p.i;
+    }
+    return this;
+  }
+
+  /** Tests to see if this represents an infinite quantity. */
+  public boolean finite()
+  {
+    return !inf;
+  }
+
+  /**
+   * Converts to a patInt to an int. Infinity is mapped Integer.MAX_VALUE;
+   */
+  public int intValue()
+  {
+    return inf ? Integer.MAX_VALUE : i;
+  }
+};
diff --git a/src/com/stevesoft/pat/wrap/CharArrayBufferWrap.java b/src/com/stevesoft/pat/wrap/CharArrayBufferWrap.java
index 19f268e..c014a57 100755
--- a/src/com/stevesoft/pat/wrap/CharArrayBufferWrap.java
+++ b/src/com/stevesoft/pat/wrap/CharArrayBufferWrap.java
@@ -1,53 +1,54 @@
-package //
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-    com.stevesoft.pat.wrap;
-
-import com.stevesoft.pat.*;
-
-/** Allows the outcome of a replaceAll() or replaceFirst()
-    to be an array of characters rather than a String.
- */
-public class CharArrayBufferWrap
-    implements BasicStringBufferLike
-{
-  StringBuffer sb = new StringBuffer();
-  public void append(char c)
-  {
-    sb.append(c);
-  }
-
-  public void append(String s)
-  {
-    sb.append(s);
-  }
-
-  public StringLike toStringLike()
-  {
-    char[] ca = new char[sb.length()];
-    for (int i = 0; i < ca.length; i++)
-    {
-      ca[i] = sb.charAt(i);
-    }
-    return new CharArrayWrap(ca);
-  }
-
-  public int length()
-  {
-    return sb.length();
-  }
-
-  public String toString()
-  {
-    return sb.toString();
-  }
-
-  public Object unwrap()
-  {
-    return sb;
-  }
-}
+package //
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+com.stevesoft.pat.wrap;
+
+import com.stevesoft.pat.*;
+
+/**
+ * Allows the outcome of a replaceAll() or replaceFirst() to be an array of
+ * characters rather than a String.
+ */
+public class CharArrayBufferWrap implements BasicStringBufferLike
+{
+  StringBuffer sb = new StringBuffer();
+
+  public void append(char c)
+  {
+    sb.append(c);
+  }
+
+  public void append(String s)
+  {
+    sb.append(s);
+  }
+
+  public StringLike toStringLike()
+  {
+    char[] ca = new char[sb.length()];
+    for (int i = 0; i < ca.length; i++)
+    {
+      ca[i] = sb.charAt(i);
+    }
+    return new CharArrayWrap(ca);
+  }
+
+  public int length()
+  {
+    return sb.length();
+  }
+
+  public String toString()
+  {
+    return sb.toString();
+  }
+
+  public Object unwrap()
+  {
+    return sb;
+  }
+}
diff --git a/src/com/stevesoft/pat/wrap/CharArrayWrap.java b/src/com/stevesoft/pat/wrap/CharArrayWrap.java
index 6de78cf..bde9bd1 100755
--- a/src/com/stevesoft/pat/wrap/CharArrayWrap.java
+++ b/src/com/stevesoft/pat/wrap/CharArrayWrap.java
@@ -1,74 +1,75 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat.wrap;
-
-import com.stevesoft.pat.*;
-
-/** This provides a wrapper for a char array so that
-    it can be searched by Regex. */
-public class CharArrayWrap
-    implements StringLike
-{
-  char[] ca;
-  public char[] getCharArray()
-  {
-    return ca;
-  }
-
-  public CharArrayWrap(char[] ca)
-  {
-    this.ca = ca;
-  }
-
-  public String toString()
-  {
-    return new String(ca);
-  }
-
-  public char charAt(int i)
-  {
-    return ca[i];
-  }
-
-  public int length()
-  {
-    return ca.length;
-  }
-
-  public String substring(int i1, int i2)
-  {
-    StringBuffer sb = new StringBuffer();
-    for (int i = i1; i < i2; i++)
-    {
-      sb.append(ca[i]);
-    }
-    return sb.toString();
-  }
-
-  public Object unwrap()
-  {
-    return ca;
-  }
-
-  public BasicStringBufferLike newStringBufferLike()
-  {
-    return new CharArrayBufferWrap();
-  }
-
-  public int indexOf(char c)
-  {
-    for (int i = 0; i < ca.length; i++)
-    {
-      if (ca[i] == c)
-      {
-        return i;
-      }
-    }
-    return -1;
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat.wrap;
+
+import com.stevesoft.pat.*;
+
+/**
+ * This provides a wrapper for a char array so that it can be searched by Regex.
+ */
+public class CharArrayWrap implements StringLike
+{
+  char[] ca;
+
+  public char[] getCharArray()
+  {
+    return ca;
+  }
+
+  public CharArrayWrap(char[] ca)
+  {
+    this.ca = ca;
+  }
+
+  public String toString()
+  {
+    return new String(ca);
+  }
+
+  public char charAt(int i)
+  {
+    return ca[i];
+  }
+
+  public int length()
+  {
+    return ca.length;
+  }
+
+  public String substring(int i1, int i2)
+  {
+    StringBuffer sb = new StringBuffer();
+    for (int i = i1; i < i2; i++)
+    {
+      sb.append(ca[i]);
+    }
+    return sb.toString();
+  }
+
+  public Object unwrap()
+  {
+    return ca;
+  }
+
+  public BasicStringBufferLike newStringBufferLike()
+  {
+    return new CharArrayBufferWrap();
+  }
+
+  public int indexOf(char c)
+  {
+    for (int i = 0; i < ca.length; i++)
+    {
+      if (ca[i] == c)
+      {
+        return i;
+      }
+    }
+    return -1;
+  }
+}
diff --git a/src/com/stevesoft/pat/wrap/RandomAccessFileWrap.java b/src/com/stevesoft/pat/wrap/RandomAccessFileWrap.java
index 90e7691..b4d38dc 100755
--- a/src/com/stevesoft/pat/wrap/RandomAccessFileWrap.java
+++ b/src/com/stevesoft/pat/wrap/RandomAccessFileWrap.java
@@ -1,173 +1,170 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat.wrap;
-
-import java.io.*;
-
-import com.stevesoft.pat.*;
-
-/** Provides a wrapper for a RandomAccessFile so that it
-    can be searched by Regex. */
-public class RandomAccessFileWrap
-    implements StringLike
-{
-
-  long offset = 0;
-  public void setOffset(long o)
-  {
-    offset = o;
-    i0 = iend = 0;
-  }
-
-  public long getOffset()
-  {
-    return offset;
-  }
-
-  RandomAccessFile raf;
-  int i0 = 0, iend = 0;
-  byte[] buf = new byte[1024];
-
-  public int getBufferSize()
-  {
-    return buf.length;
-  }
-
-  public void setBufferSize(int bs)
-  {
-    buf = new byte[bs];
-    i0 = iend = 0;
-  }
-
-  public RandomAccessFileWrap(String file)
-      throws IOException
-  {
-    this.raf = new RandomAccessFile(file, "r");
-  }
-
-  public RandomAccessFileWrap(RandomAccessFile raf)
-  {
-    this.raf = raf;
-  }
-
-  public char charAt(int i)
-  {
-    if (i >= i0 && i < iend)
-    {
-      return (char) buf[i - i0];
-    }
-
-    try
-    {
-      i0 = i - 5;
-      //if(i0+offset<0) i0=(int)(-offset);
-      if (i0 < 0)
-      {
-        i0 = 0;
-      }
-      raf.seek(i0 + offset);
-      iend = i0 + raf.read(buf, 0, buf.length);
-
-      if (i >= i0 && i < iend)
-      {
-        return (char) buf[i - i0];
-      }
-    }
-    catch (Throwable t)
-    {}
-
-    throw new ArrayIndexOutOfBoundsException("Out of bounds for file:" +
-                                             " i=" + i +
-                                             ", Final Buffer: i0=" + i0 +
-                                             " iend=" + iend);
-  }
-
-  public String toString()
-  {
-    throw new Error("Not implemented");
-  }
-
-  public int length()
-  {
-    try
-    {
-      long len = raf.length() - offset;
-      if (len > Integer.MAX_VALUE)
-      {
-        return Integer.MAX_VALUE;
-      }
-      return (int) len;
-    }
-    catch (IOException ioe)
-    {
-      return 0;
-    }
-  }
-
-  public String substring(int i1, int i2)
-  {
-    StringBuffer sb = new StringBuffer();
-    for (int i = i1; i < i2; i++)
-    {
-      sb.append(charAt(i));
-    }
-    return sb.toString();
-  }
-
-  public Object unwrap()
-  {
-    return raf;
-  }
-
-  public static void main(String[] files)
-      throws IOException
-  {
-    for (int i = 0; i < files.length; i++)
-    {
-      RandomAccessFileWrap fw =
-          new RandomAccessFileWrap(new RandomAccessFile(files[i], "r"));
-      Regex r = new Regex("toString\\(\\) *(?@{})");
-      r.setGFlag(true);
-      r.optimize();
-      System.out.print(files[i] + " ");
-      int j = 0;
-      do
-      {
-        if (r.searchFrom(fw, j))
-        {
-          System.out.println("Matched at index: " +
-                             r.matchedFrom());
-          j = r.matchedTo();
-        }
-        else
-        {
-          System.out.println("not found");
-        }
-        System.out.println(r.stringMatched());
-      }
-      while (r.didMatch());
-    }
-  }
-
-  public BasicStringBufferLike newStringBufferLike()
-  {
-    return new StringBufferWrap();
-  }
-
-  public int indexOf(char c)
-  {
-    for (int i = 0; i < length(); i++)
-    {
-      if (charAt(i) == c)
-      {
-        return i;
-      }
-    }
-    return -1;
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat.wrap;
+
+import java.io.*;
+
+import com.stevesoft.pat.*;
+
+/**
+ * Provides a wrapper for a RandomAccessFile so that it can be searched by
+ * Regex.
+ */
+public class RandomAccessFileWrap implements StringLike
+{
+
+  long offset = 0;
+
+  public void setOffset(long o)
+  {
+    offset = o;
+    i0 = iend = 0;
+  }
+
+  public long getOffset()
+  {
+    return offset;
+  }
+
+  RandomAccessFile raf;
+
+  int i0 = 0, iend = 0;
+
+  byte[] buf = new byte[1024];
+
+  public int getBufferSize()
+  {
+    return buf.length;
+  }
+
+  public void setBufferSize(int bs)
+  {
+    buf = new byte[bs];
+    i0 = iend = 0;
+  }
+
+  public RandomAccessFileWrap(String file) throws IOException
+  {
+    this.raf = new RandomAccessFile(file, "r");
+  }
+
+  public RandomAccessFileWrap(RandomAccessFile raf)
+  {
+    this.raf = raf;
+  }
+
+  public char charAt(int i)
+  {
+    if (i >= i0 && i < iend)
+    {
+      return (char) buf[i - i0];
+    }
+
+    try
+    {
+      i0 = i - 5;
+      // if(i0+offset<0) i0=(int)(-offset);
+      if (i0 < 0)
+      {
+        i0 = 0;
+      }
+      raf.seek(i0 + offset);
+      iend = i0 + raf.read(buf, 0, buf.length);
+
+      if (i >= i0 && i < iend)
+      {
+        return (char) buf[i - i0];
+      }
+    } catch (Throwable t)
+    {
+    }
+
+    throw new ArrayIndexOutOfBoundsException("Out of bounds for file:"
+            + " i=" + i + ", Final Buffer: i0=" + i0 + " iend=" + iend);
+  }
+
+  public String toString()
+  {
+    throw new Error("Not implemented");
+  }
+
+  public int length()
+  {
+    try
+    {
+      long len = raf.length() - offset;
+      if (len > Integer.MAX_VALUE)
+      {
+        return Integer.MAX_VALUE;
+      }
+      return (int) len;
+    } catch (IOException ioe)
+    {
+      return 0;
+    }
+  }
+
+  public String substring(int i1, int i2)
+  {
+    StringBuffer sb = new StringBuffer();
+    for (int i = i1; i < i2; i++)
+    {
+      sb.append(charAt(i));
+    }
+    return sb.toString();
+  }
+
+  public Object unwrap()
+  {
+    return raf;
+  }
+
+  public static void main(String[] files) throws IOException
+  {
+    for (int i = 0; i < files.length; i++)
+    {
+      RandomAccessFileWrap fw = new RandomAccessFileWrap(
+              new RandomAccessFile(files[i], "r"));
+      Regex r = new Regex("toString\\(\\) *(?@{})");
+      r.setGFlag(true);
+      r.optimize();
+      System.out.print(files[i] + " ");
+      int j = 0;
+      do
+      {
+        if (r.searchFrom(fw, j))
+        {
+          System.out.println("Matched at index: " + r.matchedFrom());
+          j = r.matchedTo();
+        }
+        else
+        {
+          System.out.println("not found");
+        }
+        System.out.println(r.stringMatched());
+      } while (r.didMatch());
+    }
+  }
+
+  public BasicStringBufferLike newStringBufferLike()
+  {
+    return new StringBufferWrap();
+  }
+
+  public int indexOf(char c)
+  {
+    for (int i = 0; i < length(); i++)
+    {
+      if (charAt(i) == c)
+      {
+        return i;
+      }
+    }
+    return -1;
+  }
+}
diff --git a/src/com/stevesoft/pat/wrap/StringBufferWrap.java b/src/com/stevesoft/pat/wrap/StringBufferWrap.java
index 40ddd65..d522461 100755
--- a/src/com/stevesoft/pat/wrap/StringBufferWrap.java
+++ b/src/com/stevesoft/pat/wrap/StringBufferWrap.java
@@ -1,47 +1,49 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat.wrap;
-
-import com.stevesoft.pat.*;
-
-/** This provides a wrapper for StringBuffer to
-    capture the output of a replacement. */
-public class StringBufferWrap
-    implements BasicStringBufferLike
-{
-  StringBuffer sb = new StringBuffer();
-  public void append(char c)
-  {
-    sb.append(c);
-  }
-
-  public void append(String s)
-  {
-    sb.append(s);
-  }
-
-  public int length()
-  {
-    return sb.length();
-  }
-
-  public String toString()
-  {
-    return sb.toString();
-  }
-
-  public StringLike toStringLike()
-  {
-    return new StringWrap(sb.toString());
-  }
-
-  public Object unwrap()
-  {
-    return sb;
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat.wrap;
+
+import com.stevesoft.pat.*;
+
+/**
+ * This provides a wrapper for StringBuffer to capture the output of a
+ * replacement.
+ */
+public class StringBufferWrap implements BasicStringBufferLike
+{
+  StringBuffer sb = new StringBuffer();
+
+  public void append(char c)
+  {
+    sb.append(c);
+  }
+
+  public void append(String s)
+  {
+    sb.append(s);
+  }
+
+  public int length()
+  {
+    return sb.length();
+  }
+
+  public String toString()
+  {
+    return sb.toString();
+  }
+
+  public StringLike toStringLike()
+  {
+    return new StringWrap(sb.toString());
+  }
+
+  public Object unwrap()
+  {
+    return sb;
+  }
+}
diff --git a/src/com/stevesoft/pat/wrap/StringWrap.java b/src/com/stevesoft/pat/wrap/StringWrap.java
index a53d18e..3ddf7c5 100755
--- a/src/com/stevesoft/pat/wrap/StringWrap.java
+++ b/src/com/stevesoft/pat/wrap/StringWrap.java
@@ -1,57 +1,59 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat.wrap;
-
-import com.stevesoft.pat.*;
-
-/** A basic wrapper for the String object. Regex does
-    not search String directly any longer, it searches StringLike. */
-public class StringWrap
-    implements StringLike
-{
-  String s;
-  public StringWrap(String s)
-  {
-    this.s = s;
-  }
-
-  public String toString()
-  {
-    return s;
-  }
-
-  public char charAt(int i)
-  {
-    return s.charAt(i);
-  }
-
-  public int length()
-  {
-    return s.length();
-  }
-
-  public String substring(int i1, int i2)
-  {
-    return s.substring(i1, i2);
-  }
-
-  public Object unwrap()
-  {
-    return s;
-  }
-
-  public BasicStringBufferLike newStringBufferLike()
-  {
-    return new StringBufferWrap();
-  }
-
-  public int indexOf(char c)
-  {
-    return s.indexOf(c);
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat.wrap;
+
+import com.stevesoft.pat.*;
+
+/**
+ * A basic wrapper for the String object. Regex does not search String directly
+ * any longer, it searches StringLike.
+ */
+public class StringWrap implements StringLike
+{
+  String s;
+
+  public StringWrap(String s)
+  {
+    this.s = s;
+  }
+
+  public String toString()
+  {
+    return s;
+  }
+
+  public char charAt(int i)
+  {
+    return s.charAt(i);
+  }
+
+  public int length()
+  {
+    return s.length();
+  }
+
+  public String substring(int i1, int i2)
+  {
+    return s.substring(i1, i2);
+  }
+
+  public Object unwrap()
+  {
+    return s;
+  }
+
+  public BasicStringBufferLike newStringBufferLike()
+  {
+    return new StringBufferWrap();
+  }
+
+  public int indexOf(char c)
+  {
+    return s.indexOf(c);
+  }
+}
diff --git a/src/com/stevesoft/pat/wrap/WriterWrap.java b/src/com/stevesoft/pat/wrap/WriterWrap.java
index 1b7f6c2..e72b5fa 100755
--- a/src/com/stevesoft/pat/wrap/WriterWrap.java
+++ b/src/com/stevesoft/pat/wrap/WriterWrap.java
@@ -1,59 +1,61 @@
-//
-// This software is now distributed according to
-// the Lesser Gnu Public License.  Please see
-// http://www.gnu.org/copyleft/lesser.txt for
-// the details.
-//    -- Happy Computing!
-//
-package com.stevesoft.pat.wrap;
-
-import java.io.*;
-
-import com.stevesoft.pat.*;
-
-/** Allows the outcome of a replaceAll() or replaceFirst()
-    to be directed to a Writer rather than a String.
-    <p>
-    The method toStringLike() cannot work, however.
-    This means that the return value of replaceAll() will
-    be null if this Object is used as the StringBufferLike.*/
-public class WriterWrap
-    implements BasicStringBufferLike
-{
-  Writer w;
-  public WriterWrap(Writer w)
-  {
-    this.w = w;
-  }
-
-  public void append(char c)
-  {
-    try
-    {
-      w.write( (int) c);
-    }
-    catch (IOException ioe)
-    {}
-  }
-
-  public void append(String s)
-  {
-    try
-    {
-      w.write(s);
-    }
-    catch (IOException ioe)
-    {}
-  }
-
-  /** This operation can't really be done. */
-  public StringLike toStringLike()
-  {
-    return null;
-  }
-
-  public Object unwrap()
-  {
-    return w;
-  }
-}
+//
+// This software is now distributed according to
+// the Lesser Gnu Public License.  Please see
+// http://www.gnu.org/copyleft/lesser.txt for
+// the details.
+//    -- Happy Computing!
+//
+package com.stevesoft.pat.wrap;
+
+import java.io.*;
+
+import com.stevesoft.pat.*;
+
+/**
+ * Allows the outcome of a replaceAll() or replaceFirst() to be directed to a
+ * Writer rather than a String.
+ * <p>
+ * The method toStringLike() cannot work, however. This means that the return
+ * value of replaceAll() will be null if this Object is used as the
+ * StringBufferLike.
+ */
+public class WriterWrap implements BasicStringBufferLike
+{
+  Writer w;
+
+  public WriterWrap(Writer w)
+  {
+    this.w = w;
+  }
+
+  public void append(char c)
+  {
+    try
+    {
+      w.write((int) c);
+    } catch (IOException ioe)
+    {
+    }
+  }
+
+  public void append(String s)
+  {
+    try
+    {
+      w.write(s);
+    } catch (IOException ioe)
+    {
+    }
+  }
+
+  /** This operation can't really be done. */
+  public StringLike toStringLike()
+  {
+    return null;
+  }
+
+  public Object unwrap()
+  {
+    return w;
+  }
+}
diff --git a/src/ext/vamsas/IRegistry.java b/src/ext/vamsas/IRegistry.java
index 9300f59..9b91b5d 100755
--- a/src/ext/vamsas/IRegistry.java
+++ b/src/ext/vamsas/IRegistry.java
@@ -1,15 +1,25 @@
-/**
- * IRegistry.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package ext.vamsas;
 
-public interface IRegistry
-    extends java.rmi.Remote
+public interface IRegistry extends java.rmi.Remote
 {
   public ext.vamsas.ServiceHandles getServices()
-      throws java.rmi.RemoteException;
+          throws java.rmi.RemoteException;
 }
diff --git a/src/ext/vamsas/IRegistryService.java b/src/ext/vamsas/IRegistryService.java
index 2590314..c99414d 100755
--- a/src/ext/vamsas/IRegistryService.java
+++ b/src/ext/vamsas/IRegistryService.java
@@ -1,20 +1,30 @@
-/**
- * IRegistryService.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package ext.vamsas;
 
-public interface IRegistryService
-    extends javax.xml.rpc.Service
+public interface IRegistryService extends javax.xml.rpc.Service
 {
   public java.lang.String getRegistryServiceAddress();
 
   public ext.vamsas.IRegistry getRegistryService()
-      throws javax.xml.rpc.ServiceException;
+          throws javax.xml.rpc.ServiceException;
 
   public ext.vamsas.IRegistry getRegistryService(java.net.URL portAddress)
-      throws javax.xml.rpc.ServiceException;
+          throws javax.xml.rpc.ServiceException;
 }
diff --git a/src/ext/vamsas/IRegistryServiceLocator.java b/src/ext/vamsas/IRegistryServiceLocator.java
index 0d7c0da..b83a9ee 100755
--- a/src/ext/vamsas/IRegistryServiceLocator.java
+++ b/src/ext/vamsas/IRegistryServiceLocator.java
@@ -1,15 +1,25 @@
-/**
- * IRegistryServiceLocator.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package ext.vamsas;
 
-public class IRegistryServiceLocator
-    extends org.apache.axis.client.Service implements ext.vamsas.
-    IRegistryService
+public class IRegistryServiceLocator extends org.apache.axis.client.Service
+        implements ext.vamsas.IRegistryService
 {
 
   public IRegistryServiceLocator()
@@ -43,14 +53,13 @@ public class IRegistryServiceLocator
   }
 
   public ext.vamsas.IRegistry getRegistryService()
-      throws javax.xml.rpc.ServiceException
+          throws javax.xml.rpc.ServiceException
   {
     java.net.URL endpoint;
     try
     {
       endpoint = new java.net.URL(RegistryService_address);
-    }
-    catch (java.net.MalformedURLException e)
+    } catch (java.net.MalformedURLException e)
     {
       throw new javax.xml.rpc.ServiceException(e);
     }
@@ -58,16 +67,15 @@ public class IRegistryServiceLocator
   }
 
   public ext.vamsas.IRegistry getRegistryService(java.net.URL portAddress)
-      throws javax.xml.rpc.ServiceException
+          throws javax.xml.rpc.ServiceException
   {
     try
     {
-      ext.vamsas.RegistryServiceSoapBindingStub _stub = new ext.vamsas.
-          RegistryServiceSoapBindingStub(portAddress, this);
+      ext.vamsas.RegistryServiceSoapBindingStub _stub = new ext.vamsas.RegistryServiceSoapBindingStub(
+              portAddress, this);
       _stub.setPortName(getRegistryServiceWSDDServiceName());
       return _stub;
-    }
-    catch (org.apache.axis.AxisFault e)
+    } catch (org.apache.axis.AxisFault e)
     {
       return null;
     }
@@ -79,42 +87,39 @@ public class IRegistryServiceLocator
   }
 
   /**
-   * For the given interface, get the stub implementation.
-   * If this service has no port for the given interface,
-   * then ServiceException is thrown.
+   * For the given interface, get the stub implementation. If this service has
+   * no port for the given interface, then ServiceException is thrown.
    */
   public java.rmi.Remote getPort(Class serviceEndpointInterface)
-      throws javax.xml.rpc.ServiceException
+          throws javax.xml.rpc.ServiceException
   {
     try
     {
-      if (ext.vamsas.IRegistry.class.isAssignableFrom(serviceEndpointInterface))
+      if (ext.vamsas.IRegistry.class
+              .isAssignableFrom(serviceEndpointInterface))
       {
-        ext.vamsas.RegistryServiceSoapBindingStub _stub = new ext.vamsas.
-            RegistryServiceSoapBindingStub(new java.net.URL(
-            RegistryService_address), this);
+        ext.vamsas.RegistryServiceSoapBindingStub _stub = new ext.vamsas.RegistryServiceSoapBindingStub(
+                new java.net.URL(RegistryService_address), this);
         _stub.setPortName(getRegistryServiceWSDDServiceName());
         return _stub;
       }
-    }
-    catch (java.lang.Throwable t)
+    } catch (java.lang.Throwable t)
     {
       throw new javax.xml.rpc.ServiceException(t);
     }
     throw new javax.xml.rpc.ServiceException(
-        "There is no stub implementation for the interface:  " +
-        (serviceEndpointInterface == null ? "null" :
-         serviceEndpointInterface.getName()));
+            "There is no stub implementation for the interface:  "
+                    + (serviceEndpointInterface == null ? "null"
+                            : serviceEndpointInterface.getName()));
   }
 
   /**
-   * For the given interface, get the stub implementation.
-   * If this service has no port for the given interface,
-   * then ServiceException is thrown.
+   * For the given interface, get the stub implementation. If this service has
+   * no port for the given interface, then ServiceException is thrown.
    */
   public java.rmi.Remote getPort(javax.xml.namespace.QName portName,
-                                 Class serviceEndpointInterface)
-      throws javax.xml.rpc.ServiceException
+          Class serviceEndpointInterface)
+          throws javax.xml.rpc.ServiceException
   {
     if (portName == null)
     {
@@ -128,7 +133,7 @@ public class IRegistryServiceLocator
     else
     {
       java.rmi.Remote _stub = getPort(serviceEndpointInterface);
-      ( (org.apache.axis.client.Stub) _stub).setPortName(portName);
+      ((org.apache.axis.client.Stub) _stub).setPortName(portName);
       return _stub;
     }
   }
@@ -154,8 +159,7 @@ public class IRegistryServiceLocator
    * Set the endpoint address for the specified port name.
    */
   public void setEndpointAddress(java.lang.String portName,
-                                 java.lang.String address)
-      throws javax.xml.rpc.ServiceException
+          java.lang.String address) throws javax.xml.rpc.ServiceException
   {
     if ("RegistryService".equals(portName))
     {
@@ -164,7 +168,7 @@ public class IRegistryServiceLocator
     else
     { // Unknown Port Name
       throw new javax.xml.rpc.ServiceException(
-          " Cannot set Endpoint Address for Unknown Port" + portName);
+              " Cannot set Endpoint Address for Unknown Port" + portName);
     }
   }
 
@@ -172,8 +176,7 @@ public class IRegistryServiceLocator
    * Set the endpoint address for the specified port name.
    */
   public void setEndpointAddress(javax.xml.namespace.QName portName,
-                                 java.lang.String address)
-      throws javax.xml.rpc.ServiceException
+          java.lang.String address) throws javax.xml.rpc.ServiceException
   {
     setEndpointAddress(portName.getLocalPart(), address);
   }
diff --git a/src/ext/vamsas/Jpred.java b/src/ext/vamsas/Jpred.java
index c3ab28b..2805a1d 100755
--- a/src/ext/vamsas/Jpred.java
+++ b/src/ext/vamsas/Jpred.java
@@ -1,24 +1,35 @@
-/**
- * Jpred.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package ext.vamsas;
 
-public interface Jpred
-    extends java.rmi.Remote
+public interface Jpred extends java.rmi.Remote
 {
   public java.lang.String predict(vamsas.objects.simple.Sequence seq)
-      throws java.rmi.RemoteException;
+          throws java.rmi.RemoteException;
 
-  public java.lang.String predictOnMsa(vamsas.objects.simple.Msfalignment msf)
-      throws java.rmi.RemoteException;
+  public java.lang.String predictOnMsa(
+          vamsas.objects.simple.Msfalignment msf)
+          throws java.rmi.RemoteException;
 
-  public vamsas.objects.simple.Secstructpred getpredict(java.lang.String job_id)
-      throws java.rmi.RemoteException;
+  public vamsas.objects.simple.Secstructpred getpredict(
+          java.lang.String job_id) throws java.rmi.RemoteException;
 
   public vamsas.objects.simple.JpredResult getresult(java.lang.String job_id)
-      throws java.rmi.RemoteException;
+          throws java.rmi.RemoteException;
 }
diff --git a/src/ext/vamsas/JpredService.java b/src/ext/vamsas/JpredService.java
index 8917d77..61ef50b 100755
--- a/src/ext/vamsas/JpredService.java
+++ b/src/ext/vamsas/JpredService.java
@@ -1,20 +1,29 @@
-/**
- * JpredService.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package ext.vamsas;
 
-public interface JpredService
-    extends javax.xml.rpc.Service
+public interface JpredService extends javax.xml.rpc.Service
 {
   public java.lang.String getjpredAddress();
 
-  public ext.vamsas.Jpred getjpred()
-      throws javax.xml.rpc.ServiceException;
+  public ext.vamsas.Jpred getjpred() throws javax.xml.rpc.ServiceException;
 
   public ext.vamsas.Jpred getjpred(java.net.URL portAddress)
-      throws javax.xml.rpc.ServiceException;
+          throws javax.xml.rpc.ServiceException;
 }
diff --git a/src/ext/vamsas/JpredServiceLocator.java b/src/ext/vamsas/JpredServiceLocator.java
index 433fa70..ec70fe6 100755
--- a/src/ext/vamsas/JpredServiceLocator.java
+++ b/src/ext/vamsas/JpredServiceLocator.java
@@ -1,14 +1,25 @@
-/**
- * JpredServiceLocator.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package ext.vamsas;
 
-public class JpredServiceLocator
-    extends org.apache.axis.client.Service implements ext.vamsas.JpredService
+public class JpredServiceLocator extends org.apache.axis.client.Service
+        implements ext.vamsas.JpredService
 {
 
   public JpredServiceLocator()
@@ -21,8 +32,7 @@ public class JpredServiceLocator
   }
 
   // Use to get a proxy class for jpred
-  private java.lang.String jpred_address =
-      "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred";
+  private java.lang.String jpred_address = "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred";
 
   public java.lang.String getjpredAddress()
   {
@@ -42,15 +52,13 @@ public class JpredServiceLocator
     jpredWSDDServiceName = name;
   }
 
-  public ext.vamsas.Jpred getjpred()
-      throws javax.xml.rpc.ServiceException
+  public ext.vamsas.Jpred getjpred() throws javax.xml.rpc.ServiceException
   {
     java.net.URL endpoint;
     try
     {
       endpoint = new java.net.URL(jpred_address);
-    }
-    catch (java.net.MalformedURLException e)
+    } catch (java.net.MalformedURLException e)
     {
       throw new javax.xml.rpc.ServiceException(e);
     }
@@ -58,16 +66,15 @@ public class JpredServiceLocator
   }
 
   public ext.vamsas.Jpred getjpred(java.net.URL portAddress)
-      throws javax.xml.rpc.ServiceException
+          throws javax.xml.rpc.ServiceException
   {
     try
     {
-      ext.vamsas.JpredSoapBindingStub _stub = new ext.vamsas.
-          JpredSoapBindingStub(portAddress, this);
+      ext.vamsas.JpredSoapBindingStub _stub = new ext.vamsas.JpredSoapBindingStub(
+              portAddress, this);
       _stub.setPortName(getjpredWSDDServiceName());
       return _stub;
-    }
-    catch (org.apache.axis.AxisFault e)
+    } catch (org.apache.axis.AxisFault e)
     {
       return null;
     }
@@ -79,41 +86,38 @@ public class JpredServiceLocator
   }
 
   /**
-   * For the given interface, get the stub implementation.
-   * If this service has no port for the given interface,
-   * then ServiceException is thrown.
+   * For the given interface, get the stub implementation. If this service has
+   * no port for the given interface, then ServiceException is thrown.
    */
   public java.rmi.Remote getPort(Class serviceEndpointInterface)
-      throws javax.xml.rpc.ServiceException
+          throws javax.xml.rpc.ServiceException
   {
     try
     {
       if (ext.vamsas.Jpred.class.isAssignableFrom(serviceEndpointInterface))
       {
-        ext.vamsas.JpredSoapBindingStub _stub = new ext.vamsas.
-            JpredSoapBindingStub(new java.net.URL(jpred_address), this);
+        ext.vamsas.JpredSoapBindingStub _stub = new ext.vamsas.JpredSoapBindingStub(
+                new java.net.URL(jpred_address), this);
         _stub.setPortName(getjpredWSDDServiceName());
         return _stub;
       }
-    }
-    catch (java.lang.Throwable t)
+    } catch (java.lang.Throwable t)
     {
       throw new javax.xml.rpc.ServiceException(t);
     }
     throw new javax.xml.rpc.ServiceException(
-        "There is no stub implementation for the interface:  " +
-        (serviceEndpointInterface == null ? "null" :
-         serviceEndpointInterface.getName()));
+            "There is no stub implementation for the interface:  "
+                    + (serviceEndpointInterface == null ? "null"
+                            : serviceEndpointInterface.getName()));
   }
 
   /**
-   * For the given interface, get the stub implementation.
-   * If this service has no port for the given interface,
-   * then ServiceException is thrown.
+   * For the given interface, get the stub implementation. If this service has
+   * no port for the given interface, then ServiceException is thrown.
    */
   public java.rmi.Remote getPort(javax.xml.namespace.QName portName,
-                                 Class serviceEndpointInterface)
-      throws javax.xml.rpc.ServiceException
+          Class serviceEndpointInterface)
+          throws javax.xml.rpc.ServiceException
   {
     if (portName == null)
     {
@@ -127,7 +131,7 @@ public class JpredServiceLocator
     else
     {
       java.rmi.Remote _stub = getPort(serviceEndpointInterface);
-      ( (org.apache.axis.client.Stub) _stub).setPortName(portName);
+      ((org.apache.axis.client.Stub) _stub).setPortName(portName);
       return _stub;
     }
   }
@@ -153,8 +157,7 @@ public class JpredServiceLocator
    * Set the endpoint address for the specified port name.
    */
   public void setEndpointAddress(java.lang.String portName,
-                                 java.lang.String address)
-      throws javax.xml.rpc.ServiceException
+          java.lang.String address) throws javax.xml.rpc.ServiceException
   {
     if ("jpred".equals(portName))
     {
@@ -163,7 +166,7 @@ public class JpredServiceLocator
     else
     { // Unknown Port Name
       throw new javax.xml.rpc.ServiceException(
-          " Cannot set Endpoint Address for Unknown Port" + portName);
+              " Cannot set Endpoint Address for Unknown Port" + portName);
     }
   }
 
@@ -171,8 +174,7 @@ public class JpredServiceLocator
    * Set the endpoint address for the specified port name.
    */
   public void setEndpointAddress(javax.xml.namespace.QName portName,
-                                 java.lang.String address)
-      throws javax.xml.rpc.ServiceException
+          java.lang.String address) throws javax.xml.rpc.ServiceException
   {
     setEndpointAddress(portName.getLocalPart(), address);
   }
diff --git a/src/ext/vamsas/JpredSoapBindingStub.java b/src/ext/vamsas/JpredSoapBindingStub.java
index 4c8fc7f..5915dca 100755
--- a/src/ext/vamsas/JpredSoapBindingStub.java
+++ b/src/ext/vamsas/JpredSoapBindingStub.java
@@ -1,18 +1,32 @@
-/**
- * JpredSoapBindingStub.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package ext.vamsas;
 
-public class JpredSoapBindingStub
-    extends org.apache.axis.client.Stub implements ext.vamsas.Jpred
+public class JpredSoapBindingStub extends org.apache.axis.client.Stub
+        implements ext.vamsas.Jpred
 {
   private java.util.Vector cachedSerClasses = new java.util.Vector();
+
   private java.util.Vector cachedSerQNames = new java.util.Vector();
+
   private java.util.Vector cachedSerFactories = new java.util.Vector();
+
   private java.util.Vector cachedDeserFactories = new java.util.Vector();
 
   static org.apache.axis.description.OperationDesc[] _operations;
@@ -29,12 +43,11 @@ public class JpredSoapBindingStub
     oper = new org.apache.axis.description.OperationDesc();
     oper.setName("predict");
     oper.addParameter(new javax.xml.namespace.QName("", "seq"),
-                      new javax.xml.
-                      namespace.QName("simple.objects.vamsas", "Sequence"),
-                      vamsas.objects.simple.Sequence.class,
-                      org.apache.axis.description.ParameterDesc.IN, false, false);
+            new javax.xml.namespace.QName("simple.objects.vamsas",
+                    "Sequence"), vamsas.objects.simple.Sequence.class,
+            org.apache.axis.description.ParameterDesc.IN, false, false);
     oper.setReturnType(new javax.xml.namespace.QName(
-        "http://www.w3.org/2001/XMLSchema", "string"));
+            "http://www.w3.org/2001/XMLSchema", "string"));
     oper.setReturnClass(java.lang.String.class);
     oper.setReturnQName(new javax.xml.namespace.QName("", "predictReturn"));
     oper.setStyle(org.apache.axis.constants.Style.RPC);
@@ -44,15 +57,15 @@ public class JpredSoapBindingStub
     oper = new org.apache.axis.description.OperationDesc();
     oper.setName("predictOnMsa");
     oper.addParameter(new javax.xml.namespace.QName("", "msf"),
-                      new javax.xml.
-                      namespace.QName("http://simple.objects.vamsas",
-                                      "Msfalignment"),
-                      vamsas.objects.simple.Msfalignment.class,
-                      org.apache.axis.description.ParameterDesc.IN, false, false);
+            new javax.xml.namespace.QName("http://simple.objects.vamsas",
+                    "Msfalignment"),
+            vamsas.objects.simple.Msfalignment.class,
+            org.apache.axis.description.ParameterDesc.IN, false, false);
     oper.setReturnType(new javax.xml.namespace.QName(
-        "http://www.w3.org/2001/XMLSchema", "string"));
+            "http://www.w3.org/2001/XMLSchema", "string"));
     oper.setReturnClass(java.lang.String.class);
-    oper.setReturnQName(new javax.xml.namespace.QName("", "predictOnMsaReturn"));
+    oper.setReturnQName(new javax.xml.namespace.QName("",
+            "predictOnMsaReturn"));
     oper.setStyle(org.apache.axis.constants.Style.RPC);
     oper.setUse(org.apache.axis.constants.Use.ENCODED);
     _operations[1] = oper;
@@ -60,14 +73,15 @@ public class JpredSoapBindingStub
     oper = new org.apache.axis.description.OperationDesc();
     oper.setName("getpredict");
     oper.addParameter(new javax.xml.namespace.QName("", "job_id"),
-                      new javax.
-                      xml.namespace.QName("http://www.w3.org/2001/XMLSchema",
-                                          "string"), java.lang.String.class,
-                      org.apache.axis.description.ParameterDesc.IN, false, false);
+            new javax.xml.namespace.QName(
+                    "http://www.w3.org/2001/XMLSchema", "string"),
+            java.lang.String.class,
+            org.apache.axis.description.ParameterDesc.IN, false, false);
     oper.setReturnType(new javax.xml.namespace.QName(
-        "http://simple.objects.vamsas", "Secstructpred"));
+            "http://simple.objects.vamsas", "Secstructpred"));
     oper.setReturnClass(vamsas.objects.simple.Secstructpred.class);
-    oper.setReturnQName(new javax.xml.namespace.QName("", "getpredictReturn"));
+    oper.setReturnQName(new javax.xml.namespace.QName("",
+            "getpredictReturn"));
     oper.setStyle(org.apache.axis.constants.Style.RPC);
     oper.setUse(org.apache.axis.constants.Use.ENCODED);
     _operations[2] = oper;
@@ -75,36 +89,36 @@ public class JpredSoapBindingStub
     oper = new org.apache.axis.description.OperationDesc();
     oper.setName("getresult");
     oper.addParameter(new javax.xml.namespace.QName("", "job_id"),
-                      new javax.
-                      xml.namespace.QName("http://www.w3.org/2001/XMLSchema",
-                                          "string"), java.lang.String.class,
-                      org.apache.axis.description.ParameterDesc.IN, false, false);
+            new javax.xml.namespace.QName(
+                    "http://www.w3.org/2001/XMLSchema", "string"),
+            java.lang.String.class,
+            org.apache.axis.description.ParameterDesc.IN, false, false);
     oper.setReturnType(new javax.xml.namespace.QName(
-        "http://simple.objects.vamsas", "JpredResult"));
+            "http://simple.objects.vamsas", "JpredResult"));
     oper.setReturnClass(vamsas.objects.simple.JpredResult.class);
-    oper.setReturnQName(new javax.xml.namespace.QName("", "getresultReturn"));
+    oper
+            .setReturnQName(new javax.xml.namespace.QName("",
+                    "getresultReturn"));
     oper.setStyle(org.apache.axis.constants.Style.RPC);
     oper.setUse(org.apache.axis.constants.Use.ENCODED);
     _operations[3] = oper;
 
   }
 
-  public JpredSoapBindingStub()
-      throws org.apache.axis.AxisFault
+  public JpredSoapBindingStub() throws org.apache.axis.AxisFault
   {
     this(null);
   }
 
   public JpredSoapBindingStub(java.net.URL endpointURL,
-                              javax.xml.rpc.Service service)
-      throws org.apache.axis.AxisFault
+          javax.xml.rpc.Service service) throws org.apache.axis.AxisFault
   {
     this(service);
     super.cachedEndpoint = endpointURL;
   }
 
   public JpredSoapBindingStub(javax.xml.rpc.Service service)
-      throws org.apache.axis.AxisFault
+          throws org.apache.axis.AxisFault
   {
     if (service == null)
     {
@@ -117,18 +131,26 @@ public class JpredSoapBindingStub
     java.lang.Class cls;
     javax.xml.namespace.QName qName;
     java.lang.Class beansf = org.apache.axis.encoding.ser.BeanSerializerFactory.class;
-    java.lang.Class beandf = org.apache.axis.encoding.ser.
-        BeanDeserializerFactory.class;
-    /*java.lang.Class enumsf = org.apache.axis.encoding.ser.EnumSerializerFactory.class;
-                 java.lang.Class enumdf = org.apache.axis.encoding.ser.EnumDeserializerFactory.class;
-                 java.lang.Class arraysf = org.apache.axis.encoding.ser.ArraySerializerFactory.class;
-                 java.lang.Class arraydf = org.apache.axis.encoding.ser.ArrayDeserializerFactory.class;
-                 java.lang.Class simplesf = org.apache.axis.encoding.ser.SimpleSerializerFactory.class;
-                 java.lang.Class simpledf = org.apache.axis.encoding.ser.SimpleDeserializerFactory.class;
-                 java.lang.Class simplelistsf = org.apache.axis.encoding.ser.SimpleListSerializerFactory.class;
-                 java.lang.Class simplelistdf = org.apache.axis.encoding.ser.SimpleListDeserializerFactory.class;*/
+    java.lang.Class beandf = org.apache.axis.encoding.ser.BeanDeserializerFactory.class;
+    /*
+     * java.lang.Class enumsf =
+     * org.apache.axis.encoding.ser.EnumSerializerFactory.class; java.lang.Class
+     * enumdf = org.apache.axis.encoding.ser.EnumDeserializerFactory.class;
+     * java.lang.Class arraysf =
+     * org.apache.axis.encoding.ser.ArraySerializerFactory.class;
+     * java.lang.Class arraydf =
+     * org.apache.axis.encoding.ser.ArrayDeserializerFactory.class;
+     * java.lang.Class simplesf =
+     * org.apache.axis.encoding.ser.SimpleSerializerFactory.class;
+     * java.lang.Class simpledf =
+     * org.apache.axis.encoding.ser.SimpleDeserializerFactory.class;
+     * java.lang.Class simplelistsf =
+     * org.apache.axis.encoding.ser.SimpleListSerializerFactory.class;
+     * java.lang.Class simplelistdf =
+     * org.apache.axis.encoding.ser.SimpleListDeserializerFactory.class;
+     */
     qName = new javax.xml.namespace.QName("http://simple.objects.vamsas",
-                                          "JpredResult");
+            "JpredResult");
     cachedSerQNames.add(qName);
     cls = vamsas.objects.simple.JpredResult.class;
     cachedSerClasses.add(cls);
@@ -143,7 +165,7 @@ public class JpredSoapBindingStub
     cachedDeserFactories.add(beandf);
 
     qName = new javax.xml.namespace.QName("http://simple.objects.vamsas",
-                                          "Secstructpred");
+            "Secstructpred");
     cachedSerQNames.add(qName);
     cls = vamsas.objects.simple.Secstructpred.class;
     cachedSerClasses.add(cls);
@@ -151,14 +173,15 @@ public class JpredSoapBindingStub
     cachedDeserFactories.add(beandf);
 
     qName = new javax.xml.namespace.QName("http://simple.objects.vamsas",
-                                          "Msfalignment");
+            "Msfalignment");
     cachedSerQNames.add(qName);
     cls = vamsas.objects.simple.Msfalignment.class;
     cachedSerClasses.add(cls);
     cachedSerFactories.add(beansf);
     cachedDeserFactories.add(beandf);
 
-    qName = new javax.xml.namespace.QName("simple.objects.vamsas", "Sequence");
+    qName = new javax.xml.namespace.QName("simple.objects.vamsas",
+            "Sequence");
     cachedSerQNames.add(qName);
     cls = vamsas.objects.simple.Sequence.class;
     cachedSerClasses.add(cls);
@@ -168,12 +191,12 @@ public class JpredSoapBindingStub
   }
 
   protected org.apache.axis.client.Call createCall()
-      throws java.rmi.RemoteException
+          throws java.rmi.RemoteException
   {
     try
     {
-      org.apache.axis.client.Call _call =
-          (org.apache.axis.client.Call)super.service.createCall();
+      org.apache.axis.client.Call _call = (org.apache.axis.client.Call) super.service
+              .createCall();
       if (super.maintainSessionSet)
       {
         _call.setMaintainSession(super.maintainSession);
@@ -214,33 +237,32 @@ public class JpredSoapBindingStub
         if (firstCall())
         {
           // must set encoding style before registering serializers
-          _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.
-                               SOAP11_CONSTANTS);
+          _call
+                  .setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
           _call.setEncodingStyle(org.apache.axis.Constants.URI_SOAP11_ENC);
           for (int i = 0; i < cachedSerFactories.size(); ++i)
           {
             java.lang.Class cls = (java.lang.Class) cachedSerClasses.get(i);
-            javax.xml.namespace.QName qName =
-                (javax.xml.namespace.QName) cachedSerQNames.get(i);
-            java.lang.Class sf = (java.lang.Class)
-                cachedSerFactories.get(i);
-            java.lang.Class df = (java.lang.Class)
-                cachedDeserFactories.get(i);
+            javax.xml.namespace.QName qName = (javax.xml.namespace.QName) cachedSerQNames
+                    .get(i);
+            java.lang.Class sf = (java.lang.Class) cachedSerFactories
+                    .get(i);
+            java.lang.Class df = (java.lang.Class) cachedDeserFactories
+                    .get(i);
             _call.registerTypeMapping(cls, qName, sf, df, false);
           }
         }
       }
       return _call;
-    }
-    catch (java.lang.Throwable _t)
+    } catch (java.lang.Throwable _t)
     {
       throw new org.apache.axis.AxisFault(
-          "Failure trying to get the Call object", _t);
+              "Failure trying to get the Call object", _t);
     }
   }
 
   public java.lang.String predict(vamsas.objects.simple.Sequence seq)
-      throws java.rmi.RemoteException
+          throws java.rmi.RemoteException
   {
     if (super.cachedEndpoint == null)
     {
@@ -250,13 +272,15 @@ public class JpredSoapBindingStub
     _call.setOperation(_operations[0]);
     _call.setUseSOAPAction(true);
     _call.setSOAPActionURI("");
-    _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
-    _call.setOperationName(new javax.xml.namespace.QName("vamsas", "predict"));
+    _call
+            .setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+    _call.setOperationName(new javax.xml.namespace.QName("vamsas",
+            "predict"));
 
     setRequestHeaders(_call);
     setAttachments(_call);
     java.lang.Object _resp = _call.invoke(new java.lang.Object[]
-                                          {seq});
+    { seq });
 
     if (_resp instanceof java.rmi.RemoteException)
     {
@@ -268,17 +292,17 @@ public class JpredSoapBindingStub
       try
       {
         return (java.lang.String) _resp;
-      }
-      catch (java.lang.Exception _exception)
+      } catch (java.lang.Exception _exception)
       {
-        return (java.lang.String) org.apache.axis.utils.JavaUtils.convert(_resp,
-            java.lang.String.class);
+        return (java.lang.String) org.apache.axis.utils.JavaUtils.convert(
+                _resp, java.lang.String.class);
       }
     }
   }
 
-  public java.lang.String predictOnMsa(vamsas.objects.simple.Msfalignment msf)
-      throws java.rmi.RemoteException
+  public java.lang.String predictOnMsa(
+          vamsas.objects.simple.Msfalignment msf)
+          throws java.rmi.RemoteException
   {
     if (super.cachedEndpoint == null)
     {
@@ -288,14 +312,15 @@ public class JpredSoapBindingStub
     _call.setOperation(_operations[1]);
     _call.setUseSOAPAction(true);
     _call.setSOAPActionURI("");
-    _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+    _call
+            .setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
     _call.setOperationName(new javax.xml.namespace.QName("vamsas",
-        "predictOnMsa"));
+            "predictOnMsa"));
 
     setRequestHeaders(_call);
     setAttachments(_call);
     java.lang.Object _resp = _call.invoke(new java.lang.Object[]
-                                          {msf});
+    { msf });
 
     if (_resp instanceof java.rmi.RemoteException)
     {
@@ -307,17 +332,16 @@ public class JpredSoapBindingStub
       try
       {
         return (java.lang.String) _resp;
-      }
-      catch (java.lang.Exception _exception)
+      } catch (java.lang.Exception _exception)
       {
-        return (java.lang.String) org.apache.axis.utils.JavaUtils.convert(_resp,
-            java.lang.String.class);
+        return (java.lang.String) org.apache.axis.utils.JavaUtils.convert(
+                _resp, java.lang.String.class);
       }
     }
   }
 
-  public vamsas.objects.simple.Secstructpred getpredict(java.lang.String job_id)
-      throws java.rmi.RemoteException
+  public vamsas.objects.simple.Secstructpred getpredict(
+          java.lang.String job_id) throws java.rmi.RemoteException
   {
     if (super.cachedEndpoint == null)
     {
@@ -327,13 +351,15 @@ public class JpredSoapBindingStub
     _call.setOperation(_operations[2]);
     _call.setUseSOAPAction(true);
     _call.setSOAPActionURI("");
-    _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
-    _call.setOperationName(new javax.xml.namespace.QName("vamsas", "getpredict"));
+    _call
+            .setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+    _call.setOperationName(new javax.xml.namespace.QName("vamsas",
+            "getpredict"));
 
     setRequestHeaders(_call);
     setAttachments(_call);
     java.lang.Object _resp = _call.invoke(new java.lang.Object[]
-                                          {job_id});
+    { job_id });
 
     if (_resp instanceof java.rmi.RemoteException)
     {
@@ -345,17 +371,16 @@ public class JpredSoapBindingStub
       try
       {
         return (vamsas.objects.simple.Secstructpred) _resp;
-      }
-      catch (java.lang.Exception _exception)
+      } catch (java.lang.Exception _exception)
       {
-        return (vamsas.objects.simple.Secstructpred) org.apache.axis.utils.
-            JavaUtils.convert(_resp, vamsas.objects.simple.Secstructpred.class);
+        return (vamsas.objects.simple.Secstructpred) org.apache.axis.utils.JavaUtils
+                .convert(_resp, vamsas.objects.simple.Secstructpred.class);
       }
     }
   }
 
   public vamsas.objects.simple.JpredResult getresult(java.lang.String job_id)
-      throws java.rmi.RemoteException
+          throws java.rmi.RemoteException
   {
     if (super.cachedEndpoint == null)
     {
@@ -365,13 +390,15 @@ public class JpredSoapBindingStub
     _call.setOperation(_operations[3]);
     _call.setUseSOAPAction(true);
     _call.setSOAPActionURI("");
-    _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
-    _call.setOperationName(new javax.xml.namespace.QName("vamsas", "getresult"));
+    _call
+            .setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+    _call.setOperationName(new javax.xml.namespace.QName("vamsas",
+            "getresult"));
 
     setRequestHeaders(_call);
     setAttachments(_call);
     java.lang.Object _resp = _call.invoke(new java.lang.Object[]
-                                          {job_id});
+    { job_id });
 
     if (_resp instanceof java.rmi.RemoteException)
     {
@@ -383,11 +410,10 @@ public class JpredSoapBindingStub
       try
       {
         return (vamsas.objects.simple.JpredResult) _resp;
-      }
-      catch (java.lang.Exception _exception)
+      } catch (java.lang.Exception _exception)
       {
-        return (vamsas.objects.simple.JpredResult) org.apache.axis.utils.
-            JavaUtils.convert(_resp, vamsas.objects.simple.JpredResult.class);
+        return (vamsas.objects.simple.JpredResult) org.apache.axis.utils.JavaUtils
+                .convert(_resp, vamsas.objects.simple.JpredResult.class);
       }
     }
   }
diff --git a/src/ext/vamsas/MuscleWS.java b/src/ext/vamsas/MuscleWS.java
index db1416e..c4e1f77 100755
--- a/src/ext/vamsas/MuscleWS.java
+++ b/src/ext/vamsas/MuscleWS.java
@@ -1,43 +1,53 @@
-/**
- * MuscleWS.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package ext.vamsas;
-
-public interface MuscleWS
-    extends java.rmi.Remote
-{
-  public vamsas.objects.simple.WsJobId align(
-      vamsas.objects.simple.SequenceSet seqSet)
-      throws java.rmi.RemoteException;
-
-  public vamsas.objects.simple.Alignment getalign(java.lang.String job_id)
-      throws java.rmi.RemoteException;
-
-  public vamsas.objects.simple.MsaResult getResult(java.lang.String job_id)
-      throws java.rmi.RemoteException;
-
-  public vamsas.objects.simple.WsJobId cancel(java.lang.String jobId)
-      throws java.rmi.RemoteException;
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package ext.vamsas;
+
+public interface MuscleWS extends java.rmi.Remote
+{
+  public vamsas.objects.simple.WsJobId align(
+          vamsas.objects.simple.SequenceSet seqSet)
+          throws java.rmi.RemoteException;
+
+  public vamsas.objects.simple.Alignment getalign(java.lang.String job_id)
+          throws java.rmi.RemoteException;
+
+  public vamsas.objects.simple.MsaResult getResult(java.lang.String job_id)
+          throws java.rmi.RemoteException;
+
+  public vamsas.objects.simple.WsJobId cancel(java.lang.String jobId)
+          throws java.rmi.RemoteException;
+}
diff --git a/src/ext/vamsas/MuscleWSService.java b/src/ext/vamsas/MuscleWSService.java
index a4dc674..76a5995 100755
--- a/src/ext/vamsas/MuscleWSService.java
+++ b/src/ext/vamsas/MuscleWSService.java
@@ -1,38 +1,48 @@
-/**
- * MuscleWSService.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package ext.vamsas;
-
-public interface MuscleWSService
-    extends javax.xml.rpc.Service
-{
-  public java.lang.String getMuscleWSAddress();
-
-  public ext.vamsas.MuscleWS getMuscleWS()
-      throws javax.xml.rpc.ServiceException;
-
-  public ext.vamsas.MuscleWS getMuscleWS(java.net.URL portAddress)
-      throws javax.xml.rpc.ServiceException;
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package ext.vamsas;
+
+public interface MuscleWSService extends javax.xml.rpc.Service
+{
+  public java.lang.String getMuscleWSAddress();
+
+  public ext.vamsas.MuscleWS getMuscleWS()
+          throws javax.xml.rpc.ServiceException;
+
+  public ext.vamsas.MuscleWS getMuscleWS(java.net.URL portAddress)
+          throws javax.xml.rpc.ServiceException;
+}
diff --git a/src/ext/vamsas/MuscleWSServiceLocator.java b/src/ext/vamsas/MuscleWSServiceLocator.java
index a269029..0f08435 100755
--- a/src/ext/vamsas/MuscleWSServiceLocator.java
+++ b/src/ext/vamsas/MuscleWSServiceLocator.java
@@ -1,208 +1,209 @@
-/**
- * MuscleWSServiceLocator.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package ext.vamsas;
-
-public class MuscleWSServiceLocator
-    extends org.apache.axis.client.Service implements ext.vamsas.
-    MuscleWSService
-{
-  // Use to get a proxy class for MuscleWS
-  private java.lang.String MuscleWS_address =
-      "http://anaplog.compbio.dundee.ac.uk:8080/axis/services/MuscleWS";
-
-  // The WSDD service name defaults to the port name.
-  private java.lang.String MuscleWSWSDDServiceName = "MuscleWS";
-  private java.util.HashSet ports = null;
-
-  public MuscleWSServiceLocator()
-  {
-  }
-
-  public MuscleWSServiceLocator(org.apache.axis.EngineConfiguration config)
-  {
-    super(config);
-  }
-
-  public java.lang.String getMuscleWSAddress()
-  {
-    return MuscleWS_address;
-  }
-
-  public java.lang.String getMuscleWSWSDDServiceName()
-  {
-    return MuscleWSWSDDServiceName;
-  }
-
-  public void setMuscleWSWSDDServiceName(java.lang.String name)
-  {
-    MuscleWSWSDDServiceName = name;
-  }
-
-  public ext.vamsas.MuscleWS getMuscleWS()
-      throws javax.xml.rpc.ServiceException
-  {
-    java.net.URL endpoint;
-
-    try
-    {
-      endpoint = new java.net.URL(MuscleWS_address);
-    }
-    catch (java.net.MalformedURLException e)
-    {
-      throw new javax.xml.rpc.ServiceException(e);
-    }
-
-    return getMuscleWS(endpoint);
-  }
-
-  public ext.vamsas.MuscleWS getMuscleWS(java.net.URL portAddress)
-      throws javax.xml.rpc.ServiceException
-  {
-    try
-    {
-      ext.vamsas.MuscleWSSoapBindingStub _stub = new ext.vamsas.
-          MuscleWSSoapBindingStub(portAddress,
-                                  this);
-      _stub.setPortName(getMuscleWSWSDDServiceName());
-
-      return _stub;
-    }
-    catch (org.apache.axis.AxisFault e)
-    {
-      return null;
-    }
-  }
-
-  public void setMuscleWSEndpointAddress(java.lang.String address)
-  {
-    MuscleWS_address = address;
-  }
-
-  /**
-   * For the given interface, get the stub implementation.
-   * If this service has no port for the given interface,
-   * then ServiceException is thrown.
-   */
-  public java.rmi.Remote getPort(Class serviceEndpointInterface)
-      throws javax.xml.rpc.ServiceException
-  {
-    try
-    {
-      if (ext.vamsas.MuscleWS.class.isAssignableFrom(
-          serviceEndpointInterface))
-      {
-        ext.vamsas.MuscleWSSoapBindingStub _stub = new ext.vamsas.
-            MuscleWSSoapBindingStub(new java.net.URL(
-                MuscleWS_address), this);
-        _stub.setPortName(getMuscleWSWSDDServiceName());
-
-        return _stub;
-      }
-    }
-    catch (java.lang.Throwable t)
-    {
-      throw new javax.xml.rpc.ServiceException(t);
-    }
-
-    throw new javax.xml.rpc.ServiceException(
-        "There is no stub implementation for the interface:  " +
-        ( (serviceEndpointInterface == null) ? "null"
-         : serviceEndpointInterface.getName()));
-  }
-
-  /**
-   * For the given interface, get the stub implementation.
-   * If this service has no port for the given interface,
-   * then ServiceException is thrown.
-   */
-  public java.rmi.Remote getPort(javax.xml.namespace.QName portName,
-                                 Class serviceEndpointInterface)
-      throws javax.xml.rpc.ServiceException
-  {
-    if (portName == null)
-    {
-      return getPort(serviceEndpointInterface);
-    }
-
-    java.lang.String inputPortName = portName.getLocalPart();
-
-    if ("MuscleWS".equals(inputPortName))
-    {
-      return getMuscleWS();
-    }
-    else
-    {
-      java.rmi.Remote _stub = getPort(serviceEndpointInterface);
-      ( (org.apache.axis.client.Stub) _stub).setPortName(portName);
-
-      return _stub;
-    }
-  }
-
-  public javax.xml.namespace.QName getServiceName()
-  {
-    return new javax.xml.namespace.QName("vamsas", "MuscleWSService");
-  }
-
-  public java.util.Iterator getPorts()
-  {
-    if (ports == null)
-    {
-      ports = new java.util.HashSet();
-      ports.add(new javax.xml.namespace.QName("vamsas", "MuscleWS"));
-    }
-
-    return ports.iterator();
-  }
-
-  /**
-   * Set the endpoint address for the specified port name.
-   */
-  public void setEndpointAddress(java.lang.String portName,
-                                 java.lang.String address)
-      throws javax.xml.rpc.ServiceException
-  {
-    if ("MuscleWS".equals(portName))
-    {
-      setMuscleWSEndpointAddress(address);
-    }
-    else
-    { // Unknown Port Name
-      throw new javax.xml.rpc.ServiceException(
-          " Cannot set Endpoint Address for Unknown Port" + portName);
-    }
-  }
-
-  /**
-   * Set the endpoint address for the specified port name.
-   */
-  public void setEndpointAddress(javax.xml.namespace.QName portName,
-                                 java.lang.String address)
-      throws javax.xml.rpc.ServiceException
-  {
-    setEndpointAddress(portName.getLocalPart(), address);
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package ext.vamsas;
+
+public class MuscleWSServiceLocator extends org.apache.axis.client.Service
+        implements ext.vamsas.MuscleWSService
+{
+  // Use to get a proxy class for MuscleWS
+  private java.lang.String MuscleWS_address = "http://anaplog.compbio.dundee.ac.uk:8080/axis/services/MuscleWS";
+
+  // The WSDD service name defaults to the port name.
+  private java.lang.String MuscleWSWSDDServiceName = "MuscleWS";
+
+  private java.util.HashSet ports = null;
+
+  public MuscleWSServiceLocator()
+  {
+  }
+
+  public MuscleWSServiceLocator(org.apache.axis.EngineConfiguration config)
+  {
+    super(config);
+  }
+
+  public java.lang.String getMuscleWSAddress()
+  {
+    return MuscleWS_address;
+  }
+
+  public java.lang.String getMuscleWSWSDDServiceName()
+  {
+    return MuscleWSWSDDServiceName;
+  }
+
+  public void setMuscleWSWSDDServiceName(java.lang.String name)
+  {
+    MuscleWSWSDDServiceName = name;
+  }
+
+  public ext.vamsas.MuscleWS getMuscleWS()
+          throws javax.xml.rpc.ServiceException
+  {
+    java.net.URL endpoint;
+
+    try
+    {
+      endpoint = new java.net.URL(MuscleWS_address);
+    } catch (java.net.MalformedURLException e)
+    {
+      throw new javax.xml.rpc.ServiceException(e);
+    }
+
+    return getMuscleWS(endpoint);
+  }
+
+  public ext.vamsas.MuscleWS getMuscleWS(java.net.URL portAddress)
+          throws javax.xml.rpc.ServiceException
+  {
+    try
+    {
+      ext.vamsas.MuscleWSSoapBindingStub _stub = new ext.vamsas.MuscleWSSoapBindingStub(
+              portAddress, this);
+      _stub.setPortName(getMuscleWSWSDDServiceName());
+
+      return _stub;
+    } catch (org.apache.axis.AxisFault e)
+    {
+      return null;
+    }
+  }
+
+  public void setMuscleWSEndpointAddress(java.lang.String address)
+  {
+    MuscleWS_address = address;
+  }
+
+  /**
+   * For the given interface, get the stub implementation. If this service has
+   * no port for the given interface, then ServiceException is thrown.
+   */
+  public java.rmi.Remote getPort(Class serviceEndpointInterface)
+          throws javax.xml.rpc.ServiceException
+  {
+    try
+    {
+      if (ext.vamsas.MuscleWS.class
+              .isAssignableFrom(serviceEndpointInterface))
+      {
+        ext.vamsas.MuscleWSSoapBindingStub _stub = new ext.vamsas.MuscleWSSoapBindingStub(
+                new java.net.URL(MuscleWS_address), this);
+        _stub.setPortName(getMuscleWSWSDDServiceName());
+
+        return _stub;
+      }
+    } catch (java.lang.Throwable t)
+    {
+      throw new javax.xml.rpc.ServiceException(t);
+    }
+
+    throw new javax.xml.rpc.ServiceException(
+            "There is no stub implementation for the interface:  "
+                    + ((serviceEndpointInterface == null) ? "null"
+                            : serviceEndpointInterface.getName()));
+  }
+
+  /**
+   * For the given interface, get the stub implementation. If this service has
+   * no port for the given interface, then ServiceException is thrown.
+   */
+  public java.rmi.Remote getPort(javax.xml.namespace.QName portName,
+          Class serviceEndpointInterface)
+          throws javax.xml.rpc.ServiceException
+  {
+    if (portName == null)
+    {
+      return getPort(serviceEndpointInterface);
+    }
+
+    java.lang.String inputPortName = portName.getLocalPart();
+
+    if ("MuscleWS".equals(inputPortName))
+    {
+      return getMuscleWS();
+    }
+    else
+    {
+      java.rmi.Remote _stub = getPort(serviceEndpointInterface);
+      ((org.apache.axis.client.Stub) _stub).setPortName(portName);
+
+      return _stub;
+    }
+  }
+
+  public javax.xml.namespace.QName getServiceName()
+  {
+    return new javax.xml.namespace.QName("vamsas", "MuscleWSService");
+  }
+
+  public java.util.Iterator getPorts()
+  {
+    if (ports == null)
+    {
+      ports = new java.util.HashSet();
+      ports.add(new javax.xml.namespace.QName("vamsas", "MuscleWS"));
+    }
+
+    return ports.iterator();
+  }
+
+  /**
+   * Set the endpoint address for the specified port name.
+   */
+  public void setEndpointAddress(java.lang.String portName,
+          java.lang.String address) throws javax.xml.rpc.ServiceException
+  {
+    if ("MuscleWS".equals(portName))
+    {
+      setMuscleWSEndpointAddress(address);
+    }
+    else
+    { // Unknown Port Name
+      throw new javax.xml.rpc.ServiceException(
+              " Cannot set Endpoint Address for Unknown Port" + portName);
+    }
+  }
+
+  /**
+   * Set the endpoint address for the specified port name.
+   */
+  public void setEndpointAddress(javax.xml.namespace.QName portName,
+          java.lang.String address) throws javax.xml.rpc.ServiceException
+  {
+    setEndpointAddress(portName.getLocalPart(), address);
+  }
+}
diff --git a/src/ext/vamsas/MuscleWSSoapBindingStub.java b/src/ext/vamsas/MuscleWSSoapBindingStub.java
index de80f9e..958a4c2 100755
--- a/src/ext/vamsas/MuscleWSSoapBindingStub.java
+++ b/src/ext/vamsas/MuscleWSSoapBindingStub.java
@@ -1,470 +1,490 @@
-/**
- * MuscleWSSoapBindingStub.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package ext.vamsas;
-
-public class MuscleWSSoapBindingStub
-    extends org.apache.axis.client.Stub implements ext.vamsas.MuscleWS
-{
-  static org.apache.axis.description.OperationDesc[] _operations;
-
-  static
-  {
-    _operations = new org.apache.axis.description.OperationDesc[4];
-    _initOperationDesc1();
-  }
-
-  private java.util.Vector cachedSerClasses = new java.util.Vector();
-  private java.util.Vector cachedSerQNames = new java.util.Vector();
-  private java.util.Vector cachedSerFactories = new java.util.Vector();
-  private java.util.Vector cachedDeserFactories = new java.util.Vector();
-
-  public MuscleWSSoapBindingStub()
-      throws org.apache.axis.AxisFault
-  {
-    this(null);
-  }
-
-  public MuscleWSSoapBindingStub(java.net.URL endpointURL,
-                                 javax.xml.rpc.Service service)
-      throws org.apache.axis.AxisFault
-  {
-    this(service);
-    super.cachedEndpoint = endpointURL;
-  }
-
-  public MuscleWSSoapBindingStub(javax.xml.rpc.Service service)
-      throws org.apache.axis.AxisFault
-  {
-    if (service == null)
-    {
-      super.service = new org.apache.axis.client.Service();
-    }
-    else
-    {
-      super.service = service;
-    }
-
-    java.lang.Class cls;
-    javax.xml.namespace.QName qName;
-    java.lang.Class beansf = org.apache.axis.encoding.ser.BeanSerializerFactory.class;
-    java.lang.Class beandf = org.apache.axis.encoding.ser.
-        BeanDeserializerFactory.class;
-    //java.lang.Class enumsf = org.apache.axis.encoding.ser.EnumSerializerFactory.class;
-    //java.lang.Class enumdf = org.apache.axis.encoding.ser.EnumDeserializerFactory.class;
-    java.lang.Class arraysf = org.apache.axis.encoding.ser.
-        ArraySerializerFactory.class;
-    java.lang.Class arraydf = org.apache.axis.encoding.ser.
-        ArrayDeserializerFactory.class;
-    //java.lang.Class simplesf = org.apache.axis.encoding.ser.SimpleSerializerFactory.class;
-    // java.lang.Class simpledf = org.apache.axis.encoding.ser.SimpleDeserializerFactory.class;
-    //java.lang.Class simplelistsf = org.apache.axis.encoding.ser.SimpleListSerializerFactory.class;
-    //java.lang.Class simplelistdf = org.apache.axis.encoding.ser.SimpleListDeserializerFactory.class;
-    qName = new javax.xml.namespace.QName("simple.objects.vamsas",
-                                          "Sequence");
-    cachedSerQNames.add(qName);
-    cls = vamsas.objects.simple.Sequence.class;
-    cachedSerClasses.add(cls);
-    cachedSerFactories.add(beansf);
-    cachedDeserFactories.add(beandf);
-
-    qName = new javax.xml.namespace.QName("vamsas", "ArrayOf_tns1_Sequence");
-    cachedSerQNames.add(qName);
-    cls = vamsas.objects.simple.Sequence[].class;
-    cachedSerClasses.add(cls);
-    cachedSerFactories.add(arraysf);
-    cachedDeserFactories.add(arraydf);
-
-    qName = new javax.xml.namespace.QName("simple.objects.vamsas",
-                                          "MsaResult");
-    cachedSerQNames.add(qName);
-    cls = vamsas.objects.simple.MsaResult.class;
-    cachedSerClasses.add(cls);
-    cachedSerFactories.add(beansf);
-    cachedDeserFactories.add(beandf);
-
-    qName = new javax.xml.namespace.QName("simple.objects.vamsas",
-                                          "SequenceSet");
-    cachedSerQNames.add(qName);
-    cls = vamsas.objects.simple.SequenceSet.class;
-    cachedSerClasses.add(cls);
-    cachedSerFactories.add(beansf);
-    cachedDeserFactories.add(beandf);
-
-    qName = new javax.xml.namespace.QName("http://simple.objects.vamsas",
-                                          "Object");
-    cachedSerQNames.add(qName);
-    cls = vamsas.objects.simple.Object.class;
-    cachedSerClasses.add(cls);
-    cachedSerFactories.add(beansf);
-    cachedDeserFactories.add(beandf);
-
-    qName = new javax.xml.namespace.QName("simple.objects.vamsas",
-                                          "Alignment");
-    cachedSerQNames.add(qName);
-    cls = vamsas.objects.simple.Alignment.class;
-    cachedSerClasses.add(cls);
-    cachedSerFactories.add(beansf);
-    cachedDeserFactories.add(beandf);
-
-    qName = new javax.xml.namespace.QName("simple.objects.vamsas", "WsJobId");
-    cachedSerQNames.add(qName);
-    cls = vamsas.objects.simple.WsJobId.class;
-    cachedSerClasses.add(cls);
-    cachedSerFactories.add(beansf);
-    cachedDeserFactories.add(beandf);
-
-    qName = new javax.xml.namespace.QName("vamsas", "ArrayOf_xsd_string");
-    cachedSerQNames.add(qName);
-    cls = java.lang.String[].class;
-    cachedSerClasses.add(cls);
-    cachedSerFactories.add(arraysf);
-    cachedDeserFactories.add(arraydf);
-
-    qName = new javax.xml.namespace.QName("simple.objects.vamsas", "Result");
-    cachedSerQNames.add(qName);
-    cls = vamsas.objects.simple.Result.class;
-    cachedSerClasses.add(cls);
-    cachedSerFactories.add(beansf);
-    cachedDeserFactories.add(beandf);
-  }
-
-  private static void _initOperationDesc1()
-  {
-    org.apache.axis.description.OperationDesc oper;
-    oper = new org.apache.axis.description.OperationDesc();
-    oper.setName("align");
-    oper.addParameter(new javax.xml.namespace.QName("", "seqSet"),
-                      new javax.xml.namespace.QName("simple.objects.vamsas",
-        "SequenceSet"),
-                      vamsas.objects.simple.SequenceSet.class,
-                      org.apache.axis.description.ParameterDesc.IN, false, false);
-    oper.setReturnType(new javax.xml.namespace.QName(
-        "simple.objects.vamsas", "WsJobId"));
-    oper.setReturnClass(vamsas.objects.simple.WsJobId.class);
-    oper.setReturnQName(new javax.xml.namespace.QName("", "alignReturn"));
-    oper.setStyle(org.apache.axis.constants.Style.RPC);
-    oper.setUse(org.apache.axis.constants.Use.ENCODED);
-    _operations[0] = oper;
-
-    oper = new org.apache.axis.description.OperationDesc();
-    oper.setName("getalign");
-    oper.addParameter(new javax.xml.namespace.QName("", "job_id"),
-                      new javax.xml.namespace.QName(
-        "http://www.w3.org/2001/XMLSchema",
-        "string"), java.lang.String.class,
-                      org.apache.axis.description.ParameterDesc.IN, false, false);
-    oper.setReturnType(new javax.xml.namespace.QName(
-        "simple.objects.vamsas", "Alignment"));
-    oper.setReturnClass(vamsas.objects.simple.Alignment.class);
-    oper.setReturnQName(new javax.xml.namespace.QName("", "getalignReturn"));
-    oper.setStyle(org.apache.axis.constants.Style.RPC);
-    oper.setUse(org.apache.axis.constants.Use.ENCODED);
-    _operations[1] = oper;
-
-    oper = new org.apache.axis.description.OperationDesc();
-    oper.setName("getResult");
-    oper.addParameter(new javax.xml.namespace.QName("", "job_id"),
-                      new javax.xml.namespace.QName(
-        "http://www.w3.org/2001/XMLSchema",
-        "string"), java.lang.String.class,
-                      org.apache.axis.description.ParameterDesc.IN, false, false);
-    oper.setReturnType(new javax.xml.namespace.QName(
-        "simple.objects.vamsas", "MsaResult"));
-    oper.setReturnClass(vamsas.objects.simple.MsaResult.class);
-    oper.setReturnQName(new javax.xml.namespace.QName("", "getResultReturn"));
-    oper.setStyle(org.apache.axis.constants.Style.RPC);
-    oper.setUse(org.apache.axis.constants.Use.ENCODED);
-    _operations[2] = oper;
-
-    oper = new org.apache.axis.description.OperationDesc();
-    oper.setName("cancel");
-    oper.addParameter(new javax.xml.namespace.QName("", "jobId"),
-                      new javax.xml.namespace.QName(
-        "http://www.w3.org/2001/XMLSchema",
-        "string"), java.lang.String.class,
-                      org.apache.axis.description.ParameterDesc.IN, false, false);
-    oper.setReturnType(new javax.xml.namespace.QName(
-        "simple.objects.vamsas", "WsJobId"));
-    oper.setReturnClass(vamsas.objects.simple.WsJobId.class);
-    oper.setReturnQName(new javax.xml.namespace.QName("", "cancelReturn"));
-    oper.setStyle(org.apache.axis.constants.Style.RPC);
-    oper.setUse(org.apache.axis.constants.Use.ENCODED);
-    _operations[3] = oper;
-  }
-
-  protected org.apache.axis.client.Call createCall()
-      throws java.rmi.RemoteException
-  {
-    try
-    {
-      org.apache.axis.client.Call _call = (org.apache.axis.client.Call)super.
-          service.createCall();
-
-      if (super.maintainSessionSet)
-      {
-        _call.setMaintainSession(super.maintainSession);
-      }
-
-      if (super.cachedUsername != null)
-      {
-        _call.setUsername(super.cachedUsername);
-      }
-
-      if (super.cachedPassword != null)
-      {
-        _call.setPassword(super.cachedPassword);
-      }
-
-      if (super.cachedEndpoint != null)
-      {
-        _call.setTargetEndpointAddress(super.cachedEndpoint);
-      }
-
-      if (super.cachedTimeout != null)
-      {
-        _call.setTimeout(super.cachedTimeout);
-      }
-
-      if (super.cachedPortName != null)
-      {
-        _call.setPortName(super.cachedPortName);
-      }
-
-      java.util.Enumeration keys = super.cachedProperties.keys();
-
-      while (keys.hasMoreElements())
-      {
-        java.lang.String key = (java.lang.String) keys.nextElement();
-        _call.setProperty(key, super.cachedProperties.get(key));
-      }
-
-      // All the type mapping information is registered
-      // when the first call is made.
-      // The type mapping information is actually registered in
-      // the TypeMappingRegistry of the service, which
-      // is the reason why registration is only needed for the first call.
-      synchronized (this)
-      {
-        if (firstCall())
-        {
-          // must set encoding style before registering serializers
-          _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.
-                               SOAP11_CONSTANTS);
-          _call.setEncodingStyle(org.apache.axis.Constants.URI_SOAP11_ENC);
-
-          for (int i = 0; i < cachedSerFactories.size(); ++i)
-          {
-            java.lang.Class cls = (java.lang.Class) cachedSerClasses.get(i);
-            javax.xml.namespace.QName qName = (javax.xml.namespace.QName)
-                cachedSerQNames.get(i);
-            java.lang.Class sf = (java.lang.Class) cachedSerFactories.get(i);
-            java.lang.Class df = (java.lang.Class) cachedDeserFactories.get(i);
-            _call.registerTypeMapping(cls, qName, sf, df, false);
-          }
-        }
-      }
-
-      return _call;
-    }
-    catch (java.lang.Throwable _t)
-    {
-      throw new org.apache.axis.AxisFault(
-          "Failure trying to get the Call object",
-          _t);
-    }
-  }
-
-  public vamsas.objects.simple.WsJobId align(
-      vamsas.objects.simple.SequenceSet seqSet)
-      throws java.rmi.RemoteException
-  {
-    if (super.cachedEndpoint == null)
-    {
-      throw new org.apache.axis.NoEndPointException();
-    }
-
-    org.apache.axis.client.Call _call = createCall();
-    _call.setOperation(_operations[0]);
-    _call.setUseSOAPAction(true);
-    _call.setSOAPActionURI("");
-    _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
-    _call.setOperationName(new javax.xml.namespace.QName("vamsas", "align"));
-
-    setRequestHeaders(_call);
-    setAttachments(_call);
-
-    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
-                                          {seqSet});
-
-    if (_resp instanceof java.rmi.RemoteException)
-    {
-      throw (java.rmi.RemoteException) _resp;
-    }
-    else
-    {
-      extractAttachments(_call);
-
-      try
-      {
-        return (vamsas.objects.simple.WsJobId) _resp;
-      }
-      catch (java.lang.Exception _exception)
-      {
-        return (vamsas.objects.simple.WsJobId) org.apache.axis.utils.JavaUtils.
-            convert(_resp,
-                    vamsas.objects.simple.WsJobId.class);
-      }
-    }
-  }
-
-  public vamsas.objects.simple.Alignment getalign(java.lang.String job_id)
-      throws java.rmi.RemoteException
-  {
-    if (super.cachedEndpoint == null)
-    {
-      throw new org.apache.axis.NoEndPointException();
-    }
-
-    org.apache.axis.client.Call _call = createCall();
-    _call.setOperation(_operations[1]);
-    _call.setUseSOAPAction(true);
-    _call.setSOAPActionURI("");
-    _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
-    _call.setOperationName(new javax.xml.namespace.QName("vamsas",
-        "getalign"));
-
-    setRequestHeaders(_call);
-    setAttachments(_call);
-
-    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
-                                          {job_id});
-
-    if (_resp instanceof java.rmi.RemoteException)
-    {
-      throw (java.rmi.RemoteException) _resp;
-    }
-    else
-    {
-      extractAttachments(_call);
-
-      try
-      {
-        return (vamsas.objects.simple.Alignment) _resp;
-      }
-      catch (java.lang.Exception _exception)
-      {
-        return (vamsas.objects.simple.Alignment) org.apache.axis.utils.
-            JavaUtils.convert(_resp,
-                              vamsas.objects.simple.Alignment.class);
-      }
-    }
-  }
-
-  public vamsas.objects.simple.MsaResult getResult(java.lang.String job_id)
-      throws java.rmi.RemoteException
-  {
-    if (super.cachedEndpoint == null)
-    {
-      throw new org.apache.axis.NoEndPointException();
-    }
-
-    org.apache.axis.client.Call _call = createCall();
-    _call.setOperation(_operations[2]);
-    _call.setUseSOAPAction(true);
-    _call.setSOAPActionURI("");
-    _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
-    _call.setOperationName(new javax.xml.namespace.QName("vamsas",
-        "getResult"));
-
-    setRequestHeaders(_call);
-    setAttachments(_call);
-
-    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
-                                          {job_id});
-
-    if (_resp instanceof java.rmi.RemoteException)
-    {
-      throw (java.rmi.RemoteException) _resp;
-    }
-    else
-    {
-      extractAttachments(_call);
-
-      try
-      {
-        return (vamsas.objects.simple.MsaResult) _resp;
-      }
-      catch (java.lang.Exception _exception)
-      {
-        return (vamsas.objects.simple.MsaResult) org.apache.axis.utils.
-            JavaUtils.convert(_resp,
-                              vamsas.objects.simple.MsaResult.class);
-      }
-    }
-  }
-
-  public vamsas.objects.simple.WsJobId cancel(java.lang.String jobId)
-      throws java.rmi.RemoteException
-  {
-    if (super.cachedEndpoint == null)
-    {
-      throw new org.apache.axis.NoEndPointException();
-    }
-
-    org.apache.axis.client.Call _call = createCall();
-    _call.setOperation(_operations[3]);
-    _call.setUseSOAPAction(true);
-    _call.setSOAPActionURI("");
-    _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
-    _call.setOperationName(new javax.xml.namespace.QName("vamsas", "cancel"));
-
-    setRequestHeaders(_call);
-    setAttachments(_call);
-
-    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
-                                          {jobId});
-
-    if (_resp instanceof java.rmi.RemoteException)
-    {
-      throw (java.rmi.RemoteException) _resp;
-    }
-    else
-    {
-      extractAttachments(_call);
-
-      try
-      {
-        return (vamsas.objects.simple.WsJobId) _resp;
-      }
-      catch (java.lang.Exception _exception)
-      {
-        return (vamsas.objects.simple.WsJobId) org.apache.axis.utils.JavaUtils.
-            convert(_resp,
-                    vamsas.objects.simple.WsJobId.class);
-      }
-    }
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package ext.vamsas;
+
+public class MuscleWSSoapBindingStub extends org.apache.axis.client.Stub
+        implements ext.vamsas.MuscleWS
+{
+  static org.apache.axis.description.OperationDesc[] _operations;
+
+  static
+  {
+    _operations = new org.apache.axis.description.OperationDesc[4];
+    _initOperationDesc1();
+  }
+
+  private java.util.Vector cachedSerClasses = new java.util.Vector();
+
+  private java.util.Vector cachedSerQNames = new java.util.Vector();
+
+  private java.util.Vector cachedSerFactories = new java.util.Vector();
+
+  private java.util.Vector cachedDeserFactories = new java.util.Vector();
+
+  public MuscleWSSoapBindingStub() throws org.apache.axis.AxisFault
+  {
+    this(null);
+  }
+
+  public MuscleWSSoapBindingStub(java.net.URL endpointURL,
+          javax.xml.rpc.Service service) throws org.apache.axis.AxisFault
+  {
+    this(service);
+    super.cachedEndpoint = endpointURL;
+  }
+
+  public MuscleWSSoapBindingStub(javax.xml.rpc.Service service)
+          throws org.apache.axis.AxisFault
+  {
+    if (service == null)
+    {
+      super.service = new org.apache.axis.client.Service();
+    }
+    else
+    {
+      super.service = service;
+    }
+
+    java.lang.Class cls;
+    javax.xml.namespace.QName qName;
+    java.lang.Class beansf = org.apache.axis.encoding.ser.BeanSerializerFactory.class;
+    java.lang.Class beandf = org.apache.axis.encoding.ser.BeanDeserializerFactory.class;
+    // java.lang.Class enumsf =
+    // org.apache.axis.encoding.ser.EnumSerializerFactory.class;
+    // java.lang.Class enumdf =
+    // org.apache.axis.encoding.ser.EnumDeserializerFactory.class;
+    java.lang.Class arraysf = org.apache.axis.encoding.ser.ArraySerializerFactory.class;
+    java.lang.Class arraydf = org.apache.axis.encoding.ser.ArrayDeserializerFactory.class;
+    // java.lang.Class simplesf =
+    // org.apache.axis.encoding.ser.SimpleSerializerFactory.class;
+    // java.lang.Class simpledf =
+    // org.apache.axis.encoding.ser.SimpleDeserializerFactory.class;
+    // java.lang.Class simplelistsf =
+    // org.apache.axis.encoding.ser.SimpleListSerializerFactory.class;
+    // java.lang.Class simplelistdf =
+    // org.apache.axis.encoding.ser.SimpleListDeserializerFactory.class;
+    qName = new javax.xml.namespace.QName("simple.objects.vamsas",
+            "Sequence");
+    cachedSerQNames.add(qName);
+    cls = vamsas.objects.simple.Sequence.class;
+    cachedSerClasses.add(cls);
+    cachedSerFactories.add(beansf);
+    cachedDeserFactories.add(beandf);
+
+    qName = new javax.xml.namespace.QName("vamsas", "ArrayOf_tns1_Sequence");
+    cachedSerQNames.add(qName);
+    cls = vamsas.objects.simple.Sequence[].class;
+    cachedSerClasses.add(cls);
+    cachedSerFactories.add(arraysf);
+    cachedDeserFactories.add(arraydf);
+
+    qName = new javax.xml.namespace.QName("simple.objects.vamsas",
+            "MsaResult");
+    cachedSerQNames.add(qName);
+    cls = vamsas.objects.simple.MsaResult.class;
+    cachedSerClasses.add(cls);
+    cachedSerFactories.add(beansf);
+    cachedDeserFactories.add(beandf);
+
+    qName = new javax.xml.namespace.QName("simple.objects.vamsas",
+            "SequenceSet");
+    cachedSerQNames.add(qName);
+    cls = vamsas.objects.simple.SequenceSet.class;
+    cachedSerClasses.add(cls);
+    cachedSerFactories.add(beansf);
+    cachedDeserFactories.add(beandf);
+
+    qName = new javax.xml.namespace.QName("http://simple.objects.vamsas",
+            "Object");
+    cachedSerQNames.add(qName);
+    cls = vamsas.objects.simple.Object.class;
+    cachedSerClasses.add(cls);
+    cachedSerFactories.add(beansf);
+    cachedDeserFactories.add(beandf);
+
+    qName = new javax.xml.namespace.QName("simple.objects.vamsas",
+            "Alignment");
+    cachedSerQNames.add(qName);
+    cls = vamsas.objects.simple.Alignment.class;
+    cachedSerClasses.add(cls);
+    cachedSerFactories.add(beansf);
+    cachedDeserFactories.add(beandf);
+
+    qName = new javax.xml.namespace.QName("simple.objects.vamsas",
+            "WsJobId");
+    cachedSerQNames.add(qName);
+    cls = vamsas.objects.simple.WsJobId.class;
+    cachedSerClasses.add(cls);
+    cachedSerFactories.add(beansf);
+    cachedDeserFactories.add(beandf);
+
+    qName = new javax.xml.namespace.QName("vamsas", "ArrayOf_xsd_string");
+    cachedSerQNames.add(qName);
+    cls = java.lang.String[].class;
+    cachedSerClasses.add(cls);
+    cachedSerFactories.add(arraysf);
+    cachedDeserFactories.add(arraydf);
+
+    qName = new javax.xml.namespace.QName("simple.objects.vamsas", "Result");
+    cachedSerQNames.add(qName);
+    cls = vamsas.objects.simple.Result.class;
+    cachedSerClasses.add(cls);
+    cachedSerFactories.add(beansf);
+    cachedDeserFactories.add(beandf);
+  }
+
+  private static void _initOperationDesc1()
+  {
+    org.apache.axis.description.OperationDesc oper;
+    oper = new org.apache.axis.description.OperationDesc();
+    oper.setName("align");
+    oper.addParameter(new javax.xml.namespace.QName("", "seqSet"),
+            new javax.xml.namespace.QName("simple.objects.vamsas",
+                    "SequenceSet"),
+            vamsas.objects.simple.SequenceSet.class,
+            org.apache.axis.description.ParameterDesc.IN, false, false);
+    oper.setReturnType(new javax.xml.namespace.QName(
+            "simple.objects.vamsas", "WsJobId"));
+    oper.setReturnClass(vamsas.objects.simple.WsJobId.class);
+    oper.setReturnQName(new javax.xml.namespace.QName("", "alignReturn"));
+    oper.setStyle(org.apache.axis.constants.Style.RPC);
+    oper.setUse(org.apache.axis.constants.Use.ENCODED);
+    _operations[0] = oper;
+
+    oper = new org.apache.axis.description.OperationDesc();
+    oper.setName("getalign");
+    oper.addParameter(new javax.xml.namespace.QName("", "job_id"),
+            new javax.xml.namespace.QName(
+                    "http://www.w3.org/2001/XMLSchema", "string"),
+            java.lang.String.class,
+            org.apache.axis.description.ParameterDesc.IN, false, false);
+    oper.setReturnType(new javax.xml.namespace.QName(
+            "simple.objects.vamsas", "Alignment"));
+    oper.setReturnClass(vamsas.objects.simple.Alignment.class);
+    oper
+            .setReturnQName(new javax.xml.namespace.QName("",
+                    "getalignReturn"));
+    oper.setStyle(org.apache.axis.constants.Style.RPC);
+    oper.setUse(org.apache.axis.constants.Use.ENCODED);
+    _operations[1] = oper;
+
+    oper = new org.apache.axis.description.OperationDesc();
+    oper.setName("getResult");
+    oper.addParameter(new javax.xml.namespace.QName("", "job_id"),
+            new javax.xml.namespace.QName(
+                    "http://www.w3.org/2001/XMLSchema", "string"),
+            java.lang.String.class,
+            org.apache.axis.description.ParameterDesc.IN, false, false);
+    oper.setReturnType(new javax.xml.namespace.QName(
+            "simple.objects.vamsas", "MsaResult"));
+    oper.setReturnClass(vamsas.objects.simple.MsaResult.class);
+    oper
+            .setReturnQName(new javax.xml.namespace.QName("",
+                    "getResultReturn"));
+    oper.setStyle(org.apache.axis.constants.Style.RPC);
+    oper.setUse(org.apache.axis.constants.Use.ENCODED);
+    _operations[2] = oper;
+
+    oper = new org.apache.axis.description.OperationDesc();
+    oper.setName("cancel");
+    oper.addParameter(new javax.xml.namespace.QName("", "jobId"),
+            new javax.xml.namespace.QName(
+                    "http://www.w3.org/2001/XMLSchema", "string"),
+            java.lang.String.class,
+            org.apache.axis.description.ParameterDesc.IN, false, false);
+    oper.setReturnType(new javax.xml.namespace.QName(
+            "simple.objects.vamsas", "WsJobId"));
+    oper.setReturnClass(vamsas.objects.simple.WsJobId.class);
+    oper.setReturnQName(new javax.xml.namespace.QName("", "cancelReturn"));
+    oper.setStyle(org.apache.axis.constants.Style.RPC);
+    oper.setUse(org.apache.axis.constants.Use.ENCODED);
+    _operations[3] = oper;
+  }
+
+  protected org.apache.axis.client.Call createCall()
+          throws java.rmi.RemoteException
+  {
+    try
+    {
+      org.apache.axis.client.Call _call = (org.apache.axis.client.Call) super.service
+              .createCall();
+
+      if (super.maintainSessionSet)
+      {
+        _call.setMaintainSession(super.maintainSession);
+      }
+
+      if (super.cachedUsername != null)
+      {
+        _call.setUsername(super.cachedUsername);
+      }
+
+      if (super.cachedPassword != null)
+      {
+        _call.setPassword(super.cachedPassword);
+      }
+
+      if (super.cachedEndpoint != null)
+      {
+        _call.setTargetEndpointAddress(super.cachedEndpoint);
+      }
+
+      if (super.cachedTimeout != null)
+      {
+        _call.setTimeout(super.cachedTimeout);
+      }
+
+      if (super.cachedPortName != null)
+      {
+        _call.setPortName(super.cachedPortName);
+      }
+
+      java.util.Enumeration keys = super.cachedProperties.keys();
+
+      while (keys.hasMoreElements())
+      {
+        java.lang.String key = (java.lang.String) keys.nextElement();
+        _call.setProperty(key, super.cachedProperties.get(key));
+      }
+
+      // All the type mapping information is registered
+      // when the first call is made.
+      // The type mapping information is actually registered in
+      // the TypeMappingRegistry of the service, which
+      // is the reason why registration is only needed for the first call.
+      synchronized (this)
+      {
+        if (firstCall())
+        {
+          // must set encoding style before registering serializers
+          _call
+                  .setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+          _call.setEncodingStyle(org.apache.axis.Constants.URI_SOAP11_ENC);
+
+          for (int i = 0; i < cachedSerFactories.size(); ++i)
+          {
+            java.lang.Class cls = (java.lang.Class) cachedSerClasses.get(i);
+            javax.xml.namespace.QName qName = (javax.xml.namespace.QName) cachedSerQNames
+                    .get(i);
+            java.lang.Class sf = (java.lang.Class) cachedSerFactories
+                    .get(i);
+            java.lang.Class df = (java.lang.Class) cachedDeserFactories
+                    .get(i);
+            _call.registerTypeMapping(cls, qName, sf, df, false);
+          }
+        }
+      }
+
+      return _call;
+    } catch (java.lang.Throwable _t)
+    {
+      throw new org.apache.axis.AxisFault(
+              "Failure trying to get the Call object", _t);
+    }
+  }
+
+  public vamsas.objects.simple.WsJobId align(
+          vamsas.objects.simple.SequenceSet seqSet)
+          throws java.rmi.RemoteException
+  {
+    if (super.cachedEndpoint == null)
+    {
+      throw new org.apache.axis.NoEndPointException();
+    }
+
+    org.apache.axis.client.Call _call = createCall();
+    _call.setOperation(_operations[0]);
+    _call.setUseSOAPAction(true);
+    _call.setSOAPActionURI("");
+    _call
+            .setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+    _call
+            .setOperationName(new javax.xml.namespace.QName("vamsas",
+                    "align"));
+
+    setRequestHeaders(_call);
+    setAttachments(_call);
+
+    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
+    { seqSet });
+
+    if (_resp instanceof java.rmi.RemoteException)
+    {
+      throw (java.rmi.RemoteException) _resp;
+    }
+    else
+    {
+      extractAttachments(_call);
+
+      try
+      {
+        return (vamsas.objects.simple.WsJobId) _resp;
+      } catch (java.lang.Exception _exception)
+      {
+        return (vamsas.objects.simple.WsJobId) org.apache.axis.utils.JavaUtils
+                .convert(_resp, vamsas.objects.simple.WsJobId.class);
+      }
+    }
+  }
+
+  public vamsas.objects.simple.Alignment getalign(java.lang.String job_id)
+          throws java.rmi.RemoteException
+  {
+    if (super.cachedEndpoint == null)
+    {
+      throw new org.apache.axis.NoEndPointException();
+    }
+
+    org.apache.axis.client.Call _call = createCall();
+    _call.setOperation(_operations[1]);
+    _call.setUseSOAPAction(true);
+    _call.setSOAPActionURI("");
+    _call
+            .setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+    _call.setOperationName(new javax.xml.namespace.QName("vamsas",
+            "getalign"));
+
+    setRequestHeaders(_call);
+    setAttachments(_call);
+
+    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
+    { job_id });
+
+    if (_resp instanceof java.rmi.RemoteException)
+    {
+      throw (java.rmi.RemoteException) _resp;
+    }
+    else
+    {
+      extractAttachments(_call);
+
+      try
+      {
+        return (vamsas.objects.simple.Alignment) _resp;
+      } catch (java.lang.Exception _exception)
+      {
+        return (vamsas.objects.simple.Alignment) org.apache.axis.utils.JavaUtils
+                .convert(_resp, vamsas.objects.simple.Alignment.class);
+      }
+    }
+  }
+
+  public vamsas.objects.simple.MsaResult getResult(java.lang.String job_id)
+          throws java.rmi.RemoteException
+  {
+    if (super.cachedEndpoint == null)
+    {
+      throw new org.apache.axis.NoEndPointException();
+    }
+
+    org.apache.axis.client.Call _call = createCall();
+    _call.setOperation(_operations[2]);
+    _call.setUseSOAPAction(true);
+    _call.setSOAPActionURI("");
+    _call
+            .setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+    _call.setOperationName(new javax.xml.namespace.QName("vamsas",
+            "getResult"));
+
+    setRequestHeaders(_call);
+    setAttachments(_call);
+
+    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
+    { job_id });
+
+    if (_resp instanceof java.rmi.RemoteException)
+    {
+      throw (java.rmi.RemoteException) _resp;
+    }
+    else
+    {
+      extractAttachments(_call);
+
+      try
+      {
+        return (vamsas.objects.simple.MsaResult) _resp;
+      } catch (java.lang.Exception _exception)
+      {
+        return (vamsas.objects.simple.MsaResult) org.apache.axis.utils.JavaUtils
+                .convert(_resp, vamsas.objects.simple.MsaResult.class);
+      }
+    }
+  }
+
+  public vamsas.objects.simple.WsJobId cancel(java.lang.String jobId)
+          throws java.rmi.RemoteException
+  {
+    if (super.cachedEndpoint == null)
+    {
+      throw new org.apache.axis.NoEndPointException();
+    }
+
+    org.apache.axis.client.Call _call = createCall();
+    _call.setOperation(_operations[3]);
+    _call.setUseSOAPAction(true);
+    _call.setSOAPActionURI("");
+    _call
+            .setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+    _call
+            .setOperationName(new javax.xml.namespace.QName("vamsas",
+                    "cancel"));
+
+    setRequestHeaders(_call);
+    setAttachments(_call);
+
+    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
+    { jobId });
+
+    if (_resp instanceof java.rmi.RemoteException)
+    {
+      throw (java.rmi.RemoteException) _resp;
+    }
+    else
+    {
+      extractAttachments(_call);
+
+      try
+      {
+        return (vamsas.objects.simple.WsJobId) _resp;
+      } catch (java.lang.Exception _exception)
+      {
+        return (vamsas.objects.simple.WsJobId) org.apache.axis.utils.JavaUtils
+                .convert(_resp, vamsas.objects.simple.WsJobId.class);
+      }
+    }
+  }
+}
diff --git a/src/ext/vamsas/RegistryServiceSoapBindingStub.java b/src/ext/vamsas/RegistryServiceSoapBindingStub.java
index 22bd8ed..c361e8d 100755
--- a/src/ext/vamsas/RegistryServiceSoapBindingStub.java
+++ b/src/ext/vamsas/RegistryServiceSoapBindingStub.java
@@ -1,18 +1,32 @@
-/**
- * RegistryServiceSoapBindingStub.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package ext.vamsas;
 
-public class RegistryServiceSoapBindingStub
-    extends org.apache.axis.client.Stub implements ext.vamsas.IRegistry
+public class RegistryServiceSoapBindingStub extends
+        org.apache.axis.client.Stub implements ext.vamsas.IRegistry
 {
   private java.util.Vector cachedSerClasses = new java.util.Vector();
+
   private java.util.Vector cachedSerQNames = new java.util.Vector();
+
   private java.util.Vector cachedSerFactories = new java.util.Vector();
+
   private java.util.Vector cachedDeserFactories = new java.util.Vector();
 
   static org.apache.axis.description.OperationDesc[] _operations;
@@ -28,32 +42,31 @@ public class RegistryServiceSoapBindingStub
     org.apache.axis.description.OperationDesc oper;
     oper = new org.apache.axis.description.OperationDesc();
     oper.setName("getServices");
-    oper.setReturnType(new javax.xml.namespace.QName("registry.objects.vamsas",
-        "ServiceHandles"));
+    oper.setReturnType(new javax.xml.namespace.QName(
+            "registry.objects.vamsas", "ServiceHandles"));
     oper.setReturnClass(ext.vamsas.ServiceHandles.class);
-    oper.setReturnQName(new javax.xml.namespace.QName("", "getServicesReturn"));
+    oper.setReturnQName(new javax.xml.namespace.QName("",
+            "getServicesReturn"));
     oper.setStyle(org.apache.axis.constants.Style.RPC);
     oper.setUse(org.apache.axis.constants.Use.ENCODED);
     _operations[0] = oper;
 
   }
 
-  public RegistryServiceSoapBindingStub()
-      throws org.apache.axis.AxisFault
+  public RegistryServiceSoapBindingStub() throws org.apache.axis.AxisFault
   {
     this(null);
   }
 
   public RegistryServiceSoapBindingStub(java.net.URL endpointURL,
-                                        javax.xml.rpc.Service service)
-      throws org.apache.axis.AxisFault
+          javax.xml.rpc.Service service) throws org.apache.axis.AxisFault
   {
     this(service);
     super.cachedEndpoint = endpointURL;
   }
 
   public RegistryServiceSoapBindingStub(javax.xml.rpc.Service service)
-      throws org.apache.axis.AxisFault
+          throws org.apache.axis.AxisFault
   {
     if (service == null)
     {
@@ -66,20 +79,23 @@ public class RegistryServiceSoapBindingStub
     java.lang.Class cls;
     javax.xml.namespace.QName qName;
     java.lang.Class beansf = org.apache.axis.encoding.ser.BeanSerializerFactory.class;
-    java.lang.Class beandf = org.apache.axis.encoding.ser.
-        BeanDeserializerFactory.class;
-    //java.lang.Class enumsf = org.apache.axis.encoding.ser.EnumSerializerFactory.class;
-    //java.lang.Class enumdf = org.apache.axis.encoding.ser.EnumDeserializerFactory.class;
-    java.lang.Class arraysf = org.apache.axis.encoding.ser.
-        ArraySerializerFactory.class;
-    java.lang.Class arraydf = org.apache.axis.encoding.ser.
-        ArrayDeserializerFactory.class;
-    //java.lang.Class simplesf = org.apache.axis.encoding.ser.SimpleSerializerFactory.class;
-    //java.lang.Class simpledf = org.apache.axis.encoding.ser.SimpleDeserializerFactory.class;
-    //java.lang.Class simplelistsf = org.apache.axis.encoding.ser.SimpleListSerializerFactory.class;
-    //java.lang.Class simplelistdf = org.apache.axis.encoding.ser.SimpleListDeserializerFactory.class;
+    java.lang.Class beandf = org.apache.axis.encoding.ser.BeanDeserializerFactory.class;
+    // java.lang.Class enumsf =
+    // org.apache.axis.encoding.ser.EnumSerializerFactory.class;
+    // java.lang.Class enumdf =
+    // org.apache.axis.encoding.ser.EnumDeserializerFactory.class;
+    java.lang.Class arraysf = org.apache.axis.encoding.ser.ArraySerializerFactory.class;
+    java.lang.Class arraydf = org.apache.axis.encoding.ser.ArrayDeserializerFactory.class;
+    // java.lang.Class simplesf =
+    // org.apache.axis.encoding.ser.SimpleSerializerFactory.class;
+    // java.lang.Class simpledf =
+    // org.apache.axis.encoding.ser.SimpleDeserializerFactory.class;
+    // java.lang.Class simplelistsf =
+    // org.apache.axis.encoding.ser.SimpleListSerializerFactory.class;
+    // java.lang.Class simplelistdf =
+    // org.apache.axis.encoding.ser.SimpleListDeserializerFactory.class;
     qName = new javax.xml.namespace.QName("vamsas",
-                                          "ArrayOf_tns1_ServiceHandle");
+            "ArrayOf_tns1_ServiceHandle");
     cachedSerQNames.add(qName);
     cls = ext.vamsas.ServiceHandle[].class;
     cachedSerClasses.add(cls);
@@ -87,7 +103,7 @@ public class RegistryServiceSoapBindingStub
     cachedDeserFactories.add(arraydf);
 
     qName = new javax.xml.namespace.QName("registry.objects.vamsas",
-                                          "ServiceHandles");
+            "ServiceHandles");
     cachedSerQNames.add(qName);
     cls = ext.vamsas.ServiceHandles.class;
     cachedSerClasses.add(cls);
@@ -95,7 +111,7 @@ public class RegistryServiceSoapBindingStub
     cachedDeserFactories.add(beandf);
 
     qName = new javax.xml.namespace.QName("registry.objects.vamsas",
-                                          "ServiceHandle");
+            "ServiceHandle");
     cachedSerQNames.add(qName);
     cls = ext.vamsas.ServiceHandle.class;
     cachedSerClasses.add(cls);
@@ -105,12 +121,12 @@ public class RegistryServiceSoapBindingStub
   }
 
   protected org.apache.axis.client.Call createCall()
-      throws java.rmi.RemoteException
+          throws java.rmi.RemoteException
   {
     try
     {
-      org.apache.axis.client.Call _call =
-          (org.apache.axis.client.Call)super.service.createCall();
+      org.apache.axis.client.Call _call = (org.apache.axis.client.Call) super.service
+              .createCall();
       if (super.maintainSessionSet)
       {
         _call.setMaintainSession(super.maintainSession);
@@ -151,33 +167,32 @@ public class RegistryServiceSoapBindingStub
         if (firstCall())
         {
           // must set encoding style before registering serializers
-          _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.
-                               SOAP11_CONSTANTS);
+          _call
+                  .setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
           _call.setEncodingStyle(org.apache.axis.Constants.URI_SOAP11_ENC);
           for (int i = 0; i < cachedSerFactories.size(); ++i)
           {
             java.lang.Class cls = (java.lang.Class) cachedSerClasses.get(i);
-            javax.xml.namespace.QName qName =
-                (javax.xml.namespace.QName) cachedSerQNames.get(i);
-            java.lang.Class sf = (java.lang.Class)
-                cachedSerFactories.get(i);
-            java.lang.Class df = (java.lang.Class)
-                cachedDeserFactories.get(i);
+            javax.xml.namespace.QName qName = (javax.xml.namespace.QName) cachedSerQNames
+                    .get(i);
+            java.lang.Class sf = (java.lang.Class) cachedSerFactories
+                    .get(i);
+            java.lang.Class df = (java.lang.Class) cachedDeserFactories
+                    .get(i);
             _call.registerTypeMapping(cls, qName, sf, df, false);
           }
         }
       }
       return _call;
-    }
-    catch (java.lang.Throwable _t)
+    } catch (java.lang.Throwable _t)
     {
       throw new org.apache.axis.AxisFault(
-          "Failure trying to get the Call object", _t);
+              "Failure trying to get the Call object", _t);
     }
   }
 
   public ext.vamsas.ServiceHandles getServices()
-      throws java.rmi.RemoteException
+          throws java.rmi.RemoteException
   {
     if (super.cachedEndpoint == null)
     {
@@ -187,14 +202,15 @@ public class RegistryServiceSoapBindingStub
     _call.setOperation(_operations[0]);
     _call.setUseSOAPAction(true);
     _call.setSOAPActionURI("");
-    _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+    _call
+            .setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
     _call.setOperationName(new javax.xml.namespace.QName("vamsas",
-        "getServices"));
+            "getServices"));
 
     setRequestHeaders(_call);
     setAttachments(_call);
     java.lang.Object _resp = _call.invoke(new java.lang.Object[]
-                                          {});
+    {});
 
     if (_resp instanceof java.rmi.RemoteException)
     {
@@ -206,11 +222,10 @@ public class RegistryServiceSoapBindingStub
       try
       {
         return (ext.vamsas.ServiceHandles) _resp;
-      }
-      catch (java.lang.Exception _exception)
+      } catch (java.lang.Exception _exception)
       {
-        return (ext.vamsas.ServiceHandles) org.apache.axis.utils.JavaUtils.
-            convert(_resp, ext.vamsas.ServiceHandles.class);
+        return (ext.vamsas.ServiceHandles) org.apache.axis.utils.JavaUtils
+                .convert(_resp, ext.vamsas.ServiceHandles.class);
       }
     }
   }
diff --git a/src/ext/vamsas/SeqSearchI.java b/src/ext/vamsas/SeqSearchI.java
index 3c89161..f8b0fb7 100644
--- a/src/ext/vamsas/SeqSearchI.java
+++ b/src/ext/vamsas/SeqSearchI.java
@@ -1,16 +1,38 @@
-/**
- * ScanPSService.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package ext.vamsas;
 
-public interface SeqSearchI extends java.rmi.Remote {
-    public java.lang.String getDatabase() throws java.rmi.RemoteException;
-    public vamsas.objects.simple.SeqSearchResult getResult(java.lang.String job_id) throws java.rmi.RemoteException;
-    public vamsas.objects.simple.WsJobId psearch(vamsas.objects.simple.Alignment al, java.lang.String database) throws java.rmi.RemoteException;
-    public vamsas.objects.simple.WsJobId search(vamsas.objects.simple.Sequence s, java.lang.String database) throws java.rmi.RemoteException;
-    public vamsas.objects.simple.WsJobId cancel(java.lang.String jobId) throws java.rmi.RemoteException;
+public interface SeqSearchI extends java.rmi.Remote
+{
+  public java.lang.String getDatabase() throws java.rmi.RemoteException;
+
+  public vamsas.objects.simple.SeqSearchResult getResult(
+          java.lang.String job_id) throws java.rmi.RemoteException;
+
+  public vamsas.objects.simple.WsJobId psearch(
+          vamsas.objects.simple.Alignment al, java.lang.String database)
+          throws java.rmi.RemoteException;
+
+  public vamsas.objects.simple.WsJobId search(
+          vamsas.objects.simple.Sequence s, java.lang.String database)
+          throws java.rmi.RemoteException;
+
+  public vamsas.objects.simple.WsJobId cancel(java.lang.String jobId)
+          throws java.rmi.RemoteException;
 }
diff --git a/src/ext/vamsas/SeqSearchServiceLocator.java b/src/ext/vamsas/SeqSearchServiceLocator.java
index 46b435b..598e1ad 100644
--- a/src/ext/vamsas/SeqSearchServiceLocator.java
+++ b/src/ext/vamsas/SeqSearchServiceLocator.java
@@ -1,136 +1,184 @@
-/**
- * ScanPSServiceServiceLocator.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package ext.vamsas;
 
-public class SeqSearchServiceLocator extends org.apache.axis.client.Service implements ext.vamsas.SeqSearchServiceService {
-
-    public SeqSearchServiceLocator() {
+public class SeqSearchServiceLocator extends org.apache.axis.client.Service
+        implements ext.vamsas.SeqSearchServiceService
+{
+
+  public SeqSearchServiceLocator()
+  {
+  }
+
+  public SeqSearchServiceLocator(org.apache.axis.EngineConfiguration config)
+  {
+    super(config);
+  }
+
+  // Use to get a proxy class for ScanPSService
+  private java.lang.String ScanPSService_address = "http://localhost:8080/TestJWS/services/ScanPSService";
+
+  public java.lang.String getSeqSeachServiceAddress()
+  {
+    return ScanPSService_address;
+  }
+
+  // The WSDD service name defaults to the port name.
+  private java.lang.String ScanPSServiceWSDDServiceName = "ScanPSService";
+
+  public java.lang.String getScanPSServiceWSDDServiceName()
+  {
+    return ScanPSServiceWSDDServiceName;
+  }
+
+  public void setScanPSServiceWSDDServiceName(java.lang.String name)
+  {
+    ScanPSServiceWSDDServiceName = name;
+  }
+
+  public ext.vamsas.SeqSearchI getSeqSearchService()
+          throws javax.xml.rpc.ServiceException
+  {
+    java.net.URL endpoint;
+    try
+    {
+      endpoint = new java.net.URL(ScanPSService_address);
+    } catch (java.net.MalformedURLException e)
+    {
+      throw new javax.xml.rpc.ServiceException(e);
     }
-
-
-    public SeqSearchServiceLocator(org.apache.axis.EngineConfiguration config) {
-        super(config);
+    return getSeqSearchService(endpoint);
+  }
+
+  public ext.vamsas.SeqSearchI getSeqSearchService(java.net.URL portAddress)
+          throws javax.xml.rpc.ServiceException
+  {
+    try
+    {
+      ext.vamsas.SeqSearchServiceSoapBindingStub _stub = new ext.vamsas.SeqSearchServiceSoapBindingStub(
+              portAddress, this);
+      _stub.setPortName(getScanPSServiceWSDDServiceName());
+      return _stub;
+    } catch (org.apache.axis.AxisFault e)
+    {
+      return null;
     }
-
-    // Use to get a proxy class for ScanPSService
-    private java.lang.String ScanPSService_address = "http://localhost:8080/TestJWS/services/ScanPSService";
-
-    public java.lang.String getSeqSeachServiceAddress() {
-        return ScanPSService_address;
+  }
+
+  public void setScanPSServiceEndpointAddress(java.lang.String address)
+  {
+    ScanPSService_address = address;
+  }
+
+  /**
+   * For the given interface, get the stub implementation. If this service has
+   * no port for the given interface, then ServiceException is thrown.
+   */
+  public java.rmi.Remote getPort(Class serviceEndpointInterface)
+          throws javax.xml.rpc.ServiceException
+  {
+    try
+    {
+      if (ext.vamsas.SeqSearchI.class
+              .isAssignableFrom(serviceEndpointInterface))
+      {
+        ext.vamsas.SeqSearchServiceSoapBindingStub _stub = new ext.vamsas.SeqSearchServiceSoapBindingStub(
+                new java.net.URL(ScanPSService_address), this);
+        _stub.setPortName(getScanPSServiceWSDDServiceName());
+        return _stub;
+      }
+    } catch (java.lang.Throwable t)
+    {
+      throw new javax.xml.rpc.ServiceException(t);
     }
-
-    // The WSDD service name defaults to the port name.
-    private java.lang.String ScanPSServiceWSDDServiceName = "ScanPSService";
-
-    public java.lang.String getScanPSServiceWSDDServiceName() {
-        return ScanPSServiceWSDDServiceName;
+    throw new javax.xml.rpc.ServiceException(
+            "There is no stub implementation for the interface:  "
+                    + (serviceEndpointInterface == null ? "null"
+                            : serviceEndpointInterface.getName()));
+  }
+
+  /**
+   * For the given interface, get the stub implementation. If this service has
+   * no port for the given interface, then ServiceException is thrown.
+   */
+  public java.rmi.Remote getPort(javax.xml.namespace.QName portName,
+          Class serviceEndpointInterface)
+          throws javax.xml.rpc.ServiceException
+  {
+    if (portName == null)
+    {
+      return getPort(serviceEndpointInterface);
     }
-
-    public void setScanPSServiceWSDDServiceName(java.lang.String name) {
-        ScanPSServiceWSDDServiceName = name;
+    java.lang.String inputPortName = portName.getLocalPart();
+    if ("ScanPSService".equals(inputPortName))
+    {
+      return getSeqSearchService();
     }
-
-    public ext.vamsas.SeqSearchI getSeqSearchService() throws javax.xml.rpc.ServiceException {
-       java.net.URL endpoint;
-        try {
-            endpoint = new java.net.URL(ScanPSService_address);
-        }
-        catch (java.net.MalformedURLException e) {
-            throw new javax.xml.rpc.ServiceException(e);
-        }
-        return getSeqSearchService(endpoint);
+    else
+    {
+      java.rmi.Remote _stub = getPort(serviceEndpointInterface);
+      ((org.apache.axis.client.Stub) _stub).setPortName(portName);
+      return _stub;
     }
+  }
 
-    public ext.vamsas.SeqSearchI getSeqSearchService(java.net.URL portAddress) throws javax.xml.rpc.ServiceException {
-        try {
-            ext.vamsas.SeqSearchServiceSoapBindingStub _stub = new ext.vamsas.SeqSearchServiceSoapBindingStub(portAddress, this);
-            _stub.setPortName(getScanPSServiceWSDDServiceName());
-            return _stub;
-        }
-        catch (org.apache.axis.AxisFault e) {
-            return null;
-        }
-    }
+  public javax.xml.namespace.QName getServiceName()
+  {
+    return new javax.xml.namespace.QName("vamsas", "ScanPSServiceService");
+  }
 
-    public void setScanPSServiceEndpointAddress(java.lang.String address) {
-        ScanPSService_address = address;
-    }
-
-    /**
-     * For the given interface, get the stub implementation.
-     * If this service has no port for the given interface,
-     * then ServiceException is thrown.
-     */
-    public java.rmi.Remote getPort(Class serviceEndpointInterface) throws javax.xml.rpc.ServiceException {
-        try {
-            if (ext.vamsas.SeqSearchI.class.isAssignableFrom(serviceEndpointInterface)) {
-                ext.vamsas.SeqSearchServiceSoapBindingStub _stub = new ext.vamsas.SeqSearchServiceSoapBindingStub(new java.net.URL(ScanPSService_address), this);
-                _stub.setPortName(getScanPSServiceWSDDServiceName());
-                return _stub;
-            }
-        }
-        catch (java.lang.Throwable t) {
-            throw new javax.xml.rpc.ServiceException(t);
-        }
-        throw new javax.xml.rpc.ServiceException("There is no stub implementation for the interface:  " + (serviceEndpointInterface == null ? "null" : serviceEndpointInterface.getName()));
-    }
-
-    /**
-     * For the given interface, get the stub implementation.
-     * If this service has no port for the given interface,
-     * then ServiceException is thrown.
-     */
-    public java.rmi.Remote getPort(javax.xml.namespace.QName portName, Class serviceEndpointInterface) throws javax.xml.rpc.ServiceException {
-        if (portName == null) {
-            return getPort(serviceEndpointInterface);
-        }
-        java.lang.String inputPortName = portName.getLocalPart();
-        if ("ScanPSService".equals(inputPortName)) {
-            return getSeqSearchService();
-        }
-        else  {
-            java.rmi.Remote _stub = getPort(serviceEndpointInterface);
-            ((org.apache.axis.client.Stub) _stub).setPortName(portName);
-            return _stub;
-        }
-    }
+  private java.util.HashSet ports = null;
 
-    public javax.xml.namespace.QName getServiceName() {
-        return new javax.xml.namespace.QName("vamsas", "ScanPSServiceService");
+  public java.util.Iterator getPorts()
+  {
+    if (ports == null)
+    {
+      ports = new java.util.HashSet();
+      ports.add(new javax.xml.namespace.QName("vamsas", "ScanPSService"));
     }
-
-    private java.util.HashSet ports = null;
-
-    public java.util.Iterator getPorts() {
-        if (ports == null) {
-            ports = new java.util.HashSet();
-            ports.add(new javax.xml.namespace.QName("vamsas", "ScanPSService"));
-        }
-        return ports.iterator();
+    return ports.iterator();
+  }
+
+  /**
+   * Set the endpoint address for the specified port name.
+   */
+  public void setEndpointAddress(java.lang.String portName,
+          java.lang.String address) throws javax.xml.rpc.ServiceException
+  {
+    if ("ScanPSService".equals(portName))
+    {
+      setScanPSServiceEndpointAddress(address);
     }
-
-    /**
-    * Set the endpoint address for the specified port name.
-    */
-    public void setEndpointAddress(java.lang.String portName, java.lang.String address) throws javax.xml.rpc.ServiceException {
-        if ("ScanPSService".equals(portName)) {
-            setScanPSServiceEndpointAddress(address);
-        }
-        else { // Unknown Port Name
-            throw new javax.xml.rpc.ServiceException(" Cannot set Endpoint Address for Unknown Port" + portName);
-        }
-    }
-
-    /**
-    * Set the endpoint address for the specified port name.
-    */
-    public void setEndpointAddress(javax.xml.namespace.QName portName, java.lang.String address) throws javax.xml.rpc.ServiceException {
-        setEndpointAddress(portName.getLocalPart(), address);
+    else
+    { // Unknown Port Name
+      throw new javax.xml.rpc.ServiceException(
+              " Cannot set Endpoint Address for Unknown Port" + portName);
     }
+  }
+
+  /**
+   * Set the endpoint address for the specified port name.
+   */
+  public void setEndpointAddress(javax.xml.namespace.QName portName,
+          java.lang.String address) throws javax.xml.rpc.ServiceException
+  {
+    setEndpointAddress(portName.getLocalPart(), address);
+  }
 
 }
diff --git a/src/ext/vamsas/SeqSearchServiceService.java b/src/ext/vamsas/SeqSearchServiceService.java
index 0dd4c14..1775b9d 100644
--- a/src/ext/vamsas/SeqSearchServiceService.java
+++ b/src/ext/vamsas/SeqSearchServiceService.java
@@ -1,16 +1,30 @@
-/**
- * ScanPSServiceService.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package ext.vamsas;
 
-public interface SeqSearchServiceService extends javax.xml.rpc.Service {
-    public java.lang.String getSeqSeachServiceAddress();
+public interface SeqSearchServiceService extends javax.xml.rpc.Service
+{
+  public java.lang.String getSeqSeachServiceAddress();
 
-    public ext.vamsas.SeqSearchI getSeqSearchService() throws javax.xml.rpc.ServiceException;
+  public ext.vamsas.SeqSearchI getSeqSearchService()
+          throws javax.xml.rpc.ServiceException;
 
-    public ext.vamsas.SeqSearchI getSeqSearchService(java.net.URL portAddress) throws javax.xml.rpc.ServiceException;
+  public ext.vamsas.SeqSearchI getSeqSearchService(java.net.URL portAddress)
+          throws javax.xml.rpc.ServiceException;
 }
diff --git a/src/ext/vamsas/SeqSearchServiceSoapBindingStub.java b/src/ext/vamsas/SeqSearchServiceSoapBindingStub.java
index 614a85f..11e307b 100644
--- a/src/ext/vamsas/SeqSearchServiceSoapBindingStub.java
+++ b/src/ext/vamsas/SeqSearchServiceSoapBindingStub.java
@@ -1,366 +1,501 @@
-/**
- * ScanPSServiceSoapBindingStub.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package ext.vamsas;
 
-public class SeqSearchServiceSoapBindingStub extends org.apache.axis.client.Stub implements ext.vamsas.SeqSearchI {
-    private java.util.Vector cachedSerClasses = new java.util.Vector();
-    private java.util.Vector cachedSerQNames = new java.util.Vector();
-    private java.util.Vector cachedSerFactories = new java.util.Vector();
-    private java.util.Vector cachedDeserFactories = new java.util.Vector();
-
-    static org.apache.axis.description.OperationDesc [] _operations;
-
-    static {
-        _operations = new org.apache.axis.description.OperationDesc[5];
-        _initOperationDesc1();
-    }
-
-    private static void _initOperationDesc1(){
-        org.apache.axis.description.OperationDesc oper;
-        oper = new org.apache.axis.description.OperationDesc();
-        oper.setName("getDatabase");
-        oper.setReturnType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
-        oper.setReturnClass(java.lang.String.class);
-        oper.setReturnQName(new javax.xml.namespace.QName("", "getDatabaseReturn"));
-        oper.setStyle(org.apache.axis.constants.Style.RPC);
-        oper.setUse(org.apache.axis.constants.Use.ENCODED);
-        _operations[0] = oper;
-
-        oper = new org.apache.axis.description.OperationDesc();
-        oper.setName("getResult");
-        oper.addParameter(new javax.xml.namespace.QName("", "job_id"), new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"), java.lang.String.class, org.apache.axis.description.ParameterDesc.IN, false, false);
-        oper.setReturnType(new javax.xml.namespace.QName("simple.objects.vamsas", "SeqSearchResult"));
-        oper.setReturnClass(vamsas.objects.simple.SeqSearchResult.class);
-        oper.setReturnQName(new javax.xml.namespace.QName("", "getResultReturn"));
-        oper.setStyle(org.apache.axis.constants.Style.RPC);
-        oper.setUse(org.apache.axis.constants.Use.ENCODED);
-        _operations[1] = oper;
-
-        oper = new org.apache.axis.description.OperationDesc();
-        oper.setName("psearch");
-        oper.addParameter(new javax.xml.namespace.QName("", "al"), new javax.xml.namespace.QName("simple.objects.vamsas", "Alignment"), vamsas.objects.simple.Alignment.class, org.apache.axis.description.ParameterDesc.IN, false, false);
-        oper.addParameter(new javax.xml.namespace.QName("", "database"), new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"), java.lang.String.class, org.apache.axis.description.ParameterDesc.IN, false, false);
-        oper.setReturnType(new javax.xml.namespace.QName("simple.objects.vamsas", "WsJobId"));
-        oper.setReturnClass(vamsas.objects.simple.WsJobId.class);
-        oper.setReturnQName(new javax.xml.namespace.QName("", "psearchReturn"));
-        oper.setStyle(org.apache.axis.constants.Style.RPC);
-        oper.setUse(org.apache.axis.constants.Use.ENCODED);
-        _operations[2] = oper;
-
-        oper = new org.apache.axis.description.OperationDesc();
-        oper.setName("search");
-        oper.addParameter(new javax.xml.namespace.QName("", "s"), new javax.xml.namespace.QName("simple.objects.vamsas", "Sequence"), vamsas.objects.simple.Sequence.class, org.apache.axis.description.ParameterDesc.IN, false, false);
-        oper.addParameter(new javax.xml.namespace.QName("", "database"), new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"), java.lang.String.class, org.apache.axis.description.ParameterDesc.IN, false, false);
-        oper.setReturnType(new javax.xml.namespace.QName("simple.objects.vamsas", "WsJobId"));
-        oper.setReturnClass(vamsas.objects.simple.WsJobId.class);
-        oper.setReturnQName(new javax.xml.namespace.QName("", "searchReturn"));
-        oper.setStyle(org.apache.axis.constants.Style.RPC);
-        oper.setUse(org.apache.axis.constants.Use.ENCODED);
-        _operations[3] = oper;
-
-        oper = new org.apache.axis.description.OperationDesc();
-        oper.setName("cancel");
-        oper.addParameter(new javax.xml.namespace.QName("", "jobId"), new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"), java.lang.String.class, org.apache.axis.description.ParameterDesc.IN, false, false);
-        oper.setReturnType(new javax.xml.namespace.QName("simple.objects.vamsas", "WsJobId"));
-        oper.setReturnClass(vamsas.objects.simple.WsJobId.class);
-        oper.setReturnQName(new javax.xml.namespace.QName("", "cancelReturn"));
-        oper.setStyle(org.apache.axis.constants.Style.RPC);
-        oper.setUse(org.apache.axis.constants.Use.ENCODED);
-        _operations[4] = oper;
-
+public class SeqSearchServiceSoapBindingStub extends
+        org.apache.axis.client.Stub implements ext.vamsas.SeqSearchI
+{
+  private java.util.Vector cachedSerClasses = new java.util.Vector();
+
+  private java.util.Vector cachedSerQNames = new java.util.Vector();
+
+  private java.util.Vector cachedSerFactories = new java.util.Vector();
+
+  private java.util.Vector cachedDeserFactories = new java.util.Vector();
+
+  static org.apache.axis.description.OperationDesc[] _operations;
+
+  static
+  {
+    _operations = new org.apache.axis.description.OperationDesc[5];
+    _initOperationDesc1();
+  }
+
+  private static void _initOperationDesc1()
+  {
+    org.apache.axis.description.OperationDesc oper;
+    oper = new org.apache.axis.description.OperationDesc();
+    oper.setName("getDatabase");
+    oper.setReturnType(new javax.xml.namespace.QName(
+            "http://www.w3.org/2001/XMLSchema", "string"));
+    oper.setReturnClass(java.lang.String.class);
+    oper.setReturnQName(new javax.xml.namespace.QName("",
+            "getDatabaseReturn"));
+    oper.setStyle(org.apache.axis.constants.Style.RPC);
+    oper.setUse(org.apache.axis.constants.Use.ENCODED);
+    _operations[0] = oper;
+
+    oper = new org.apache.axis.description.OperationDesc();
+    oper.setName("getResult");
+    oper.addParameter(new javax.xml.namespace.QName("", "job_id"),
+            new javax.xml.namespace.QName(
+                    "http://www.w3.org/2001/XMLSchema", "string"),
+            java.lang.String.class,
+            org.apache.axis.description.ParameterDesc.IN, false, false);
+    oper.setReturnType(new javax.xml.namespace.QName(
+            "simple.objects.vamsas", "SeqSearchResult"));
+    oper.setReturnClass(vamsas.objects.simple.SeqSearchResult.class);
+    oper
+            .setReturnQName(new javax.xml.namespace.QName("",
+                    "getResultReturn"));
+    oper.setStyle(org.apache.axis.constants.Style.RPC);
+    oper.setUse(org.apache.axis.constants.Use.ENCODED);
+    _operations[1] = oper;
+
+    oper = new org.apache.axis.description.OperationDesc();
+    oper.setName("psearch");
+    oper.addParameter(new javax.xml.namespace.QName("", "al"),
+            new javax.xml.namespace.QName("simple.objects.vamsas",
+                    "Alignment"), vamsas.objects.simple.Alignment.class,
+            org.apache.axis.description.ParameterDesc.IN, false, false);
+    oper.addParameter(new javax.xml.namespace.QName("", "database"),
+            new javax.xml.namespace.QName(
+                    "http://www.w3.org/2001/XMLSchema", "string"),
+            java.lang.String.class,
+            org.apache.axis.description.ParameterDesc.IN, false, false);
+    oper.setReturnType(new javax.xml.namespace.QName(
+            "simple.objects.vamsas", "WsJobId"));
+    oper.setReturnClass(vamsas.objects.simple.WsJobId.class);
+    oper.setReturnQName(new javax.xml.namespace.QName("", "psearchReturn"));
+    oper.setStyle(org.apache.axis.constants.Style.RPC);
+    oper.setUse(org.apache.axis.constants.Use.ENCODED);
+    _operations[2] = oper;
+
+    oper = new org.apache.axis.description.OperationDesc();
+    oper.setName("search");
+    oper.addParameter(new javax.xml.namespace.QName("", "s"),
+            new javax.xml.namespace.QName("simple.objects.vamsas",
+                    "Sequence"), vamsas.objects.simple.Sequence.class,
+            org.apache.axis.description.ParameterDesc.IN, false, false);
+    oper.addParameter(new javax.xml.namespace.QName("", "database"),
+            new javax.xml.namespace.QName(
+                    "http://www.w3.org/2001/XMLSchema", "string"),
+            java.lang.String.class,
+            org.apache.axis.description.ParameterDesc.IN, false, false);
+    oper.setReturnType(new javax.xml.namespace.QName(
+            "simple.objects.vamsas", "WsJobId"));
+    oper.setReturnClass(vamsas.objects.simple.WsJobId.class);
+    oper.setReturnQName(new javax.xml.namespace.QName("", "searchReturn"));
+    oper.setStyle(org.apache.axis.constants.Style.RPC);
+    oper.setUse(org.apache.axis.constants.Use.ENCODED);
+    _operations[3] = oper;
+
+    oper = new org.apache.axis.description.OperationDesc();
+    oper.setName("cancel");
+    oper.addParameter(new javax.xml.namespace.QName("", "jobId"),
+            new javax.xml.namespace.QName(
+                    "http://www.w3.org/2001/XMLSchema", "string"),
+            java.lang.String.class,
+            org.apache.axis.description.ParameterDesc.IN, false, false);
+    oper.setReturnType(new javax.xml.namespace.QName(
+            "simple.objects.vamsas", "WsJobId"));
+    oper.setReturnClass(vamsas.objects.simple.WsJobId.class);
+    oper.setReturnQName(new javax.xml.namespace.QName("", "cancelReturn"));
+    oper.setStyle(org.apache.axis.constants.Style.RPC);
+    oper.setUse(org.apache.axis.constants.Use.ENCODED);
+    _operations[4] = oper;
+
+  }
+
+  public SeqSearchServiceSoapBindingStub() throws org.apache.axis.AxisFault
+  {
+    this(null);
+  }
+
+  public SeqSearchServiceSoapBindingStub(java.net.URL endpointURL,
+          javax.xml.rpc.Service service) throws org.apache.axis.AxisFault
+  {
+    this(service);
+    super.cachedEndpoint = endpointURL;
+  }
+
+  public SeqSearchServiceSoapBindingStub(javax.xml.rpc.Service service)
+          throws org.apache.axis.AxisFault
+  {
+    if (service == null)
+    {
+      super.service = new org.apache.axis.client.Service();
     }
-
-    public SeqSearchServiceSoapBindingStub() throws org.apache.axis.AxisFault {
-         this(null);
-    }
-
-    public SeqSearchServiceSoapBindingStub(java.net.URL endpointURL, javax.xml.rpc.Service service) throws org.apache.axis.AxisFault {
-         this(service);
-         super.cachedEndpoint = endpointURL;
+    else
+    {
+      super.service = service;
     }
-
-    public SeqSearchServiceSoapBindingStub(javax.xml.rpc.Service service) throws org.apache.axis.AxisFault {
-        if (service == null) {
-            super.service = new org.apache.axis.client.Service();
-        } else {
-            super.service = service;
+    java.lang.Class cls;
+    javax.xml.namespace.QName qName;
+    java.lang.Class beansf = org.apache.axis.encoding.ser.BeanSerializerFactory.class;
+    java.lang.Class beandf = org.apache.axis.encoding.ser.BeanDeserializerFactory.class;
+    java.lang.Class enumsf = org.apache.axis.encoding.ser.EnumSerializerFactory.class;
+    java.lang.Class enumdf = org.apache.axis.encoding.ser.EnumDeserializerFactory.class;
+    java.lang.Class arraysf = org.apache.axis.encoding.ser.ArraySerializerFactory.class;
+    java.lang.Class arraydf = org.apache.axis.encoding.ser.ArrayDeserializerFactory.class;
+    java.lang.Class simplesf = org.apache.axis.encoding.ser.SimpleSerializerFactory.class;
+    java.lang.Class simpledf = org.apache.axis.encoding.ser.SimpleDeserializerFactory.class;
+    java.lang.Class simplelistsf = org.apache.axis.encoding.ser.SimpleListSerializerFactory.class;
+    java.lang.Class simplelistdf = org.apache.axis.encoding.ser.SimpleListDeserializerFactory.class;
+    qName = new javax.xml.namespace.QName("simple.objects.vamsas", "Result");
+    cachedSerQNames.add(qName);
+    cls = vamsas.objects.simple.Result.class;
+    cachedSerClasses.add(cls);
+    cachedSerFactories.add(beansf);
+    cachedDeserFactories.add(beandf);
+
+    qName = new javax.xml.namespace.QName("simple.objects.vamsas",
+            "WsJobId");
+    cachedSerQNames.add(qName);
+    cls = vamsas.objects.simple.WsJobId.class;
+    cachedSerClasses.add(cls);
+    cachedSerFactories.add(beansf);
+    cachedDeserFactories.add(beandf);
+
+    qName = new javax.xml.namespace.QName("http://simple.objects.vamsas",
+            "Object");
+    cachedSerQNames.add(qName);
+    cls = vamsas.objects.simple.Object.class;
+    cachedSerClasses.add(cls);
+    cachedSerFactories.add(beansf);
+    cachedDeserFactories.add(beandf);
+
+    qName = new javax.xml.namespace.QName("vamsas", "ArrayOf_xsd_string");
+    cachedSerQNames.add(qName);
+    cls = java.lang.String[].class;
+    cachedSerClasses.add(cls);
+    cachedSerFactories.add(arraysf);
+    cachedDeserFactories.add(arraydf);
+
+    qName = new javax.xml.namespace.QName("simple.objects.vamsas",
+            "Alignment");
+    cachedSerQNames.add(qName);
+    cls = vamsas.objects.simple.Alignment.class;
+    cachedSerClasses.add(cls);
+    cachedSerFactories.add(beansf);
+    cachedDeserFactories.add(beandf);
+
+    qName = new javax.xml.namespace.QName("simple.objects.vamsas",
+            "Sequence");
+    cachedSerQNames.add(qName);
+    cls = vamsas.objects.simple.Sequence.class;
+    cachedSerClasses.add(cls);
+    cachedSerFactories.add(beansf);
+    cachedDeserFactories.add(beandf);
+
+    qName = new javax.xml.namespace.QName("vamsas", "ArrayOf_tns1_Sequence");
+    cachedSerQNames.add(qName);
+    cls = vamsas.objects.simple.Sequence[].class;
+    cachedSerClasses.add(cls);
+    cachedSerFactories.add(arraysf);
+    cachedDeserFactories.add(arraydf);
+
+    qName = new javax.xml.namespace.QName("simple.objects.vamsas",
+            "SeqSearchResult");
+    cachedSerQNames.add(qName);
+    cls = vamsas.objects.simple.SeqSearchResult.class;
+    cachedSerClasses.add(cls);
+    cachedSerFactories.add(beansf);
+    cachedDeserFactories.add(beandf);
+
+    qName = new javax.xml.namespace.QName("simple.objects.vamsas",
+            "SequenceSet");
+    cachedSerQNames.add(qName);
+    cls = vamsas.objects.simple.SequenceSet.class;
+    cachedSerClasses.add(cls);
+    cachedSerFactories.add(beansf);
+    cachedDeserFactories.add(beandf);
+
+  }
+
+  protected org.apache.axis.client.Call createCall()
+          throws java.rmi.RemoteException
+  {
+    try
+    {
+      org.apache.axis.client.Call _call = (org.apache.axis.client.Call) super.service
+              .createCall();
+      if (super.maintainSessionSet)
+      {
+        _call.setMaintainSession(super.maintainSession);
+      }
+      if (super.cachedUsername != null)
+      {
+        _call.setUsername(super.cachedUsername);
+      }
+      if (super.cachedPassword != null)
+      {
+        _call.setPassword(super.cachedPassword);
+      }
+      if (super.cachedEndpoint != null)
+      {
+        _call.setTargetEndpointAddress(super.cachedEndpoint);
+      }
+      if (super.cachedTimeout != null)
+      {
+        _call.setTimeout(super.cachedTimeout);
+      }
+      if (super.cachedPortName != null)
+      {
+        _call.setPortName(super.cachedPortName);
+      }
+      java.util.Enumeration keys = super.cachedProperties.keys();
+      while (keys.hasMoreElements())
+      {
+        java.lang.String key = (java.lang.String) keys.nextElement();
+        _call.setProperty(key, super.cachedProperties.get(key));
+      }
+      // All the type mapping information is registered
+      // when the first call is made.
+      // The type mapping information is actually registered in
+      // the TypeMappingRegistry of the service, which
+      // is the reason why registration is only needed for the first call.
+      synchronized (this)
+      {
+        if (firstCall())
+        {
+          // must set encoding style before registering serializers
+          _call
+                  .setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+          _call.setEncodingStyle(org.apache.axis.Constants.URI_SOAP11_ENC);
+          for (int i = 0; i < cachedSerFactories.size(); ++i)
+          {
+            java.lang.Class cls = (java.lang.Class) cachedSerClasses.get(i);
+            javax.xml.namespace.QName qName = (javax.xml.namespace.QName) cachedSerQNames
+                    .get(i);
+            java.lang.Class sf = (java.lang.Class) cachedSerFactories
+                    .get(i);
+            java.lang.Class df = (java.lang.Class) cachedDeserFactories
+                    .get(i);
+            _call.registerTypeMapping(cls, qName, sf, df, false);
+          }
         }
-            java.lang.Class cls;
-            javax.xml.namespace.QName qName;
-            java.lang.Class beansf = org.apache.axis.encoding.ser.BeanSerializerFactory.class;
-            java.lang.Class beandf = org.apache.axis.encoding.ser.BeanDeserializerFactory.class;
-            java.lang.Class enumsf = org.apache.axis.encoding.ser.EnumSerializerFactory.class;
-            java.lang.Class enumdf = org.apache.axis.encoding.ser.EnumDeserializerFactory.class;
-            java.lang.Class arraysf = org.apache.axis.encoding.ser.ArraySerializerFactory.class;
-            java.lang.Class arraydf = org.apache.axis.encoding.ser.ArrayDeserializerFactory.class;
-            java.lang.Class simplesf = org.apache.axis.encoding.ser.SimpleSerializerFactory.class;
-            java.lang.Class simpledf = org.apache.axis.encoding.ser.SimpleDeserializerFactory.class;
-            java.lang.Class simplelistsf = org.apache.axis.encoding.ser.SimpleListSerializerFactory.class;
-            java.lang.Class simplelistdf = org.apache.axis.encoding.ser.SimpleListDeserializerFactory.class;
-            qName = new javax.xml.namespace.QName("simple.objects.vamsas", "Result");
-            cachedSerQNames.add(qName);
-            cls = vamsas.objects.simple.Result.class;
-            cachedSerClasses.add(cls);
-            cachedSerFactories.add(beansf);
-            cachedDeserFactories.add(beandf);
-
-            qName = new javax.xml.namespace.QName("simple.objects.vamsas", "WsJobId");
-            cachedSerQNames.add(qName);
-            cls = vamsas.objects.simple.WsJobId.class;
-            cachedSerClasses.add(cls);
-            cachedSerFactories.add(beansf);
-            cachedDeserFactories.add(beandf);
-
-            qName = new javax.xml.namespace.QName("http://simple.objects.vamsas", "Object");
-            cachedSerQNames.add(qName);
-            cls = vamsas.objects.simple.Object.class;
-            cachedSerClasses.add(cls);
-            cachedSerFactories.add(beansf);
-            cachedDeserFactories.add(beandf);
-
-            qName = new javax.xml.namespace.QName("vamsas", "ArrayOf_xsd_string");
-            cachedSerQNames.add(qName);
-            cls = java.lang.String[].class;
-            cachedSerClasses.add(cls);
-            cachedSerFactories.add(arraysf);
-            cachedDeserFactories.add(arraydf);
-
-            qName = new javax.xml.namespace.QName("simple.objects.vamsas", "Alignment");
-            cachedSerQNames.add(qName);
-            cls = vamsas.objects.simple.Alignment.class;
-            cachedSerClasses.add(cls);
-            cachedSerFactories.add(beansf);
-            cachedDeserFactories.add(beandf);
-
-            qName = new javax.xml.namespace.QName("simple.objects.vamsas", "Sequence");
-            cachedSerQNames.add(qName);
-            cls = vamsas.objects.simple.Sequence.class;
-            cachedSerClasses.add(cls);
-            cachedSerFactories.add(beansf);
-            cachedDeserFactories.add(beandf);
-
-            qName = new javax.xml.namespace.QName("vamsas", "ArrayOf_tns1_Sequence");
-            cachedSerQNames.add(qName);
-            cls = vamsas.objects.simple.Sequence[].class;
-            cachedSerClasses.add(cls);
-            cachedSerFactories.add(arraysf);
-            cachedDeserFactories.add(arraydf);
-
-            qName = new javax.xml.namespace.QName("simple.objects.vamsas", "SeqSearchResult");
-            cachedSerQNames.add(qName);
-            cls = vamsas.objects.simple.SeqSearchResult.class;
-            cachedSerClasses.add(cls);
-            cachedSerFactories.add(beansf);
-            cachedDeserFactories.add(beandf);
-
-            qName = new javax.xml.namespace.QName("simple.objects.vamsas", "SequenceSet");
-            cachedSerQNames.add(qName);
-            cls = vamsas.objects.simple.SequenceSet.class;
-            cachedSerClasses.add(cls);
-            cachedSerFactories.add(beansf);
-            cachedDeserFactories.add(beandf);
-
+      }
+      return _call;
+    } catch (java.lang.Throwable _t)
+    {
+      throw new org.apache.axis.AxisFault(
+              "Failure trying to get the Call object", _t);
     }
+  }
 
-    protected org.apache.axis.client.Call createCall() throws java.rmi.RemoteException {
-        try {
-            org.apache.axis.client.Call _call =
-                    (org.apache.axis.client.Call) super.service.createCall();
-            if (super.maintainSessionSet) {
-                _call.setMaintainSession(super.maintainSession);
-            }
-            if (super.cachedUsername != null) {
-                _call.setUsername(super.cachedUsername);
-            }
-            if (super.cachedPassword != null) {
-                _call.setPassword(super.cachedPassword);
-            }
-            if (super.cachedEndpoint != null) {
-                _call.setTargetEndpointAddress(super.cachedEndpoint);
-            }
-            if (super.cachedTimeout != null) {
-                _call.setTimeout(super.cachedTimeout);
-            }
-            if (super.cachedPortName != null) {
-                _call.setPortName(super.cachedPortName);
-            }
-            java.util.Enumeration keys = super.cachedProperties.keys();
-            while (keys.hasMoreElements()) {
-                java.lang.String key = (java.lang.String) keys.nextElement();
-                _call.setProperty(key, super.cachedProperties.get(key));
-            }
-            // All the type mapping information is registered
-            // when the first call is made.
-            // The type mapping information is actually registered in
-            // the TypeMappingRegistry of the service, which
-            // is the reason why registration is only needed for the first call.
-            synchronized (this) {
-                if (firstCall()) {
-                    // must set encoding style before registering serializers
-                    _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
-                    _call.setEncodingStyle(org.apache.axis.Constants.URI_SOAP11_ENC);
-                    for (int i = 0; i < cachedSerFactories.size(); ++i) {
-                        java.lang.Class cls = (java.lang.Class) cachedSerClasses.get(i);
-                        javax.xml.namespace.QName qName =
-                                (javax.xml.namespace.QName) cachedSerQNames.get(i);
-                        java.lang.Class sf = (java.lang.Class)
-                                 cachedSerFactories.get(i);
-                        java.lang.Class df = (java.lang.Class)
-                                 cachedDeserFactories.get(i);
-                        _call.registerTypeMapping(cls, qName, sf, df, false);
-                    }
-                }
-            }
-            return _call;
-        }
-        catch (java.lang.Throwable _t) {
-            throw new org.apache.axis.AxisFault("Failure trying to get the Call object", _t);
-        }
+  public java.lang.String getDatabase() throws java.rmi.RemoteException
+  {
+    if (super.cachedEndpoint == null)
+    {
+      throw new org.apache.axis.NoEndPointException();
     }
-
-    public java.lang.String getDatabase() throws java.rmi.RemoteException {
-        if (super.cachedEndpoint == null) {
-            throw new org.apache.axis.NoEndPointException();
-        }
-        org.apache.axis.client.Call _call = createCall();
-        _call.setOperation(_operations[0]);
-        _call.setUseSOAPAction(true);
-        _call.setSOAPActionURI("");
-        _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
-        _call.setOperationName(new javax.xml.namespace.QName("vamsas", "getDatabase"));
-
-        setRequestHeaders(_call);
-        setAttachments(_call);
-        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {});
-
-        if (_resp instanceof java.rmi.RemoteException) {
-            throw (java.rmi.RemoteException)_resp;
-        }
-        else {
-            extractAttachments(_call);
-            try {
-                return (java.lang.String) _resp;
-            } catch (java.lang.Exception _exception) {
-                return (java.lang.String) org.apache.axis.utils.JavaUtils.convert(_resp, java.lang.String.class);
-            }
-        }
+    org.apache.axis.client.Call _call = createCall();
+    _call.setOperation(_operations[0]);
+    _call.setUseSOAPAction(true);
+    _call.setSOAPActionURI("");
+    _call
+            .setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+    _call.setOperationName(new javax.xml.namespace.QName("vamsas",
+            "getDatabase"));
+
+    setRequestHeaders(_call);
+    setAttachments(_call);
+    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
+    {});
+
+    if (_resp instanceof java.rmi.RemoteException)
+    {
+      throw (java.rmi.RemoteException) _resp;
     }
-
-    public vamsas.objects.simple.SeqSearchResult getResult(java.lang.String job_id) throws java.rmi.RemoteException {
-        if (super.cachedEndpoint == null) {
-            throw new org.apache.axis.NoEndPointException();
-        }
-        org.apache.axis.client.Call _call = createCall();
-        _call.setOperation(_operations[1]);
-        _call.setUseSOAPAction(true);
-        _call.setSOAPActionURI("");
-        _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
-        _call.setOperationName(new javax.xml.namespace.QName("vamsas", "getResult"));
-
-        setRequestHeaders(_call);
-        setAttachments(_call);
-        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {job_id});
-
-        if (_resp instanceof java.rmi.RemoteException) {
-            throw (java.rmi.RemoteException)_resp;
-        }
-        else {
-            extractAttachments(_call);
-            try {
-                return (vamsas.objects.simple.SeqSearchResult) _resp;
-            } catch (java.lang.Exception _exception) {
-                return (vamsas.objects.simple.SeqSearchResult) org.apache.axis.utils.JavaUtils.convert(_resp, vamsas.objects.simple.SeqSearchResult.class);
-            }
-        }
+    else
+    {
+      extractAttachments(_call);
+      try
+      {
+        return (java.lang.String) _resp;
+      } catch (java.lang.Exception _exception)
+      {
+        return (java.lang.String) org.apache.axis.utils.JavaUtils.convert(
+                _resp, java.lang.String.class);
+      }
     }
-
-    public vamsas.objects.simple.WsJobId psearch(vamsas.objects.simple.Alignment al, java.lang.String database) throws java.rmi.RemoteException {
-        if (super.cachedEndpoint == null) {
-            throw new org.apache.axis.NoEndPointException();
-        }
-        org.apache.axis.client.Call _call = createCall();
-        _call.setOperation(_operations[2]);
-        _call.setUseSOAPAction(true);
-        _call.setSOAPActionURI("");
-        _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
-        _call.setOperationName(new javax.xml.namespace.QName("vamsas", "psearch"));
-
-        setRequestHeaders(_call);
-        setAttachments(_call);
-        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {al, database});
-
-        if (_resp instanceof java.rmi.RemoteException) {
-            throw (java.rmi.RemoteException)_resp;
-        }
-        else {
-            extractAttachments(_call);
-            try {
-                return (vamsas.objects.simple.WsJobId) _resp;
-            } catch (java.lang.Exception _exception) {
-                return (vamsas.objects.simple.WsJobId) org.apache.axis.utils.JavaUtils.convert(_resp, vamsas.objects.simple.WsJobId.class);
-            }
-        }
+  }
+
+  public vamsas.objects.simple.SeqSearchResult getResult(
+          java.lang.String job_id) throws java.rmi.RemoteException
+  {
+    if (super.cachedEndpoint == null)
+    {
+      throw new org.apache.axis.NoEndPointException();
     }
-
-    public vamsas.objects.simple.WsJobId search(vamsas.objects.simple.Sequence s, java.lang.String database) throws java.rmi.RemoteException {
-        if (super.cachedEndpoint == null) {
-            throw new org.apache.axis.NoEndPointException();
-        }
-        org.apache.axis.client.Call _call = createCall();
-        _call.setOperation(_operations[3]);
-        _call.setUseSOAPAction(true);
-        _call.setSOAPActionURI("");
-        _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
-        _call.setOperationName(new javax.xml.namespace.QName("vamsas", "search"));
-
-        setRequestHeaders(_call);
-        setAttachments(_call);
-        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {s, database});
-
-        if (_resp instanceof java.rmi.RemoteException) {
-            throw (java.rmi.RemoteException)_resp;
-        }
-        else {
-            extractAttachments(_call);
-            try {
-                return (vamsas.objects.simple.WsJobId) _resp;
-            } catch (java.lang.Exception _exception) {
-                return (vamsas.objects.simple.WsJobId) org.apache.axis.utils.JavaUtils.convert(_resp, vamsas.objects.simple.WsJobId.class);
-            }
-        }
+    org.apache.axis.client.Call _call = createCall();
+    _call.setOperation(_operations[1]);
+    _call.setUseSOAPAction(true);
+    _call.setSOAPActionURI("");
+    _call
+            .setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+    _call.setOperationName(new javax.xml.namespace.QName("vamsas",
+            "getResult"));
+
+    setRequestHeaders(_call);
+    setAttachments(_call);
+    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
+    { job_id });
+
+    if (_resp instanceof java.rmi.RemoteException)
+    {
+      throw (java.rmi.RemoteException) _resp;
     }
-
-    public vamsas.objects.simple.WsJobId cancel(java.lang.String jobId) throws java.rmi.RemoteException {
-        if (super.cachedEndpoint == null) {
-            throw new org.apache.axis.NoEndPointException();
-        }
-        org.apache.axis.client.Call _call = createCall();
-        _call.setOperation(_operations[4]);
-        _call.setUseSOAPAction(true);
-        _call.setSOAPActionURI("");
-        _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
-        _call.setOperationName(new javax.xml.namespace.QName("vamsas", "cancel"));
-
-        setRequestHeaders(_call);
-        setAttachments(_call);
-        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {jobId});
-
-        if (_resp instanceof java.rmi.RemoteException) {
-            throw (java.rmi.RemoteException)_resp;
-        }
-        else {
-            extractAttachments(_call);
-            try {
-                return (vamsas.objects.simple.WsJobId) _resp;
-            } catch (java.lang.Exception _exception) {
-                return (vamsas.objects.simple.WsJobId) org.apache.axis.utils.JavaUtils.convert(_resp, vamsas.objects.simple.WsJobId.class);
-            }
-        }
+    else
+    {
+      extractAttachments(_call);
+      try
+      {
+        return (vamsas.objects.simple.SeqSearchResult) _resp;
+      } catch (java.lang.Exception _exception)
+      {
+        return (vamsas.objects.simple.SeqSearchResult) org.apache.axis.utils.JavaUtils
+                .convert(_resp, vamsas.objects.simple.SeqSearchResult.class);
+      }
+    }
+  }
+
+  public vamsas.objects.simple.WsJobId psearch(
+          vamsas.objects.simple.Alignment al, java.lang.String database)
+          throws java.rmi.RemoteException
+  {
+    if (super.cachedEndpoint == null)
+    {
+      throw new org.apache.axis.NoEndPointException();
+    }
+    org.apache.axis.client.Call _call = createCall();
+    _call.setOperation(_operations[2]);
+    _call.setUseSOAPAction(true);
+    _call.setSOAPActionURI("");
+    _call
+            .setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+    _call.setOperationName(new javax.xml.namespace.QName("vamsas",
+            "psearch"));
+
+    setRequestHeaders(_call);
+    setAttachments(_call);
+    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
+    { al, database });
+
+    if (_resp instanceof java.rmi.RemoteException)
+    {
+      throw (java.rmi.RemoteException) _resp;
+    }
+    else
+    {
+      extractAttachments(_call);
+      try
+      {
+        return (vamsas.objects.simple.WsJobId) _resp;
+      } catch (java.lang.Exception _exception)
+      {
+        return (vamsas.objects.simple.WsJobId) org.apache.axis.utils.JavaUtils
+                .convert(_resp, vamsas.objects.simple.WsJobId.class);
+      }
+    }
+  }
+
+  public vamsas.objects.simple.WsJobId search(
+          vamsas.objects.simple.Sequence s, java.lang.String database)
+          throws java.rmi.RemoteException
+  {
+    if (super.cachedEndpoint == null)
+    {
+      throw new org.apache.axis.NoEndPointException();
+    }
+    org.apache.axis.client.Call _call = createCall();
+    _call.setOperation(_operations[3]);
+    _call.setUseSOAPAction(true);
+    _call.setSOAPActionURI("");
+    _call
+            .setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+    _call
+            .setOperationName(new javax.xml.namespace.QName("vamsas",
+                    "search"));
+
+    setRequestHeaders(_call);
+    setAttachments(_call);
+    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
+    { s, database });
+
+    if (_resp instanceof java.rmi.RemoteException)
+    {
+      throw (java.rmi.RemoteException) _resp;
+    }
+    else
+    {
+      extractAttachments(_call);
+      try
+      {
+        return (vamsas.objects.simple.WsJobId) _resp;
+      } catch (java.lang.Exception _exception)
+      {
+        return (vamsas.objects.simple.WsJobId) org.apache.axis.utils.JavaUtils
+                .convert(_resp, vamsas.objects.simple.WsJobId.class);
+      }
+    }
+  }
+
+  public vamsas.objects.simple.WsJobId cancel(java.lang.String jobId)
+          throws java.rmi.RemoteException
+  {
+    if (super.cachedEndpoint == null)
+    {
+      throw new org.apache.axis.NoEndPointException();
+    }
+    org.apache.axis.client.Call _call = createCall();
+    _call.setOperation(_operations[4]);
+    _call.setUseSOAPAction(true);
+    _call.setSOAPActionURI("");
+    _call
+            .setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+    _call
+            .setOperationName(new javax.xml.namespace.QName("vamsas",
+                    "cancel"));
+
+    setRequestHeaders(_call);
+    setAttachments(_call);
+    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
+    { jobId });
+
+    if (_resp instanceof java.rmi.RemoteException)
+    {
+      throw (java.rmi.RemoteException) _resp;
+    }
+    else
+    {
+      extractAttachments(_call);
+      try
+      {
+        return (vamsas.objects.simple.WsJobId) _resp;
+      } catch (java.lang.Exception _exception)
+      {
+        return (vamsas.objects.simple.WsJobId) org.apache.axis.utils.JavaUtils
+                .convert(_resp, vamsas.objects.simple.WsJobId.class);
+      }
     }
+  }
 
 }
diff --git a/src/ext/vamsas/ServiceHandle.java b/src/ext/vamsas/ServiceHandle.java
index 994ea5c..8b15688 100755
--- a/src/ext/vamsas/ServiceHandle.java
+++ b/src/ext/vamsas/ServiceHandle.java
@@ -1,29 +1,40 @@
-/**
- * ServiceHandle.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package ext.vamsas;
 
-public class ServiceHandle
-    implements java.io.Serializable
+public class ServiceHandle implements java.io.Serializable
 {
   private java.lang.String abstractName;
+
   private java.lang.String description;
+
   private java.lang.String endpointURL;
+
   private java.lang.String name;
 
   public ServiceHandle()
   {
   }
 
-  public ServiceHandle(
-      java.lang.String abstractName,
-      java.lang.String description,
-      java.lang.String endpointURL,
-      java.lang.String name)
+  public ServiceHandle(java.lang.String abstractName,
+          java.lang.String description, java.lang.String endpointURL,
+          java.lang.String name)
   {
     this.abstractName = abstractName;
     this.description = description;
@@ -33,7 +44,7 @@ public class ServiceHandle
 
   /**
    * Gets the abstractName value for this ServiceHandle.
-   *
+   * 
    * @return abstractName
    */
   public java.lang.String getAbstractName()
@@ -43,7 +54,7 @@ public class ServiceHandle
 
   /**
    * Sets the abstractName value for this ServiceHandle.
-   *
+   * 
    * @param abstractName
    */
   public void setAbstractName(java.lang.String abstractName)
@@ -53,7 +64,7 @@ public class ServiceHandle
 
   /**
    * Gets the description value for this ServiceHandle.
-   *
+   * 
    * @return description
    */
   public java.lang.String getDescription()
@@ -63,7 +74,7 @@ public class ServiceHandle
 
   /**
    * Sets the description value for this ServiceHandle.
-   *
+   * 
    * @param description
    */
   public void setDescription(java.lang.String description)
@@ -73,7 +84,7 @@ public class ServiceHandle
 
   /**
    * Gets the endpointURL value for this ServiceHandle.
-   *
+   * 
    * @return endpointURL
    */
   public java.lang.String getEndpointURL()
@@ -83,7 +94,7 @@ public class ServiceHandle
 
   /**
    * Sets the endpointURL value for this ServiceHandle.
-   *
+   * 
    * @param endpointURL
    */
   public void setEndpointURL(java.lang.String endpointURL)
@@ -93,7 +104,7 @@ public class ServiceHandle
 
   /**
    * Gets the name value for this ServiceHandle.
-   *
+   * 
    * @return name
    */
   public java.lang.String getName()
@@ -103,7 +114,7 @@ public class ServiceHandle
 
   /**
    * Sets the name value for this ServiceHandle.
-   *
+   * 
    * @param name
    */
   public void setName(java.lang.String name)
@@ -112,9 +123,10 @@ public class ServiceHandle
   }
 
   private java.lang.Object __equalsCalc = null;
+
   public synchronized boolean equals(java.lang.Object obj)
   {
-    if (! (obj instanceof ServiceHandle))
+    if (!(obj instanceof ServiceHandle))
     {
       return false;
     }
@@ -133,24 +145,21 @@ public class ServiceHandle
     }
     __equalsCalc = obj;
     boolean _equals;
-    _equals = true &&
-        ( (this.abstractName == null && other.getAbstractName() == null) ||
-         (this.abstractName != null &&
-          this.abstractName.equals(other.getAbstractName()))) &&
-        ( (this.description == null && other.getDescription() == null) ||
-         (this.description != null &&
-          this.description.equals(other.getDescription()))) &&
-        ( (this.endpointURL == null && other.getEndpointURL() == null) ||
-         (this.endpointURL != null &&
-          this.endpointURL.equals(other.getEndpointURL()))) &&
-        ( (this.name == null && other.getName() == null) ||
-         (this.name != null &&
-          this.name.equals(other.getName())));
+    _equals = true
+            && ((this.abstractName == null && other.getAbstractName() == null) || (this.abstractName != null && this.abstractName
+                    .equals(other.getAbstractName())))
+            && ((this.description == null && other.getDescription() == null) || (this.description != null && this.description
+                    .equals(other.getDescription())))
+            && ((this.endpointURL == null && other.getEndpointURL() == null) || (this.endpointURL != null && this.endpointURL
+                    .equals(other.getEndpointURL())))
+            && ((this.name == null && other.getName() == null) || (this.name != null && this.name
+                    .equals(other.getName())));
     __equalsCalc = null;
     return _equals;
   }
 
   private boolean __hashCodeCalc = false;
+
   public synchronized int hashCode()
   {
     if (__hashCodeCalc)
@@ -180,37 +189,36 @@ public class ServiceHandle
   }
 
   // Type metadata
-  private static org.apache.axis.description.TypeDesc typeDesc =
-      new org.apache.axis.description.TypeDesc(ServiceHandle.class, true);
+  private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(
+          ServiceHandle.class, true);
 
   static
   {
-    typeDesc.setXmlType(new javax.xml.namespace.QName("registry.objects.vamsas",
-        "ServiceHandle"));
-    org.apache.axis.description.ElementDesc elemField = new org.apache.axis.
-        description.ElementDesc();
+    typeDesc.setXmlType(new javax.xml.namespace.QName(
+            "registry.objects.vamsas", "ServiceHandle"));
+    org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
     elemField.setFieldName("abstractName");
     elemField.setXmlName(new javax.xml.namespace.QName("", "abstractName"));
     elemField.setXmlType(new javax.xml.namespace.QName(
-        "http://schemas.xmlsoap.org/soap/encoding/", "string"));
+            "http://schemas.xmlsoap.org/soap/encoding/", "string"));
     typeDesc.addFieldDesc(elemField);
     elemField = new org.apache.axis.description.ElementDesc();
     elemField.setFieldName("description");
     elemField.setXmlName(new javax.xml.namespace.QName("", "description"));
     elemField.setXmlType(new javax.xml.namespace.QName(
-        "http://schemas.xmlsoap.org/soap/encoding/", "string"));
+            "http://schemas.xmlsoap.org/soap/encoding/", "string"));
     typeDesc.addFieldDesc(elemField);
     elemField = new org.apache.axis.description.ElementDesc();
     elemField.setFieldName("endpointURL");
     elemField.setXmlName(new javax.xml.namespace.QName("", "endpointURL"));
     elemField.setXmlType(new javax.xml.namespace.QName(
-        "http://schemas.xmlsoap.org/soap/encoding/", "string"));
+            "http://schemas.xmlsoap.org/soap/encoding/", "string"));
     typeDesc.addFieldDesc(elemField);
     elemField = new org.apache.axis.description.ElementDesc();
     elemField.setFieldName("name");
     elemField.setXmlName(new javax.xml.namespace.QName("", "name"));
     elemField.setXmlType(new javax.xml.namespace.QName(
-        "http://schemas.xmlsoap.org/soap/encoding/", "string"));
+            "http://schemas.xmlsoap.org/soap/encoding/", "string"));
     typeDesc.addFieldDesc(elemField);
   }
 
@@ -226,26 +234,22 @@ public class ServiceHandle
    * Get Custom Serializer
    */
   public static org.apache.axis.encoding.Serializer getSerializer(
-      java.lang.String mechType,
-      java.lang.Class _javaType,
-      javax.xml.namespace.QName _xmlType)
+          java.lang.String mechType, java.lang.Class _javaType,
+          javax.xml.namespace.QName _xmlType)
   {
-    return
-        new org.apache.axis.encoding.ser.BeanSerializer(
-            _javaType, _xmlType, typeDesc);
+    return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,
+            _xmlType, typeDesc);
   }
 
   /**
    * Get Custom Deserializer
    */
   public static org.apache.axis.encoding.Deserializer getDeserializer(
-      java.lang.String mechType,
-      java.lang.Class _javaType,
-      javax.xml.namespace.QName _xmlType)
+          java.lang.String mechType, java.lang.Class _javaType,
+          javax.xml.namespace.QName _xmlType)
   {
-    return
-        new org.apache.axis.encoding.ser.BeanDeserializer(
-            _javaType, _xmlType, typeDesc);
+    return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,
+            _xmlType, typeDesc);
   }
 
 }
diff --git a/src/ext/vamsas/ServiceHandles.java b/src/ext/vamsas/ServiceHandles.java
index 1de1345..60e4ffd 100755
--- a/src/ext/vamsas/ServiceHandles.java
+++ b/src/ext/vamsas/ServiceHandles.java
@@ -1,14 +1,24 @@
-/**
- * ServiceHandles.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package ext.vamsas;
 
-public class ServiceHandles
-    implements java.io.Serializable
+public class ServiceHandles implements java.io.Serializable
 {
   private ext.vamsas.ServiceHandle[] services;
 
@@ -16,15 +26,14 @@ public class ServiceHandles
   {
   }
 
-  public ServiceHandles(
-      ext.vamsas.ServiceHandle[] services)
+  public ServiceHandles(ext.vamsas.ServiceHandle[] services)
   {
     this.services = services;
   }
 
   /**
    * Gets the services value for this ServiceHandles.
-   *
+   * 
    * @return services
    */
   public ext.vamsas.ServiceHandle[] getServices()
@@ -34,7 +43,7 @@ public class ServiceHandles
 
   /**
    * Sets the services value for this ServiceHandles.
-   *
+   * 
    * @param services
    */
   public void setServices(ext.vamsas.ServiceHandle[] services)
@@ -43,9 +52,10 @@ public class ServiceHandles
   }
 
   private java.lang.Object __equalsCalc = null;
+
   public synchronized boolean equals(java.lang.Object obj)
   {
-    if (! (obj instanceof ServiceHandles))
+    if (!(obj instanceof ServiceHandles))
     {
       return false;
     }
@@ -64,15 +74,14 @@ public class ServiceHandles
     }
     __equalsCalc = obj;
     boolean _equals;
-    _equals = true &&
-        ( (this.services == null && other.getServices() == null) ||
-         (this.services != null &&
-          java.util.Arrays.equals(this.services, other.getServices())));
+    _equals = true && ((this.services == null && other.getServices() == null) || (this.services != null && java.util.Arrays
+            .equals(this.services, other.getServices())));
     __equalsCalc = null;
     return _equals;
   }
 
   private boolean __hashCodeCalc = false;
+
   public synchronized int hashCode()
   {
     if (__hashCodeCalc)
@@ -83,13 +92,11 @@ public class ServiceHandles
     int _hashCode = 1;
     if (getServices() != null)
     {
-      for (int i = 0;
-           i < java.lang.reflect.Array.getLength(getServices());
-           i++)
+      for (int i = 0; i < java.lang.reflect.Array.getLength(getServices()); i++)
       {
-        java.lang.Object obj = java.lang.reflect.Array.get(getServices(), i);
-        if (obj != null &&
-            !obj.getClass().isArray())
+        java.lang.Object obj = java.lang.reflect.Array
+                .get(getServices(), i);
+        if (obj != null && !obj.getClass().isArray())
         {
           _hashCode += obj.hashCode();
         }
@@ -100,19 +107,18 @@ public class ServiceHandles
   }
 
   // Type metadata
-  private static org.apache.axis.description.TypeDesc typeDesc =
-      new org.apache.axis.description.TypeDesc(ServiceHandles.class, true);
+  private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(
+          ServiceHandles.class, true);
 
   static
   {
-    typeDesc.setXmlType(new javax.xml.namespace.QName("registry.objects.vamsas",
-        "ServiceHandles"));
-    org.apache.axis.description.ElementDesc elemField = new org.apache.axis.
-        description.ElementDesc();
+    typeDesc.setXmlType(new javax.xml.namespace.QName(
+            "registry.objects.vamsas", "ServiceHandles"));
+    org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
     elemField.setFieldName("services");
     elemField.setXmlName(new javax.xml.namespace.QName("", "services"));
     elemField.setXmlType(new javax.xml.namespace.QName(
-        "registry.objects.vamsas", "ServiceHandle"));
+            "registry.objects.vamsas", "ServiceHandle"));
     typeDesc.addFieldDesc(elemField);
   }
 
@@ -128,26 +134,22 @@ public class ServiceHandles
    * Get Custom Serializer
    */
   public static org.apache.axis.encoding.Serializer getSerializer(
-      java.lang.String mechType,
-      java.lang.Class _javaType,
-      javax.xml.namespace.QName _xmlType)
+          java.lang.String mechType, java.lang.Class _javaType,
+          javax.xml.namespace.QName _xmlType)
   {
-    return
-        new org.apache.axis.encoding.ser.BeanSerializer(
-            _javaType, _xmlType, typeDesc);
+    return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,
+            _xmlType, typeDesc);
   }
 
   /**
    * Get Custom Deserializer
    */
   public static org.apache.axis.encoding.Deserializer getDeserializer(
-      java.lang.String mechType,
-      java.lang.Class _javaType,
-      javax.xml.namespace.QName _xmlType)
+          java.lang.String mechType, java.lang.Class _javaType,
+          javax.xml.namespace.QName _xmlType)
   {
-    return
-        new org.apache.axis.encoding.ser.BeanDeserializer(
-            _javaType, _xmlType, typeDesc);
+    return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,
+            _xmlType, typeDesc);
   }
 
 }
diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 03cdc15..36534a3 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -1,156 +1,159 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.analysis;
-
-import java.util.*;
-
-import jalview.datamodel.*;
-
-/**
- * Takes in a vector or array of sequences and column start and column end
- * and returns a new Hashtable[] of size maxSeqLength, if Hashtable not supplied.
- * This class is used extensively in calculating alignment colourschemes
- * that depend on the amount of conservation in each alignment column.
- * @author $author$
- * @version $Revision$
- */
-public class AAFrequency
-{
-  //No need to store 1000s of strings which are not
-  //visible to the user.
-  public static final String MAXCOUNT = "C";
-  public static final String MAXRESIDUE = "R";
-  public static final String PID_GAPS = "G";
-  public static final String PID_NOGAPS = "N";
-
-  public static final Hashtable[] calculate(Vector sequences, int start,
-                                            int end)
-  {
-    SequenceI[] seqs = new SequenceI[sequences.size()];
-    int width = 0;
-    for (int i = 0; i < sequences.size(); i++)
-    {
-      seqs[i] = (SequenceI) sequences.elementAt(i);
-      if (seqs[i].getLength() > width)
-      {
-        width = seqs[i].getLength();
-      }
-    }
-
-    Hashtable[] reply = new Hashtable[width];
-
-    if (end >= width)
-    {
-      end = width;
-    }
-
-    calculate(seqs, start, end, reply);
-
-    return reply;
-  }
-
-  public static final void calculate(SequenceI[] sequences,
-                                     int start, int end,
-                                     Hashtable[] result)
-  {
-    Hashtable residueHash;
-    int maxCount, nongap, i, j, v, jSize = sequences.length;
-    String maxResidue;
-    char c;
-    float percentage;
-
-    int[] values = new int[255];
-
-    char[] seq;
-
-    for (i = start; i < end; i++)
-    {
-      residueHash = new Hashtable();
-      maxCount = 0;
-      maxResidue = "";
-      nongap = 0;
-      values = new int[255];
-
-      for (j = 0; j < jSize; j++)
-      {
-        seq = sequences[j].getSequence();
-        if (seq.length > i)
-        {
-          c = seq[i];
-
-          if (c == '.' || c == ' ')
-          {
-            c = '-';
-          }
-
-          if (c == '-')
-          {
-            values['-']++;
-            continue;
-          }
-          else if ('a' <= c && c <= 'z')
-          {
-            c -= 32; //('a' - 'A');
-          }
-
-          nongap++;
-          values[c]++;
-
-        }
-        else
-        {
-          values['-']++;
-        }
-      }
-
-      for (v = 'A'; v < 'Z'; v++)
-      {
-        if (values[v] < 2 || values[v] < maxCount)
-        {
-          continue;
-        }
-
-        if (values[v] > maxCount)
-        {
-          maxResidue = String.valueOf( (char) v);
-        }
-        else if (values[v] == maxCount)
-        {
-          maxResidue += String.valueOf( (char) v);
-        }
-        maxCount = values[v];
-      }
-
-      if (maxResidue.length() == 0)
-      {
-        maxResidue = "-";
-      }
-
-      residueHash.put(MAXCOUNT, new Integer(maxCount));
-      residueHash.put(MAXRESIDUE, maxResidue);
-
-      percentage = ( (float) maxCount * 100) / (float) jSize;
-      residueHash.put(PID_GAPS, new Float(percentage));
-
-      percentage = ( (float) maxCount * 100) / (float) nongap;
-      residueHash.put(PID_NOGAPS, new Float(percentage));
-      result[i] = residueHash;
-    }
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.analysis;
+
+import java.util.*;
+
+import jalview.datamodel.*;
+
+/**
+ * Takes in a vector or array of sequences and column start and column end and
+ * returns a new Hashtable[] of size maxSeqLength, if Hashtable not supplied.
+ * This class is used extensively in calculating alignment colourschemes that
+ * depend on the amount of conservation in each alignment column.
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class AAFrequency
+{
+  // No need to store 1000s of strings which are not
+  // visible to the user.
+  public static final String MAXCOUNT = "C";
+
+  public static final String MAXRESIDUE = "R";
+
+  public static final String PID_GAPS = "G";
+
+  public static final String PID_NOGAPS = "N";
+
+  public static final Hashtable[] calculate(Vector sequences, int start,
+          int end)
+  {
+    SequenceI[] seqs = new SequenceI[sequences.size()];
+    int width = 0;
+    for (int i = 0; i < sequences.size(); i++)
+    {
+      seqs[i] = (SequenceI) sequences.elementAt(i);
+      if (seqs[i].getLength() > width)
+      {
+        width = seqs[i].getLength();
+      }
+    }
+
+    Hashtable[] reply = new Hashtable[width];
+
+    if (end >= width)
+    {
+      end = width;
+    }
+
+    calculate(seqs, start, end, reply);
+
+    return reply;
+  }
+
+  public static final void calculate(SequenceI[] sequences, int start,
+          int end, Hashtable[] result)
+  {
+    Hashtable residueHash;
+    int maxCount, nongap, i, j, v, jSize = sequences.length;
+    String maxResidue;
+    char c;
+    float percentage;
+
+    int[] values = new int[255];
+
+    char[] seq;
+
+    for (i = start; i < end; i++)
+    {
+      residueHash = new Hashtable();
+      maxCount = 0;
+      maxResidue = "";
+      nongap = 0;
+      values = new int[255];
+
+      for (j = 0; j < jSize; j++)
+      {
+        seq = sequences[j].getSequence();
+        if (seq.length > i)
+        {
+          c = seq[i];
+
+          if (c == '.' || c == ' ')
+          {
+            c = '-';
+          }
+
+          if (c == '-')
+          {
+            values['-']++;
+            continue;
+          }
+          else if ('a' <= c && c <= 'z')
+          {
+            c -= 32; // ('a' - 'A');
+          }
+
+          nongap++;
+          values[c]++;
+
+        }
+        else
+        {
+          values['-']++;
+        }
+      }
+
+      for (v = 'A'; v < 'Z'; v++)
+      {
+        if (values[v] < 2 || values[v] < maxCount)
+        {
+          continue;
+        }
+
+        if (values[v] > maxCount)
+        {
+          maxResidue = String.valueOf((char) v);
+        }
+        else if (values[v] == maxCount)
+        {
+          maxResidue += String.valueOf((char) v);
+        }
+        maxCount = values[v];
+      }
+
+      if (maxResidue.length() == 0)
+      {
+        maxResidue = "-";
+      }
+
+      residueHash.put(MAXCOUNT, new Integer(maxCount));
+      residueHash.put(MAXRESIDUE, maxResidue);
+
+      percentage = ((float) maxCount * 100) / (float) jSize;
+      residueHash.put(PID_GAPS, new Float(percentage));
+
+      percentage = ((float) maxCount * 100) / (float) nongap;
+      residueHash.put(PID_NOGAPS, new Float(percentage));
+      result[i] = residueHash;
+    }
+  }
+}
diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 0de8167..c9a8077 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -27,40 +27,55 @@ import jalview.schemes.*;
 import jalview.util.*;
 
 /**
- *
- *
+ * 
+ * 
  * @author $author$
  * @version $Revision$
  */
 public class AlignSeq
 {
   public static final String PEP = "pep";
+
   public static final String DNA = "dna";
-  
+
   static String[] dna =
-      {
-    "A", "C", "G", "T", "-"};
-    //"C", "T", "A", "G", "-"};
+  { "A", "C", "G", "T", "-" };
+
+  // "C", "T", "A", "G", "-"};
   static String[] pep =
-      {
-      "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F",
-      "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "-"
-  };
+  { "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F",
+      "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "-" };
+
   int[][] score;
+
   int[][] E;
+
   int[][] F;
+
   int[][] traceback;
+
   int[] seq1;
+
   int[] seq2;
+
   SequenceI s1;
+
   SequenceI s2;
+
   public String s1str;
+
   public String s2str;
+
   int maxi;
+
   int maxj;
+
   int[] aseq1;
+
   int[] aseq2;
+
   public String astr1 = "";
+
   public String astr2 = "";
 
   /** DOCUMENT ME!! */
@@ -74,51 +89,65 @@ public class AlignSeq
 
   /** DOCUMENT ME!! */
   public int seq2end;
+
   int count;
 
   /** DOCUMENT ME!! */
   public int maxscore;
+
   float pid;
+
   int prev = 0;
+
   int gapOpen = 120;
+
   int gapExtend = 20;
+
   int[][] lookup = ResidueProperties.getBLOSUM62();
+
   String[] intToStr = pep;
+
   int defInt = 23;
+
   StringBuffer output = new StringBuffer();
+
   String type;
 
   /**
    * Creates a new AlignSeq object.
-   *
-   * @param s1 DOCUMENT ME!
-   * @param s2 DOCUMENT ME!
-   * @param type DOCUMENT ME!
+   * 
+   * @param s1
+   *                DOCUMENT ME!
+   * @param s2
+   *                DOCUMENT ME!
+   * @param type
+   *                DOCUMENT ME!
    */
   public AlignSeq(SequenceI s1, SequenceI s2, String type)
   {
-    SeqInit(s1, s1.getSequenceAsString(), s2, s2.getSequenceAsString(), type);
+    SeqInit(s1, s1.getSequenceAsString(), s2, s2.getSequenceAsString(),
+            type);
   }
 
   /**
    * Creates a new AlignSeq object.
-   *
-   * @param s1 DOCUMENT ME!
-   * @param s2 DOCUMENT ME!
-   * @param type DOCUMENT ME!
+   * 
+   * @param s1
+   *                DOCUMENT ME!
+   * @param s2
+   *                DOCUMENT ME!
+   * @param type
+   *                DOCUMENT ME!
    */
-  public AlignSeq(SequenceI s1,
-                  String string1,
-                  SequenceI s2,
-                  String string2,
-                  String type)
+  public AlignSeq(SequenceI s1, String string1, SequenceI s2,
+          String string2, String type)
   {
     SeqInit(s1, string1, s2, string2, type);
   }
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public int getMaxScore()
@@ -128,7 +157,7 @@ public class AlignSeq
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public int getSeq2Start()
@@ -138,7 +167,7 @@ public class AlignSeq
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public int getSeq2End()
@@ -148,7 +177,7 @@ public class AlignSeq
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public int getSeq1Start()
@@ -158,7 +187,7 @@ public class AlignSeq
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public int getSeq1End()
@@ -168,7 +197,7 @@ public class AlignSeq
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public String getOutput()
@@ -178,7 +207,7 @@ public class AlignSeq
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public String getAStr1()
@@ -188,7 +217,7 @@ public class AlignSeq
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public String getAStr2()
@@ -198,7 +227,7 @@ public class AlignSeq
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public int[] getASeq1()
@@ -208,7 +237,7 @@ public class AlignSeq
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public int[] getASeq2()
@@ -218,7 +247,7 @@ public class AlignSeq
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public SequenceI getS1()
@@ -228,7 +257,7 @@ public class AlignSeq
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public SequenceI getS2()
@@ -238,18 +267,20 @@ public class AlignSeq
 
   /**
    * DOCUMENT ME!
-   *
-   * @param s1 DOCUMENT ME!
-   * @param string1 -  string to align for sequence1
-   * @param s2 sequence 2
-   * @param string2 -  string to align for sequence2
-   * @param type DNA or PEPTIDE
+   * 
+   * @param s1
+   *                DOCUMENT ME!
+   * @param string1 -
+   *                string to align for sequence1
+   * @param s2
+   *                sequence 2
+   * @param string2 -
+   *                string to align for sequence2
+   * @param type
+   *                DNA or PEPTIDE
    */
-  public void SeqInit(SequenceI s1,
-                      String string1,
-                      SequenceI s2,
-                      String string2,
-                      String type)
+  public void SeqInit(SequenceI s1, String string1, SequenceI s2,
+          String string2, String type)
   {
     this.s1 = s1;
     this.s2 = s2;
@@ -257,11 +288,8 @@ public class AlignSeq
     SeqInit(string1, string2);
   }
 
-  public void SeqInit(SequenceI s1,
-                      String string1,
-                      SequenceI s2,
-                      String string2,
-                      ScoreMatrix scoreMatrix)
+  public void SeqInit(SequenceI s1, String string1, SequenceI s2,
+          String string2, ScoreMatrix scoreMatrix)
   {
     this.s1 = s1;
     this.s2 = s2;
@@ -270,7 +298,9 @@ public class AlignSeq
   }
 
   /**
-   * construct score matrix for string1 and string2 (after removing any existing gaps
+   * construct score matrix for string1 and string2 (after removing any existing
+   * gaps
+   * 
    * @param string1
    * @param string2
    */
@@ -281,51 +311,53 @@ public class AlignSeq
 
     if (s1str.length() == 0 || s2str.length() == 0)
     {
-      output.append("ALL GAPS: " +
-                    (s1str.length() == 0 ? s1.getName() : " ")
-                    + (s2str.length() == 0 ? s2.getName() : ""));
+      output.append("ALL GAPS: "
+              + (s1str.length() == 0 ? s1.getName() : " ")
+              + (s2str.length() == 0 ? s2.getName() : ""));
       return;
     }
 
-    //System.out.println("lookuip " + rt.freeMemory() + " "+  rt.totalMemory());
+    // System.out.println("lookuip " + rt.freeMemory() + " "+ rt.totalMemory());
     seq1 = new int[s1str.length()];
 
-    //System.out.println("seq1 " + rt.freeMemory() +" "  + rt.totalMemory());
+    // System.out.println("seq1 " + rt.freeMemory() +" " + rt.totalMemory());
     seq2 = new int[s2str.length()];
 
-    //System.out.println("seq2 " + rt.freeMemory() + " " + rt.totalMemory());
+    // System.out.println("seq2 " + rt.freeMemory() + " " + rt.totalMemory());
     score = new int[s1str.length()][s2str.length()];
 
-    //System.out.println("score " + rt.freeMemory() + " " + rt.totalMemory());
+    // System.out.println("score " + rt.freeMemory() + " " + rt.totalMemory());
     E = new int[s1str.length()][s2str.length()];
 
-    //System.out.println("E " + rt.freeMemory() + " " + rt.totalMemory());
+    // System.out.println("E " + rt.freeMemory() + " " + rt.totalMemory());
     F = new int[s1str.length()][s2str.length()];
     traceback = new int[s1str.length()][s2str.length()];
 
-    //System.out.println("F " + rt.freeMemory() + " " + rt.totalMemory());
+    // System.out.println("F " + rt.freeMemory() + " " + rt.totalMemory());
     seq1 = stringToInt(s1str, type);
 
-    //System.out.println("seq1 " + rt.freeMemory() + " " + rt.totalMemory());
+    // System.out.println("seq1 " + rt.freeMemory() + " " + rt.totalMemory());
     seq2 = stringToInt(s2str, type);
 
-    //System.out.println("Seq2 " + rt.freeMemory() + " " + rt.totalMemory());
-    //   long tstart = System.currentTimeMillis();
-    //    calcScoreMatrix();
-    //long tend = System.currentTimeMillis();
-    //System.out.println("Time take to calculate score matrix = " + (tend-tstart) + " ms");
-    //   printScoreMatrix(score);
-    //System.out.println();
-    //printScoreMatrix(traceback);
-    //System.out.println();
-    //  printScoreMatrix(E);
-    //System.out.println();
-    ///printScoreMatrix(F);
-    //System.out.println();
+    // System.out.println("Seq2 " + rt.freeMemory() + " " + rt.totalMemory());
+    // long tstart = System.currentTimeMillis();
+    // calcScoreMatrix();
+    // long tend = System.currentTimeMillis();
+    // System.out.println("Time take to calculate score matrix = " +
+    // (tend-tstart) + " ms");
+    // printScoreMatrix(score);
+    // System.out.println();
+    // printScoreMatrix(traceback);
+    // System.out.println();
+    // printScoreMatrix(E);
+    // System.out.println();
+    // /printScoreMatrix(F);
+    // System.out.println();
     // tstart = System.currentTimeMillis();
-    //traceAlignment();
-    //tend = System.currentTimeMillis();
-    //System.out.println("Time take to traceback alignment = " + (tend-tstart) + " ms");
+    // traceAlignment();
+    // tend = System.currentTimeMillis();
+    // System.out.println("Time take to traceback alignment = " + (tend-tstart)
+    // + " ms");
   }
 
   private void setDefaultParams(String type)
@@ -358,8 +390,8 @@ public class AlignSeq
     else
     {
       output.append("Wrong type = dna or pep only");
-      throw new Error("Unknown Type " + type2 +
-                      " - dna or pep are the only allowed values.");
+      throw new Error("Unknown Type " + type2
+              + " - dna or pep are the only allowed values.");
     }
   }
 
@@ -391,7 +423,7 @@ public class AlignSeq
       }
     }
 
-    //  System.out.println(maxi + " " + maxj + " " + score[maxi][maxj]);
+    // System.out.println(maxi + " " + maxj + " " + score[maxi][maxj]);
     int i = maxi;
     int j = maxj;
     int trace;
@@ -405,15 +437,15 @@ public class AlignSeq
 
     count = (seq1.length + seq2.length) - 1;
 
-    while ( (i > 0) && (j > 0))
+    while ((i > 0) && (j > 0))
     {
-      if ( (aseq1[count] != defInt) && (i >= 0))
+      if ((aseq1[count] != defInt) && (i >= 0))
       {
         aseq1[count] = seq1[i];
         astr1 = s1str.charAt(i) + astr1;
       }
 
-      if ( (aseq2[count] != defInt) && (j > 0))
+      if ((aseq2[count] != defInt) && (j > 0))
       {
         aseq2[count] = seq2[j];
         astr2 = s2str.charAt(j) + astr2;
@@ -463,7 +495,8 @@ public class AlignSeq
    */
   public void printAlignment(java.io.PrintStream os)
   {
-    // TODO: Use original sequence characters rather than re-translated characters in output
+    // TODO: Use original sequence characters rather than re-translated
+    // characters in output
     // Find the biggest id length for formatting purposes
     int maxid = s1.getName().length();
     if (s2.getName().length() > maxid)
@@ -472,33 +505,31 @@ public class AlignSeq
     }
 
     int len = 72 - maxid - 1;
-    int nochunks = ( (aseq1.length - count) / len) + 1;
+    int nochunks = ((aseq1.length - count) / len) + 1;
     pid = 0;
 
     output.append("Score = " + score[maxi][maxj] + "\n");
     output.append("Length of alignment = " + (aseq1.length - count) + "\n");
     output.append("Sequence ");
     output.append(new Format("%" + maxid + "s").form(s1.getName()));
-    output.append(" :  " + s1.getStart() + " - " + s1.getEnd() +
-                  " (Sequence length = " +
-                  s1str.length() + ")\n");
+    output.append(" :  " + s1.getStart() + " - " + s1.getEnd()
+            + " (Sequence length = " + s1str.length() + ")\n");
     output.append("Sequence ");
     output.append(new Format("%" + maxid + "s").form(s2.getName()));
-    output.append(" :  " + s2.getStart() + " - " + s2.getEnd() +
-                  " (Sequence length = " +
-                  s2str.length() + ")\n\n");
-    
+    output.append(" :  " + s2.getStart() + " - " + s2.getEnd()
+            + " (Sequence length = " + s2str.length() + ")\n\n");
+
     for (int j = 0; j < nochunks; j++)
     {
       // Print the first aligned sequence
-      output.append(new Format("%" + (maxid) + "s").form(s1.getName()) + " ");
+      output.append(new Format("%" + (maxid) + "s").form(s1.getName())
+              + " ");
 
       for (int i = 0; i < len; i++)
       {
-        if ( (i + (j * len)) < astr1.length())
+        if ((i + (j * len)) < astr1.length())
         {
-          output.append(astr1.charAt(i +
-                                              (j * len)));
+          output.append(astr1.charAt(i + (j * len)));
         }
       }
 
@@ -508,19 +539,19 @@ public class AlignSeq
       // Print out the matching chars
       for (int i = 0; i < len; i++)
       {
-        if ( (i + (j * len)) < astr1.length())
+        if ((i + (j * len)) < astr1.length())
         {
-          if (astr1.charAt(i + (j * len))==astr2.charAt(i + (j * len)) &&
-              !jalview.util.Comparison.isGap(astr1.charAt(i + (j * len))))
+          if (astr1.charAt(i + (j * len)) == astr2.charAt(i + (j * len))
+                  && !jalview.util.Comparison.isGap(astr1.charAt(i
+                          + (j * len))))
           {
             pid++;
             output.append("|");
           }
           else if (type.equals("pep"))
           {
-            if (ResidueProperties.getPAM250(
-                    astr1.charAt(i + (j * len)),
-                    astr2.charAt(i + (j * len)))>0)
+            if (ResidueProperties.getPAM250(astr1.charAt(i + (j * len)),
+                    astr2.charAt(i + (j * len))) > 0)
             {
               output.append(".");
             }
@@ -538,12 +569,13 @@ public class AlignSeq
 
       // Now print the second aligned sequence
       output = output.append("\n");
-      output = output.append(new Format("%" + (maxid) + "s").form(s2.getName()) +
-                             " ");
+      output = output.append(new Format("%" + (maxid) + "s").form(s2
+              .getName())
+              + " ");
 
       for (int i = 0; i < len; i++)
       {
-        if ( (i + (j * len)) < astr2.length())
+        if ((i + (j * len)) < astr2.length())
         {
           output.append(astr2.charAt(i + (j * len)));
         }
@@ -553,20 +585,22 @@ public class AlignSeq
     }
 
     pid = pid / (float) (aseq1.length - count) * 100;
-    output = output.append(new Format("Percentage ID = %2.2f\n\n").form(pid));
+    output = output.append(new Format("Percentage ID = %2.2f\n\n")
+            .form(pid));
 
     try
     {
       os.print(output.toString());
+    } catch (Exception ex)
+    {
     }
-    catch (Exception ex)
-    {}
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param mat DOCUMENT ME!
+   * 
+   * @param mat
+   *                DOCUMENT ME!
    */
   public void printScoreMatrix(int[][] mat)
   {
@@ -604,10 +638,12 @@ public class AlignSeq
 
   /**
    * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
-   * @param j DOCUMENT ME!
-   *
+   * 
+   * @param i
+   *                DOCUMENT ME!
+   * @param j
+   *                DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   public int findTrace(int i, int j)
@@ -668,8 +704,7 @@ public class AlignSeq
       E[0][j] = max(score[0][j - 1] - gapOpen, E[0][j - 1] - gapExtend);
       F[0][j] = -gapExtend;
 
-      score[0][j] = max(lookup[seq1[0]][seq2[j]] * 10, -gapOpen,
-                        -gapExtend);
+      score[0][j] = max(lookup[seq1[0]][seq2[j]] * 10, -gapOpen, -gapExtend);
 
       traceback[0][j] = 1;
     }
@@ -689,13 +724,11 @@ public class AlignSeq
     {
       for (int j = 1; j < m; j++)
       {
-        E[i][j] = max(score[i][j - 1] - gapOpen, E[i][j - 1] -
-                      gapExtend);
-        F[i][j] = max(score[i - 1][j] - gapOpen, F[i - 1][j] -
-                      gapExtend);
+        E[i][j] = max(score[i][j - 1] - gapOpen, E[i][j - 1] - gapExtend);
+        F[i][j] = max(score[i - 1][j] - gapOpen, F[i - 1][j] - gapExtend);
 
-        score[i][j] = max(score[i - 1][j - 1] +
-                          (lookup[seq1[i]][seq2[j]] * 10), E[i][j], F[i][j]);
+        score[i][j] = max(score[i - 1][j - 1]
+                + (lookup[seq1[i]][seq2[j]] * 10), E[i][j], F[i][j]);
         traceback[i][j] = findTrace(i, j);
       }
     }
@@ -703,10 +736,12 @@ public class AlignSeq
 
   /**
    * DOCUMENT ME!
-   *
-   * @param gapChar DOCUMENT ME!
-   * @param seq DOCUMENT ME!
-   *
+   * 
+   * @param gapChar
+   *                DOCUMENT ME!
+   * @param seq
+   *                DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   public static String extractGaps(String gapChar, String seq)
@@ -724,11 +759,14 @@ public class AlignSeq
 
   /**
    * DOCUMENT ME!
-   *
-   * @param i1 DOCUMENT ME!
-   * @param i2 DOCUMENT ME!
-   * @param i3 DOCUMENT ME!
-   *
+   * 
+   * @param i1
+   *                DOCUMENT ME!
+   * @param i2
+   *                DOCUMENT ME!
+   * @param i3
+   *                DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   public int max(int i1, int i2, int i3)
@@ -750,10 +788,12 @@ public class AlignSeq
 
   /**
    * DOCUMENT ME!
-   *
-   * @param i1 DOCUMENT ME!
-   * @param i2 DOCUMENT ME!
-   *
+   * 
+   * @param i1
+   *                DOCUMENT ME!
+   * @param i2
+   *                DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   public int max(int i1, int i2)
@@ -770,10 +810,12 @@ public class AlignSeq
 
   /**
    * DOCUMENT ME!
-   *
-   * @param s DOCUMENT ME!
-   * @param type DOCUMENT ME!
-   *
+   * 
+   * @param s
+   *                DOCUMENT ME!
+   * @param type
+   *                DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   public int[] stringToInt(String s, String type)
@@ -809,8 +851,7 @@ public class AlignSeq
           }
         }
 
-      }
-      catch (Exception e)
+      } catch (Exception e)
       {
         if (type.equals("dna"))
         {
@@ -828,15 +869,20 @@ public class AlignSeq
 
   /**
    * DOCUMENT ME!
-   *
-   * @param g DOCUMENT ME!
-   * @param mat DOCUMENT ME!
-   * @param n DOCUMENT ME!
-   * @param m DOCUMENT ME!
-   * @param psize DOCUMENT ME!
+   * 
+   * @param g
+   *                DOCUMENT ME!
+   * @param mat
+   *                DOCUMENT ME!
+   * @param n
+   *                DOCUMENT ME!
+   * @param m
+   *                DOCUMENT ME!
+   * @param psize
+   *                DOCUMENT ME!
    */
   public static void displayMatrix(Graphics g, int[][] mat, int n, int m,
-                                   int psize)
+          int psize)
   {
     int max = -1000;
     int min = 1000;
@@ -866,12 +912,12 @@ public class AlignSeq
         int x = psize * i;
         int y = psize * j;
 
-        //	System.out.println(mat[i][j]);
+        // System.out.println(mat[i][j]);
         float score = (float) (mat[i][j] - min) / (float) (max - min);
         g.setColor(new Color(score, 0, 0));
         g.fillRect(x, y, psize, psize);
 
-        //	System.out.println(x + " " + y + " " + score);
+        // System.out.println(x + " " + y + " " + score);
       }
     }
   }
diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index a3493f7..fe2cfc7 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -23,34 +23,51 @@ import java.util.*;
 import jalview.datamodel.*;
 import jalview.util.*;
 
-/** 
- * Routines for manipulating the order of a multiple sequence alignment
- * TODO: this class retains some global states concerning sort-order which should be made attributes for the caller's alignment visualization.
- * TODO: refactor to allow a subset of selected sequences to be sorted within the context of a whole alignment.
- * Sort method template is: SequenceI[] tobesorted, [ input data mapping to each tobesorted element to use ], Alignment context of tobesorted that are to be re-ordered, boolean sortinplace, [special data - ie seuqence to be sorted w.r.t.])
- * sortinplace implies that the sorted vector resulting from applying the operation to tobesorted should be mapped back to the original positions in alignment.
- * Otherwise, normal behaviour is to re order alignment so that tobesorted is sorted and grouped together starting from the first tobesorted position in the alignment.
- * e.g. (a,tb2,b,tb1,c,tb3 becomes a,tb1,tb2,tb3,b,c)
+/**
+ * Routines for manipulating the order of a multiple sequence alignment TODO:
+ * this class retains some global states concerning sort-order which should be
+ * made attributes for the caller's alignment visualization. TODO: refactor to
+ * allow a subset of selected sequences to be sorted within the context of a
+ * whole alignment. Sort method template is: SequenceI[] tobesorted, [ input
+ * data mapping to each tobesorted element to use ], Alignment context of
+ * tobesorted that are to be re-ordered, boolean sortinplace, [special data - ie
+ * seuqence to be sorted w.r.t.]) sortinplace implies that the sorted vector
+ * resulting from applying the operation to tobesorted should be mapped back to
+ * the original positions in alignment. Otherwise, normal behaviour is to re
+ * order alignment so that tobesorted is sorted and grouped together starting
+ * from the first tobesorted position in the alignment. e.g. (a,tb2,b,tb1,c,tb3
+ * becomes a,tb1,tb2,tb3,b,c)
  */
 public class AlignmentSorter
 {
   static boolean sortIdAscending = true;
+
   static int lastGroupHash = 0;
+
   static boolean sortGroupAscending = true;
+
   static AlignmentOrder lastOrder = null;
+
   static boolean sortOrderAscending = true;
+
   static NJTree lastTree = null;
+
   static boolean sortTreeAscending = true;
+
   private static String lastSortByScore;
 
   /**
    * Sort by Percentage Identity w.r.t. s
-   *
-   * @param align AlignmentI
-   * @param s SequenceI
-   * @param tosort sequences from align that are to be sorted.
+   * 
+   * @param align
+   *                AlignmentI
+   * @param s
+   *                SequenceI
+   * @param tosort
+   *                sequences from align that are to be sorted.
    */
-  public static void sortByPID(AlignmentI align, SequenceI s, SequenceI[] tosort)
+  public static void sortByPID(AlignmentI align, SequenceI s,
+          SequenceI[] tosort)
   {
     int nSeq = align.getHeight();
 
@@ -59,8 +76,8 @@ public class AlignmentSorter
 
     for (int i = 0; i < nSeq; i++)
     {
-      scores[i] = Comparison.PID(align.getSequenceAt(i).getSequenceAsString(),
-                                 s.getSequenceAsString());
+      scores[i] = Comparison.PID(align.getSequenceAt(i)
+              .getSequenceAsString(), s.getSequenceAsString());
       seqs[i] = align.getSequenceAt(i);
     }
 
@@ -71,9 +88,11 @@ public class AlignmentSorter
 
   /**
    * Reverse the order of the sort
-   *
-   * @param align DOCUMENT ME!
-   * @param seqs DOCUMENT ME!
+   * 
+   * @param align
+   *                DOCUMENT ME!
+   * @param seqs
+   *                DOCUMENT ME!
    */
   private static void setReverseOrder(AlignmentI align, SequenceI[] seqs)
   {
@@ -81,7 +100,7 @@ public class AlignmentSorter
 
     int len = 0;
 
-    if ( (nSeq % 2) == 0)
+    if ((nSeq % 2) == 0)
     {
       len = nSeq / 2;
     }
@@ -93,7 +112,7 @@ public class AlignmentSorter
     // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
     for (int i = 0; i < len; i++)
     {
-      //SequenceI tmp = seqs[i];
+      // SequenceI tmp = seqs[i];
       align.getSequences().setElementAt(seqs[nSeq - i - 1], i);
       align.getSequences().setElementAt(seqs[i], nSeq - i - 1);
     }
@@ -101,9 +120,11 @@ public class AlignmentSorter
 
   /**
    * Sets the Alignment object with the given sequences
-   *
-   * @param align Alignment object to be updated
-   * @param tmp sequences as a vector
+   * 
+   * @param align
+   *                Alignment object to be updated
+   * @param tmp
+   *                sequences as a vector
    */
   private static void setOrder(AlignmentI align, Vector tmp)
   {
@@ -112,9 +133,11 @@ public class AlignmentSorter
 
   /**
    * Sets the Alignment object with the given sequences
-   *
-   * @param align DOCUMENT ME!
-   * @param seqs sequences as an array
+   * 
+   * @param align
+   *                DOCUMENT ME!
+   * @param seqs
+   *                sequences as an array
    */
   public static void setOrder(AlignmentI align, SequenceI[] seqs)
   {
@@ -131,7 +154,7 @@ public class AlignmentSorter
     }
 
     algn.removeAllElements();
-    //User may have hidden seqs, then clicked undo or redo
+    // User may have hidden seqs, then clicked undo or redo
     for (int i = 0; i < tmp.size(); i++)
     {
       algn.addElement(tmp.elementAt(i));
@@ -141,8 +164,9 @@ public class AlignmentSorter
 
   /**
    * Sorts by ID. Numbers are sorted before letters.
-   *
-   * @param align The alignment object to sort
+   * 
+   * @param align
+   *                The alignment object to sort
    */
   public static void sortByID(AlignmentI align)
   {
@@ -172,16 +196,17 @@ public class AlignmentSorter
   }
 
   /**
-   * Sorts the alignment by size of group.
-   * <br>Maintains the order of sequences in each group
-   * by order in given alignment object.
-   *
-   * @param align sorts the given alignment object by group
+   * Sorts the alignment by size of group. <br>
+   * Maintains the order of sequences in each group by order in given alignment
+   * object.
+   * 
+   * @param align
+   *                sorts the given alignment object by group
    */
   public static void sortByGroup(AlignmentI align)
   {
-    //MAINTAINS ORIGNAL SEQUENCE ORDER,
-    //ORDERS BY GROUP SIZE
+    // MAINTAINS ORIGNAL SEQUENCE ORDER,
+    // ORDERS BY GROUP SIZE
     Vector groups = new Vector();
 
     if (groups.hashCode() != lastGroupHash)
@@ -194,8 +219,8 @@ public class AlignmentSorter
       sortGroupAscending = !sortGroupAscending;
     }
 
-    //SORTS GROUPS BY SIZE
-    //////////////////////
+    // SORTS GROUPS BY SIZE
+    // ////////////////////
     for (int i = 0; i < align.getGroups().size(); i++)
     {
       SequenceGroup sg = (SequenceGroup) align.getGroups().elementAt(i);
@@ -218,8 +243,8 @@ public class AlignmentSorter
       }
     }
 
-    //NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER
-    ///////////////////////////////////////////////
+    // NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER
+    // /////////////////////////////////////////////
     Vector seqs = new Vector();
 
     for (int i = 0; i < groups.size(); i++)
@@ -240,16 +265,16 @@ public class AlignmentSorter
     else
     {
       setReverseOrder(align,
-                      vectorSubsetToArray(seqs, align.getSequences()));
+              vectorSubsetToArray(seqs, align.getSequences()));
     }
   }
 
   /**
-   * Converts Vector to array.
-   * java 1.18 does not have Vector.toArray()
-   *
-   * @param tmp Vector of SequenceI objects
-   *
+   * Converts Vector to array. java 1.18 does not have Vector.toArray()
+   * 
+   * @param tmp
+   *                Vector of SequenceI objects
+   * 
    * @return array of Sequence[]
    */
   private static SequenceI[] vectorToArray(Vector tmp)
@@ -266,10 +291,12 @@ public class AlignmentSorter
 
   /**
    * DOCUMENT ME!
-   *
-   * @param tmp DOCUMENT ME!
-   * @param mask DOCUMENT ME!
-   *
+   * 
+   * @param tmp
+   *                DOCUMENT ME!
+   * @param mask
+   *                DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   private static SequenceI[] vectorSubsetToArray(Vector tmp, Vector mask)
@@ -307,9 +334,11 @@ public class AlignmentSorter
 
   /**
    * Sorts by a given AlignmentOrder object
-   *
-   * @param align Alignment to order
-   * @param order specified order for alignment
+   * 
+   * @param align
+   *                Alignment to order
+   * @param order
+   *                specified order for alignment
    */
   public static void sortBy(AlignmentI align, AlignmentOrder order)
   {
@@ -331,17 +360,18 @@ public class AlignmentSorter
     }
     else
     {
-      setReverseOrder(align,
-                      vectorSubsetToArray(tmp, align.getSequences()));
+      setReverseOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
     }
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param align alignment to order
-   * @param tree tree which has
-   *
+   * 
+   * @param align
+   *                alignment to order
+   * @param tree
+   *                tree which has
+   * 
    * @return DOCUMENT ME!
    */
   private static Vector getOrderByTree(AlignmentI align, NJTree tree)
@@ -356,7 +386,7 @@ public class AlignmentSorter
     {
       // TODO: JBPNote - decide if this is always an error
       // (eg. not when a tree is associated to another alignment which has more
-      //  sequences)
+      // sequences)
       if (tmp.size() < nSeq)
       {
         addStrays(align, tmp);
@@ -364,8 +394,8 @@ public class AlignmentSorter
 
       if (tmp.size() != nSeq)
       {
-        System.err.println("ERROR: tmp.size()=" + tmp.size() +
-                           " != nseq=" + nSeq + " in getOrderByTree");
+        System.err.println("ERROR: tmp.size()=" + tmp.size() + " != nseq="
+                + nSeq + " in getOrderByTree");
       }
     }
 
@@ -374,9 +404,11 @@ public class AlignmentSorter
 
   /**
    * Sorts the alignment by a given tree
-   *
-   * @param align alignment to order
-   * @param tree tree which has
+   * 
+   * @param align
+   *                alignment to order
+   * @param tree
+   *                tree which has
    */
   public static void sortByTree(AlignmentI align, NJTree tree)
   {
@@ -399,16 +431,17 @@ public class AlignmentSorter
     }
     else
     {
-      setReverseOrder(align,
-                      vectorSubsetToArray(tmp, align.getSequences()));
+      setReverseOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
     }
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param align DOCUMENT ME!
-   * @param seqs DOCUMENT ME!
+   * 
+   * @param align
+   *                DOCUMENT ME!
+   * @param seqs
+   *                DOCUMENT ME!
    */
   private static void addStrays(AlignmentI align, Vector seqs)
   {
@@ -424,22 +457,25 @@ public class AlignmentSorter
 
     if (nSeq != seqs.size())
     {
-      System.err.println(
-          "ERROR: Size still not right even after addStrays");
+      System.err
+              .println("ERROR: Size still not right even after addStrays");
     }
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param node DOCUMENT ME!
-   * @param tmp DOCUMENT ME!
-   * @param seqset DOCUMENT ME!
-   *
+   * 
+   * @param node
+   *                DOCUMENT ME!
+   * @param tmp
+   *                DOCUMENT ME!
+   * @param seqset
+   *                DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   private static Vector _sortByTree(SequenceNode node, Vector tmp,
-                                    Vector seqset)
+          Vector seqset)
   {
     if (node == null)
     {
@@ -449,7 +485,7 @@ public class AlignmentSorter
     SequenceNode left = (SequenceNode) node.left();
     SequenceNode right = (SequenceNode) node.right();
 
-    if ( (left == null) && (right == null))
+    if ((left == null) && (right == null))
     {
       if (!node.isPlaceholder() && (node.element() != null))
       {
@@ -457,7 +493,7 @@ public class AlignmentSorter
         {
           if (!tmp.contains(node.element()))
           {
-            tmp.addElement( (SequenceI) node.element());
+            tmp.addElement((SequenceI) node.element());
           }
         }
       }
@@ -474,7 +510,8 @@ public class AlignmentSorter
   }
 
   // Ordering Objects
-  // Alignment.sortBy(OrderObj) - sequence of sequence pointer refs in appropriate order
+  // Alignment.sortBy(OrderObj) - sequence of sequence pointer refs in
+  // appropriate order
   //
 
   /**
@@ -487,42 +524,52 @@ public class AlignmentSorter
 
     for (int i = 0; i < alignment.length; i++)
     {
-      ids[i] = (new Float(alignment[i].getName().substring(8))).floatValue();
+      ids[i] = (new Float(alignment[i].getName().substring(8)))
+              .floatValue();
     }
 
     jalview.util.QuickSort.sort(ids, alignment);
   }
+
   /**
-   * Sort sequence in order of increasing score attribute for annotation with a particular
-   * scoreLabel. Or reverse if same label was used previously
-   * @param scoreLabel exact label for sequence associated AlignmentAnnotation scores to use for sorting.
-   * @param alignment sequences to be sorted
+   * Sort sequence in order of increasing score attribute for annotation with a
+   * particular scoreLabel. Or reverse if same label was used previously
+   * 
+   * @param scoreLabel
+   *                exact label for sequence associated AlignmentAnnotation
+   *                scores to use for sorting.
+   * @param alignment
+   *                sequences to be sorted
    */
-  public static void sortByAnnotationScore(String scoreLabel, AlignmentI alignment)
+  public static void sortByAnnotationScore(String scoreLabel,
+          AlignmentI alignment)
   {
     SequenceI[] seqs = alignment.getSequencesArray();
-    boolean[] hasScore = new boolean[seqs.length]; // per sequence score presence
-    int hasScores=0; // number of scores present on set
+    boolean[] hasScore = new boolean[seqs.length]; // per sequence score
+                                                    // presence
+    int hasScores = 0; // number of scores present on set
     double[] scores = new double[seqs.length];
-    double min=0,max=0;
+    double min = 0, max = 0;
     for (int i = 0; i < seqs.length; i++)
     {
       AlignmentAnnotation[] scoreAnn = seqs[i].getAnnotation(scoreLabel);
-      if (scoreAnn!=null)
+      if (scoreAnn != null)
       {
         hasScores++;
         hasScore[i] = true;
-        scores[i] = scoreAnn[0].getScore(); // take the first instance of this score.
-        if (hasScores==1)
+        scores[i] = scoreAnn[0].getScore(); // take the first instance of this
+                                            // score.
+        if (hasScores == 1)
         {
           max = min = scores[i];
-        } else
+        }
+        else
         {
-          if (max<scores[i])
+          if (max < scores[i])
           {
             max = scores[i];
           }
-          if (min>scores[i])
+          if (min > scores[i])
           {
             min = scores[i];
           }
@@ -533,27 +580,29 @@ public class AlignmentSorter
         hasScore[i] = false;
       }
     }
-    if (hasScores==0)
+    if (hasScores == 0)
     {
       return; // do nothing - no scores present to sort by.
     }
-    if (hasScores<seqs.length)
+    if (hasScores < seqs.length)
     {
-      for (int i=0; i<seqs.length;i++)
+      for (int i = 0; i < seqs.length; i++)
       {
         if (!hasScore[i])
         {
-          scores[i] = (max+i);
+          scores[i] = (max + i);
         }
       }
     }
-    
+
     jalview.util.QuickSort.sort(scores, seqs);
-    if (lastSortByScore!=scoreLabel)
+    if (lastSortByScore != scoreLabel)
     {
       lastSortByScore = scoreLabel;
       setOrder(alignment, seqs);
-    } else {
+    }
+    else
+    {
       setReverseOrder(alignment, seqs);
     }
   }
diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index c216471..31a4b66 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -45,9 +45,10 @@ public class Conservation
   Hashtable[] total;
 
   boolean canonicaliseAa = true; // if true then conservation calculation will
-                                  // map all symbols to canonical aa numbering
-                                  // rather than consider conservation of that
-                                  // symbol
+
+  // map all symbols to canonical aa numbering
+  // rather than consider conservation of that
+  // symbol
 
   /** Stores calculated quality values */
   public Vector quality;
@@ -95,7 +96,7 @@ public class Conservation
     this.end = end;
 
     maxLength = end - start + 1; // default width includes bounds of
-                                  // calculation
+    // calculation
 
     int s, sSize = sequences.size();
     SequenceI[] sarray = new SequenceI[sSize];
@@ -112,8 +113,8 @@ public class Conservation
   }
 
   /**
-   * Translate sequence i into a numerical 
-   * representation and store it in the i'th position of the seqNums array.
+   * Translate sequence i into a numerical representation and store it in the
+   * i'th position of the seqNums array.
    * 
    * @param i
    */
@@ -146,7 +147,7 @@ public class Conservation
         }
 
         sqnum = new int[len + 1]; // better to always make a new array -
-                                  // sequence can change its length
+        // sequence can change its length
         sqnum[0] = sq.hashCode();
 
         for (j = 1; j <= len; j++)
@@ -276,7 +277,8 @@ public class Conservation
   }
 
   /*****************************************************************************
-   * count conservation  for the j'th column of the alignment
+   * count conservation for the j'th column of the alignment
+   * 
    * @return { gap count, conserved residue count}
    */
   public int[] countConsNGaps(int j)
@@ -477,8 +479,7 @@ public class Conservation
        * maxj = -1;
        * 
        * for (int j=0;j<24;j++) { if (cons2[i][j] > max) { max = cons2[i][j];
-       * maxi = i; maxj = j; }
-       *  } }
+       * maxi = i; maxj = j; } } }
        */
     }
   }
diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 159d96a..8bc844b 100644
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.analysis;
 
 import java.util.Enumeration;
@@ -158,7 +176,8 @@ public class CrossRef
       {
         if (cdna[c].getSource().equals(DBRefSource.EMBLCDS))
         {
-          System.err.println("TODO: unimplemented sequence retrieval for coding region sequence.");
+          System.err
+                  .println("TODO: unimplemented sequence retrieval for coding region sequence.");
           // TODO: retrieve CDS dataset sequences
           // need global dataset sequence retriever/resolver to reuse refs
           // and construct Mapping entry.
@@ -306,7 +325,10 @@ public class CrossRef
             xrfs = t;
             try
             {
-              retrieved = sftch.getSequences(xrfs); // problem here is we don't know which of xrfs resulted in which retrieved element
+              retrieved = sftch.getSequences(xrfs); // problem here is we don't
+                                                    // know which of xrfs
+                                                    // resulted in which
+                                                    // retrieved element
             } catch (Exception e)
             {
               System.err
@@ -319,32 +341,39 @@ public class CrossRef
               for (int rs = 0; rs < retrieved.length; rs++)
               {
                 // TODO: examine each sequence for 'redundancy'
-                jalview.datamodel.DBRefEntry[] dbr = retrieved[rs].getDBRef();
+                jalview.datamodel.DBRefEntry[] dbr = retrieved[rs]
+                        .getDBRef();
                 if (dbr != null && dbr.length > 0)
                 {
                   for (int di = 0; di < dbr.length; di++)
                   {
-                    // find any entry where we should put in the sequence being cross-referenced into the map
+                    // find any entry where we should put in the sequence being
+                    // cross-referenced into the map
                     jalview.datamodel.Mapping map = dbr[di].getMap();
                     if (map != null)
                     {
                       if (map.getTo() != null && map.getMap() != null)
                       {
-                        // should search the local dataset to find any existing candidates for To !
+                        // should search the local dataset to find any existing
+                        // candidates for To !
                         try
                         {
-                          // compare ms with dss and replace with dss in mapping if map is congruent
+                          // compare ms with dss and replace with dss in mapping
+                          // if map is congruent
                           SequenceI ms = map.getTo();
                           int sf = map.getMap().getToLowest();
                           int st = map.getMap().getToHighest();
                           SequenceI mappedrg = ms.getSubSequence(sf, st);
                           SequenceI loc = dss.getSubSequence(sf, st);
-                          if (mappedrg.getLength()>0 && mappedrg.getSequenceAsString().equals(
-                                  loc.getSequenceAsString()))
+                          if (mappedrg.getLength() > 0
+                                  && mappedrg.getSequenceAsString().equals(
+                                          loc.getSequenceAsString()))
                           {
                             System.err
                                     .println("Mapping updated for retrieved crossreference");
-                            // method to update all refs of existing To on retrieved sequence with dss and merge any props on To onto dss.
+                            // method to update all refs of existing To on
+                            // retrieved sequence with dss and merge any props
+                            // on To onto dss.
                             map.setTo(dss);
                           }
                         } catch (Exception e)
@@ -445,7 +474,7 @@ public class CrossRef
           boolean direct, boolean dna)
   {
     boolean found = false;
-    SequenceI[] typer=new SequenceI[1];
+    SequenceI[] typer = new SequenceI[1];
     if (dataset == null)
       return false;
     if (dataset.getSequences() == null)
@@ -470,7 +499,7 @@ public class CrossRef
           {
             typer[0] = nxt;
             boolean isDna = jalview.util.Comparison.isNucleotide(typer);
-            if ((direct && isDna == dna) || (!direct && isDna!=dna))
+            if ((direct && isDna == dna) || (!direct && isDna != dna))
             {
               // skip this sequence because it is same molecule type
               continue;
@@ -550,16 +579,17 @@ public class CrossRef
    *         System.out.println("Found " + ((prod == null) ? "no" : "" +
    *         prod.length) + " products"); if (prod!=null) { for (int p=0; p<prod.length;
    *         p++) { System.out.println("Prod "+p+":
-   *         "+prod[p].getDisplayId(true)); } } }
-   *  } else { System.out.println("Trying getProducts for
-   * "+al.getSequenceAt(0).getDisplayId(true)); System.out.println("Search DS
-   * Xref for: "+(dna ? "dna" : "prot")); // have a bash at finding the products
-   * amongst all the retrieved sequences. SequenceI[] prod =
-   * jalview.analysis.CrossRef.findXrefSequences(al .getSequencesArray(), dna,
-   * null, ds); System.out.println("Found " + ((prod == null) ? "no" : "" +
-   * prod.length) + " products"); if (prod!=null) { // select non-equivalent
-   * sequences from dataset list for (int p=0; p<prod.length; p++) {
-   * System.out.println("Prod "+p+": "+prod[p].getDisplayId(true)); } }
-   *  } }
+   *         "+prod[p].getDisplayId(true)); } } } } else {
+   *         System.out.println("Trying getProducts for
+   *         "+al.getSequenceAt(0).getDisplayId(true));
+   *         System.out.println("Search DS Xref for: "+(dna ? "dna" : "prot")); //
+   *         have a bash at finding the products amongst all the retrieved
+   *         sequences. SequenceI[] prod =
+   *         jalview.analysis.CrossRef.findXrefSequences(al
+   *         .getSequencesArray(), dna, null, ds); System.out.println("Found " +
+   *         ((prod == null) ? "no" : "" + prod.length) + " products"); if
+   *         (prod!=null) { // select non-equivalent sequences from dataset list
+   *         for (int p=0; p<prod.length; p++) { System.out.println("Prod
+   *         "+p+": "+prod[p].getDisplayId(true)); } } } }
    */
-}
\ No newline at end of file
+}
diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index c6bcfda..8bf8962 100644
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.analysis;
 
 import java.util.Enumeration;
@@ -66,7 +84,8 @@ public class Dna
    * @param gapCharacter
    * @param annotations
    * @param aWidth
-   * @param dataset destination dataset for translated sequences and mappings
+   * @param dataset
+   *                destination dataset for translated sequences and mappings
    * @return
    */
   public static AlignmentI CdnaTranslate(SequenceI[] selection,
@@ -81,7 +100,9 @@ public class Dna
    * 
    * @param selection
    * @param seqstring
-   * @param product - array of DbRefEntry objects from which exon map in seqstring is derived
+   * @param product -
+   *                array of DbRefEntry objects from which exon map in seqstring
+   *                is derived
    * @param viscontigs
    * @param gapCharacter
    * @param annotations
@@ -91,7 +112,8 @@ public class Dna
    */
   public static AlignmentI CdnaTranslate(SequenceI[] selection,
           String[] seqstring, DBRefEntry[] product, int viscontigs[],
-          char gapCharacter, AlignmentAnnotation[] annotations, int aWidth, Alignment dataset)
+          char gapCharacter, AlignmentAnnotation[] annotations, int aWidth,
+          Alignment dataset)
   {
     AlignedCodonFrame codons = new AlignedCodonFrame(aWidth); // stores hash of
     // subsequent
@@ -104,12 +126,14 @@ public class Dna
     for (s = 0; s < sSize; s++)
     {
       SequenceI newseq = translateCodingRegion(selection[s], seqstring[s],
-              viscontigs, codons, gapCharacter, (product!=null) ? product[s] : null); // possibly anonymous product
+              viscontigs, codons, gapCharacter,
+              (product != null) ? product[s] : null); // possibly anonymous
+                                                      // product
       if (newseq != null)
       {
         pepseqs.addElement(newseq);
         SequenceI ds = newseq;
-        while (ds.getDatasetSequence()!=null)
+        while (ds.getDatasetSequence() != null)
         {
           ds = ds.getDatasetSequence();
         }
@@ -127,31 +151,36 @@ public class Dna
     al.addCodonFrame(codons);
     return al;
   }
+
   /**
-   * fake the collection of DbRefs with associated exon mappings to identify
-   * if a translation would generate distinct product in the currently selected region.
+   * fake the collection of DbRefs with associated exon mappings to identify if
+   * a translation would generate distinct product in the currently selected
+   * region.
+   * 
    * @param selection
    * @param viscontigs
    * @return
    */
-  public static boolean canTranslate(SequenceI[] selection, int viscontigs[])
+  public static boolean canTranslate(SequenceI[] selection,
+          int viscontigs[])
   {
-    for (int gd=0; gd<selection.length; gd++)
+    for (int gd = 0; gd < selection.length; gd++)
     {
       SequenceI dna = selection[gd];
       jalview.datamodel.DBRefEntry[] dnarefs = jalview.util.DBRefUtils
-      .selectRefs(dna.getDBRef(),
-              jalview.datamodel.DBRefSource.DNACODINGDBS);
+              .selectRefs(dna.getDBRef(),
+                      jalview.datamodel.DBRefSource.DNACODINGDBS);
       if (dnarefs != null)
       {
         // intersect with pep
         // intersect with pep
         Vector mappedrefs = new Vector();
-        DBRefEntry[] refs=dna.getDBRef();
-        for (int d=0; d<refs.length; d++)
+        DBRefEntry[] refs = dna.getDBRef();
+        for (int d = 0; d < refs.length; d++)
         {
-          if (refs[d].getMap()!=null && refs[d].getMap().getMap()!=null && refs[d].getMap().getMap().getFromRatio()==3
-                  && refs[d].getMap().getMap().getToRatio()==1)
+          if (refs[d].getMap() != null && refs[d].getMap().getMap() != null
+                  && refs[d].getMap().getMap().getFromRatio() == 3
+                  && refs[d].getMap().getMap().getToRatio() == 1)
           {
             mappedrefs.addElement(refs[d]); // add translated protein maps
           }
@@ -163,10 +192,12 @@ public class Dna
           Mapping mp = dnarefs[d].getMap();
           if (mp != null)
           {
-            for (int vc=0; vc<viscontigs.length; vc+=2)
+            for (int vc = 0; vc < viscontigs.length; vc += 2)
             {
-              int[] mpr=mp.locateMappedRange(viscontigs[vc], viscontigs[vc+1]);
-              if (mpr!=null) {
+              int[] mpr = mp.locateMappedRange(viscontigs[vc],
+                      viscontigs[vc + 1]);
+              if (mpr != null)
+              {
                 return true;
               }
             }
@@ -176,12 +207,15 @@ public class Dna
     }
     return false;
   }
+
   /**
    * generate a set of translated protein products from annotated sequenceI
+   * 
    * @param selection
    * @param viscontigs
    * @param gapCharacter
-   * @param dataset destination dataset for translated sequences
+   * @param dataset
+   *                destination dataset for translated sequences
    * @param annotations
    * @param aWidth
    * @return
@@ -189,25 +223,26 @@ public class Dna
   public static AlignmentI CdnaTranslate(SequenceI[] selection,
           int viscontigs[], char gapCharacter, Alignment dataset)
   {
-    int alwidth=0;
-    Vector cdnasqs=new Vector();
-    Vector cdnasqi=new Vector();
-    Vector cdnaprod=new Vector();
-    for (int gd=0; gd<selection.length; gd++)
+    int alwidth = 0;
+    Vector cdnasqs = new Vector();
+    Vector cdnasqi = new Vector();
+    Vector cdnaprod = new Vector();
+    for (int gd = 0; gd < selection.length; gd++)
     {
       SequenceI dna = selection[gd];
       jalview.datamodel.DBRefEntry[] dnarefs = jalview.util.DBRefUtils
-      .selectRefs(dna.getDBRef(),
-              jalview.datamodel.DBRefSource.DNACODINGDBS);
+              .selectRefs(dna.getDBRef(),
+                      jalview.datamodel.DBRefSource.DNACODINGDBS);
       if (dnarefs != null)
       {
         // intersect with pep
         Vector mappedrefs = new Vector();
-        DBRefEntry[] refs=dna.getDBRef();
-        for (int d=0; d<refs.length; d++)
+        DBRefEntry[] refs = dna.getDBRef();
+        for (int d = 0; d < refs.length; d++)
         {
-          if (refs[d].getMap()!=null && refs[d].getMap().getMap()!=null && refs[d].getMap().getMap().getFromRatio()==3
-                  && refs[d].getMap().getMap().getToRatio()==1)
+          if (refs[d].getMap() != null && refs[d].getMap().getMap() != null
+                  && refs[d].getMap().getMap().getFromRatio() == 3
+                  && refs[d].getMap().getMap().getToRatio() == 1)
           {
             mappedrefs.addElement(refs[d]); // add translated protein maps
           }
@@ -217,13 +252,13 @@ public class Dna
         for (int d = 0; d < dnarefs.length; d++)
         {
           Mapping mp = dnarefs[d].getMap();
-          StringBuffer sqstr=new StringBuffer();
+          StringBuffer sqstr = new StringBuffer();
           if (mp != null)
           {
             Mapping intersect = mp.intersectVisContigs(viscontigs);
             // generate seqstring for this sequence based on mapping
-            
-            if (sqstr.length()>alwidth)
+
+            if (sqstr.length() > alwidth)
               alwidth = sqstr.length();
             cdnasqs.addElement(sqstr.toString());
             cdnasqi.addElement(dna);
@@ -237,7 +272,8 @@ public class Dna
       cdnasqs.copyInto(xons);
       cdnaprod.copyInto(prods);
       cdnasqi.copyInto(cdna);
-      return CdnaTranslate(cdna, xons, prods, viscontigs, gapCharacter, null, alwidth, dataset);
+      return CdnaTranslate(cdna, xons, prods, viscontigs, gapCharacter,
+              null, alwidth, dataset);
     }
     return null;
   }
@@ -282,7 +318,8 @@ public class Dna
             if (codons.codons[a] != null
                     && codons.codons[a][0] == (codons.codons[a][2] - 2))
             {
-              anots[a] = getCodonAnnotation(codons.codons[a], annotations[i].annotations);
+              anots[a] = getCodonAnnotation(codons.codons[a],
+                      annotations[i].annotations);
             }
           }
         }
@@ -292,9 +329,10 @@ public class Dna
         aa.graph = annotations[i].graph;
         aa.graphGroup = annotations[i].graphGroup;
         aa.graphHeight = annotations[i].graphHeight;
-        if (annotations[i].getThreshold()!=null)
+        if (annotations[i].getThreshold() != null)
         {
-          aa.setThreshold(new jalview.datamodel.GraphLine(annotations[i].getThreshold()));        
+          aa.setThreshold(new jalview.datamodel.GraphLine(annotations[i]
+                  .getThreshold()));
         }
         if (annotations[i].hasScore)
         {
@@ -321,13 +359,14 @@ public class Dna
     }
   }
 
-  private static Annotation getCodonAnnotation(int[] is, Annotation[] annotations)
-  { 
+  private static Annotation getCodonAnnotation(int[] is,
+          Annotation[] annotations)
+  {
     // Have a look at all the codon positions for annotation and put the first
     // one found into the translated annotation pos.
-    for (int p=0; p<3; p++)
+    for (int p = 0; p < 3; p++)
     {
-      if (annotations[is[p]]!=null)
+      if (annotations[is[p]] != null)
       {
         return new Annotation(annotations[is[p]]);
       }
@@ -338,10 +377,15 @@ public class Dna
   /**
    * Translate a na sequence
    * 
-   * @param selection sequence displayed under viscontigs visible columns
-   * @param seqstring ORF read in some global alignment reference frame
-   * @param viscontigs mapping from global reference frame to visible seqstring ORF read
-   * @param codons Definition of global ORF alignment reference frame
+   * @param selection
+   *                sequence displayed under viscontigs visible columns
+   * @param seqstring
+   *                ORF read in some global alignment reference frame
+   * @param viscontigs
+   *                mapping from global reference frame to visible seqstring ORF
+   *                read
+   * @param codons
+   *                Definition of global ORF alignment reference frame
    * @param gapCharacter
    * @param newSeq
    * @return sequence ready to be added to alignment.
@@ -350,22 +394,25 @@ public class Dna
           String seqstring, int[] viscontigs, AlignedCodonFrame codons,
           char gapCharacter, DBRefEntry product)
   {
-    Vector skip=new Vector();
-    int skipint[]=null;
+    Vector skip = new Vector();
+    int skipint[] = null;
     ShiftList vismapping = new ShiftList(); // map from viscontigs to seqstring
     // intervals
     int vc, scontigs[] = new int[viscontigs.length];
     int npos = 0;
     for (vc = 0; vc < viscontigs.length; vc += 2)
     {
-      if (vc==0) {
-      vismapping.addShift(npos, viscontigs[vc]);
-      } else {
+      if (vc == 0)
+      {
+        vismapping.addShift(npos, viscontigs[vc]);
+      }
+      else
+      {
         // hidden region
-        vismapping.addShift(npos, viscontigs[vc]-viscontigs[vc-1]+1);
+        vismapping.addShift(npos, viscontigs[vc] - viscontigs[vc - 1] + 1);
       }
       scontigs[vc] = viscontigs[vc];
-      scontigs[vc + 1] = viscontigs[vc+1];
+      scontigs[vc + 1] = viscontigs[vc + 1];
     }
 
     StringBuffer protein = new StringBuffer();
@@ -389,37 +436,42 @@ public class Dna
         if (aa == null)
         {
           aa = String.valueOf(gapCharacter);
-          if (skipint==null)
+          if (skipint == null)
           {
-            skipint = new int[] { cdp[0],cdp[2] };
+            skipint = new int[]
+            { cdp[0], cdp[2] };
           }
           skipint[1] = cdp[2];
-        } else {
-          if (skipint!=null)
+        }
+        else
+        {
+          if (skipint != null)
           {
             // edit scontigs
             skipint[0] = vismapping.shift(skipint[0]);
             skipint[1] = vismapping.shift(skipint[1]);
-            for (vc=0; vc<scontigs.length; vc+=2)
+            for (vc = 0; vc < scontigs.length; vc += 2)
             {
-              if (scontigs[vc+1]<skipint[0])
+              if (scontigs[vc + 1] < skipint[0])
               {
                 continue;
               }
-              if (scontigs[vc]<=skipint[0])
+              if (scontigs[vc] <= skipint[0])
               {
-               if (skipint[0]==scontigs[vc])
-               {
-                 
-               } else {
-                 int[] t = new int[scontigs.length+2];
-                 System.arraycopy(scontigs, 0, t, 0, vc-1);
-                 // scontigs[vc]; //
-               }
+                if (skipint[0] == scontigs[vc])
+                {
+
+                }
+                else
+                {
+                  int[] t = new int[scontigs.length + 2];
+                  System.arraycopy(scontigs, 0, t, 0, vc - 1);
+                  // scontigs[vc]; //
+                }
               }
             }
             skip.addElement(skipint);
-            skipint=null;
+            skipint = null;
           }
           if (aa.equals("STOP"))
           {
@@ -446,8 +498,8 @@ public class Dna
             // with a gap
             aa = "" + gapCharacter + aa;
             aspos++;
-            //if (aspos >= codons.aaWidth)
-            //  codons.aaWidth = aspos + 1;
+            // if (aspos >= codons.aaWidth)
+            // codons.aaWidth = aspos + 1;
             break; // check the next position for alignment
           case 0:
             // codon aligns at aspos position.
@@ -515,8 +567,7 @@ public class Dna
         for (vc = 0; vc < scontigs.length; vc += 2)
         {
           scontigs[vc] = selection.findPosition(scontigs[vc]); // not from 1!
-          scontigs[vc + 1] = selection
-                  .findPosition(scontigs[vc + 1]); // exclusive
+          scontigs[vc + 1] = selection.findPosition(scontigs[vc + 1]); // exclusive
           if (scontigs[vc + 1] == selection.getEnd())
             break;
         }
@@ -528,62 +579,35 @@ public class Dna
           scontigs = t;
         }
         /*
-         * delete intervals in scontigs which are not translated.
-         * 1. map skip into sequence position intervals
-         * 2. truncate existing ranges and add new ranges to exclude untranslated regions.
-        if (skip.size()>0)
-        {
-          Vector narange = new Vector();
-          for (vc=0; vc<scontigs.length; vc++)
-          {
-            narange.addElement(new int[] {scontigs[vc]});
-          }
-          int sint=0,iv[];
-          vc = 0;
-          while (sint<skip.size())
-          {
-            skipint = (int[]) skip.elementAt(sint);
-            do {
-              iv = (int[]) narange.elementAt(vc);
-              if (iv[0]>=skipint[0] && iv[0]<=skipint[1])
-              {
-                if (iv[0]==skipint[0])
-                {
-                  // delete beginning of range
-                } else {
-                  // truncate range and create new one if necessary
-                  iv = (int[]) narange.elementAt(vc+1);
-                  if (iv[0]<=skipint[1])
-                  {
-                    // truncate range
-                    iv[0] = skipint[1];
-                  } else {
-                    
-                  }
-                }
-              } else
-                if (iv[0]<skipint[0])
-                {
-                  iv = (int[]) narange.elementAt(vc+1);
-                }
-            } while (iv[0])
-          }
-        }*/
+         * delete intervals in scontigs which are not translated. 1. map skip
+         * into sequence position intervals 2. truncate existing ranges and add
+         * new ranges to exclude untranslated regions. if (skip.size()>0) {
+         * Vector narange = new Vector(); for (vc=0; vc<scontigs.length; vc++) {
+         * narange.addElement(new int[] {scontigs[vc]}); } int sint=0,iv[]; vc =
+         * 0; while (sint<skip.size()) { skipint = (int[])
+         * skip.elementAt(sint); do { iv = (int[]) narange.elementAt(vc); if
+         * (iv[0]>=skipint[0] && iv[0]<=skipint[1]) { if (iv[0]==skipint[0]) { //
+         * delete beginning of range } else { // truncate range and create new
+         * one if necessary iv = (int[]) narange.elementAt(vc+1); if (iv[0]<=skipint[1]) { //
+         * truncate range iv[0] = skipint[1]; } else {
+         *  } } } else if (iv[0]<skipint[0]) { iv = (int[])
+         * narange.elementAt(vc+1); } } while (iv[0]) } }
+         */
         MapList map = new MapList(scontigs, new int[]
-                                                    { 1, resSize }, 3, 1);
-        
+        { 1, resSize }, 3, 1);
+
         // update newseq as if it was generated as mapping from product
-        
+
         if (product != null)
         {
           newseq.setName(product.getSource() + "|"
                   + product.getAccessionId());
           if (product.getMap() != null)
           {
-            //Mapping mp = product.getMap();
-            //newseq.setStart(mp.getPosition(scontigs[0]));
-            //newseq.setEnd(mp
-            //        .getPosition(scontigs[scontigs.length - 1]));
+            // Mapping mp = product.getMap();
+            // newseq.setStart(mp.getPosition(scontigs[0]));
+            // newseq.setEnd(mp
+            // .getPosition(scontigs[scontigs.length - 1]));
           }
         }
         transferCodedFeatures(selection, newseq, map, null, null);
@@ -611,10 +635,10 @@ public class Dna
    * @param pep
    * @param map
    * @param featureTypes
-   *          hash who's keys are the displayed feature type strings
+   *                hash who's keys are the displayed feature type strings
    * @param featureGroups
-   *          hash where keys are feature groups and values are Boolean objects
-   *          indicating if they are displayed.
+   *                hash where keys are feature groups and values are Boolean
+   *                objects indicating if they are displayed.
    */
   private static void transferCodedFeatures(SequenceI dna, SequenceI pep,
           MapList map, Hashtable featureTypes, Hashtable featureGroups)
diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index 5280467..756897c 100644
--- a/src/jalview/analysis/Finder.java
+++ b/src/jalview/analysis/Finder.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.analysis;
 
 import java.util.*;
@@ -10,16 +28,24 @@ public class Finder
    * Implements the search algorithms for the Find dialog box.
    */
   SearchResults searchResults;
+
   AlignmentI alignment;
+
   jalview.datamodel.SequenceGroup selection = null;
+
   Vector idMatch = null;
+
   boolean caseSensitive = false;
+
   boolean findAll = false;
+
   com.stevesoft.pat.Regex regex = null;
+
   /**
    * hold's last-searched position between calles to find(false)
    */
   int seqIndex = 0, resIndex = 0;
+
   public Finder(AlignmentI alignment, SequenceGroup selection)
   {
     this.alignment = alignment;
@@ -27,7 +53,7 @@ public class Finder
   }
 
   public Finder(AlignmentI alignment, SequenceGroup selectionGroup,
-                int seqIndex, int resIndex)
+          int seqIndex, int resIndex)
   {
     this(alignment, selectionGroup);
     this.seqIndex = seqIndex;
@@ -48,7 +74,7 @@ public class Finder
     String item = null;
     boolean found = false;
 
-    ////// is the searchString a residue number?
+    // //// is the searchString a residue number?
     try
     {
       int res = Integer.parseInt(searchString);
@@ -64,19 +90,18 @@ public class Finder
 
       searchResults.addResult(seq, res, res);
       hasResults = true;
-    }
-    catch (NumberFormatException ex)
+    } catch (NumberFormatException ex)
     {
     }
 
-    ///////////////////////////////////////////////
+    // /////////////////////////////////////////////
 
     int end = alignment.getHeight();
 
     if (selection != null)
     {
-      if ( (selection.getSize() < 1) ||
-          ( (selection.getEndRes() - selection.getStartRes()) < 2))
+      if ((selection.getSize() < 1)
+              || ((selection.getEndRes() - selection.getStartRes()) < 2))
       {
         selection = null;
       }
@@ -86,7 +111,8 @@ public class Finder
     {
       seq = (Sequence) alignment.getSequenceAt(seqIndex);
 
-      if ( (selection != null) && !selection.getSequences(null).contains(seq))
+      if ((selection != null)
+              && !selection.getSequences(null).contains(seq))
       {
         seqIndex++;
         resIndex = 0;
@@ -95,16 +121,16 @@ public class Finder
       }
 
       item = seq.getSequenceAsString();
-      if(!caseSensitive)
+      if (!caseSensitive)
         item = item.toUpperCase();
 
-      if ( (selection != null) &&
-          (selection.getEndRes() < alignment.getWidth() - 1))
+      if ((selection != null)
+              && (selection.getEndRes() < alignment.getWidth() - 1))
       {
         item = item.substring(0, selection.getEndRes() + 1);
       }
 
-      ///Shall we ignore gaps???? - JBPNote: Add Flag for forcing this or not
+      // /Shall we ignore gaps???? - JBPNote: Add Flag for forcing this or not
       StringBuffer noGapsSB = new StringBuffer();
       int insertCount = 0;
       Vector spaces = new Vector();
@@ -131,22 +157,21 @@ public class Finder
         {
           resIndex = regex.matchedFrom();
 
-          if ( (selection != null) &&
-              ( (resIndex +
-                 Integer.parseInt(spaces.elementAt(resIndex).toString())) <
-               selection.getStartRes()))
+          if ((selection != null)
+                  && ((resIndex + Integer.parseInt(spaces.elementAt(
+                          resIndex).toString())) < selection.getStartRes()))
           {
             continue;
           }
 
-          int sres = seq.findPosition(resIndex +
-                                      Integer.parseInt(spaces.elementAt(
-              resIndex)
-              .toString()));
-          int eres = seq.findPosition(regex.matchedTo() - 1 +
-                                      Integer.parseInt(spaces.elementAt(regex.
-              matchedTo() -
-              1).toString()));
+          int sres = seq
+                  .findPosition(resIndex
+                          + Integer.parseInt(spaces.elementAt(resIndex)
+                                  .toString()));
+          int eres = seq.findPosition(regex.matchedTo()
+                  - 1
+                  + Integer.parseInt(spaces
+                          .elementAt(regex.matchedTo() - 1).toString()));
 
           searchResults.addResult(seq, sres, eres);
           hasResults = true;
@@ -194,7 +219,8 @@ public class Finder
   }
 
   /**
-   * @param alignment the alignment to set
+   * @param alignment
+   *                the alignment to set
    */
   public void setAlignment(AlignmentI alignment)
   {
@@ -210,7 +236,8 @@ public class Finder
   }
 
   /**
-   * @param caseSensitive the caseSensitive to set
+   * @param caseSensitive
+   *                the caseSensitive to set
    */
   public void setCaseSensitive(boolean caseSensitive)
   {
@@ -226,7 +253,8 @@ public class Finder
   }
 
   /**
-   * @param findAll the findAll to set
+   * @param findAll
+   *                the findAll to set
    */
   public void setFindAll(boolean findAll)
   {
@@ -242,7 +270,8 @@ public class Finder
   }
 
   /**
-   * @param selection the selection to set
+   * @param selection
+   *                the selection to set
    */
   public void setSelection(jalview.datamodel.SequenceGroup selection)
   {
@@ -282,7 +311,8 @@ public class Finder
   }
 
   /**
-   * @param resIndex the resIndex to set
+   * @param resIndex
+   *                the resIndex to set
    */
   public void setResIndex(int resIndex)
   {
@@ -298,7 +328,8 @@ public class Finder
   }
 
   /**
-   * @param seqIndex the seqIndex to set
+   * @param seqIndex
+   *                the seqIndex to set
    */
   public void setSeqIndex(int seqIndex)
   {
diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 3569be1..fe0df1a 100755
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -27,40 +27,60 @@ import jalview.util.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
 public class NJTree
 {
   Vector cluster;
+
   SequenceI[] sequence;
 
-  //SequenceData is a string representation of what the user
-  //sees. The display may contain hidden columns.
+  // SequenceData is a string representation of what the user
+  // sees. The display may contain hidden columns.
   public AlignmentView seqData = null;
 
   int[] done;
+
   int noseqs;
+
   int noClus;
+
   float[][] distance;
+
   int mini;
+
   int minj;
+
   float ri;
+
   float rj;
+
   Vector groups = new Vector();
+
   SequenceNode maxdist;
+
   SequenceNode top;
+
   float maxDistValue;
+
   float maxheight;
+
   int ycount;
+
   Vector node;
+
   String type;
+
   String pwtype;
+
   Object found = null;
+
   Object leaves = null;
 
   boolean hasDistances = true; // normal case for jalview trees
+
   boolean hasBootstrap = false; // normal case for jalview trees
 
   private boolean hasRootDistance = true;
@@ -68,9 +88,13 @@ public class NJTree
   /**
    * Create a new NJTree object with leaves associated with sequences in seqs,
    * and original alignment data represented by Cigar strings.
-   * @param seqs SequenceI[]
-   * @param odata Cigar[]
-   * @param treefile NewickFile
+   * 
+   * @param seqs
+   *                SequenceI[]
+   * @param odata
+   *                Cigar[]
+   * @param treefile
+   *                NewickFile
    */
   public NJTree(SequenceI[] seqs, AlignmentView odata, NewickFile treefile)
   {
@@ -80,20 +104,20 @@ public class NJTree
       seqData = odata;
     }
     /*
-           sequenceString = new String[odata.length];
-           char gapChar = jalview.util.Comparison.GapChars.charAt(0);
-           for (int i = 0; i < odata.length; i++)
-           {
-      SequenceI oseq_aligned = odata[i].getSeq(gapChar);
-        sequenceString[i] = oseq_aligned.getSequence();
-           } */
+     * sequenceString = new String[odata.length]; char gapChar =
+     * jalview.util.Comparison.GapChars.charAt(0); for (int i = 0; i <
+     * odata.length; i++) { SequenceI oseq_aligned = odata[i].getSeq(gapChar);
+     * sequenceString[i] = oseq_aligned.getSequence(); }
+     */
   }
 
   /**
    * Creates a new NJTree object from a tree from an external source
-   *
-   * @param seqs SequenceI which should be associated with leafs of treefile
-   * @param treefile A parsed tree
+   * 
+   * @param seqs
+   *                SequenceI which should be associated with leafs of treefile
+   * @param treefile
+   *                A parsed tree
    */
   public NJTree(SequenceI[] seqs, NewickFile treefile)
   {
@@ -101,17 +125,11 @@ public class NJTree
     top = treefile.getTree();
 
     /**
-     * There is no dependent alignment to be recovered from an
-     * imported tree.
-     *
-             if (sequenceString == null)
-             {
-      sequenceString = new String[seqs.length];
-      for (int i = 0; i < seqs.length; i++)
-      {
-        sequenceString[i] = seqs[i].getSequence();
-      }
-             }
+     * There is no dependent alignment to be recovered from an imported tree.
+     * 
+     * if (sequenceString == null) { sequenceString = new String[seqs.length];
+     * for (int i = 0; i < seqs.length; i++) { sequenceString[i] =
+     * seqs[i].getSequence(); } }
      */
 
     hasDistances = treefile.HasDistances();
@@ -150,8 +168,9 @@ public class NJTree
         if (one2many.contains(nam))
         {
           countOne2Many++;
-          //  if (jalview.bin.Cache.log.isDebugEnabled())
-          //    jalview.bin.Cache.log.debug("One 2 many relationship for "+nam.getName());
+          // if (jalview.bin.Cache.log.isDebugEnabled())
+          // jalview.bin.Cache.log.debug("One 2 many relationship for
+          // "+nam.getName());
         }
         else
         {
@@ -165,26 +184,30 @@ public class NJTree
         j.setPlaceholder(true);
       }
     }
-    //  if (jalview.bin.Cache.log.isDebugEnabled() && countOne2Many>0) {
-    //    jalview.bin.Cache.log.debug("There were "+countOne2Many+" alignment sequence ids (out of "+one2many.size()+" unique ids) linked to two or more leaves.");
-    //  }
-    //  one2many.clear();
+    // if (jalview.bin.Cache.log.isDebugEnabled() && countOne2Many>0) {
+    // jalview.bin.Cache.log.debug("There were "+countOne2Many+" alignment
+    // sequence ids (out of "+one2many.size()+" unique ids) linked to two or
+    // more leaves.");
+    // }
+    // one2many.clear();
   }
 
   /**
    * Creates a new NJTree object.
-   *
-   * @param sequence DOCUMENT ME!
-   * @param type DOCUMENT ME!
-   * @param pwtype DOCUMENT ME!
-   * @param start DOCUMENT ME!
-   * @param end DOCUMENT ME!
+   * 
+   * @param sequence
+   *                DOCUMENT ME!
+   * @param type
+   *                DOCUMENT ME!
+   * @param pwtype
+   *                DOCUMENT ME!
+   * @param start
+   *                DOCUMENT ME!
+   * @param end
+   *                DOCUMENT ME!
    */
-  public NJTree(SequenceI[] sequence,
-                AlignmentView seqData,
-                String type,
-                String pwtype,
-                int start, int end)
+  public NJTree(SequenceI[] sequence, AlignmentView seqData, String type,
+          String pwtype, int start, int end)
   {
     this.sequence = sequence;
     this.node = new Vector();
@@ -206,12 +229,12 @@ public class NJTree
       this.seqData = new AlignmentView(sdata, start);
     }
 
-    if (! (type.equals("NJ")))
+    if (!(type.equals("NJ")))
     {
       type = "AV";
     }
 
-    if (! (pwtype.equals("PID")))
+    if (!(pwtype.equals("PID")))
     {
       if (ResidueProperties.getScoreMatrix(pwtype) == null)
       {
@@ -223,7 +246,7 @@ public class NJTree
 
     done = new int[sequence.length];
 
-    while ( (i < sequence.length) && (sequence[i] != null))
+    while ((i < sequence.length) && (sequence[i] != null))
     {
       done[i] = 0;
       i++;
@@ -231,8 +254,8 @@ public class NJTree
 
     noseqs = i++;
 
-    distance = findDistances(this.seqData.getSequenceStrings(Comparison.
-        GapChars.charAt(0)));
+    distance = findDistances(this.seqData
+            .getSequenceStrings(Comparison.GapChars.charAt(0)));
 
     makeLeaves();
 
@@ -243,7 +266,7 @@ public class NJTree
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public String toString()
@@ -254,10 +277,11 @@ public class NJTree
   }
 
   /**
-   *
+   * 
    * used when the alignment associated to a tree has changed.
-   *
-   * @param alignment Vector
+   * 
+   * @param alignment
+   *                Vector
    */
   public void UpdatePlaceHolders(Vector alignment)
   {
@@ -297,8 +321,10 @@ public class NJTree
         {
           if (!leaf.isPlaceholder())
           {
-            // remapping the node to a new sequenceI - should remove any refs to old one.
-            // TODO - make many sequenceI to one leaf mappings possible! (JBPNote)
+            // remapping the node to a new sequenceI - should remove any refs to
+            // old one.
+            // TODO - make many sequenceI to one leaf mappings possible!
+            // (JBPNote)
           }
           leaf.setPlaceholder(false);
           leaf.setElement(nam);
@@ -308,7 +334,8 @@ public class NJTree
           if (!leaf.isPlaceholder())
           {
             // Construct a new placeholder sequence object for this leaf
-            leaf.setElement(new Sequence(leaf.getName(), "THISISAPLACEHLDER"));
+            leaf.setElement(new Sequence(leaf.getName(),
+                    "THISISAPLACEHLDER"));
           }
           leaf.setPlaceholder(true);
 
@@ -374,29 +401,31 @@ public class NJTree
 
   /**
    * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
-   * @param j DOCUMENT ME!
-   *
+   * 
+   * @param i
+   *                DOCUMENT ME!
+   * @param j
+   *                DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   public Cluster joinClusters(int i, int j)
   {
     float dist = distance[i][j];
 
-    int noi = ( (Cluster) cluster.elementAt(i)).value.length;
-    int noj = ( (Cluster) cluster.elementAt(j)).value.length;
+    int noi = ((Cluster) cluster.elementAt(i)).value.length;
+    int noj = ((Cluster) cluster.elementAt(j)).value.length;
 
     int[] value = new int[noi + noj];
 
     for (int ii = 0; ii < noi; ii++)
     {
-      value[ii] = ( (Cluster) cluster.elementAt(i)).value[ii];
+      value[ii] = ((Cluster) cluster.elementAt(i)).value[ii];
     }
 
     for (int ii = noi; ii < (noi + noj); ii++)
     {
-      value[ii] = ( (Cluster) cluster.elementAt(j)).value[ii - noi];
+      value[ii] = ((Cluster) cluster.elementAt(j)).value[ii - noi];
     }
 
     Cluster c = new Cluster(value);
@@ -415,8 +444,8 @@ public class NJTree
 
     SequenceNode sn = new SequenceNode();
 
-    sn.setLeft( (SequenceNode) (node.elementAt(i)));
-    sn.setRight( (SequenceNode) (node.elementAt(j)));
+    sn.setLeft((SequenceNode) (node.elementAt(i)));
+    sn.setRight((SequenceNode) (node.elementAt(j)));
 
     SequenceNode tmpi = (SequenceNode) (node.elementAt(i));
     SequenceNode tmpj = (SequenceNode) (node.elementAt(j));
@@ -440,16 +469,19 @@ public class NJTree
 
   /**
    * DOCUMENT ME!
-   *
-   * @param tmpi DOCUMENT ME!
-   * @param tmpj DOCUMENT ME!
-   * @param dist DOCUMENT ME!
+   * 
+   * @param tmpi
+   *                DOCUMENT ME!
+   * @param tmpj
+   *                DOCUMENT ME!
+   * @param dist
+   *                DOCUMENT ME!
    */
   public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj,
-                                 float dist)
+          float dist)
   {
 
-    tmpi.dist = ( (dist + ri) - rj) / 2;
+    tmpi.dist = ((dist + ri) - rj) / 2;
     tmpj.dist = (dist - tmpi.dist);
 
     if (tmpi.dist < 0)
@@ -465,13 +497,16 @@ public class NJTree
 
   /**
    * DOCUMENT ME!
-   *
-   * @param tmpi DOCUMENT ME!
-   * @param tmpj DOCUMENT ME!
-   * @param dist DOCUMENT ME!
+   * 
+   * @param tmpi
+   *                DOCUMENT ME!
+   * @param tmpj
+   *                DOCUMENT ME!
+   * @param dist
+   *                DOCUMENT ME!
    */
   public void findNewDistances(SequenceNode tmpi, SequenceNode tmpj,
-                               float dist)
+          float dist)
   {
     float ih = 0;
     float jh = 0;
@@ -491,30 +526,32 @@ public class NJTree
       snj = (SequenceNode) snj.left();
     }
 
-    tmpi.dist = ( (dist / 2) - ih);
-    tmpj.dist = ( (dist / 2) - jh);
+    tmpi.dist = ((dist / 2) - ih);
+    tmpj.dist = ((dist / 2) - jh);
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
-   * @param j DOCUMENT ME!
+   * 
+   * @param i
+   *                DOCUMENT ME!
+   * @param j
+   *                DOCUMENT ME!
    */
   public void findClusterDistance(int i, int j)
   {
-    int noi = ( (Cluster) cluster.elementAt(i)).value.length;
-    int noj = ( (Cluster) cluster.elementAt(j)).value.length;
+    int noi = ((Cluster) cluster.elementAt(i)).value.length;
+    int noj = ((Cluster) cluster.elementAt(j)).value.length;
 
     // New distances from cluster to others
     float[] newdist = new float[noseqs];
 
     for (int l = 0; l < noseqs; l++)
     {
-      if ( (l != i) && (l != j))
+      if ((l != i) && (l != j))
       {
-        newdist[l] = ( (distance[i][l] * noi) + (distance[j][l] * noj)) / (noi +
-            noj);
+        newdist[l] = ((distance[i][l] * noi) + (distance[j][l] * noj))
+                / (noi + noj);
       }
       else
       {
@@ -531,9 +568,11 @@ public class NJTree
 
   /**
    * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
-   * @param j DOCUMENT ME!
+   * 
+   * @param i
+   *                DOCUMENT ME!
+   * @param j
+   *                DOCUMENT ME!
    */
   public void findClusterNJDistance(int i, int j)
   {
@@ -543,10 +582,9 @@ public class NJTree
 
     for (int l = 0; l < noseqs; l++)
     {
-      if ( (l != i) && (l != j))
+      if ((l != i) && (l != j))
       {
-        newdist[l] = ( (distance[i][l] + distance[j][l]) -
-                      distance[i][j]) / 2;
+        newdist[l] = ((distance[i][l] + distance[j][l]) - distance[i][j]) / 2;
       }
       else
       {
@@ -563,10 +601,12 @@ public class NJTree
 
   /**
    * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
-   * @param j DOCUMENT ME!
-   *
+   * 
+   * @param i
+   *                DOCUMENT ME!
+   * @param j
+   *                DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   public float findr(int i, int j)
@@ -575,7 +615,7 @@ public class NJTree
 
     for (int k = 0; k < noseqs; k++)
     {
-      if ( (k != i) && (k != j) && (done[k] != 1))
+      if ((k != i) && (k != j) && (done[k] != 1))
       {
         tmp = tmp + distance[i][k];
       }
@@ -591,7 +631,7 @@ public class NJTree
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public float findMinNJDistance()
@@ -602,7 +642,7 @@ public class NJTree
     {
       for (int j = i + 1; j < noseqs; j++)
       {
-        if ( (done[i] != 1) && (done[j] != 1))
+        if ((done[i] != 1) && (done[j] != 1))
         {
           float tmp = distance[i][j] - (findr(i, j) + findr(j, i));
 
@@ -622,7 +662,7 @@ public class NJTree
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public float findMinDistance()
@@ -633,7 +673,7 @@ public class NJTree
     {
       for (int j = i + 1; j < noseqs; j++)
       {
-        if ( (done[i] != 1) && (done[j] != 1))
+        if ((done[i] != 1) && (done[j] != 1))
         {
           if (distance[i][j] < min)
           {
@@ -651,7 +691,7 @@ public class NJTree
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public float[][] findDistances(String[] sequenceString)
@@ -670,8 +710,8 @@ public class NJTree
           }
           else
           {
-            distance[i][j] = 100 -
-                Comparison.PID(sequenceString[i], sequenceString[j]);
+            distance[i][j] = 100 - Comparison.PID(sequenceString[i],
+                    sequenceString[j]);
 
             distance[j][i] = distance[i][j];
           }
@@ -698,10 +738,9 @@ public class NJTree
           {
             try
             {
-              score += pwmatrix.getPairwiseScore(sequenceString[i].charAt(k),
-                                                 sequenceString[j].charAt(k));
-            }
-            catch (Exception ex)
+              score += pwmatrix.getPairwiseScore(sequenceString[i]
+                      .charAt(k), sequenceString[j].charAt(k));
+            } catch (Exception ex)
             {
               System.err.println("err creating BLOSUM62 tree");
               ex.printStackTrace();
@@ -729,37 +768,20 @@ public class NJTree
     }
     return distance;
 
-    //   else
-    /*  else if (pwtype.equals("SW"))
-      {
-          float max = -1;
-
-          for (int i = 0; i < (noseqs - 1); i++)
-          {
-              for (int j = i; j < noseqs; j++)
-              {
-                  AlignSeq as = new AlignSeq(sequence[i], sequence[j], "pep");
-                  as.calcScoreMatrix();
-                  as.traceAlignment();
-                  as.printAlignment(System.out);
-                  distance[i][j] = (float) as.maxscore;
-
-                  if (max < distance[i][j])
-                  {
-                      max = distance[i][j];
-                  }
-              }
-          }
-
-          for (int i = 0; i < (noseqs - 1); i++)
-          {
-              for (int j = i; j < noseqs; j++)
-              {
-                  distance[i][j] = max - distance[i][j];
-                  distance[j][i] = distance[i][j];
-              }
-          }
-      }/*/
+    // else
+    /*
+     * else if (pwtype.equals("SW")) { float max = -1;
+     * 
+     * for (int i = 0; i < (noseqs - 1); i++) { for (int j = i; j < noseqs; j++) {
+     * AlignSeq as = new AlignSeq(sequence[i], sequence[j], "pep");
+     * as.calcScoreMatrix(); as.traceAlignment(); as.printAlignment(System.out);
+     * distance[i][j] = (float) as.maxscore;
+     * 
+     * if (max < distance[i][j]) { max = distance[i][j]; } } }
+     * 
+     * for (int i = 0; i < (noseqs - 1); i++) { for (int j = i; j < noseqs; j++) {
+     * distance[i][j] = max - distance[i][j]; distance[j][i] = distance[i][j]; } } }/
+     */
   }
 
   /**
@@ -787,20 +809,23 @@ public class NJTree
 
   /**
    * Search for leaf nodes.
-   *
-   * @param node root node to search from
-   * @param leaves Vector of leaves to add leaf node objects too.
-   *
+   * 
+   * @param node
+   *                root node to search from
+   * @param leaves
+   *                Vector of leaves to add leaf node objects too.
+   * 
    * @return Vector of leaf nodes on binary tree
    */
   public Vector findLeaves(SequenceNode node, Vector leaves)
-  { 
+  {
     if (node == null)
     {
       return leaves;
     }
 
-    if ( (node.left() == null) && (node.right() == null)) // Interior node detection
+    if ((node.left() == null) && (node.right() == null)) // Interior node
+                                                          // detection
     {
       leaves.addElement(node);
 
@@ -808,23 +833,25 @@ public class NJTree
     }
     else
     {
-/*  TODO: Identify internal nodes...    if (node.isSequenceLabel())
-      {
-        leaves.addElement(node);
-      }*/
-      findLeaves( (SequenceNode) node.left(), leaves);
-      findLeaves( (SequenceNode) node.right(), leaves);
+      /*
+       * TODO: Identify internal nodes... if (node.isSequenceLabel()) {
+       * leaves.addElement(node); }
+       */
+      findLeaves((SequenceNode) node.left(), leaves);
+      findLeaves((SequenceNode) node.right(), leaves);
     }
 
     return leaves;
   }
 
   /**
-   * Find the leaf node with a particular ycount 
-   *
-   * @param node initial point on tree to search from
-   * @param count value to search for
-   *
+   * Find the leaf node with a particular ycount
+   * 
+   * @param node
+   *                initial point on tree to search from
+   * @param count
+   *                value to search for
+   * 
    * @return null or the node with ycound=count
    */
   public Object findLeaf(SequenceNode node, int count)
@@ -834,8 +861,9 @@ public class NJTree
     return found;
   }
 
-  /*#see findLeaf(SequenceNode node, count)
-   *
+  /*
+   * #see findLeaf(SequenceNode node, count)
+   * 
    */
   public Object _findLeaf(SequenceNode node, int count)
   {
@@ -852,8 +880,8 @@ public class NJTree
     }
     else
     {
-      _findLeaf( (SequenceNode) node.left(), count);
-      _findLeaf( (SequenceNode) node.right(), count);
+      _findLeaf((SequenceNode) node.left(), count);
+      _findLeaf((SequenceNode) node.right(), count);
     }
 
     return found;
@@ -861,8 +889,9 @@ public class NJTree
 
   /**
    * printNode is mainly for debugging purposes.
-   *
-   * @param node SequenceNode
+   * 
+   * @param node
+   *                SequenceNode
    */
   public void printNode(SequenceNode node)
   {
@@ -871,25 +900,26 @@ public class NJTree
       return;
     }
 
-    if ( (node.left() == null) && (node.right() == null))
+    if ((node.left() == null) && (node.right() == null))
     {
-      System.out.println("Leaf = " +
-                         ( (SequenceI) node.element()).getName());
-      System.out.println("Dist " + ( (SequenceNode) node).dist);
+      System.out
+              .println("Leaf = " + ((SequenceI) node.element()).getName());
+      System.out.println("Dist " + ((SequenceNode) node).dist);
       System.out.println("Boot " + node.getBootstrap());
     }
     else
     {
-      System.out.println("Dist " + ( (SequenceNode) node).dist);
-      printNode( (SequenceNode) node.left());
-      printNode( (SequenceNode) node.right());
+      System.out.println("Dist " + ((SequenceNode) node).dist);
+      printNode((SequenceNode) node.left());
+      printNode((SequenceNode) node.right());
     }
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param node DOCUMENT ME!
+   * 
+   * @param node
+   *                DOCUMENT ME!
    */
   public void findMaxDist(SequenceNode node)
   {
@@ -898,9 +928,9 @@ public class NJTree
       return;
     }
 
-    if ( (node.left() == null) && (node.right() == null))
+    if ((node.left() == null) && (node.right() == null))
     {
-      float dist = ( (SequenceNode) node).dist;
+      float dist = ((SequenceNode) node).dist;
 
       if (dist > maxDistValue)
       {
@@ -910,14 +940,14 @@ public class NJTree
     }
     else
     {
-      findMaxDist( (SequenceNode) node.left());
-      findMaxDist( (SequenceNode) node.right());
+      findMaxDist((SequenceNode) node.left());
+      findMaxDist((SequenceNode) node.right());
     }
   }
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public Vector getGroups()
@@ -927,7 +957,7 @@ public class NJTree
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public float getMaxHeight()
@@ -937,9 +967,11 @@ public class NJTree
 
   /**
    * DOCUMENT ME!
-   *
-   * @param node DOCUMENT ME!
-   * @param threshold DOCUMENT ME!
+   * 
+   * @param node
+   *                DOCUMENT ME!
+   * @param threshold
+   *                DOCUMENT ME!
    */
   public void groupNodes(SequenceNode node, float threshold)
   {
@@ -948,22 +980,23 @@ public class NJTree
       return;
     }
 
-    if ( (node.height / maxheight) > threshold)
+    if ((node.height / maxheight) > threshold)
     {
       groups.addElement(node);
     }
     else
     {
-      groupNodes( (SequenceNode) node.left(), threshold);
-      groupNodes( (SequenceNode) node.right(), threshold);
+      groupNodes((SequenceNode) node.left(), threshold);
+      groupNodes((SequenceNode) node.right(), threshold);
     }
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param node DOCUMENT ME!
-   *
+   * 
+   * @param node
+   *                DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   public float findHeight(SequenceNode node)
@@ -973,9 +1006,9 @@ public class NJTree
       return maxheight;
     }
 
-    if ( (node.left() == null) && (node.right() == null))
+    if ((node.left() == null) && (node.right() == null))
     {
-      node.height = ( (SequenceNode) node.parent()).height + node.dist;
+      node.height = ((SequenceNode) node.parent()).height + node.dist;
 
       if (node.height > maxheight)
       {
@@ -990,8 +1023,7 @@ public class NJTree
     {
       if (node.parent() != null)
       {
-        node.height = ( (SequenceNode) node.parent()).height +
-            node.dist;
+        node.height = ((SequenceNode) node.parent()).height + node.dist;
       }
       else
       {
@@ -999,8 +1031,8 @@ public class NJTree
         node.height = (float) 0.0;
       }
 
-      maxheight = findHeight( (SequenceNode) (node.left()));
-      maxheight = findHeight( (SequenceNode) (node.right()));
+      maxheight = findHeight((SequenceNode) (node.left()));
+      maxheight = findHeight((SequenceNode) (node.right()));
     }
 
     return maxheight;
@@ -1008,7 +1040,7 @@ public class NJTree
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public SequenceNode reRoot()
@@ -1048,7 +1080,7 @@ public class NJTree
   }
 
   /**
-   *
+   * 
    * @return true if original sequence data can be recovered
    */
   public boolean hasOriginalSequenceData()
@@ -1057,9 +1089,9 @@ public class NJTree
   }
 
   /**
-   * Returns original alignment data used for calculation - or null where
-   * not available.
-   *
+   * Returns original alignment data used for calculation - or null where not
+   * available.
+   * 
    * @return null or cut'n'pasteable alignment
    */
   public String printOriginalSequenceData(char gapChar)
@@ -1073,8 +1105,8 @@ public class NJTree
     String[] seqdatas = seqData.getSequenceStrings(gapChar);
     for (int i = 0; i < seqdatas.length; i++)
     {
-      sb.append(new jalview.util.Format("%-" + 15 + "s").form(
-          sequence[i].getName()));
+      sb.append(new jalview.util.Format("%-" + 15 + "s").form(sequence[i]
+              .getName()));
       sb.append(" " + seqdatas[i] + "\n");
     }
     return sb.toString();
@@ -1082,8 +1114,9 @@ public class NJTree
 
   /**
    * DOCUMENT ME!
-   *
-   * @param node DOCUMENT ME!
+   * 
+   * @param node
+   *                DOCUMENT ME!
    */
   public void printN(SequenceNode node)
   {
@@ -1092,26 +1125,27 @@ public class NJTree
       return;
     }
 
-    if ( (node.left() != null) && (node.right() != null))
+    if ((node.left() != null) && (node.right() != null))
     {
-      printN( (SequenceNode) node.left());
-      printN( (SequenceNode) node.right());
+      printN((SequenceNode) node.left());
+      printN((SequenceNode) node.right());
     }
     else
     {
-      System.out.println(" name = " +
-                         ( (SequenceI) node.element()).getName());
+      System.out.println(" name = "
+              + ((SequenceI) node.element()).getName());
     }
 
-    System.out.println(" dist = " + ( (SequenceNode) node).dist + " " +
-                       ( (SequenceNode) node).count + " " +
-                       ( (SequenceNode) node).height);
+    System.out.println(" dist = " + ((SequenceNode) node).dist + " "
+            + ((SequenceNode) node).count + " "
+            + ((SequenceNode) node).height);
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param node DOCUMENT ME!
+   * 
+   * @param node
+   *                DOCUMENT ME!
    */
   public void reCount(SequenceNode node)
   {
@@ -1121,8 +1155,9 @@ public class NJTree
 
   /**
    * DOCUMENT ME!
-   *
-   * @param node DOCUMENT ME!
+   * 
+   * @param node
+   *                DOCUMENT ME!
    */
   public void _reCount(SequenceNode node)
   {
@@ -1131,28 +1166,29 @@ public class NJTree
       return;
     }
 
-    if ( (node.left() != null) && (node.right() != null))
+    if ((node.left() != null) && (node.right() != null))
     {
-      _reCount( (SequenceNode) node.left());
-      _reCount( (SequenceNode) node.right());
+      _reCount((SequenceNode) node.left());
+      _reCount((SequenceNode) node.right());
 
       SequenceNode l = (SequenceNode) node.left();
       SequenceNode r = (SequenceNode) node.right();
 
-      ( (SequenceNode) node).count = l.count + r.count;
-      ( (SequenceNode) node).ycount = (l.ycount + r.ycount) / 2;
+      ((SequenceNode) node).count = l.count + r.count;
+      ((SequenceNode) node).ycount = (l.ycount + r.ycount) / 2;
     }
     else
     {
-      ( (SequenceNode) node).count = 1;
-      ( (SequenceNode) node).ycount = ycount++;
+      ((SequenceNode) node).count = 1;
+      ((SequenceNode) node).ycount = ycount++;
     }
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param node DOCUMENT ME!
+   * 
+   * @param node
+   *                DOCUMENT ME!
    */
   public void swapNodes(SequenceNode node)
   {
@@ -1169,9 +1205,11 @@ public class NJTree
 
   /**
    * DOCUMENT ME!
-   *
-   * @param node DOCUMENT ME!
-   * @param dir DOCUMENT ME!
+   * 
+   * @param node
+   *                DOCUMENT ME!
+   * @param dir
+   *                DOCUMENT ME!
    */
   public void changeDirection(SequenceNode node, SequenceNode dir)
   {
@@ -1182,7 +1220,7 @@ public class NJTree
 
     if (node.parent() != top)
     {
-      changeDirection( (SequenceNode) node.parent(), node);
+      changeDirection((SequenceNode) node.parent(), node);
 
       SequenceNode tmp = (SequenceNode) node.parent();
 
@@ -1230,7 +1268,7 @@ public class NJTree
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public SequenceNode getMaxDist()
@@ -1240,7 +1278,7 @@ public class NJTree
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public SequenceNode getTopNode()
@@ -1249,7 +1287,7 @@ public class NJTree
   }
 
   /**
-   *
+   * 
    * @return true if tree has real distances
    */
   public boolean isHasDistances()
@@ -1258,7 +1296,7 @@ public class NJTree
   }
 
   /**
-   *
+   * 
    * @return true if tree has real bootstrap values
    */
   public boolean isHasBootstrap()
@@ -1275,7 +1313,7 @@ public class NJTree
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
@@ -1285,8 +1323,9 @@ class Cluster
 
   /**
    * Creates a new Cluster object.
-   *
-   * @param value DOCUMENT ME!
+   * 
+   * @param value
+   *                DOCUMENT ME!
    */
   public Cluster(int[] value)
   {
diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java
index c11610a..f9a0343 100755
--- a/src/jalview/analysis/PCA.java
+++ b/src/jalview/analysis/PCA.java
@@ -1,239 +1,252 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.analysis;
-
-import java.io.*;
-
-import jalview.datamodel.*;
-import jalview.math.*;
-
-/**
- * Performs Principal Component Analysis on given sequences
- *
- * @author $author$
- * @version $Revision$
- */
-public class PCA
-    implements Runnable
-{
-  Matrix m;
-  Matrix symm;
-  Matrix m2;
-  double[] eigenvalue;
-  Matrix eigenvector;
-  StringBuffer details = new StringBuffer();
-
-  /**
-   * Creates a new PCA object.
-   *
-   * @param s Set of sequences to perform PCA on
-   */
-  public PCA(String[] s)
-  {
-
-    BinarySequence[] bs = new BinarySequence[s.length];
-    int ii = 0;
-
-    while ( (ii < s.length) && (s[ii] != null))
-    {
-      bs[ii] = new BinarySequence(s[ii]);
-      bs[ii].encode();
-      ii++;
-    }
-
-    BinarySequence[] bs2 = new BinarySequence[s.length];
-    ii = 0;
-
-    while ( (ii < s.length) && (s[ii] != null))
-    {
-      bs2[ii] = new BinarySequence(s[ii]);
-      bs2[ii].blosumEncode();
-      ii++;
-    }
-
-    //System.out.println("Created binary encoding");
-    //printMemory(rt);
-    int count = 0;
-
-    while ( (count < bs.length) && (bs[count] != null))
-    {
-      count++;
-    }
-
-    double[][] seqmat = new double[count][bs[0].getDBinary().length];
-    double[][] seqmat2 = new double[count][bs2[0].getDBinary().length];
-    int i = 0;
-
-    while (i < count)
-    {
-      seqmat[i] = bs[i].getDBinary();
-      seqmat2[i] = bs2[i].getDBinary();
-      i++;
-    }
-
-    //System.out.println("Created array");
-    //printMemory(rt);
-    //    System.out.println(" --- Original matrix ---- ");
-    m = new Matrix(seqmat, count, bs[0].getDBinary().length);
-    m2 = new Matrix(seqmat2, count, bs2[0].getDBinary().length);
-
-  }
-
-  /**
-   * Returns the matrix used in PCA calculation
-   *
-   * @return java.math.Matrix object
-   */
-
-  public Matrix getM()
-  {
-    return m;
-  }
-
-  /**
-   * Returns Eigenvalue
-   *
-   * @param i Index of diagonal within matrix
-   *
-   * @return Returns value of diagonal from matrix
-   */
-  public double getEigenvalue(int i)
-  {
-    return eigenvector.d[i];
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param l DOCUMENT ME!
-   * @param n DOCUMENT ME!
-   * @param mm DOCUMENT ME!
-   * @param factor DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public float[][] getComponents(int l, int n, int mm, float factor)
-  {
-    float[][] out = new float[m.rows][3];
-
-    for (int i = 0; i < m.rows; i++)
-    {
-      out[i][0] = (float) component(i, l) * factor;
-      out[i][1] = (float) component(i, n) * factor;
-      out[i][2] = (float) component(i, mm) * factor;
-    }
-
-    return out;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param n DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public double[] component(int n)
-  {
-    // n = index of eigenvector
-    double[] out = new double[m.rows];
-
-    for (int i = 0; i < m.rows; i++)
-    {
-      out[i] = component(i, n);
-    }
-
-    return out;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param row DOCUMENT ME!
-   * @param n DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  double component(int row, int n)
-  {
-    double out = 0.0;
-
-    for (int i = 0; i < symm.cols; i++)
-    {
-      out += (symm.value[row][i] * eigenvector.value[i][n]);
-    }
-
-    return out / eigenvector.d[n];
-  }
-
-  public String getDetails()
-  {
-    return details.toString();
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  public void run()
-  {
-    Matrix mt = m.transpose();
-
-    details.append(" --- OrigT * Orig ---- \n");
-    eigenvector = mt.preMultiply(m2);
-
-    PrintStream ps = new PrintStream(System.out)
-    {
-      public void print(String x)
-      {
-        details.append(x);
-      }
-
-      public void println()
-      {
-        details.append("\n");
-      }
-    };
-
-    eigenvector.print(ps);
-
-    symm = eigenvector.copy();
-
-    eigenvector.tred();
-
-    details.append(" ---Tridiag transform matrix ---\n");
-    details.append(" --- D vector ---\n");
-    eigenvector.printD(ps);
-    ps.println();
-    details.append("--- E vector ---\n");
-    eigenvector.printE(ps);
-    ps.println();
-
-    // Now produce the diagonalization matrix
-    eigenvector.tqli();
-
-    details.append(" --- New diagonalization matrix ---\n");
-    details.append(" --- Eigenvalues ---\n");
-    eigenvector.printD(ps);
-    ps.println();
-    //  taps.println();
-    //  taps.println("Transformed sequences = ");
-    // Matrix trans =  m.preMultiply(eigenvector);
-    //  trans.print(System.out);
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.analysis;
+
+import java.io.*;
+
+import jalview.datamodel.*;
+import jalview.math.*;
+
+/**
+ * Performs Principal Component Analysis on given sequences
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class PCA implements Runnable
+{
+  Matrix m;
+
+  Matrix symm;
+
+  Matrix m2;
+
+  double[] eigenvalue;
+
+  Matrix eigenvector;
+
+  StringBuffer details = new StringBuffer();
+
+  /**
+   * Creates a new PCA object.
+   * 
+   * @param s
+   *                Set of sequences to perform PCA on
+   */
+  public PCA(String[] s)
+  {
+
+    BinarySequence[] bs = new BinarySequence[s.length];
+    int ii = 0;
+
+    while ((ii < s.length) && (s[ii] != null))
+    {
+      bs[ii] = new BinarySequence(s[ii]);
+      bs[ii].encode();
+      ii++;
+    }
+
+    BinarySequence[] bs2 = new BinarySequence[s.length];
+    ii = 0;
+
+    while ((ii < s.length) && (s[ii] != null))
+    {
+      bs2[ii] = new BinarySequence(s[ii]);
+      bs2[ii].blosumEncode();
+      ii++;
+    }
+
+    // System.out.println("Created binary encoding");
+    // printMemory(rt);
+    int count = 0;
+
+    while ((count < bs.length) && (bs[count] != null))
+    {
+      count++;
+    }
+
+    double[][] seqmat = new double[count][bs[0].getDBinary().length];
+    double[][] seqmat2 = new double[count][bs2[0].getDBinary().length];
+    int i = 0;
+
+    while (i < count)
+    {
+      seqmat[i] = bs[i].getDBinary();
+      seqmat2[i] = bs2[i].getDBinary();
+      i++;
+    }
+
+    // System.out.println("Created array");
+    // printMemory(rt);
+    // System.out.println(" --- Original matrix ---- ");
+    m = new Matrix(seqmat, count, bs[0].getDBinary().length);
+    m2 = new Matrix(seqmat2, count, bs2[0].getDBinary().length);
+
+  }
+
+  /**
+   * Returns the matrix used in PCA calculation
+   * 
+   * @return java.math.Matrix object
+   */
+
+  public Matrix getM()
+  {
+    return m;
+  }
+
+  /**
+   * Returns Eigenvalue
+   * 
+   * @param i
+   *                Index of diagonal within matrix
+   * 
+   * @return Returns value of diagonal from matrix
+   */
+  public double getEigenvalue(int i)
+  {
+    return eigenvector.d[i];
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param l
+   *                DOCUMENT ME!
+   * @param n
+   *                DOCUMENT ME!
+   * @param mm
+   *                DOCUMENT ME!
+   * @param factor
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public float[][] getComponents(int l, int n, int mm, float factor)
+  {
+    float[][] out = new float[m.rows][3];
+
+    for (int i = 0; i < m.rows; i++)
+    {
+      out[i][0] = (float) component(i, l) * factor;
+      out[i][1] = (float) component(i, n) * factor;
+      out[i][2] = (float) component(i, mm) * factor;
+    }
+
+    return out;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param n
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public double[] component(int n)
+  {
+    // n = index of eigenvector
+    double[] out = new double[m.rows];
+
+    for (int i = 0; i < m.rows; i++)
+    {
+      out[i] = component(i, n);
+    }
+
+    return out;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param row
+   *                DOCUMENT ME!
+   * @param n
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  double component(int row, int n)
+  {
+    double out = 0.0;
+
+    for (int i = 0; i < symm.cols; i++)
+    {
+      out += (symm.value[row][i] * eigenvector.value[i][n]);
+    }
+
+    return out / eigenvector.d[n];
+  }
+
+  public String getDetails()
+  {
+    return details.toString();
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void run()
+  {
+    Matrix mt = m.transpose();
+
+    details.append(" --- OrigT * Orig ---- \n");
+    eigenvector = mt.preMultiply(m2);
+
+    PrintStream ps = new PrintStream(System.out)
+    {
+      public void print(String x)
+      {
+        details.append(x);
+      }
+
+      public void println()
+      {
+        details.append("\n");
+      }
+    };
+
+    eigenvector.print(ps);
+
+    symm = eigenvector.copy();
+
+    eigenvector.tred();
+
+    details.append(" ---Tridiag transform matrix ---\n");
+    details.append(" --- D vector ---\n");
+    eigenvector.printD(ps);
+    ps.println();
+    details.append("--- E vector ---\n");
+    eigenvector.printE(ps);
+    ps.println();
+
+    // Now produce the diagonalization matrix
+    eigenvector.tqli();
+
+    details.append(" --- New diagonalization matrix ---\n");
+    details.append(" --- Eigenvalues ---\n");
+    eigenvector.printD(ps);
+    ps.println();
+    // taps.println();
+    // taps.println("Transformed sequences = ");
+    // Matrix trans = m.preMultiply(eigenvector);
+    // trans.print(System.out);
+  }
+}
diff --git a/src/jalview/analysis/ParseProperties.java b/src/jalview/analysis/ParseProperties.java
index 79c1325..211f4e2 100644
--- a/src/jalview/analysis/ParseProperties.java
+++ b/src/jalview/analysis/ParseProperties.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.analysis;
 
 import com.stevesoft.pat.Regex;
@@ -7,102 +25,124 @@ import jalview.datamodel.*;
 public class ParseProperties
 {
   /**
-   * Methods for parsing free text properties on alignments and sequences.
-   * There are a number of ways we might want to do this:
-   * arbitrary regex. and an associated score name for the number that's extracted.
-   * Regex that provides both score and name.
+   * Methods for parsing free text properties on alignments and sequences. There
+   * are a number of ways we might want to do this: arbitrary regex. and an
+   * associated score name for the number that's extracted. Regex that provides
+   * both score and name.
    * 
-   * We may also want to :
-   * - modify description to remove parsed numbers (this behaviour is dangerous since exporting the alignment would lose the original form then)
-   * - 
+   * We may also want to : - modify description to remove parsed numbers (this
+   * behaviour is dangerous since exporting the alignment would lose the
+   * original form then) -
    * 
    */
   /**
    * The alignment being operated on
    */
-  private AlignmentI al=null;
-  
+  private AlignmentI al = null;
+
   /**
    * initialise a new property parser
+   * 
    * @param al
    */
-  public ParseProperties(AlignmentI al) {
+  public ParseProperties(AlignmentI al)
+  {
     this.al = al;
   }
 
-  public int getScoresFromDescription(String ScoreName, String ScoreDescriptions, String regex, boolean repeat)
+  public int getScoresFromDescription(String ScoreName,
+          String ScoreDescriptions, String regex, boolean repeat)
   {
-    return getScoresFromDescription(new String[] { ScoreName }, new String[] { ScoreDescriptions}, regex, repeat);
+    return getScoresFromDescription(new String[]
+    { ScoreName }, new String[]
+    { ScoreDescriptions }, regex, repeat);
   }
 
-  public int getScoresFromDescription(String[] ScoreNames, String[] ScoreDescriptions, String regex, boolean repeat) 
+  public int getScoresFromDescription(String[] ScoreNames,
+          String[] ScoreDescriptions, String regex, boolean repeat)
   {
-    return getScoresFromDescription(al.getSequencesArray(), ScoreNames, ScoreDescriptions, regex, repeat);
+    return getScoresFromDescription(al.getSequencesArray(), ScoreNames,
+            ScoreDescriptions, regex, repeat);
   }
+
   /**
    * Extract scores for sequences by applying regex to description string.
-   * @param seqs seuqences to extract annotation from.
-   * @param ScoreNames labels for each numeric field in regex match
-   * @param ScoreDescriptions description for each numeric field in regex match
-   * @param regex Regular Expression string for passing to <code>new com.stevesoft.patt.Regex(regex)</code>
-   * @param repeat true means the regex will be applied multiple times along the description string of each sequence
+   * 
+   * @param seqs
+   *                seuqences to extract annotation from.
+   * @param ScoreNames
+   *                labels for each numeric field in regex match
+   * @param ScoreDescriptions
+   *                description for each numeric field in regex match
+   * @param regex
+   *                Regular Expression string for passing to
+   *                <code>new com.stevesoft.patt.Regex(regex)</code>
+   * @param repeat
+   *                true means the regex will be applied multiple times along
+   *                the description string of each sequence
    * @return total number of sequences that matched the regex
    */
-  public int getScoresFromDescription(SequenceI[] seqs, String[] ScoreNames, String[] ScoreDescriptions, String regex, boolean repeat) 
+  public int getScoresFromDescription(SequenceI[] seqs,
+          String[] ScoreNames, String[] ScoreDescriptions, String regex,
+          boolean repeat)
   {
-    int count=0;
+    int count = 0;
     Regex pattern = new Regex(regex);
-    if (pattern.numSubs()>ScoreNames.length)
+    if (pattern.numSubs() > ScoreNames.length)
     {
-      // Check that we have enough labels and descriptions for any parsed scores.
+      // Check that we have enough labels and descriptions for any parsed
+      // scores.
       int onamelen = ScoreNames.length;
-      String[] tnames = new String[pattern.numSubs()+1];
+      String[] tnames = new String[pattern.numSubs() + 1];
       System.arraycopy(ScoreNames, 0, tnames, 0, ScoreNames.length);
-      String base = tnames[ScoreNames.length-1];
+      String base = tnames[ScoreNames.length - 1];
       ScoreNames = tnames;
-      String descrbase = ScoreDescriptions[onamelen-1];
+      String descrbase = ScoreDescriptions[onamelen - 1];
       if (descrbase == null)
-        descrbase = "Score parsed from ("+regex+")";
-      tnames = new String[pattern.numSubs()+1];
-      System.arraycopy(ScoreDescriptions, 0, tnames, 0, ScoreDescriptions.length);
+        descrbase = "Score parsed from (" + regex + ")";
+      tnames = new String[pattern.numSubs() + 1];
+      System.arraycopy(ScoreDescriptions, 0, tnames, 0,
+              ScoreDescriptions.length);
       ScoreDescriptions = tnames;
-      for (int i=onamelen; i<ScoreNames.length; i++)
+      for (int i = onamelen; i < ScoreNames.length; i++)
       {
-        ScoreNames[i] = base+"_"+i;
-        ScoreDescriptions[i] = descrbase+" (column "+i+")";
+        ScoreNames[i] = base + "_" + i;
+        ScoreDescriptions[i] = descrbase + " (column " + i + ")";
       }
     }
-    for (int i=0; i<seqs.length; i++)
+    for (int i = 0; i < seqs.length; i++)
     {
       String descr = seqs[i].getDescription();
-      if (descr==null)
+      if (descr == null)
         continue;
-      int pos=0;
-      boolean added=false;
-      int reps=0;
-      while ((repeat || pos==0) && pattern.searchFrom(descr, pos))
+      int pos = 0;
+      boolean added = false;
+      int reps = 0;
+      while ((repeat || pos == 0) && pattern.searchFrom(descr, pos))
       {
         pos = pattern.matchedTo();
-        for (int cols=0; cols<pattern.numSubs(); cols++)
+        for (int cols = 0; cols < pattern.numSubs(); cols++)
         {
-          String sstring = pattern.stringMatched(cols+1);
-          double score=Double.NaN;
-          try {
+          String sstring = pattern.stringMatched(cols + 1);
+          double score = Double.NaN;
+          try
+          {
             score = new Double(sstring).doubleValue();
-          }
-          catch (Exception e)
+          } catch (Exception e)
           {
             // don't try very hard to parse if regex was wrong.
             continue;
           }
           // add score to sequence annotation.
-          AlignmentAnnotation an = new AlignmentAnnotation(ScoreNames[cols] +((reps>0) ? "_"+reps : ""), ScoreDescriptions[cols], null);
+          AlignmentAnnotation an = new AlignmentAnnotation(ScoreNames[cols]
+                  + ((reps > 0) ? "_" + reps : ""),
+                  ScoreDescriptions[cols], null);
           an.setScore(score);
-          System.out.println("Score: "+ScoreNames[cols]+"="+score); // DEBUG
+          System.out.println("Score: " + ScoreNames[cols] + "=" + score); // DEBUG
           an.setSequenceRef(seqs[i]);
           seqs[i].addAlignmentAnnotation(an);
           al.addAnnotation(an);
-          added=true;
+          added = true;
         }
         reps++; // repeated matches
       }
@@ -111,24 +151,31 @@ public class ParseProperties
         count++;
       }
     }
-    return count; 
+    return count;
   }
-  public static void main(String argv[]) {
-    SequenceI[] seqs = new SequenceI[] { new Sequence("sq1","THISISAPLACEHOLDER"),
-            new Sequence("sq2","THISISAPLACEHOLDER"),
-            new Sequence("sq3","THISISAPLACEHOLDER"),
-            new Sequence("sq4","THISISAPLACEHOLDER")};
+
+  public static void main(String argv[])
+  {
+    SequenceI[] seqs = new SequenceI[]
+    { new Sequence("sq1", "THISISAPLACEHOLDER"),
+        new Sequence("sq2", "THISISAPLACEHOLDER"),
+        new Sequence("sq3", "THISISAPLACEHOLDER"),
+        new Sequence("sq4", "THISISAPLACEHOLDER") };
     seqs[0].setDescription("1 mydescription1");
     seqs[1].setDescription("mydescription2");
     seqs[2].setDescription("2. 0.1 mydescription3");
     seqs[3].setDescription("3 0.01 mydescription4");
-    //seqs[4].setDescription("5 mydescription5");
+    // seqs[4].setDescription("5 mydescription5");
     Alignment al = new Alignment(seqs);
     ParseProperties pp = new ParseProperties(al);
     String regex = ".*([-0-9.+]+)";
-    System.out.println("Matched "+pp.getScoresFromDescription("my Score", "my Score Description",regex, true)+" for "+regex);
+    System.out.println("Matched "
+            + pp.getScoresFromDescription("my Score",
+                    "my Score Description", regex, true) + " for " + regex);
     regex = ".*([-0-9.+]+).+([-0-9.+]+).*";
-    System.out.println("Matched "+pp.getScoresFromDescription("my Score", "my Score Description",regex, true)+" for "+regex);
+    System.out.println("Matched "
+            + pp.getScoresFromDescription("my Score",
+                    "my Score Description", regex, true) + " for " + regex);
     System.out.println("Finished.");
   }
 }
diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index 0aa2bd5..a86775d 100755
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -23,14 +23,22 @@ import java.util.*;
 import jalview.datamodel.*;
 
 /**
- * <p>Title: </p>
- *
- * <p>Description: </p>
- *
- * <p>Copyright: Copyright (c) 2004</p>
- *
- * <p>Company: Dundee University</p>
- *
+ * <p>
+ * Title:
+ * </p>
+ * 
+ * <p>
+ * Description:
+ * </p>
+ * 
+ * <p>
+ * Copyright: Copyright (c) 2004
+ * </p>
+ * 
+ * <p>
+ * Company: Dundee University
+ * </p>
+ * 
  * @author not attributable
  * @version 1.0
  */
@@ -39,8 +47,10 @@ public class SeqsetUtils
 
   /**
    * Store essential properties of a sequence in a hashtable for later recovery
-   *  Keys are Name, Start, End, SeqFeatures, PdbId
-   * @param seq SequenceI
+   * Keys are Name, Start, End, SeqFeatures, PdbId
+   * 
+   * @param seq
+   *                SequenceI
    * @return Hashtable
    */
   public static Hashtable SeqCharacterHash(SequenceI seq)
@@ -63,19 +73,21 @@ public class SeqsetUtils
       }
     }
     sqinfo.put("SeqFeatures", sfeat);
-    sqinfo.put("PdbId",
-               (seq.getPDBId() != null) ? seq.getPDBId() : new Vector());
-    sqinfo.put("datasetSequence",
-               (seq.getDatasetSequence() != null) ? seq.getDatasetSequence() :
-               new Sequence("THISISAPLACEHOLDER", ""));
+    sqinfo.put("PdbId", (seq.getPDBId() != null) ? seq.getPDBId()
+            : new Vector());
+    sqinfo.put("datasetSequence", (seq.getDatasetSequence() != null) ? seq
+            .getDatasetSequence() : new Sequence("THISISAPLACEHOLDER", ""));
     return sqinfo;
   }
 
   /**
-   * Recover essential properties of a sequence from a hashtable
-   * TODO: replace these methods with something more elegant.
-   * @param sq SequenceI
-   * @param sqinfo Hashtable
+   * Recover essential properties of a sequence from a hashtable TODO: replace
+   * these methods with something more elegant.
+   * 
+   * @param sq
+   *                SequenceI
+   * @param sqinfo
+   *                Hashtable
    * @return boolean true if name was not updated from sqinfo Name entry
    */
   public static boolean SeqCharacterUnhash(SequenceI sq, Hashtable sqinfo)
@@ -88,8 +100,7 @@ public class SeqsetUtils
     String oldname = (String) sqinfo.get("Name");
     Integer start = (Integer) sqinfo.get("Start");
     Integer end = (Integer) sqinfo.get("End");
-    Vector sfeatures = (Vector) sqinfo.get(
-        "SeqFeatures");
+    Vector sfeatures = (Vector) sqinfo.get("SeqFeatures");
     Vector pdbid = (Vector) sqinfo.get("PdbId");
     String description = (String) sqinfo.get("Description");
     Sequence seqds = (Sequence) sqinfo.get("datasetSequence");
@@ -106,17 +117,17 @@ public class SeqsetUtils
       sq.setPDBId(pdbid);
     }
 
-    if ( (start != null) && (end != null))
+    if ((start != null) && (end != null))
     {
       sq.setStart(start.intValue());
       sq.setEnd(end.intValue());
     }
 
-    if ( (sfeatures != null) && (sfeatures.size() > 0))
+    if ((sfeatures != null) && (sfeatures.size() > 0))
     {
       SequenceFeature[] sfarray = new SequenceFeature[sfeatures.size()];
-      for (int is=0,isize=sfeatures.size();is<isize;is++)
-      { 
+      for (int is = 0, isize = sfeatures.size(); is < isize; is++)
+      {
         sfarray[is] = (SequenceFeature) sfeatures.elementAt(is);
       }
       sq.setSequenceFeatures(sfarray);
@@ -125,9 +136,9 @@ public class SeqsetUtils
     {
       sq.setDescription(description);
     }
-    if ( (seqds != null) &&
-        ! (seqds.getName().equals("THISISAPLACEHOLDER") &&
-           seqds.getLength() == 0))
+    if ((seqds != null)
+            && !(seqds.getName().equals("THISISAPLACEHOLDER") && seqds
+                    .getLength() == 0))
     {
       sq.setDatasetSequence(seqds);
     }
@@ -136,8 +147,11 @@ public class SeqsetUtils
   }
 
   /**
-   * Form of the unique name used in uniquify for the i'th sequence in an ordered vector of sequences.
-   * @param i int
+   * Form of the unique name used in uniquify for the i'th sequence in an
+   * ordered vector of sequences.
+   * 
+   * @param i
+   *                int
    * @return String
    */
   public static String unique_name(int i)
@@ -146,18 +160,26 @@ public class SeqsetUtils
   }
 
   /**
-   * Generates a hash of SeqCharacterHash properties for each sequence
-   * in a sequence set, and optionally renames the sequences to an
-   * unambiguous 'safe' name.
-   * @param sequences SequenceI[]
-   * @param write_names boolean set this to rename each of the sequences to its unique_name(index) name
-   * @return Hashtable to be passed to @see deuniquify to recover original names (and properties) for renamed sequences
+   * Generates a hash of SeqCharacterHash properties for each sequence in a
+   * sequence set, and optionally renames the sequences to an unambiguous 'safe'
+   * name.
+   * 
+   * @param sequences
+   *                SequenceI[]
+   * @param write_names
+   *                boolean set this to rename each of the sequences to its
+   *                unique_name(index) name
+   * @return Hashtable to be passed to
+   * @see deuniquify to recover original names (and properties) for renamed
+   *      sequences
    */
-  public static Hashtable uniquify(SequenceI[] sequences, boolean write_names)
+  public static Hashtable uniquify(SequenceI[] sequences,
+          boolean write_names)
   {
-    // Generate a safely named sequence set and a hash to recover the sequence names
+    // Generate a safely named sequence set and a hash to recover the sequence
+    // names
     Hashtable map = new Hashtable();
-    //String[] un_names = new String[sequences.length];
+    // String[] un_names = new String[sequences.length];
 
     for (int i = 0; i < sequences.length; i++)
     {
@@ -174,28 +196,40 @@ public class SeqsetUtils
   }
 
   /**
-   * recover unsafe sequence names and original properties for a sequence
-   * set using a map generated by @see uniquify(sequences,true)
-   * @param map Hashtable
-   * @param sequences SequenceI[]
+   * recover unsafe sequence names and original properties for a sequence set
+   * using a map generated by
+   * 
+   * @see uniquify(sequences,true)
+   * @param map
+   *                Hashtable
+   * @param sequences
+   *                SequenceI[]
    * @return boolean
    */
   public static boolean deuniquify(Hashtable map, SequenceI[] sequences)
   {
     return deuniquify(map, sequences, true);
   }
+
   /**
-   * recover unsafe sequence names and original properties for a sequence
-   * set using a map generated by @see uniquify(sequences,true)
-   * @param map Hashtable
-   * @param sequences SequenceI[]
-   * @param quiet when false, don't complain about sequences without any data in the map. 
+   * recover unsafe sequence names and original properties for a sequence set
+   * using a map generated by
+   * 
+   * @see uniquify(sequences,true)
+   * @param map
+   *                Hashtable
+   * @param sequences
+   *                SequenceI[]
+   * @param quiet
+   *                when false, don't complain about sequences without any data
+   *                in the map.
    * @return boolean
    */
-    public static boolean deuniquify(Hashtable map, SequenceI[] sequences, boolean quiet)
-    {
-          jalview.analysis.SequenceIdMatcher matcher = new SequenceIdMatcher(
-        sequences);
+  public static boolean deuniquify(Hashtable map, SequenceI[] sequences,
+          boolean quiet)
+  {
+    jalview.analysis.SequenceIdMatcher matcher = new SequenceIdMatcher(
+            sequences);
     SequenceI msq = null;
     Enumeration keys = map.keys();
     Vector unmatched = new Vector();
@@ -208,7 +242,7 @@ public class SeqsetUtils
       Object key = keys.nextElement();
       if (key instanceof String)
       {
-        if ( (msq = matcher.findIdMatch( (String) key)) != null)
+        if ((msq = matcher.findIdMatch((String) key)) != null)
         {
           Hashtable sqinfo = (Hashtable) map.get(key);
           unmatched.removeElement(msq);
@@ -217,18 +251,18 @@ public class SeqsetUtils
         else
         {
           if (!quiet)
-            {
-            System.err.println("Can't find '" + ( (String) key) +
-                             "' in uniquified alignment");
-            }
+          {
+            System.err.println("Can't find '" + ((String) key)
+                    + "' in uniquified alignment");
+          }
         }
       }
     }
     if (unmatched.size() > 0 && !quiet)
     {
       System.err.println("Did not find matches for :");
-      for (Enumeration i = unmatched.elements(); i.hasMoreElements();
-           System.out.println( ( (SequenceI) i.nextElement()).getName()))
+      for (Enumeration i = unmatched.elements(); i.hasMoreElements(); System.out
+              .println(((SequenceI) i.nextElement()).getName()))
       {
         ;
       }
@@ -239,9 +273,11 @@ public class SeqsetUtils
   }
 
   /**
-   * returns a subset of the sequenceI seuqences,
-   * including only those that contain at least one residue.
-   * @param sequences SequenceI[]
+   * returns a subset of the sequenceI seuqences, including only those that
+   * contain at least one residue.
+   * 
+   * @param sequences
+   *                SequenceI[]
    * @return SequenceI[]
    */
   public static SequenceI[] getNonEmptySequenceSet(SequenceI[] sequences)
@@ -252,8 +288,8 @@ public class SeqsetUtils
     for (int i = 0, j = sequences.length; i < j; i++)
     {
       String tempseq = jalview.analysis.AlignSeq.extractGaps(
-          jalview.util.Comparison.GapChars,
-          sequences[i].getSequenceAsString());
+              jalview.util.Comparison.GapChars, sequences[i]
+                      .getSequenceAsString());
 
       if (tempseq.length() == 0)
       {
diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java
index 0744937..240f9cf 100755
--- a/src/jalview/analysis/SequenceIdMatcher.java
+++ b/src/jalview/analysis/SequenceIdMatcher.java
@@ -1,246 +1,258 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.analysis;
-
-import java.util.*;
-
-import jalview.datamodel.*;
-
-/**
- * <p>Title: </p>
- * SequenceIdMatcher
- * <p>Description: </p>
- * Routine which does approximate Sequence Id resolution by name using
- * string containment (on word boundaries) rather than equivalence. It also
- * attempts to resolve ties where no exact match is available by picking the
- * the id closest to the query.
- * <p>Copyright: Copyright (c) 2004</p>
- *
- * <p>Company: Dundee University</p>
- *
- * @author not attributable
- * @version 1.0
- */
-public class SequenceIdMatcher
-{
-  private Hashtable names;
-
-  public SequenceIdMatcher(SequenceI[] seqs)
-  {
-    names = new Hashtable();
-    for (int i = 0; i < seqs.length; i++)
-    {
-      names.put(new SeqIdName(seqs[i].getName()), seqs[i]);
-    }
-  }
-
-  /**
-   * returns the closest SequenceI in matches to SeqIdName and returns all the matches
-   * to the names hash.
-   * @param candName SeqIdName
-   * @param matches Vector of SequenceI objects
-   * @return SequenceI closest SequenceI to SeqIdName
-   */
-  private SequenceI pickbestMatch(SeqIdName candName, Vector matches)
-  {
-    SequenceI match = null;
-    if (candName == null || matches == null || matches.size() == 0)
-    {
-      return null;
-    }
-    match = (SequenceI) matches.elementAt(0);
-    matches.removeElementAt(0);
-    names.put(new SeqIdName(match.getName()), match);
-    int matchlen = match.getName().length();
-    int namlen = candName.id.length();
-    while (matches.size() > 0)
-    {
-      // look through for a better one.
-      SequenceI cand = (SequenceI) matches.elementAt(0);
-      names.put(new SeqIdName(cand.getName()), cand);
-      int candlen = cand.getName().length();
-      // keep the one with an id 'closer' to the given seqnam string
-      if (Math.abs(matchlen - namlen) > Math.abs(candlen - namlen) &&
-          candlen > matchlen)
-      {
-        match = cand;
-        matchlen = candlen;
-      }
-    }
-    return match;
-  }
-
-  /**
-   * get SequenceI with closest SequenceI.getName() to seq.getName()
-   * @param seq SequenceI
-   * @return SequenceI
-   */
-  SequenceI findIdMatch(SequenceI seq)
-  {
-    SeqIdName nam = new SeqIdName(seq.getName());
-    return findIdMatch(nam);
-  }
-
-  SequenceI findIdMatch(String seqnam)
-  {
-    SeqIdName nam = new SeqIdName(seqnam);
-    return findIdMatch(nam);
-  }
-
-  /**
-   * findIdMatch
-   *
-   * Return pointers to sequences (or sequence object containers)
-   * which have same Id as a given set of different sequence objects
-   *
-   * @param seqs SequenceI[]
-   * @return SequenceI[]
-   */
-  SequenceI[] findIdMatch(SequenceI[] seqs)
-  {
-    SequenceI[] namedseqs = null;
-    int i = 0;
-    SeqIdName nam;
-
-    if (seqs.length > 0)
-    {
-      namedseqs = new SequenceI[seqs.length];
-      do
-      {
-        nam = new SeqIdName(seqs[i].getName());
-
-        if (names.containsKey(nam))
-        {
-          namedseqs[i] = findIdMatch(nam);
-        }
-        else
-        {
-          namedseqs[i] = null;
-        }
-      }
-      while (++i < seqs.length);
-    }
-
-    return namedseqs;
-  }
-
-  /**
-   * core findIdMatch search method
-   * @param nam SeqIdName
-   * @return SequenceI
-   */
-  private SequenceI findIdMatch(jalview.analysis.SequenceIdMatcher.SeqIdName
-                                nam)
-  {
-    Vector matches = new Vector();
-    while (names.containsKey(nam))
-    {
-      matches.addElement(names.remove(nam));
-    }
-    return pickbestMatch(nam, matches);
-  }
-
-  private class SeqIdName
-  {
-    String id;
-
-    SeqIdName(String s)
-    {
-      if (s != null)
-      {
-        id = new String(s);
-      }
-      else
-      {
-        id = "";
-      }
-    }
-
-    public int hashCode()
-    {
-      return ( (id.length() >= 4) ? id.substring(0, 4).hashCode() : id.hashCode());
-    }
-
-    public boolean equals(Object s)
-    {
-      if (s instanceof SeqIdName)
-      {
-        return this.equals( (SeqIdName) s);
-      }
-      else
-      {
-        if (s instanceof String)
-        {
-          return this.equals( (String) s);
-        }
-      }
-
-      return false;
-    }
-
-    /**
-     * Characters that define the end of a unique sequence ID at
-     * the beginning of an arbitrary ID string
-     * JBPNote: This is a heuristic that will fail for arbritrarily extended sequence id's
-     * (like portions of an aligned set of repeats from one sequence)
-     */
-    private String WORD_SEP = "~. |#\\/<>!\"£$%^*)}[@',?_";
-
-    /**
-     * matches if one ID properly contains another at a whitespace boundary.
-     * TODO: (JBPNote) These are not efficient. should use char[] for speed
-     * todo: (JBPNote) Set separator characters appropriately
-     * @param s SeqIdName
-     * @return boolean
-     */
-    public boolean equals(SeqIdName s)
-    {
-      if (id.length() > s.id.length())
-      {
-        return id.startsWith(s.id) ?
-            (WORD_SEP.indexOf(id.charAt(s.id.length())) > -1)
-            : false;
-      }
-      else
-      {
-        return s.id.startsWith(id) ?
-            (s.id.equals(id) ? true :
-             (WORD_SEP.indexOf(s.id.charAt(id.length())) > -1))
-            : false;
-      }
-    }
-
-    public boolean equals(String s)
-    {
-      if (id.length() > s.length())
-      {
-        return id.startsWith(s) ?
-            (WORD_SEP.indexOf(id.charAt(s.length())) > -1)
-            : false;
-      }
-      else
-      {
-        return s.startsWith(id) ?
-            (s.equals(id) ? true :
-             (WORD_SEP.indexOf(s.charAt(id.length())) > -1))
-            : false;
-      }
-    }
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.analysis;
+
+import java.util.*;
+
+import jalview.datamodel.*;
+
+/**
+ * <p>
+ * Title:
+ * </p>
+ * SequenceIdMatcher
+ * <p>
+ * Description:
+ * </p>
+ * Routine which does approximate Sequence Id resolution by name using string
+ * containment (on word boundaries) rather than equivalence. It also attempts to
+ * resolve ties where no exact match is available by picking the the id closest
+ * to the query.
+ * <p>
+ * Copyright: Copyright (c) 2004
+ * </p>
+ * 
+ * <p>
+ * Company: Dundee University
+ * </p>
+ * 
+ * @author not attributable
+ * @version 1.0
+ */
+public class SequenceIdMatcher
+{
+  private Hashtable names;
+
+  public SequenceIdMatcher(SequenceI[] seqs)
+  {
+    names = new Hashtable();
+    for (int i = 0; i < seqs.length; i++)
+    {
+      names.put(new SeqIdName(seqs[i].getName()), seqs[i]);
+    }
+  }
+
+  /**
+   * returns the closest SequenceI in matches to SeqIdName and returns all the
+   * matches to the names hash.
+   * 
+   * @param candName
+   *                SeqIdName
+   * @param matches
+   *                Vector of SequenceI objects
+   * @return SequenceI closest SequenceI to SeqIdName
+   */
+  private SequenceI pickbestMatch(SeqIdName candName, Vector matches)
+  {
+    SequenceI match = null;
+    if (candName == null || matches == null || matches.size() == 0)
+    {
+      return null;
+    }
+    match = (SequenceI) matches.elementAt(0);
+    matches.removeElementAt(0);
+    names.put(new SeqIdName(match.getName()), match);
+    int matchlen = match.getName().length();
+    int namlen = candName.id.length();
+    while (matches.size() > 0)
+    {
+      // look through for a better one.
+      SequenceI cand = (SequenceI) matches.elementAt(0);
+      names.put(new SeqIdName(cand.getName()), cand);
+      int candlen = cand.getName().length();
+      // keep the one with an id 'closer' to the given seqnam string
+      if (Math.abs(matchlen - namlen) > Math.abs(candlen - namlen)
+              && candlen > matchlen)
+      {
+        match = cand;
+        matchlen = candlen;
+      }
+    }
+    return match;
+  }
+
+  /**
+   * get SequenceI with closest SequenceI.getName() to seq.getName()
+   * 
+   * @param seq
+   *                SequenceI
+   * @return SequenceI
+   */
+  SequenceI findIdMatch(SequenceI seq)
+  {
+    SeqIdName nam = new SeqIdName(seq.getName());
+    return findIdMatch(nam);
+  }
+
+  SequenceI findIdMatch(String seqnam)
+  {
+    SeqIdName nam = new SeqIdName(seqnam);
+    return findIdMatch(nam);
+  }
+
+  /**
+   * findIdMatch
+   * 
+   * Return pointers to sequences (or sequence object containers) which have
+   * same Id as a given set of different sequence objects
+   * 
+   * @param seqs
+   *                SequenceI[]
+   * @return SequenceI[]
+   */
+  SequenceI[] findIdMatch(SequenceI[] seqs)
+  {
+    SequenceI[] namedseqs = null;
+    int i = 0;
+    SeqIdName nam;
+
+    if (seqs.length > 0)
+    {
+      namedseqs = new SequenceI[seqs.length];
+      do
+      {
+        nam = new SeqIdName(seqs[i].getName());
+
+        if (names.containsKey(nam))
+        {
+          namedseqs[i] = findIdMatch(nam);
+        }
+        else
+        {
+          namedseqs[i] = null;
+        }
+      } while (++i < seqs.length);
+    }
+
+    return namedseqs;
+  }
+
+  /**
+   * core findIdMatch search method
+   * 
+   * @param nam
+   *                SeqIdName
+   * @return SequenceI
+   */
+  private SequenceI findIdMatch(
+          jalview.analysis.SequenceIdMatcher.SeqIdName nam)
+  {
+    Vector matches = new Vector();
+    while (names.containsKey(nam))
+    {
+      matches.addElement(names.remove(nam));
+    }
+    return pickbestMatch(nam, matches);
+  }
+
+  private class SeqIdName
+  {
+    String id;
+
+    SeqIdName(String s)
+    {
+      if (s != null)
+      {
+        id = new String(s);
+      }
+      else
+      {
+        id = "";
+      }
+    }
+
+    public int hashCode()
+    {
+      return ((id.length() >= 4) ? id.substring(0, 4).hashCode() : id
+              .hashCode());
+    }
+
+    public boolean equals(Object s)
+    {
+      if (s instanceof SeqIdName)
+      {
+        return this.equals((SeqIdName) s);
+      }
+      else
+      {
+        if (s instanceof String)
+        {
+          return this.equals((String) s);
+        }
+      }
+
+      return false;
+    }
+
+    /**
+     * Characters that define the end of a unique sequence ID at the beginning
+     * of an arbitrary ID string JBPNote: This is a heuristic that will fail for
+     * arbritrarily extended sequence id's (like portions of an aligned set of
+     * repeats from one sequence)
+     */
+    private String WORD_SEP = "~. |#\\/<>!\"£$%^*)}[@',?_";
+
+    /**
+     * matches if one ID properly contains another at a whitespace boundary.
+     * TODO: (JBPNote) These are not efficient. should use char[] for speed
+     * todo: (JBPNote) Set separator characters appropriately
+     * 
+     * @param s
+     *                SeqIdName
+     * @return boolean
+     */
+    public boolean equals(SeqIdName s)
+    {
+      if (id.length() > s.id.length())
+      {
+        return id.startsWith(s.id) ? (WORD_SEP.indexOf(id.charAt(s.id
+                .length())) > -1) : false;
+      }
+      else
+      {
+        return s.id.startsWith(id) ? (s.id.equals(id) ? true : (WORD_SEP
+                .indexOf(s.id.charAt(id.length())) > -1)) : false;
+      }
+    }
+
+    public boolean equals(String s)
+    {
+      if (id.length() > s.length())
+      {
+        return id.startsWith(s) ? (WORD_SEP.indexOf(id.charAt(s.length())) > -1)
+                : false;
+      }
+      else
+      {
+        return s.startsWith(id) ? (s.equals(id) ? true : (WORD_SEP
+                .indexOf(s.charAt(id.length())) > -1)) : false;
+      }
+    }
+  }
+}
diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 7c1ea3f..f7ecfda 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.appletgui;
 
 import java.util.*;
@@ -31,60 +30,97 @@ import jalview.schemes.*;
 import jalview.util.UrlLink;
 import jalview.io.AppletFormatAdapter;
 
-public class APopupMenu
-    extends java.awt.PopupMenu implements ActionListener, ItemListener
+public class APopupMenu extends java.awt.PopupMenu implements
+        ActionListener, ItemListener
 {
   Menu groupMenu = new Menu();
+
   MenuItem editGroupName = new MenuItem();
+
   protected MenuItem clustalColour = new MenuItem();
+
   protected MenuItem zappoColour = new MenuItem();
+
   protected MenuItem taylorColour = new MenuItem();
+
   protected MenuItem hydrophobicityColour = new MenuItem();
+
   protected MenuItem helixColour = new MenuItem();
+
   protected MenuItem strandColour = new MenuItem();
+
   protected MenuItem turnColour = new MenuItem();
+
   protected MenuItem buriedColour = new MenuItem();
+
   protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
+
   protected MenuItem userDefinedColour = new MenuItem();
+
   protected MenuItem PIDColour = new MenuItem();
+
   protected MenuItem BLOSUM62Colour = new MenuItem();
+
   MenuItem noColourmenuItem = new MenuItem();
+
   protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
 
   final AlignmentPanel ap;
+
   MenuItem unGroupMenuItem = new MenuItem();
+
   MenuItem nucleotideMenuItem = new MenuItem();
+
   Menu colourMenu = new Menu();
+
   CheckboxMenuItem showBoxes = new CheckboxMenuItem();
+
   CheckboxMenuItem showText = new CheckboxMenuItem();
+
   CheckboxMenuItem showColourText = new CheckboxMenuItem();
+
   Menu editMenu = new Menu("Edit");
+
   MenuItem copy = new MenuItem("Copy (Jalview Only)");
+
   MenuItem cut = new MenuItem("Cut (Jalview Only)");
+
   MenuItem toUpper = new MenuItem("To Upper Case");
+
   MenuItem toLower = new MenuItem("To Lower Case");
+
   MenuItem toggleCase = new MenuItem("Toggle Case");
+
   Menu outputmenu = new Menu();
+
   Menu seqMenu = new Menu();
+
   MenuItem pdb = new MenuItem();
+
   MenuItem hideSeqs = new MenuItem();
+
   MenuItem repGroup = new MenuItem();
+
   MenuItem sequenceName = new MenuItem("Edit Name/Description");
+
   MenuItem sequenceFeature = new MenuItem("Create Sequence Feature");
+
   MenuItem editSequence = new MenuItem("Edit Sequence");
 
   Sequence seq;
+
   MenuItem revealAll = new MenuItem();
+
   Menu menu1 = new Menu();
 
   public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
   {
-    ///////////////////////////////////////////////////////////
+    // /////////////////////////////////////////////////////////
     // If this is activated from the sequence panel, the user may want to
     // edit or annotate a particular residue. Therefore display the residue menu
     //
     // If from the IDPanel, we must display the sequence menu
-    //////////////////////////////////////////////////////////
+    // ////////////////////////////////////////////////////////
 
     this.ap = apanel;
     this.seq = seq;
@@ -92,17 +128,15 @@ public class APopupMenu
     try
     {
       jbInit();
-    }
-    catch (Exception e)
+    } catch (Exception e)
     {
       e.printStackTrace();
     }
 
-    for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length;
-         i++)
+    for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
     {
-      MenuItem item = new MenuItem(jalview.io.AppletFormatAdapter.
-                                   WRITEABLE_FORMATS[i]);
+      MenuItem item = new MenuItem(
+              jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
 
       item.addActionListener(this);
       outputmenu.add(item);
@@ -128,7 +162,7 @@ public class APopupMenu
       remove(groupMenu);
     }
 
-    if (links != null && links.size()>0)
+    if (links != null && links.size() > 0)
     {
       Menu linkMenu = new Menu("Link");
       String link;
@@ -141,92 +175,82 @@ public class APopupMenu
           System.err.println(urlLink.getInvalidMessage());
           continue;
         }
-        final String target = urlLink.getTarget(); // link.substring(0, link.indexOf("|"));
+        final String target = urlLink.getTarget(); // link.substring(0,
+                                                    // link.indexOf("|"));
         final String label = urlLink.getLabel();
         if (urlLink.isDynamic())
         {
 
           // collect matching db-refs
-          DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new String[]{target});
+          DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq
+                  .getDBRef(), new String[]
+          { target });
           // collect id string too
           String id = seq.getName();
-          if (dbr!=null)
+          if (dbr != null)
           {
-            for (int r=0;r<dbr.length; r++)
+            for (int r = 0; r < dbr.length; r++)
             {
-              if (id!=null && dbr[r].getAccessionId().equals(id))
+              if (id != null && dbr[r].getAccessionId().equals(id))
               {
-                // suppress duplicate link creation for the bare sequence ID string with this link
+                // suppress duplicate link creation for the bare sequence ID
+                // string with this link
                 id = null;
               }
               // create Bare ID link for this RUL
-              String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(), true);
-              if (urls!=null)
+              String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
+                      true);
+              if (urls != null)
               {
-                for (int u=0; u<urls.length; u+=2)
+                for (int u = 0; u < urls.length; u += 2)
                 {
-                  addshowLink(linkMenu, label+"|"+urls[u],urls[u+1]);
+                  addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
                 }
               }
             }
           }
-          if (id!=null)
+          if (id != null)
           {
             // create Bare ID link for this RUL
             String[] urls = urlLink.makeUrls(id, true);
-            if (urls!=null)
+            if (urls != null)
             {
-              for (int u=0; u<urls.length; u+=2)
+              for (int u = 0; u < urls.length; u += 2)
               {
-                addshowLink(linkMenu, label,urls[u+1]);
+                addshowLink(linkMenu, label, urls[u + 1]);
               }
             }
-            // addshowLink(linkMenu, target,  url_pref + id + url_suff);
+            // addshowLink(linkMenu, target, url_pref + id + url_suff);
           }
-        } else {
-          addshowLink(linkMenu, target, urlLink.getUrl_prefix()); // link.substring(link.lastIndexOf("|")+1));
         }
-        /*final String url;
-        
-        if (link.indexOf("$SEQUENCE_ID$") > -1)
+        else
         {
-          // Substitute SEQUENCE_ID string and any matching database reference accessions
-          String url_pref = link.substring(link.indexOf("|") + 1,
-                  link.indexOf("$SEQUENCE_ID$"));
-          
-          String url_suff = link.substring(link.indexOf("$SEQUENCE_ID$") + 13); 
-
-          // collect matching db-refs
-          DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new String[]{target});
-          // collect id string too
-          String id = seq.getName();
-          if (id.indexOf("|") > -1)
-          {
-            id = id.substring(id.lastIndexOf("|") + 1);
-          }
-          if (dbr!=null)
-          {
-            for (int r=0;r<dbr.length; r++)
-            {
-              if (dbr[r].getAccessionId().equals(id))
-              {
-                // suppress duplicate link creation for the bare sequence ID string with this link
-                id = null;
-              }
-              addshowLink(linkMenu, dbr[r].getSource()+"|"+dbr[r].getAccessionId(), target,
-                      url_pref+dbr[r].getAccessionId()+url_suff);
-            }
-          }
-          if (id!=null)
-          {
-            // create Bare ID link for this RUL
-            addshowLink(linkMenu, target,  url_pref + id + url_suff);
-          }
-        } else {
-          addshowLink(linkMenu, target, link.substring(link.lastIndexOf("|")+1));
-        } */
+          addshowLink(linkMenu, target, urlLink.getUrl_prefix()); // link.substring(link.lastIndexOf("|")+1));
+        }
+        /*
+         * final String url;
+         * 
+         * if (link.indexOf("$SEQUENCE_ID$") > -1) { // Substitute SEQUENCE_ID
+         * string and any matching database reference accessions String url_pref =
+         * link.substring(link.indexOf("|") + 1, link.indexOf("$SEQUENCE_ID$"));
+         * 
+         * String url_suff = link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
+         *  // collect matching db-refs DBRefEntry[] dbr =
+         * jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new
+         * String[]{target}); // collect id string too String id =
+         * seq.getName(); if (id.indexOf("|") > -1) { id =
+         * id.substring(id.lastIndexOf("|") + 1); } if (dbr!=null) { for (int
+         * r=0;r<dbr.length; r++) { if (dbr[r].getAccessionId().equals(id)) { //
+         * suppress duplicate link creation for the bare sequence ID string with
+         * this link id = null; } addshowLink(linkMenu,
+         * dbr[r].getSource()+"|"+dbr[r].getAccessionId(), target,
+         * url_pref+dbr[r].getAccessionId()+url_suff); } } if (id!=null) { //
+         * create Bare ID link for this RUL addshowLink(linkMenu, target,
+         * url_pref + id + url_suff); } } else { addshowLink(linkMenu, target,
+         * link.substring(link.lastIndexOf("|")+1)); }
+         */
       }
-    
+
       if (seq != null)
       {
         seqMenu.add(linkMenu);
@@ -251,24 +275,35 @@ public class APopupMenu
       remove(revealAll);
     }
   }
+
   /**
    * add a show URL menu item to the given linkMenu
+   * 
    * @param linkMenu
-   * @param target - menu label string
-   * @param url - url to open
+   * @param target -
+   *                menu label string
+   * @param url -
+   *                url to open
    */
-  private void addshowLink(Menu linkMenu, final String target, final String url)
+  private void addshowLink(Menu linkMenu, final String target,
+          final String url)
   {
     addshowLink(linkMenu, target, target, url);
   }
+
   /**
    * add a show URL menu item to the given linkMenu
+   * 
    * @param linkMenu
-   * @param target - URL target window
-   * @param label - menu label string
-   * @param url - url to open
+   * @param target -
+   *                URL target window
+   * @param label -
+   *                menu label string
+   * @param url -
+   *                url to open
    */
-  private void addshowLink(Menu linkMenu, final String target, final String label, final String url)
+  private void addshowLink(Menu linkMenu, final String target,
+          final String label, final String url)
   {
     MenuItem item = new MenuItem(label);
     item.addActionListener(new java.awt.event.ActionListener()
@@ -280,7 +315,6 @@ public class APopupMenu
     });
     linkMenu.add(item);
   }
- 
 
   public void itemStateChanged(ItemEvent evt)
   {
@@ -390,14 +424,10 @@ public class APopupMenu
 
     else if (source == editGroupName)
     {
-      EditNameDialog dialog = new EditNameDialog(
-          getGroup().getName(),
-          getGroup().getDescription(),
-          "       Group Name",
-          "Group Description",
-          ap.alignFrame,
-          "Edit Group Name / Description",
-          500,100, true);
+      EditNameDialog dialog = new EditNameDialog(getGroup().getName(),
+              getGroup().getDescription(), "       Group Name",
+              "Group Description", ap.alignFrame,
+              "Edit Group Name / Description", 500, 100, true);
 
       if (dialog.accept)
       {
@@ -414,39 +444,33 @@ public class APopupMenu
     {
       ap.alignFrame.cut_actionPerformed();
     }
-    else if(source == editSequence)
+    else if (source == editSequence)
     {
       SequenceGroup sg = ap.av.getSelectionGroup();
 
-      if(sg!=null)
+      if (sg != null)
       {
         if (seq == null)
           seq = (Sequence) sg.getSequenceAt(0);
 
         EditNameDialog dialog = new EditNameDialog(seq.getSequenceAsString(
-            sg.getStartRes(),
-            sg.getEndRes() + 1),
-                                                   null,
-                                                   "Edit Sequence ",
-                                                   null,
+                sg.getStartRes(), sg.getEndRes() + 1), null,
+                "Edit Sequence ", null,
 
-                                                   ap.alignFrame,
-                                                   "Edit Sequence",
-                                                   500, 100, true);
+                ap.alignFrame, "Edit Sequence", 500, 100, true);
 
         if (dialog.accept)
         {
-          EditCommand editCommand = new EditCommand(
-              "Edit Sequences", EditCommand.REPLACE,
-              dialog.getName().replace(' ', ap.av.getGapCharacter()),
-              sg.getSequencesAsArray(ap.av.hiddenRepSequences),
-              sg.getStartRes(), sg.getEndRes()+1, ap.av.alignment
-              );
+          EditCommand editCommand = new EditCommand("Edit Sequences",
+                  EditCommand.REPLACE, dialog.getName().replace(' ',
+                          ap.av.getGapCharacter()), sg
+                          .getSequencesAsArray(ap.av.hiddenRepSequences),
+                  sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment);
 
           ap.alignFrame.addHistoryItem(editCommand);
 
-          ap.av.firePropertyChange("alignment", null,
-                                 ap.av.getAlignment().getSequences());
+          ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+                  .getSequences());
         }
       }
     }
@@ -480,15 +504,14 @@ public class APopupMenu
           }
 
           regions.addElement(new int[]
-                             {start, end});
+          { start, end });
 
           if (ap.av.hasHiddenColumns)
           {
             start = ap.av.colSel.adjustForHiddenColumns(end);
             start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
           }
-        }
-        while (end < sg.getEndRes());
+        } while (end < sg.getEndRes());
 
         int[][] startEnd = new int[regions.size()][2];
         for (int i = 0; i < regions.size(); i++)
@@ -515,19 +538,18 @@ public class APopupMenu
           caseChange = ChangeCaseCommand.TO_LOWER;
         }
 
-        ChangeCaseCommand caseCommand = new ChangeCaseCommand(
-            description, sg.getSequencesAsArray(ap.av.hiddenRepSequences),
-            startEnd, caseChange
-            );
+        ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
+                sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd,
+                caseChange);
 
         ap.alignFrame.addHistoryItem(caseCommand);
 
-        ap.av.firePropertyChange("alignment", null,
-                                 ap.av.getAlignment().getSequences());
+        ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+                .getSequences());
 
       }
     }
-    else if(source == sequenceFeature)
+    else if (source == sequenceFeature)
     {
       SequenceGroup sg = ap.av.getSelectionGroup();
       if (sg == null)
@@ -545,11 +567,11 @@ public class APopupMenu
         int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
         int end = sg.findEndRes(sg.getSequenceAt(i));
         features[i] = new SequenceFeature(null, null, null, start, end,
-                                          "Jalview");
+                "Jalview");
       }
 
-      if (ap.seqPanel.seqCanvas.getFeatureRenderer()
-          .amendFeatures(seqs, features, true, ap))
+      if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
+              features, true, ap))
       {
         ap.alignFrame.sequenceFeatures.setState(true);
         ap.av.showSequenceFeatures(true);
@@ -569,27 +591,21 @@ public class APopupMenu
 
     Frame frame = new Frame();
     frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame,
-                                     "Selection output - " + e.getActionCommand(),
-                                     600, 500);
+    jalview.bin.JalviewLite.addFrame(frame, "Selection output - "
+            + e.getActionCommand(), 600, 500);
 
-    cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
-        e.getActionCommand(),
-        new Alignment(ap.av.getSelectionAsNewSequence()),
-        ap.av.showJVSuffix));
+    cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(e
+            .getActionCommand(), new Alignment(ap.av
+            .getSelectionAsNewSequence()), ap.av.showJVSuffix));
 
   }
 
   void editName()
   {
-    EditNameDialog dialog = new EditNameDialog(
-        seq.getName(),
-        seq.getDescription(),
-        "       Sequence Name",
-        "Sequence Description",
-        ap.alignFrame,
-        "Edit Sequence Name / Description",
-        500,100, true);
+    EditNameDialog dialog = new EditNameDialog(seq.getName(), seq
+            .getDescription(), "       Sequence Name",
+            "Sequence Description", ap.alignFrame,
+            "Edit Sequence Name / Description", 500, 100, true);
 
     if (dialog.accept)
     {
@@ -601,22 +617,16 @@ public class APopupMenu
 
   void addPDB()
   {
-    if(seq.getPDBId()!=null)
+    if (seq.getPDBId() != null)
     {
-      PDBEntry entry = (PDBEntry)seq.getPDBId().firstElement();
+      PDBEntry entry = (PDBEntry) seq.getPDBId().firstElement();
 
-      if ( ap.av.applet.jmolAvailable )
-       new jalview.appletgui.AppletJmol(entry,
-                                        new Sequence[]{seq},
-                                        null,
-                                        ap,
-                                        AppletFormatAdapter.URL);
-     else
-       new MCview.AppletPDBViewer(entry,
-                                  new Sequence[]{seq},
-                                  null,
-                                  ap,
-                                  AppletFormatAdapter.URL);
+      if (ap.av.applet.jmolAvailable)
+        new jalview.appletgui.AppletJmol(entry, new Sequence[]
+        { seq }, null, ap, AppletFormatAdapter.URL);
+      else
+        new MCview.AppletPDBViewer(entry, new Sequence[]
+        { seq }, null, ap, AppletFormatAdapter.URL);
 
     }
     else
@@ -630,8 +640,7 @@ public class APopupMenu
     }
   }
 
-  private void jbInit()
-      throws Exception
+  private void jbInit() throws Exception
   {
     groupMenu.setLabel("Group");
     groupMenu.setLabel("Selection");
@@ -754,8 +763,9 @@ public class APopupMenu
   protected void clustalColour_actionPerformed()
   {
     SequenceGroup sg = getGroup();
-    sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),
-                                     ap.av.alignment.getWidth());
+    sg.cs = new ClustalxColourScheme(sg
+            .getSequences(ap.av.hiddenRepSequences), ap.av.alignment
+            .getWidth());
     refresh();
   }
 
@@ -817,18 +827,19 @@ public class APopupMenu
 
     if (abovePIDColour.getState())
     {
-      sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
-          hiddenRepSequences), 0,
-                                               ap.av.alignment.getWidth()));
-      int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
-          getGroup().getName());
+      sg.cs.setConsensus(AAFrequency.calculate(sg
+              .getSequences(ap.av.hiddenRepSequences), 0, ap.av.alignment
+              .getWidth()));
+      int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
+              .getName());
 
       sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
 
       SliderPanel.showPIDSlider();
 
     }
-    else // remove PIDColouring
+    else
+    // remove PIDColouring
     {
       sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
     }
@@ -846,9 +857,9 @@ public class APopupMenu
   {
     SequenceGroup sg = getGroup();
     sg.cs = new PIDColourScheme();
-    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
-        hiddenRepSequences), 0,
-                                             ap.av.alignment.getWidth()));
+    sg.cs.setConsensus(AAFrequency.calculate(sg
+            .getSequences(ap.av.hiddenRepSequences), 0, ap.av.alignment
+            .getWidth()));
     refresh();
   }
 
@@ -858,9 +869,9 @@ public class APopupMenu
 
     sg.cs = new Blosum62ColourScheme();
 
-    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
-        hiddenRepSequences), 0,
-                                             ap.av.alignment.getWidth()));
+    sg.cs.setConsensus(AAFrequency.calculate(sg
+            .getSequences(ap.av.hiddenRepSequences), 0, ap.av.alignment
+            .getWidth()));
 
     refresh();
   }
@@ -883,10 +894,9 @@ public class APopupMenu
     {
 
       Conservation c = new Conservation("Group",
-                                        ResidueProperties.propHash, 3,
-                                        sg.getSequences(ap.av.
-          hiddenRepSequences), 0,
-                                        ap.av.alignment.getWidth());
+              ResidueProperties.propHash, 3, sg
+                      .getSequences(ap.av.hiddenRepSequences), 0,
+              ap.av.alignment.getWidth());
 
       c.calculate();
       c.verdict(false, ap.av.ConsPercGaps);
@@ -896,7 +906,8 @@ public class APopupMenu
       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
       SliderPanel.showConservationSlider();
     }
-    else // remove ConservationColouring
+    else
+    // remove ConservationColouring
     {
       sg.cs.setConservation(null);
     }
@@ -949,7 +960,7 @@ public class APopupMenu
     if (sg == null || sg.getSize() < 1)
     {
       ap.av.hideSequence(new SequenceI[]
-                         {seq});
+      { seq });
       return;
     }
 
diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index d7c2b43..3e214b8 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.appletgui;
 
 import java.io.*;
@@ -32,21 +31,21 @@ import jalview.datamodel.*;
 import jalview.io.*;
 import jalview.schemes.*;
 
-public class AlignFrame
-    extends EmbmenuFrame implements ActionListener,
-    ItemListener, KeyListener
+public class AlignFrame extends EmbmenuFrame implements ActionListener,
+        ItemListener, KeyListener
 {
   public AlignmentPanel alignPanel;
+
   public AlignViewport viewport;
+
   int DEFAULT_WIDTH = 700;
+
   int DEFAULT_HEIGHT = 500;
 
   String jalviewServletURL;
 
-  public AlignFrame(AlignmentI al,
-                    jalview.bin.JalviewLite applet,
-                    String title,
-                    boolean embedded)
+  public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
+          String title, boolean embedded)
   {
 
     if (applet != null)
@@ -57,8 +56,7 @@ public class AlignFrame
     try
     {
       jbInit();
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       ex.printStackTrace();
     }
@@ -118,14 +116,15 @@ public class AlignFrame
           int height = Integer.parseInt(param);
           DEFAULT_HEIGHT = height;
         }
+      } catch (Exception ex)
+      {
       }
-      catch (Exception ex)
-      {}
 
     }
 
-    //Some JVMS send keyevents to Top frame or lowest panel,
-    //Havent worked out why yet. So add to both this frame and seqCanvas for now
+    // Some JVMS send keyevents to Top frame or lowest panel,
+    // Havent worked out why yet. So add to both this frame and seqCanvas for
+    // now
     this.addKeyListener(this);
     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
     alignPanel.idPanel.idCanvas.addKeyListener(this);
@@ -148,8 +147,9 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param String DOCUMENT ME!
+   * 
+   * @param String
+   *                DOCUMENT ME!
    */
 
   public void parseFeaturesFile(String file, String type)
@@ -158,14 +158,11 @@ public class AlignFrame
     boolean featuresFile = false;
     try
     {
-      featuresFile = new jalview.io.FeaturesFile(file,
-          type).parse(viewport.alignment,
-                      alignPanel.seqPanel.seqCanvas.
-                      getFeatureRenderer().featureColours,
-                      featureLinks,
-                      true);
-    }
-    catch (Exception ex)
+      featuresFile = new jalview.io.FeaturesFile(file, type).parse(
+              viewport.alignment, alignPanel.seqPanel.seqCanvas
+                      .getFeatureRenderer().featureColours, featureLinks,
+              true);
+    } catch (Exception ex)
     {
       ex.printStackTrace();
     }
@@ -174,8 +171,7 @@ public class AlignFrame
     {
       if (featureLinks.size() > 0)
       {
-        alignPanel.seqPanel.seqCanvas
-            .getFeatureRenderer().featureLinks = featureLinks;
+        alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
       }
       viewport.showSequenceFeatures = true;
       sequenceFeatures.setState(true);
@@ -186,307 +182,298 @@ public class AlignFrame
 
   public void keyPressed(KeyEvent evt)
   {
-    if (viewport.cursorMode &&
-        ( (evt.getKeyCode() >= KeyEvent.VK_0 &&
-           evt.getKeyCode() <= KeyEvent.VK_9)
-         ||
-         (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0 &&
-          evt.getKeyCode() <= KeyEvent.VK_NUMPAD9)
-        )
-        && Character.isDigit(evt.getKeyChar()))
-            alignPanel.seqPanel.numberPressed(evt.getKeyChar());
-
+    if (viewport.cursorMode
+            && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
+                    .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
+                    .getKeyCode() <= KeyEvent.VK_NUMPAD9))
+            && Character.isDigit(evt.getKeyChar()))
+      alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 
     switch (evt.getKeyCode())
     {
-      case 27: // escape key
-        deselectAllSequenceMenuItem_actionPerformed();
-        break;
-      case KeyEvent.VK_X:
-        if (evt.isControlDown() || evt.isMetaDown())
-        {
-          cut_actionPerformed();
-        }
-        break;
-      case KeyEvent.VK_C:
-        if (viewport.cursorMode && !evt.isControlDown())
-        {
-          alignPanel.seqPanel.setCursorColumn();
-        }
-        if (evt.isControlDown() || evt.isMetaDown())
-        {
-          copy_actionPerformed();
-        }
-        break;
-      case KeyEvent.VK_V:
-        if (evt.isControlDown())
-        {
-          paste(evt.isShiftDown());
-        }
-        break;
-      case KeyEvent.VK_A:
-        if (evt.isControlDown() || evt.isMetaDown())
-        {
-          selectAllSequenceMenuItem_actionPerformed();
-        }
-        break;
-      case KeyEvent.VK_DOWN:
-        if (viewport.cursorMode)
-        {
-          alignPanel.seqPanel.moveCursor(0, 1);
-        }
-        else
-        {
-          moveSelectedSequences(false);
-        }
-        break;
+    case 27: // escape key
+      deselectAllSequenceMenuItem_actionPerformed();
+      break;
+    case KeyEvent.VK_X:
+      if (evt.isControlDown() || evt.isMetaDown())
+      {
+        cut_actionPerformed();
+      }
+      break;
+    case KeyEvent.VK_C:
+      if (viewport.cursorMode && !evt.isControlDown())
+      {
+        alignPanel.seqPanel.setCursorColumn();
+      }
+      if (evt.isControlDown() || evt.isMetaDown())
+      {
+        copy_actionPerformed();
+      }
+      break;
+    case KeyEvent.VK_V:
+      if (evt.isControlDown())
+      {
+        paste(evt.isShiftDown());
+      }
+      break;
+    case KeyEvent.VK_A:
+      if (evt.isControlDown() || evt.isMetaDown())
+      {
+        selectAllSequenceMenuItem_actionPerformed();
+      }
+      break;
+    case KeyEvent.VK_DOWN:
+      if (viewport.cursorMode)
+      {
+        alignPanel.seqPanel.moveCursor(0, 1);
+      }
+      else
+      {
+        moveSelectedSequences(false);
+      }
+      break;
 
-      case KeyEvent.VK_UP:
-        if (viewport.cursorMode)
-        {
-          alignPanel.seqPanel.moveCursor(0, -1);
-        }
-        else
-        {
-          moveSelectedSequences(true);
-        }
-        break;
+    case KeyEvent.VK_UP:
+      if (viewport.cursorMode)
+      {
+        alignPanel.seqPanel.moveCursor(0, -1);
+      }
+      else
+      {
+        moveSelectedSequences(true);
+      }
+      break;
 
-      case KeyEvent.VK_LEFT:
-        if (evt.isAltDown() || !viewport.cursorMode)
-          slideSequences(false,
-                         alignPanel.seqPanel.getKeyboardNo1());
-        else
-          alignPanel.seqPanel.moveCursor( -1, 0);
-        break;
+    case KeyEvent.VK_LEFT:
+      if (evt.isAltDown() || !viewport.cursorMode)
+        slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
+      else
+        alignPanel.seqPanel.moveCursor(-1, 0);
+      break;
 
-      case KeyEvent.VK_RIGHT:
-        if (evt.isAltDown() || !viewport.cursorMode)
-          slideSequences(true,
-                         alignPanel.seqPanel.getKeyboardNo1());
-        else
-          alignPanel.seqPanel.moveCursor( 1, 0);
-            break;
+    case KeyEvent.VK_RIGHT:
+      if (evt.isAltDown() || !viewport.cursorMode)
+        slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
+      else
+        alignPanel.seqPanel.moveCursor(1, 0);
+      break;
 
-      case KeyEvent.VK_SPACE:
-        if (viewport.cursorMode)
-        {
-          alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
-                                                || evt.isShiftDown()
-                                                || evt.isAltDown()
-              );
-        }
-        break;
+    case KeyEvent.VK_SPACE:
+      if (viewport.cursorMode)
+      {
+        alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
+                || evt.isShiftDown() || evt.isAltDown());
+      }
+      break;
 
-      case KeyEvent.VK_DELETE:
-      case KeyEvent.VK_BACK_SPACE:
-        if (viewport.cursorMode)
-        {
-          alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
-                                                || evt.isShiftDown()
-                                                || evt.isAltDown());
-        }
-        else
-        {
-          cut_actionPerformed();
-          alignPanel.seqPanel.seqCanvas.repaint();
-        }
-        break;
+    case KeyEvent.VK_DELETE:
+    case KeyEvent.VK_BACK_SPACE:
+      if (viewport.cursorMode)
+      {
+        alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
+                || evt.isShiftDown() || evt.isAltDown());
+      }
+      else
+      {
+        cut_actionPerformed();
+        alignPanel.seqPanel.seqCanvas.repaint();
+      }
+      break;
 
-      case KeyEvent.VK_S:
-        if (viewport.cursorMode)
-        {
-          alignPanel.seqPanel.setCursorRow();
-        }
-        break;
-      case KeyEvent.VK_P:
-        if (viewport.cursorMode)
-        {
-          alignPanel.seqPanel.setCursorPosition();
-        }
-        break;
+    case KeyEvent.VK_S:
+      if (viewport.cursorMode)
+      {
+        alignPanel.seqPanel.setCursorRow();
+      }
+      break;
+    case KeyEvent.VK_P:
+      if (viewport.cursorMode)
+      {
+        alignPanel.seqPanel.setCursorPosition();
+      }
+      break;
 
-      case KeyEvent.VK_ENTER:
-      case KeyEvent.VK_COMMA:
-        if (viewport.cursorMode)
-        {
-          alignPanel.seqPanel.setCursorRowAndColumn();
-        }
-        break;
+    case KeyEvent.VK_ENTER:
+    case KeyEvent.VK_COMMA:
+      if (viewport.cursorMode)
+      {
+        alignPanel.seqPanel.setCursorRowAndColumn();
+      }
+      break;
 
-      case KeyEvent.VK_Q:
-        if (viewport.cursorMode)
-        {
-          alignPanel.seqPanel.setSelectionAreaAtCursor(true);
-        }
-        break;
-      case KeyEvent.VK_M:
-        if (viewport.cursorMode)
-        {
-          alignPanel.seqPanel.setSelectionAreaAtCursor(false);
-        }
-        break;
+    case KeyEvent.VK_Q:
+      if (viewport.cursorMode)
+      {
+        alignPanel.seqPanel.setSelectionAreaAtCursor(true);
+      }
+      break;
+    case KeyEvent.VK_M:
+      if (viewport.cursorMode)
+      {
+        alignPanel.seqPanel.setSelectionAreaAtCursor(false);
+      }
+      break;
+
+    case KeyEvent.VK_F2:
+      viewport.cursorMode = !viewport.cursorMode;
+      statusBar.setText("Keyboard editing mode is "
+              + (viewport.cursorMode ? "on" : "off"));
+      if (viewport.cursorMode)
+      {
+        alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
+        alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
+      }
+      break;
+
+    case KeyEvent.VK_F:
+      if (evt.isControlDown())
+      {
+        findMenuItem_actionPerformed();
+      }
+      break;
+
+    case KeyEvent.VK_H:
+    {
+      boolean toggleSeqs = !evt.isControlDown();
+      boolean toggleCols = !evt.isShiftDown();
+      boolean hide = false;
+      SequenceGroup sg = viewport.getSelectionGroup();
 
-      case KeyEvent.VK_F2:
-        viewport.cursorMode = !viewport.cursorMode;
-        statusBar.setText("Keyboard editing mode is " +
-                          (viewport.cursorMode ? "on" : "off"));
-        if (viewport.cursorMode)
+      if (toggleSeqs)
+      {
+        if (sg != null && sg.getSize() != viewport.alignment.getHeight())
         {
-          alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
-          alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
+          hide = true;
+          viewport.hideAllSelectedSeqs();
         }
-        break;
-
-      case KeyEvent.VK_F:
-        if (evt.isControlDown())
+        else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
         {
-          findMenuItem_actionPerformed();
+          viewport.showAllHiddenSeqs();
         }
-        break;
+      }
 
-      case KeyEvent.VK_H:
+      if (toggleCols)
       {
-        boolean toggleSeqs = !evt.isControlDown();
-        boolean toggleCols = !evt.isShiftDown();
-        boolean hide = false;
-        SequenceGroup sg = viewport.getSelectionGroup();
-
-        if (toggleSeqs)
+        if (viewport.colSel.getSelected().size() > 0)
         {
-          if (sg != null && sg.getSize() != viewport.alignment.getHeight())
-          {
-            hide = true;
-            viewport.hideAllSelectedSeqs();
-          }
-          else if (! (toggleCols && viewport.colSel.getSelected().size() > 0))
+          viewport.hideSelectedColumns();
+          if (!toggleSeqs)
           {
-            viewport.showAllHiddenSeqs();
+            viewport.selectionGroup = sg;
           }
         }
-
-        if (toggleCols)
+        else if (!hide)
         {
-          if (viewport.colSel.getSelected().size() > 0)
-          {
-            viewport.hideSelectedColumns();
-            if (!toggleSeqs)
-            {
-              viewport.selectionGroup = sg;
-            }
-          }
-          else if (!hide)
-          {
-            viewport.showAllHiddenColumns();
-          }
+          viewport.showAllHiddenColumns();
         }
-        break;
       }
+      break;
+    }
 
-      case KeyEvent.VK_PAGE_UP:
-        if (viewport.wrapAlignment)
-        {
-          alignPanel.scrollUp(true);
-        }
-        else
-        {
-          alignPanel.setScrollValues(viewport.startRes,
-                                     viewport.startSeq
-                                     - viewport.endSeq + viewport.startSeq);
-        }
-        break;
+    case KeyEvent.VK_PAGE_UP:
+      if (viewport.wrapAlignment)
+      {
+        alignPanel.scrollUp(true);
+      }
+      else
+      {
+        alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
+                - viewport.endSeq + viewport.startSeq);
+      }
+      break;
 
-      case KeyEvent.VK_PAGE_DOWN:
-        if (viewport.wrapAlignment)
-        {
-          alignPanel.scrollUp(false);
-        }
-        else
-        {
-          alignPanel.setScrollValues(viewport.startRes,
-                                     viewport.startSeq
-                                     + viewport.endSeq - viewport.startSeq);
-        }
-        break;
+    case KeyEvent.VK_PAGE_DOWN:
+      if (viewport.wrapAlignment)
+      {
+        alignPanel.scrollUp(false);
+      }
+      else
+      {
+        alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
+                + viewport.endSeq - viewport.startSeq);
+      }
+      break;
 
-      case KeyEvent.VK_Z:
-        if (evt.isControlDown())
-        {
-          undoMenuItem_actionPerformed();
-        }
-        break;
+    case KeyEvent.VK_Z:
+      if (evt.isControlDown())
+      {
+        undoMenuItem_actionPerformed();
+      }
+      break;
 
-      case KeyEvent.VK_Y:
-        if (evt.isControlDown())
-        {
-          redoMenuItem_actionPerformed();
-        }
-        break;
+    case KeyEvent.VK_Y:
+      if (evt.isControlDown())
+      {
+        redoMenuItem_actionPerformed();
+      }
+      break;
 
-      case KeyEvent.VK_L:
-        if (evt.isControlDown())
-        {
-          trimAlignment(true);
-        }
-        break;
+    case KeyEvent.VK_L:
+      if (evt.isControlDown())
+      {
+        trimAlignment(true);
+      }
+      break;
 
-      case KeyEvent.VK_R:
-        if (evt.isControlDown())
-        {
-          trimAlignment(false);
-        }
-        break;
+    case KeyEvent.VK_R:
+      if (evt.isControlDown())
+      {
+        trimAlignment(false);
+      }
+      break;
 
-      case KeyEvent.VK_E:
-        if (evt.isControlDown())
+    case KeyEvent.VK_E:
+      if (evt.isControlDown())
+      {
+        if (evt.isShiftDown())
         {
-          if (evt.isShiftDown())
-          {
-            this.removeAllGapsMenuItem_actionPerformed();
-          }
-          else
-          {
-            removeGappedColumnMenuItem_actionPerformed();
-          }
+          this.removeAllGapsMenuItem_actionPerformed();
         }
-        break;
-      case KeyEvent.VK_I:
-        if (evt.isControlDown())
+        else
         {
-          if (evt.isAltDown())
-          {
-            viewport.invertColumnSelection();
-          }
-          else
-          {
-            this.invertSequenceMenuItem_actionPerformed();
-          }
+          removeGappedColumnMenuItem_actionPerformed();
         }
-        break;
-
-      case KeyEvent.VK_U:
-        if (evt.isControlDown())
+      }
+      break;
+    case KeyEvent.VK_I:
+      if (evt.isControlDown())
+      {
+        if (evt.isAltDown())
         {
-          this.deleteGroups_actionPerformed();
+          viewport.invertColumnSelection();
         }
-        break;
-
-      case KeyEvent.VK_T:
-        if (evt.isControlDown())
+        else
         {
-          newView(null);
+          this.invertSequenceMenuItem_actionPerformed();
         }
-        break;
+      }
+      break;
+
+    case KeyEvent.VK_U:
+      if (evt.isControlDown())
+      {
+        this.deleteGroups_actionPerformed();
+      }
+      break;
+
+    case KeyEvent.VK_T:
+      if (evt.isControlDown())
+      {
+        newView(null);
+      }
+      break;
 
     }
     alignPanel.paintAlignment(true);
   }
 
   public void keyReleased(KeyEvent evt)
-  {}
+  {
+  }
 
   public void keyTyped(KeyEvent evt)
-  {}
+  {
+  }
 
   public void itemStateChanged(ItemEvent evt)
   {
@@ -551,11 +538,12 @@ public class AlignFrame
     else if (evt.getSource() == autoCalculate)
     {
       viewport.autocalculateConsensus = autoCalculate.getState();
-    } else if (evt.getSource() == this.centreColumnLabelFlag)
+    }
+    else if (evt.getSource() == this.centreColumnLabelFlag)
     {
       centreColumnLabelFlag_stateChanged();
     }
-    
+
     alignPanel.paintAlignment(true);
   }
 
@@ -708,7 +696,8 @@ public class AlignFrame
       viewport.hideSelectedColumns();
       alignPanel.paintAlignment(true);
     }
-    else if (source == hideSequences && viewport.getSelectionGroup() != null)
+    else if (source == hideSequences
+            && viewport.getSelectionGroup() != null)
     {
       viewport.hideAllSelectedSeqs();
     }
@@ -716,47 +705,46 @@ public class AlignFrame
     {
       new FeatureSettings(alignPanel);
     }
-    else if(source== alProperties)
+    else if (source == alProperties)
     {
-        StringBuffer contents = new StringBuffer();
+      StringBuffer contents = new StringBuffer();
 
-        float avg  = 0;
-        int min=Integer.MAX_VALUE, max=0;
-        for(int i=0; i<viewport.alignment.getHeight(); i++)
-        {
-          int size = viewport.alignment.getSequenceAt(i).getEnd()
-              -viewport.alignment.getSequenceAt(i).getStart();
-          avg += size;
-          if(size>max)
-            max = size;
-          if(size<min)
-            min = size;
-        }
-        avg = avg/(float)viewport.alignment.getHeight();
+      float avg = 0;
+      int min = Integer.MAX_VALUE, max = 0;
+      for (int i = 0; i < viewport.alignment.getHeight(); i++)
+      {
+        int size = viewport.alignment.getSequenceAt(i).getEnd()
+                - viewport.alignment.getSequenceAt(i).getStart();
+        avg += size;
+        if (size > max)
+          max = size;
+        if (size < min)
+          min = size;
+      }
+      avg = avg / (float) viewport.alignment.getHeight();
 
-        contents.append("\nSequences: "+ viewport.alignment.getHeight());
-        contents.append("\nMinimum Sequence Length: "+min);
-        contents.append("\nMaximum Sequence Length: "+max);
-        contents.append("\nAverage Length: "+(int)avg);
+      contents.append("\nSequences: " + viewport.alignment.getHeight());
+      contents.append("\nMinimum Sequence Length: " + min);
+      contents.append("\nMaximum Sequence Length: " + max);
+      contents.append("\nAverage Length: " + (int) avg);
 
-        if (((Alignment)viewport.alignment).alignmentProperties != null)
+      if (((Alignment) viewport.alignment).alignmentProperties != null)
+      {
+        Hashtable props = ((Alignment) viewport.alignment).alignmentProperties;
+        Enumeration en = props.keys();
+        while (en.hasMoreElements())
         {
-          Hashtable props = ((Alignment)viewport.alignment).alignmentProperties;
-          Enumeration en = props.keys();
-          while(en.hasMoreElements())
-          {
-            String key = en.nextElement().toString();
-            contents.append("\n"+key+"\t"+props.get(key));
-          }
+          String key = en.nextElement().toString();
+          contents.append("\n" + key + "\t" + props.get(key));
         }
+      }
 
-        CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
-        cap.setText(contents.toString());
-        Frame frame = new Frame();
-        frame.add(cap);
-        jalview.bin.JalviewLite.addFrame(frame,
-                                         "Alignment Properties: "+getTitle()
-                                         , 400, 250);
+      CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
+      cap.setText(contents.toString());
+      Frame frame = new Frame();
+      frame.add(cap);
+      jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
+              + getTitle(), 400, 250);
     }
     else if (source == overviewMenuItem)
     {
@@ -769,8 +757,8 @@ public class AlignFrame
     else if (source == clustalColour)
     {
       abovePIDThreshold.setState(false);
-      changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
-                                            viewport.alignment.getWidth()));
+      changeColour(new ClustalxColourScheme(viewport.alignment
+              .getSequences(), viewport.alignment.getWidth()));
     }
     else if (source == zappoColour)
     {
@@ -892,12 +880,11 @@ public class AlignFrame
     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
     Frame frame = new Frame();
     frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame,
-                                     "Alignment output - " + e.getActionCommand(),
-                                     600, 500);
-    cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),
-        viewport.getAlignment(),
-        viewport.showJVSuffix));
+    jalview.bin.JalviewLite.addFrame(frame, "Alignment output - "
+            + e.getActionCommand(), 600, 500);
+    cap.setText(new AppletFormatAdapter().formatSequences(e
+            .getActionCommand(), viewport.getAlignment(),
+            viewport.showJVSuffix));
   }
 
   public void loadAnnotations()
@@ -914,18 +901,17 @@ public class AlignFrame
   public String outputAnnotations(boolean displayTextbox)
   {
     String annotation = new AnnotationFile().printAnnotations(
-        viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null,
-        viewport.alignment.getGroups(),
-         ((Alignment) viewport.alignment).alignmentProperties);
+            viewport.showAnnotation ? viewport.alignment
+                    .getAlignmentAnnotation() : null, viewport.alignment
+                    .getGroups(),
+            ((Alignment) viewport.alignment).alignmentProperties);
 
     if (displayTextbox)
     {
       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
       Frame frame = new Frame();
       frame.add(cap);
-      jalview.bin.JalviewLite.addFrame(frame,
-                                       "Annotations",
-                                       600, 500);
+      jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
       cap.setText(annotation);
     }
 
@@ -937,15 +923,13 @@ public class AlignFrame
     String features;
     if (format.equalsIgnoreCase("Jalview"))
     {
-      features = new FeaturesFile().printJalviewFormat(
-          viewport.alignment.getSequencesArray(),
-          viewport.featuresDisplayed);
+      features = new FeaturesFile().printJalviewFormat(viewport.alignment
+              .getSequencesArray(), viewport.featuresDisplayed);
     }
     else
     {
-      features = new FeaturesFile().printGFFFormat(
-          viewport.alignment.getSequencesArray(),
-          viewport.featuresDisplayed);
+      features = new FeaturesFile().printGFFFormat(viewport.alignment
+              .getSequencesArray(), viewport.featuresDisplayed);
     }
 
     if (displayTextbox)
@@ -953,9 +937,7 @@ public class AlignFrame
       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
       Frame frame = new Frame();
       frame.add(cap);
-      jalview.bin.JalviewLite.addFrame(frame,
-                                       "Features",
-                                       600, 500);
+      jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
 
       cap.setText(features);
     }
@@ -967,8 +949,8 @@ public class AlignFrame
   {
     StringBuffer url = new StringBuffer(jalviewServletURL);
 
-    url.append("?open=" +
-               appendProtocol(viewport.applet.getParameter("file")));
+    url.append("?open="
+            + appendProtocol(viewport.applet.getParameter("file")));
 
     if (viewport.applet.getParameter("features") != null)
     {
@@ -979,7 +961,9 @@ public class AlignFrame
     if (viewport.applet.getParameter("annotations") != null)
     {
       url.append("&annotations=");
-      url.append(appendProtocol(viewport.applet.getParameter("annotations")));
+      url
+              .append(appendProtocol(viewport.applet
+                      .getParameter("annotations")));
     }
 
     if (viewport.applet.getParameter("jnetfile") != null)
@@ -990,25 +974,26 @@ public class AlignFrame
 
     if (viewport.applet.getParameter("defaultColour") != null)
     {
-      url.append("&colour=" +
-                 removeWhiteSpace(viewport.applet.getParameter("defaultColour"))
-          );
+      url.append("&colour="
+              + removeWhiteSpace(viewport.applet
+                      .getParameter("defaultColour")));
     }
 
     if (viewport.applet.getParameter("userDefinedColour") != null)
     {
-      url.append("&colour=" +
-                 removeWhiteSpace(viewport.applet.getParameter(
-          "userDefinedColour"))
-          );
+      url.append("&colour="
+              + removeWhiteSpace(viewport.applet
+                      .getParameter("userDefinedColour")));
     }
-    if (viewport.applet.getParameter("tree")!=null)
+    if (viewport.applet.getParameter("tree") != null)
     {
-      url.append("&tree="+appendProtocol(viewport.applet.getParameter("tree")));
+      url.append("&tree="
+              + appendProtocol(viewport.applet.getParameter("tree")));
     }
-    if (viewport.applet.getParameter("treeFile")!=null)
+    if (viewport.applet.getParameter("treeFile") != null)
     {
-      url.append("&tree="+appendProtocol(viewport.applet.getParameter("treeFile")));
+      url.append("&tree="
+              + appendProtocol(viewport.applet.getParameter("treeFile")));
     }
 
     showURL(url.toString(), "FULL_APP");
@@ -1039,14 +1024,13 @@ public class AlignFrame
       new URL(url);
       url = URLEncoder.encode(url);
     }
-    /* When we finally deprecate 1.1 compatibility, 
-     * we can start to use URLEncoder.encode(url,"UTF-8") 
-     * and then we'll need this catch:
-     * catch (UnsupportedEncodingException ex)
-    {
-      System.err.println("WARNING - IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
-      ex.printStackTrace();
-    } */
+    /*
+     * When we finally deprecate 1.1 compatibility, we can start to use
+     * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
+     * (UnsupportedEncodingException ex) { System.err.println("WARNING -
+     * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
+     * ex.printStackTrace(); }
+     */
     catch (java.net.MalformedURLException ex)
     {
       url = viewport.applet.getCodeBase() + url;
@@ -1110,10 +1094,12 @@ public class AlignFrame
       viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
     }
   }
+
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void undoMenuItem_actionPerformed()
   {
@@ -1131,13 +1117,14 @@ public class AlignFrame
     originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
     updateEditMenuBar();
     originalSource.firePropertyChange("alignment", null,
-                                      originalSource.alignment.getSequences());
+            originalSource.alignment.getSequences());
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void redoMenuItem_actionPerformed()
   {
@@ -1155,29 +1142,29 @@ public class AlignFrame
 
     updateEditMenuBar();
     originalSource.firePropertyChange("alignment", null,
-                                      originalSource.alignment.getSequences());
+            originalSource.alignment.getSequences());
   }
 
   AlignViewport getOriginatingSource(CommandI command)
   {
     AlignViewport originalSource = null;
-    //For sequence removal and addition, we need to fire
-    //the property change event FROM the viewport where the
-    //original alignment was altered
+    // For sequence removal and addition, we need to fire
+    // the property change event FROM the viewport where the
+    // original alignment was altered
     AlignmentI al = null;
     if (command instanceof EditCommand)
     {
       EditCommand editCommand = (EditCommand) command;
       al = editCommand.getAlignment();
-      Vector comps = (Vector) PaintRefresher.components
-          .get(viewport.getSequenceSetId());
+      Vector comps = (Vector) PaintRefresher.components.get(viewport
+              .getSequenceSetId());
       for (int i = 0; i < comps.size(); i++)
       {
         if (comps.elementAt(i) instanceof AlignmentPanel)
         {
-          if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)
+          if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
           {
-            originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;
+            originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
             break;
           }
         }
@@ -1186,8 +1173,8 @@ public class AlignFrame
 
     if (originalSource == null)
     {
-      //The original view is closed, we must validate
-      //the current view against the closed view first
+      // The original view is closed, we must validate
+      // the current view against the closed view first
       if (al != null)
       {
         PaintRefresher.validateSequences(al, viewport.alignment);
@@ -1254,19 +1241,20 @@ public class AlignFrame
   synchronized void slideSequences(boolean right, int size)
   {
     Vector sg = new Vector();
-    if(viewport.cursorMode)
+    if (viewport.cursorMode)
+    {
+      sg.addElement(viewport.alignment
+              .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
+    }
+    else if (viewport.getSelectionGroup() != null
+            && viewport.getSelectionGroup().getSize() != viewport.alignment
+                    .getHeight())
     {
-      sg.addElement(viewport.alignment.getSequenceAt(
-          alignPanel.seqPanel.seqCanvas.cursorY));
+      sg = viewport.getSelectionGroup().getSequences(
+              viewport.hiddenRepSequences);
     }
-    else if(viewport.getSelectionGroup()!=null
-        && viewport.getSelectionGroup().getSize()!=viewport.alignment.getHeight())
-   {
-     sg = viewport.getSelectionGroup().getSequences(
-         viewport.hiddenRepSequences);
-   }
 
-    if(sg.size()<1)
+    if (sg.size() < 1)
     {
       return;
     }
@@ -1275,8 +1263,8 @@ public class AlignFrame
 
     for (int i = 0; i < viewport.alignment.getHeight(); i++)
     {
-      if(!sg.contains(viewport.alignment.getSequenceAt(i)))
-         invertGroup.addElement(viewport.alignment.getSequenceAt(i));
+      if (!sg.contains(viewport.alignment.getSequenceAt(i)))
+        invertGroup.addElement(viewport.alignment.getSequenceAt(i));
     }
 
     SequenceI[] seqs1 = new SequenceI[sg.size()];
@@ -1289,15 +1277,11 @@ public class AlignFrame
 
     SlideSequencesCommand ssc;
     if (right)
-      ssc = new SlideSequencesCommand("Slide Sequences",
-                                      seqs2, seqs1, size,
-                                      viewport.getGapCharacter()
-          );
+      ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
+              size, viewport.getGapCharacter());
     else
-      ssc = new SlideSequencesCommand("Slide Sequences",
-                                      seqs1, seqs2, size,
-                                      viewport.getGapCharacter()
-          );
+      ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
+              size, viewport.getGapCharacter());
 
     int groupAdjustment = 0;
     if (ssc.getGapsInsertedBegin() && right)
@@ -1310,7 +1294,7 @@ public class AlignFrame
     else if (!ssc.getGapsInsertedBegin() && !right)
     {
       if (viewport.cursorMode)
-        alignPanel.seqPanel.moveCursor( -size, 0);
+        alignPanel.seqPanel.moveCursor(-size, 0);
       else
         groupAdjustment = -size;
     }
@@ -1318,30 +1302,30 @@ public class AlignFrame
     if (groupAdjustment != 0)
     {
       viewport.getSelectionGroup().setStartRes(
-          viewport.getSelectionGroup().getStartRes() + groupAdjustment);
+              viewport.getSelectionGroup().getStartRes() + groupAdjustment);
       viewport.getSelectionGroup().setEndRes(
-          viewport.getSelectionGroup().getEndRes() + groupAdjustment);
+              viewport.getSelectionGroup().getEndRes() + groupAdjustment);
     }
 
-
     boolean appendHistoryItem = false;
-    if(viewport.historyList!=null
-       && viewport.historyList.size()>0
-      && viewport.historyList.peek() instanceof SlideSequencesCommand)
+    if (viewport.historyList != null && viewport.historyList.size() > 0
+            && viewport.historyList.peek() instanceof SlideSequencesCommand)
     {
-      appendHistoryItem = ssc.appendSlideCommand(
-          (SlideSequencesCommand)viewport.historyList.peek())
-          ;
+      appendHistoryItem = ssc
+              .appendSlideCommand((SlideSequencesCommand) viewport.historyList
+                      .peek());
     }
 
-    if(!appendHistoryItem)
+    if (!appendHistoryItem)
       addHistoryItem(ssc);
 
     repaint();
   }
 
   static StringBuffer copiedSequences;
+
   static Vector copiedHiddenColumns;
+
   protected void copy_actionPerformed()
   {
     if (viewport.getSelectionGroup() == null)
@@ -1366,15 +1350,14 @@ public class AlignFrame
     {
       copiedHiddenColumns = new Vector();
       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
-      for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();
-           i++)
+      for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
+              .size(); i++)
       {
-        int[] region = (int[])
-            viewport.getColumnSelection().getHiddenColumns().elementAt(i);
+        int[] region = (int[]) viewport.getColumnSelection()
+                .getHiddenColumns().elementAt(i);
 
         copiedHiddenColumns.addElement(new int[]
-                                       {region[0] - hiddenOffset,
-                                       region[1] - hiddenOffset});
+        { region[0] - hiddenOffset, region[1] - hiddenOffset });
       }
     }
     else
@@ -1401,18 +1384,18 @@ public class AlignFrame
         }
       }
 
-      //FIND START RES
-      //Returns residue following index if gap
+      // FIND START RES
+      // Returns residue following index if gap
       startRes = seq.findPosition(sg.getStartRes());
 
-      //FIND END RES
-      //Need to find the residue preceeding index if gap
+      // FIND END RES
+      // Need to find the residue preceeding index if gap
       endRes = 0;
 
       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
       {
         ch = seq.getCharAt(j);
-        if (!jalview.util.Comparison.isGap( (ch)))
+        if (!jalview.util.Comparison.isGap((ch)))
         {
           endRes++;
         }
@@ -1423,11 +1406,14 @@ public class AlignFrame
         endRes += seq.getStart() - 1;
       }
 
-      copiedSequences.append(seq.getName() + "\t" +
-                             startRes + "\t" +
-                             endRes + "\t" +
-                             seq.getSequenceAsString(sg.getStartRes(),
-          sg.getEndRes() + 1) + "\n");
+      copiedSequences.append(seq.getName()
+              + "\t"
+              + startRes
+              + "\t"
+              + endRes
+              + "\t"
+              + seq.getSequenceAsString(sg.getStartRes(),
+                      sg.getEndRes() + 1) + "\n");
     }
 
   }
@@ -1479,9 +1465,7 @@ public class AlignFrame
           newtitle = newtitle.concat("- from " + getTitle());
         }
         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
-                                       viewport.applet,
-                                       newtitle,
-                                       false);
+                viewport.applet, newtitle, false);
         if (copiedHiddenColumns != null)
         {
           for (int i = 0; i < copiedHiddenColumns.size(); i++)
@@ -1492,16 +1476,16 @@ public class AlignFrame
         }
 
         jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
-                                         DEFAULT_HEIGHT);
+                DEFAULT_HEIGHT);
       }
       else
       {
         addSequences(newSeqs);
       }
 
-    }
-    catch (Exception ex)
-    {} // could be anything being pasted in here
+    } catch (Exception ex)
+    {
+    } // could be anything being pasted in here
 
   }
 
@@ -1512,20 +1496,14 @@ public class AlignFrame
       viewport.alignment.addSequence(seqs[i]);
     }
 
-    //!newAlignment
-    addHistoryItem(new EditCommand(
-        "Add sequences",
-        EditCommand.PASTE,
-        seqs,
-        0,
-        viewport.alignment.getWidth(),
-        viewport.alignment)
-        );
+    // !newAlignment
+    addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
+            seqs, 0, viewport.alignment.getWidth(), viewport.alignment));
 
     viewport.setEndSeq(viewport.alignment.getHeight());
     viewport.alignment.getWidth();
-    viewport.firePropertyChange("alignment", null,
-                                viewport.alignment.getSequences());
+    viewport.firePropertyChange("alignment", null, viewport.alignment
+            .getSequences());
 
   }
 
@@ -1556,7 +1534,7 @@ public class AlignFrame
     if (sg.getSize() == viewport.alignment.getHeight())
     {
       viewport.getColumnSelection().removeElements(sg.getStartRes(),
-          sg.getEndRes() + 1);
+              sg.getEndRes() + 1);
     }
 
     SequenceI[] cut = new SequenceI[seqs.size()];
@@ -1566,20 +1544,17 @@ public class AlignFrame
     }
 
     /*
-         //ADD HISTORY ITEM
+     * //ADD HISTORY ITEM
      */
-    addHistoryItem(new EditCommand("Cut Sequences",
-                                   EditCommand.CUT,
-                                   cut,
-                                   sg.getStartRes(),
-                                   sg.getEndRes() - sg.getStartRes() + 1,
-                                   viewport.alignment));
+    addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
+            sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
+            viewport.alignment));
 
     viewport.setSelectionGroup(null);
     viewport.alignment.deleteGroup(sg);
 
-    viewport.firePropertyChange("alignment", null,
-                                viewport.getAlignment().getSequences());
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment()
+            .getSequences());
 
     if (viewport.getAlignment().getHeight() < 1)
     {
@@ -1655,8 +1630,8 @@ public class AlignFrame
       SequenceI[] seqs;
       if (viewport.getSelectionGroup() != null)
       {
-        seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
-            hiddenRepSequences);
+        seqs = viewport.getSelectionGroup().getSequencesAsArray(
+                viewport.hiddenRepSequences);
       }
       else
       {
@@ -1667,23 +1642,17 @@ public class AlignFrame
       if (trimLeft)
       {
         trimRegion = new TrimRegionCommand("Remove Left",
-                                           TrimRegionCommand.TRIM_LEFT,
-                                           seqs,
-                                           column,
-                                           viewport.alignment,
-                                           viewport.colSel,
-                                           viewport.selectionGroup);
+                TrimRegionCommand.TRIM_LEFT, seqs, column,
+                viewport.alignment, viewport.colSel,
+                viewport.selectionGroup);
         viewport.setStartRes(0);
       }
       else
       {
         trimRegion = new TrimRegionCommand("Remove Right",
-                                           TrimRegionCommand.TRIM_RIGHT,
-                                           seqs,
-                                           column,
-                                           viewport.alignment,
-                                           viewport.colSel,
-                                           viewport.selectionGroup);
+                TrimRegionCommand.TRIM_RIGHT, seqs, column,
+                viewport.alignment, viewport.colSel,
+                viewport.selectionGroup);
       }
 
       statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
@@ -1696,15 +1665,15 @@ public class AlignFrame
       {
         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
 
-        if ( (trimLeft && !sg.adjustForRemoveLeft(column))
-            || (!trimLeft && !sg.adjustForRemoveRight(column)))
+        if ((trimLeft && !sg.adjustForRemoveLeft(column))
+                || (!trimLeft && !sg.adjustForRemoveRight(column)))
         {
           viewport.alignment.deleteGroup(sg);
         }
       }
 
-      viewport.firePropertyChange("alignment", null,
-                                  viewport.getAlignment().getSequences());
+      viewport.firePropertyChange("alignment", null, viewport
+              .getAlignment().getSequences());
     }
   }
 
@@ -1715,8 +1684,8 @@ public class AlignFrame
     SequenceI[] seqs;
     if (viewport.getSelectionGroup() != null)
     {
-      seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
-          hiddenRepSequences);
+      seqs = viewport.getSelectionGroup().getSequencesAsArray(
+              viewport.hiddenRepSequences);
       start = viewport.getSelectionGroup().getStartRes();
       end = viewport.getSelectionGroup().getEndRes();
     }
@@ -1725,28 +1694,26 @@ public class AlignFrame
       seqs = viewport.alignment.getSequencesArray();
     }
 
-    RemoveGapColCommand removeGapCols =
-        new RemoveGapColCommand("Remove Gapped Columns",
-                                seqs,
-                                start, end,
-                                viewport.alignment);
+    RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
+            "Remove Gapped Columns", seqs, start, end, viewport.alignment);
 
     addHistoryItem(removeGapCols);
 
-    statusBar.setText("Removed " + removeGapCols.getSize() + " empty columns.");
+    statusBar.setText("Removed " + removeGapCols.getSize()
+            + " empty columns.");
 
-    //This is to maintain viewport position on first residue
-    //of first sequence
+    // This is to maintain viewport position on first residue
+    // of first sequence
     SequenceI seq = viewport.alignment.getSequenceAt(0);
     int startRes = seq.findPosition(viewport.startRes);
     // ShiftList shifts;
     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
     // edit.alColumnChanges=shifts.getInverse();
     // if (viewport.hasHiddenColumns)
-    //   viewport.getColumnSelection().compensateForEdits(shifts);
+    // viewport.getColumnSelection().compensateForEdits(shifts);
     viewport.setStartRes(seq.findIndex(startRes) - 1);
-    viewport.firePropertyChange("alignment", null,
-                                viewport.getAlignment().getSequences());
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment()
+            .getSequences());
 
   }
 
@@ -1757,8 +1724,8 @@ public class AlignFrame
     SequenceI[] seqs;
     if (viewport.getSelectionGroup() != null)
     {
-      seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
-          hiddenRepSequences);
+      seqs = viewport.getSelectionGroup().getSequencesAsArray(
+              viewport.hiddenRepSequences);
       start = viewport.getSelectionGroup().getStartRes();
       end = viewport.getSelectionGroup().getEndRes();
     }
@@ -1767,20 +1734,18 @@ public class AlignFrame
       seqs = viewport.alignment.getSequencesArray();
     }
 
-    //This is to maintain viewport position on first residue
-    //of first sequence
+    // This is to maintain viewport position on first residue
+    // of first sequence
     SequenceI seq = viewport.alignment.getSequenceAt(0);
     int startRes = seq.findPosition(viewport.startRes);
 
-    addHistoryItem(new RemoveGapsCommand("Remove Gaps",
-                                         seqs,
-                                         start, end,
-                                         viewport.alignment));
+    addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
+            viewport.alignment));
 
     viewport.setStartRes(seq.findIndex(startRes) - 1);
 
-    viewport.firePropertyChange("alignment", null,
-                                viewport.getAlignment().getSequences());
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment()
+            .getSequences());
 
   }
 
@@ -1788,8 +1753,10 @@ public class AlignFrame
   {
     new Finder(alignPanel);
   }
+
   /**
    * create a new view derived from the current view
+   * 
    * @param viewtitle
    * @return frame for the new view
    */
@@ -1798,10 +1765,8 @@ public class AlignFrame
     AlignmentI newal;
     if (viewport.hasHiddenRows)
     {
-      newal = new Alignment(viewport.getAlignment().
-                            getHiddenSequences()
-                            .getFullAlignment().
-                            getSequencesArray());
+      newal = new Alignment(viewport.getAlignment().getHiddenSequences()
+              .getFullAlignment().getSequencesArray());
     }
     else
     {
@@ -1814,28 +1779,27 @@ public class AlignFrame
       {
         if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)
         {
-          newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);
+          newal
+                  .addAnnotation(viewport.alignment
+                          .getAlignmentAnnotation()[i]);
         }
       }
     }
 
-    AlignFrame newaf = new AlignFrame(newal,
-                                      viewport.applet,
-                                      "",
-                                      false);
+    AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
 
     newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();
     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
-    PaintRefresher.Register(newaf.alignPanel,
-                            newaf.alignPanel.av.getSequenceSetId());
+    PaintRefresher.Register(newaf.alignPanel, newaf.alignPanel.av
+            .getSequenceSetId());
 
     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
-                            newaf.alignPanel.av.getSequenceSetId());
+            newaf.alignPanel.av.getSequenceSetId());
     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
-                            newaf.alignPanel.av.getSequenceSetId());
+            newaf.alignPanel.av.getSequenceSetId());
 
-    Vector comps = (Vector) PaintRefresher.components.get(viewport.
-        getSequenceSetId());
+    Vector comps = (Vector) PaintRefresher.components.get(viewport
+            .getSequenceSetId());
     int viewSize = -1;
     for (int i = 0; i < comps.size(); i++)
     {
@@ -1846,10 +1810,12 @@ public class AlignFrame
     }
 
     String title = new String(this.getTitle());
-    if (viewtitle!=null)
+    if (viewtitle != null)
+    {
+      title = viewtitle + " ( " + title + ")";
+    }
+    else
     {
-      title = viewtitle+" ( "+title+")";
-    } else {
       if (title.indexOf("(View") > -1)
       {
         title = title.substring(0, title.indexOf("(View"));
@@ -1863,6 +1829,7 @@ public class AlignFrame
     newaf.viewport.redoList = viewport.redoList;
     return newaf;
   }
+
   /**
    * 
    * @return list of feature groups on the view
@@ -1870,36 +1837,47 @@ public class AlignFrame
   public String[] getFeatureGroups()
   {
     FeatureRenderer fr = null;
-    if (alignPanel!=null && (fr=alignPanel.getFeatureRenderer())!=null)
+    if (alignPanel != null
+            && (fr = alignPanel.getFeatureRenderer()) != null)
     {
       return fr.getGroups();
     }
     return null;
   }
+
   /**
    * get sequence feature groups that are hidden or shown
-   * @param visible true is visible
+   * 
+   * @param visible
+   *                true is visible
    * @return list
    */
   public String[] getFeatureGroupsOfState(boolean visible)
   {
     FeatureRenderer fr = null;
-    if (alignPanel!=null && (fr=alignPanel.getFeatureRenderer())!=null)
+    if (alignPanel != null
+            && (fr = alignPanel.getFeatureRenderer()) != null)
     {
       return fr.getGroups(visible);
     }
     return null;
   }
+
   /**
    * Change the display state for the given feature groups
-   * @param groups list of group strings
-   * @param state visible or invisible
+   * 
+   * @param groups
+   *                list of group strings
+   * @param state
+   *                visible or invisible
    */
-  public void setFeatureGroupState(String[] groups, boolean state) {
+  public void setFeatureGroupState(String[] groups, boolean state)
+  {
     FeatureRenderer fr = null;
     this.sequenceFeatures.setState(true);
     viewport.showSequenceFeatures(true);
-    if (alignPanel!=null && (fr=alignPanel.getFeatureRenderer())!=null)
+    if (alignPanel != null
+            && (fr = alignPanel.getFeatureRenderer()) != null)
     {
       fr.setGroupState(groups, state);
       alignPanel.seqPanel.seqCanvas.repaint();
@@ -1909,6 +1887,7 @@ public class AlignFrame
       }
     }
   }
+
   public void seqLimits_itemStateChanged()
   {
     viewport.setShowJVSuffix(seqLimits.getState());
@@ -1944,8 +1923,8 @@ public class AlignFrame
     frame.add(overview);
     // +50 must allow for applet frame window
     jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
-                                     overview.getPreferredSize().width,
-                                     overview.getPreferredSize().height + 50);
+            overview.getPreferredSize().width,
+            overview.getPreferredSize().height + 50);
 
     frame.pack();
     frame.addWindowListener(new WindowAdapter()
@@ -1968,7 +1947,8 @@ public class AlignFrame
     {
       if (viewport.getAbovePIDThreshold())
       {
-        threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
+        threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
+                "Background");
 
         cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
 
@@ -1984,17 +1964,16 @@ public class AlignFrame
 
         Alignment al = (Alignment) viewport.alignment;
         Conservation c = new Conservation("All",
-                                          ResidueProperties.propHash, 3,
-                                          al.getSequences(), 0,
-                                          al.getWidth() - 1);
+                ResidueProperties.propHash, 3, al.getSequences(), 0, al
+                        .getWidth() - 1);
 
         c.calculate();
         c.verdict(false, viewport.ConsPercGaps);
 
         cs.setConservation(c);
 
-        cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
-            "Background"));
+        cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
+                cs, "Background"));
 
       }
       else
@@ -2021,17 +2000,15 @@ public class AlignFrame
         }
         if (cs instanceof ClustalxColourScheme)
         {
-          sg.cs = new ClustalxColourScheme(
-              sg.getSequences(viewport.hiddenRepSequences),
-              sg.getWidth());
+          sg.cs = new ClustalxColourScheme(sg
+                  .getSequences(viewport.hiddenRepSequences), sg.getWidth());
         }
         else
         {
           try
           {
             sg.cs = (ColourSchemeI) cs.getClass().newInstance();
-          }
-          catch (Exception ex)
+          } catch (Exception ex)
           {
             ex.printStackTrace();
             sg.cs = cs;
@@ -2039,12 +2016,13 @@ public class AlignFrame
         }
 
         if (viewport.getAbovePIDThreshold()
-            || cs instanceof PIDColourScheme
-            || cs instanceof Blosum62ColourScheme)
+                || cs instanceof PIDColourScheme
+                || cs instanceof Blosum62ColourScheme)
         {
           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
-          sg.cs.setConsensus(AAFrequency.calculate(
-              sg.getSequences(viewport.hiddenRepSequences), 0, sg.getWidth()));
+          sg.cs.setConsensus(AAFrequency.calculate(sg
+                  .getSequences(viewport.hiddenRepSequences), 0, sg
+                  .getWidth()));
         }
         else
         {
@@ -2054,10 +2032,9 @@ public class AlignFrame
         if (viewport.getConservationSelected())
         {
           Conservation c = new Conservation("Group",
-                                            ResidueProperties.propHash, 3,
-                                            sg.getSequences(viewport.
-              hiddenRepSequences), 0,
-                                            viewport.alignment.getWidth() - 1);
+                  ResidueProperties.propHash, 3, sg
+                          .getSequences(viewport.hiddenRepSequences), 0,
+                  viewport.alignment.getWidth() - 1);
           c.calculate();
           c.verdict(false, viewport.ConsPercGaps);
           sg.cs.setConservation(c);
@@ -2076,28 +2053,31 @@ public class AlignFrame
       alignPanel.getOverviewPanel().updateOverviewImage();
     }
 
-    jalview.structure.StructureSelectionManager.getStructureSelectionManager()
-        .sequenceColoursChanged(alignPanel);
+    jalview.structure.StructureSelectionManager
+            .getStructureSelectionManager().sequenceColoursChanged(
+                    alignPanel);
 
     alignPanel.paintAlignment(true);
   }
 
   protected void modifyPID_actionPerformed()
   {
-    if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme != null)
+    if (viewport.getAbovePIDThreshold()
+            && viewport.globalColourScheme != null)
     {
-      SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
-                                     "Background");
+      SliderPanel.setPIDSliderSource(alignPanel, viewport
+              .getGlobalColourScheme(), "Background");
       SliderPanel.showPIDSlider();
     }
   }
 
   protected void modifyConservation_actionPerformed()
   {
-    if (viewport.getConservationSelected() && viewport.globalColourScheme != null)
+    if (viewport.getConservationSelected()
+            && viewport.globalColourScheme != null)
     {
-      SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
-                                        "Background");
+      SliderPanel.setConservationSlider(alignPanel,
+              viewport.globalColourScheme, "Background");
       SliderPanel.showConservationSlider();
     }
   }
@@ -2129,25 +2109,25 @@ public class AlignFrame
   public void sortPairwiseMenuItem_actionPerformed()
   {
     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
-    AlignmentSorter.sortByPID(viewport.getAlignment(),
-                              viewport.getAlignment().getSequenceAt(0), null);
+    AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
+            .getAlignment().getSequenceAt(0), null);
     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
-                                    viewport.alignment));
+            viewport.alignment));
     alignPanel.paintAlignment(true);
   }
 
   public void sortIDMenuItem_actionPerformed()
   {
-    //  addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
-    //                                HistoryItem.SORT));
+    // addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
+    // HistoryItem.SORT));
     AlignmentSorter.sortByID(viewport.getAlignment());
     alignPanel.paintAlignment(true);
   }
 
   public void sortGroupMenuItem_actionPerformed()
   {
-    //  addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
-    //                                 HistoryItem.SORT));
+    // addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
+    // HistoryItem.SORT));
     AlignmentSorter.sortByGroup(viewport.getAlignment());
     alignPanel.paintAlignment(true);
 
@@ -2161,24 +2141,24 @@ public class AlignFrame
   public void pairwiseAlignmentMenuItem_actionPerformed()
   {
     if (viewport.getSelectionGroup() != null
-        && viewport.getSelectionGroup().getSize() > 1)
+            && viewport.getSelectionGroup().getSize() > 1)
     {
       Frame frame = new Frame();
       frame.add(new PairwiseAlignPanel(alignPanel));
-      jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
+      jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
+              500);
     }
   }
 
   public void PCAMenuItem_actionPerformed()
   {
-    //are the sequences aligned?
+    // are the sequences aligned?
     if (!viewport.alignment.isAligned())
     {
       SequenceI current;
       int Width = viewport.getAlignment().getWidth();
 
-      for (int i = 0; i < viewport.getAlignment().getSequences().size();
-           i++)
+      for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
       {
         current = viewport.getAlignment().getSequenceAt(i);
 
@@ -2190,10 +2170,10 @@ public class AlignFrame
       alignPanel.paintAlignment(true);
     }
 
-    if ( (viewport.getSelectionGroup() != null &&
-          viewport.getSelectionGroup().getSize() < 4 &&
-          viewport.getSelectionGroup().getSize() > 0)
-        || viewport.getAlignment().getHeight() < 4)
+    if ((viewport.getSelectionGroup() != null
+            && viewport.getSelectionGroup().getSize() < 4 && viewport
+            .getSelectionGroup().getSize() > 0)
+            || viewport.getAlignment().getHeight() < 4)
     {
       return;
     }
@@ -2201,8 +2181,7 @@ public class AlignFrame
     try
     {
       new PCAPanel(viewport);
-    }
-    catch (java.lang.OutOfMemoryError ex)
+    } catch (java.lang.OutOfMemoryError ex)
     {
     }
 
@@ -2230,14 +2209,13 @@ public class AlignFrame
 
   void NewTreePanel(String type, String pwType, String title)
   {
-    //are the sequences aligned?
+    // are the sequences aligned?
     if (!viewport.alignment.isAligned())
     {
       SequenceI current;
       int Width = viewport.getAlignment().getWidth();
 
-      for (int i = 0; i < viewport.getAlignment().getSequences().size();
-           i++)
+      for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
       {
         current = viewport.getAlignment().getSequenceAt(i);
 
@@ -2250,14 +2228,12 @@ public class AlignFrame
 
     }
 
-    if ( (viewport.getSelectionGroup() != null &&
-          viewport.getSelectionGroup().getSize() > 1)
-        || (viewport.getSelectionGroup() == null
-            && viewport.alignment.getHeight() > 1))
+    if ((viewport.getSelectionGroup() != null && viewport
+            .getSelectionGroup().getSize() > 1)
+            || (viewport.getSelectionGroup() == null && viewport.alignment
+                    .getHeight() > 1))
     {
-      final TreePanel tp = new TreePanel(viewport,
-                                         type,
-                                         pwType);
+      final TreePanel tp = new TreePanel(viewport, type, pwType);
 
       addTreeMenuItem(tp, title);
 
@@ -2277,10 +2253,7 @@ public class AlignFrame
 
   public void loadTree(jalview.io.NewickFile tree, String treeFile)
   {
-    TreePanel tp = new TreePanel(viewport,
-                                 treeFile,
-                                 "From File - ",
-                                 tree);
+    TreePanel tp = new TreePanel(viewport, treeFile, "From File - ", tree);
     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
     addTreeMenuItem(tp, treeFile);
   }
@@ -2293,9 +2266,10 @@ public class AlignFrame
     {
       public void actionPerformed(ActionEvent evt)
       {
-        //  addHistoryItem(new HistoryItem("Sort", viewport.alignment,
-        //                                 HistoryItem.SORT));
-        AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
+        // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
+        // HistoryItem.SORT));
+        AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel
+                .getTree());
         alignPanel.paintAlignment(true);
       }
     });
@@ -2317,10 +2291,10 @@ public class AlignFrame
   protected void about_actionPerformed()
   {
 
-    class AboutPanel
-        extends Canvas
+    class AboutPanel extends Canvas
     {
       String version;
+
       public AboutPanel(String version)
       {
         this.version = version;
@@ -2335,19 +2309,29 @@ public class AlignFrame
         int fh = fm.getHeight();
         int y = 5, x = 7;
         g.setColor(Color.black);
+        // TODO: update this text for each release or centrally store it for
+        // lite and application
         g.setFont(new Font("Helvetica", Font.BOLD, 14));
-        g.drawString("Jalview - Release " + version, 200, y += fh);
+        g.drawString("JalviewLite - Release " + version, x, y += fh);
         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
-        g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
-                     x, y += fh * 2);
-        g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
-                     x, y += fh);
-        g.drawString(
-            "For any issues relating to Jalview, email help@jalview.org", x,
-            y += fh);
-        g.drawString("If  you use JalView, please cite:", x, y += fh + 8);
-        g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
-                     x, y += fh);
+        g
+                .drawString(
+                        "Authors:  Andrew Waterhouse, Jim Procter, Michele Clamp, James Cuff, Steve Searle,",
+                        x, y += fh * 1.5);
+        g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);
+        g
+                .drawString(
+                        "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
+                        x, y += fh);
+        g
+                .drawString(
+                        "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
+                        x, y += fh);
+        g.drawString("If  you use Jalview, please cite:", x, y += fh + 8);
+        g
+                .drawString(
+                        "\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
+                        x, y += fh);
         g.drawString("Bioinformatics,  2004 20;426-7.", x, y += fh);
       }
     }
@@ -2359,17 +2343,16 @@ public class AlignFrame
       try
       {
         BufferedReader reader = new BufferedReader(new InputStreamReader(
-            url.openStream()));
+                url.openStream()));
         String line;
-        while ( (line = reader.readLine()) != null)
+        while ((line = reader.readLine()) != null)
         {
           if (line.indexOf("VERSION") > -1)
           {
             version = line.substring(line.indexOf("=") + 1);
           }
         }
-      }
-      catch (Exception ex)
+      } catch (Exception ex)
       {
         ex.printStackTrace();
       }
@@ -2377,7 +2360,7 @@ public class AlignFrame
 
     Frame frame = new Frame();
     frame.add(new AboutPanel(version));
-    jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
+    jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
 
   }
 
@@ -2391,108 +2374,198 @@ public class AlignFrame
     {
       try
       {
-        System.out.println("Show url: " + url);
-        viewport.applet.getAppletContext().showDocument(new java.net.URL(url),
-            target);
-      }
-      catch (Exception ex)
+        if (url.indexOf(":")==-1)
+        {
+          // TODO: verify (Bas Vroling bug) prepend codebase or server URL to form valid URL
+          if (url.indexOf("/")==0)
+          {
+            String codebase = viewport.applet.getCodeBase().toString();
+            url = codebase.substring(0,codebase.length()-viewport.applet.getCodeBase().getFile().length())+url;
+          } else {
+            url = viewport.applet.getCodeBase()+url;
+          }
+          System.out.println("Show url (prepended codebase): " + url);
+        } else {
+          System.out.println("Show url: " + url);
+        }
+        viewport.applet.getAppletContext().showDocument(
+                new java.net.URL(url), target);
+      } catch (Exception ex)
       {
         ex.printStackTrace();
       }
     }
   }
 
-  //////////////////////////////////////////////////////////////////////////////////
-  //JBuilder Graphics here
-
-   MenuBar alignFrameMenuBar = new MenuBar();
-   Menu fileMenu = new Menu("File");
-   MenuItem loadApplication = new MenuItem("View in Full Application");
-   MenuItem loadTree = new MenuItem("Load Associated Tree ...");
-   MenuItem loadAnnotations = new MenuItem(
-      "Load Features/Annotations ...");
-   MenuItem outputFeatures = new MenuItem("Export Features ...");
-   MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
-
-   MenuItem closeMenuItem = new MenuItem("Close");
-   Menu editMenu = new Menu("Edit");
-   Menu viewMenu = new Menu("View");
-   Menu colourMenu = new Menu("Colour");
-   Menu calculateMenu = new Menu("Calculate");
-   MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
-   MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
-   MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
-   MenuItem remove2LeftMenuItem = new MenuItem();
-   MenuItem remove2RightMenuItem = new MenuItem();
-   MenuItem removeGappedColumnMenuItem = new MenuItem();
-   MenuItem removeAllGapsMenuItem = new MenuItem();
-   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
-   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
-   MenuItem sortPairwiseMenuItem = new MenuItem();
-   MenuItem sortIDMenuItem = new MenuItem();
-   MenuItem sortGroupMenuItem = new MenuItem();
-   MenuItem removeRedundancyMenuItem = new MenuItem();
-   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
-   MenuItem PCAMenuItem = new MenuItem();
-   MenuItem averageDistanceTreeMenuItem = new MenuItem();
-   MenuItem neighbourTreeMenuItem = new MenuItem();
+  // ////////////////////////////////////////////////////////////////////////////////
+  // JBuilder Graphics here
+
+  MenuBar alignFrameMenuBar = new MenuBar();
+
+  Menu fileMenu = new Menu("File");
+
+  MenuItem loadApplication = new MenuItem("View in Full Application");
+
+  MenuItem loadTree = new MenuItem("Load Associated Tree ...");
+
+  MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
+
+  MenuItem outputFeatures = new MenuItem("Export Features ...");
+
+  MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
+
+  MenuItem closeMenuItem = new MenuItem("Close");
+
+  Menu editMenu = new Menu("Edit");
+
+  Menu viewMenu = new Menu("View");
+
+  Menu colourMenu = new Menu("Colour");
+
+  Menu calculateMenu = new Menu("Calculate");
+
+  MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
+
+  MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
+
+  MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
+
+  MenuItem remove2LeftMenuItem = new MenuItem();
+
+  MenuItem remove2RightMenuItem = new MenuItem();
+
+  MenuItem removeGappedColumnMenuItem = new MenuItem();
+
+  MenuItem removeAllGapsMenuItem = new MenuItem();
+
+  CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
+
+  CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
+
+  MenuItem sortPairwiseMenuItem = new MenuItem();
+
+  MenuItem sortIDMenuItem = new MenuItem();
+
+  MenuItem sortGroupMenuItem = new MenuItem();
+
+  MenuItem removeRedundancyMenuItem = new MenuItem();
+
+  MenuItem pairwiseAlignmentMenuItem = new MenuItem();
+
+  MenuItem PCAMenuItem = new MenuItem();
+
+  MenuItem averageDistanceTreeMenuItem = new MenuItem();
+
+  MenuItem neighbourTreeMenuItem = new MenuItem();
+
   BorderLayout borderLayout1 = new BorderLayout();
+
   public Label statusBar = new Label();
-   Menu outputTextboxMenu = new Menu();
-   MenuItem clustalColour = new MenuItem();
-   MenuItem zappoColour = new MenuItem();
-   MenuItem taylorColour = new MenuItem();
-   MenuItem hydrophobicityColour = new MenuItem();
-   MenuItem helixColour = new MenuItem();
-   MenuItem strandColour = new MenuItem();
-   MenuItem turnColour = new MenuItem();
-   MenuItem buriedColour = new MenuItem();
-   MenuItem userDefinedColour = new MenuItem();
-   MenuItem PIDColour = new MenuItem();
-   MenuItem BLOSUM62Colour = new MenuItem();
+
+  Menu outputTextboxMenu = new Menu();
+
+  MenuItem clustalColour = new MenuItem();
+
+  MenuItem zappoColour = new MenuItem();
+
+  MenuItem taylorColour = new MenuItem();
+
+  MenuItem hydrophobicityColour = new MenuItem();
+
+  MenuItem helixColour = new MenuItem();
+
+  MenuItem strandColour = new MenuItem();
+
+  MenuItem turnColour = new MenuItem();
+
+  MenuItem buriedColour = new MenuItem();
+
+  MenuItem userDefinedColour = new MenuItem();
+
+  MenuItem PIDColour = new MenuItem();
+
+  MenuItem BLOSUM62Colour = new MenuItem();
+
   MenuItem njTreeBlosumMenuItem = new MenuItem();
+
   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
-   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
-   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
-   MenuItem alProperties = new MenuItem("Alignment Properties...");
+
+  CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
+
+  CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
+
+  MenuItem alProperties = new MenuItem("Alignment Properties...");
+
   MenuItem overviewMenuItem = new MenuItem();
-   MenuItem undoMenuItem = new MenuItem();
-   MenuItem redoMenuItem = new MenuItem();
-   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
+
+  MenuItem undoMenuItem = new MenuItem();
+
+  MenuItem redoMenuItem = new MenuItem();
+
+  CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
+
   MenuItem noColourmenuItem = new MenuItem();
-   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
-   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
+
+  CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
+
+  CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
+
   MenuItem findMenuItem = new MenuItem();
-   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
-   MenuItem nucleotideColour = new MenuItem();
+
+  CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
+
+  MenuItem nucleotideColour = new MenuItem();
+
   MenuItem deleteGroups = new MenuItem();
+
   MenuItem delete = new MenuItem();
+
   MenuItem copy = new MenuItem();
+
   MenuItem cut = new MenuItem();
+
   Menu pasteMenu = new Menu();
+
   MenuItem pasteNew = new MenuItem();
+
   MenuItem pasteThis = new MenuItem();
-   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
-   MenuItem font = new MenuItem();
-   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
-   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
-   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
+
+  CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
+
+  MenuItem font = new MenuItem();
+
+  CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
+
+  CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
+
+  CheckboxMenuItem scaleRight = new CheckboxMenuItem();
+
   MenuItem modifyPID = new MenuItem();
+
   MenuItem modifyConservation = new MenuItem();
-   CheckboxMenuItem autoCalculate
-      = new CheckboxMenuItem("Autocalculate Consensus", true);
-   Menu sortByTreeMenu = new Menu();
+
+  CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
+          "Autocalculate Consensus", true);
+
+  Menu sortByTreeMenu = new Menu();
+
   Menu sort = new Menu();
+
   Menu calculate = new Menu();
+
   MenuItem inputText = new MenuItem();
+
   Menu helpMenu = new Menu();
+
   MenuItem documentation = new MenuItem();
+
   MenuItem about = new MenuItem();
-   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
-   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
 
-  private void jbInit()
-      throws Exception
+  CheckboxMenuItem seqLimits = new CheckboxMenuItem();
+
+  CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
+
+  private void jbInit() throws Exception
   {
 
     setMenuBar(alignFrameMenuBar);
@@ -2500,11 +2573,11 @@ public class AlignFrame
     MenuItem item;
 
     // dynamically fill save as menu with available formats
-    for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length;
-         i++)
+    for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
     {
 
-      item = new MenuItem(jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
+      item = new MenuItem(
+              jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
 
       item.addActionListener(new java.awt.event.ActionListener()
       {
@@ -2552,8 +2625,8 @@ public class AlignFrame
     pairwiseAlignmentMenuItem.addActionListener(this);
     PCAMenuItem.setLabel("Principal Component Analysis");
     PCAMenuItem.addActionListener(this);
-    averageDistanceTreeMenuItem.setLabel(
-        "Average Distance Using % Identity");
+    averageDistanceTreeMenuItem
+            .setLabel("Average Distance Using % Identity");
     averageDistanceTreeMenuItem.addActionListener(this);
     neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
     neighbourTreeMenuItem.addActionListener(this);
@@ -2584,8 +2657,8 @@ public class AlignFrame
     PIDColour.addActionListener(this);
     BLOSUM62Colour.setLabel("BLOSUM62 Score");
     BLOSUM62Colour.addActionListener(this);
-    avDistanceTreeBlosumMenuItem.setLabel(
-        "Average Distance Using BLOSUM62");
+    avDistanceTreeBlosumMenuItem
+            .setLabel("Average Distance Using BLOSUM62");
     avDistanceTreeBlosumMenuItem.addActionListener(this);
     njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
     njTreeBlosumMenuItem.addActionListener(this);
@@ -2659,7 +2732,7 @@ public class AlignFrame
     inputText.addActionListener(this);
     centreColumnLabelFlag.setLabel("Centre column labels");
     centreColumnLabelFlag.addItemListener(this);
-    
+
     helpMenu.setLabel("Help");
     documentation.setLabel("Documentation");
     documentation.addActionListener(this);
@@ -2807,63 +2880,80 @@ public class AlignFrame
     selectMenu.add(invertColSel);
     selectMenu.add(deleteGroups);
   }
+
   MenuItem featureSettings = new MenuItem();
+
   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
+
   MenuItem annotationColour = new MenuItem();
+
   MenuItem invertColSel = new MenuItem();
+
   Menu menu1 = new Menu();
+
   MenuItem showColumns = new MenuItem();
+
   MenuItem showSeqs = new MenuItem();
+
   Menu menu2 = new Menu();
+
   MenuItem hideColumns = new MenuItem();
+
   MenuItem hideSequences = new MenuItem();
+
   Menu formatMenu = new Menu();
+
   Menu selectMenu = new Menu();
+
   MenuItem newView = new MenuItem();
 
   /**
-   * Attach the alignFrame panels after embedding menus, if necessary.
-   * This used to be called setEmbedded, but is now creates the 
-   * dropdown menus in a platform independent manner
-   * to avoid OSX/Mac menu appendage daftness.
-   *  
-   * @param reallyEmbedded true to attach the view to the applet area on the page rather than in a new window
+   * Attach the alignFrame panels after embedding menus, if necessary. This used
+   * to be called setEmbedded, but is now creates the dropdown menus in a
+   * platform independent manner to avoid OSX/Mac menu appendage daftness.
+   * 
+   * @param reallyEmbedded
+   *                true to attach the view to the applet area on the page
+   *                rather than in a new window
    */
   public void createAlignFrameWindow(boolean reallyEmbedded, String title)
   {
     if (reallyEmbedded)
     {
-      //////
+      // ////
       // Explicly build the embedded menu panel for the on-page applet
       //
       // view cannot be closed if its actually on the page
       fileMenu.remove(closeMenuItem);
       fileMenu.remove(3); // Remove Seperator
-      embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial", Font.PLAIN, 10, false); // use our own fonts.
+      embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
+              Font.PLAIN, 10, false); // use our own fonts.
       // and actually add the components to the applet area
       viewport.applet.setLayout(new BorderLayout());
       viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
       viewport.applet.add(statusBar, BorderLayout.SOUTH);
-      alignPanel.setSize(viewport.applet.getSize().width,
-              viewport.applet.getSize().height
+      alignPanel.setSize(viewport.applet.getSize().width, viewport.applet
+              .getSize().height
               - embeddedMenu.HEIGHT - statusBar.HEIGHT);
       viewport.applet.add(alignPanel, BorderLayout.CENTER);
       viewport.applet.validate();
-    } else {
-      ////////
+    }
+    else
+    {
+      // //////
       // test and embed menu bar if necessary.
       //
-      if (embedMenuIfNeeded(alignPanel)) {
+      if (embedMenuIfNeeded(alignPanel))
+      {
         // adjust for status bar height too
-        alignPanel.setSize(getSize().width,
-              getSize().height
+        alignPanel.setSize(getSize().width, getSize().height
                 - statusBar.HEIGHT);
       }
       add(statusBar, BorderLayout.SOUTH);
       add(alignPanel, BorderLayout.CENTER);
       // and register with the applet so it can pass external API calls to us
       jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
-                                         DEFAULT_HEIGHT);
+              DEFAULT_HEIGHT);
     }
   }
 }
diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 33a73d3..b39aaeb 100755
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.appletgui;
 
 import java.util.*;
@@ -31,50 +30,73 @@ import jalview.schemes.*;
 public class AlignViewport
 {
   int startRes;
+
   int endRes;
 
   int startSeq;
+
   int endSeq;
 
   boolean cursorMode = false;
 
   boolean showJVSuffix = true;
+
   boolean showText = true;
+
   boolean showColourText = false;
+
   boolean showBoxes = true;
+
   boolean wrapAlignment = false;
+
   boolean renderGaps = true;
+
   boolean showSequenceFeatures = false;
+
   boolean showAnnotation = true;
+
   boolean showConservation = true;
+
   boolean showQuality = true;
+
   boolean showConsensus = true;
+
   boolean upperCasebold = false;
 
   boolean colourAppliesToAllGroups = true;
+
   ColourSchemeI globalColourScheme = null;
+
   boolean conservationColourSelected = false;
+
   boolean abovePIDThreshold = false;
 
   SequenceGroup selectionGroup;
 
   int charHeight;
+
   int charWidth;
+
   int wrappedWidth;
 
   Font font = new Font("SansSerif", Font.PLAIN, 10);
+
   boolean validCharWidth = true;
+
   AlignmentI alignment;
 
   ColumnSelection colSel = new ColumnSelection();
 
   int threshold;
+
   int increment;
 
   NJTree currentTree = null;
 
   boolean scaleAboveWrapped = true;
+
   boolean scaleLeftWrapped = true;
+
   boolean scaleRightWrapped = true;
 
   // The following vector holds the features which are
@@ -82,20 +104,25 @@ public class AlignViewport
   public Hashtable featuresDisplayed;
 
   boolean hasHiddenColumns = false;
+
   boolean hasHiddenRows = false;
+
   boolean showHiddenMarkers = true;
 
   public Hashtable[] hconsensus;
+
   AlignmentAnnotation consensus;
+
   AlignmentAnnotation conservation;
+
   AlignmentAnnotation quality;
 
   boolean autocalculateConsensus = true;
 
   public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
 
-  private java.beans.PropertyChangeSupport changeSupport = new java.beans.
-      PropertyChangeSupport(this);
+  private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
+          this);
 
   boolean ignoreGapsInConsensusCalculation = false;
 
@@ -106,6 +133,7 @@ public class AlignViewport
   boolean MAC = false;
 
   Stack historyList = new Stack();
+
   Stack redoList = new Stack();
 
   String sequenceSetID;
@@ -123,7 +151,7 @@ public class AlignViewport
     setFont(font);
 
     MAC = new jalview.util.Platform().isAMac();
-    
+
     if (applet != null)
     {
       String param = applet.getParameter("showFullId");
@@ -164,7 +192,6 @@ public class AlignViewport
           upperCasebold = true;
         }
       }
-      
 
     }
 
@@ -183,7 +210,8 @@ public class AlignViewport
 
       if (colour != null)
       {
-        globalColourScheme = ColourSchemeProperty.getColour(alignment, colour);
+        globalColourScheme = ColourSchemeProperty.getColour(alignment,
+                colour);
         if (globalColourScheme != null)
         {
           globalColourScheme.setConsensus(hconsensus);
@@ -192,8 +220,8 @@ public class AlignViewport
 
       if (applet.getParameter("userDefinedColour") != null)
       {
-        ( (UserColourScheme) globalColourScheme).parseAppletParameter(
-            applet.getParameter("userDefinedColour"));
+        ((UserColourScheme) globalColourScheme).parseAppletParameter(applet
+                .getParameter("userDefinedColour"));
       }
     }
     if (hconsensus == null)
@@ -201,10 +229,8 @@ public class AlignViewport
       if (!alignment.isNucleotide())
       {
         conservation = new AlignmentAnnotation("Conservation",
-                "Conservation of total alignment less than " +
-                ConsPercGaps + "% gaps",
-                new Annotation[1], 0f,
-                11f,
+                "Conservation of total alignment less than " + ConsPercGaps
+                        + "% gaps", new Annotation[1], 0f, 11f,
                 AlignmentAnnotation.BAR_GRAPH);
         conservation.hasText = true;
         conservation.autoCalculated = true;
@@ -218,10 +244,7 @@ public class AlignViewport
         {
           quality = new AlignmentAnnotation("Quality",
                   "Alignment Quality based on Blosum62 scores",
-                  new Annotation[1],
-                  0f,
-                  11f,
-                  AlignmentAnnotation.BAR_GRAPH);
+                  new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
           quality.hasText = true;
           quality.autoCalculated = true;
 
@@ -230,8 +253,7 @@ public class AlignViewport
       }
 
       consensus = new AlignmentAnnotation("Consensus", "PID",
-              new Annotation[1], 0f, 100f,
-              AlignmentAnnotation.BAR_GRAPH);
+              new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
       consensus.hasText = true;
       consensus.autoCalculated = true;
 
@@ -253,10 +275,10 @@ public class AlignViewport
     return showSequenceFeatures;
   }
 
-  class ConservationThread
-      extends Thread
+  class ConservationThread extends Thread
   {
     AlignmentPanel ap;
+
     public ConservationThread(AlignmentPanel ap)
     {
       this.ap = ap;
@@ -277,8 +299,7 @@ public class AlignViewport
               ap.paintAlignment(false);
             }
             Thread.sleep(200);
-          }
-          catch (Exception ex)
+          } catch (Exception ex)
           {
             ex.printStackTrace();
           }
@@ -293,8 +314,8 @@ public class AlignViewport
         }
 
         Conservation cons = new jalview.analysis.Conservation("All",
-            jalview.schemes.ResidueProperties.propHash, 3,
-            alignment.getSequences(), 0, alWidth - 1);
+                jalview.schemes.ResidueProperties.propHash, 3, alignment
+                        .getSequences(), 0, alWidth - 1);
 
         cons.calculate();
         cons.verdict(false, ConsPercGaps);
@@ -316,7 +337,8 @@ public class AlignViewport
         minB = 0f;
         maxR = 1.0f - minR;
         maxG = 0.9f - minG;
-        maxB = 0f - minB; // scalable range for colouring both Conservation and Quality
+        maxB = 0f - minB; // scalable range for colouring both Conservation and
+                          // Quality
 
         float min = 0f;
         float max = 11f;
@@ -356,29 +378,24 @@ public class AlignViewport
 
           float vprop = value - min;
           vprop /= max;
-          conservation.annotations[i] =
-              new Annotation(String.valueOf(c),
-                             String.valueOf(value), ' ', value,
-                             new Color(minR + (maxR * vprop),
-                                       minG + (maxG * vprop),
-                                       minB + (maxB * vprop)));
+          conservation.annotations[i] = new Annotation(String.valueOf(c),
+                  String.valueOf(value), ' ', value, new Color(minR
+                          + (maxR * vprop), minG + (maxG * vprop), minB
+                          + (maxB * vprop)));
 
           // Quality calc
           if (quality != null)
           {
-            value = ( (Double) cons.quality.elementAt(i)).floatValue();
+            value = ((Double) cons.quality.elementAt(i)).floatValue();
             vprop = value - qmin;
             vprop /= qmax;
-            quality.annotations[i] = new Annotation(" ", String.valueOf(value),
-                ' ',
-                value,
-                new Color(minR + (maxR * vprop),
-                          minG + (maxG * vprop),
-                          minB + (maxB * vprop)));
+            quality.annotations[i] = new Annotation(" ", String
+                    .valueOf(value), ' ', value, new Color(minR
+                    + (maxR * vprop), minG + (maxG * vprop), minB
+                    + (maxB * vprop)));
           }
         }
-      }
-      catch (OutOfMemoryError error)
+      } catch (OutOfMemoryError error)
       {
         System.out.println("Out of memory calculating conservation!!");
         conservation = null;
@@ -434,10 +451,10 @@ public class AlignViewport
     consensusThread.start();
   }
 
-  class ConsensusThread
-      extends Thread
+  class ConsensusThread extends Thread
   {
     AlignmentPanel ap;
+
     public ConsensusThread(AlignmentPanel ap)
     {
       this.ap = ap;
@@ -456,8 +473,7 @@ public class AlignViewport
           }
 
           Thread.sleep(200);
-        }
-        catch (Exception ex)
+        } catch (Exception ex)
         {
           ex.printStackTrace();
         }
@@ -477,27 +493,27 @@ public class AlignViewport
         consensus.annotations = new Annotation[aWidth];
 
         hconsensus = new Hashtable[aWidth];
-        AAFrequency.calculate(alignment.getSequencesArray(),
-                              0,
-                              alignment.getWidth(),
-                              hconsensus);
+        AAFrequency.calculate(alignment.getSequencesArray(), 0, alignment
+                .getWidth(), hconsensus);
 
         for (int i = 0; i < aWidth; i++)
         {
           float value = 0;
           if (ignoreGapsInConsensusCalculation)
           {
-            value = ( (Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)).
-                floatValue();
+            value = ((Float) hconsensus[i].get(AAFrequency.PID_NOGAPS))
+                    .floatValue();
           }
           else
           {
-            value = ( (Float) hconsensus[i].get(AAFrequency.PID_GAPS)).
-                floatValue();
+            value = ((Float) hconsensus[i].get(AAFrequency.PID_GAPS))
+                    .floatValue();
           }
 
-          String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString();
-          String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " ";
+          String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE)
+                  .toString();
+          String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE)
+                  + " ";
 
           if (maxRes.length() > 1)
           {
@@ -505,9 +521,9 @@ public class AlignViewport
             maxRes = "+";
           }
 
-          mouseOver += ( (int) value + "%");
+          mouseOver += ((int) value + "%");
           consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
-              value);
+                  value);
         }
 
         if (globalColourScheme != null)
@@ -515,8 +531,7 @@ public class AlignViewport
           globalColourScheme.setConsensus(hconsensus);
         }
 
-      }
-      catch (OutOfMemoryError error)
+      } catch (OutOfMemoryError error)
       {
         alignment.deleteAnnotation(consensus);
 
@@ -536,11 +551,15 @@ public class AlignViewport
   }
 
   /**
-   * get the consensus sequence as displayed under the PID consensus annotation row.
+   * get the consensus sequence as displayed under the PID consensus annotation
+   * row.
+   * 
    * @return consensus sequence as a new sequence object
    */
   /**
-   * get the consensus sequence as displayed under the PID consensus annotation row.
+   * get the consensus sequence as displayed under the PID consensus annotation
+   * row.
+   * 
    * @return consensus sequence as a new sequence object
    */
   public SequenceI getConsensusSeq()
@@ -565,9 +584,8 @@ public class AlignViewport
       }
     }
     SequenceI sq = new Sequence("Consensus", seqs.toString());
-    sq.setDescription("Percentage Identity Consensus " +
-                      ( (ignoreGapsInConsensusCalculation) ? " without gaps" :
-                       ""));
+    sq.setDescription("Percentage Identity Consensus "
+            + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
     return sq;
   }
 
@@ -640,7 +658,8 @@ public class AlignViewport
   {
     if (res > alignment.getWidth() - 1)
     {
-      // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
+      // log.System.out.println(" Corrected res from " + res + " to maximum " +
+      // (alignment.getWidth()-1));
       res = alignment.getWidth() - 1;
     }
     if (res < 0)
@@ -669,7 +688,9 @@ public class AlignViewport
   }
 
   java.awt.Frame nullFrame;
-  protected FeatureSettings featureSettings=null;
+
+  protected FeatureSettings featureSettings = null;
+
   public void setFont(Font f)
   {
     font = f;
@@ -905,41 +926,47 @@ public class AlignViewport
     if (globalColourScheme != null)
     {
       globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
-                                      ignoreGapsInConsensusCalculation);
+              ignoreGapsInConsensusCalculation);
 
     }
   }
 
   /**
    * Property change listener for changes in alignment
-   *
-   * @param listener DOCUMENT ME!
+   * 
+   * @param listener
+   *                DOCUMENT ME!
    */
   public void addPropertyChangeListener(
-      java.beans.PropertyChangeListener listener)
+          java.beans.PropertyChangeListener listener)
   {
     changeSupport.addPropertyChangeListener(listener);
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param listener DOCUMENT ME!
+   * 
+   * @param listener
+   *                DOCUMENT ME!
    */
   public void removePropertyChangeListener(
-      java.beans.PropertyChangeListener listener)
+          java.beans.PropertyChangeListener listener)
   {
     changeSupport.removePropertyChangeListener(listener);
   }
 
   /**
    * Property change listener for changes in alignment
-   *
-   * @param prop DOCUMENT ME!
-   * @param oldvalue DOCUMENT ME!
-   * @param newvalue DOCUMENT ME!
+   * 
+   * @param prop
+   *                DOCUMENT ME!
+   * @param oldvalue
+   *                DOCUMENT ME!
+   * @param newvalue
+   *                DOCUMENT ME!
    */
-  public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
+  public void firePropertyChange(String prop, Object oldvalue,
+          Object newvalue)
   {
     changeSupport.firePropertyChange(prop, oldvalue, newvalue);
   }
@@ -1009,7 +1036,7 @@ public class AlignViewport
 
     hiddenRepSequences.put(repSequence, sg);
 
-    //Hide all sequences except the repSequence
+    // Hide all sequences except the repSequence
     SequenceI[] seqs = new SequenceI[sSize - 1];
     int index = 0;
     for (int i = 0; i < sSize; i++)
@@ -1031,7 +1058,7 @@ public class AlignViewport
 
   public void hideAllSelectedSeqs()
   {
-    if (selectionGroup == null  || selectionGroup.getSize()<1)
+    if (selectionGroup == null || selectionGroup.getSize() < 1)
     {
       return;
     }
@@ -1081,12 +1108,11 @@ public class AlignViewport
         selectionGroup = new SequenceGroup();
         selectionGroup.setEndRes(alignment.getWidth() - 1);
       }
-      Vector tmp = alignment.getHiddenSequences().showAll(hiddenRepSequences);
+      Vector tmp = alignment.getHiddenSequences().showAll(
+              hiddenRepSequences);
       for (int t = 0; t < tmp.size(); t++)
       {
-        selectionGroup.addSequence(
-            (SequenceI) tmp.elementAt(t), false
-            );
+        selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false);
       }
       firePropertyChange("alignment", null, alignment.getSequences());
       hasHiddenRows = false;
@@ -1096,12 +1122,14 @@ public class AlignViewport
 
   public int adjustForHiddenSeqs(int alignmentIndex)
   {
-    return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
+    return alignment.getHiddenSequences().adjustForHiddenSeqs(
+            alignmentIndex);
   }
 
   /**
-   * This method returns the a new SequenceI [] with
-   * the selection sequence and start and end points adjusted
+   * This method returns the a new SequenceI [] with the selection sequence and
+   * start and end points adjusted
+   * 
    * @return String[]
    */
   public SequenceI[] getSelectionAsNewSequence()
@@ -1121,15 +1149,15 @@ public class AlignViewport
   }
 
   /**
-   * This method returns the visible alignment as text, as
-   * seen on the GUI, ie if columns are hidden they will not
-   * be returned in the result.
-   * Use this for calculating trees, PCA, redundancy etc on views
-   * which contain hidden columns.
+   * This method returns the visible alignment as text, as seen on the GUI, ie
+   * if columns are hidden they will not be returned in the result. Use this for
+   * calculating trees, PCA, redundancy etc on views which contain hidden
+   * columns.
+   * 
    * @return String[]
    */
-  public jalview.datamodel.CigarArray getViewAsCigars(boolean
-      selectedRegionOnly)
+  public jalview.datamodel.CigarArray getViewAsCigars(
+          boolean selectedRegionOnly)
   {
     CigarArray selection = null;
     SequenceI[] seqs = null;
@@ -1140,7 +1168,8 @@ public class AlignViewport
       iSize = selectionGroup.getSize();
       seqs = selectionGroup.getSequencesInOrder(alignment);
       start = selectionGroup.getStartRes();
-      end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor
+      end = selectionGroup.getEndRes(); // inclusive for start and end in
+                                        // SeqCigar constructor
     }
     else
     {
@@ -1217,33 +1246,36 @@ public class AlignViewport
   }
 
   /**
-   * return a compact representation of the current alignment selection to
-   * pass to an analysis function
-   * @param selectedOnly boolean true to just return the selected view
+   * return a compact representation of the current alignment selection to pass
+   * to an analysis function
+   * 
+   * @param selectedOnly
+   *                boolean true to just return the selected view
    * @return AlignmentView
    */
   jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly)
   {
     // JBPNote:
-    // this is here because the AlignmentView constructor modifies the CigarArray
+    // this is here because the AlignmentView constructor modifies the
+    // CigarArray
     // object. Refactoring of Cigar and alignment view representation should
     // be done to remove redundancy.
     CigarArray aligview = getViewAsCigars(selectedOnly);
     if (aligview != null)
     {
       return new AlignmentView(aligview,
-                               (selectedOnly && selectionGroup != null) ?
-                               selectionGroup.getStartRes() : 0);
+              (selectedOnly && selectionGroup != null) ? selectionGroup
+                      .getStartRes() : 0);
     }
     return null;
   }
 
   /**
-   * This method returns the visible alignment as text, as
-   * seen on the GUI, ie if columns are hidden they will not
-   * be returned in the result.
-   * Use this for calculating trees, PCA, redundancy etc on views
-   * which contain hidden columns.
+   * This method returns the visible alignment as text, as seen on the GUI, ie
+   * if columns are hidden they will not be returned in the result. Use this for
+   * calculating trees, PCA, redundancy etc on views which contain hidden
+   * columns.
+   * 
    * @return String[]
    */
   public String[] getViewAsString(boolean selectedRegionOnly)
@@ -1379,7 +1411,7 @@ public class AlignViewport
       updateConservation(ap);
     }
 
-    //Reset endRes of groups if beyond alignment width
+    // Reset endRes of groups if beyond alignment width
     int alWidth = alignment.getWidth();
     Vector groups = alignment.getGroups();
     if (groups != null)
@@ -1401,7 +1433,7 @@ public class AlignViewport
 
     resetAllColourSchemes();
 
-    //AW  alignment.adjustSequenceAnnotations();
+    // AW alignment.adjustSequenceAnnotations();
   }
 
   void resetAllColourSchemes()
@@ -1411,9 +1443,8 @@ public class AlignViewport
     {
       if (cs instanceof ClustalxColourScheme)
       {
-        ( (ClustalxColourScheme) cs).
-            resetClustalX(alignment.getSequences(),
-                          alignment.getWidth());
+        ((ClustalxColourScheme) cs).resetClustalX(alignment.getSequences(),
+                alignment.getWidth());
       }
 
       cs.setConsensus(hconsensus);
@@ -1421,9 +1452,8 @@ public class AlignViewport
       {
         Alignment al = (Alignment) alignment;
         Conservation c = new Conservation("All",
-                                          ResidueProperties.propHash, 3,
-                                          al.getSequences(), 0,
-                                          al.getWidth() - 1);
+                ResidueProperties.propHash, 3, al.getSequences(), 0, al
+                        .getWidth() - 1);
         c.calculate();
         c.verdict(false, ConsPercGaps);
 
@@ -1437,13 +1467,15 @@ public class AlignViewport
       SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s);
       if (sg.cs != null && sg.cs instanceof ClustalxColourScheme)
       {
-        ( (ClustalxColourScheme) sg.cs).resetClustalX(
-            sg.getSequences(hiddenRepSequences), sg.getWidth());
+        ((ClustalxColourScheme) sg.cs).resetClustalX(sg
+                .getSequences(hiddenRepSequences), sg.getWidth());
       }
       sg.recalcConservation();
     }
   }
+
   boolean centreColumnLabels;
+
   public boolean getCentreColumnLabels()
   {
     return centreColumnLabels;
@@ -1452,16 +1484,16 @@ public class AlignViewport
   public void updateSequenceIdColours()
   {
     Vector groups = alignment.getGroups();
-    for (int ig=0,igSize=groups.size(); ig<igSize; ig++)
+    for (int ig = 0, igSize = groups.size(); ig < igSize; ig++)
     {
       SequenceGroup sg = (SequenceGroup) groups.elementAt(ig);
-      if (sg.idColour!=null)
+      if (sg.idColour != null)
       {
         Vector sqs = sg.getSequences(hiddenRepSequences);
-        for (int s=0,sSize=sqs.size();s<sSize;s++)
+        for (int s = 0, sSize = sqs.size(); s < sSize; s++)
         {
           this.setSequenceColour((SequenceI) sqs.elementAt(s), sg.idColour);
-        } 
+        }
       }
     }
   }
diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 6b292e9..c2bdaf0 100755
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.appletgui;
 
 import java.awt.*;
@@ -24,18 +23,25 @@ import java.awt.event.*;
 
 import jalview.datamodel.*;
 
-public class AlignmentPanel
-    extends Panel implements AdjustmentListener
+public class AlignmentPanel extends Panel implements AdjustmentListener
 {
 
   public AlignViewport av;
+
   OverviewPanel overviewPanel;
+
   SeqPanel seqPanel;
+
   IdPanel idPanel;
+
   IdwidthAdjuster idwidthAdjuster;
+
   public AlignFrame alignFrame;
+
   ScalePanel scalePanel;
+
   AnnotationPanel annotationPanel;
+
   AnnotationLabels alabels;
 
   // this value is set false when selection area being dragged
@@ -46,8 +52,7 @@ public class AlignmentPanel
     try
     {
       jbInit();
-    }
-    catch (Exception e)
+    } catch (Exception e)
     {
       e.printStackTrace();
     }
@@ -94,7 +99,7 @@ public class AlignmentPanel
 
     idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
     annotationSpaceFillerHolder.setSize(d.width,
-                                        annotationPanel.getSize().height);
+            annotationPanel.getSize().height);
     alabels.setSize(d.width, annotationPanel.getSize().height);
 
     final AlignmentPanel ap = this;
@@ -104,10 +109,7 @@ public class AlignmentPanel
       {
         if (evt.getPropertyName().equals("alignment"))
         {
-          PaintRefresher.Refresh(ap,
-                                 av.getSequenceSetId(),
-                                 true,
-                                 true);
+          PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true);
           alignmentChanged();
         }
       }
@@ -147,7 +149,8 @@ public class AlignmentPanel
     FontMetrics fm = getFontMetrics(av.getFont());
 
     scalePanel.setSize(new Dimension(10, av.charHeight + fm.getDescent()));
-    idwidthAdjuster.setSize(new Dimension(10, av.charHeight + fm.getDescent()));
+    idwidthAdjuster.setSize(new Dimension(10, av.charHeight
+            + fm.getDescent()));
     av.updateSequenceIdColours();
     annotationPanel.image = null;
     int ap = annotationPanel.adjustPanelHeight();
@@ -236,8 +239,9 @@ public class AlignmentPanel
 
       if (!av.wrapAlignment)
       {
-        if ( (av.getStartRes() > end) || (av.getEndRes() < start) ||
-            ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
+        if ((av.getStartRes() > end)
+                || (av.getEndRes() < start)
+                || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
         {
           if (start > av.alignment.getWidth() - hextent)
           {
@@ -269,8 +273,8 @@ public class AlignmentPanel
 
   void scrollToWrappedVisible(int res)
   {
-    int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.
-        getSize().width);
+    int cwidth = seqPanel.seqCanvas
+            .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
     if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
     {
       vscroll.setValue(res / cwidth);
@@ -321,7 +325,7 @@ public class AlignmentPanel
 
     idSpaceFillerPanel1.setVisible(!wrap);
 
-    fontChanged(); //This is so that the scalePanel is resized correctly
+    fontChanged(); // This is so that the scalePanel is resized correctly
 
     validate();
     repaint();
@@ -329,6 +333,7 @@ public class AlignmentPanel
   }
 
   int hextent = 0;
+
   int vextent = 0;
 
   // return value is true if the scroll is valid
@@ -389,7 +394,8 @@ public class AlignmentPanel
     }
 
     av.setStartRes(x);
-    av.setEndRes( (x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) - 1);
+    av
+            .setEndRes((x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) - 1);
 
     hextent = seqPanel.seqCanvas.getSize().width / av.charWidth;
     vextent = seqPanel.seqCanvas.getSize().height / av.charHeight;
@@ -404,12 +410,12 @@ public class AlignmentPanel
       vextent = height;
     }
 
-    if ( (hextent + x) > width)
+    if ((hextent + x) > width)
     {
       x = width - hextent;
     }
 
-    if ( (vextent + y) > height)
+    if ((vextent + y) > height)
     {
       y = height - vextent;
     }
@@ -452,8 +458,8 @@ public class AlignmentPanel
     {
       int x = hscroll.getValue();
       av.setStartRes(x);
-      av.setEndRes(x + seqPanel.seqCanvas.getSize().width / av.getCharWidth() -
-                   1);
+      av.setEndRes(x + seqPanel.seqCanvas.getSize().width
+              / av.getCharWidth() - 1);
     }
 
     if (evt == null || evt.getSource() == vscroll)
@@ -461,16 +467,16 @@ public class AlignmentPanel
       int offy = vscroll.getValue();
       if (av.getWrapAlignment())
       {
-        int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
-            seqCanvas.getSize().width);
+        int rowSize = seqPanel.seqCanvas
+                .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
         av.setStartRes(vscroll.getValue() * rowSize);
-        av.setEndRes( (vscroll.getValue() + 1) * rowSize);
+        av.setEndRes((vscroll.getValue() + 1) * rowSize);
       }
       else
       {
         av.setStartSeq(offy);
-        av.setEndSeq(offy +
-                     seqPanel.seqCanvas.getSize().height / av.getCharHeight());
+        av.setEndSeq(offy + seqPanel.seqCanvas.getSize().height
+                / av.getCharHeight());
       }
     }
 
@@ -500,8 +506,7 @@ public class AlignmentPanel
       }
 
       idPanel.idCanvas.fastPaint(scrollY);
-      seqPanel.seqCanvas.fastPaint(scrollX,
-                                   scrollY);
+      seqPanel.seqCanvas.fastPaint(scrollX, scrollY);
 
       scalePanel.repaint();
       if (av.getShowAnnotation())
@@ -516,10 +521,10 @@ public class AlignmentPanel
   {
     repaint();
 
-    if(updateOverview)
+    if (updateOverview)
     {
-      jalview.structure.StructureSelectionManager.getStructureSelectionManager()
-          .sequenceColoursChanged(this);
+      jalview.structure.StructureSelectionManager
+              .getStructureSelectionManager().sequenceColoursChanged(this);
 
       if (overviewPanel != null)
       {
@@ -539,7 +544,7 @@ public class AlignmentPanel
     Dimension d = idPanel.idCanvas.getSize();
     idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
     annotationSpaceFillerHolder.setSize(d.width,
-                                        annotationPanel.getSize().height);
+            annotationPanel.getSize().height);
 
     alabels.setSize(d.width, annotationPanel.getSize().height);
 
@@ -552,8 +557,8 @@ public class AlignmentPanel
         maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
       }
 
-      int canvasWidth = seqPanel.seqCanvas.getWrappedCanvasWidth
-          (seqPanel.seqCanvas.getSize().width);
+      int canvasWidth = seqPanel.seqCanvas
+              .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
 
       if (canvasWidth > 0)
       {
@@ -577,32 +582,49 @@ public class AlignmentPanel
   }
 
   protected Panel sequenceHolderPanel = new Panel();
+
   protected Scrollbar vscroll = new Scrollbar();
+
   protected Scrollbar hscroll = new Scrollbar();
+
   protected Panel seqPanelHolder = new Panel();
+
   BorderLayout borderLayout1 = new BorderLayout();
+
   BorderLayout borderLayout3 = new BorderLayout();
+
   protected Panel scalePanelHolder = new Panel();
+
   protected Panel idPanelHolder = new Panel();
+
   BorderLayout borderLayout5 = new BorderLayout();
+
   protected Panel idSpaceFillerPanel1 = new Panel();
+
   public Panel annotationSpaceFillerHolder = new Panel();
+
   BorderLayout borderLayout6 = new BorderLayout();
+
   BorderLayout borderLayout7 = new BorderLayout();
+
   Panel hscrollHolder = new Panel();
+
   BorderLayout borderLayout10 = new BorderLayout();
+
   protected Panel hscrollFillerPanel = new Panel();
+
   BorderLayout borderLayout11 = new BorderLayout();
+
   BorderLayout borderLayout4 = new BorderLayout();
+
   BorderLayout borderLayout2 = new BorderLayout();
 
-  private void jbInit()
-      throws Exception
+  private void jbInit() throws Exception
   {
-    //  idPanelHolder.setPreferredSize(new Dimension(70, 10));
+    // idPanelHolder.setPreferredSize(new Dimension(70, 10));
     this.setLayout(borderLayout7);
 
-    //   sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
+    // sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
     sequenceHolderPanel.setLayout(borderLayout3);
     seqPanelHolder.setLayout(borderLayout1);
     scalePanelHolder.setBackground(Color.white);
@@ -612,28 +634,28 @@ public class AlignmentPanel
     idPanelHolder.setLayout(borderLayout5);
     idSpaceFillerPanel1.setBackground(Color.white);
 
-    //  idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
+    // idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
     idSpaceFillerPanel1.setLayout(borderLayout11);
     annotationSpaceFillerHolder.setBackground(Color.white);
 
-    //  annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
+    // annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
     annotationSpaceFillerHolder.setLayout(borderLayout4);
     hscroll.setOrientation(Scrollbar.HORIZONTAL);
     hscrollHolder.setLayout(borderLayout10);
     hscrollFillerPanel.setBackground(Color.white);
 
-    //  hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
+    // hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
     hscrollHolder.setBackground(Color.white);
 
-    //    annotationScroller.setPreferredSize(new Dimension(10, 80));
-    //  this.setPreferredSize(new Dimension(220, 166));
+    // annotationScroller.setPreferredSize(new Dimension(10, 80));
+    // this.setPreferredSize(new Dimension(220, 166));
     seqPanelHolder.setBackground(Color.white);
     idPanelHolder.setBackground(Color.white);
     sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);
     sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);
     seqPanelHolder.add(vscroll, BorderLayout.EAST);
 
-    //  Panel3.add(secondaryPanelHolder,  BorderLayout.SOUTH);
+    // Panel3.add(secondaryPanelHolder, BorderLayout.SOUTH);
     this.add(idPanelHolder, BorderLayout.WEST);
     idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);
     idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);
diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java
index c932962..4416ec3 100755
--- a/src/jalview/appletgui/AnnotationColourChooser.java
+++ b/src/jalview/appletgui/AnnotationColourChooser.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -27,16 +27,21 @@ import jalview.datamodel.*;
 import jalview.schemes.*;
 import java.awt.Rectangle;
 
-public class AnnotationColourChooser
-    extends Panel implements ActionListener,
-    AdjustmentListener, ItemListener, MouseListener
+public class AnnotationColourChooser extends Panel implements
+        ActionListener, AdjustmentListener, ItemListener, MouseListener
 {
   Frame frame;
+
   AlignViewport av;
+
   AlignmentPanel ap;
+
   ColourSchemeI oldcs;
+
   Hashtable oldgroupColours;
+
   jalview.datamodel.AlignmentAnnotation currentAnnotation;
+
   boolean adjusting = false;
 
   public AnnotationColourChooser(AlignViewport av, AlignmentPanel ap)
@@ -44,9 +49,9 @@ public class AnnotationColourChooser
     try
     {
       jbInit();
+    } catch (Exception ex)
+    {
     }
-    catch (Exception ex)
-    {}
 
     oldcs = av.getGlobalColourScheme();
     if (av.alignment.getGroups() != null)
@@ -57,10 +62,12 @@ public class AnnotationColourChooser
       for (int g = 0; g < allGroups.size(); g++)
       {
         sg = (SequenceGroup) allGroups.elementAt(g);
-        if (sg.cs!=null)
+        if (sg.cs != null)
+        {
+          oldgroupColours.put(sg, sg.cs);
+        }
+        else
         {
-            oldgroupColours.put(sg, sg.cs);
-        } else {
           oldgroupColours.put(sg, "null");
         }
       }
@@ -98,12 +105,12 @@ public class AnnotationColourChooser
       if (!list.contains(label))
         list.addElement(label);
       else
-        list.addElement(label+"_"+(index++));
+        list.addElement(label + "_" + (index++));
     }
 
     for (int i = 0; i < list.size(); i++)
     {
-        annotations.addItem(list.elementAt(i).toString());
+      annotations.addItem(list.elementAt(i).toString());
     }
 
     threshold.addItem("No Threshold");
@@ -116,7 +123,8 @@ public class AnnotationColourChooser
 
     frame = new Frame();
     frame.add(this);
-    jalview.bin.JalviewLite.addFrame(frame, "Colour by Annotation", 480, 145);
+    jalview.bin.JalviewLite.addFrame(frame, "Colour by Annotation", 480,
+            145);
     validate();
   }
 
@@ -125,15 +133,13 @@ public class AnnotationColourChooser
     try
     {
       jbInit();
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       ex.printStackTrace();
     }
   }
 
-  private void jbInit()
-      throws Exception
+  private void jbInit() throws Exception
   {
     minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
     minColour.setLabel("Min Colour");
@@ -191,19 +197,33 @@ public class AnnotationColourChooser
   }
 
   Choice annotations = new Choice();
+
   Button minColour = new Button();
+
   Button maxColour = new Button();
+
   Button ok = new Button();
+
   Button cancel = new Button();
+
   Panel jPanel1 = new Panel();
+
   Panel jPanel2 = new Panel();
+
   Choice threshold = new Choice();
+
   FlowLayout flowLayout1 = new FlowLayout();
+
   Panel jPanel3 = new Panel();
+
   Scrollbar slider = new Scrollbar(Scrollbar.HORIZONTAL);
+
   TextField thresholdValue = new TextField(20);
+
   Checkbox currentColours = new Checkbox();
+
   BorderLayout borderLayout1 = new BorderLayout();
+
   Checkbox thresholdIsMin = new Checkbox();
 
   public void actionPerformed(ActionEvent evt)
@@ -213,11 +233,11 @@ public class AnnotationColourChooser
       try
       {
         float f = new Float(thresholdValue.getText()).floatValue();
-        slider.setValue( (int) (f * 1000));
+        slider.setValue((int) (f * 1000));
         adjustmentValueChanged(null);
+      } catch (NumberFormatException ex)
+      {
       }
-      catch (NumberFormatException ex)
-      {}
     }
     else if (evt.getSource() == minColour)
     {
@@ -267,9 +287,9 @@ public class AnnotationColourChooser
   {
     if (!adjusting)
     {
-      thresholdValue.setText( ( (float) slider.getValue() / 1000f) + "");
+      thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
       if (currentColours.getState()
-          && ! (av.getGlobalColourScheme() instanceof AnnotationColourGradient))
+              && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
       {
         changeColour();
       }
@@ -289,8 +309,7 @@ public class AnnotationColourChooser
     }
     else
     {
-      new UserDefinedColours(this, "Min Colour",
-                             minColour.getBackground());
+      new UserDefinedColours(this, "Min Colour", minColour.getBackground());
     }
 
   }
@@ -305,8 +324,7 @@ public class AnnotationColourChooser
     }
     else
     {
-      new UserDefinedColours(this, "Max Colour",
-                             maxColour.getBackground());
+      new UserDefinedColours(this, "Max Colour", maxColour.getBackground());
     }
   }
 
@@ -318,9 +336,8 @@ public class AnnotationColourChooser
       return;
     }
 
-
-    currentAnnotation = av.alignment.getAlignmentAnnotation()
-        [annotations.getSelectedIndex()];
+    currentAnnotation = av.alignment.getAlignmentAnnotation()[annotations
+            .getSelectedIndex()];
 
     int aboveThreshold = -1;
     if (threshold.getSelectedItem().equals("Above Threshold"))
@@ -341,23 +358,22 @@ public class AnnotationColourChooser
       thresholdValue.setEnabled(false);
       thresholdValue.setText("");
     }
-    else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD &&
-             currentAnnotation.threshold == null)
-    {
-      currentAnnotation.setThreshold(new jalview.datamodel.GraphLine
-                                     ( (currentAnnotation.graphMax -
-                                        currentAnnotation.graphMin) / 2f,
-                                      "Threshold",
-                                      Color.black));
+    else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
+            && currentAnnotation.threshold == null)
+    {
+      currentAnnotation
+              .setThreshold(new jalview.datamodel.GraphLine(
+                      (currentAnnotation.graphMax - currentAnnotation.graphMin) / 2f,
+                      "Threshold", Color.black));
     }
 
     if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
     {
       adjusting = true;
 
-      slider.setMinimum( (int) (currentAnnotation.graphMin * 1000));
-      slider.setMaximum( (int) (currentAnnotation.graphMax * 1000));
-      slider.setValue( (int) (currentAnnotation.threshold.value * 1000));
+      slider.setMinimum((int) (currentAnnotation.graphMin * 1000));
+      slider.setMaximum((int) (currentAnnotation.graphMax * 1000));
+      slider.setValue((int) (currentAnnotation.threshold.value * 1000));
       thresholdValue.setText(currentAnnotation.threshold.value + "");
       slider.setEnabled(true);
       thresholdValue.setEnabled(true);
@@ -367,21 +383,17 @@ public class AnnotationColourChooser
     AnnotationColourGradient acg = null;
     if (currentColours.getState())
     {
-      acg = new AnnotationColourGradient(
-          currentAnnotation,
-          av.getGlobalColourScheme(), aboveThreshold);
+      acg = new AnnotationColourGradient(currentAnnotation, av
+              .getGlobalColourScheme(), aboveThreshold);
     }
     else
     {
-      acg =
-          new AnnotationColourGradient(
-              currentAnnotation,
-              minColour.getBackground(),
-              maxColour.getBackground(),
-              aboveThreshold);
+      acg = new AnnotationColourGradient(currentAnnotation, minColour
+              .getBackground(), maxColour.getBackground(), aboveThreshold);
     }
 
-    if (currentAnnotation.graphMin == 0f && currentAnnotation.graphMax == 0f)
+    if (currentAnnotation.graphMin == 0f
+            && currentAnnotation.graphMax == 0f)
     {
       acg.predefinedColours = true;
     }
@@ -405,17 +417,14 @@ public class AnnotationColourChooser
 
         if (currentColours.getState())
         {
-          sg.cs = new AnnotationColourGradient(
-              currentAnnotation,
-              sg.cs, aboveThreshold);
+          sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
+                  aboveThreshold);
         }
         else
         {
-          sg.cs = new AnnotationColourGradient(
-              currentAnnotation,
-              minColour.getBackground(),
-              maxColour.getBackground(),
-              aboveThreshold);
+          sg.cs = new AnnotationColourGradient(currentAnnotation, minColour
+                  .getBackground(), maxColour.getBackground(),
+                  aboveThreshold);
         }
 
       }
@@ -437,8 +446,10 @@ public class AnnotationColourChooser
         Object cs = oldgroupColours.get(sg);
         if (cs instanceof ColourSchemeI)
         {
-          sg.cs = (ColourSchemeI) cs; 
-        } else {
+          sg.cs = (ColourSchemeI) cs;
+        }
+        else
+        {
           // probably the "null" string we set it to if it was null originally.
           sg.cs = null;
         }
@@ -448,11 +459,25 @@ public class AnnotationColourChooser
 
   }
 
-  public void mouseClicked(MouseEvent evt){}
-  public void mousePressed(MouseEvent evt){}
-  public void mouseReleased(MouseEvent evt){ ap.paintAlignment(true);}
-  public void mouseEntered(MouseEvent evt){}
-  public void mouseExited(MouseEvent evt){}
+  public void mouseClicked(MouseEvent evt)
+  {
+  }
+
+  public void mousePressed(MouseEvent evt)
+  {
+  }
+
+  public void mouseReleased(MouseEvent evt)
+  {
+    ap.paintAlignment(true);
+  }
 
+  public void mouseEntered(MouseEvent evt)
+  {
+  }
+
+  public void mouseExited(MouseEvent evt)
+  {
+  }
 
 }
diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index 2d2d748..28270c9 100755
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.appletgui;
 
 import java.util.*;
@@ -26,24 +25,35 @@ import java.awt.event.*;
 
 import jalview.datamodel.*;
 
-public class AnnotationLabels
-    extends Panel implements ActionListener, MouseListener, MouseMotionListener
+public class AnnotationLabels extends Panel implements ActionListener,
+        MouseListener, MouseMotionListener
 {
   Image image;
+
   boolean active = false;
+
   AlignmentPanel ap;
+
   AlignViewport av;
+
   boolean resizing = false;
+
   int oldY, mouseX;
 
   static String ADDNEW = "Add New Row";
+
   static String EDITNAME = "Edit Label/Description";
+
   static String HIDE = "Hide This Row";
+
   static String SHOWALL = "Show All Hidden Rows";
+
   static String OUTPUT_TEXT = "Show Values In Textbox";
+
   static String COPYCONS_SEQ = "Copy Consensus Sequence";
 
   int scrollOffset = 0;
+
   int selectedRow = -1;
 
   Tooltip tooltip;
@@ -103,9 +113,8 @@ public class AnnotationLabels
 
     if (evt.getActionCommand().equals(ADDNEW))
     {
-      AlignmentAnnotation newAnnotation = new AlignmentAnnotation("",
-          null,
-          new Annotation[ap.av.alignment.getWidth()]);
+      AlignmentAnnotation newAnnotation = new AlignmentAnnotation("", null,
+              new Annotation[ap.av.alignment.getWidth()]);
 
       if (!editLabelDescription(newAnnotation))
       {
@@ -127,17 +136,17 @@ public class AnnotationLabels
     {
       for (int i = 0; i < aa.length; i++)
       {
-        aa[i].visible = (aa[i].annotations==null) ? false : true;
+        aa[i].visible = (aa[i].annotations == null) ? false : true;
       }
     }
     else if (evt.getActionCommand().equals(OUTPUT_TEXT))
     {
-      CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
+      CutAndPasteTransfer cap = new CutAndPasteTransfer(false,
+              ap.alignFrame);
       Frame frame = new Frame();
       frame.add(cap);
-      jalview.bin.JalviewLite.addFrame(frame,
-                                       ap.alignFrame.getTitle() + " - " +
-                                       aa[selectedRow].label, 500, 100);
+      jalview.bin.JalviewLite.addFrame(frame, ap.alignFrame.getTitle()
+              + " - " + aa[selectedRow].label, 500, 100);
       cap.setText(aa[selectedRow].toString());
     }
     else if (evt.getActionCommand().equals(COPYCONS_SEQ))
@@ -158,17 +167,12 @@ public class AnnotationLabels
   boolean editLabelDescription(AlignmentAnnotation annotation)
   {
     Checkbox padGaps = new Checkbox("Fill Empty Gaps With \""
-                                    +ap.av.getGapCharacter()+"\"",
-                                    annotation.padGaps);
-
-    EditNameDialog dialog = new EditNameDialog(
-        annotation.label,
-        annotation.description,
-        "      Annotation Label",
-        "Annotation Description",
-        ap.alignFrame,
-        "Edit Annotation Name / Description",
-        500, 180, false);
+            + ap.av.getGapCharacter() + "\"", annotation.padGaps);
+
+    EditNameDialog dialog = new EditNameDialog(annotation.label,
+            annotation.description, "      Annotation Label",
+            "Annotation Description", ap.alignFrame,
+            "Edit Annotation Name / Description", 500, 180, false);
 
     Panel empty = new Panel(new FlowLayout());
     empty.add(padGaps);
@@ -198,14 +202,13 @@ public class AnnotationLabels
     {
       if (tooltip == null)
       {
-        tooltip = new Tooltip(ap.av.alignment.
-                              getAlignmentAnnotation()[row].getDescription(true),
-                              this);
+        tooltip = new Tooltip(ap.av.alignment.getAlignmentAnnotation()[row]
+                .getDescription(true), this);
       }
       else
       {
-        tooltip.setTip(ap.av.alignment.
-                       getAlignmentAnnotation()[row].getDescription(true));
+        tooltip.setTip(ap.av.alignment.getAlignmentAnnotation()[row]
+                .getDescription(true));
       }
     }
     else if (tooltip != null)
@@ -216,19 +219,24 @@ public class AnnotationLabels
   }
 
   public void mouseDragged(MouseEvent evt)
-  {}
+  {
+  }
 
   public void mouseClicked(MouseEvent evt)
-  {}
+  {
+  }
 
   public void mouseReleased(MouseEvent evt)
-  {}
+  {
+  }
 
   public void mouseEntered(MouseEvent evt)
-  {}
+  {
+  }
 
   public void mouseExited(MouseEvent evt)
-  {}
+  {
+  }
 
   public void mousePressed(MouseEvent evt)
   {
@@ -259,8 +267,7 @@ public class AnnotationLabels
     {
       popup.addSeparator();
       final CheckboxMenuItem cbmi = new CheckboxMenuItem(
-          "Ignore Gaps In Consensus",
-          ap.av.getIgnoreGapsConsensus());
+              "Ignore Gaps In Consensus", ap.av.getIgnoreGapsConsensus());
 
       cbmi.addItemListener(new ItemListener()
       {
@@ -282,8 +289,9 @@ public class AnnotationLabels
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void copy_annotseqtoclipboard(SequenceI sq)
   {
@@ -292,21 +300,20 @@ public class AnnotationLabels
       return;
     }
     jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer();
-    jalview.appletgui.AlignFrame.copiedSequences.append(sq.getName() + "\t" +
-        sq.getStart() + "\t" +
-        sq.getEnd() + "\t" +
-        sq.getSequenceAsString() + "\n");
+    jalview.appletgui.AlignFrame.copiedSequences.append(sq.getName() + "\t"
+            + sq.getStart() + "\t" + sq.getEnd() + "\t"
+            + sq.getSequenceAsString() + "\n");
     if (av.hasHiddenColumns)
     {
       jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector();
       for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
       {
-        int[] region = (int[])
-            av.getColumnSelection().getHiddenColumns().elementAt(i);
+        int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
+                .elementAt(i);
 
-        jalview.appletgui.AlignFrame.copiedHiddenColumns.addElement(new int[]
-            {region[0],
-            region[1]});
+        jalview.appletgui.AlignFrame.copiedHiddenColumns
+                .addElement(new int[]
+                { region[0], region[1] });
       }
     }
   }
diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index 909ce78..13db915 100755
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.appletgui;
 
 import java.util.*;
@@ -26,29 +25,41 @@ import java.awt.event.*;
 
 import jalview.datamodel.*;
 
-public class AnnotationPanel
-    extends Panel
-    implements AdjustmentListener, ActionListener, MouseListener, MouseMotionListener
+public class AnnotationPanel extends Panel implements AdjustmentListener,
+        ActionListener, MouseListener, MouseMotionListener
 {
   AlignViewport av;
+
   AlignmentPanel ap;
+
   int activeRow = -1;
 
   Vector activeRes;
+
   static String HELIX = "Helix";
+
   static String SHEET = "Sheet";
+
   static String LABEL = "Label";
+
   static String REMOVE = "Remove Annotation";
+
   static String COLOUR = "Colour";
+
   static Color HELIX_COLOUR = Color.red.darker();
+
   static Color SHEET_COLOUR = Color.green.darker().darker();
-  
+
   Image image;
+
   Graphics gg;
+
   FontMetrics fm;
+
   int imgWidth = 0;
 
   boolean fastPaint = false;
+
   public static int GRAPH_HEIGHT = 40;
 
   boolean MAC = false;
@@ -65,7 +76,6 @@ public class AnnotationPanel
 
     addMouseListener(this);
 
-
     // ap.annotationScroller.getVAdjustable().addAdjustmentListener( this );
   }
 
@@ -76,13 +86,14 @@ public class AnnotationPanel
 
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
-    ap.alabels.setScrollOffset( -evt.getValue());
+    ap.alabels.setScrollOffset(-evt.getValue());
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
    */
   public void actionPerformed(ActionEvent evt)
   {
@@ -99,10 +110,9 @@ public class AnnotationPanel
 
     String label = "";
     if (av.colSel != null && av.colSel.size() > 0
-        && anot[av.colSel.getMin()] != null)
+            && anot[av.colSel.getMin()] != null)
       label = anot[av.getColumnSelection().getMin()].displayCharacter;
 
-
     if (evt.getActionCommand().equals(REMOVE))
     {
       for (int i = 0; i < av.getColumnSelection().size(); i++)
@@ -119,7 +129,7 @@ public class AnnotationPanel
         return;
       }
 
-      if ( (label.length() > 0) && !aa[activeRow].hasText)
+      if ((label.length() > 0) && !aa[activeRow].hasText)
       {
         aa[activeRow].hasText = true;
       }
@@ -128,7 +138,7 @@ public class AnnotationPanel
       {
         int index = av.getColumnSelection().columnAt(i);
 
-        if(!av.colSel.isVisible(index))
+        if (!av.colSel.isVisible(index))
           continue;
 
         if (anot[index] == null)
@@ -141,9 +151,8 @@ public class AnnotationPanel
     }
     else if (evt.getActionCommand().equals(COLOUR))
     {
-      UserDefinedColours udc = new UserDefinedColours(
-          this,
-         Color.black, ap.alignFrame);
+      UserDefinedColours udc = new UserDefinedColours(this, Color.black,
+              ap.alignFrame);
 
       Color col = udc.getColor();
 
@@ -151,7 +160,7 @@ public class AnnotationPanel
       {
         int index = av.getColumnSelection().columnAt(i);
 
-        if(!av.colSel.isVisible(index))
+        if (!av.colSel.isVisible(index))
           continue;
 
         if (anot[index] == null)
@@ -162,7 +171,8 @@ public class AnnotationPanel
         anot[index].colour = col;
       }
     }
-    else // HELIX OR SHEET
+    else
+    // HELIX OR SHEET
     {
       char type = 0;
       String symbol = "\u03B1";
@@ -189,7 +199,7 @@ public class AnnotationPanel
         return;
       }
 
-      if ( (label.length() > 0) && !aa[activeRow].hasText)
+      if ((label.length() > 0) && !aa[activeRow].hasText)
       {
         aa[activeRow].hasText = true;
       }
@@ -198,7 +208,7 @@ public class AnnotationPanel
       {
         int index = av.getColumnSelection().columnAt(i);
 
-        if(!av.colSel.isVisible(index))
+        if (!av.colSel.isVisible(index))
           continue;
 
         if (anot[index] == null)
@@ -219,10 +229,10 @@ public class AnnotationPanel
 
   String enterLabel(String text, String label)
   {
-    EditNameDialog dialog = new EditNameDialog(text,null,label,null,
-        ap.alignFrame,"Enter Label", 400,200, true);
+    EditNameDialog dialog = new EditNameDialog(text, null, label, null,
+            ap.alignFrame, "Enter Label", 400, 200, true);
 
-    if(dialog.accept)
+    if (dialog.accept)
       return dialog.getName();
     else
       return null;
@@ -230,70 +240,69 @@ public class AnnotationPanel
 
   public void mousePressed(MouseEvent evt)
   {
-      AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-      if (aa == null)
-      {
-        return;
-      }
-
-      int height = 0;
-      activeRow = -1;
+    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+    if (aa == null)
+    {
+      return;
+    }
 
+    int height = 0;
+    activeRow = -1;
 
-      for (int i = 0; i < aa.length; i++)
+    for (int i = 0; i < aa.length; i++)
+    {
+      if (aa[i].visible)
       {
-        if (aa[i].visible)
-        {
-          height += aa[i].height;
-        }
-
-        if (evt.getY() < height)
-        {
-          if (aa[i].editable)
-          {
-            activeRow = i;
-          }
-
-          break;
-        }
+        height += aa[i].height;
       }
 
-      if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==
-        InputEvent.BUTTON3_MASK  && activeRow != -1)
+      if (evt.getY() < height)
       {
-        if (av.getColumnSelection() == null)
+        if (aa[i].editable)
         {
-          return;
+          activeRow = i;
         }
 
-        PopupMenu pop = new PopupMenu("Structure type");
-        MenuItem item = new MenuItem(HELIX);
-        item.addActionListener(this);
-        pop.add(item);
-        item = new MenuItem(SHEET);
-        item.addActionListener(this);
-        pop.add(item);
-        item = new MenuItem(LABEL);
-        item.addActionListener(this);
-        pop.add(item);
-        item = new MenuItem(COLOUR);
-        item.addActionListener(this);
-        pop.add(item);
-        item = new MenuItem(REMOVE);
-        item.addActionListener(this);
-        pop.add(item);
-        ap.alignFrame.add(pop);
-        pop.show(this, evt.getX(), evt.getY());
-
-        return;
+        break;
       }
+    }
 
-      if (aa == null)
+    if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK
+            && activeRow != -1)
+    {
+      if (av.getColumnSelection() == null)
       {
         return;
       }
 
-      ap.scalePanel.mousePressed(evt);
+      PopupMenu pop = new PopupMenu("Structure type");
+      MenuItem item = new MenuItem(HELIX);
+      item.addActionListener(this);
+      pop.add(item);
+      item = new MenuItem(SHEET);
+      item.addActionListener(this);
+      pop.add(item);
+      item = new MenuItem(LABEL);
+      item.addActionListener(this);
+      pop.add(item);
+      item = new MenuItem(COLOUR);
+      item.addActionListener(this);
+      pop.add(item);
+      item = new MenuItem(REMOVE);
+      item.addActionListener(this);
+      pop.add(item);
+      ap.alignFrame.add(pop);
+      pop.show(this, evt.getX(), evt.getY());
+
+      return;
+    }
+
+    if (aa == null)
+    {
+      return;
+    }
+
+    ap.scalePanel.mousePressed(evt);
   }
 
   public void mouseReleased(MouseEvent evt)
@@ -302,7 +311,8 @@ public class AnnotationPanel
   }
 
   public void mouseClicked(MouseEvent evt)
-  {}
+  {
+  }
 
   public void mouseDragged(MouseEvent evt)
   {
@@ -341,7 +351,8 @@ public class AnnotationPanel
       res = av.getColumnSelection().adjustForHiddenColumns(res);
     }
 
-    if (row > -1 && res < aa[row].annotations.length && aa[row].annotations[res] != null)
+    if (row > -1 && res < aa[row].annotations.length
+            && aa[row].annotations[res] != null)
     {
       StringBuffer text = new StringBuffer("Sequence position " + (res + 1));
       if (aa[row].annotations[res].description != null)
@@ -351,16 +362,17 @@ public class AnnotationPanel
       ap.alignFrame.statusBar.setText(text.toString());
     }
   }
+
   public void mouseEntered(MouseEvent evt)
   {
     ap.scalePanel.mouseEntered(evt);
   }
+
   public void mouseExited(MouseEvent evt)
   {
     ap.scalePanel.mouseExited(evt);
   }
 
-
   public int adjustPanelHeight()
   {
     // setHeight of panels
@@ -444,7 +456,6 @@ public class AnnotationPanel
     activeRes.addElement(String.valueOf(i));
   }
 
-
   public void update(Graphics g)
   {
     paint(g);
@@ -454,7 +465,7 @@ public class AnnotationPanel
   {
 
     imgWidth = getSize().width;
-    //(av.endRes - av.startRes + 1) * av.charWidth;
+    // (av.endRes - av.startRes + 1) * av.charWidth;
 
     if (image == null || imgWidth != image.getWidth(this))
     {
@@ -481,16 +492,15 @@ public class AnnotationPanel
 
   public void fastPaint(int horizontal)
   {
-    if (horizontal == 0
-        || av.alignment.getAlignmentAnnotation() == null
-        || av.alignment.getAlignmentAnnotation().length < 1
-        )
+    if (horizontal == 0 || av.alignment.getAlignmentAnnotation() == null
+            || av.alignment.getAlignmentAnnotation().length < 1)
     {
       repaint();
       return;
     }
 
-    gg.copyArea(0, 0, imgWidth, getSize().height, -horizontal * av.charWidth, 0);
+    gg.copyArea(0, 0, imgWidth, getSize().height, -horizontal
+            * av.charWidth, 0);
     int sr = av.startRes, er = av.endRes + 1, transX = 0;
 
     if (horizontal > 0) // scrollbar pulled right, image to the left
@@ -507,7 +517,7 @@ public class AnnotationPanel
 
     drawComponent(gg, sr, er);
 
-    gg.translate( -transX, 0);
+    gg.translate(-transX, 0);
 
     fastPaint = true;
     repaint();
@@ -515,10 +525,13 @@ public class AnnotationPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param g DOCUMENT ME!
-   * @param startRes DOCUMENT ME!
-   * @param endRes DOCUMENT ME!
+   * 
+   * @param g
+   *                DOCUMENT ME!
+   * @param startRes
+   *                DOCUMENT ME!
+   * @param endRes
+   *                DOCUMENT ME!
    */
   public void drawComponent(Graphics g, int startRes, int endRes)
   {
@@ -532,8 +545,8 @@ public class AnnotationPanel
       fm = g.getFontMetrics();
     }
 
-    if ( (av.alignment.getAlignmentAnnotation() == null) ||
-        (av.alignment.getAlignmentAnnotation().length < 1))
+    if ((av.alignment.getAlignmentAnnotation() == null)
+            || (av.alignment.getAlignmentAnnotation().length < 1))
     {
       g.setColor(Color.white);
       g.fillRect(0, 0, getSize().width, getSize().height);
@@ -558,7 +571,7 @@ public class AnnotationPanel
     boolean validEnd = false;
     boolean[] graphGroupDrawn = new boolean[aa.length];
 
-    //\u03B2 \u03B1
+    // \u03B2 \u03B1
     for (int i = 0; i < aa.length; i++)
     {
       AlignmentAnnotation row = aa[i];
@@ -601,7 +614,8 @@ public class AnnotationPanel
       {
         if (av.hasHiddenColumns)
         {
-          column = av.getColumnSelection().adjustForHiddenColumns(startRes + x);
+          column = av.getColumnSelection().adjustForHiddenColumns(
+                  startRes + x);
           if (column > row.annotations.length - 1)
           {
             break;
@@ -612,8 +626,8 @@ public class AnnotationPanel
           column = startRes + x;
         }
 
-        if ( (row.annotations.length <= column) ||
-            (row.annotations[column] == null))
+        if ((row.annotations.length <= column)
+                || (row.annotations[column] == null))
         {
           validRes = false;
         }
@@ -634,25 +648,26 @@ public class AnnotationPanel
 
               if (v == column)
               {
-                g.fillRect(x * av.charWidth, y,
-                           av.charWidth, av.charHeight);
+                g
+                        .fillRect(x * av.charWidth, y, av.charWidth,
+                                av.charHeight);
               }
             }
           }
         }
 
-
-
-        if (av.validCharWidth && validRes &&
-            (row.annotations[column].displayCharacter!=null && row.annotations[column].displayCharacter.length() > 0))
+        if (av.validCharWidth
+                && validRes
+                && (row.annotations[column].displayCharacter != null && row.annotations[column].displayCharacter
+                        .length() > 0))
         {
-          int charOffset = (av.getCentreColumnLabels()) ? ((av.charWidth -
-                  fm.charsWidth(row.annotations[column].
-                               displayCharacter.toCharArray(),0,
-                               row.annotations[column].
-                               displayCharacter.length())) / 2)
-                               : (av.charWidth - fm.charWidth(row.annotations[column].
-                                       displayCharacter.charAt(0))) / 2;
+          int charOffset = (av.getCentreColumnLabels()) ? ((av.charWidth - fm
+                  .charsWidth(row.annotations[column].displayCharacter
+                          .toCharArray(), 0,
+                          row.annotations[column].displayCharacter.length())) / 2)
+                  : (av.charWidth - fm
+                          .charWidth(row.annotations[column].displayCharacter
+                                  .charAt(0))) / 2;
 
           if (row.annotations[column].colour == null)
             g.setColor(Color.black);
@@ -662,87 +677,78 @@ public class AnnotationPanel
           if (column == 0 || row.graph > 0)
           {
             g.drawString(row.annotations[column].displayCharacter,
-                         (x * av.charWidth) + charOffset,
-                         y + iconOffset + 3);
+                    (x * av.charWidth) + charOffset, y + iconOffset + 3);
           }
-          else if (
-              row.annotations[column - 1] == null
-              || (!row.annotations[column].displayCharacter.equals(
-                  row.annotations[column - 1].displayCharacter)
-                  ||
-                  (row.annotations[column].displayCharacter.length() < 2 &&
-                   row.annotations[column].secondaryStructure == ' ')))
+          else if (row.annotations[column - 1] == null
+                  || (!row.annotations[column].displayCharacter
+                          .equals(row.annotations[column - 1].displayCharacter) || (row.annotations[column].displayCharacter
+                          .length() < 2 && row.annotations[column].secondaryStructure == ' ')))
           {
             g.drawString(row.annotations[column].displayCharacter,
-                         (x * av.charWidth) + charOffset,
-                         y + iconOffset + 3);
+                    (x * av.charWidth) + charOffset, y + iconOffset + 3);
           }
         }
 
         if (row.hasIcons)
         {
-          if (!validRes ||
-              (row.annotations[column].secondaryStructure != lastSS))
+          if (!validRes
+                  || (row.annotations[column].secondaryStructure != lastSS))
           {
             switch (lastSS)
             {
-              case 'H':
-                g.setColor(HELIX_COLOUR);
-                if (MAC)
-                {
-                  //Off by 1 offset when drawing rects and ovals
-                  //to offscreen image on the MAC
-                  g.fillRoundRect(lastSSX, y + 4 + iconOffset,
-                                  (x * av.charWidth) - lastSSX, 7, 8, 8);
-                  break;
-                }
-
-                int sCol = (lastSSX / av.charWidth) + startRes;
-                int x1 = lastSSX;
-                int x2 = (x * av.charWidth);
-
-                if (sCol == 0 ||
-                    row.annotations[sCol - 1] == null ||
-                    row.annotations[sCol - 1].secondaryStructure != 'H')
-                {
-                  g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90,
-                            180);
-                  x1 += av.charWidth / 2;
-                }
-
-                if (row.annotations[column] == null ||
-                    row.annotations[column].secondaryStructure != 'H')
-                {
-                  g.fillArc( (x * av.charWidth) - av.charWidth,
-                            y + 4 + iconOffset, av.charWidth, 8, 270, 180);
-                  x2 -= av.charWidth / 2;
-                }
-
-                g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
+            case 'H':
+              g.setColor(HELIX_COLOUR);
+              if (MAC)
+              {
+                // Off by 1 offset when drawing rects and ovals
+                // to offscreen image on the MAC
+                g.fillRoundRect(lastSSX, y + 4 + iconOffset,
+                        (x * av.charWidth) - lastSSX, 7, 8, 8);
                 break;
+              }
 
-              case 'E':
-                g.setColor(SHEET_COLOUR);
-                g.fillRect(lastSSX, y + 4 + iconOffset,
-                           (x * av.charWidth) - lastSSX - 4, 7);
-                g.fillPolygon(new int[]
-                              { (x * av.charWidth) - 4,
-                              (x * av.charWidth) - 4,
-                              (x * av.charWidth)},
-                              new int[]
-                              {
-                              y + iconOffset, y + 14 + iconOffset,
-                              y + 8 + iconOffset
-                }, 3);
+              int sCol = (lastSSX / av.charWidth) + startRes;
+              int x1 = lastSSX;
+              int x2 = (x * av.charWidth);
 
-                break;
+              if (sCol == 0
+                      || row.annotations[sCol - 1] == null
+                      || row.annotations[sCol - 1].secondaryStructure != 'H')
+              {
+                g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90,
+                        180);
+                x1 += av.charWidth / 2;
+              }
+
+              if (row.annotations[column] == null
+                      || row.annotations[column].secondaryStructure != 'H')
+              {
+                g.fillArc((x * av.charWidth) - av.charWidth, y + 4
+                        + iconOffset, av.charWidth, 8, 270, 180);
+                x2 -= av.charWidth / 2;
+              }
 
-              default:
-                g.setColor(Color.gray);
-                g.fillRect(lastSSX, y + 6 + iconOffset,
-                           (x * av.charWidth) - lastSSX, 2);
+              g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
+              break;
 
-                break;
+            case 'E':
+              g.setColor(SHEET_COLOUR);
+              g.fillRect(lastSSX, y + 4 + iconOffset, (x * av.charWidth)
+                      - lastSSX - 4, 7);
+              g.fillPolygon(new int[]
+              { (x * av.charWidth) - 4, (x * av.charWidth) - 4,
+                  (x * av.charWidth) }, new int[]
+              { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
+                      3);
+
+              break;
+
+            default:
+              g.setColor(Color.gray);
+              g.fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth)
+                      - lastSSX, 2);
+
+              break;
             }
 
             if (validRes)
@@ -766,86 +772,83 @@ public class AnnotationPanel
       {
         column = row.annotations.length - 1;
         validEnd = false;
-      } else {
+      }
+      else
+      {
         validEnd = true;
       }
 
-      //  x ++;
+      // x ++;
 
       if (row.hasIcons)
       {
         switch (lastSS)
         {
-          case 'H':
-            g.setColor(HELIX_COLOUR);
-            if (MAC)
-            {
-              //Off by 1 offset when drawing rects and ovals
-              //to offscreen image on the MAC
-              g.fillRoundRect(lastSSX, y + 4 + iconOffset,
-                              (x * av.charWidth) - lastSSX, 7, 8, 8);
-              break;
-            }
+        case 'H':
+          g.setColor(HELIX_COLOUR);
+          if (MAC)
+          {
+            // Off by 1 offset when drawing rects and ovals
+            // to offscreen image on the MAC
+            g.fillRoundRect(lastSSX, y + 4 + iconOffset, (x * av.charWidth)
+                    - lastSSX, 7, 8, 8);
+            break;
+          }
 
-            int sCol = (lastSSX / av.charWidth) + startRes;
-            int x1 = lastSSX;
-            int x2 = (x * av.charWidth);
+          int sCol = (lastSSX / av.charWidth) + startRes;
+          int x1 = lastSSX;
+          int x2 = (x * av.charWidth);
 
-            if (sCol == 0 ||
-                row.annotations[sCol - 1] == null ||
-                row.annotations[sCol - 1].secondaryStructure != 'H')
-            {
-              g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90, 180);
-              x1 += av.charWidth / 2;
-            }
+          if (sCol == 0 || row.annotations[sCol - 1] == null
+                  || row.annotations[sCol - 1].secondaryStructure != 'H')
+          {
+            g
+                    .fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8,
+                            90, 180);
+            x1 += av.charWidth / 2;
+          }
 
-            if (row.annotations[column] == null ||
-                row.annotations[column].secondaryStructure != 'H')
-            {
-              g.fillArc( (x * av.charWidth) - av.charWidth,
-                        y + 4 + iconOffset, av.charWidth, 8, 270,
-                        180);
-              x2 -= av.charWidth / 2;
-            }
+          if (row.annotations[column] == null
+                  || row.annotations[column].secondaryStructure != 'H')
+          {
+            g.fillArc((x * av.charWidth) - av.charWidth,
+                    y + 4 + iconOffset, av.charWidth, 8, 270, 180);
+            x2 -= av.charWidth / 2;
+          }
 
-            g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
+          g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
 
-            break;
+          break;
 
-          case 'E':
-            g.setColor(SHEET_COLOUR);
+        case 'E':
+          g.setColor(SHEET_COLOUR);
 
-            if (!validEnd || row.annotations[endRes] == null
-                || row.annotations[endRes].secondaryStructure != 'E')
-            {
-              g.fillRect(lastSSX, y + 4 + iconOffset,
-                         (x * av.charWidth) - lastSSX - 4, 7);
-              g.fillPolygon(new int[]
-                            { (x * av.charWidth) - 4,
-                            (x * av.charWidth) - 4,
-                            (x * av.charWidth)},
-                            new int[]
-                            {
-                            y + iconOffset, y + 14 + iconOffset,
-                            y + 7 + iconOffset
-              }, 3);
-            }
-            else
-            {
-              g.fillRect(lastSSX, y + 4 + iconOffset,
-                         x * av.charWidth - lastSSX, 7);
-            }
-            break;
+          if (!validEnd || row.annotations[endRes] == null
+                  || row.annotations[endRes].secondaryStructure != 'E')
+          {
+            g.fillRect(lastSSX, y + 4 + iconOffset, (x * av.charWidth)
+                    - lastSSX - 4, 7);
+            g.fillPolygon(new int[]
+            { (x * av.charWidth) - 4, (x * av.charWidth) - 4,
+                (x * av.charWidth) }, new int[]
+            { y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset }, 3);
+          }
+          else
+          {
+            g.fillRect(lastSSX, y + 4 + iconOffset, x * av.charWidth
+                    - lastSSX, 7);
+          }
+          break;
 
-          default:
-            g.setColor(Color.gray);
-            if (!av.wrapAlignment || endRes == av.endRes)
-            {
-              g.fillRect(lastSSX, y + 6 + iconOffset,
-                         (x * av.charWidth) - lastSSX, 2);
-            }
+        default:
+          g.setColor(Color.gray);
+          if (!av.wrapAlignment || endRes == av.endRes)
+          {
+            g.fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth)
+                    - lastSSX, 2);
+          }
 
-            break;
+          break;
         }
       }
 
@@ -882,9 +885,8 @@ public class AnnotationPanel
             {
               if (aa[gg].graphGroup == row.graphGroup)
               {
-                drawLineGraph(g, aa[gg], startRes, endRes, y,
-                              groupmin, groupmax,
-                              row.graphHeight);
+                drawLineGraph(g, aa[gg], startRes, endRes, y, groupmin,
+                        groupmax, row.graphHeight);
               }
             }
 
@@ -892,14 +894,14 @@ public class AnnotationPanel
           }
           else
           {
-            drawLineGraph(g, row, startRes, endRes,
-                          y, row.graphMin, row.graphMax, row.graphHeight);
+            drawLineGraph(g, row, startRes, endRes, y, row.graphMin,
+                    row.graphMax, row.graphHeight);
           }
         }
         else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
         {
-          drawBarGraph(g, row, startRes, endRes,
-                       row.graphMin, row.graphMax, y);
+          drawBarGraph(g, row, startRes, endRes, row.graphMin,
+                  row.graphMax, y);
         }
       }
 
@@ -915,11 +917,8 @@ public class AnnotationPanel
     }
   }
 
-  public void drawLineGraph(Graphics g, AlignmentAnnotation aa,
-                            int sRes, int eRes,
-                            int y,
-                            float min, float max,
-                            int graphHeight)
+  public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes,
+          int eRes, int y, float min, float max, int graphHeight)
   {
     if (sRes > aa.annotations.length)
     {
@@ -928,7 +927,7 @@ public class AnnotationPanel
 
     int x = 0;
 
-    //Adjustment for fastpaint to left
+    // Adjustment for fastpaint to left
     if (eRes < av.endRes)
     {
       eRes++;
@@ -939,10 +938,10 @@ public class AnnotationPanel
     int y1 = y, y2 = y;
     float range = max - min;
 
-    ////Draw origin
+    // //Draw origin
     if (min < 0)
     {
-      y2 = y - (int) ( (0 - min / range) * graphHeight);
+      y2 = y - (int) ((0 - min / range) * graphHeight);
     }
 
     g.setColor(Color.gray);
@@ -965,8 +964,9 @@ public class AnnotationPanel
       {
         break;
       }
-      
-      if (aa.annotations[column] == null) //  || coaa.annotations[column - 1] == null)
+
+      if (aa.annotations[column] == null) // || coaa.annotations[column - 1] ==
+                                          // null)
       {
         x++;
         continue;
@@ -976,19 +976,21 @@ public class AnnotationPanel
         g.setColor(Color.black);
       else
         g.setColor(aa.annotations[column].colour);
-      if (column==0 || aa.annotations[column-1]==null)
+      if (column == 0 || aa.annotations[column - 1] == null)
+      {
+        y1 = y
+                - (int) (((aa.annotations[column].value - min) / range) * graphHeight);
+      }
+      else
       {
-        y1 = y -
-        (int) ( ( (aa.annotations[column].value - min) / range) * graphHeight);
-      } else {
-        y1 = y -
-        (int) ( ( (aa.annotations[column-1].value - min) / range) * graphHeight);        
+        y1 = y
+                - (int) (((aa.annotations[column - 1].value - min) / range) * graphHeight);
       }
-      y2 = y -
-          (int) ( ( (aa.annotations[column].value - min) / range) * graphHeight);
+      y2 = y
+              - (int) (((aa.annotations[column].value - min) / range) * graphHeight);
 
-      g.drawLine(x * av.charWidth - av.charWidth / 2, y1,
-                 x * av.charWidth + av.charWidth / 2, y2);
+      g.drawLine(x * av.charWidth - av.charWidth / 2, y1, x * av.charWidth
+              + av.charWidth / 2, y2);
       x++;
     }
 
@@ -996,15 +998,13 @@ public class AnnotationPanel
     {
       g.setColor(aa.threshold.colour);
 
-      y2 = (int) (y - ( (aa.threshold.value - min) / range) * graphHeight);
+      y2 = (int) (y - ((aa.threshold.value - min) / range) * graphHeight);
       g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2);
     }
   }
 
-  public void drawBarGraph(Graphics g, AlignmentAnnotation aa,
-                           int sRes, int eRes,
-                           float min, float max,
-                           int y)
+  public void drawBarGraph(Graphics g, AlignmentAnnotation aa, int sRes,
+          int eRes, float min, float max, int y)
   {
     if (sRes > aa.annotations.length)
     {
@@ -1019,7 +1019,7 @@ public class AnnotationPanel
 
     if (min < 0)
     {
-      y2 = y - (int) ( (0 - min / (range)) * aa.graphHeight);
+      y2 = y - (int) ((0 - min / (range)) * aa.graphHeight);
     }
 
     g.setColor(Color.gray);
@@ -1053,8 +1053,8 @@ public class AnnotationPanel
       else
         g.setColor(aa.annotations[column].colour);
 
-      y1 = y -
-          (int) ( ( (aa.annotations[column].value - min) / (range)) * aa.graphHeight);
+      y1 = y
+              - (int) (((aa.annotations[column].value - min) / (range)) * aa.graphHeight);
 
       if (y1 - y2 > 0)
       {
@@ -1071,14 +1071,14 @@ public class AnnotationPanel
     if (aa.threshold != null)
     {
       g.setColor(aa.threshold.colour);
-      y2 = (int) (y - ( (aa.threshold.value - min) / range) * aa.graphHeight);
+      y2 = (int) (y - ((aa.threshold.value - min) / range) * aa.graphHeight);
       g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2);
     }
   }
 
   // used by overview window
-  public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y,
-                        int sRes, int eRes)
+  public void drawGraph(Graphics g, AlignmentAnnotation aa, int width,
+          int y, int sRes, int eRes)
   {
     eRes = Math.min(eRes, aa.annotations.length);
     g.setColor(Color.white);
@@ -1094,7 +1094,7 @@ public class AnnotationPanel
       else
         g.setColor(aa.annotations[j].colour);
 
-      height = (int) ( (aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT);
+      height = (int) ((aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT);
       if (height > y)
       {
         height = y;
diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 82a5911..7939d9b 100644
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.appletgui;
 
 import java.util.*;
@@ -33,71 +32,121 @@ import org.jmol.adapter.smarter.SmarterJmolAdapter;
 import org.jmol.popup.*;
 import jalview.schemes.*;
 
-
-public class AppletJmol extends EmbmenuFrame
-    implements  StructureListener, JmolStatusListener,
-    KeyListener, ActionListener, ItemListener
+public class AppletJmol extends EmbmenuFrame implements StructureListener,
+        JmolStatusListener, KeyListener, ActionListener, ItemListener
 
 {
   Menu fileMenu = new Menu("File");
+
   Menu viewMenu = new Menu("View");
+
   Menu coloursMenu = new Menu("Colours");
+
   Menu chainMenu = new Menu("Show Chain");
+
   Menu helpMenu = new Menu("Help");
+
   MenuItem mappingMenuItem = new MenuItem("View Mapping");
 
   CheckboxMenuItem seqColour = new CheckboxMenuItem("By Sequence", true);
+
   MenuItem chain = new MenuItem("By Chain");
+
   MenuItem charge = new MenuItem("Charge & Cysteine");
+
   MenuItem zappo = new MenuItem("Zappo");
+
   MenuItem taylor = new MenuItem("Taylor");
+
   MenuItem hydro = new MenuItem("Hydrophobicity");
+
   MenuItem helix = new MenuItem("Helix Propensity");
+
   MenuItem strand = new MenuItem("Strand Propensity");
+
   MenuItem turn = new MenuItem("Turn Propensity");
+
   MenuItem buried = new MenuItem("Buried Index");
+
   MenuItem user = new MenuItem("User Defined Colours");
 
   MenuItem jmolHelp = new MenuItem("Jmol Help");
 
   JmolViewer viewer;
+
   JmolPopup jmolpopup;
 
   Panel scriptWindow;
+
   TextField inputLine;
+
   TextArea history;
+
   SequenceI[] sequence;
-  String [] chains;
+
+  String[] chains;
+
   StructureSelectionManager ssm;
+
   RenderPanel renderPanel;
+
   AlignmentPanel ap;
+
   String fileLoadingError;
+
   boolean loadedInline;
+
   PDBEntry pdbentry;
+
   boolean colourBySequence = true;
+
   Vector atomsPicked = new Vector();
 
-  public AppletJmol(PDBEntry pdbentry,
-                    SequenceI[] seq,
-                    String[] chains,
-                    AlignmentPanel ap,
-                    String protocol)
+  /**
+   * datasource protocol for access to PDBEntry
+   */
+  String protocol = null;
+
+  public AppletJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
+          AlignmentPanel ap, String protocol)
   {
     this.ap = ap;
     this.sequence = seq;
     this.chains = chains;
     this.pdbentry = pdbentry;
+    this.protocol = protocol;
+    if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
+    {
+      if (jalview.bin.JalviewLite.debug)
+      {
+        System.err.println("Setting PDB id for file " + pdbentry.getFile());
+        if (protocol.equals(AppletFormatAdapter.PASTE))
+        {
+          pdbentry.setId("PASTED PDB"
+                  + (chains == null ? "_" : chains.toString()));
+        }
+        else
+        {
+          pdbentry.setId(pdbentry.getFile());
+        }
+      }
+    }
+    if (jalview.bin.JalviewLite.debug)
+    {
+      System.err
+              .println("AppletJmol: PDB ID is '" + pdbentry.getId() + "'");
+    }
 
-   String alreadyMapped = StructureSelectionManager
-        .getStructureSelectionManager()
-        .alreadyMappedToFile(pdbentry.getId());
-
+    String alreadyMapped = StructureSelectionManager
+            .getStructureSelectionManager().alreadyMappedToFile(
+                    pdbentry.getId());
+    MCview.PDBfile reader = null;
     if (alreadyMapped != null)
     {
-       StructureSelectionManager.getStructureSelectionManager()
-            .setMapping(seq, chains, pdbentry.getFile(), protocol);
-       //PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW?
-       //FOR NOW, LETS JUST OPEN A NEW WINDOW
+      reader = StructureSelectionManager.getStructureSelectionManager()
+              .setMapping(seq, chains, pdbentry.getFile(), protocol);
+      // PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW?
+      // FOR NOW, LETS JUST OPEN A NEW WINDOW
     }
     MenuBar menuBar = new MenuBar();
     menuBar.add(fileMenu);
@@ -141,57 +190,90 @@ public class AppletJmol extends EmbmenuFrame
     renderPanel = new RenderPanel();
     embedMenuIfNeeded(renderPanel);
     this.add(renderPanel, BorderLayout.CENTER);
-    viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter());
+    viewer = JmolViewer.allocateViewer(renderPanel,
+            new SmarterJmolAdapter());
 
-    viewer.setAppletContext("jalview",
-                       ap.av.applet.getDocumentBase(),
-                            ap.av.applet.getCodeBase(),
-                            null);
+    viewer.setAppletContext("jalview", ap.av.applet.getDocumentBase(),
+            ap.av.applet.getCodeBase(), null);
 
     viewer.setJmolStatusListener(this);
 
     jmolpopup = JmolPopup.newJmolPopup(viewer);
 
     this.addWindowListener(new WindowAdapter()
-        {
-          public void windowClosing(WindowEvent evt)
-          {
-            closeViewer();
-          }
-        });
-
+    {
+      public void windowClosing(WindowEvent evt)
+      {
+        closeViewer();
+      }
+    });
 
-    if(pdbentry.getFile()!=null)
+    if (pdbentry.getFile() != null)
     {
       // import structure data from pdbentry.getFile based on given protocol
       if (protocol.equals(AppletFormatAdapter.PASTE))
-      { 
+      {
         loadInline(pdbentry.getFile());
-      } else
-      if (protocol.equals(AppletFormatAdapter.FILE) || protocol.equals(AppletFormatAdapter.URL)){
-          viewer.openFile(pdbentry.getFile());
+      }
+      else if (protocol.equals(AppletFormatAdapter.FILE)
+              || protocol.equals(AppletFormatAdapter.URL))
+      {
+        viewer.openFile(pdbentry.getFile());
       }
       else
-        {
+      {
         // probably CLASSLOADER based datasource..
         // Try and get a reader on the datasource, and pass that to Jmol
-        try {
-          FileParse fparser = new jalview.io.FileParse(protocol, pdbentry.getFile());
-          if (!fparser.isValid())
+        try
+        {
+          java.io.Reader freader = null;
+          if (reader != null)
+          {
+            if (jalview.bin.JalviewLite.debug)
+            {
+              System.err
+                      .println("AppletJmol:Trying to reuse existing PDBfile IO parser.");
+            }
+            // re-use the one we opened earlier
+            freader = reader.getReader();
+          }
+          if (freader == null)
+          {
+            if (jalview.bin.JalviewLite.debug)
+            {
+              System.err
+                      .println("AppletJmol:Creating new PDBfile IO parser.");
+            }
+            FileParse fp = new FileParse(pdbentry.getFile(), protocol);
+            fp.mark();
+            // reader = new MCview.PDBfile(fp);
+            // could set ID, etc.
+            // if (!reader.isValid())
+            // {
+            // throw new Exception("Invalid datasource.
+            // "+reader.getWarningMessage());
+            // }
+            // fp.reset();
+            freader = fp.getReader();
+          }
+          if (freader == null)
           {
-            throw new Exception("Invalid datasource. "+fparser.getWarningMessage());
+            throw new Exception(
+                    "Invalid datasource. Could not obtain Reader.");
           }
-          viewer.openReader(pdbentry.getFile(), pdbentry.getId(), fparser.getReader());
+          viewer.openReader(pdbentry.getFile(), pdbentry.getId(), freader);
         } catch (Exception e)
         {
           // give up!
-          System.err.println("Couldn't access pdbentry id="+pdbentry.getId()+" and file="+pdbentry.getFile()+" using protocol="+protocol);
+          System.err.println("Couldn't access pdbentry id="
+                  + pdbentry.getId() + " and file=" + pdbentry.getFile()
+                  + " using protocol=" + protocol);
           e.printStackTrace();
         }
-        }
+      }
     }
-    
-    jalview.bin.JalviewLite.addFrame(this, "Jmol", 400,400);
+
+    jalview.bin.JalviewLite.addFrame(this, "Jmol", 400, 400);
   }
 
   public void loadInline(String string)
@@ -200,7 +282,6 @@ public class AppletJmol extends EmbmenuFrame
     viewer.openStringInline(string);
   }
 
-
   void setChainMenuItems(Vector chains)
   {
     chainMenu.removeAll();
@@ -213,13 +294,15 @@ public class AppletJmol extends EmbmenuFrame
     CheckboxMenuItem menuItemCB;
     for (int c = 0; c < chains.size(); c++)
     {
-      menuItemCB = new CheckboxMenuItem(chains.elementAt(c).toString(), true);
+      menuItemCB = new CheckboxMenuItem(chains.elementAt(c).toString(),
+              true);
       menuItemCB.addItemListener(this);
       chainMenu.add(menuItemCB);
     }
   }
 
   boolean allChainsSelected = false;
+
   void centerViewer()
   {
     StringBuffer cmd = new StringBuffer();
@@ -236,11 +319,11 @@ public class AppletJmol extends EmbmenuFrame
     if (cmd.length() > 0)
       cmd.setLength(cmd.length() - 4);
 
-    viewer.evalString("select *;restrict "
-                      + cmd + ";cartoon;center " + cmd);
+    viewer
+            .evalString("select *;restrict " + cmd + ";cartoon;center "
+                    + cmd);
   }
 
-
   void closeViewer()
   {
     viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);
@@ -248,37 +331,35 @@ public class AppletJmol extends EmbmenuFrame
     viewer.setJmolStatusListener(null);
     viewer = null;
 
-    //We'll need to find out what other
+    // We'll need to find out what other
     // listeners need to be shut down in Jmol
-    StructureSelectionManager
-        .getStructureSelectionManager()
-        .removeStructureViewerListener(this, pdbentry.getId());
+    StructureSelectionManager.getStructureSelectionManager()
+            .removeStructureViewerListener(this, pdbentry.getId());
 
     this.setVisible(false);
   }
 
   public void actionPerformed(ActionEvent evt)
   {
-    if(evt.getSource()==mappingMenuItem)
+    if (evt.getSource() == mappingMenuItem)
     {
-      jalview.appletgui.CutAndPasteTransfer cap
-          = new jalview.appletgui.CutAndPasteTransfer(false, null);
+      jalview.appletgui.CutAndPasteTransfer cap = new jalview.appletgui.CutAndPasteTransfer(
+              false, null);
       Frame frame = new Frame();
       frame.add(cap);
 
-      jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping", 550,
-                                       600);
-      cap.setText(
-          StructureSelectionManager.getStructureSelectionManager().printMapping(
-              pdbentry.getFile())
-          );
+      jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping",
+              550, 600);
+      cap.setText(StructureSelectionManager.getStructureSelectionManager()
+              .printMapping(pdbentry.getFile()));
     }
     else if (evt.getSource() == charge)
     {
       colourBySequence = false;
       seqColour.setState(false);
-      viewer.evalStringQuiet("select *;color white;select ASP,GLU;color red;"
-                      +"select LYS,ARG;color blue;select CYS;color yellow");
+      viewer
+              .evalStringQuiet("select *;color white;select ASP,GLU;color red;"
+                      + "select LYS,ARG;color blue;select CYS;color yellow");
     }
 
     else if (evt.getSource() == chain)
@@ -293,7 +374,7 @@ public class AppletJmol extends EmbmenuFrame
     }
     else if (evt.getSource() == taylor)
     {
-     setJalviewColourScheme(new TaylorColourScheme());
+      setJalviewColourScheme(new TaylorColourScheme());
     }
     else if (evt.getSource() == hydro)
     {
@@ -319,13 +400,17 @@ public class AppletJmol extends EmbmenuFrame
     {
       new UserDefinedColours(this);
     }
-    else if(evt.getSource() == jmolHelp)
+    else if (evt.getSource() == jmolHelp)
     {
-      try{
+      try
+      {
         ap.av.applet.getAppletContext().showDocument(
-            new java.net.URL("http://jmol.sourceforge.net/docs/JmolUserGuide/"),
-            "jmolHelp");
-      }catch(java.net.MalformedURLException ex){}
+                new java.net.URL(
+                        "http://jmol.sourceforge.net/docs/JmolUserGuide/"),
+                "jmolHelp");
+      } catch (java.net.MalformedURLException ex)
+      {
+      }
     }
     else
     {
@@ -333,7 +418,7 @@ public class AppletJmol extends EmbmenuFrame
       for (int i = 0; i < chainMenu.getItemCount(); i++)
       {
         if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
-          ( (CheckboxMenuItem) chainMenu.getItem(i)).setState(true);
+          ((CheckboxMenuItem) chainMenu.getItem(i)).setState(true);
       }
       centerViewer();
       allChainsSelected = false;
@@ -345,7 +430,7 @@ public class AppletJmol extends EmbmenuFrame
     colourBySequence = false;
     seqColour.setState(false);
 
-    if(cs==null)
+    if (cs == null)
       return;
 
     String res;
@@ -354,19 +439,17 @@ public class AppletJmol extends EmbmenuFrame
 
     Enumeration en = ResidueProperties.aa3Hash.keys();
     StringBuffer command = new StringBuffer("select *;color white;");
-    while(en.hasMoreElements())
+    while (en.hasMoreElements())
     {
       res = en.nextElement().toString();
       index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();
-      if(index>20)
+      if (index > 20)
         continue;
 
       col = cs.findColour(ResidueProperties.aa[index].charAt(0));
 
-      command.append("select "+res+";color["
-                        + col.getRed() + ","
-                        + col.getGreen() + ","
-                        + col.getBlue() + "];");
+      command.append("select " + res + ";color[" + col.getRed() + ","
+              + col.getGreen() + "," + col.getBlue() + "];");
     }
 
     viewer.evalStringQuiet(command.toString());
@@ -386,63 +469,66 @@ public class AppletJmol extends EmbmenuFrame
 
   public void keyPressed(KeyEvent evt)
   {
-    if (evt.getKeyCode() == KeyEvent.VK_ENTER
-        && scriptWindow.isVisible())
+    if (evt.getKeyCode() == KeyEvent.VK_ENTER && scriptWindow.isVisible())
     {
       viewer.evalString(inputLine.getText());
-      history.append("\n$ "+inputLine.getText());
+      history.append("\n$ " + inputLine.getText());
       inputLine.setText("");
     }
 
   }
 
   public void keyTyped(KeyEvent evt)
-  {  }
+  {
+  }
 
-  public void keyReleased(KeyEvent evt){}
+  public void keyReleased(KeyEvent evt)
+  {
+  }
 
-  //////////////////////////////////
-  ///StructureListener
+  // ////////////////////////////////
+  // /StructureListener
   public String getPdbFile()
   {
     return "???";
   }
 
-
-
   String lastMessage;
+
   public void mouseOverStructure(int atomIndex, String strInfo)
   {
-      int pdbResNum;
+    int pdbResNum;
 
-      int chainSeparator = strInfo.indexOf(":");
+    int chainSeparator = strInfo.indexOf(":");
 
-      if(chainSeparator==-1)
-        chainSeparator = strInfo.indexOf(".");
+    if (chainSeparator == -1)
+      chainSeparator = strInfo.indexOf(".");
 
-      pdbResNum = Integer.parseInt(
-          strInfo.substring(strInfo.indexOf("]")+ 1, chainSeparator));
+    pdbResNum = Integer.parseInt(strInfo.substring(
+            strInfo.indexOf("]") + 1, chainSeparator));
 
-      String chainId;
+    String chainId;
 
-      if (strInfo.indexOf(":") > -1)
-        chainId = strInfo.substring
-            (strInfo.indexOf(":")+1, strInfo.indexOf("."));
-      else
-      {
-        chainId = " ";
-      }
+    if (strInfo.indexOf(":") > -1)
+      chainId = strInfo.substring(strInfo.indexOf(":") + 1, strInfo
+              .indexOf("."));
+    else
+    {
+      chainId = " ";
+    }
 
-      if (lastMessage == null || !lastMessage.equals(strInfo))
-        ssm.mouseOverStructure(pdbResNum, chainId, pdbentry.getFile());
+    if (lastMessage == null || !lastMessage.equals(strInfo))
+      ssm.mouseOverStructure(pdbResNum, chainId, pdbentry.getFile());
 
-      lastMessage = strInfo;
+    lastMessage = strInfo;
   }
 
   StringBuffer resetLastRes = new StringBuffer();
+
   StringBuffer eval = new StringBuffer();
 
-  public void highlightAtom(int atomIndex, int pdbResNum, String chain, String pdbfile)
+  public void highlightAtom(int atomIndex, int pdbResNum, String chain,
+          String pdbfile)
   {
     if (!pdbfile.equals(pdbentry.getFile()))
       return;
@@ -464,9 +550,10 @@ public class AppletJmol extends EmbmenuFrame
       resetLastRes.append(":" + chain);
     }
 
-    eval.append(";wireframe 100;"+eval.toString()+".CA;");
+    eval.append(";wireframe 100;" + eval.toString() + ".CA;");
 
-    resetLastRes.append(";wireframe 0;"+resetLastRes.toString()+".CA;spacefill 0;");
+    resetLastRes.append(";wireframe 0;" + resetLastRes.toString()
+            + ".CA;spacefill 0;");
 
     eval.append("spacefill 200;select none");
 
@@ -476,13 +563,14 @@ public class AppletJmol extends EmbmenuFrame
 
   public void updateColours(Object source)
   {
-    colourBySequence( (AlignmentPanel) source);
+    colourBySequence((AlignmentPanel) source);
   }
 
-//End StructureListener
-////////////////////////////
+  // End StructureListener
+  // //////////////////////////
 
-  public Color getColour(int atomIndex, int pdbResNum, String chain, String pdbfile)
+  public Color getColour(int atomIndex, int pdbResNum, String chain,
+          String pdbfile)
   {
     if (!pdbfile.equals(pdbentry.getFile()))
       return null;
@@ -491,7 +579,9 @@ public class AppletJmol extends EmbmenuFrame
   }
 
   String lastCommand;
-  FeatureRenderer fr=null;
+
+  FeatureRenderer fr = null;
+
   public void colourBySequence(AlignmentPanel sourceap)
   {
     this.ap = sourceap;
@@ -524,10 +614,10 @@ public class AppletJmol extends EmbmenuFrame
     int lastPos = -1;
     for (int s = 0; s < sequence.length; s++)
     {
-      for (int sp,m = 0; m < mapping.length; m++)
+      for (int sp, m = 0; m < mapping.length; m++)
       {
         if (mapping[m].getSequence() == sequence[s]
-            && (sp=ap.av.alignment.findIndex(sequence[s])) > -1)
+                && (sp = ap.av.alignment.findIndex(sequence[s])) > -1)
         {
           SequenceI asp = ap.av.alignment.getSequenceAt(sp);
           for (int r = 0; r < asp.getLength(); r++)
@@ -537,9 +627,7 @@ public class AppletJmol extends EmbmenuFrame
             {
               continue;
             }
-            int pos = mapping[m].getPDBResNum(
-                    asp.findPosition(r));
-
+            int pos = mapping[m].getPDBResNum(asp.findPosition(r));
 
             if (pos < 1 || pos == lastPos)
               continue;
@@ -551,11 +639,10 @@ public class AppletJmol extends EmbmenuFrame
             if (showFeatures)
               col = fr.findFeatureColour(col, sequence[s], r);
 
-            if (command.toString().endsWith(":" + mapping[m].getChain() +
-                                            ";color["
-                                            + col.getRed() + ","
-                                            + col.getGreen() + ","
-                                            + col.getBlue() + "]"))
+            if (command.toString().endsWith(
+                    ":" + mapping[m].getChain() + ";color[" + col.getRed()
+                            + "," + col.getGreen() + "," + col.getBlue()
+                            + "]"))
             {
               command = condenseCommand(command.toString(), pos);
               continue;
@@ -568,10 +655,8 @@ public class AppletJmol extends EmbmenuFrame
               command.append(":" + mapping[m].getChain());
             }
 
-            command.append(";color["
-                           + col.getRed() + ","
-                           + col.getGreen() + ","
-                           + col.getBlue() + "]");
+            command.append(";color[" + col.getRed() + "," + col.getGreen()
+                    + "," + col.getBlue() + "]");
           }
           break;
         }
@@ -585,11 +670,11 @@ public class AppletJmol extends EmbmenuFrame
     lastCommand = command.toString();
   }
 
-
   StringBuffer condenseCommand(String command, int pos)
   {
 
-    StringBuffer sb = new StringBuffer(command.substring(0, command.lastIndexOf("select")+7));
+    StringBuffer sb = new StringBuffer(command.substring(0, command
+            .lastIndexOf("select") + 7));
 
     command = command.substring(sb.length());
 
@@ -597,40 +682,41 @@ public class AppletJmol extends EmbmenuFrame
 
     if (command.indexOf("-") > -1)
     {
-      start = command.substring(0,command.indexOf("-"));
+      start = command.substring(0, command.indexOf("-"));
     }
     else
     {
       start = command.substring(0, command.indexOf(":"));
     }
 
-    sb.append(start+"-"+pos+command.substring(command.indexOf(":")));
+    sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
 
     return sb;
   }
 
-  /////////////////////////////////
-  //JmolStatusListener
+  // ///////////////////////////////
+  // JmolStatusListener
 
   public String eval(String strEval)
   {
-   // System.out.println(strEval);
-   //"# 'eval' is implemented only for the applet.";
+    // System.out.println(strEval);
+    // "# 'eval' is implemented only for the applet.";
     return null;
   }
 
   public void createImage(String file, String type, int quality)
-  {}
+  {
+  }
 
   public void setCallbackFunction(String callbackType,
-                                  String callbackFunction)
-  {}
+          String callbackFunction)
+  {
+  }
 
   public void notifyFileLoaded(String fullPathName, String fileName,
-                               String modelName, Object clientFile,
-                               String errorMsg)
+          String modelName, Object clientFile, String errorMsg)
   {
-    if(errorMsg!=null)
+    if (errorMsg != null)
     {
       fileLoadingError = errorMsg;
       repaint();
@@ -641,26 +727,28 @@ public class AppletJmol extends EmbmenuFrame
 
     if (fileName != null)
     {
-      //FILE LOADED OK
+      // FILE LOADED OK
       jmolpopup.updateComputedMenus();
-            viewer.evalStringQuiet(
-          "select backbone;restrict;cartoon;wireframe off;spacefill off");
+      viewer
+              .evalStringQuiet("select backbone;restrict;cartoon;wireframe off;spacefill off");
 
       ssm = StructureSelectionManager.getStructureSelectionManager();
-
       MCview.PDBfile pdb;
       if (loadedInline)
       {
-        pdb = ssm.setMapping(sequence,chains,
-                                pdbentry.getFile(),
-                                AppletFormatAdapter.PASTE);
-        pdbentry.setFile("INLINE"+pdb.id);
+        pdb = ssm.setMapping(sequence, chains, pdbentry.getFile(),
+                AppletFormatAdapter.PASTE);
+        pdbentry.setFile("INLINE" + pdb.id);
       }
       else
       {
-         pdb = ssm.setMapping(sequence,chains,
-                              pdbentry.getFile(),
-                              AppletFormatAdapter.URL);
+        // TODO: Jmol can in principle retrieve from CLASSLOADER but this needs
+        // to be tested. See mantis bug
+        // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
+
+        pdb = ssm.setMapping(sequence, chains, pdbentry.getFile(),
+                AppletFormatAdapter.URL);
+
       }
 
       pdbentry.setId(pdb.id);
@@ -670,14 +758,14 @@ public class AppletJmol extends EmbmenuFrame
       Vector chains = new Vector();
       for (int i = 0; i < pdb.chains.size(); i++)
       {
-        chains.addElement( ( (MCview.PDBChain) pdb.chains.elementAt(i)).id);
+        chains.addElement(((MCview.PDBChain) pdb.chains.elementAt(i)).id);
       }
       setChainMenuItems(chains);
 
       colourBySequence(ap);
 
-      StringBuffer title = new StringBuffer(sequence[0].getName() + ":" +
-                                            pdbentry.getId());
+      StringBuffer title = new StringBuffer(sequence[0].getName() + ":"
+              + pdbentry.getId());
 
       if (pdbentry.getProperty() != null)
       {
@@ -706,27 +794,29 @@ public class AppletJmol extends EmbmenuFrame
   }
 
   public void notifyScriptStart(String statusMessage, String additionalInfo)
-  {}
+  {
+  }
 
   public void sendConsoleEcho(String strEcho)
   {
     if (scriptWindow == null)
       showConsole(true);
 
-    history.append("\n"+strEcho);
+    history.append("\n" + strEcho);
   }
 
   public void sendConsoleMessage(String strStatus)
   {
-    if(history!=null && strStatus!=null
-       && !strStatus.equals("Script completed"))
+    if (history != null && strStatus != null
+            && !strStatus.equals("Script completed"))
     {
-      history.append("\n"+strStatus);
+      history.append("\n" + strStatus);
     }
   }
 
   public void notifyScriptTermination(String strStatus, int msWalltime)
-  {  }
+  {
+  }
 
   public void handlePopupMenu(int x, int y)
   {
@@ -739,34 +829,34 @@ public class AppletJmol extends EmbmenuFrame
   }
 
   public void notifyNewDefaultModeMeasurement(int count, String strInfo)
-  {}
+  {
+  }
 
   public void notifyAtomPicked(int atomIndex, String strInfo)
   {
 
     int chainSeparator = strInfo.indexOf(":");
 
-    if(chainSeparator==-1)
+    if (chainSeparator == -1)
       chainSeparator = strInfo.indexOf(".");
 
-    String picked =
-        strInfo.substring(strInfo.indexOf("]")+ 1, chainSeparator);
-
+    String picked = strInfo.substring(strInfo.indexOf("]") + 1,
+            chainSeparator);
 
     if (strInfo.indexOf(":") > -1)
-      picked+=strInfo.substring(strInfo.indexOf(":")+1,
-                               strInfo.indexOf("."));
+      picked += strInfo.substring(strInfo.indexOf(":") + 1, strInfo
+              .indexOf("."));
 
-    picked+=".CA";
+    picked += ".CA";
 
     if (!atomsPicked.contains(picked))
     {
-      viewer.evalString("select "+picked+";label %n %r:%c");
+      viewer.evalString("select " + picked + ";label %n %r:%c");
       atomsPicked.addElement(picked);
     }
     else
     {
-      viewer.evalString("select "+picked+";label off");
+      viewer.evalString("select " + picked + ";label off");
       atomsPicked.removeElement(picked);
     }
   }
@@ -777,15 +867,18 @@ public class AppletJmol extends EmbmenuFrame
   }
 
   public void sendSyncScript(String script, String appletName)
-  {}
+  {
+  }
 
   public void showUrl(String url)
   {
-    try{
+    try
+    {
       ap.av.applet.getAppletContext().showDocument(new java.net.URL(url),
-          "jmolOutput");
-    }catch(java.net.MalformedURLException ex)
-    {}
+              "jmolOutput");
+    } catch (java.net.MalformedURLException ex)
+    {
+    }
   }
 
   public void showConsole(boolean showConsole)
@@ -812,19 +905,20 @@ public class AppletJmol extends EmbmenuFrame
     return 0;
   }
 
-  ///End JmolStatusListener
-  ///////////////////////////////
-
+  // /End JmolStatusListener
+  // /////////////////////////////
 
-  class RenderPanel
-      extends Panel
+  class RenderPanel extends Panel
   {
     Dimension currentSize = new Dimension();
+
     Rectangle rectClip = new Rectangle();
 
-    public void update(Graphics g) {
+    public void update(Graphics g)
+    {
       paint(g);
     }
+
     public void paint(Graphics g)
     {
       currentSize = this.getSize();
diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java
index 78d7ba7..6f5498d 100755
--- a/src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/src/jalview/appletgui/CutAndPasteTransfer.java
@@ -1,279 +1,278 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.appletgui;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
-import jalview.io.*;
-
-public class CutAndPasteTransfer
-    extends Panel implements ActionListener, MouseListener
-{
-  boolean pdbImport = false;
-  boolean treeImport = false;
-  boolean annotationImport = false;
-  Sequence  seq;
-  AlignFrame alignFrame;
-
-  public CutAndPasteTransfer(boolean forImport, AlignFrame alignFrame)
-  {
-    try
-    {
-      jbInit();
-    }
-    catch (Exception e)
-    {
-      e.printStackTrace();
-    }
-
-    this.alignFrame = alignFrame;
-
-    if (!forImport)
-    {
-      buttonPanel.setVisible(false);
-    }
-  }
-
-  public String getText()
-  {
-    return textarea.getText();
-  }
-
-  public void setText(String text)
-  {
-    textarea.setText(text);
-  }
-
-  public void setPDBImport(Sequence seq)
-  {
-    this.seq = seq;
-    accept.setLabel("Accept");
-    addSequences.setVisible(false);
-    pdbImport = true;
-  }
-
-  public void setTreeImport()
-  {
-    treeImport = true;
-    accept.setLabel("Accept");
-    addSequences.setVisible(false);
-  }
-
-  public void setAnnotationImport()
-  {
-    annotationImport = true;
-    accept.setLabel("Accept");
-    addSequences.setVisible(false);
-  }
-
-  public void actionPerformed(ActionEvent evt)
-  {
-    if (evt.getSource() == accept)
-    {
-      ok(true);
-    }
-    else if (evt.getSource() == addSequences)
-    {
-      ok(false);
-    }
-    else if (evt.getSource() == cancel)
-    {
-      cancel();
-    }
-  }
-
-  protected void ok(boolean newWindow)
-  {
-    String text = getText();
-    int length = text.length();
-    textarea.append("\n");
-    if (textarea.getText().length() == length)
-    {
-      String warning =
-          "\n\n#################################################\n"
-          + "WARNING!! THIS IS THE MAXIMUM SIZE OF TEXTAREA!!\n"
-          + "\nCAN'T INPUT FULL ALIGNMENT"
-          + "\n\nYOU MUST DELETE THIS WARNING TO CONTINUE"
-          + "\n\nMAKE SURE LAST SEQUENCE PASTED IS COMPLETE"
-          + "\n#################################################\n";
-      textarea.setText(text.substring(0, text.length() - warning.length())
-                       + warning);
-
-      textarea.setCaretPosition(text.length());
-    }
-
-    if (pdbImport)
-    {
-      PDBEntry pdb = new PDBEntry();
-      pdb.setFile(text);
-
-      if ( alignFrame.alignPanel.av.applet.jmolAvailable )
-        new jalview.appletgui.AppletJmol(pdb,
-                                         new Sequence[]{seq},
-                                         null,
-                                         alignFrame.alignPanel,
-                                         AppletFormatAdapter.PASTE);
-      else
-
-        new MCview.AppletPDBViewer(pdb,
-                                   new Sequence[]{seq},
-                                   null,
-                                   alignFrame.alignPanel,
-                                   AppletFormatAdapter.PASTE);
-
-    }
-    else if (treeImport)
-    {
-      try
-      {
-        jalview.io.NewickFile fin = new jalview.io.NewickFile(textarea.getText(),
-            "Paste");
-
-        fin.parse();
-        if (fin.getTree() != null)
-        {
-          alignFrame.loadTree(fin, "Pasted tree file");
-        }
-
-      }
-      catch (Exception ex)
-      {
-        textarea.setText("Could not parse Newick file!\n" + ex);
-        return;
-      }
-    }
-    else if (annotationImport)
-    {
-      if (new AnnotationFile().readAnnotationFile(
-          alignFrame.viewport.alignment, textarea.getText(),
-          jalview.io.AppletFormatAdapter.PASTE))
-      {
-        alignFrame.alignPanel.fontChanged();
-        alignFrame.alignPanel.setScrollValues(0, 0);
-
-      }
-      else
-      {
-        alignFrame.parseFeaturesFile(textarea.getText(),
-                                     jalview.io.AppletFormatAdapter.PASTE);
-      }
-    }
-    else if (alignFrame != null)
-    {
-      Alignment al = null;
-
-      String format = new IdentifyFile().Identify(text,
-                                                  AppletFormatAdapter.PASTE);
-      try
-      {
-        al = new AppletFormatAdapter().readFile(text, AppletFormatAdapter.PASTE,
-                                                format);
-      }
-      catch (java.io.IOException ex)
-      {
-        ex.printStackTrace();
-      }
-
-      if (al != null)
-      {
-        if (newWindow)
-        {
-          AlignFrame af = new AlignFrame(al, alignFrame.viewport.applet,
-                                         "Cut & Paste input - " + format,
-                                         false);
-          af.statusBar.setText("Successfully pasted alignment file");
-        }
-        else
-        {
-          alignFrame.addSequences(al.getSequencesArray());
-        }
-      }
-    }
-
-    if (this.getParent() instanceof Frame)
-    {
-      ( (Frame)this.getParent()).setVisible(false);
-    }
-    else
-    {
-      ( (Dialog)this.getParent()).setVisible(false);
-    }
-  }
-
-  protected void cancel()
-  {
-    textarea.setText("");
-    if (this.getParent() instanceof Frame)
-    {
-      ( (Frame)this.getParent()).setVisible(false);
-    }
-    else
-    {
-      ( (Dialog)this.getParent()).setVisible(false);
-    }
-  }
-
-  protected TextArea textarea = new TextArea();
-  Button accept = new Button("New Window");
-  Button addSequences = new Button("Add to Current Alignment");
-  Button cancel = new Button("Close");
-
-  protected Panel buttonPanel = new Panel();
-  BorderLayout borderLayout1 = new BorderLayout();
-
-  private void jbInit()
-      throws Exception
-  {
-    textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 10));
-    textarea.setText("Paste your alignment file here");
-    textarea.addMouseListener(this);
-    this.setLayout(borderLayout1);
-    accept.addActionListener(this);
-    addSequences.addActionListener(this);
-    cancel.addActionListener(this);
-    this.add(buttonPanel, BorderLayout.SOUTH);
-    buttonPanel.add(accept, null);
-    buttonPanel.add(addSequences);
-    buttonPanel.add(cancel, null);
-    this.add(textarea, java.awt.BorderLayout.CENTER);
-  }
-
-  public void mousePressed(MouseEvent evt)
-  {
-    if (textarea.getText().startsWith("Paste your"))
-    {
-      textarea.setText("");
-    }
-  }
-
-  public void mouseReleased(MouseEvent evt)
-  {}
-
-  public void mouseClicked(MouseEvent evt)
-  {}
-
-  public void mouseEntered(MouseEvent evt)
-  {}
-
-  public void mouseExited(MouseEvent evt)
-  {}
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.appletgui;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import jalview.datamodel.*;
+import jalview.io.*;
+
+public class CutAndPasteTransfer extends Panel implements ActionListener,
+        MouseListener
+{
+  boolean pdbImport = false;
+
+  boolean treeImport = false;
+
+  boolean annotationImport = false;
+
+  Sequence seq;
+
+  AlignFrame alignFrame;
+
+  public CutAndPasteTransfer(boolean forImport, AlignFrame alignFrame)
+  {
+    try
+    {
+      jbInit();
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+
+    this.alignFrame = alignFrame;
+
+    if (!forImport)
+    {
+      buttonPanel.setVisible(false);
+    }
+  }
+
+  public String getText()
+  {
+    return textarea.getText();
+  }
+
+  public void setText(String text)
+  {
+    textarea.setText(text);
+  }
+
+  public void setPDBImport(Sequence seq)
+  {
+    this.seq = seq;
+    accept.setLabel("Accept");
+    addSequences.setVisible(false);
+    pdbImport = true;
+  }
+
+  public void setTreeImport()
+  {
+    treeImport = true;
+    accept.setLabel("Accept");
+    addSequences.setVisible(false);
+  }
+
+  public void setAnnotationImport()
+  {
+    annotationImport = true;
+    accept.setLabel("Accept");
+    addSequences.setVisible(false);
+  }
+
+  public void actionPerformed(ActionEvent evt)
+  {
+    if (evt.getSource() == accept)
+    {
+      ok(true);
+    }
+    else if (evt.getSource() == addSequences)
+    {
+      ok(false);
+    }
+    else if (evt.getSource() == cancel)
+    {
+      cancel();
+    }
+  }
+
+  protected void ok(boolean newWindow)
+  {
+    String text = getText();
+    int length = text.length();
+    textarea.append("\n");
+    if (textarea.getText().length() == length)
+    {
+      String warning = "\n\n#################################################\n"
+              + "WARNING!! THIS IS THE MAXIMUM SIZE OF TEXTAREA!!\n"
+              + "\nCAN'T INPUT FULL ALIGNMENT"
+              + "\n\nYOU MUST DELETE THIS WARNING TO CONTINUE"
+              + "\n\nMAKE SURE LAST SEQUENCE PASTED IS COMPLETE"
+              + "\n#################################################\n";
+      textarea.setText(text.substring(0, text.length() - warning.length())
+              + warning);
+
+      textarea.setCaretPosition(text.length());
+    }
+
+    if (pdbImport)
+    {
+      PDBEntry pdb = new PDBEntry();
+      pdb.setFile(text);
+
+      if (alignFrame.alignPanel.av.applet.jmolAvailable)
+        new jalview.appletgui.AppletJmol(pdb, new Sequence[]
+        { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE);
+      else
+
+        new MCview.AppletPDBViewer(pdb, new Sequence[]
+        { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE);
+
+    }
+    else if (treeImport)
+    {
+      try
+      {
+        jalview.io.NewickFile fin = new jalview.io.NewickFile(textarea
+                .getText(), "Paste");
+
+        fin.parse();
+        if (fin.getTree() != null)
+        {
+          alignFrame.loadTree(fin, "Pasted tree file");
+        }
+
+      } catch (Exception ex)
+      {
+        textarea.setText("Could not parse Newick file!\n" + ex);
+        return;
+      }
+    }
+    else if (annotationImport)
+    {
+      if (new AnnotationFile().readAnnotationFile(
+              alignFrame.viewport.alignment, textarea.getText(),
+              jalview.io.AppletFormatAdapter.PASTE))
+      {
+        alignFrame.alignPanel.fontChanged();
+        alignFrame.alignPanel.setScrollValues(0, 0);
+
+      }
+      else
+      {
+        alignFrame.parseFeaturesFile(textarea.getText(),
+                jalview.io.AppletFormatAdapter.PASTE);
+      }
+    }
+    else if (alignFrame != null)
+    {
+      Alignment al = null;
+
+      String format = new IdentifyFile().Identify(text,
+              AppletFormatAdapter.PASTE);
+      try
+      {
+        al = new AppletFormatAdapter().readFile(text,
+                AppletFormatAdapter.PASTE, format);
+      } catch (java.io.IOException ex)
+      {
+        ex.printStackTrace();
+      }
+
+      if (al != null)
+      {
+        if (newWindow)
+        {
+          AlignFrame af = new AlignFrame(al, alignFrame.viewport.applet,
+                  "Cut & Paste input - " + format, false);
+          af.statusBar.setText("Successfully pasted alignment file");
+        }
+        else
+        {
+          alignFrame.addSequences(al.getSequencesArray());
+        }
+      }
+    }
+
+    if (this.getParent() instanceof Frame)
+    {
+      ((Frame) this.getParent()).setVisible(false);
+    }
+    else
+    {
+      ((Dialog) this.getParent()).setVisible(false);
+    }
+  }
+
+  protected void cancel()
+  {
+    textarea.setText("");
+    if (this.getParent() instanceof Frame)
+    {
+      ((Frame) this.getParent()).setVisible(false);
+    }
+    else
+    {
+      ((Dialog) this.getParent()).setVisible(false);
+    }
+  }
+
+  protected TextArea textarea = new TextArea();
+
+  Button accept = new Button("New Window");
+
+  Button addSequences = new Button("Add to Current Alignment");
+
+  Button cancel = new Button("Close");
+
+  protected Panel buttonPanel = new Panel();
+
+  BorderLayout borderLayout1 = new BorderLayout();
+
+  private void jbInit() throws Exception
+  {
+    textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 10));
+    textarea.setText("Paste your alignment file here");
+    textarea.addMouseListener(this);
+    this.setLayout(borderLayout1);
+    accept.addActionListener(this);
+    addSequences.addActionListener(this);
+    cancel.addActionListener(this);
+    this.add(buttonPanel, BorderLayout.SOUTH);
+    buttonPanel.add(accept, null);
+    buttonPanel.add(addSequences);
+    buttonPanel.add(cancel, null);
+    this.add(textarea, java.awt.BorderLayout.CENTER);
+  }
+
+  public void mousePressed(MouseEvent evt)
+  {
+    if (textarea.getText().startsWith("Paste your"))
+    {
+      textarea.setText("");
+    }
+  }
+
+  public void mouseReleased(MouseEvent evt)
+  {
+  }
+
+  public void mouseClicked(MouseEvent evt)
+  {
+  }
+
+  public void mouseEntered(MouseEvent evt)
+  {
+  }
+
+  public void mouseExited(MouseEvent evt)
+  {
+  }
+}
diff --git a/src/jalview/appletgui/EditNameDialog.java b/src/jalview/appletgui/EditNameDialog.java
index 46325d9..b1cd40e 100644
--- a/src/jalview/appletgui/EditNameDialog.java
+++ b/src/jalview/appletgui/EditNameDialog.java
@@ -1,84 +1,77 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.appletgui;
-
-import java.awt.*;
-
-
-public class EditNameDialog extends JVDialog
-{
-  TextField id, description;
-
-  public String getName()
-  {
-    return id.getText();
-  }
-
-  public String getDescription()
-  {
-    if (description.getText().length() < 1)
-    {
-      return null;
-    }
-    else
-    {
-      return description.getText();
-    }
-  }
-
-  public EditNameDialog(String name,
-                        String desc,
-                        String label1,
-                        String label2,
-                        Frame owner,
-                        String title,
-                        int width, int height, boolean display)
-  {
-    super(owner, title, true, width, height);
-
-    Font mono = new Font("Monospaced", Font.PLAIN, 12);
-    Panel panel = new Panel(new BorderLayout());
-    Panel panel2 = new Panel(new BorderLayout());
-
-    id = new TextField(name, 40);
-    id.setFont(mono);
-    Label label = new Label(label1);
-    label.setFont(mono);
-
-    panel2.add(label, BorderLayout.WEST);
-    panel2.add(id, BorderLayout.CENTER);
-    panel.add(panel2, BorderLayout.NORTH);
-
-
-    if(label2!=null)
-    {
-      panel2 = new Panel(new BorderLayout());
-      description = new TextField(desc, 40);
-      description.setFont(mono);
-      label = new Label(label2);
-      label.setFont(mono);
-      panel2.add(label, BorderLayout.WEST);
-      panel2.add(description, BorderLayout.CENTER);
-      panel.add(panel2, BorderLayout.CENTER);
-    }
-    setMainPanel(panel);
-    setVisible(display);
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.appletgui;
+
+import java.awt.*;
+
+public class EditNameDialog extends JVDialog
+{
+  TextField id, description;
+
+  public String getName()
+  {
+    return id.getText();
+  }
+
+  public String getDescription()
+  {
+    if (description.getText().length() < 1)
+    {
+      return null;
+    }
+    else
+    {
+      return description.getText();
+    }
+  }
+
+  public EditNameDialog(String name, String desc, String label1,
+          String label2, Frame owner, String title, int width, int height,
+          boolean display)
+  {
+    super(owner, title, true, width, height);
+
+    Font mono = new Font("Monospaced", Font.PLAIN, 12);
+    Panel panel = new Panel(new BorderLayout());
+    Panel panel2 = new Panel(new BorderLayout());
+
+    id = new TextField(name, 40);
+    id.setFont(mono);
+    Label label = new Label(label1);
+    label.setFont(mono);
+
+    panel2.add(label, BorderLayout.WEST);
+    panel2.add(id, BorderLayout.CENTER);
+    panel.add(panel2, BorderLayout.NORTH);
+
+    if (label2 != null)
+    {
+      panel2 = new Panel(new BorderLayout());
+      description = new TextField(desc, 40);
+      description.setFont(mono);
+      label = new Label(label2);
+      label.setFont(mono);
+      panel2.add(label, BorderLayout.WEST);
+      panel2.add(description, BorderLayout.CENTER);
+      panel.add(panel2, BorderLayout.CENTER);
+    }
+    setMainPanel(panel);
+    setVisible(display);
+  }
+}
diff --git a/src/jalview/appletgui/EmbmenuFrame.java b/src/jalview/appletgui/EmbmenuFrame.java
index 23f6aa2..df59ef4 100644
--- a/src/jalview/appletgui/EmbmenuFrame.java
+++ b/src/jalview/appletgui/EmbmenuFrame.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.appletgui;
 
 import java.awt.BorderLayout;
@@ -19,18 +37,19 @@ import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.util.Enumeration;
 import java.util.Hashtable;
+
 /**
- * This class implements a pattern form embedding toolbars as a panel with popups
- * for situations where the system menu bar is either invisible or inappropriate.
- * It was derived from the code for embedding the jalview applet alignFrame as
- * a component on the web-page, which requires the local alignFrame menu to be
- * attached to that panel rather than placed on the parent (which isn't allowed
- * anyhow).
- * TODO: try to modify the embeddedMenu display so it looks like a real toolbar menu
- * TODO: modify click/mouse handler for embeddedMenu so it behaves more like a real pulldown menu toolbar
+ * This class implements a pattern form embedding toolbars as a panel with
+ * popups for situations where the system menu bar is either invisible or
+ * inappropriate. It was derived from the code for embedding the jalview applet
+ * alignFrame as a component on the web-page, which requires the local
+ * alignFrame menu to be attached to that panel rather than placed on the parent
+ * (which isn't allowed anyhow). TODO: try to modify the embeddedMenu display so
+ * it looks like a real toolbar menu TODO: modify click/mouse handler for
+ * embeddedMenu so it behaves more like a real pulldown menu toolbar
  * 
  * @author Jim Procter and Andrew Waterhouse
- *
+ * 
  */
 public class EmbmenuFrame extends Frame implements MouseListener
 {
@@ -38,9 +57,10 @@ public class EmbmenuFrame extends Frame implements MouseListener
    * map from labels to popup menus for the embedded menubar
    */
   protected Hashtable embeddedPopup;
+
   /**
-   * the embedded menu is built on this and should be 
-   * added to the frame at the appropriate position.
+   * the embedded menu is built on this and should be added to the frame at the
+   * appropriate position.
    * 
    */
   protected Panel embeddedMenu;
@@ -49,20 +69,25 @@ public class EmbmenuFrame extends Frame implements MouseListener
   {
     super();
   }
+
   public EmbmenuFrame(String title) throws HeadlessException
   {
     super(title);
   }
+
   /**
-   * Check if the applet is running on a platform that requires the Frame menuBar to be embedded,
-   * and if so, embeds it.
-   * @param tobeAdjusted the panel that is to be reduced to make space for the embedded menu bar
+   * Check if the applet is running on a platform that requires the Frame
+   * menuBar to be embedded, and if so, embeds it.
+   * 
+   * @param tobeAdjusted
+   *                the panel that is to be reduced to make space for the
+   *                embedded menu bar
    * @return true if menuBar was embedded and tobeAdjusted's height modified
    */
   protected boolean embedMenuIfNeeded(Panel tobeAdjusted)
   {
     MenuBar topMenuBar = getMenuBar();
-    if (topMenuBar==null)
+    if (topMenuBar == null)
     {
       return false;
     }
@@ -70,43 +95,53 @@ public class EmbmenuFrame extends Frame implements MouseListener
     if (new jalview.util.Platform().isAMac())
     {
       // Build the embedded menu panel
-      embeddedMenu = makeEmbeddedPopupMenu(topMenuBar, "Arial", Font.PLAIN, 10, true); // try to pickup system font.
+      embeddedMenu = makeEmbeddedPopupMenu(topMenuBar, "Arial", Font.PLAIN,
+              10, true); // try to pickup system font.
       setMenuBar(null);
       // add the components to the TreePanel area.
       add(embeddedMenu, BorderLayout.NORTH);
-      tobeAdjusted.setSize(getSize().width,
-              getSize().height
-              - embeddedMenu.HEIGHT);        
+      tobeAdjusted.setSize(getSize().width, getSize().height
+              - embeddedMenu.HEIGHT);
       return true;
     }
     return false;
   }
+
   /**
-   * move all menus on menuBar onto embeddedMenu.
-   * embeddedPopup is used to store the popups for each menu removed from the menuBar and added
-   * to the panel.
-   * NOTE: it is up to the caller to remove menuBar from the Frame if it is already attached.
+   * move all menus on menuBar onto embeddedMenu. embeddedPopup is used to store
+   * the popups for each menu removed from the menuBar and added to the panel.
+   * NOTE: it is up to the caller to remove menuBar from the Frame if it is
+   * already attached.
+   * 
    * @param menuBar
    * @param fn
    * @param fstyle
    * @param fsz
-   * @param overrideFonts true if we take the menuBar fonts in preference to the supplied defaults
+   * @param overrideFonts
+   *                true if we take the menuBar fonts in preference to the
+   *                supplied defaults
    * @return the embedded menu instance to be added to the frame.
    */
   protected Panel makeEmbeddedPopupMenu(MenuBar menuBar, String fn,
           int fstyle, int fsz, boolean overrideFonts)
   {
-    return makeEmbeddedPopupMenu(menuBar, fn, fstyle, fsz, overrideFonts, false);
+    return makeEmbeddedPopupMenu(menuBar, fn, fstyle, fsz, overrideFonts,
+            false);
   }
+
   /**
-   * Create or add elements to the embedded menu from menuBar. This removes all menu from
-   * menuBar and it is up to the caller to remove the now useless menuBar from the Frame if it is already attached. 
+   * Create or add elements to the embedded menu from menuBar. This removes all
+   * menu from menuBar and it is up to the caller to remove the now useless
+   * menuBar from the Frame if it is already attached.
+   * 
    * @param menuBar
    * @param fn
    * @param fstyle
    * @param fsz
-   * @param overrideFonts 
-   * @param append true means existing menu will be emptied before adding new elements
+   * @param overrideFonts
+   * @param append
+   *                true means existing menu will be emptied before adding new
+   *                elements
    * @return
    */
   protected Panel makeEmbeddedPopupMenu(MenuBar menuBar, String fn,
@@ -117,59 +152,71 @@ public class EmbmenuFrame extends Frame implements MouseListener
       if (embeddedPopup != null)
       {
         embeddedPopup.clear(); // TODO: check if j1.1
-      } 
-      if (embeddedMenu!=null)
+      }
+      if (embeddedMenu != null)
       {
-        embeddedMenu.removeAll(); 
+        embeddedMenu.removeAll();
       }
     }
-    if (embeddedPopup==null)
+    if (embeddedPopup == null)
     {
       embeddedPopup = new Hashtable();
     }
-    
-    embeddedMenu = makeEmbeddedPopupMenu(menuBar, fn, fstyle, fsz, overrideFonts, embeddedPopup, new Panel(), this);
+
+    embeddedMenu = makeEmbeddedPopupMenu(menuBar, fn, fstyle, fsz,
+            overrideFonts, embeddedPopup, new Panel(), this);
     return embeddedMenu;
   }
+
   /**
-   * Generic method to move elements from menubar onto embeddedMenu using the existing or the supplied font, 
-   * and adds binding from panel to attached menus in embeddedPopup
-   * This removes all menu from
-   * menuBar and it is up to the caller to remove the now useless menuBar from the Frame if it is already attached.
-   * @param menuBar must be non-null
+   * Generic method to move elements from menubar onto embeddedMenu using the
+   * existing or the supplied font, and adds binding from panel to attached
+   * menus in embeddedPopup This removes all menu from menuBar and it is up to
+   * the caller to remove the now useless menuBar from the Frame if it is
+   * already attached.
+   * 
+   * @param menuBar
+   *                must be non-null
    * @param fn
    * @param fstyle
    * @param fsz
    * @param overrideFonts
-   * @param embeddedPopup must be non-null
-   * @param embeddedMenu if null, a new panel will be created and returned
-   * @param clickHandler - usually the instance of EmbmenuFrame that holds references to embeddedPopup and embeddedMenu
+   * @param embeddedPopup
+   *                must be non-null
+   * @param embeddedMenu
+   *                if null, a new panel will be created and returned
+   * @param clickHandler -
+   *                usually the instance of EmbmenuFrame that holds references
+   *                to embeddedPopup and embeddedMenu
    * @return the panel instance for convenience.
    */
   protected Panel makeEmbeddedPopupMenu(MenuBar menuBar, String fn,
-          int fstyle, int fsz, boolean overrideFonts, Hashtable embeddedPopup, Panel embeddedMenu, MouseListener clickHandler)
+          int fstyle, int fsz, boolean overrideFonts,
+          Hashtable embeddedPopup, Panel embeddedMenu,
+          MouseListener clickHandler)
   {
-    if (embeddedPopup==null)
+    if (embeddedPopup == null)
     {
-      throw new Error("Implementation error - embeddedPopup must be non-null");
+      throw new Error(
+              "Implementation error - embeddedPopup must be non-null");
     }
     if (overrideFonts)
     {
       Font mbf = menuBar.getFont();
-      if (mbf!=null)
+      if (mbf != null)
       {
         fn = mbf.getName();
         fstyle = mbf.getStyle();
         fsz = mbf.getSize();
       }
     }
-    if (embeddedMenu==null)
+    if (embeddedMenu == null)
       embeddedMenu = new Panel();
     FlowLayout flowLayout1 = new FlowLayout();
     embeddedMenu.setBackground(Color.lightGray);
     embeddedMenu.setLayout(flowLayout1);
     // loop thru
-    for (int mbi = 0,nMbi=menuBar.getMenuCount(); mbi<nMbi; mbi++)
+    for (int mbi = 0, nMbi = menuBar.getMenuCount(); mbi < nMbi; mbi++)
     {
       Menu mi = menuBar.getMenu(mbi);
       Label elab = new Label(mi.getLabel());
@@ -198,18 +245,19 @@ public class EmbmenuFrame extends Frame implements MouseListener
     PopupMenu popup = null;
     Label source = (Label) evt.getSource();
     popup = getPopupMenu(source);
-    if (popup!=null)
+    if (popup != null)
     {
       embeddedMenu.add(popup);
-      popup.show(embeddedMenu,
-               source.getBounds().x,
-               source.getBounds().y + source.getBounds().getSize().height);
+      popup.show(embeddedMenu, source.getBounds().x, source.getBounds().y
+              + source.getBounds().getSize().height);
     }
   }
 
   /**
    * get the menu for source from the hash.
-   * @param source what was clicked on.
+   * 
+   * @param source
+   *                what was clicked on.
    */
   PopupMenu getPopupMenu(Label source)
   {
@@ -217,24 +265,28 @@ public class EmbmenuFrame extends Frame implements MouseListener
   }
 
   public void mouseClicked(MouseEvent evt)
-  {}
+  {
+  }
 
   public void mouseReleased(MouseEvent evt)
-  {}
+  {
+  }
 
   public void mouseEntered(MouseEvent evt)
-  {}
+  {
+  }
 
   public void mouseExited(MouseEvent evt)
-  {}
+  {
+  }
 
   /**
-   * called to clear the GUI resources taken up for embedding
-   * and remove any self references so we can be garbage collected.
+   * called to clear the GUI resources taken up for embedding and remove any
+   * self references so we can be garbage collected.
    */
   public void destroyMenus()
   {
-    if (embeddedPopup!=null)
+    if (embeddedPopup != null)
     {
       Enumeration e = embeddedPopup.keys();
       while (e.hasMoreElements())
@@ -244,18 +296,20 @@ public class EmbmenuFrame extends Frame implements MouseListener
       }
       embeddedPopup.clear();
     }
-    if (embeddedMenu!=null)
+    if (embeddedMenu != null)
     {
       embeddedMenu.removeAll();
     }
   }
+
   /**
    * calls destroyMenus()
    */
-  public void finalize() throws Throwable {
+  public void finalize() throws Throwable
+  {
     destroyMenus();
-    embeddedPopup=null;
-    embeddedMenu=null;
+    embeddedPopup = null;
+    embeddedMenu = null;
     super.finalize();
   }
-}
\ No newline at end of file
+}
diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index 5e65409..cb9736e 100755
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -24,13 +24,12 @@ import java.awt.*;
 
 import java.awt.event.*;
 
-
 import jalview.appletgui.FeatureSettings.MyCheckbox;
 import jalview.datamodel.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
@@ -55,6 +54,7 @@ public class FeatureRenderer
   String[] renderOrder;
 
   FontMetrics fm;
+
   int charOffset;
 
   float transparency = 1f;
@@ -63,8 +63,9 @@ public class FeatureRenderer
 
   /**
    * Creates a new FeatureRenderer object.
-   *
-   * @param av DOCUMENT ME!
+   * 
+   * @param av
+   *                DOCUMENT ME!
    */
   public FeatureRenderer(AlignViewport av)
   {
@@ -84,18 +85,21 @@ public class FeatureRenderer
     transparency = fr.transparency;
   }
 
-
   static String lastFeatureAdded;
+
   static String lastFeatureGroupAdded;
+
   static String lastDescriptionAdded;
 
   int featureIndex = 0;
+
   boolean deleteFeature = false;
+
   Panel colourPanel;
+
   boolean amendFeatures(final SequenceI[] sequences,
-                        final SequenceFeature[] features,
-                        boolean newFeatures,
-                        final AlignmentPanel ap)
+          final SequenceFeature[] features, boolean newFeatures,
+          final AlignmentPanel ap)
   {
     Panel bigPanel = new Panel(new BorderLayout());
     final TextField name = new TextField(16);
@@ -108,74 +112,70 @@ public class FeatureRenderer
     deleteFeature = false;
 
     colourPanel = new Panel(null);
-    colourPanel.setSize(110,15);
+    colourPanel.setSize(110, 15);
     final FeatureRenderer fr = this;
 
     Panel panel = new Panel(new GridLayout(3, 1));
 
     Panel tmp;
 
-    ///////////////////////////////////////
-    ///MULTIPLE FEATURES AT SELECTED RESIDUE
-    if(!newFeatures && features.length>1)
+    // /////////////////////////////////////
+    // /MULTIPLE FEATURES AT SELECTED RESIDUE
+    if (!newFeatures && features.length > 1)
     {
-     panel = new Panel(new GridLayout(4, 1));
-     tmp = new Panel();
-     tmp.add(new Label("Select Feature: "));
-     overlaps = new Choice();
-     for(int i=0; i<features.length; i++)
-     {
-       String item = features[i].getType()
-        +"/"+features[i].getBegin()+"-"+features[i].getEnd();
-
-       if(features[i].getFeatureGroup()!=null)
-         item += " ("+features[i].getFeatureGroup()+")";
+      panel = new Panel(new GridLayout(4, 1));
+      tmp = new Panel();
+      tmp.add(new Label("Select Feature: "));
+      overlaps = new Choice();
+      for (int i = 0; i < features.length; i++)
+      {
+        String item = features[i].getType() + "/" + features[i].getBegin()
+                + "-" + features[i].getEnd();
 
-       overlaps.addItem(item);
-     }
+        if (features[i].getFeatureGroup() != null)
+          item += " (" + features[i].getFeatureGroup() + ")";
 
-     tmp.add(overlaps);
+        overlaps.addItem(item);
+      }
 
-     overlaps.addItemListener(new java.awt.event.ItemListener()
-     {
-       public void itemStateChanged(java.awt.event.ItemEvent e)
-       {
-         int index = overlaps.getSelectedIndex();
-         if (index != -1)
-         {
-           featureIndex = index;
-           name.setText(features[index].getType());
-           description.setText(features[index].getDescription());
-           source.setText(features[index].getFeatureGroup());
-           start.setText(features[index].getBegin()+"");
-           end.setText(features[index].getEnd()+"");
+      tmp.add(overlaps);
 
-           SearchResults highlight = new SearchResults();
-           highlight.addResult(sequences[0],
-                               features[index].getBegin(),
-                               features[index].getEnd());
+      overlaps.addItemListener(new java.awt.event.ItemListener()
+      {
+        public void itemStateChanged(java.awt.event.ItemEvent e)
+        {
+          int index = overlaps.getSelectedIndex();
+          if (index != -1)
+          {
+            featureIndex = index;
+            name.setText(features[index].getType());
+            description.setText(features[index].getDescription());
+            source.setText(features[index].getFeatureGroup());
+            start.setText(features[index].getBegin() + "");
+            end.setText(features[index].getEnd() + "");
 
-           ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
+            SearchResults highlight = new SearchResults();
+            highlight.addResult(sequences[0], features[index].getBegin(),
+                    features[index].getEnd());
 
-         }
-         Color col = getColour(name.getText());
-         if (col == null)
-         {
-           col = new
-               jalview.schemes.UserColourScheme()
-               .createColourFromName(name.getText());
-         }
+            ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
 
-         colourPanel.setBackground(col);
-       }
-     });
+          }
+          Color col = getColour(name.getText());
+          if (col == null)
+          {
+            col = new jalview.schemes.UserColourScheme()
+                    .createColourFromName(name.getText());
+          }
 
+          colourPanel.setBackground(col);
+        }
+      });
 
-     panel.add(tmp);
+      panel.add(tmp);
     }
-    //////////
-    //////////////////////////////////////
-
+    // ////////
+    // ////////////////////////////////////
 
     tmp = new Panel();
     panel.add(tmp);
@@ -184,7 +184,7 @@ public class FeatureRenderer
 
     tmp = new Panel();
     panel.add(tmp);
-    tmp.add(new Label("Group: ",Label.RIGHT));
+    tmp.add(new Label("Group: ", Label.RIGHT));
     tmp.add(source);
 
     tmp = new Panel();
@@ -238,19 +238,15 @@ public class FeatureRenderer
       }
     }
 
+    String title = newFeatures ? "Create New Sequence Feature(s)"
+            : "Amend/Delete Features for " + sequences[0].getName();
 
-    String title = newFeatures ? "Create New Sequence Feature(s)" :
-        "Amend/Delete Features for "
-        + sequences[0].getName();
-
-    final JVDialog dialog = new JVDialog(ap.alignFrame,
-                               title,
-                               true,
-                               385,240);
+    final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385,
+            240);
 
     dialog.setMainPanel(bigPanel);
 
-    if(newFeatures)
+    if (newFeatures)
     {
       name.setText(lastFeatureAdded);
       source.setText(lastFeatureGroupAdded);
@@ -260,34 +256,32 @@ public class FeatureRenderer
       dialog.ok.setLabel("Amend");
       dialog.buttonPanel.add(deleteButton, 1);
       deleteButton.addActionListener(new ActionListener()
-          {
-            public void actionPerformed(ActionEvent evt)
-            {
-              deleteFeature = true;
-              dialog.setVisible(false);
-            }
-          });
+      {
+        public void actionPerformed(ActionEvent evt)
+        {
+          deleteFeature = true;
+          dialog.setVisible(false);
+        }
+      });
       name.setText(features[0].getType());
       source.setText(features[0].getFeatureGroup());
     }
 
-    start.setText(features[0].getBegin()+"");
-    end.setText(features[0].getEnd()+"");
+    start.setText(features[0].getBegin() + "");
+    end.setText(features[0].getEnd() + "");
     description.setText(features[0].getDescription());
 
     Color col = getColour(name.getText());
     if (col == null)
     {
-      col = new
-          jalview.schemes.UserColourScheme()
-          .createColourFromName(name.getText());
+      col = new jalview.schemes.UserColourScheme()
+              .createColourFromName(name.getText());
     }
 
     colourPanel.setBackground(col);
 
     dialog.setResizable(true);
 
-
     colourPanel.addMouseListener(new java.awt.event.MouseAdapter()
     {
       public void mousePressed(java.awt.event.MouseEvent evt)
@@ -302,18 +296,17 @@ public class FeatureRenderer
 
     if (dialog.accept)
     {
-      //This ensures that the last sequence
-      //is refreshed and new features are rendered
+      // This ensures that the last sequence
+      // is refreshed and new features are rendered
       lastSeq = null;
       lastFeatureAdded = name.getText().trim();
       lastFeatureGroupAdded = source.getText().trim();
       lastDescriptionAdded = description.getText().replace('\n', ' ');
     }
 
-    if(lastFeatureGroupAdded !=null && lastFeatureGroupAdded.length()<1)
+    if (lastFeatureGroupAdded != null && lastFeatureGroupAdded.length() < 1)
       lastFeatureGroupAdded = null;
 
-
     if (!newFeatures)
     {
       SequenceFeature sf = features[featureIndex];
@@ -327,10 +320,10 @@ public class FeatureRenderer
         try
         {
           sf.begin = Integer.parseInt(start.getText());
-          sf.end =  Integer.parseInt(end.getText());
+          sf.end = Integer.parseInt(end.getText());
+        } catch (NumberFormatException ex)
+        {
         }
-        catch (NumberFormatException ex)
-        {}
 
         ffile.parseDescriptionHTML(sf, false);
       }
@@ -342,7 +335,7 @@ public class FeatureRenderer
     }
     else
     {
-      if (dialog.accept && name.getText().length()>0)
+      if (dialog.accept && name.getText().length() > 0)
       {
         for (int i = 0; i < sequences.length; i++)
         {
@@ -366,17 +359,17 @@ public class FeatureRenderer
         col = colourPanel.getBackground();
         setColour(lastFeatureAdded, col);
 
-        if(lastFeatureGroupAdded!=null)
+        if (lastFeatureGroupAdded != null)
         {
           featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
-          av.featuresDisplayed.put(lastFeatureGroupAdded,
-                                   new Integer(col.getRGB()));
+          av.featuresDisplayed.put(lastFeatureGroupAdded, new Integer(col
+                  .getRGB()));
         }
         findAllFeatures();
 
-        String [] tro = new String[renderOrder.length];
-        tro[0] = renderOrder[renderOrder.length-1];
-        System.arraycopy(renderOrder,0,tro,1,renderOrder.length-1);
+        String[] tro = new String[renderOrder.length];
+        tro[0] = renderOrder[renderOrder.length - 1];
+        System.arraycopy(renderOrder, 0, tro, 1, renderOrder.length - 1);
         renderOrder = tro;
 
         ap.paintAlignment(true);
@@ -396,7 +389,6 @@ public class FeatureRenderer
     return true;
   }
 
-
   public Color findFeatureColour(Color initialCol, SequenceI seq, int i)
   {
     overview = true;
@@ -428,41 +420,50 @@ public class FeatureRenderer
       return initialCol;
     }
 
-    return new Color( ( (Integer) currentColour).intValue());
+    return new Color(((Integer) currentColour).intValue());
   }
 
   /**
-   * This is used by the Molecule Viewer to get the accurate colour
-   * of the rendered sequence
+   * This is used by the Molecule Viewer to get the accurate colour of the
+   * rendered sequence
    */
   boolean overview = false;
 
-
   /**
    * DOCUMENT ME!
-   *
-   * @param g DOCUMENT ME!
-   * @param seq DOCUMENT ME!
-   * @param sg DOCUMENT ME!
-   * @param start DOCUMENT ME!
-   * @param end DOCUMENT ME!
-   * @param x1 DOCUMENT ME!
-   * @param y1 DOCUMENT ME!
-   * @param width DOCUMENT ME!
-   * @param height DOCUMENT ME!
+   * 
+   * @param g
+   *                DOCUMENT ME!
+   * @param seq
+   *                DOCUMENT ME!
+   * @param sg
+   *                DOCUMENT ME!
+   * @param start
+   *                DOCUMENT ME!
+   * @param end
+   *                DOCUMENT ME!
+   * @param x1
+   *                DOCUMENT ME!
+   * @param y1
+   *                DOCUMENT ME!
+   * @param width
+   *                DOCUMENT ME!
+   * @param height
+   *                DOCUMENT ME!
    */
   // String type;
   // SequenceFeature sf;
-
   SequenceI lastSeq;
+
   SequenceFeature[] sequenceFeatures;
+
   int sfSize, sfindex, spos, epos;
 
   synchronized public void drawSequence(Graphics g, SequenceI seq,
-                           int start, int end, int y1)
+          int start, int end, int y1)
   {
     if (seq.getSequenceFeatures() == null
-        || seq.getSequenceFeatures().length == 0)
+            || seq.getSequenceFeatures().length == 0)
     {
       return;
     }
@@ -472,7 +473,8 @@ public class FeatureRenderer
       transparencySetter.setTransparency(g, transparency);
     }
 
-    if (lastSeq == null || seq != lastSeq || sequenceFeatures!=seq.getSequenceFeatures())
+    if (lastSeq == null || seq != lastSeq
+            || sequenceFeatures != seq.getSequenceFeatures())
     {
       lastSeq = seq;
       sequenceFeatures = seq.getSequenceFeatures();
@@ -518,57 +520,60 @@ public class FeatureRenderer
         }
 
         if (featureGroups != null
-            && sequenceFeatures[sfindex].featureGroup != null
-            &&
-            featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
-            &&
-            ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].
-                                            featureGroup)).
-            booleanValue())
+                && sequenceFeatures[sfindex].featureGroup != null
+                && featureGroups
+                        .containsKey(sequenceFeatures[sfindex].featureGroup)
+                && !((Boolean) featureGroups
+                        .get(sequenceFeatures[sfindex].featureGroup))
+                        .booleanValue())
         {
           continue;
         }
 
-        if (!overview && (sequenceFeatures[sfindex].getBegin() > epos
-                          || sequenceFeatures[sfindex].getEnd() < spos))
+        if (!overview
+                && (sequenceFeatures[sfindex].getBegin() > epos || sequenceFeatures[sfindex]
+                        .getEnd() < spos))
         {
           continue;
         }
 
         if (overview)
         {
-          if (sequenceFeatures[sfindex].begin <= start &&
-              sequenceFeatures[sfindex].end >= start)
+          if (sequenceFeatures[sfindex].begin <= start
+                  && sequenceFeatures[sfindex].end >= start)
           {
-            currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].
-                type);
+            currentColour = av.featuresDisplayed
+                    .get(sequenceFeatures[sfindex].type);
           }
 
         }
         else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
         {
 
-          renderFeature(g, seq,
-                        seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
-                        seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
-                        new Color( ( (Integer) av.featuresDisplayed.get(
-                            sequenceFeatures[sfindex].type)).intValue()),
-                        start, end, y1);
-          renderFeature(g, seq,
-                        seq.findIndex(sequenceFeatures[sfindex].end) - 1,
-                        seq.findIndex(sequenceFeatures[sfindex].end) - 1,
-                        new Color( ( (Integer) av.featuresDisplayed.get(
-                            sequenceFeatures[sfindex].type)).intValue()),
-                        start, end, y1);
+          renderFeature(
+                  g,
+                  seq,
+                  seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+                  seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+                  new Color(((Integer) av.featuresDisplayed
+                          .get(sequenceFeatures[sfindex].type)).intValue()),
+                  start, end, y1);
+          renderFeature(
+                  g,
+                  seq,
+                  seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+                  seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+                  new Color(((Integer) av.featuresDisplayed
+                          .get(sequenceFeatures[sfindex].type)).intValue()),
+                  start, end, y1);
 
         }
         else
         {
-          renderFeature(g, seq,
-                        seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
-                        seq.findIndex(sequenceFeatures[sfindex].end) - 1,
-                        getColour(sequenceFeatures[sfindex].type),
-                        start, end, y1);
+          renderFeature(g, seq, seq
+                  .findIndex(sequenceFeatures[sfindex].begin) - 1, seq
+                  .findIndex(sequenceFeatures[sfindex].end) - 1,
+                  getColour(sequenceFeatures[sfindex].type), start, end, y1);
         }
 
       }
@@ -581,13 +586,14 @@ public class FeatureRenderer
   }
 
   char s;
+
   int i;
-  void renderFeature(Graphics g, SequenceI seq,
-                     int fstart, int fend, Color featureColour, int start,
-                     int end, int y1)
+
+  void renderFeature(Graphics g, SequenceI seq, int fstart, int fend,
+          Color featureColour, int start, int end, int y1)
   {
 
-    if ( ( (fstart <= end) && (fend >= start)))
+    if (((fstart <= end) && (fend >= start)))
     {
       if (fstart < start)
       { // fix for if the feature we have starts before the sequence start,
@@ -610,7 +616,8 @@ public class FeatureRenderer
 
         g.setColor(featureColour);
 
-        g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight);
+        g.fillRect((i - start) * av.charWidth, y1, av.charWidth,
+                av.charHeight);
 
         if (!av.validCharWidth)
         {
@@ -619,9 +626,9 @@ public class FeatureRenderer
 
         g.setColor(Color.white);
         charOffset = (av.charWidth - fm.charWidth(s)) / 2;
-        g.drawString(String.valueOf(s),
-                     charOffset + (av.charWidth * (i - start)),
-                     (y1 + av.charHeight) - av.charHeight / 5); //pady = height / 5;
+        g.drawString(String.valueOf(s), charOffset
+                + (av.charWidth * (i - start)), (y1 + av.charHeight)
+                - av.charHeight / 5); // pady = height / 5;
 
       }
     }
@@ -629,15 +636,14 @@ public class FeatureRenderer
 
   void findAllFeatures()
   {
-    jalview.schemes.UserColourScheme ucs = new
-        jalview.schemes.UserColourScheme();
+    jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
 
     av.featuresDisplayed = new Hashtable();
     Vector allfeatures = new Vector();
     for (int i = 0; i < av.alignment.getHeight(); i++)
     {
-      SequenceFeature[] features = av.alignment.getSequenceAt(i).
-          getSequenceFeatures();
+      SequenceFeature[] features = av.alignment.getSequenceAt(i)
+              .getSequenceFeatures();
 
       if (features == null)
       {
@@ -651,14 +657,12 @@ public class FeatureRenderer
         {
           if (getColour(features[index].getType()) == null)
           {
-            featureColours.put(features[index].getType(),
-                               ucs.createColourFromName(features[index].
-                getType()));
+            featureColours.put(features[index].getType(), ucs
+                    .createColourFromName(features[index].getType()));
           }
 
-          av.featuresDisplayed.put(features[index].getType(),
-                                   new Integer(getColour(features[index].
-              getType()).getRGB()));
+          av.featuresDisplayed.put(features[index].getType(), new Integer(
+                  getColour(features[index].getType()).getRGB()));
           allfeatures.addElement(features[index].getType());
         }
         index++;
@@ -679,8 +683,7 @@ public class FeatureRenderer
   {
     if (!featureColours.containsKey(featureType))
     {
-      jalview.schemes.UserColourScheme ucs = new
-          jalview.schemes.UserColourScheme();
+      jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
       Color col = ucs.createColourFromName(featureType);
       featureColours.put(featureType, col);
       return col;
@@ -689,7 +692,6 @@ public class FeatureRenderer
       return (Color) featureColours.get(featureType);
   }
 
-
   public void setColour(String featureType, Color col)
   {
     featureColours.put(featureType, col);
@@ -705,22 +707,11 @@ public class FeatureRenderer
       av.featuresDisplayed.clear();
     }
 
-   /* if (visibleNew)
-    {
-      if (av.featuresDisplayed != null)
-      {
-        av.featuresDisplayed.clear();
-      }
-      else
-      {
-        av.featuresDisplayed = new Hashtable();
-      }
-    }
-    if (data == null)
-    {
-      return;
-    }*/
-
+    /*
+     * if (visibleNew) { if (av.featuresDisplayed != null) {
+     * av.featuresDisplayed.clear(); } else { av.featuresDisplayed = new
+     * Hashtable(); } } if (data == null) { return; }
+     */
 
     renderOrder = new String[data.length];
 
@@ -730,113 +721,126 @@ public class FeatureRenderer
       {
         String type = data[i][0].toString();
         setColour(type, (Color) data[i][1]);
-        if ( ( (Boolean) data[i][2]).booleanValue())
+        if (((Boolean) data[i][2]).booleanValue())
         {
-          av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));
+          av.featuresDisplayed.put(type, new Integer(getColour(type)
+                  .getRGB()));
         }
 
         renderOrder[data.length - i - 1] = type;
       }
     }
   }
+
   /**
-   * @return a simple list of feature group names or null 
+   * @return a simple list of feature group names or null
    */
   public String[] getGroups()
   {
     buildGroupHash();
-    if (featureGroups!=null)
+    if (featureGroups != null)
     {
       String[] gps = new String[featureGroups.size()];
       Enumeration gn = featureGroups.keys();
-      int i=0;
+      int i = 0;
       while (gn.hasMoreElements())
       {
-        gps[i++]  = (String) gn.nextElement();
+        gps[i++] = (String) gn.nextElement();
       }
       return gps;
     }
     return null;
   }
+
   /**
    * get visible or invisible groups
-   * @param visible true to return visible groups, false to return hidden ones.
+   * 
+   * @param visible
+   *                true to return visible groups, false to return hidden ones.
    * @return list of groups
    */
-  public String[] getGroups(boolean visible) 
+  public String[] getGroups(boolean visible)
   {
     buildGroupHash();
-    if (featureGroups!=null)
+    if (featureGroups != null)
     {
       Vector gp = new Vector();
-      
+
       Enumeration gn = featureGroups.keys();
       while (gn.hasMoreElements())
       {
         String nm = (String) gn.nextElement();
         Boolean state = (Boolean) featureGroups.get(nm);
-        if (state.booleanValue()==visible)
+        if (state.booleanValue() == visible)
         {
           gp.addElement(nm);
         }
       }
       String[] gps = new String[gp.size()];
       gp.copyInto(gps);
-      
-      int i=0;
+
+      int i = 0;
       while (gn.hasMoreElements())
       {
-        gps[i++]  = (String) gn.nextElement();
+        gps[i++] = (String) gn.nextElement();
       }
       return gps;
     }
     return null;
   }
+
   /**
    * set all feature groups in toset to be visible or invisible
-   * @param toset group names
-   * @param visible the state of the named groups to set
+   * 
+   * @param toset
+   *                group names
+   * @param visible
+   *                the state of the named groups to set
    */
   public void setGroupState(String[] toset, boolean visible)
   {
     buildGroupHash();
-    if (toset!=null && toset.length>0 && featureGroups!=null)
+    if (toset != null && toset.length > 0 && featureGroups != null)
     {
       boolean rdrw = false;
-      for (int i=0;i<toset.length; i++)
+      for (int i = 0; i < toset.length; i++)
       {
         Object st = featureGroups.get(toset[i]);
-        if (st!=null)
+        if (st != null)
         {
           featureGroups.put(toset[i], new Boolean(visible));
-          rdrw = rdrw || (visible!=((Boolean) st).booleanValue());
+          rdrw = rdrw || (visible != ((Boolean) st).booleanValue());
         }
       }
       if (rdrw)
       {
-        if (this.av!=null)
-          if (this.av.featureSettings!=null)
+        if (this.av != null)
+          if (this.av.featureSettings != null)
           {
             av.featureSettings.rebuildGroups();
             this.av.featureSettings.resetTable(true);
-          } else {
-            buildFeatureHash();
           }
-          if (av!=null)
+          else
           {
-            av.alignmentChanged(null);
+            buildFeatureHash();
           }
+        if (av != null)
+        {
+          av.alignmentChanged(null);
+        }
       }
     }
   }
+
   /**
-   * analyse alignment for groups and hash tables
-   * (used to be embedded in FeatureSettings.setTableData)
+   * analyse alignment for groups and hash tables (used to be embedded in
+   * FeatureSettings.setTableData)
+   * 
    * @return true if features are on the alignment
    */
   public boolean buildGroupHash()
   {
-    boolean alignmentHasFeatures=false;
+    boolean alignmentHasFeatures = false;
     if (featureGroups == null)
     {
       featureGroups = new Hashtable();
@@ -868,8 +872,10 @@ public class FeatureRenderer
             boolean visible = true;
             if (featureGroups.containsKey(group))
             {
-              visible = ( (Boolean) featureGroups.get(group)).booleanValue();
-            } else {
+              visible = ((Boolean) featureGroups.get(group)).booleanValue();
+            }
+            else
+            {
               featureGroups.put(group, new Boolean(visible));
             }
           }
@@ -882,17 +888,21 @@ public class FeatureRenderer
         index++;
       }
     }
-    
+
     return alignmentHasFeatures;
   }
+
   /**
-   * rebuild the featuresDisplayed and renderorder list based on the featureGroups hash and any existing display state
-   * and force a repaint if necessary
+   * rebuild the featuresDisplayed and renderorder list based on the
+   * featureGroups hash and any existing display state and force a repaint if
+   * necessary
+   * 
    * @return true if alignment has visible features
    */
-  public boolean buildFeatureHash() {
-    boolean alignmentHasFeatures=false;
-    if (featureGroups==null)
+  public boolean buildFeatureHash()
+  {
+    boolean alignmentHasFeatures = false;
+    if (featureGroups == null)
     {
       alignmentHasFeatures = buildGroupHash();
     }
@@ -921,10 +931,10 @@ public class FeatureRenderer
           group = tmpfeatures[index].featureGroup;
           if (featureGroups.containsKey(group))
           {
-            visible = ( (Boolean) featureGroups.get(group)).booleanValue();
+            visible = ((Boolean) featureGroups.get(group)).booleanValue();
           }
         }
-        
+
         if (visible && !allFeatures.contains(tmpfeatures[index].getType()))
         {
           allFeatures.addElement(tmpfeatures[index].getType());
@@ -932,33 +942,35 @@ public class FeatureRenderer
         index++;
       }
     }
-    if (allFeatures.size()>0)
+    if (allFeatures.size() > 0)
     {
       String[] neworder = new String[allFeatures.size()];
-      int p=neworder.length-1;
-      for (int i=renderOrder.length-1; i>=0; i--)
+      int p = neworder.length - 1;
+      for (int i = renderOrder.length - 1; i >= 0; i--)
       {
         if (allFeatures.contains(renderOrder[i]))
         {
           neworder[p--] = renderOrder[i];
           allFeatures.removeElement(renderOrder[i]);
-        } else {
+        }
+        else
+        {
           av.featuresDisplayed.remove(renderOrder[i]);
         }
       }
-      for (int i=allFeatures.size()-1; i>0; i++)
+      for (int i = allFeatures.size() - 1; i > 0; i++)
       {
         Object e = allFeatures.elementAt(i);
-        if (e!=null)
+        if (e != null)
         {
           neworder[p--] = (String) e;
-          av.featuresDisplayed.put(e, getColour((String)e));
+          av.featuresDisplayed.put(e, getColour((String) e));
         }
       }
       renderOrder = neworder;
       return true;
     }
-    
+
     return alignmentHasFeatures;
   }
 }
@@ -967,9 +979,8 @@ class TransparencySetter
 {
   void setTransparency(Graphics g, float value)
   {
-     Graphics2D g2 = (Graphics2D) g;
-     g2.setComposite(
-        AlphaComposite.getInstance(
-             AlphaComposite.SRC_OVER, value));
+    Graphics2D g2 = (Graphics2D) g;
+    g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
+            value));
   }
 }
diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index 6670d2f..4649786 100755
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -25,19 +25,28 @@ import java.awt.event.*;
 
 import jalview.datamodel.*;
 
-public class FeatureSettings
-    extends Panel implements ItemListener,
-    MouseListener, MouseMotionListener, ActionListener, AdjustmentListener
+public class FeatureSettings extends Panel implements ItemListener,
+        MouseListener, MouseMotionListener, ActionListener,
+        AdjustmentListener
 {
   FeatureRenderer fr;
+
   AlignmentPanel ap;
+
   AlignViewport av;
+
   Frame frame;
+
   Panel groupPanel;
+
   Panel featurePanel = new Panel();
+
   ScrollPane scrollPane;
+
   boolean alignmentHasFeatures = false;
+
   Image linkImage;
+
   Scrollbar transparency;
 
   public FeatureSettings(final AlignmentPanel ap)
@@ -48,7 +57,7 @@ public class FeatureSettings
     fr = ap.seqPanel.seqCanvas.getFeatureRenderer();
 
     transparency = new Scrollbar(Scrollbar.HORIZONTAL,
-                                 100 - (int) (fr.transparency * 100), 1, 1, 100);
+            100 - (int) (fr.transparency * 100), 1, 1, 100);
 
     if (fr.transparencySetter != null)
     {
@@ -95,8 +104,9 @@ public class FeatureSettings
     }
     else
     {
-      tPanel.add(new Label("Transparency not available in this web browser"),
-                 BorderLayout.CENTER);
+      tPanel.add(
+              new Label("Transparency not available in this web browser"),
+              BorderLayout.CENTER);
     }
 
     lowerPanel.add(tPanel, BorderLayout.SOUTH);
@@ -105,8 +115,8 @@ public class FeatureSettings
 
     if (groupPanel != null)
     {
-      groupPanel.setLayout(
-          new GridLayout(fr.featureGroups.size() / 4 + 1, 4));
+      groupPanel.setLayout(new GridLayout(fr.featureGroups.size() / 4 + 1,
+              4));
       groupPanel.validate();
 
       add(groupPanel, BorderLayout.NORTH);
@@ -118,22 +128,21 @@ public class FeatureSettings
     {
       public void windowClosing(WindowEvent e)
       {
-        if (me.av.featureSettings==me)
+        if (me.av.featureSettings == me)
         {
           me.av.featureSettings = null;
           me.ap = null;
           me.av = null;
         }
       }
-    }
-    );
+    });
     int height = featurePanel.getComponentCount() * 50 + 60;
 
     height = Math.max(200, height);
     height = Math.min(400, height);
     int width = 300;
     jalview.bin.JalviewLite.addFrame(frame, "Feature Settings", width,
-                                     height);
+            height);
   }
 
   public void paint(Graphics g)
@@ -150,10 +159,11 @@ public class FeatureSettings
     if (alignmentHasFeatures)
     {
       rebuildGroups();
-      
+
     }
     resetTable(false);
   }
+
   /**
    * rebuilds the group panel
    */
@@ -163,21 +173,21 @@ public class FeatureSettings
     if (groupPanel == null)
     {
       groupPanel = new Panel();
-    } else {
+    }
+    else
+    {
       rdrw = true;
       groupPanel.removeAll();
     }
-    
+
     Enumeration gps = fr.featureGroups.keys();
     while (gps.hasMoreElements())
     {
       String group = (String) gps.nextElement();
       Boolean vis = (Boolean) fr.featureGroups.get(group);
-      Checkbox check = new MyCheckbox(
-              group,
-              vis.booleanValue(),
-              (fr.featureLinks != null && fr.featureLinks.containsKey(group))
-        );    
+      Checkbox check = new MyCheckbox(group, vis.booleanValue(),
+              (fr.featureLinks != null && fr.featureLinks
+                      .containsKey(group)));
       check.addMouseListener(this);
       check.setFont(new Font("Serif", Font.BOLD, 12));
       check.addItemListener(this);
@@ -189,8 +199,8 @@ public class FeatureSettings
     }
   }
 
-  //This routine adds and removes checkboxes depending on
-  //Group selection states
+  // This routine adds and removes checkboxes depending on
+  // Group selection states
   void resetTable(boolean groupsChanged)
   {
     SequenceFeature[] tmpfeatures;
@@ -210,8 +220,8 @@ public class FeatureSettings
       {
         group = tmpfeatures[index].featureGroup;
 
-        if (group == null || fr.featureGroups.get(group) == null ||
-            ( (Boolean) fr.featureGroups.get(group)).booleanValue())
+        if (group == null || fr.featureGroups.get(group) == null
+                || ((Boolean) fr.featureGroups.get(group)).booleanValue())
         {
           type = tmpfeatures[index].getType();
           if (!visibleChecks.contains(type))
@@ -226,8 +236,8 @@ public class FeatureSettings
     Component[] comps;
     int cSize = featurePanel.getComponentCount();
     Checkbox check;
-    //This will remove any checkboxes which shouldn't be
-    //visible
+    // This will remove any checkboxes which shouldn't be
+    // visible
     for (int i = 0; i < cSize; i++)
     {
       comps = featurePanel.getComponents();
@@ -242,8 +252,8 @@ public class FeatureSettings
 
     if (fr.renderOrder != null)
     {
-      //First add the checks in the previous render order,
-      //in case the window has been closed and reopened
+      // First add the checks in the previous render order,
+      // in case the window has been closed and reopened
       for (int ro = fr.renderOrder.length - 1; ro > -1; ro--)
       {
         String item = fr.renderOrder[ro];
@@ -268,8 +278,8 @@ public class FeatureSettings
       addCheck(groupsChanged, en.nextElement().toString());
     }
 
-    featurePanel.setLayout(new GridLayout(featurePanel.getComponentCount(), 1,
-                                          10, 5));
+    featurePanel.setLayout(new GridLayout(featurePanel.getComponentCount(),
+            1, 10, 5));
     featurePanel.validate();
 
     if (scrollPane != null)
@@ -279,10 +289,15 @@ public class FeatureSettings
 
     itemStateChanged(null);
   }
+
   /**
    * update the checklist of feature types with the given type
-   * @param groupsChanged true means if the type is not in the display list then it will be added and displayed
-   * @param type feature type to be checked for in the list.
+   * 
+   * @param groupsChanged
+   *                true means if the type is not in the display list then it
+   *                will be added and displayed
+   * @param type
+   *                feature type to be checked for in the list.
    */
   void addCheck(boolean groupsChanged, String type)
   {
@@ -308,11 +323,10 @@ public class FeatureSettings
         selected = true;
       }
 
-      check = new MyCheckbox(type,
-                             selected,
-                             (fr.featureLinks != null &&
-                              fr.featureLinks.containsKey(type))
-          );
+      check = new MyCheckbox(
+              type,
+              selected,
+              (fr.featureLinks != null && fr.featureLinks.containsKey(type)));
 
       check.addMouseListener(this);
       check.addMouseMotionListener(this);
@@ -345,11 +359,12 @@ public class FeatureSettings
   {
     if (evt != null)
     {
-      //Is the source a top level featureGroup?
+      // Is the source a top level featureGroup?
       Checkbox source = (Checkbox) evt.getSource();
       if (fr.featureGroups.containsKey(source.getLabel()))
       {
-        fr.featureGroups.put(source.getLabel(), new Boolean(source.getState()));
+        fr.featureGroups.put(source.getLabel(), new Boolean(source
+                .getState()));
         ap.seqPanel.seqCanvas.repaint();
         if (ap.overviewPanel != null)
         {
@@ -388,6 +403,7 @@ public class FeatureSettings
   }
 
   MyCheckbox selectedCheck;
+
   boolean dragging = false;
 
   public void mousePressed(MouseEvent evt)
@@ -396,8 +412,7 @@ public class FeatureSettings
     selectedCheck = (MyCheckbox) evt.getSource();
 
     if (fr.featureLinks != null
-        && fr.featureLinks.containsKey(selectedCheck.getLabel())
-        )
+            && fr.featureLinks.containsKey(selectedCheck.getLabel()))
     {
       if (evt.getX() > selectedCheck.stringWidth + 20)
       {
@@ -409,7 +424,7 @@ public class FeatureSettings
 
   public void mouseDragged(MouseEvent evt)
   {
-    if ( ( (Component) evt.getSource()).getParent() != featurePanel)
+    if (((Component) evt.getSource()).getParent() != featurePanel)
     {
       return;
     }
@@ -418,7 +433,7 @@ public class FeatureSettings
 
   public void mouseReleased(MouseEvent evt)
   {
-    if ( ( (Component) evt.getSource()).getParent() != featurePanel)
+    if (((Component) evt.getSource()).getParent() != featurePanel)
     {
       return;
     }
@@ -431,7 +446,8 @@ public class FeatureSettings
     if (height > featurePanel.getSize().height)
     {
 
-      comp = featurePanel.getComponent(featurePanel.getComponentCount() - 1);
+      comp = featurePanel
+              .getComponent(featurePanel.getComponentCount() - 1);
     }
     else if (height < 0)
     {
@@ -439,9 +455,8 @@ public class FeatureSettings
     }
     else
     {
-      comp = featurePanel.getComponentAt(evt.getX(),
-                                         evt.getY() +
-                                         evt.getComponent().getLocation().y);
+      comp = featurePanel.getComponentAt(evt.getX(), evt.getY()
+              + evt.getComponent().getLocation().y);
     }
 
     if (comp != null && comp instanceof Checkbox)
@@ -449,9 +464,7 @@ public class FeatureSettings
       target = (Checkbox) comp;
     }
 
-    if (selectedCheck != null
-        && target != null
-        && selectedCheck != target)
+    if (selectedCheck != null && target != null && selectedCheck != target)
     {
       int targetIndex = -1;
       for (int i = 0; i < featurePanel.getComponentCount(); i++)
@@ -479,24 +492,26 @@ public class FeatureSettings
   }
 
   public void mouseEntered(MouseEvent evt)
-  {}
+  {
+  }
 
   public void mouseExited(MouseEvent evt)
-  {}
+  {
+  }
 
   public void mouseClicked(MouseEvent evt)
   {
     MyCheckbox check = (MyCheckbox) evt.getSource();
 
     if (fr.featureLinks != null
-        && fr.featureLinks.containsKey(check.getLabel()))
+            && fr.featureLinks.containsKey(check.getLabel()))
     {
       if (evt.getX() > check.stringWidth + 20)
       {
         evt.consume();
         String link = fr.featureLinks.get(check.getLabel()).toString();
-        ap.alignFrame.showURL(link.substring(link.indexOf("|") + 1),
-                              link.substring(0, link.indexOf("|")));
+        ap.alignFrame.showURL(link.substring(link.indexOf("|") + 1), link
+                .substring(0, link.indexOf("|")));
       }
     }
 
@@ -507,26 +522,28 @@ public class FeatureSettings
 
     if (evt.getClickCount() > 1)
     {
-      new UserDefinedColours(this, check.getLabel(),
-                             fr.getColour(check.getLabel()));
+      new UserDefinedColours(this, check.getLabel(), fr.getColour(check
+              .getLabel()));
     }
   }
 
   public void mouseMoved(MouseEvent evt)
-  {}
+  {
+  }
 
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
-    fr.transparency = ( (float) (100 - transparency.getValue()) / 100f);
+    fr.transparency = ((float) (100 - transparency.getValue()) / 100f);
     ap.seqPanel.seqCanvas.repaint();
 
   }
 
-  class MyCheckbox
-      extends Checkbox
+  class MyCheckbox extends Checkbox
   {
     public int stringWidth;
+
     boolean hasLink;
+
     public MyCheckbox(String label, boolean checked, boolean haslink)
     {
       super(label, checked);
@@ -540,9 +557,8 @@ public class FeatureSettings
     {
       if (hasLink)
       {
-        g.drawImage(linkImage, stringWidth + 25, (
-            getSize().height - linkImage.getHeight(this)) / 2,
-                    this);
+        g.drawImage(linkImage, stringWidth + 25,
+                (getSize().height - linkImage.getHeight(this)) / 2, this);
       }
     }
   }
diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index 9e974e9..6d205b6 100755
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.appletgui;
 
 import java.util.*;
@@ -26,25 +25,27 @@ import java.awt.event.*;
 
 import jalview.datamodel.*;
 
-public class Finder
-    extends Panel implements ActionListener
+public class Finder extends Panel implements ActionListener
 {
   AlignViewport av;
+
   AlignmentPanel ap;
+
   Frame frame;
 
   SearchResults searchResults;
 
   int seqIndex = 0;
+
   int resIndex = 0;
+
   public Finder(final AlignmentPanel ap)
   {
     try
     {
       jbInit();
 
-    }
-    catch (Exception e)
+    } catch (Exception e)
     {
       e.printStackTrace();
     }
@@ -92,21 +93,20 @@ public class Finder
   public void createNewGroup_actionPerformed()
   {
     SequenceI[] seqs = new SequenceI[searchResults.getSize()];
-    SequenceFeature[] features = new SequenceFeature[searchResults.getSize()];
+    SequenceFeature[] features = new SequenceFeature[searchResults
+            .getSize()];
 
     for (int i = 0; i < searchResults.getSize(); i++)
     {
       seqs[i] = searchResults.getResultSequence(i);
 
       features[i] = new SequenceFeature(textfield.getText().trim(),
-                                        "Search Results", null,
-                                        searchResults.getResultStart(i),
-                                        searchResults.getResultEnd(i),
-                                        "Search Results");
+              "Search Results", null, searchResults.getResultStart(i),
+              searchResults.getResultEnd(i), "Search Results");
     }
 
-    if (ap.seqPanel.seqCanvas.getFeatureRenderer()
-        .amendFeatures(seqs, features, true, ap))
+    if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
+            features, true, ap))
     {
       ap.alignFrame.sequenceFeatures.setState(true);
       av.showSequenceFeatures(true);
@@ -122,8 +122,8 @@ public class Finder
       av = ap.av;
     }
     createNewGroup.setEnabled(false);
-    jalview.analysis.Finder finder = new jalview.analysis.Finder(av.
-        getAlignment(), av.getSelectionGroup(), seqIndex, resIndex);
+    jalview.analysis.Finder finder = new jalview.analysis.Finder(av
+            .getAlignment(), av.getSelectionGroup(), seqIndex, resIndex);
     finder.setCaseSensitive(caseSensitive.getState());
     finder.setFindAll(findAll);
 
@@ -152,30 +152,37 @@ public class Finder
       seqIndex = 0;
     }
 
-    // if allResults is null, this effectively switches displaySearch flag in seqCanvas
+    // if allResults is null, this effectively switches displaySearch flag in
+    // seqCanvas
     ap.highlightSearchResults(searchResults);
 
     if (findAll)
     {
-      String message = (searchResults == null ? 0 : searchResults.getSize()) +
-          " matches found.";
-      ap.alignFrame.statusBar.setText("Search results: " + searchString + " : " +
-                                      message);
+      String message = (searchResults == null ? 0 : searchResults.getSize())
+              + " matches found.";
+      ap.alignFrame.statusBar.setText("Search results: " + searchString
+              + " : " + message);
     }
 
   }
 
   Label jLabel1 = new Label();
+
   protected TextField textfield = new TextField();
+
   protected Button findAll = new Button();
+
   protected Button findNext = new Button();
+
   Panel jPanel1 = new Panel();
+
   GridLayout gridLayout1 = new GridLayout();
+
   protected Button createNewGroup = new Button();
+
   Checkbox caseSensitive = new Checkbox();
 
-  private void jbInit()
-      throws Exception
+  private void jbInit() throws Exception
   {
     jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
     jLabel1.setText("Find");
diff --git a/src/jalview/appletgui/FontChooser.java b/src/jalview/appletgui/FontChooser.java
index 87fa50f..514b059 100755
--- a/src/jalview/appletgui/FontChooser.java
+++ b/src/jalview/appletgui/FontChooser.java
@@ -1,268 +1,282 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.appletgui;
-
-import java.awt.*;
-import java.awt.event.*;
-
-public class FontChooser
-    extends Panel implements ActionListener, ItemListener
-{
-  AlignmentPanel ap;
-  TreePanel tp;
-  Font oldFont;
-  boolean init = true;
-  Frame frame;
-
-  public FontChooser(TreePanel tp)
-  {
-    try
-    {
-      jbInit();
-    }
-    catch (Exception e)
-    {
-      e.printStackTrace();
-    }
-
-    this.tp = tp;
-    oldFont = tp.getTreeFont();
-    init();
-  }
-
-  public FontChooser(AlignmentPanel ap)
-  {
-    try
-    {
-      jbInit();
-    }
-    catch (Exception e)
-    {
-      e.printStackTrace();
-    }
-
-    this.ap = ap;
-    oldFont = ap.av.getFont();
-    init();
-  }
-
-  void init()
-  {
-    String fonts[] = Toolkit.getDefaultToolkit().getFontList();
-    for (int i = 0; i < fonts.length; i++)
-    {
-      fontName.addItem(fonts[i]);
-    }
-
-    for (int i = 1; i < 31; i++)
-    {
-      fontSize.addItem(i + "");
-    }
-
-    fontStyle.addItem("plain");
-    fontStyle.addItem("bold");
-    fontStyle.addItem("italic");
-
-    fontName.select(oldFont.getName());
-    fontSize.select(oldFont.getSize() + "");
-    fontStyle.select(oldFont.getStyle());
-
-    Frame frame = new Frame();
-    this.frame = frame;
-    frame.add(this);
-    jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 115);
-
-    init = false;
-  }
-
-  public void actionPerformed(ActionEvent evt)
-  {
-    if (evt.getSource() == ok)
-    {
-      ok_actionPerformed();
-    }
-    else if (evt.getSource() == cancel)
-    {
-      cancel_actionPerformed();
-    }
-  }
-
-  public void itemStateChanged(ItemEvent evt)
-  {
-    if (evt.getSource() == fontName)
-    {
-      fontName_actionPerformed();
-    }
-    else if (evt.getSource() == fontSize)
-    {
-      fontSize_actionPerformed();
-    }
-    else if (evt.getSource() == fontStyle)
-    {
-      fontStyle_actionPerformed();
-    }
-  }
-
-  protected void ok_actionPerformed()
-  {
-    frame.setVisible(false);
-    if (ap != null)
-    {
-      if (ap.getOverviewPanel() != null)
-      {
-        ap.getOverviewPanel().updateOverviewImage();
-      }
-    }
-
-  }
-
-  protected void cancel_actionPerformed()
-  {
-    if (ap != null)
-    {
-      ap.av.setFont(oldFont);
-      ap.paintAlignment(true);
-    }
-    else if (tp != null)
-    {
-      tp.setTreeFont(oldFont);
-      tp.treeCanvas.repaint();
-    }
-
-    fontName.select(oldFont.getName());
-    fontSize.select(oldFont.getSize() + "");
-    fontStyle.select(oldFont.getStyle());
-
-    frame.setVisible(false);
-  }
-
-  void changeFont()
-  {
-    Font newFont = new Font(fontName.getSelectedItem().toString(),
-                            fontStyle.getSelectedIndex(),
-                            Integer.parseInt(fontSize.getSelectedItem().
-                                             toString())
-        );
-    if (ap != null)
-    {
-      ap.av.setFont(newFont);
-      ap.fontChanged();
-    }
-    else if (tp != null)
-    {
-      tp.setTreeFont(newFont);
-    }
-  }
-
-  protected void fontName_actionPerformed()
-  {
-    if (init)
-    {
-      return;
-    }
-    changeFont();
-  }
-
-  protected void fontSize_actionPerformed()
-  {
-    if (init)
-    {
-      return;
-    }
-    changeFont();
-  }
-
-  protected void fontStyle_actionPerformed()
-  {
-    if (init)
-    {
-      return;
-    }
-    changeFont();
-  }
-
-  Label label1 = new Label();
-  protected Choice fontSize = new Choice();
-  protected Choice fontStyle = new Choice();
-  Label label2 = new Label();
-  Label label3 = new Label();
-  protected Choice fontName = new Choice();
-  Button ok = new Button();
-  Button cancel = new Button();
-  Panel panel1 = new Panel();
-  Panel panel2 = new Panel();
-  Panel panel3 = new Panel();
-  BorderLayout borderLayout1 = new BorderLayout();
-  BorderLayout borderLayout2 = new BorderLayout();
-  BorderLayout borderLayout3 = new BorderLayout();
-  Panel panel4 = new Panel();
-  Panel panel5 = new Panel();
-  BorderLayout borderLayout4 = new BorderLayout();
-
-  private void jbInit()
-      throws Exception
-  {
-    label1.setFont(new java.awt.Font("Verdana", 0, 11));
-    label1.setAlignment(Label.RIGHT);
-    label1.setText("Font: ");
-    this.setLayout(borderLayout4);
-    fontSize.setFont(new java.awt.Font("Verdana", 0, 11));
-    fontSize.addItemListener(this);
-    fontStyle.setFont(new java.awt.Font("Verdana", 0, 11));
-    fontStyle.addItemListener(this);
-    label2.setAlignment(Label.RIGHT);
-    label2.setFont(new java.awt.Font("Verdana", 0, 11));
-    label2.setText("Size: ");
-    label3.setAlignment(Label.RIGHT);
-    label3.setFont(new java.awt.Font("Verdana", 0, 11));
-    label3.setText("Style: ");
-    fontName.setFont(new java.awt.Font("Verdana", 0, 11));
-    fontName.addItemListener(this);
-    ok.setFont(new java.awt.Font("Verdana", 0, 11));
-    ok.setLabel("OK");
-    ok.addActionListener(this);
-    cancel.setFont(new java.awt.Font("Verdana", 0, 11));
-    cancel.setLabel("Cancel");
-    cancel.addActionListener(this);
-    this.setBackground(Color.white);
-    panel1.setLayout(borderLayout1);
-    panel2.setLayout(borderLayout3);
-    panel3.setLayout(borderLayout2);
-    panel5.setBackground(Color.white);
-    panel4.setBackground(Color.white);
-    panel1.setBackground(Color.white);
-    panel2.setBackground(Color.white);
-    panel3.setBackground(Color.white);
-    panel1.add(label1, BorderLayout.WEST);
-    panel1.add(fontName, BorderLayout.CENTER);
-    panel5.add(panel1, null);
-    panel5.add(panel3, null);
-    panel5.add(panel2, null);
-    panel2.add(label3, BorderLayout.WEST);
-    panel2.add(fontStyle, BorderLayout.CENTER);
-    panel3.add(label2, BorderLayout.WEST);
-    panel3.add(fontSize, BorderLayout.CENTER);
-    this.add(panel4, BorderLayout.SOUTH);
-    panel4.add(ok, null);
-    panel4.add(cancel, null);
-    this.add(panel5, BorderLayout.CENTER);
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.appletgui;
+
+import java.awt.*;
+import java.awt.event.*;
+
+public class FontChooser extends Panel implements ActionListener,
+        ItemListener
+{
+  AlignmentPanel ap;
+
+  TreePanel tp;
+
+  Font oldFont;
+
+  boolean init = true;
+
+  Frame frame;
+
+  public FontChooser(TreePanel tp)
+  {
+    try
+    {
+      jbInit();
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+
+    this.tp = tp;
+    oldFont = tp.getTreeFont();
+    init();
+  }
+
+  public FontChooser(AlignmentPanel ap)
+  {
+    try
+    {
+      jbInit();
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+
+    this.ap = ap;
+    oldFont = ap.av.getFont();
+    init();
+  }
+
+  void init()
+  {
+    String fonts[] = Toolkit.getDefaultToolkit().getFontList();
+    for (int i = 0; i < fonts.length; i++)
+    {
+      fontName.addItem(fonts[i]);
+    }
+
+    for (int i = 1; i < 31; i++)
+    {
+      fontSize.addItem(i + "");
+    }
+
+    fontStyle.addItem("plain");
+    fontStyle.addItem("bold");
+    fontStyle.addItem("italic");
+
+    fontName.select(oldFont.getName());
+    fontSize.select(oldFont.getSize() + "");
+    fontStyle.select(oldFont.getStyle());
+
+    Frame frame = new Frame();
+    this.frame = frame;
+    frame.add(this);
+    jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 115);
+
+    init = false;
+  }
+
+  public void actionPerformed(ActionEvent evt)
+  {
+    if (evt.getSource() == ok)
+    {
+      ok_actionPerformed();
+    }
+    else if (evt.getSource() == cancel)
+    {
+      cancel_actionPerformed();
+    }
+  }
+
+  public void itemStateChanged(ItemEvent evt)
+  {
+    if (evt.getSource() == fontName)
+    {
+      fontName_actionPerformed();
+    }
+    else if (evt.getSource() == fontSize)
+    {
+      fontSize_actionPerformed();
+    }
+    else if (evt.getSource() == fontStyle)
+    {
+      fontStyle_actionPerformed();
+    }
+  }
+
+  protected void ok_actionPerformed()
+  {
+    frame.setVisible(false);
+    if (ap != null)
+    {
+      if (ap.getOverviewPanel() != null)
+      {
+        ap.getOverviewPanel().updateOverviewImage();
+      }
+    }
+
+  }
+
+  protected void cancel_actionPerformed()
+  {
+    if (ap != null)
+    {
+      ap.av.setFont(oldFont);
+      ap.paintAlignment(true);
+    }
+    else if (tp != null)
+    {
+      tp.setTreeFont(oldFont);
+      tp.treeCanvas.repaint();
+    }
+
+    fontName.select(oldFont.getName());
+    fontSize.select(oldFont.getSize() + "");
+    fontStyle.select(oldFont.getStyle());
+
+    frame.setVisible(false);
+  }
+
+  void changeFont()
+  {
+    Font newFont = new Font(fontName.getSelectedItem().toString(),
+            fontStyle.getSelectedIndex(), Integer.parseInt(fontSize
+                    .getSelectedItem().toString()));
+    if (ap != null)
+    {
+      ap.av.setFont(newFont);
+      ap.fontChanged();
+    }
+    else if (tp != null)
+    {
+      tp.setTreeFont(newFont);
+    }
+  }
+
+  protected void fontName_actionPerformed()
+  {
+    if (init)
+    {
+      return;
+    }
+    changeFont();
+  }
+
+  protected void fontSize_actionPerformed()
+  {
+    if (init)
+    {
+      return;
+    }
+    changeFont();
+  }
+
+  protected void fontStyle_actionPerformed()
+  {
+    if (init)
+    {
+      return;
+    }
+    changeFont();
+  }
+
+  Label label1 = new Label();
+
+  protected Choice fontSize = new Choice();
+
+  protected Choice fontStyle = new Choice();
+
+  Label label2 = new Label();
+
+  Label label3 = new Label();
+
+  protected Choice fontName = new Choice();
+
+  Button ok = new Button();
+
+  Button cancel = new Button();
+
+  Panel panel1 = new Panel();
+
+  Panel panel2 = new Panel();
+
+  Panel panel3 = new Panel();
+
+  BorderLayout borderLayout1 = new BorderLayout();
+
+  BorderLayout borderLayout2 = new BorderLayout();
+
+  BorderLayout borderLayout3 = new BorderLayout();
+
+  Panel panel4 = new Panel();
+
+  Panel panel5 = new Panel();
+
+  BorderLayout borderLayout4 = new BorderLayout();
+
+  private void jbInit() throws Exception
+  {
+    label1.setFont(new java.awt.Font("Verdana", 0, 11));
+    label1.setAlignment(Label.RIGHT);
+    label1.setText("Font: ");
+    this.setLayout(borderLayout4);
+    fontSize.setFont(new java.awt.Font("Verdana", 0, 11));
+    fontSize.addItemListener(this);
+    fontStyle.setFont(new java.awt.Font("Verdana", 0, 11));
+    fontStyle.addItemListener(this);
+    label2.setAlignment(Label.RIGHT);
+    label2.setFont(new java.awt.Font("Verdana", 0, 11));
+    label2.setText("Size: ");
+    label3.setAlignment(Label.RIGHT);
+    label3.setFont(new java.awt.Font("Verdana", 0, 11));
+    label3.setText("Style: ");
+    fontName.setFont(new java.awt.Font("Verdana", 0, 11));
+    fontName.addItemListener(this);
+    ok.setFont(new java.awt.Font("Verdana", 0, 11));
+    ok.setLabel("OK");
+    ok.addActionListener(this);
+    cancel.setFont(new java.awt.Font("Verdana", 0, 11));
+    cancel.setLabel("Cancel");
+    cancel.addActionListener(this);
+    this.setBackground(Color.white);
+    panel1.setLayout(borderLayout1);
+    panel2.setLayout(borderLayout3);
+    panel3.setLayout(borderLayout2);
+    panel5.setBackground(Color.white);
+    panel4.setBackground(Color.white);
+    panel1.setBackground(Color.white);
+    panel2.setBackground(Color.white);
+    panel3.setBackground(Color.white);
+    panel1.add(label1, BorderLayout.WEST);
+    panel1.add(fontName, BorderLayout.CENTER);
+    panel5.add(panel1, null);
+    panel5.add(panel3, null);
+    panel5.add(panel2, null);
+    panel2.add(label3, BorderLayout.WEST);
+    panel2.add(fontStyle, BorderLayout.CENTER);
+    panel3.add(label2, BorderLayout.WEST);
+    panel3.add(fontSize, BorderLayout.CENTER);
+    this.add(panel4, BorderLayout.SOUTH);
+    panel4.add(ok, null);
+    panel4.add(cancel, null);
+    this.add(panel5, BorderLayout.CENTER);
+  }
+
+}
diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index bec3c63..d530fd8 100755
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -1,40 +1,43 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.appletgui;
 
 import java.awt.*;
 
 import jalview.datamodel.*;
 
-public class IdCanvas
-    extends Panel
+public class IdCanvas extends Panel
 {
   protected AlignViewport av;
 
   protected boolean showScores = true;
 
   protected int maxIdLength = -1;
+
   protected String maxIdStr = null;
+
   Image image;
+
   Graphics gg;
+
   int imgHeight = 0;
+
   boolean fastPaint = false;
 
   java.util.Vector searchResults;
@@ -47,36 +50,36 @@ public class IdCanvas
   }
 
   public void drawIdString(Graphics gg, SequenceI s, int i, int starty,
-                           int ypos)
+          int ypos)
   {
     int charHeight = av.getCharHeight();
 
     if (searchResults != null && searchResults.contains(s))
     {
       gg.setColor(Color.black);
-      gg.fillRect(0, ( (i - starty) * charHeight) + ypos,
-                  getSize().width, charHeight);
+      gg.fillRect(0, ((i - starty) * charHeight) + ypos, getSize().width,
+              charHeight);
       gg.setColor(Color.white);
     }
-    else if (av.getSelectionGroup() != null &&
-             av.getSelectionGroup().getSequences(null).contains(s))
+    else if (av.getSelectionGroup() != null
+            && av.getSelectionGroup().getSequences(null).contains(s))
     {
       gg.setColor(Color.lightGray);
-      gg.fillRect(0, ( (i - starty) * charHeight) + ypos,
-                  getSize().width, charHeight);
+      gg.fillRect(0, ((i - starty) * charHeight) + ypos, getSize().width,
+              charHeight);
       gg.setColor(Color.white);
     }
     else
     {
       gg.setColor(av.getSequenceColour(s));
-      gg.fillRect(0, ( (i - starty) * charHeight) + ypos,
-                  getSize().width, charHeight);
+      gg.fillRect(0, ((i - starty) * charHeight) + ypos, getSize().width,
+              charHeight);
       gg.setColor(Color.black);
     }
 
     gg.drawString(s.getDisplayId(av.getShowJVSuffix()), 0,
-                  ( (i - starty) * charHeight) + ypos +
-                  charHeight - (charHeight / 5));
+            ((i - starty) * charHeight) + ypos + charHeight
+                    - (charHeight / 5));
 
     if (av.hasHiddenRows && av.showHiddenMarkers)
     {
@@ -93,7 +96,8 @@ public class IdCanvas
       return;
     }
 
-    gg.copyArea(0, 0, getSize().width, imgHeight, 0, -vertical * av.charHeight);
+    gg.copyArea(0, 0, getSize().width, imgHeight, 0, -vertical
+            * av.charHeight);
 
     int ss = av.startSeq, es = av.endSeq, transY = 0;
     if (vertical > 0) // scroll down
@@ -160,21 +164,21 @@ public class IdCanvas
       gg.setFont(av.getFont());
     }
 
-    //Fill in the background
+    // Fill in the background
     gg.setColor(Color.white);
-    Font italic = new Font(av.getFont().getName(), Font.ITALIC,
-                           av.getFont().getSize());
+    Font italic = new Font(av.getFont().getName(), Font.ITALIC, av
+            .getFont().getSize());
     gg.setFont(italic);
 
     gg.fillRect(0, 0, getSize().width, getSize().height);
     drawIds(av.startSeq, av.endSeq);
     g.drawImage(image, 0, 0, this);
   }
-  
+
   void drawIds(int starty, int endy)
   {
-    Font italic = new Font(av.getFont().getName(), Font.ITALIC,
-                           av.getFont().getSize());
+    Font italic = new Font(av.getFont().getName(), Font.ITALIC, av
+            .getFont().getSize());
 
     gg.setFont(italic);
 
@@ -207,16 +211,13 @@ public class IdCanvas
         hgap += av.charHeight;
       }
 
-      int cHeight = alheight * av.charHeight
-          + hgap
-          + annotationHeight;
+      int cHeight = alheight * av.charHeight + hgap + annotationHeight;
 
       int rowSize = av.getEndRes() - av.getStartRes();
 
       // Draw the rest of the panels
-      for (int ypos = hgap, row = av.startRes;
-           (ypos <= getSize().height) && (row < maxwidth);
-           ypos += cHeight, row += rowSize)
+      for (int ypos = hgap, row = av.startRes; (ypos <= getSize().height)
+              && (row < maxwidth); ypos += cHeight, row += rowSize)
       {
         for (int i = starty; i < alheight; i++)
         {
@@ -241,7 +242,7 @@ public class IdCanvas
     }
     else
     {
-      //Now draw the id strings
+      // Now draw the id strings
       SequenceI seq;
       for (int i = starty; i < endy; i++)
       {
@@ -252,22 +253,21 @@ public class IdCanvas
           continue;
         }
         gg.setFont(italic);
-        //boolean isrep=false;
+        // boolean isrep=false;
         if (av.hasHiddenRows)
         {
-          //isrep = 
+          // isrep =
           setHiddenFont(seq);
         }
 
         // Selected sequence colours
-        if ( (searchResults != null) &&
-            searchResults.contains(seq))
+        if ((searchResults != null) && searchResults.contains(seq))
         {
           currentColor = Color.black;
           currentTextColor = Color.white;
         }
-        else if ( (av.getSelectionGroup() != null) &&
-                 av.getSelectionGroup().getSequences(null).contains(seq))
+        else if ((av.getSelectionGroup() != null)
+                && av.getSelectionGroup().getSequences(null).contains(seq))
         {
           currentColor = Color.lightGray;
           currentTextColor = Color.black;
@@ -279,15 +279,15 @@ public class IdCanvas
         }
 
         gg.setColor(currentColor);
-        // TODO: isrep could be used to highlight the representative in a different way
+        // TODO: isrep could be used to highlight the representative in a
+        // different way
         gg.fillRect(0, (i - starty) * av.charHeight, getSize().width,
-                    av.charHeight);
+                av.charHeight);
         gg.setColor(currentTextColor);
 
-        gg.drawString(seq.getDisplayId(av.getShowJVSuffix()),
-                      0,
-                      ( ( (i - starty) * av.charHeight) + av.charHeight) -
-                      (av.charHeight / 5));
+        gg.drawString(seq.getDisplayId(av.getShowJVSuffix()), 0,
+                (((i - starty) * av.charHeight) + av.charHeight)
+                        - (av.charHeight / 5));
 
         if (av.hasHiddenRows && av.showHiddenMarkers)
         {
@@ -306,15 +306,14 @@ public class IdCanvas
   void drawMarker(int i, int starty, int yoffset)
   {
     SequenceI[] hseqs = av.alignment.getHiddenSequences().hiddenSequences;
-    //Use this method here instead of calling hiddenSeq adjust
-    //3 times.
+    // Use this method here instead of calling hiddenSeq adjust
+    // 3 times.
     int hSize = hseqs.length;
 
     int hiddenIndex = i;
     int lastIndex = i - 1;
     int nextIndex = i + 1;
 
-
     for (int j = 0; j < hSize; j++)
     {
       if (hseqs[j] != null)
@@ -341,40 +340,31 @@ public class IdCanvas
     if (below)
     {
       gg.fillPolygon(new int[]
-                     {getSize().width - av.charHeight,
-                     getSize().width - av.charHeight,
-                     getSize().width},
-                     new int[]
-                     {
-                     (i - starty) * av.charHeight + yoffset,
-                     (i - starty) * av.charHeight + yoffset + av.charHeight / 4,
-                     (i - starty) * av.charHeight + yoffset
-      }, 3);
+      { getSize().width - av.charHeight, getSize().width - av.charHeight,
+          getSize().width }, new int[]
+      { (i - starty) * av.charHeight + yoffset,
+          (i - starty) * av.charHeight + yoffset + av.charHeight / 4,
+          (i - starty) * av.charHeight + yoffset }, 3);
     }
     if (above)
     {
       gg.fillPolygon(new int[]
-                     {getSize().width - av.charHeight,
-                     getSize().width - av.charHeight,
-                     getSize().width},
-                     new int[]
-                     {
-                     (i - starty + 1) * av.charHeight + yoffset,
-                     (i - starty + 1) * av.charHeight + yoffset -
-                     av.charHeight / 4,
-                     (i - starty + 1) * av.charHeight + yoffset
-      }, 3);
+      { getSize().width - av.charHeight, getSize().width - av.charHeight,
+          getSize().width }, new int[]
+      { (i - starty + 1) * av.charHeight + yoffset,
+          (i - starty + 1) * av.charHeight + yoffset - av.charHeight / 4,
+          (i - starty + 1) * av.charHeight + yoffset }, 3);
 
     }
   }
+
   boolean setHiddenFont(SequenceI seq)
   {
-    Font bold = new Font(av.getFont().getName(), Font.BOLD
-            ,
-                         av.getFont().getSize());
+    Font bold = new Font(av.getFont().getName(), Font.BOLD, av.getFont()
+            .getSize());
 
-    if (av.hiddenRepSequences != null &&
-        av.hiddenRepSequences.containsKey(seq))
+    if (av.hiddenRepSequences != null
+            && av.hiddenRepSequences.containsKey(seq))
     {
       gg.setFont(bold);
       return true;
diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index 44a03ec..9bf2374 100755
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.appletgui;
 
 import java.awt.*;
@@ -25,19 +24,26 @@ import java.awt.event.*;
 import jalview.datamodel.*;
 import jalview.util.UrlLink;
 
-public class IdPanel
-    extends Panel implements MouseListener, MouseMotionListener
+public class IdPanel extends Panel implements MouseListener,
+        MouseMotionListener
 {
 
   protected IdCanvas idCanvas;
+
   protected AlignViewport av;
+
   protected AlignmentPanel alignPanel;
+
   ScrollThread scrollThread = null;
 
   int offy;
+
   int width;
+
   int lastid = -1;
+
   boolean mouseDragging = false;
+
   java.util.Vector links = new java.util.Vector();
 
   public IdPanel(AlignViewport av, AlignmentPanel parent)
@@ -68,11 +74,13 @@ public class IdPanel
     if (links.size() < 1)
     {
       links = new java.util.Vector();
-      links.addElement("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
+      links
+              .addElement("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
     }
   }
 
   Tooltip tooltip;
+
   public void mouseMoved(MouseEvent e)
   {
     int seq = alignPanel.seqPanel.findSeq(e);
@@ -91,14 +99,13 @@ public class IdPanel
 
     if (tooltip == null)
     {
-      tooltip = new Tooltip(
-          sequence.getDisplayId(true)
-          + "\n" + sequence.getDescription(), idCanvas);
+      tooltip = new Tooltip(sequence.getDisplayId(true) + "\n"
+              + sequence.getDescription(), idCanvas);
     }
     else
     {
-      tooltip.setTip(sequence.getDisplayId(true)
-                     + "\n" + sequence.getDescription());
+      tooltip.setTip(sequence.getDisplayId(true) + "\n"
+              + sequence.getDescription());
     }
   }
 
@@ -128,13 +135,13 @@ public class IdPanel
       return;
     }
 
-    //DEFAULT LINK IS FIRST IN THE LINK LIST
+    // DEFAULT LINK IS FIRST IN THE LINK LIST
     int seq = alignPanel.seqPanel.findSeq(e);
     String id = av.getAlignment().getSequenceAt(seq).getName();
-    
+
     String target = null;
     String url = null;
-    int i=0;
+    int i = 0;
     while (url == null && i < links.size())
     {
       // DEFAULT LINK IS FIRST IN THE LINK LIST
@@ -161,7 +168,7 @@ public class IdPanel
       }
 
       String urls[] = urlLink.makeUrls(id, true);
-      if (urls == null || urls[0]==null || urls[0].length()<1)
+      if (urls == null || urls[0] == null || urls[0].length() < 1)
       {
         url = null;
         continue;
@@ -173,8 +180,7 @@ public class IdPanel
     {
 
       alignPanel.alignFrame.showURL(url, target);
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       ex.printStackTrace();
     }
@@ -200,8 +206,8 @@ public class IdPanel
       scrollThread = new ScrollThread(true);
     }
 
-    if (mouseDragging && e.getY() >= getSize().height &&
-        av.alignment.getHeight() > av.getEndSeq())
+    if (mouseDragging && e.getY() >= getSize().height
+            && av.alignment.getHeight() > av.getEndSeq())
     {
       scrollThread = new ScrollThread(false);
     }
@@ -222,19 +228,18 @@ public class IdPanel
 
     int seq = alignPanel.seqPanel.findSeq(e);
 
-    if ( (e.getModifiers() & InputEvent.BUTTON3_MASK) ==
-        InputEvent.BUTTON3_MASK)
+    if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
     {
-      APopupMenu popup = new APopupMenu(alignPanel,
-                                        (Sequence) av.getAlignment().
-                                        getSequenceAt(seq), links);
+      APopupMenu popup = new APopupMenu(alignPanel, (Sequence) av
+              .getAlignment().getSequenceAt(seq), links);
       this.add(popup);
       popup.show(this, e.getX(), e.getY());
       return;
     }
 
-    if ( (av.getSelectionGroup() == null) ||
-        ( (!e.isControlDown() && !e.isShiftDown()) && av.getSelectionGroup() != null))
+    if ((av.getSelectionGroup() == null)
+            || ((!e.isControlDown() && !e.isShiftDown()) && av
+                    .getSelectionGroup() != null))
     {
       av.setSelectionGroup(new SequenceGroup());
       av.getSelectionGroup().setStartRes(0);
@@ -280,7 +285,8 @@ public class IdPanel
 
     for (int i = start; i <= end; i++)
     {
-      av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i), false);
+      av.getSelectionGroup().addSequence(
+              av.getAlignment().getSequenceAt(i), false);
     }
 
   }
@@ -310,7 +316,7 @@ public class IdPanel
       return;
     }
 
-    int index = av.alignment.findIndex( (SequenceI) found.elementAt(0));
+    int index = av.alignment.findIndex((SequenceI) found.elementAt(0));
 
     // do we need to scroll the panel?
     if (av.getStartSeq() > index || av.getEndSeq() < index)
@@ -320,11 +326,12 @@ public class IdPanel
   }
 
   // this class allows scrolling off the bottom of the visible alignment
-  class ScrollThread
-      extends Thread
+  class ScrollThread extends Thread
   {
     boolean running = false;
+
     boolean up = true;
+
     public ScrollThread(boolean up)
     {
       this.up = up;
@@ -370,9 +377,9 @@ public class IdPanel
         try
         {
           Thread.sleep(100);
+        } catch (Exception ex)
+        {
         }
-        catch (Exception ex)
-        {}
       }
     }
   }
diff --git a/src/jalview/appletgui/IdwidthAdjuster.java b/src/jalview/appletgui/IdwidthAdjuster.java
index 052a95e..4a9f9ef 100755
--- a/src/jalview/appletgui/IdwidthAdjuster.java
+++ b/src/jalview/appletgui/IdwidthAdjuster.java
@@ -1,104 +1,108 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.appletgui;
-
-import java.awt.*;
-import java.awt.event.*;
-
-public class IdwidthAdjuster
-    extends Panel implements MouseListener, MouseMotionListener
-{
-  boolean active = false;
-  int oldX = 0;
-  Image image;
-  AlignmentPanel ap;
-
-  public IdwidthAdjuster(AlignmentPanel ap)
-  {
-    setLayout(null);
-    this.ap = ap;
-    java.net.URL url = getClass().getResource("/images/idwidth.gif");
-    if (url != null)
-    {
-      image = java.awt.Toolkit.getDefaultToolkit().getImage(url);
-    }
-
-    addMouseListener(this);
-    addMouseMotionListener(this);
-  }
-
-  public void mousePressed(MouseEvent evt)
-  {
-    oldX = evt.getX();
-  }
-
-  public void mouseReleased(MouseEvent evt)
-  {
-    active = false;
-    repaint();
-  }
-
-  public void mouseEntered(MouseEvent evt)
-  {
-    active = true;
-    repaint();
-  }
-
-  public void mouseExited(MouseEvent evt)
-  {
-    active = false;
-    repaint();
-  }
-
-  public void mouseDragged(MouseEvent evt)
-  {
-    active = true;
-    Dimension d = ap.idPanel.idCanvas.getSize();
-    int dif = evt.getX() - oldX;
-
-    if (d.width + dif > 20 || dif > 0)
-    {
-      ap.setIdWidth(d.width + dif, d.height);
-      this.setSize(d.width + dif, getSize().height);
-    }
-
-    oldX = evt.getX();
-  }
-
-  public void mouseMoved(MouseEvent evt)
-  {}
-
-  public void mouseClicked(MouseEvent evt)
-  {}
-
-  public void paint(Graphics g)
-  {
-    g.setColor(Color.white);
-    g.fillRect(0, 0, getSize().width, getSize().height);
-    if (active)
-    {
-      if (image != null)
-      {
-        g.drawImage(image, getSize().width - 20, 2, this);
-      }
-    }
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.appletgui;
+
+import java.awt.*;
+import java.awt.event.*;
+
+public class IdwidthAdjuster extends Panel implements MouseListener,
+        MouseMotionListener
+{
+  boolean active = false;
+
+  int oldX = 0;
+
+  Image image;
+
+  AlignmentPanel ap;
+
+  public IdwidthAdjuster(AlignmentPanel ap)
+  {
+    setLayout(null);
+    this.ap = ap;
+    java.net.URL url = getClass().getResource("/images/idwidth.gif");
+    if (url != null)
+    {
+      image = java.awt.Toolkit.getDefaultToolkit().getImage(url);
+    }
+
+    addMouseListener(this);
+    addMouseMotionListener(this);
+  }
+
+  public void mousePressed(MouseEvent evt)
+  {
+    oldX = evt.getX();
+  }
+
+  public void mouseReleased(MouseEvent evt)
+  {
+    active = false;
+    repaint();
+  }
+
+  public void mouseEntered(MouseEvent evt)
+  {
+    active = true;
+    repaint();
+  }
+
+  public void mouseExited(MouseEvent evt)
+  {
+    active = false;
+    repaint();
+  }
+
+  public void mouseDragged(MouseEvent evt)
+  {
+    active = true;
+    Dimension d = ap.idPanel.idCanvas.getSize();
+    int dif = evt.getX() - oldX;
+
+    if (d.width + dif > 20 || dif > 0)
+    {
+      ap.setIdWidth(d.width + dif, d.height);
+      this.setSize(d.width + dif, getSize().height);
+    }
+
+    oldX = evt.getX();
+  }
+
+  public void mouseMoved(MouseEvent evt)
+  {
+  }
+
+  public void mouseClicked(MouseEvent evt)
+  {
+  }
+
+  public void paint(Graphics g)
+  {
+    g.setColor(Color.white);
+    g.fillRect(0, 0, getSize().width, getSize().height);
+    if (active)
+    {
+      if (image != null)
+      {
+        g.drawImage(image, getSize().width - 20, 2, this);
+      }
+    }
+  }
+
+}
diff --git a/src/jalview/appletgui/JVDialog.java b/src/jalview/appletgui/JVDialog.java
index b8e0abc..b85424c 100644
--- a/src/jalview/appletgui/JVDialog.java
+++ b/src/jalview/appletgui/JVDialog.java
@@ -1,79 +1,78 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.appletgui;
-
-import java.awt.*;
-import java.awt.event.*;
-
-public class JVDialog extends Dialog implements ActionListener
-{
-  AlignmentPanel ap;
-  Panel buttonPanel;
-  Button ok = new Button("Accept");
-  Button cancel = new Button("Cancel");
-  boolean accept = false;
-  Frame owner;
-
-  public JVDialog(Frame owner,
-                  String title,
-                  boolean modal,
-                  int width, int height)
-  {
-      super(owner, title, modal);
-      this.owner = owner;
-
-      height += owner.getInsets().top + getInsets().bottom;
-
-      setBounds(owner.getBounds().x
-                + (owner.getSize().width - width) / 2,
-                owner.getBounds().y
-                + (owner.getSize().height - height) / 2,
-                width, height);
-  }
-
-  void setMainPanel(Panel panel)
-  {
-    add(panel, BorderLayout.NORTH);
-
-    buttonPanel = new Panel(new FlowLayout());
-
-    buttonPanel.add(ok);
-    buttonPanel.add(cancel);
-    ok.addActionListener(this);
-    cancel.addActionListener(this);
-
-    add(buttonPanel, BorderLayout.SOUTH);
-
-    pack();
-
-  }
-
-  public void actionPerformed(ActionEvent evt)
-  {
-    if (evt.getSource() == ok)
-    {
-      accept = true;
-    }
-
-    setVisible(false);
-  }
-
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.appletgui;
+
+import java.awt.*;
+import java.awt.event.*;
+
+public class JVDialog extends Dialog implements ActionListener
+{
+  AlignmentPanel ap;
+
+  Panel buttonPanel;
+
+  Button ok = new Button("Accept");
+
+  Button cancel = new Button("Cancel");
+
+  boolean accept = false;
+
+  Frame owner;
+
+  public JVDialog(Frame owner, String title, boolean modal, int width,
+          int height)
+  {
+    super(owner, title, modal);
+    this.owner = owner;
+
+    height += owner.getInsets().top + getInsets().bottom;
+
+    setBounds(owner.getBounds().x + (owner.getSize().width - width) / 2,
+            owner.getBounds().y + (owner.getSize().height - height) / 2,
+            width, height);
+  }
+
+  void setMainPanel(Panel panel)
+  {
+    add(panel, BorderLayout.NORTH);
+
+    buttonPanel = new Panel(new FlowLayout());
+
+    buttonPanel.add(ok);
+    buttonPanel.add(cancel);
+    ok.addActionListener(this);
+    cancel.addActionListener(this);
+
+    add(buttonPanel, BorderLayout.SOUTH);
+
+    pack();
+
+  }
+
+  public void actionPerformed(ActionEvent evt)
+  {
+    if (evt.getSource() == ok)
+    {
+      accept = true;
+    }
+
+    setVisible(false);
+  }
+
+}
diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 7265489..ef7c16d 100755
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -1,449 +1,455 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.appletgui;
-
-import java.awt.*;
-import java.awt.event.*;
-
-public class OverviewPanel
-    extends Panel implements Runnable, MouseMotionListener, MouseListener
-{
-  Image miniMe;
-  Image offscreen;
-  AlignViewport av;
-  AlignmentPanel ap;
-  float scalew = 1f;
-  float scaleh = 1f;
-
-  public int width, sequencesHeight;
-  int graphHeight = 20;
-  int boxX = -1, boxY = -1, boxWidth = -1, boxHeight = -1;
-
-  boolean resizing = false;
-
-  // Can set different properties in this seqCanvas than
-  // main visible SeqCanvas
-  SequenceRenderer sr;
-  FeatureRenderer fr;
-
-  Frame nullFrame;
-
-  public OverviewPanel(AlignmentPanel ap)
-  {
-    this.av = ap.av;
-    this.ap = ap;
-    setLayout(null);
-    nullFrame = new Frame();
-    nullFrame.addNotify();
-
-    sr = new SequenceRenderer(av);
-    sr.graphics = nullFrame.getGraphics();
-    sr.renderGaps = false;
-    sr.forOverview = true;
-    fr = new FeatureRenderer(av);
-    fr.overview = true;
-
-    // scale the initial size of overviewpanel to shape of alignment
-    float initialScale = (float) av.alignment.getWidth() /
-        (float) av.alignment.getHeight();
-
-    if (av.hconsensus == null)
-    {
-      graphHeight = 0;
-    }
-
-    if (av.alignment.getWidth() > av.alignment.getHeight())
-    {
-      // wider
-      width = 400;
-      sequencesHeight = (int) (400f / initialScale);
-      if (sequencesHeight < 40)
-      {
-        sequencesHeight = 40;
-      }
-    }
-    else
-    {
-      // taller
-      width = (int) (400f * initialScale);
-      sequencesHeight = 300;
-      if (width < 120)
-      {
-        width = 120;
-      }
-    }
-
-    setSize(new Dimension(width, sequencesHeight + graphHeight));
-    addComponentListener(new ComponentAdapter()
-    {
-
-      public void componentResized(ComponentEvent evt)
-      {
-        if (getSize().width != width ||
-            getSize().height != sequencesHeight + graphHeight)
-        {
-          updateOverviewImage();
-        }
-      }
-    });
-
-    addMouseMotionListener(this);
-
-    addMouseListener(this);
-
-    updateOverviewImage();
-
-  }
-
-  public void mouseEntered(MouseEvent evt)
-  {}
-
-  public void mouseExited(MouseEvent evt)
-  {}
-
-  public void mouseClicked(MouseEvent evt)
-  {}
-
-  public void mouseMoved(MouseEvent evt)
-  {}
-
-  public void mousePressed(MouseEvent evt)
-  {
-    boxX = evt.getX();
-    boxY = evt.getY();
-    checkValid();
-  }
-
-  public void mouseReleased(MouseEvent evt)
-  {
-    boxX = evt.getX();
-    boxY = evt.getY();
-    checkValid();
-  }
-
-  public void mouseDragged(MouseEvent evt)
-  {
-    boxX = evt.getX();
-    boxY = evt.getY();
-    checkValid();
-  }
-
-  void checkValid()
-  {
-    if (boxY < 0)
-    {
-      boxY = 0;
-    }
-
-    if (boxY > (sequencesHeight - boxHeight))
-    {
-      boxY = sequencesHeight - boxHeight + 1;
-    }
-
-    if (boxX < 0)
-    {
-      boxX = 0;
-    }
-
-    if (boxX > (width - boxWidth))
-    {
-      if (av.hasHiddenColumns)
-      {
-        //Try smallest possible box
-        boxWidth = (int) ( (av.endRes - av.startRes + 1) *
-                          av.getCharWidth() * scalew);
-      }
-      boxX = width - boxWidth;
-    }
-
-    int col = (int) (boxX / scalew / av.getCharWidth());
-    int row = (int) (boxY / scaleh / av.getCharHeight());
-
-    if (av.hasHiddenColumns)
-    {
-      if (!av.getColumnSelection().isVisible(col))
-      {
-        return;
-      }
-
-      col = av.getColumnSelection().findColumnPosition(col);
-    }
-
-    if (av.hasHiddenRows)
-    {
-      row = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(row);
-    }
-
-    ap.setScrollValues(col, row);
-    ap.paintAlignment(false);
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  public void updateOverviewImage()
-  {
-    if (resizing)
-    {
-      resizeAgain = true;
-      return;
-    }
-
-    if (av.showSequenceFeatures)
-    {
-      fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().
-          featureGroups;
-      fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().
-          featureColours;
-    }
-
-    resizing = true;
-
-    if ( (getSize().width > 0) && (getSize().height > 0))
-    {
-      width = getSize().width;
-      sequencesHeight = getSize().height - graphHeight;
-    }
-    setSize(new Dimension(width, sequencesHeight + graphHeight));
-
-    Thread thread = new Thread(this);
-    thread.start();
-    repaint();
-  }
-
-  // This is set true if the user resizes whilst
-  // the overview is being calculated
-  boolean resizeAgain = false;
-
-  public void run()
-  {
-    miniMe = null;
-    int alwidth = av.alignment.getWidth();
-    int alheight = av.alignment.getHeight();
-
-    if (av.showSequenceFeatures)
-    {
-      fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
-    }
-
-    if (getSize().width > 0 && getSize().height > 0)
-    {
-      width = getSize().width;
-      sequencesHeight = getSize().height - graphHeight;
-    }
-
-    setSize(new Dimension(width, sequencesHeight + graphHeight));
-
-    int fullsizeWidth = alwidth * av.getCharWidth();
-    int fullsizeHeight = alheight * av.getCharHeight();
-
-    scalew = (float) width / (float) fullsizeWidth;
-    scaleh = (float) sequencesHeight / (float) fullsizeHeight;
-
-    miniMe = nullFrame.createImage(width, sequencesHeight + graphHeight);
-    offscreen = nullFrame.createImage(width, sequencesHeight + graphHeight);
-
-    Graphics mg = miniMe.getGraphics();
-    float sampleCol = (float) alwidth / (float) width;
-    float sampleRow = (float) alheight / (float) sequencesHeight;
-
-    int lastcol = 0, lastrow = 0;
-    int xstart = 0, ystart = 0;
-    Color color = Color.yellow;
-    int row, col, sameRow = 0, sameCol = 0;
-    jalview.datamodel.SequenceI seq;
-    boolean hiddenRow = false;
-    for (row = 0; row <= sequencesHeight; row++)
-    {
-      if ( (int) (row * sampleRow) == lastrow)
-      {
-        sameRow++;
-        continue;
-      }
-
-      hiddenRow = false;
-      if (av.hasHiddenRows)
-      {
-        seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow);
-        if (seq == null)
-        {
-          int index =
-              av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(
-              lastrow);
-
-          seq = av.alignment.getSequenceAt(index);
-        }
-        else
-        {
-          hiddenRow = true;
-        }
-      }
-      else
-      {
-        seq = av.alignment.getSequenceAt(lastrow);
-      }
-
-      for (col = 0; col < width; col++)
-      {
-        if ( (int) (col * sampleCol) == lastcol &&
-            (int) (row * sampleRow) == lastrow)
-        {
-          sameCol++;
-          continue;
-        }
-
-        lastcol = (int) (col * sampleCol);
-
-        if (seq.getLength() > lastcol)
-        {
-          color = sr.getResidueBoxColour(
-              seq, lastcol);
-
-          if (av.showSequenceFeatures)
-          {
-            color = fr.findFeatureColour(color, seq, lastcol);
-          }
-        }
-        else
-        {
-          color = Color.white; //White
-        }
-
-        if (hiddenRow ||
-            (av.hasHiddenColumns && !av.getColumnSelection().isVisible(lastcol)))
-        {
-          color = color.darker().darker();
-        }
-
-        mg.setColor(color);
-        if (sameCol == 1 && sameRow == 1)
-        {
-          mg.drawLine(xstart, ystart, xstart, ystart);
-        }
-        else
-        {
-          mg.fillRect(xstart, ystart, sameCol, sameRow);
-        }
-
-        xstart = col;
-        sameCol = 1;
-      }
-      lastrow = (int) (row * sampleRow);
-      ystart = row;
-      sameRow = 1;
-    }
-
-    if (av.conservation != null)
-    {
-      for (col = 0; col < width; col++)
-      {
-        lastcol = (int) (col * sampleCol);
-        {
-          mg.translate(col, sequencesHeight);
-          ap.annotationPanel.drawGraph(mg, av.conservation,
-                                       (int) (sampleCol) + 1,
-                                       graphHeight,
-                                       (int) (col * sampleCol),
-                                       (int) (col * sampleCol) + 1);
-          mg.translate( -col, -sequencesHeight);
-        }
-      }
-    }
-    System.gc();
-
-    resizing = false;
-
-    setBoxPosition();
-
-    if (resizeAgain)
-    {
-      resizeAgain = false;
-      updateOverviewImage();
-    }
-  }
-
-  public void setBoxPosition()
-  {
-    int fullsizeWidth = av.alignment.getWidth() * av.getCharWidth();
-    int fullsizeHeight = (av.alignment.getHeight()
-                          + av.alignment.getHiddenSequences().getSize()) *
-        av.getCharHeight();
-
-    int startRes = av.getStartRes();
-    int endRes = av.getEndRes();
-
-    if (av.hasHiddenColumns)
-    {
-      startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);
-      endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);
-    }
-
-    int startSeq = av.startSeq;
-    int endSeq = av.endSeq;
-
-    if (av.hasHiddenRows)
-    {
-      startSeq =
-          av.alignment.getHiddenSequences().adjustForHiddenSeqs(startSeq);
-
-      endSeq =
-          av.alignment.getHiddenSequences().adjustForHiddenSeqs(endSeq);
-
-    }
-
-    scalew = (float) width / (float) fullsizeWidth;
-    scaleh = (float) sequencesHeight / (float) fullsizeHeight;
-
-    boxX = (int) (startRes * av.getCharWidth() * scalew);
-    boxY = (int) (startSeq * av.getCharHeight() * scaleh);
-
-    if (av.hasHiddenColumns)
-    {
-      boxWidth = (int) ( (endRes - startRes + 1) * av.getCharWidth() * scalew);
-    }
-    else
-    {
-      boxWidth = (int) ( (endRes - startRes + 1) * av.getCharWidth() * scalew);
-    }
-
-    boxHeight = (int) ( (endSeq - startSeq) * av.getCharHeight() * scaleh);
-
-    repaint();
-  }
-
-  public void update(Graphics g)
-  {
-    paint(g);
-  }
-
-  public void paint(Graphics g)
-  {
-    Graphics og = offscreen.getGraphics();
-    if (miniMe != null)
-    {
-      og.drawImage(miniMe, 0, 0, this);
-      og.setColor(Color.red);
-      og.drawRect(boxX, boxY, boxWidth, boxHeight);
-      og.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
-      g.drawImage(offscreen, 0, 0, this);
-    }
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.appletgui;
+
+import java.awt.*;
+import java.awt.event.*;
+
+public class OverviewPanel extends Panel implements Runnable,
+        MouseMotionListener, MouseListener
+{
+  Image miniMe;
+
+  Image offscreen;
+
+  AlignViewport av;
+
+  AlignmentPanel ap;
+
+  float scalew = 1f;
+
+  float scaleh = 1f;
+
+  public int width, sequencesHeight;
+
+  int graphHeight = 20;
+
+  int boxX = -1, boxY = -1, boxWidth = -1, boxHeight = -1;
+
+  boolean resizing = false;
+
+  // Can set different properties in this seqCanvas than
+  // main visible SeqCanvas
+  SequenceRenderer sr;
+
+  FeatureRenderer fr;
+
+  Frame nullFrame;
+
+  public OverviewPanel(AlignmentPanel ap)
+  {
+    this.av = ap.av;
+    this.ap = ap;
+    setLayout(null);
+    nullFrame = new Frame();
+    nullFrame.addNotify();
+
+    sr = new SequenceRenderer(av);
+    sr.graphics = nullFrame.getGraphics();
+    sr.renderGaps = false;
+    sr.forOverview = true;
+    fr = new FeatureRenderer(av);
+    fr.overview = true;
+
+    // scale the initial size of overviewpanel to shape of alignment
+    float initialScale = (float) av.alignment.getWidth()
+            / (float) av.alignment.getHeight();
+
+    if (av.hconsensus == null)
+    {
+      graphHeight = 0;
+    }
+
+    if (av.alignment.getWidth() > av.alignment.getHeight())
+    {
+      // wider
+      width = 400;
+      sequencesHeight = (int) (400f / initialScale);
+      if (sequencesHeight < 40)
+      {
+        sequencesHeight = 40;
+      }
+    }
+    else
+    {
+      // taller
+      width = (int) (400f * initialScale);
+      sequencesHeight = 300;
+      if (width < 120)
+      {
+        width = 120;
+      }
+    }
+
+    setSize(new Dimension(width, sequencesHeight + graphHeight));
+    addComponentListener(new ComponentAdapter()
+    {
+
+      public void componentResized(ComponentEvent evt)
+      {
+        if (getSize().width != width
+                || getSize().height != sequencesHeight + graphHeight)
+        {
+          updateOverviewImage();
+        }
+      }
+    });
+
+    addMouseMotionListener(this);
+
+    addMouseListener(this);
+
+    updateOverviewImage();
+
+  }
+
+  public void mouseEntered(MouseEvent evt)
+  {
+  }
+
+  public void mouseExited(MouseEvent evt)
+  {
+  }
+
+  public void mouseClicked(MouseEvent evt)
+  {
+  }
+
+  public void mouseMoved(MouseEvent evt)
+  {
+  }
+
+  public void mousePressed(MouseEvent evt)
+  {
+    boxX = evt.getX();
+    boxY = evt.getY();
+    checkValid();
+  }
+
+  public void mouseReleased(MouseEvent evt)
+  {
+    boxX = evt.getX();
+    boxY = evt.getY();
+    checkValid();
+  }
+
+  public void mouseDragged(MouseEvent evt)
+  {
+    boxX = evt.getX();
+    boxY = evt.getY();
+    checkValid();
+  }
+
+  void checkValid()
+  {
+    if (boxY < 0)
+    {
+      boxY = 0;
+    }
+
+    if (boxY > (sequencesHeight - boxHeight))
+    {
+      boxY = sequencesHeight - boxHeight + 1;
+    }
+
+    if (boxX < 0)
+    {
+      boxX = 0;
+    }
+
+    if (boxX > (width - boxWidth))
+    {
+      if (av.hasHiddenColumns)
+      {
+        // Try smallest possible box
+        boxWidth = (int) ((av.endRes - av.startRes + 1) * av.getCharWidth() * scalew);
+      }
+      boxX = width - boxWidth;
+    }
+
+    int col = (int) (boxX / scalew / av.getCharWidth());
+    int row = (int) (boxY / scaleh / av.getCharHeight());
+
+    if (av.hasHiddenColumns)
+    {
+      if (!av.getColumnSelection().isVisible(col))
+      {
+        return;
+      }
+
+      col = av.getColumnSelection().findColumnPosition(col);
+    }
+
+    if (av.hasHiddenRows)
+    {
+      row = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(
+              row);
+    }
+
+    ap.setScrollValues(col, row);
+    ap.paintAlignment(false);
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void updateOverviewImage()
+  {
+    if (resizing)
+    {
+      resizeAgain = true;
+      return;
+    }
+
+    if (av.showSequenceFeatures)
+    {
+      fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups;
+      fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours;
+    }
+
+    resizing = true;
+
+    if ((getSize().width > 0) && (getSize().height > 0))
+    {
+      width = getSize().width;
+      sequencesHeight = getSize().height - graphHeight;
+    }
+    setSize(new Dimension(width, sequencesHeight + graphHeight));
+
+    Thread thread = new Thread(this);
+    thread.start();
+    repaint();
+  }
+
+  // This is set true if the user resizes whilst
+  // the overview is being calculated
+  boolean resizeAgain = false;
+
+  public void run()
+  {
+    miniMe = null;
+    int alwidth = av.alignment.getWidth();
+    int alheight = av.alignment.getHeight();
+
+    if (av.showSequenceFeatures)
+    {
+      fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
+    }
+
+    if (getSize().width > 0 && getSize().height > 0)
+    {
+      width = getSize().width;
+      sequencesHeight = getSize().height - graphHeight;
+    }
+
+    setSize(new Dimension(width, sequencesHeight + graphHeight));
+
+    int fullsizeWidth = alwidth * av.getCharWidth();
+    int fullsizeHeight = alheight * av.getCharHeight();
+
+    scalew = (float) width / (float) fullsizeWidth;
+    scaleh = (float) sequencesHeight / (float) fullsizeHeight;
+
+    miniMe = nullFrame.createImage(width, sequencesHeight + graphHeight);
+    offscreen = nullFrame.createImage(width, sequencesHeight + graphHeight);
+
+    Graphics mg = miniMe.getGraphics();
+    float sampleCol = (float) alwidth / (float) width;
+    float sampleRow = (float) alheight / (float) sequencesHeight;
+
+    int lastcol = 0, lastrow = 0;
+    int xstart = 0, ystart = 0;
+    Color color = Color.yellow;
+    int row, col, sameRow = 0, sameCol = 0;
+    jalview.datamodel.SequenceI seq;
+    boolean hiddenRow = false;
+    for (row = 0; row <= sequencesHeight; row++)
+    {
+      if ((int) (row * sampleRow) == lastrow)
+      {
+        sameRow++;
+        continue;
+      }
+
+      hiddenRow = false;
+      if (av.hasHiddenRows)
+      {
+        seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow);
+        if (seq == null)
+        {
+          int index = av.alignment.getHiddenSequences()
+                  .findIndexWithoutHiddenSeqs(lastrow);
+
+          seq = av.alignment.getSequenceAt(index);
+        }
+        else
+        {
+          hiddenRow = true;
+        }
+      }
+      else
+      {
+        seq = av.alignment.getSequenceAt(lastrow);
+      }
+
+      for (col = 0; col < width; col++)
+      {
+        if ((int) (col * sampleCol) == lastcol
+                && (int) (row * sampleRow) == lastrow)
+        {
+          sameCol++;
+          continue;
+        }
+
+        lastcol = (int) (col * sampleCol);
+
+        if (seq.getLength() > lastcol)
+        {
+          color = sr.getResidueBoxColour(seq, lastcol);
+
+          if (av.showSequenceFeatures)
+          {
+            color = fr.findFeatureColour(color, seq, lastcol);
+          }
+        }
+        else
+        {
+          color = Color.white; // White
+        }
+
+        if (hiddenRow
+                || (av.hasHiddenColumns && !av.getColumnSelection()
+                        .isVisible(lastcol)))
+        {
+          color = color.darker().darker();
+        }
+
+        mg.setColor(color);
+        if (sameCol == 1 && sameRow == 1)
+        {
+          mg.drawLine(xstart, ystart, xstart, ystart);
+        }
+        else
+        {
+          mg.fillRect(xstart, ystart, sameCol, sameRow);
+        }
+
+        xstart = col;
+        sameCol = 1;
+      }
+      lastrow = (int) (row * sampleRow);
+      ystart = row;
+      sameRow = 1;
+    }
+
+    if (av.conservation != null)
+    {
+      for (col = 0; col < width; col++)
+      {
+        lastcol = (int) (col * sampleCol);
+        {
+          mg.translate(col, sequencesHeight);
+          ap.annotationPanel.drawGraph(mg, av.conservation,
+                  (int) (sampleCol) + 1, graphHeight,
+                  (int) (col * sampleCol), (int) (col * sampleCol) + 1);
+          mg.translate(-col, -sequencesHeight);
+        }
+      }
+    }
+    System.gc();
+
+    resizing = false;
+
+    setBoxPosition();
+
+    if (resizeAgain)
+    {
+      resizeAgain = false;
+      updateOverviewImage();
+    }
+  }
+
+  public void setBoxPosition()
+  {
+    int fullsizeWidth = av.alignment.getWidth() * av.getCharWidth();
+    int fullsizeHeight = (av.alignment.getHeight() + av.alignment
+            .getHiddenSequences().getSize())
+            * av.getCharHeight();
+
+    int startRes = av.getStartRes();
+    int endRes = av.getEndRes();
+
+    if (av.hasHiddenColumns)
+    {
+      startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);
+      endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);
+    }
+
+    int startSeq = av.startSeq;
+    int endSeq = av.endSeq;
+
+    if (av.hasHiddenRows)
+    {
+      startSeq = av.alignment.getHiddenSequences().adjustForHiddenSeqs(
+              startSeq);
+
+      endSeq = av.alignment.getHiddenSequences()
+              .adjustForHiddenSeqs(endSeq);
+
+    }
+
+    scalew = (float) width / (float) fullsizeWidth;
+    scaleh = (float) sequencesHeight / (float) fullsizeHeight;
+
+    boxX = (int) (startRes * av.getCharWidth() * scalew);
+    boxY = (int) (startSeq * av.getCharHeight() * scaleh);
+
+    if (av.hasHiddenColumns)
+    {
+      boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
+    }
+    else
+    {
+      boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
+    }
+
+    boxHeight = (int) ((endSeq - startSeq) * av.getCharHeight() * scaleh);
+
+    repaint();
+  }
+
+  public void update(Graphics g)
+  {
+    paint(g);
+  }
+
+  public void paint(Graphics g)
+  {
+    Graphics og = offscreen.getGraphics();
+    if (miniMe != null)
+    {
+      og.drawImage(miniMe, 0, 0, this);
+      og.setColor(Color.red);
+      og.drawRect(boxX, boxY, boxWidth, boxHeight);
+      og.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
+      g.drawImage(offscreen, 0, 0, this);
+    }
+  }
+
+}
diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index ee54478..922941b 100755
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.appletgui;
 
 import java.util.*;
@@ -27,14 +26,19 @@ import java.awt.event.*;
 import jalview.analysis.*;
 import jalview.datamodel.*;
 
-public class PCAPanel
-    extends EmbmenuFrame implements Runnable, ActionListener, ItemListener
+public class PCAPanel extends EmbmenuFrame implements Runnable,
+        ActionListener, ItemListener
 {
   PCA pca;
+
   int top;
+
   RotatableCanvas rc;
+
   AlignViewport av;
+
   SequenceI[] seqs;
+
   AlignmentView seqstrings;
 
   public PCAPanel(AlignViewport av)
@@ -42,8 +46,7 @@ public class PCAPanel
     try
     {
       jbInit();
-    }
-    catch (Exception e)
+    } catch (Exception e)
     {
       e.printStackTrace();
     }
@@ -72,7 +75,8 @@ public class PCAPanel
     {
       if (sq[i].getWidth() != length)
       {
-        System.out.println("Sequences must be equal length for PCA analysis");
+        System.out
+                .println("Sequences must be equal length for PCA analysis");
         return;
       }
     }
@@ -82,7 +86,7 @@ public class PCAPanel
     add(rc, BorderLayout.CENTER);
 
     jalview.bin.JalviewLite.addFrame(this, "Principal component analysis",
-                                     400, 400);
+            400, 400);
 
     Thread worker = new Thread(this);
     worker.start();
@@ -99,7 +103,7 @@ public class PCAPanel
     // Now find the component coordinates
     int ii = 0;
 
-    while ( (ii < seqs.length) && (seqs[ii] != null))
+    while ((ii < seqs.length) && (seqs[ii] != null))
     {
       ii++;
     }
@@ -114,7 +118,7 @@ public class PCAPanel
       }
     }
 
-    //////////////////
+    // ////////////////
     xCombobox.select(0);
     yCombobox.select(1);
     zCombobox.select(2);
@@ -150,7 +154,7 @@ public class PCAPanel
     float[][] scores = pca.getComponents(dim1, dim2, dim3, 100);
     for (int i = 0; i < pca.getM().rows; i++)
     {
-      ( (SequencePoint) rc.points.elementAt(i)).coord = scores[i];
+      ((SequencePoint) rc.points.elementAt(i)).coord = scores[i];
     }
 
     rc.img = null;
@@ -215,28 +219,31 @@ public class PCAPanel
 
   void showOriginalData()
   {
-    // decide if av alignment is sufficiently different to original data to warrant a new window to be created
-    // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)
+    // decide if av alignment is sufficiently different to original data to
+    // warrant a new window to be created
+    // create new alignmnt window with hidden regions (unhiding hidden regions
+    // yields unaligned seqs)
     // or create a selection box around columns in alignment view
     // test Alignment(SeqCigar[])
     char gc = '-';
-    try {
+    try
+    {
       // we try to get the associated view's gap character
       // but this may fail if the view was closed...
-      gc = av.
-      getGapCharacter();
-    } catch (Exception ex) {};
+      gc = av.getGapCharacter();
+    } catch (Exception ex)
+    {
+    }
+    ;
     Object[] alAndColsel = seqstrings.getAlignmentAndColumnSelection(gc);
 
     if (alAndColsel != null && alAndColsel[0] != null)
     {
-      Alignment al = new Alignment( (SequenceI[]) alAndColsel[0]);
-      AlignFrame af = new AlignFrame(al,
-                                     av.applet,
-                                     "Original Data for PCA",
-                                     false);
+      Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
+      AlignFrame af = new AlignFrame(al, av.applet,
+              "Original Data for PCA", false);
 
-      af.viewport.setHiddenColumns( (ColumnSelection) alAndColsel[1]);
+      af.viewport.setHiddenColumns((ColumnSelection) alAndColsel[1]);
     }
   }
 
@@ -246,23 +253,36 @@ public class PCAPanel
   }
 
   Panel jPanel2 = new Panel();
+
   Label jLabel1 = new Label();
+
   Label jLabel2 = new Label();
+
   Label jLabel3 = new Label();
+
   protected Choice xCombobox = new Choice();
+
   protected Choice yCombobox = new Choice();
+
   protected Choice zCombobox = new Choice();
+
   FlowLayout flowLayout1 = new FlowLayout();
+
   BorderLayout borderLayout1 = new BorderLayout();
+
   MenuBar menuBar1 = new MenuBar();
+
   Menu menu1 = new Menu();
+
   Menu menu2 = new Menu();
+
   protected CheckboxMenuItem labels = new CheckboxMenuItem();
+
   MenuItem values = new MenuItem();
+
   MenuItem inputData = new MenuItem();
 
-  private void jbInit()
-      throws Exception
+  private void jbInit() throws Exception
   {
     this.setLayout(borderLayout1);
     jPanel2.setLayout(flowLayout1);
diff --git a/src/jalview/appletgui/PaintRefresher.java b/src/jalview/appletgui/PaintRefresher.java
index 7e0edf7..20edeeb 100755
--- a/src/jalview/appletgui/PaintRefresher.java
+++ b/src/jalview/appletgui/PaintRefresher.java
@@ -1,228 +1,229 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.appletgui;
-
-import java.util.*;
-
-import java.awt.*;
-
-import jalview.datamodel.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class PaintRefresher
-{
-  static Hashtable components;
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param comp DOCUMENT ME!
-   * @param al DOCUMENT ME!
-   */
-  public static void Register(Component comp, String seqSetId)
-  {
-    if (components == null)
-    {
-      components = new Hashtable();
-    }
-
-    if (components.containsKey(seqSetId))
-    {
-      Vector comps = (Vector) components.get(seqSetId);
-      if (!comps.contains(comp))
-      {
-        comps.addElement(comp);
-      }
-    }
-    else
-    {
-      Vector vcoms = new Vector();
-      vcoms.addElement(comp);
-      components.put(seqSetId, vcoms);
-    }
-  }
-
-  public static void RemoveComponent(Component comp)
-  {
-    if (components == null)
-    {
-      return;
-    }
-
-    Enumeration en = components.keys();
-    while (en.hasMoreElements())
-    {
-      String id = en.nextElement().toString();
-      Vector comps = (Vector) components.get(id);
-      comps.removeElement(comp);
-      if (comps.size() == 0)
-      {
-        components.remove(id);
-      }
-    }
-  }
-
-  public static void Refresh(Component source, String id)
-  {
-    Refresh(source, id, false, false);
-  }
-
-  public static void Refresh(Component source,
-                             String id,
-                             boolean alignmentChanged,
-                             boolean validateSequences)
-  {
-    if (components == null)
-    {
-      return;
-    }
-
-    Component comp;
-    Vector comps = (Vector) components.get(id);
-
-    if (comps == null)
-    {
-      return;
-    }
-
-    Enumeration e = comps.elements();
-    while (e.hasMoreElements())
-    {
-      comp = (Component) e.nextElement();
-
-      if (comp == source)
-      {
-        continue;
-      }
-
-      if (!comp.isValid())
-      {
-        comps.removeElement(comp);
-      }
-      else if (validateSequences
-               && comp instanceof AlignmentPanel
-               && source instanceof AlignmentPanel)
-      {
-        validateSequences( ( (AlignmentPanel) source).av.alignment,
-                          ( (AlignmentPanel) comp).av.alignment);
-      }
-
-      if (comp instanceof AlignmentPanel && alignmentChanged)
-      {
-        ( (AlignmentPanel) comp).alignmentChanged();
-      }
-
-      comp.repaint();
-    }
-  }
-
-  static void validateSequences(AlignmentI source, AlignmentI comp)
-  {
-    SequenceI[] a1;
-    if (source.getHiddenSequences().getSize() > 0)
-    {
-      a1 = source.getHiddenSequences().getFullAlignment().getSequencesArray();
-    }
-    else
-    {
-      a1 = source.getSequencesArray();
-    }
-
-    SequenceI[] a2;
-    if (comp.getHiddenSequences().getSize() > 0)
-    {
-      a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();
-    }
-    else
-    {
-      a2 = comp.getSequencesArray();
-    }
-
-    int i, iSize = a1.length, j, jSize = a2.length;
-
-    if (iSize == jSize)
-    {
-      return;
-    }
-
-    boolean exists = false;
-    for (i = 0; i < iSize; i++)
-    {
-      exists = false;
-
-      for (j = 0; j < jSize; j++)
-      {
-        if (a2[j] == a1[i])
-        {
-          exists = true;
-          break;
-        }
-      }
-
-      if (!exists)
-      {
-        if (i < comp.getHeight())
-        {
-          comp.getSequences().insertElementAt(a1[i], i);
-        }
-        else
-        {
-          comp.addSequence(a1[i]);
-        }
-
-        if (comp.getHiddenSequences().getSize() > 0)
-        {
-          a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();
-        }
-        else
-        {
-          a2 = comp.getSequencesArray();
-        }
-
-        jSize = a2.length;
-      }
-    }
-
-    iSize = a1.length;
-    jSize = a2.length;
-
-    for (j = 0; j < jSize; j++)
-    {
-      exists = false;
-      for (i = 0; i < iSize; i++)
-      {
-        if (a2[j] == a1[i])
-        {
-          exists = true;
-          break;
-        }
-      }
-
-      if (!exists)
-      {
-        comp.deleteSequence(a2[j]);
-      }
-    }
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.appletgui;
+
+import java.util.*;
+
+import java.awt.*;
+
+import jalview.datamodel.*;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class PaintRefresher
+{
+  static Hashtable components;
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param comp
+   *                DOCUMENT ME!
+   * @param al
+   *                DOCUMENT ME!
+   */
+  public static void Register(Component comp, String seqSetId)
+  {
+    if (components == null)
+    {
+      components = new Hashtable();
+    }
+
+    if (components.containsKey(seqSetId))
+    {
+      Vector comps = (Vector) components.get(seqSetId);
+      if (!comps.contains(comp))
+      {
+        comps.addElement(comp);
+      }
+    }
+    else
+    {
+      Vector vcoms = new Vector();
+      vcoms.addElement(comp);
+      components.put(seqSetId, vcoms);
+    }
+  }
+
+  public static void RemoveComponent(Component comp)
+  {
+    if (components == null)
+    {
+      return;
+    }
+
+    Enumeration en = components.keys();
+    while (en.hasMoreElements())
+    {
+      String id = en.nextElement().toString();
+      Vector comps = (Vector) components.get(id);
+      comps.removeElement(comp);
+      if (comps.size() == 0)
+      {
+        components.remove(id);
+      }
+    }
+  }
+
+  public static void Refresh(Component source, String id)
+  {
+    Refresh(source, id, false, false);
+  }
+
+  public static void Refresh(Component source, String id,
+          boolean alignmentChanged, boolean validateSequences)
+  {
+    if (components == null)
+    {
+      return;
+    }
+
+    Component comp;
+    Vector comps = (Vector) components.get(id);
+
+    if (comps == null)
+    {
+      return;
+    }
+
+    Enumeration e = comps.elements();
+    while (e.hasMoreElements())
+    {
+      comp = (Component) e.nextElement();
+
+      if (comp == source)
+      {
+        continue;
+      }
+
+      if (!comp.isValid())
+      {
+        comps.removeElement(comp);
+      }
+      else if (validateSequences && comp instanceof AlignmentPanel
+              && source instanceof AlignmentPanel)
+      {
+        validateSequences(((AlignmentPanel) source).av.alignment,
+                ((AlignmentPanel) comp).av.alignment);
+      }
+
+      if (comp instanceof AlignmentPanel && alignmentChanged)
+      {
+        ((AlignmentPanel) comp).alignmentChanged();
+      }
+
+      comp.repaint();
+    }
+  }
+
+  static void validateSequences(AlignmentI source, AlignmentI comp)
+  {
+    SequenceI[] a1;
+    if (source.getHiddenSequences().getSize() > 0)
+    {
+      a1 = source.getHiddenSequences().getFullAlignment()
+              .getSequencesArray();
+    }
+    else
+    {
+      a1 = source.getSequencesArray();
+    }
+
+    SequenceI[] a2;
+    if (comp.getHiddenSequences().getSize() > 0)
+    {
+      a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();
+    }
+    else
+    {
+      a2 = comp.getSequencesArray();
+    }
+
+    int i, iSize = a1.length, j, jSize = a2.length;
+
+    if (iSize == jSize)
+    {
+      return;
+    }
+
+    boolean exists = false;
+    for (i = 0; i < iSize; i++)
+    {
+      exists = false;
+
+      for (j = 0; j < jSize; j++)
+      {
+        if (a2[j] == a1[i])
+        {
+          exists = true;
+          break;
+        }
+      }
+
+      if (!exists)
+      {
+        if (i < comp.getHeight())
+        {
+          comp.getSequences().insertElementAt(a1[i], i);
+        }
+        else
+        {
+          comp.addSequence(a1[i]);
+        }
+
+        if (comp.getHiddenSequences().getSize() > 0)
+        {
+          a2 = comp.getHiddenSequences().getFullAlignment()
+                  .getSequencesArray();
+        }
+        else
+        {
+          a2 = comp.getSequencesArray();
+        }
+
+        jSize = a2.length;
+      }
+    }
+
+    iSize = a1.length;
+    jSize = a2.length;
+
+    for (j = 0; j < jSize; j++)
+    {
+      exists = false;
+      for (i = 0; i < iSize; i++)
+      {
+        if (a2[j] == a1[i])
+        {
+          exists = true;
+          break;
+        }
+      }
+
+      if (!exists)
+      {
+        comp.deleteSequence(a2[j]);
+      }
+    }
+  }
+}
diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java
index 05372a4..c122b3f 100755
--- a/src/jalview/appletgui/PairwiseAlignPanel.java
+++ b/src/jalview/appletgui/PairwiseAlignPanel.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.appletgui;
 
 import java.util.*;
@@ -27,10 +26,10 @@ import java.awt.event.*;
 import jalview.analysis.*;
 import jalview.datamodel.*;
 
-public class PairwiseAlignPanel
-    extends Panel implements ActionListener
+public class PairwiseAlignPanel extends Panel implements ActionListener
 {
   Vector sequences = new Vector();
+
   AlignmentPanel ap;
 
   public PairwiseAlignPanel(AlignmentPanel ap)
@@ -38,8 +37,7 @@ public class PairwiseAlignPanel
     try
     {
       jbInit();
-    }
-    catch (Exception e)
+    } catch (Exception e)
     {
       e.printStackTrace();
     }
@@ -61,8 +59,8 @@ public class PairwiseAlignPanel
     float scores[][] = new float[seqs.length][seqs.length];
     double totscore = 0;
     int count = ap.av.getSelectionGroup().getSize();
-    String type = (ap.av.alignment.isNucleotide()) ? AlignSeq.DNA :
-        AlignSeq.PEP;
+    String type = (ap.av.alignment.isNucleotide()) ? AlignSeq.DNA
+            : AlignSeq.PEP;
     Sequence seq;
 
     for (int i = 1; i < count; i++)
@@ -70,8 +68,8 @@ public class PairwiseAlignPanel
       for (int j = 0; j < i; j++)
       {
 
-        AlignSeq as = new AlignSeq(seqs[i], seqStrings[i],
-                                   seqs[j], seqStrings[j], type);
+        AlignSeq as = new AlignSeq(seqs[i], seqStrings[i], seqs[j],
+                seqStrings[j], type);
 
         if (as.s1str.length() == 0 || as.s2str.length() == 0)
         {
@@ -82,35 +80,30 @@ public class PairwiseAlignPanel
         as.traceAlignment();
 
         as.printAlignment(System.out);
-        scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;
+        scores[i][j] = (float) as.getMaxScore()
+                / (float) as.getASeq1().length;
         totscore = totscore + scores[i][j];
 
         textarea.append(as.getOutput());
-        seq = new Sequence(as.getS1().getName(),
-                           as.getAStr1(),
-                           as.getS1().getStart(),
-                           as.getS1().getEnd()
-            );
+        seq = new Sequence(as.getS1().getName(), as.getAStr1(), as.getS1()
+                .getStart(), as.getS1().getEnd());
         sequences.addElement(seq);
 
-        seq = new Sequence(as.getS2().getName(),
-                           as.getAStr2(),
-                           as.getS2().getStart(),
-                           as.getS2().getEnd());
+        seq = new Sequence(as.getS2().getName(), as.getAStr2(), as.getS2()
+                .getStart(), as.getS2().getEnd());
         sequences.addElement(seq);
       }
     }
 
     if (count > 2)
     {
-      System.out.println(
-          "Pairwise alignment scaled similarity score matrix\n");
+      System.out
+              .println("Pairwise alignment scaled similarity score matrix\n");
 
       for (int i = 0; i < count; i++)
       {
-        jalview.util.Format.print(System.out, "%s \n",
-                                  ("" + i) + " " +
-                                  seqs[i].getName());
+        jalview.util.Format.print(System.out, "%s \n", ("" + i) + " "
+                + seqs[i].getName());
       }
 
       System.out.println("\n");
@@ -119,8 +112,8 @@ public class PairwiseAlignPanel
       {
         for (int j = 0; j < i; j++)
         {
-          jalview.util.Format.print(System.out, "%7.3f",
-                                    scores[i][j] / totscore);
+          jalview.util.Format.print(System.out, "%7.3f", scores[i][j]
+                  / totscore);
         }
       }
 
@@ -146,21 +139,22 @@ public class PairwiseAlignPanel
       seq[i] = (Sequence) sequences.elementAt(i);
     }
 
-    new AlignFrame(new Alignment(seq),
-                   ap.av.applet,
-                   "Pairwise Aligned Sequences",
-                   false);
+    new AlignFrame(new Alignment(seq), ap.av.applet,
+            "Pairwise Aligned Sequences", false);
 
   }
 
   protected ScrollPane scrollPane = new ScrollPane();
+
   protected TextArea textarea = new TextArea();
+
   protected Button viewInEditorButton = new Button();
+
   Panel jPanel1 = new Panel();
+
   BorderLayout borderLayout1 = new BorderLayout();
 
-  private void jbInit()
-      throws Exception
+  private void jbInit() throws Exception
   {
     this.setLayout(borderLayout1);
     textarea.setFont(new java.awt.Font("Monospaced", 0, 12));
diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
index 9881b64..9682000 100755
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/RedundancyPanel.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.appletgui;
 
 import java.util.*;
@@ -27,15 +26,19 @@ import java.awt.event.*;
 import jalview.commands.*;
 import jalview.datamodel.*;
 
-public class RedundancyPanel
-    extends SliderPanel implements Runnable, WindowListener
+public class RedundancyPanel extends SliderPanel implements Runnable,
+        WindowListener
 {
   AlignmentPanel ap;
 
   Stack historyList = new Stack(); // simpler than synching with alignFrame.
+
   float[] redundancy;
+
   SequenceI[] originalSequences;
+
   Frame frame;
+
   Vector redundantSeqs;
 
   public RedundancyPanel(AlignmentPanel ap)
@@ -67,8 +70,8 @@ public class RedundancyPanel
 
     frame = new Frame();
     frame.add(this);
-    jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",
-                                     400, 100);
+    jalview.bin.JalviewLite.addFrame(frame,
+            "Redundancy threshold selection", 400, 100);
 
     frame.addWindowListener(this);
 
@@ -77,13 +80,15 @@ public class RedundancyPanel
   }
 
   /**
-   * This is a copy of remove redundancy in jalivew.datamodel.Alignment
-   * except we dont want to remove redundancy, just calculate once
-   * so we can use the slider to dynamically hide redundant sequences
-   *
-   * @param threshold DOCUMENT ME!
-   * @param sel DOCUMENT ME!
-   *
+   * This is a copy of remove redundancy in jalivew.datamodel.Alignment except
+   * we dont want to remove redundancy, just calculate once so we can use the
+   * slider to dynamically hide redundant sequences
+   * 
+   * @param threshold
+   *                DOCUMENT ME!
+   * @param sel
+   *                DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   public void run()
@@ -103,7 +108,7 @@ public class RedundancyPanel
 
     int start, end;
 
-    if ( (sg != null) && (sg.getSize() >= 1))
+    if ((sg != null) && (sg.getSize() >= 1))
     {
       originalSequences = sg.getSequencesInOrder(ap.av.alignment);
       start = sg.getStartRes();
@@ -124,9 +129,9 @@ public class RedundancyPanel
       redundancy[i] = 0f;
     }
 
-    //  if (ap.av.hasHiddenColumns)
+    // if (ap.av.hasHiddenColumns)
     {
-      //   omitHidden = ap.av.getSelectionAsString();
+      // omitHidden = ap.av.getSelectionAsString();
     }
 
     // long start = System.currentTimeMillis();
@@ -198,10 +203,7 @@ public class RedundancyPanel
     }
 
     ap.idPanel.idCanvas.setHighlighted(redundantSeqs);
-    PaintRefresher.Refresh(this,
-                           ap.av.getSequenceSetId(),
-                           true,
-                           true);
+    PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
 
   }
 
@@ -222,7 +224,8 @@ public class RedundancyPanel
       }
     }
 
-    // This has to be done before the restoreHistoryItem method of alignFrame will
+    // This has to be done before the restoreHistoryItem method of alignFrame
+    // will
     // actually restore these sequences.
     if (del.size() > 0)
     {
@@ -239,16 +242,12 @@ public class RedundancyPanel
       }
 
       EditCommand cut = new EditCommand("Remove Redundancy",
-                                        EditCommand.CUT, deleted, 0, width,
-                                        ap.av.alignment);
+              EditCommand.CUT, deleted, 0, width, ap.av.alignment);
 
       for (int i = 0; i < del.size(); i++)
       {
         ap.av.alignment.deleteSequence(deleted[i]);
-        PaintRefresher.Refresh(this,
-                               ap.av.getSequenceSetId(),
-                               true,
-                               true);
+        PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
         if (sg != null)
         {
           sg.deleteSequence(deleted[i], false);
@@ -259,8 +258,8 @@ public class RedundancyPanel
 
       ap.alignFrame.addHistoryItem(cut);
 
-      ap.av.firePropertyChange("alignment", null,
-                               ap.av.getAlignment().getSequences());
+      ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+              .getSequences());
     }
 
   }
@@ -290,15 +289,15 @@ public class RedundancyPanel
     {
       int i = Integer.parseInt(valueField.getText());
       slider.setValue(i);
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       valueField.setText(slider.getValue() + "");
     }
   }
 
   public void windowOpened(WindowEvent evt)
-  {}
+  {
+  }
 
   public void windowClosing(WindowEvent evt)
   {
@@ -306,17 +305,22 @@ public class RedundancyPanel
   }
 
   public void windowClosed(WindowEvent evt)
-  {}
+  {
+  }
 
   public void windowActivated(WindowEvent evt)
-  {}
+  {
+  }
 
   public void windowDeactivated(WindowEvent evt)
-  {}
+  {
+  }
 
   public void windowIconified(WindowEvent evt)
-  {}
+  {
+  }
 
   public void windowDeiconified(WindowEvent evt)
-  {}
+  {
+  }
 }
diff --git a/src/jalview/appletgui/RotatableCanvas.java b/src/jalview/appletgui/RotatableCanvas.java
index a2463e8..4f54670 100755
--- a/src/jalview/appletgui/RotatableCanvas.java
+++ b/src/jalview/appletgui/RotatableCanvas.java
@@ -1,622 +1,641 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.appletgui;
-
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
-import jalview.math.*;
-import jalview.util.*;
-
-public class RotatableCanvas
-    extends Panel implements MouseListener,
-    MouseMotionListener,
-    KeyListener
-{
-  RotatableMatrix idmat = new RotatableMatrix(3, 3);
-  RotatableMatrix objmat = new RotatableMatrix(3, 3);
-  RotatableMatrix rotmat = new RotatableMatrix(3, 3);
-  String tooltip;
-  int toolx, tooly;
-
-  //RubberbandRectangle rubberband;
-
-  boolean drawAxes = true;
-
-  int omx = 0;
-  int mx = 0;
-  int omy = 0;
-  int my = 0;
-
-  Image img;
-  Graphics ig;
-
-  Dimension prefsize;
-
-  float centre[] = new float[3];
-  float width[] = new float[3];
-
-  float max[] = new float[3];
-  float min[] = new float[3];
-
-  float maxwidth;
-  float scale;
-
-  int npoint;
-
-  Vector points;
-  float[][] orig;
-  float[][] axes;
-
-  int startx;
-  int starty;
-
-  int lastx;
-  int lasty;
-
-  int rectx1;
-  int recty1;
-  int rectx2;
-  int recty2;
-
-  float scalefactor = 1;
-
-  AlignViewport av;
-  boolean showLabels = false;
-
-  public RotatableCanvas(AlignViewport av)
-  {
-    this.av = av;
-  }
-
-  public void showLabels(boolean b)
-  {
-    showLabels = b;
-    repaint();
-  }
-
-  public void setPoints(Vector points, int npoint)
-  {
-    this.points = points;
-    this.npoint = npoint;
-    PaintRefresher.Register(this, av.getSequenceSetId());
-
-    prefsize = getPreferredSize();
-    orig = new float[npoint][3];
-
-    for (int i = 0; i < npoint; i++)
-    {
-      SequencePoint sp = (SequencePoint) points.elementAt(i);
-      for (int j = 0; j < 3; j++)
-      {
-        orig[i][j] = sp.coord[j];
-      }
-    }
-    //Initialize the matrices to identity
-
-    for (int i = 0; i < 3; i++)
-    {
-      for (int j = 0; j < 3; j++)
-      {
-        if (i != j)
-        {
-          idmat.addElement(i, j, 0);
-          objmat.addElement(i, j, 0);
-          rotmat.addElement(i, j, 0);
-        }
-        else
-        {
-          idmat.addElement(i, j, 0);
-          objmat.addElement(i, j, 0);
-          rotmat.addElement(i, j, 0);
-        }
-      }
-    }
-
-    axes = new float[3][3];
-    initAxes();
-
-    findCentre();
-    findWidth();
-
-    scale = findScale();
-
-    //    System.out.println("Scale factor = " + scale);
-
-    addMouseListener(this);
-    addKeyListener(this);
-    // if (getParent() != null) {
-    //   getParent().addKeyListener(this);
-    //}
-    addMouseMotionListener(this);
-
-    // Add rubberband
-    //   rubberband  = new RubberbandRectangle(this);
-    //  rubberband.setActive(true);
-    //   rubberband.addListener(this);
-  }
-
-  /* public boolean handleSequenceSelectionEvent(SequenceSelectionEvent evt) {
-     redrawneeded = true;
-     repaint();
-     return true;
-   }
-
-   public void removeNotify() {
-     controller.removeListener(this);
-     super.removeNotify();
-   }*/
-
-  public void initAxes()
-  {
-    for (int i = 0; i < 3; i++)
-    {
-      for (int j = 0; j < 3; j++)
-      {
-        if (i != j)
-        {
-          axes[i][j] = 0;
-        }
-        else
-        {
-          axes[i][j] = 1;
-        }
-      }
-    }
-  }
-
-  public void findWidth()
-  {
-    max = new float[3];
-    min = new float[3];
-
-    max[0] = (float) - 1e30;
-    max[1] = (float) - 1e30;
-    max[2] = (float) - 1e30;
-
-    min[0] = (float) 1e30;
-    min[1] = (float) 1e30;
-    min[2] = (float) 1e30;
-
-    for (int i = 0; i < 3; i++)
-    {
-      for (int j = 0; j < npoint; j++)
-      {
-        SequencePoint sp = (SequencePoint) points.elementAt(j);
-        if (sp.coord[i] >= max[i])
-        {
-          max[i] = sp.coord[i];
-        }
-        if (sp.coord[i] <= min[i])
-        {
-          min[i] = sp.coord[i];
-        }
-      }
-    }
-
-    //    System.out.println("xmax " + max[0] + " min " + min[0]);
-    //System.out.println("ymax " + max[1] + " min " + min[1]);
-    //System.out.println("zmax " + max[2] + " min " + min[2]);
-
-    width[0] = Math.abs(max[0] - min[0]);
-    width[1] = Math.abs(max[1] - min[1]);
-    width[2] = Math.abs(max[2] - min[2]);
-
-    maxwidth = width[0];
-
-    if (width[1] > width[0])
-    {
-      maxwidth = width[1];
-    }
-    if (width[2] > width[1])
-    {
-      maxwidth = width[2];
-    }
-
-    //System.out.println("Maxwidth = " + maxwidth);
-  }
-
-  public float findScale()
-  {
-    int dim, width, height;
-    if (getSize().width != 0)
-    {
-      width = getSize().width;
-      height = getSize().height;
-    }
-    else
-    {
-      width = prefsize.width;
-      height = prefsize.height;
-    }
-
-    if (width < height)
-    {
-      dim = width;
-    }
-    else
-    {
-      dim = height;
-    }
-
-    return (float) (dim * scalefactor / (2 * maxwidth));
-  }
-
-  public void findCentre()
-  {
-    //Find centre coordinate
-    findWidth();
-
-    centre[0] = (max[0] + min[0]) / 2;
-    centre[1] = (max[1] + min[1]) / 2;
-    centre[2] = (max[2] + min[2]) / 2;
-
-    //    System.out.println("Centre x " + centre[0]);
-    //System.out.println("Centre y " + centre[1]);
-    //System.out.println("Centre z " + centre[2]);
-  }
-
-  public Dimension getPreferredSize()
-  {
-    if (prefsize != null)
-    {
-      return prefsize;
-    }
-    else
-    {
-      return new Dimension(400, 400);
-    }
-  }
-
-  public Dimension getMinimumSize()
-  {
-    return getPreferredSize();
-  }
-
-  public void update(Graphics g)
-  {
-    paint(g);
-  }
-
-  public void paint(Graphics g)
-  {
-    if (points == null)
-    {
-      g.setFont(new Font("Verdana", Font.PLAIN, 18));
-      g.drawString("Calculating PCA....", 20, getSize().height / 2);
-    }
-    else
-    {
-
-      //Only create the image at the beginning -
-      if ( (img == null) || (prefsize.width != getSize().width) ||
-          (prefsize.height != getSize().height))
-      {
-        prefsize.width = getSize().width;
-        prefsize.height = getSize().height;
-
-        scale = findScale();
-
-        //      System.out.println("New scale = " + scale);
-        img = createImage(getSize().width, getSize().height);
-        ig = img.getGraphics();
-
-      }
-
-      drawBackground(ig, Color.black);
-      drawScene(ig);
-      if (drawAxes == true)
-      {
-        drawAxes(ig);
-      }
-
-      if (tooltip != null)
-      {
-        ig.setColor(Color.red);
-        ig.drawString(tooltip, toolx, tooly);
-      }
-
-      g.drawImage(img, 0, 0, this);
-    }
-  }
-
-  public void drawAxes(Graphics g)
-  {
-
-    g.setColor(Color.yellow);
-    for (int i = 0; i < 3; i++)
-    {
-      g.drawLine(getSize().width / 2, getSize().height / 2,
-                 (int) (axes[i][0] * scale * max[0] + getSize().width / 2),
-                 (int) (axes[i][1] * scale * max[1] + getSize().height / 2));
-    }
-  }
-
-  public void drawBackground(Graphics g, Color col)
-  {
-    g.setColor(col);
-    g.fillRect(0, 0, prefsize.width, prefsize.height);
-  }
-
-  public void drawScene(Graphics g)
-  {
-    //boolean darker = false;
-
-    int halfwidth = getSize().width / 2;
-    int halfheight = getSize().height / 2;
-
-    for (int i = 0; i < npoint; i++)
-    {
-      SequencePoint sp = (SequencePoint) points.elementAt(i);
-      int x = (int) ( (float) (sp.coord[0] - centre[0]) * scale) + halfwidth;
-      int y = (int) ( (float) (sp.coord[1] - centre[1]) * scale) + halfheight;
-      float z = sp.coord[1] - centre[2];
-
-      if (av.getSequenceColour(sp.sequence) == Color.black)
-      {
-        g.setColor(Color.white);
-      }
-      else
-      {
-        g.setColor(av.getSequenceColour(sp.sequence));
-      }
-
-      if (av.getSelectionGroup() != null)
-      {
-        if (av.getSelectionGroup().getSequences(null).contains( ( (
-            SequencePoint) points.
-            elementAt(i)).sequence))
-        {
-          g.setColor(Color.gray);
-        }
-      }
-      if (z < 0)
-      {
-        g.setColor(g.getColor().darker());
-      }
-
-      g.fillRect(x - 3, y - 3, 6, 6);
-      if (showLabels)
-      {
-        g.setColor(Color.red);
-        g.drawString( ( (SequencePoint) points.elementAt(i)).sequence.
-                     getName(),
-                     x - 3, y - 4);
-      }
-    }
-  }
-
-  public Dimension minimumsize()
-  {
-    return prefsize;
-  }
-
-  public Dimension preferredsize()
-  {
-    return prefsize;
-  }
-
-  public void keyTyped(KeyEvent evt)
-  {}
-
-  public void keyReleased(KeyEvent evt)
-  {}
-
-  public void keyPressed(KeyEvent evt)
-  {
-    if (evt.getKeyCode() == KeyEvent.VK_UP)
-    {
-      scalefactor = (float) (scalefactor * 1.1);
-      scale = findScale();
-    }
-    else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
-    {
-      scalefactor = (float) (scalefactor * 0.9);
-      scale = findScale();
-    }
-    else if (evt.getKeyChar() == 's')
-    {
-      System.err.println("DEBUG: Rectangle selection"); // log.debug
-      if (rectx2 != -1 && recty2 != -1)
-      {
-        rectSelect(rectx1, recty1, rectx2, recty2);
-
-      }
-    }
-    repaint();
-  }
-
-  public void printPoints()
-  {
-    for (int i = 0; i < npoint; i++)
-    {
-      SequencePoint sp = (SequencePoint) points.elementAt(i);
-      Format.print(System.out, "%5d ", i);
-      for (int j = 0; j < 3; j++)
-      {
-        Format.print(System.out, "%13.3f  ", sp.coord[j]);
-      }
-      System.out.println();
-    }
-  }
-
-  public void mouseClicked(MouseEvent evt)
-  {}
-
-  public void mouseEntered(MouseEvent evt)
-  {}
-
-  public void mouseExited(MouseEvent evt)
-  {}
-
-  public void mouseReleased(MouseEvent evt)
-  {}
-
-  public void mousePressed(MouseEvent evt)
-  {
-    int x = evt.getX();
-    int y = evt.getY();
-
-    mx = x;
-    my = y;
-
-    omx = mx;
-    omy = my;
-
-    startx = x;
-    starty = y;
-
-    rectx1 = x;
-    recty1 = y;
-
-    rectx2 = -1;
-    recty2 = -1;
-
-    SequenceI found = findPoint(x, y);
-
-    if (found != null)
-    {
-      if (av.getSelectionGroup() != null)
-      {
-        av.getSelectionGroup().addOrRemove(found, true);
-        av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
-        PaintRefresher.Refresh(this, av.getSequenceSetId());
-      }
-      else
-      {
-        av.setSelectionGroup(new SequenceGroup());
-        av.getSelectionGroup().addOrRemove(found, true);
-        av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
-
-      }
-    }
-    repaint();
-  }
-
-  public void mouseMoved(MouseEvent evt)
-  {
-    SequenceI found = findPoint(evt.getX(), evt.getY());
-    if (found == null)
-    {
-      tooltip = null;
-    }
-    else
-    {
-      tooltip = found.getName();
-      toolx = evt.getX();
-      tooly = evt.getY();
-    }
-    repaint();
-  }
-
-  public void mouseDragged(MouseEvent evt)
-  {
-    mx = evt.getX();
-    my = evt.getY();
-
-    rotmat.setIdentity();
-
-    rotmat.rotate( (float) (my - omy), 'x');
-    rotmat.rotate( (float) (mx - omx), 'y');
-
-    for (int i = 0; i < npoint; i++)
-    {
-      SequencePoint sp = (SequencePoint) points.elementAt(i);
-      sp.coord[0] -= centre[0];
-      sp.coord[1] -= centre[1];
-      sp.coord[2] -= centre[2];
-
-      //Now apply the rotation matrix
-      sp.coord = rotmat.vectorMultiply(sp.coord);
-
-      //Now translate back again
-      sp.coord[0] += centre[0];
-      sp.coord[1] += centre[1];
-      sp.coord[2] += centre[2];
-    }
-
-    for (int i = 0; i < 3; i++)
-    {
-      axes[i] = rotmat.vectorMultiply(axes[i]);
-    }
-    omx = mx;
-    omy = my;
-
-    paint(this.getGraphics());
-  }
-
-  public void rectSelect(int x1, int y1, int x2, int y2)
-  {
-    //boolean changedSel = false;
-    for (int i = 0; i < npoint; i++)
-    {
-      SequencePoint sp = (SequencePoint) points.elementAt(i);
-      int tmp1 = (int) ( (sp.coord[0] - centre[0]) * scale +
-                        (float) getSize().width / 2.0);
-      int tmp2 = (int) ( (sp.coord[1] - centre[1]) * scale +
-                        (float) getSize().height / 2.0);
-
-      if (tmp1 > x1 && tmp1 < x2 && tmp2 > y1 && tmp2 < y2)
-      {
-        if (av != null)
-        {
-          if (!av.getSelectionGroup().getSequences(null).contains(sp.sequence))
-          {
-            av.getSelectionGroup().addSequence(sp.sequence, true);
-          }
-        }
-      }
-    }
-  }
-
-  public SequenceI findPoint(int x, int y)
-  {
-
-    int halfwidth = getSize().width / 2;
-    int halfheight = getSize().height / 2;
-
-    int found = -1;
-
-    for (int i = 0; i < npoint; i++)
-    {
-
-      SequencePoint sp = (SequencePoint) points.elementAt(i);
-      int px = (int) ( (float) (sp.coord[0] - centre[0]) * scale) + halfwidth;
-      int py = (int) ( (float) (sp.coord[1] - centre[1]) * scale) + halfheight;
-
-      if (Math.abs(px - x) < 3 && Math.abs(py - y) < 3)
-      {
-        found = i;
-      }
-    }
-    if (found != -1)
-    {
-      return ( (SequencePoint) points.elementAt(found)).sequence;
-    }
-    else
-    {
-      return null;
-    }
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.appletgui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import jalview.datamodel.*;
+import jalview.math.*;
+import jalview.util.*;
+
+public class RotatableCanvas extends Panel implements MouseListener,
+        MouseMotionListener, KeyListener
+{
+  RotatableMatrix idmat = new RotatableMatrix(3, 3);
+
+  RotatableMatrix objmat = new RotatableMatrix(3, 3);
+
+  RotatableMatrix rotmat = new RotatableMatrix(3, 3);
+
+  String tooltip;
+
+  int toolx, tooly;
+
+  // RubberbandRectangle rubberband;
+
+  boolean drawAxes = true;
+
+  int omx = 0;
+
+  int mx = 0;
+
+  int omy = 0;
+
+  int my = 0;
+
+  Image img;
+
+  Graphics ig;
+
+  Dimension prefsize;
+
+  float centre[] = new float[3];
+
+  float width[] = new float[3];
+
+  float max[] = new float[3];
+
+  float min[] = new float[3];
+
+  float maxwidth;
+
+  float scale;
+
+  int npoint;
+
+  Vector points;
+
+  float[][] orig;
+
+  float[][] axes;
+
+  int startx;
+
+  int starty;
+
+  int lastx;
+
+  int lasty;
+
+  int rectx1;
+
+  int recty1;
+
+  int rectx2;
+
+  int recty2;
+
+  float scalefactor = 1;
+
+  AlignViewport av;
+
+  boolean showLabels = false;
+
+  public RotatableCanvas(AlignViewport av)
+  {
+    this.av = av;
+  }
+
+  public void showLabels(boolean b)
+  {
+    showLabels = b;
+    repaint();
+  }
+
+  public void setPoints(Vector points, int npoint)
+  {
+    this.points = points;
+    this.npoint = npoint;
+    PaintRefresher.Register(this, av.getSequenceSetId());
+
+    prefsize = getPreferredSize();
+    orig = new float[npoint][3];
+
+    for (int i = 0; i < npoint; i++)
+    {
+      SequencePoint sp = (SequencePoint) points.elementAt(i);
+      for (int j = 0; j < 3; j++)
+      {
+        orig[i][j] = sp.coord[j];
+      }
+    }
+    // Initialize the matrices to identity
+
+    for (int i = 0; i < 3; i++)
+    {
+      for (int j = 0; j < 3; j++)
+      {
+        if (i != j)
+        {
+          idmat.addElement(i, j, 0);
+          objmat.addElement(i, j, 0);
+          rotmat.addElement(i, j, 0);
+        }
+        else
+        {
+          idmat.addElement(i, j, 0);
+          objmat.addElement(i, j, 0);
+          rotmat.addElement(i, j, 0);
+        }
+      }
+    }
+
+    axes = new float[3][3];
+    initAxes();
+
+    findCentre();
+    findWidth();
+
+    scale = findScale();
+
+    // System.out.println("Scale factor = " + scale);
+
+    addMouseListener(this);
+    addKeyListener(this);
+    // if (getParent() != null) {
+    // getParent().addKeyListener(this);
+    // }
+    addMouseMotionListener(this);
+
+    // Add rubberband
+    // rubberband = new RubberbandRectangle(this);
+    // rubberband.setActive(true);
+    // rubberband.addListener(this);
+  }
+
+  /*
+   * public boolean handleSequenceSelectionEvent(SequenceSelectionEvent evt) {
+   * redrawneeded = true; repaint(); return true; }
+   * 
+   * public void removeNotify() { controller.removeListener(this);
+   * super.removeNotify(); }
+   */
+
+  public void initAxes()
+  {
+    for (int i = 0; i < 3; i++)
+    {
+      for (int j = 0; j < 3; j++)
+      {
+        if (i != j)
+        {
+          axes[i][j] = 0;
+        }
+        else
+        {
+          axes[i][j] = 1;
+        }
+      }
+    }
+  }
+
+  public void findWidth()
+  {
+    max = new float[3];
+    min = new float[3];
+
+    max[0] = (float) -1e30;
+    max[1] = (float) -1e30;
+    max[2] = (float) -1e30;
+
+    min[0] = (float) 1e30;
+    min[1] = (float) 1e30;
+    min[2] = (float) 1e30;
+
+    for (int i = 0; i < 3; i++)
+    {
+      for (int j = 0; j < npoint; j++)
+      {
+        SequencePoint sp = (SequencePoint) points.elementAt(j);
+        if (sp.coord[i] >= max[i])
+        {
+          max[i] = sp.coord[i];
+        }
+        if (sp.coord[i] <= min[i])
+        {
+          min[i] = sp.coord[i];
+        }
+      }
+    }
+
+    // System.out.println("xmax " + max[0] + " min " + min[0]);
+    // System.out.println("ymax " + max[1] + " min " + min[1]);
+    // System.out.println("zmax " + max[2] + " min " + min[2]);
+
+    width[0] = Math.abs(max[0] - min[0]);
+    width[1] = Math.abs(max[1] - min[1]);
+    width[2] = Math.abs(max[2] - min[2]);
+
+    maxwidth = width[0];
+
+    if (width[1] > width[0])
+    {
+      maxwidth = width[1];
+    }
+    if (width[2] > width[1])
+    {
+      maxwidth = width[2];
+    }
+
+    // System.out.println("Maxwidth = " + maxwidth);
+  }
+
+  public float findScale()
+  {
+    int dim, width, height;
+    if (getSize().width != 0)
+    {
+      width = getSize().width;
+      height = getSize().height;
+    }
+    else
+    {
+      width = prefsize.width;
+      height = prefsize.height;
+    }
+
+    if (width < height)
+    {
+      dim = width;
+    }
+    else
+    {
+      dim = height;
+    }
+
+    return (float) (dim * scalefactor / (2 * maxwidth));
+  }
+
+  public void findCentre()
+  {
+    // Find centre coordinate
+    findWidth();
+
+    centre[0] = (max[0] + min[0]) / 2;
+    centre[1] = (max[1] + min[1]) / 2;
+    centre[2] = (max[2] + min[2]) / 2;
+
+    // System.out.println("Centre x " + centre[0]);
+    // System.out.println("Centre y " + centre[1]);
+    // System.out.println("Centre z " + centre[2]);
+  }
+
+  public Dimension getPreferredSize()
+  {
+    if (prefsize != null)
+    {
+      return prefsize;
+    }
+    else
+    {
+      return new Dimension(400, 400);
+    }
+  }
+
+  public Dimension getMinimumSize()
+  {
+    return getPreferredSize();
+  }
+
+  public void update(Graphics g)
+  {
+    paint(g);
+  }
+
+  public void paint(Graphics g)
+  {
+    if (points == null)
+    {
+      g.setFont(new Font("Verdana", Font.PLAIN, 18));
+      g.drawString("Calculating PCA....", 20, getSize().height / 2);
+    }
+    else
+    {
+
+      // Only create the image at the beginning -
+      if ((img == null) || (prefsize.width != getSize().width)
+              || (prefsize.height != getSize().height))
+      {
+        prefsize.width = getSize().width;
+        prefsize.height = getSize().height;
+
+        scale = findScale();
+
+        // System.out.println("New scale = " + scale);
+        img = createImage(getSize().width, getSize().height);
+        ig = img.getGraphics();
+
+      }
+
+      drawBackground(ig, Color.black);
+      drawScene(ig);
+      if (drawAxes == true)
+      {
+        drawAxes(ig);
+      }
+
+      if (tooltip != null)
+      {
+        ig.setColor(Color.red);
+        ig.drawString(tooltip, toolx, tooly);
+      }
+
+      g.drawImage(img, 0, 0, this);
+    }
+  }
+
+  public void drawAxes(Graphics g)
+  {
+
+    g.setColor(Color.yellow);
+    for (int i = 0; i < 3; i++)
+    {
+      g.drawLine(getSize().width / 2, getSize().height / 2,
+              (int) (axes[i][0] * scale * max[0] + getSize().width / 2),
+              (int) (axes[i][1] * scale * max[1] + getSize().height / 2));
+    }
+  }
+
+  public void drawBackground(Graphics g, Color col)
+  {
+    g.setColor(col);
+    g.fillRect(0, 0, prefsize.width, prefsize.height);
+  }
+
+  public void drawScene(Graphics g)
+  {
+    // boolean darker = false;
+
+    int halfwidth = getSize().width / 2;
+    int halfheight = getSize().height / 2;
+
+    for (int i = 0; i < npoint; i++)
+    {
+      SequencePoint sp = (SequencePoint) points.elementAt(i);
+      int x = (int) ((float) (sp.coord[0] - centre[0]) * scale) + halfwidth;
+      int y = (int) ((float) (sp.coord[1] - centre[1]) * scale)
+              + halfheight;
+      float z = sp.coord[1] - centre[2];
+
+      if (av.getSequenceColour(sp.sequence) == Color.black)
+      {
+        g.setColor(Color.white);
+      }
+      else
+      {
+        g.setColor(av.getSequenceColour(sp.sequence));
+      }
+
+      if (av.getSelectionGroup() != null)
+      {
+        if (av.getSelectionGroup().getSequences(null).contains(
+                ((SequencePoint) points.elementAt(i)).sequence))
+        {
+          g.setColor(Color.gray);
+        }
+      }
+      if (z < 0)
+      {
+        g.setColor(g.getColor().darker());
+      }
+
+      g.fillRect(x - 3, y - 3, 6, 6);
+      if (showLabels)
+      {
+        g.setColor(Color.red);
+        g.drawString(((SequencePoint) points.elementAt(i)).sequence
+                .getName(), x - 3, y - 4);
+      }
+    }
+  }
+
+  public Dimension minimumsize()
+  {
+    return prefsize;
+  }
+
+  public Dimension preferredsize()
+  {
+    return prefsize;
+  }
+
+  public void keyTyped(KeyEvent evt)
+  {
+  }
+
+  public void keyReleased(KeyEvent evt)
+  {
+  }
+
+  public void keyPressed(KeyEvent evt)
+  {
+    if (evt.getKeyCode() == KeyEvent.VK_UP)
+    {
+      scalefactor = (float) (scalefactor * 1.1);
+      scale = findScale();
+    }
+    else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
+    {
+      scalefactor = (float) (scalefactor * 0.9);
+      scale = findScale();
+    }
+    else if (evt.getKeyChar() == 's')
+    {
+      System.err.println("DEBUG: Rectangle selection"); // log.debug
+      if (rectx2 != -1 && recty2 != -1)
+      {
+        rectSelect(rectx1, recty1, rectx2, recty2);
+
+      }
+    }
+    repaint();
+  }
+
+  public void printPoints()
+  {
+    for (int i = 0; i < npoint; i++)
+    {
+      SequencePoint sp = (SequencePoint) points.elementAt(i);
+      Format.print(System.out, "%5d ", i);
+      for (int j = 0; j < 3; j++)
+      {
+        Format.print(System.out, "%13.3f  ", sp.coord[j]);
+      }
+      System.out.println();
+    }
+  }
+
+  public void mouseClicked(MouseEvent evt)
+  {
+  }
+
+  public void mouseEntered(MouseEvent evt)
+  {
+  }
+
+  public void mouseExited(MouseEvent evt)
+  {
+  }
+
+  public void mouseReleased(MouseEvent evt)
+  {
+  }
+
+  public void mousePressed(MouseEvent evt)
+  {
+    int x = evt.getX();
+    int y = evt.getY();
+
+    mx = x;
+    my = y;
+
+    omx = mx;
+    omy = my;
+
+    startx = x;
+    starty = y;
+
+    rectx1 = x;
+    recty1 = y;
+
+    rectx2 = -1;
+    recty2 = -1;
+
+    SequenceI found = findPoint(x, y);
+
+    if (found != null)
+    {
+      if (av.getSelectionGroup() != null)
+      {
+        av.getSelectionGroup().addOrRemove(found, true);
+        av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
+        PaintRefresher.Refresh(this, av.getSequenceSetId());
+      }
+      else
+      {
+        av.setSelectionGroup(new SequenceGroup());
+        av.getSelectionGroup().addOrRemove(found, true);
+        av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
+
+      }
+    }
+    repaint();
+  }
+
+  public void mouseMoved(MouseEvent evt)
+  {
+    SequenceI found = findPoint(evt.getX(), evt.getY());
+    if (found == null)
+    {
+      tooltip = null;
+    }
+    else
+    {
+      tooltip = found.getName();
+      toolx = evt.getX();
+      tooly = evt.getY();
+    }
+    repaint();
+  }
+
+  public void mouseDragged(MouseEvent evt)
+  {
+    mx = evt.getX();
+    my = evt.getY();
+
+    rotmat.setIdentity();
+
+    rotmat.rotate((float) (my - omy), 'x');
+    rotmat.rotate((float) (mx - omx), 'y');
+
+    for (int i = 0; i < npoint; i++)
+    {
+      SequencePoint sp = (SequencePoint) points.elementAt(i);
+      sp.coord[0] -= centre[0];
+      sp.coord[1] -= centre[1];
+      sp.coord[2] -= centre[2];
+
+      // Now apply the rotation matrix
+      sp.coord = rotmat.vectorMultiply(sp.coord);
+
+      // Now translate back again
+      sp.coord[0] += centre[0];
+      sp.coord[1] += centre[1];
+      sp.coord[2] += centre[2];
+    }
+
+    for (int i = 0; i < 3; i++)
+    {
+      axes[i] = rotmat.vectorMultiply(axes[i]);
+    }
+    omx = mx;
+    omy = my;
+
+    paint(this.getGraphics());
+  }
+
+  public void rectSelect(int x1, int y1, int x2, int y2)
+  {
+    // boolean changedSel = false;
+    for (int i = 0; i < npoint; i++)
+    {
+      SequencePoint sp = (SequencePoint) points.elementAt(i);
+      int tmp1 = (int) ((sp.coord[0] - centre[0]) * scale + (float) getSize().width / 2.0);
+      int tmp2 = (int) ((sp.coord[1] - centre[1]) * scale + (float) getSize().height / 2.0);
+
+      if (tmp1 > x1 && tmp1 < x2 && tmp2 > y1 && tmp2 < y2)
+      {
+        if (av != null)
+        {
+          if (!av.getSelectionGroup().getSequences(null).contains(
+                  sp.sequence))
+          {
+            av.getSelectionGroup().addSequence(sp.sequence, true);
+          }
+        }
+      }
+    }
+  }
+
+  public SequenceI findPoint(int x, int y)
+  {
+
+    int halfwidth = getSize().width / 2;
+    int halfheight = getSize().height / 2;
+
+    int found = -1;
+
+    for (int i = 0; i < npoint; i++)
+    {
+
+      SequencePoint sp = (SequencePoint) points.elementAt(i);
+      int px = (int) ((float) (sp.coord[0] - centre[0]) * scale)
+              + halfwidth;
+      int py = (int) ((float) (sp.coord[1] - centre[1]) * scale)
+              + halfheight;
+
+      if (Math.abs(px - x) < 3 && Math.abs(py - y) < 3)
+      {
+        found = i;
+      }
+    }
+    if (found != -1)
+    {
+      return ((SequencePoint) points.elementAt(found)).sequence;
+    }
+    else
+    {
+      return null;
+    }
+  }
+
+}
diff --git a/src/jalview/appletgui/ScalePanel.java b/src/jalview/appletgui/ScalePanel.java
index a1d0bf7..431bc66 100755
--- a/src/jalview/appletgui/ScalePanel.java
+++ b/src/jalview/appletgui/ScalePanel.java
@@ -1,453 +1,457 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.appletgui;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
-
-public class ScalePanel
-    extends Panel implements MouseMotionListener, MouseListener
-{
-
-  protected int offy = 4;
-  public int width;
-
-  protected AlignViewport av;
-  AlignmentPanel ap;
-
-  boolean stretchingGroup = false;
-  int min; //used by mouseDragged to see if user
-  int max; //used by mouseDragged to see if user
-  boolean mouseDragging = false;
-  int[] reveal;
-
-  public ScalePanel(AlignViewport av, AlignmentPanel ap)
-  {
-    setLayout(null);
-    this.av = av;
-    this.ap = ap;
-
-    addMouseListener(this);
-    addMouseMotionListener(this);
-
-  }
-
-  public void mousePressed(MouseEvent evt)
-  {
-    int x = (evt.getX() / av.getCharWidth()) + av.getStartRes();
-    final int res;
-
-    if (av.hasHiddenColumns)
-    {
-      res = av.getColumnSelection().adjustForHiddenColumns(x);
-    }
-    else
-    {
-      res = x;
-    }
-
-    min = res;
-    max = res;
-    if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK)
-        == InputEvent.BUTTON3_MASK)
-    {
-      PopupMenu pop = new PopupMenu();
-      if (reveal != null)
-      {
-        MenuItem item = new MenuItem("Reveal");
-        item.addActionListener(new ActionListener()
-        {
-          public void actionPerformed(ActionEvent e)
-          {
-            av.showColumn(reveal[0]);
-            reveal = null;
-            ap.paintAlignment(true);
-            if (ap.overviewPanel != null)
-            {
-              ap.overviewPanel.updateOverviewImage();
-            }
-          }
-        });
-        pop.add(item);
-
-        if (av.getColumnSelection().getHiddenColumns().size() > 1)
-        {
-          item = new MenuItem("Reveal All");
-          item.addActionListener(new ActionListener()
-          {
-            public void actionPerformed(ActionEvent e)
-            {
-              av.showAllHiddenColumns();
-              reveal = null;
-              ap.paintAlignment(true);
-              if (ap.overviewPanel != null)
-              {
-                ap.overviewPanel.updateOverviewImage();
-              }
-            }
-          });
-          pop.add(item);
-        }
-        this.add(pop);
-        pop.show(this, evt.getX(), evt.getY());
-      }
-      else if (av.getColumnSelection().contains(res))
-      {
-        MenuItem item = new MenuItem("Hide Columns");
-        item.addActionListener(new ActionListener()
-        {
-          public void actionPerformed(ActionEvent e)
-          {
-            av.hideColumns(res, res);
-            if (av.getSelectionGroup() != null
-                &&
-                av.getSelectionGroup().getSize() == av.alignment.getHeight())
-            {
-              av.setSelectionGroup(null);
-            }
-
-            ap.paintAlignment(true);
-            if (ap.overviewPanel != null)
-            {
-              ap.overviewPanel.updateOverviewImage();
-            }
-          }
-        });
-        pop.add(item);
-        this.add(pop);
-        pop.show(this, evt.getX(), evt.getY());
-      }
-    }
-    else // LEFT MOUSE TO SELECT
-    {
-      if (!evt.isControlDown() && !evt.isShiftDown())
-      {
-        av.getColumnSelection().clear();
-      }
-
-      av.getColumnSelection().addElement(res);
-      SequenceGroup sg = new SequenceGroup();
-      for (int i = 0; i < av.alignment.getSequences().size(); i++)
-      {
-        sg.addSequence(av.alignment.getSequenceAt(i), false);
-      }
-
-      sg.setStartRes(res);
-      sg.setEndRes(res);
-      av.setSelectionGroup(sg);
-
-      if (evt.isShiftDown())
-      {
-        int min = Math.min(av.getColumnSelection().getMin(), res);
-        int max = Math.max(av.getColumnSelection().getMax(), res);
-        for (int i = min; i < max; i++)
-        {
-          av.getColumnSelection().addElement(i);
-        }
-        sg.setStartRes(min);
-        sg.setEndRes(max);
-      }
-    }
-
-    ap.paintAlignment(true);
-  }
-
-  public void mouseReleased(MouseEvent evt)
-  {
-    mouseDragging = false;
-
-    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
-
-    if (res > av.alignment.getWidth())
-    {
-      res = av.alignment.getWidth() - 1;
-    }
-
-    if (av.hasHiddenColumns)
-    {
-      res = av.getColumnSelection().adjustForHiddenColumns(res);
-    }
-
-    if (!stretchingGroup)
-    {
-      ap.paintAlignment(false);
-
-      return;
-    }
-
-    SequenceGroup sg = av.getSelectionGroup();
-
-    if (res > sg.getStartRes())
-    {
-      sg.setEndRes(res);
-    }
-    else if (res < sg.getStartRes())
-    {
-      sg.setStartRes(res);
-    }
-
-    stretchingGroup = false;
-    ap.paintAlignment(false);
-  }
-
-  public void mouseDragged(MouseEvent evt)
-  {
-    mouseDragging = true;
-
-    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
-    if (res < 0)
-    {
-      res = 0;
-    }
-
-    if (av.hasHiddenColumns)
-    {
-      res = av.getColumnSelection().adjustForHiddenColumns(res);
-    }
-
-    if (res > av.alignment.getWidth())
-    {
-      res = av.alignment.getWidth() - 1;
-    }
-
-    if (res < min)
-    {
-      min = res;
-    }
-
-    if (res > max)
-    {
-      max = res;
-    }
-
-    SequenceGroup sg = av.getSelectionGroup();
-
-    if (sg != null)
-    {
-      stretchingGroup = true;
-
-      if (!av.getColumnSelection().contains(res))
-      {
-        av.getColumnSelection().addElement(res);
-      }
-
-      if (res > sg.getStartRes())
-      {
-        sg.setEndRes(res);
-      }
-      if (res < sg.getStartRes())
-      {
-        sg.setStartRes(res);
-      }
-
-      int col;
-      for (int i = min; i <= max; i++)
-      {
-        col = av.getColumnSelection().adjustForHiddenColumns(i);
-
-        if ( (col < sg.getStartRes()) || (col > sg.getEndRes()))
-        {
-          av.getColumnSelection().removeElement(col);
-        }
-        else
-        {
-          av.getColumnSelection().addElement(col);
-        }
-      }
-
-      ap.paintAlignment(false);
-    }
-  }
-
-  public void mouseEntered(MouseEvent evt)
-  {
-    if (mouseDragging)
-    {
-      ap.seqPanel.scrollCanvas(null);
-    }
-  }
-
-  public void mouseExited(MouseEvent evt)
-  {
-    if (mouseDragging)
-    {
-      ap.seqPanel.scrollCanvas(evt);
-    }
-  }
-
-  public void mouseClicked(MouseEvent evt)
-  {
-
-  }
-
-  public void mouseMoved(MouseEvent evt)
-  {
-    if (!av.hasHiddenColumns)
-    {
-      return;
-    }
-
-    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
-
-    res = av.getColumnSelection().adjustForHiddenColumns(res);
-
-    reveal = null;
-    for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
-    {
-      int[] region = (int[]) av.getColumnSelection().getHiddenColumns().
-          elementAt(i);
-      if (res + 1 == region[0] || res - 1 == region[1])
-      {
-        reveal = region;
-        break;
-      }
-    }
-
-    repaint();
-  }
-
-  public void update(Graphics g)
-  {
-    paint(g);
-  }
-
-  public void paint(Graphics g)
-  {
-    drawScale(g, av.getStartRes(), av.getEndRes(), getSize().width,
-              getSize().height);
-  }
-
-// scalewidth will normally be screenwidth,
-  public void drawScale(Graphics gg, int startx, int endx, int width,
-                        int height)
-  {
-    gg.setFont(av.getFont());
-
-    //Fill in the background
-    gg.setColor(Color.white);
-    gg.fillRect(0, 0, width, height);
-    gg.setColor(Color.black);
-
-    //Fill the selected columns
-    ColumnSelection cs = av.getColumnSelection();
-    gg.setColor(new Color(220, 0, 0));
-
-    for (int i = 0; i < cs.size(); i++)
-    {
-      int sel = cs.columnAt(i);
-      if (av.hasHiddenColumns)
-      {
-        sel = av.getColumnSelection().findColumnPosition(sel);
-      }
-
-      if ( (sel >= startx) && (sel <= endx))
-      {
-        gg.fillRect( (sel - startx) * av.charWidth, 0, av.charWidth,
-                    getSize().height);
-      }
-    }
-
-    // Draw the scale numbers
-    gg.setColor(Color.black);
-
-    int scalestartx = (startx / 10) * 10;
-
-    FontMetrics fm = gg.getFontMetrics(av.getFont());
-    int y = av.charHeight - fm.getDescent();
-
-    if ( (scalestartx % 10) == 0)
-    {
-      scalestartx += 5;
-    }
-
-    String string;
-    int maxX = 0;
-
-    for (int i = scalestartx; i < endx; i += 5)
-    {
-      if ( (i % 10) == 0)
-      {
-        string = String.valueOf(av.getColumnSelection().adjustForHiddenColumns(
-            i));
-        if ( (i - startx - 1) * av.charWidth > maxX)
-        {
-          gg.drawString(string,
-                        (i - startx - 1) * av.charWidth, y);
-          maxX = (i - startx + 1) * av.charWidth + fm.stringWidth(string);
-        }
-
-        gg.drawLine( (int) ( ( (i - startx - 1) * av.charWidth) +
-                            (av.charWidth / 2)), y + 2,
-                    (int) ( ( (i - startx - 1) * av.charWidth) +
-                           (av.charWidth / 2)),
-                    y + (fm.getDescent() * 2));
-
-      }
-      else
-      {
-        gg.drawLine( (int) ( ( (i - startx - 1) * av.charWidth) +
-                            (av.charWidth / 2)), y + fm.getDescent(),
-                    (int) ( ( (i - startx - 1) * av.charWidth) +
-                           (av.charWidth / 2)), y + (fm.getDescent() * 2));
-      }
-    }
-
-    if (av.hasHiddenColumns)
-    {
-      gg.setColor(Color.blue);
-      int res;
-      if (av.getShowHiddenMarkers())
-      {
-        for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size();
-             i++)
-        {
-
-          res = av.getColumnSelection().findHiddenRegionPosition(i) -
-              startx;
-
-          if (res < 0 || res > endx - scalestartx)
-          {
-            continue;
-          }
-
-          gg.fillPolygon(new int[]
-                         {res * av.charWidth - av.charHeight / 4,
-                         res * av.charWidth + av.charHeight / 4,
-                         res * av.charWidth},
-                         new int[]
-                         {
-                         y - av.charHeight / 2, y - av.charHeight / 2,
-                         y + 8
-          }, 3);
-
-        }
-      }
-
-      if (reveal != null && reveal[0] > startx && reveal[0] < endx)
-      {
-        gg.drawString("Reveal Columns", reveal[0] * av.charWidth, 0);
-      }
-    }
-
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.appletgui;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import jalview.datamodel.*;
+
+public class ScalePanel extends Panel implements MouseMotionListener,
+        MouseListener
+{
+
+  protected int offy = 4;
+
+  public int width;
+
+  protected AlignViewport av;
+
+  AlignmentPanel ap;
+
+  boolean stretchingGroup = false;
+
+  int min; // used by mouseDragged to see if user
+
+  int max; // used by mouseDragged to see if user
+
+  boolean mouseDragging = false;
+
+  int[] reveal;
+
+  public ScalePanel(AlignViewport av, AlignmentPanel ap)
+  {
+    setLayout(null);
+    this.av = av;
+    this.ap = ap;
+
+    addMouseListener(this);
+    addMouseMotionListener(this);
+
+  }
+
+  public void mousePressed(MouseEvent evt)
+  {
+    int x = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    final int res;
+
+    if (av.hasHiddenColumns)
+    {
+      res = av.getColumnSelection().adjustForHiddenColumns(x);
+    }
+    else
+    {
+      res = x;
+    }
+
+    min = res;
+    max = res;
+    if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+    {
+      PopupMenu pop = new PopupMenu();
+      if (reveal != null)
+      {
+        MenuItem item = new MenuItem("Reveal");
+        item.addActionListener(new ActionListener()
+        {
+          public void actionPerformed(ActionEvent e)
+          {
+            av.showColumn(reveal[0]);
+            reveal = null;
+            ap.paintAlignment(true);
+            if (ap.overviewPanel != null)
+            {
+              ap.overviewPanel.updateOverviewImage();
+            }
+          }
+        });
+        pop.add(item);
+
+        if (av.getColumnSelection().getHiddenColumns().size() > 1)
+        {
+          item = new MenuItem("Reveal All");
+          item.addActionListener(new ActionListener()
+          {
+            public void actionPerformed(ActionEvent e)
+            {
+              av.showAllHiddenColumns();
+              reveal = null;
+              ap.paintAlignment(true);
+              if (ap.overviewPanel != null)
+              {
+                ap.overviewPanel.updateOverviewImage();
+              }
+            }
+          });
+          pop.add(item);
+        }
+        this.add(pop);
+        pop.show(this, evt.getX(), evt.getY());
+      }
+      else if (av.getColumnSelection().contains(res))
+      {
+        MenuItem item = new MenuItem("Hide Columns");
+        item.addActionListener(new ActionListener()
+        {
+          public void actionPerformed(ActionEvent e)
+          {
+            av.hideColumns(res, res);
+            if (av.getSelectionGroup() != null
+                    && av.getSelectionGroup().getSize() == av.alignment
+                            .getHeight())
+            {
+              av.setSelectionGroup(null);
+            }
+
+            ap.paintAlignment(true);
+            if (ap.overviewPanel != null)
+            {
+              ap.overviewPanel.updateOverviewImage();
+            }
+          }
+        });
+        pop.add(item);
+        this.add(pop);
+        pop.show(this, evt.getX(), evt.getY());
+      }
+    }
+    else
+    // LEFT MOUSE TO SELECT
+    {
+      if (!evt.isControlDown() && !evt.isShiftDown())
+      {
+        av.getColumnSelection().clear();
+      }
+
+      av.getColumnSelection().addElement(res);
+      SequenceGroup sg = new SequenceGroup();
+      for (int i = 0; i < av.alignment.getSequences().size(); i++)
+      {
+        sg.addSequence(av.alignment.getSequenceAt(i), false);
+      }
+
+      sg.setStartRes(res);
+      sg.setEndRes(res);
+      av.setSelectionGroup(sg);
+
+      if (evt.isShiftDown())
+      {
+        int min = Math.min(av.getColumnSelection().getMin(), res);
+        int max = Math.max(av.getColumnSelection().getMax(), res);
+        for (int i = min; i < max; i++)
+        {
+          av.getColumnSelection().addElement(i);
+        }
+        sg.setStartRes(min);
+        sg.setEndRes(max);
+      }
+    }
+
+    ap.paintAlignment(true);
+  }
+
+  public void mouseReleased(MouseEvent evt)
+  {
+    mouseDragging = false;
+
+    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+
+    if (res > av.alignment.getWidth())
+    {
+      res = av.alignment.getWidth() - 1;
+    }
+
+    if (av.hasHiddenColumns)
+    {
+      res = av.getColumnSelection().adjustForHiddenColumns(res);
+    }
+
+    if (!stretchingGroup)
+    {
+      ap.paintAlignment(false);
+
+      return;
+    }
+
+    SequenceGroup sg = av.getSelectionGroup();
+
+    if (res > sg.getStartRes())
+    {
+      sg.setEndRes(res);
+    }
+    else if (res < sg.getStartRes())
+    {
+      sg.setStartRes(res);
+    }
+
+    stretchingGroup = false;
+    ap.paintAlignment(false);
+  }
+
+  public void mouseDragged(MouseEvent evt)
+  {
+    mouseDragging = true;
+
+    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    if (res < 0)
+    {
+      res = 0;
+    }
+
+    if (av.hasHiddenColumns)
+    {
+      res = av.getColumnSelection().adjustForHiddenColumns(res);
+    }
+
+    if (res > av.alignment.getWidth())
+    {
+      res = av.alignment.getWidth() - 1;
+    }
+
+    if (res < min)
+    {
+      min = res;
+    }
+
+    if (res > max)
+    {
+      max = res;
+    }
+
+    SequenceGroup sg = av.getSelectionGroup();
+
+    if (sg != null)
+    {
+      stretchingGroup = true;
+
+      if (!av.getColumnSelection().contains(res))
+      {
+        av.getColumnSelection().addElement(res);
+      }
+
+      if (res > sg.getStartRes())
+      {
+        sg.setEndRes(res);
+      }
+      if (res < sg.getStartRes())
+      {
+        sg.setStartRes(res);
+      }
+
+      int col;
+      for (int i = min; i <= max; i++)
+      {
+        col = av.getColumnSelection().adjustForHiddenColumns(i);
+
+        if ((col < sg.getStartRes()) || (col > sg.getEndRes()))
+        {
+          av.getColumnSelection().removeElement(col);
+        }
+        else
+        {
+          av.getColumnSelection().addElement(col);
+        }
+      }
+
+      ap.paintAlignment(false);
+    }
+  }
+
+  public void mouseEntered(MouseEvent evt)
+  {
+    if (mouseDragging)
+    {
+      ap.seqPanel.scrollCanvas(null);
+    }
+  }
+
+  public void mouseExited(MouseEvent evt)
+  {
+    if (mouseDragging)
+    {
+      ap.seqPanel.scrollCanvas(evt);
+    }
+  }
+
+  public void mouseClicked(MouseEvent evt)
+  {
+
+  }
+
+  public void mouseMoved(MouseEvent evt)
+  {
+    if (!av.hasHiddenColumns)
+    {
+      return;
+    }
+
+    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+
+    res = av.getColumnSelection().adjustForHiddenColumns(res);
+
+    reveal = null;
+    for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
+    {
+      int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
+              .elementAt(i);
+      if (res + 1 == region[0] || res - 1 == region[1])
+      {
+        reveal = region;
+        break;
+      }
+    }
+
+    repaint();
+  }
+
+  public void update(Graphics g)
+  {
+    paint(g);
+  }
+
+  public void paint(Graphics g)
+  {
+    drawScale(g, av.getStartRes(), av.getEndRes(), getSize().width,
+            getSize().height);
+  }
+
+  // scalewidth will normally be screenwidth,
+  public void drawScale(Graphics gg, int startx, int endx, int width,
+          int height)
+  {
+    gg.setFont(av.getFont());
+
+    // Fill in the background
+    gg.setColor(Color.white);
+    gg.fillRect(0, 0, width, height);
+    gg.setColor(Color.black);
+
+    // Fill the selected columns
+    ColumnSelection cs = av.getColumnSelection();
+    gg.setColor(new Color(220, 0, 0));
+
+    for (int i = 0; i < cs.size(); i++)
+    {
+      int sel = cs.columnAt(i);
+      if (av.hasHiddenColumns)
+      {
+        sel = av.getColumnSelection().findColumnPosition(sel);
+      }
+
+      if ((sel >= startx) && (sel <= endx))
+      {
+        gg.fillRect((sel - startx) * av.charWidth, 0, av.charWidth,
+                getSize().height);
+      }
+    }
+
+    // Draw the scale numbers
+    gg.setColor(Color.black);
+
+    int scalestartx = (startx / 10) * 10;
+
+    FontMetrics fm = gg.getFontMetrics(av.getFont());
+    int y = av.charHeight - fm.getDescent();
+
+    if ((scalestartx % 10) == 0)
+    {
+      scalestartx += 5;
+    }
+
+    String string;
+    int maxX = 0;
+
+    for (int i = scalestartx; i < endx; i += 5)
+    {
+      if ((i % 10) == 0)
+      {
+        string = String.valueOf(av.getColumnSelection()
+                .adjustForHiddenColumns(i));
+        if ((i - startx - 1) * av.charWidth > maxX)
+        {
+          gg.drawString(string, (i - startx - 1) * av.charWidth, y);
+          maxX = (i - startx + 1) * av.charWidth + fm.stringWidth(string);
+        }
+
+        gg
+                .drawLine(
+                        (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
+                        y + 2,
+                        (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
+                        y + (fm.getDescent() * 2));
+
+      }
+      else
+      {
+        gg
+                .drawLine(
+                        (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
+                        y + fm.getDescent(),
+                        (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
+                        y + (fm.getDescent() * 2));
+      }
+    }
+
+    if (av.hasHiddenColumns)
+    {
+      gg.setColor(Color.blue);
+      int res;
+      if (av.getShowHiddenMarkers())
+      {
+        for (int i = 0; i < av.getColumnSelection().getHiddenColumns()
+                .size(); i++)
+        {
+
+          res = av.getColumnSelection().findHiddenRegionPosition(i)
+                  - startx;
+
+          if (res < 0 || res > endx - scalestartx)
+          {
+            continue;
+          }
+
+          gg.fillPolygon(new int[]
+          { res * av.charWidth - av.charHeight / 4,
+              res * av.charWidth + av.charHeight / 4, res * av.charWidth },
+                  new int[]
+                  { y - av.charHeight / 2, y - av.charHeight / 2, y + 8 },
+                  3);
+
+        }
+      }
+
+      if (reveal != null && reveal[0] > startx && reveal[0] < endx)
+      {
+        gg.drawString("Reveal Columns", reveal[0] * av.charWidth, 0);
+      }
+    }
+
+  }
+
+}
diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 5fb956c..68b8501 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -1,825 +1,818 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.appletgui;
-
-import java.awt.*;
-
-import jalview.datamodel.*;
-
-public class SeqCanvas
-    extends Panel
-{
-  FeatureRenderer fr;
-  SequenceRenderer sr;
-  Image img;
-  Graphics gg;
-  int imgWidth;
-  int imgHeight;
-
-  AlignViewport av;
-
-  SearchResults searchResults = null;
-
-  boolean fastPaint = false;
-
-  int cursorX = 0;
-  int cursorY = 0;
-
-  public SeqCanvas(AlignViewport av)
-  {
-    this.av = av;
-    fr = new FeatureRenderer(av);
-    sr = new SequenceRenderer(av);
-    PaintRefresher.Register(this, av.getSequenceSetId());
-  }
-
-  public AlignViewport getViewport()
-  {
-    return av;
-  }
-
-  public FeatureRenderer getFeatureRenderer()
-  {
-    return fr;
-  }
-
-  public SequenceRenderer getSequenceRenderer()
-  {
-    return sr;
-  }
-
-  void drawNorthScale(Graphics g, int startx, int endx, int ypos)
-  {
-    int scalestartx = startx - startx % 10 + 10;
-
-    g.setColor(Color.black);
-
-    // NORTH SCALE
-    for (int i = scalestartx; i < endx; i += 10)
-    {
-      int value = i;
-      if (av.hasHiddenColumns)
-      {
-        value = av.getColumnSelection().adjustForHiddenColumns(value);
-      }
-
-      g.drawString(String.valueOf(value), (i - startx - 1) * av.charWidth,
-                   ypos - (av.charHeight / 2));
-
-      g.drawLine( ( (i - startx - 1) * av.charWidth) + (av.charWidth / 2),
-                 (ypos + 2) - (av.charHeight / 2),
-                 ( (i - startx - 1) * av.charWidth) + (av.charWidth / 2), ypos -
-                 2);
-    }
-  }
-
-  void drawWestScale(Graphics g, int startx, int endx, int ypos)
-  {
-    FontMetrics fm = getFontMetrics(av.getFont());
-    ypos += av.charHeight;
-    if (av.hasHiddenColumns)
-    {
-      startx = av.getColumnSelection().adjustForHiddenColumns(startx);
-      endx = av.getColumnSelection().adjustForHiddenColumns(endx);
-    }
-
-    int maxwidth = av.alignment.getWidth();
-    if (av.hasHiddenColumns)
-    {
-      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
-    }
-
-    // WEST SCALE
-    for (int i = 0; i < av.alignment.getHeight(); i++)
-    {
-      SequenceI seq = av.alignment.getSequenceAt(i);
-      int index = startx;
-      int value = -1;
-
-      while (index < endx)
-      {
-        if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
-        {
-          index++;
-
-          continue;
-        }
-
-        value = av.alignment.getSequenceAt(i).findPosition(index);
-
-        break;
-      }
-
-      if (value != -1)
-      {
-        int x = LABEL_WEST - fm.stringWidth(String.valueOf(value)) -
-            av.charWidth / 2;
-        g.drawString(value + "", x,
-                     (ypos + (i * av.charHeight)) - (av.charHeight / 5));
-      }
-    }
-  }
-
-  void drawEastScale(Graphics g, int startx, int endx, int ypos)
-  {
-    ypos += av.charHeight;
-
-    if (av.hasHiddenColumns)
-    {
-      endx = av.getColumnSelection().adjustForHiddenColumns(endx);
-    }
-
-    SequenceI seq;
-    // EAST SCALE
-    for (int i = 0; i < av.alignment.getHeight(); i++)
-    {
-      seq = av.alignment.getSequenceAt(i);
-      int index = endx;
-      int value = -1;
-
-      while (index > startx)
-      {
-        if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
-        {
-          index--;
-
-          continue;
-        }
-
-        value = seq.findPosition(index);
-
-        break;
-      }
-
-      if (value != -1)
-      {
-        g.drawString(String.valueOf(value), 0,
-                     (ypos + (i * av.charHeight)) - (av.charHeight / 5));
-      }
-    }
-  }
-
-  int lastsr = 0;
-  void fastPaint(int horizontal, int vertical)
-  {
-    if (fastPaint || gg == null)
-    {
-      return;
-    }
-
-    // Its possible on certain browsers that the call to fastpaint
-    // is faster than it can paint, so this check here catches
-    // this possibility
-    if (lastsr + horizontal != av.startRes)
-    {
-      horizontal = av.startRes - lastsr;
-    }
-
-    lastsr = av.startRes;
-
-    fastPaint = true;
-    gg.copyArea(horizontal * av.charWidth,
-                vertical * av.charHeight,
-                imgWidth - horizontal * av.charWidth,
-                imgHeight - vertical * av.charHeight,
-                -horizontal * av.charWidth,
-                -vertical * av.charHeight);
-
-    int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq,
-        transX = 0, transY = 0;
-
-    if (horizontal > 0) // scrollbar pulled right, image to the left
-    {
-      transX = (er - sr - horizontal) * av.charWidth;
-      sr = er - horizontal;
-    }
-    else if (horizontal < 0)
-    {
-      er = sr - horizontal;
-    }
-
-    else if (vertical > 0) // scroll down
-    {
-      ss = es - vertical;
-      if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time
-      {
-        ss = av.startSeq;
-      }
-      else
-      {
-        transY = imgHeight - vertical * av.charHeight;
-      }
-    }
-    else if (vertical < 0)
-    {
-      es = ss - vertical;
-      if (es > av.endSeq)
-      {
-        es = av.endSeq;
-      }
-    }
-
-    gg.translate(transX, transY);
-
-    drawPanel(gg, sr, er, ss, es, 0);
-    gg.translate( -transX, -transY);
-
-    repaint();
-
-  }
-
-  /**
-   * Definitions of startx and endx (hopefully):
-   * SMJS This is what I'm working towards!
-   *   startx is the first residue (starting at 0) to display.
-   *   endx   is the last residue to display (starting at 0).
-   *   starty is the first sequence to display (starting at 0).
-   *   endy   is the last sequence to display (starting at 0).
-   * NOTE 1: The av limits are set in setFont in this class and
-   * in the adjustment listener in SeqPanel when the scrollbars move.
-   */
-  public void update(Graphics g)
-  {
-    paint(g);
-  }
-
-  public void paint(Graphics g)
-  {
-
-    if (img != null && (fastPaint
-                        || (getSize().width != g.getClipBounds().width)
-                        || (getSize().height != g.getClipBounds().height)))
-    {
-      g.drawImage(img, 0, 0, this);
-      fastPaint = false;
-      return;
-    }
-
-    if (fastPaint)
-    {
-      g.drawImage(img, 0, 0, this);
-      fastPaint = false;
-      return;
-    }
-
-    // this draws the whole of the alignment
-    imgWidth = this.getSize().width;
-    imgHeight = this.getSize().height;
-
-    imgWidth -= imgWidth % av.charWidth;
-    imgHeight -= imgHeight % av.charHeight;
-
-    if (imgWidth < 1 || imgHeight < 1)
-    {
-      return;
-    }
-
-    if (img == null || imgWidth != img.getWidth(this) ||
-        imgHeight != img.getHeight(this))
-    {
-      img = createImage(imgWidth, imgHeight);
-      gg = img.getGraphics();
-      gg.setFont(av.getFont());
-    }
-
-    gg.setColor(Color.white);
-    gg.fillRect(0, 0, imgWidth, imgHeight);
-
-    if (av.getWrapAlignment())
-    {
-      drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes);
-    }
-    else
-    {
-      drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);
-    }
-
-    g.drawImage(img, 0, 0, this);
-
-  }
-
-  int LABEL_WEST, LABEL_EAST;
-  public int getWrappedCanvasWidth(int cwidth)
-  {
-    cwidth -= cwidth % av.charWidth;
-
-    FontMetrics fm = getFontMetrics(av.getFont());
-
-    LABEL_EAST = 0;
-    LABEL_WEST = 0;
-
-    if (av.scaleRightWrapped)
-    {
-      LABEL_EAST = fm.stringWidth(getMask());
-    }
-
-    if (av.scaleLeftWrapped)
-    {
-      LABEL_WEST = fm.stringWidth(getMask());
-    }
-
-    return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
-  }
-
-  /**
-   * Generates a string of zeroes.
-   * @return String
-   */
-  String getMask()
-  {
-    String mask = "0";
-    int maxWidth = 0;
-    int tmp;
-    for (int i = 0; i < av.alignment.getHeight(); i++)
-    {
-      tmp = av.alignment.getSequenceAt(i).getEnd();
-      if (tmp > maxWidth)
-      {
-        maxWidth = tmp;
-      }
-    }
-
-    for (int i = maxWidth; i > 0; i /= 10)
-    {
-      mask += "0";
-    }
-    return mask;
-  }
-
-  public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,
-                               int startRes)
-  {
-    AlignmentI al = av.getAlignment();
-
-    FontMetrics fm = getFontMetrics(av.getFont());
-
-    if (av.scaleRightWrapped)
-    {
-      LABEL_EAST = fm.stringWidth(getMask());
-    }
-
-    if (av.scaleLeftWrapped)
-    {
-      LABEL_WEST = fm.stringWidth(getMask());
-    }
-
-    int hgap = av.charHeight;
-    if (av.scaleAboveWrapped)
-    {
-      hgap += av.charHeight;
-    }
-
-    int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
-    int cHeight = av.getAlignment().getHeight() * av.charHeight;
-
-    av.setWrappedWidth(cWidth);
-
-    av.endRes = av.startRes + cWidth;
-
-    int endx;
-    int ypos = hgap;
-
-    int maxwidth = av.alignment.getWidth() - 1;
-
-    if (av.hasHiddenColumns)
-    {
-      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
-    }
-
-    while ( (ypos <= canvasHeight) && (startRes < maxwidth))
-    {
-      endx = startRes + cWidth - 1;
-
-      if (endx > maxwidth)
-      {
-        endx = maxwidth;
-      }
-
-      g.setColor(Color.black);
-
-      if (av.scaleLeftWrapped)
-      {
-        drawWestScale(g, startRes, endx, ypos);
-      }
-
-      if (av.scaleRightWrapped)
-      {
-        g.translate(canvasWidth - LABEL_EAST, 0);
-        drawEastScale(g, startRes, endx, ypos);
-        g.translate( - (canvasWidth - LABEL_EAST), 0);
-      }
-
-      g.translate(LABEL_WEST, 0);
-
-      if (av.scaleAboveWrapped)
-      {
-        drawNorthScale(g, startRes, endx, ypos);
-      }
-      if (av.hasHiddenColumns && av.showHiddenMarkers)
-      {
-        g.setColor(Color.blue);
-        int res;
-        for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size();
-             i++)
-        {
-          res = av.getColumnSelection().findHiddenRegionPosition(i) -
-              startRes;
-
-          if (res < 0 || res > endx - startRes)
-          {
-            continue;
-          }
-
-          gg.fillPolygon(new int[]
-                         {res * av.charWidth - av.charHeight / 4,
-                         res * av.charWidth + av.charHeight / 4,
-                         res * av.charWidth},
-                         new int[]
-                         {
-                         ypos - (av.charHeight / 2),
-                         ypos - (av.charHeight / 2),
-                         ypos - (av.charHeight / 2) + 8
-          }, 3);
-
-        }
-      }
-
-      if (g.getClip() == null)
-      {
-        g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);
-      }
-
-      drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
-      g.setClip(null);
-
-      if (av.showAnnotation)
-      {
-        g.translate(0, cHeight + ypos + 4);
-        if (annotations == null)
-        {
-          annotations = new AnnotationPanel(av);
-        }
-
-        annotations.drawComponent(g, startRes, endx + 1);
-        g.translate(0, -cHeight - ypos - 4);
-      }
-      g.translate( -LABEL_WEST, 0);
-
-      ypos += cHeight + getAnnotationHeight() + hgap;
-
-      startRes += cWidth;
-    }
-
-  }
-
-  AnnotationPanel annotations;
-  int getAnnotationHeight()
-  {
-    if (!av.showAnnotation)
-    {
-      return 0;
-    }
-
-    if (annotations == null)
-    {
-      annotations = new AnnotationPanel(av);
-    }
-
-    return annotations.adjustPanelHeight();
-  }
-
-  void drawPanel(Graphics g1, int startRes, int endRes,
-                 int startSeq, int endSeq, int offset)
-  {
-    if (!av.hasHiddenColumns)
-    {
-      draw(g1, startRes, endRes, startSeq, endSeq, offset);
-    }
-    else
-    {
-      java.util.Vector regions = av.getColumnSelection().getHiddenColumns();
-
-      int screenY = 0;
-      int blockStart = startRes;
-      int blockEnd = endRes;
-
-      for (int i = 0; i < regions.size(); i++)
-      {
-        int[] region = (int[]) regions.elementAt(i);
-        int hideStart = region[0];
-        int hideEnd = region[1];
-
-        if (hideStart <= blockStart)
-        {
-          blockStart += (hideEnd - hideStart) + 1;
-          continue;
-        }
-
-        blockEnd = hideStart - 1;
-
-        g1.translate(screenY * av.charWidth, 0);
-
-        draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
-
-        if (av.getShowHiddenMarkers())
-        {
-          g1.setColor(Color.blue);
-          g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth - 1,
-                      0 + offset,
-                      (blockEnd - blockStart + 1) * av.charWidth - 1,
-                      (endSeq - startSeq) * av.charHeight + offset);
-        }
-
-        g1.translate( -screenY * av.charWidth, 0);
-        screenY += blockEnd - blockStart + 1;
-        blockStart = hideEnd + 1;
-      }
-
-      if (screenY <= (endRes - startRes))
-      {
-        blockEnd = blockStart + (endRes - startRes) - screenY;
-        g1.translate(screenY * av.charWidth, 0);
-        draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
-
-        g1.translate( -screenY * av.charWidth, 0);
-      }
-    }
-
-  }
-
-  //int startRes, int endRes, int startSeq, int endSeq, int x, int y,
-  // int x1, int x2, int y1, int y2, int startx, int starty,
-  void draw(Graphics g,
-            int startRes, int endRes,
-            int startSeq, int endSeq,
-            int offset)
-  {
-    g.setFont(av.getFont());
-    sr.prepare(g, av.renderGaps);
-
-    SequenceI nextSeq;
-
-    /// First draw the sequences
-    /////////////////////////////
-    for (int i = startSeq; i < endSeq; i++)
-    {
-      nextSeq = av.alignment.getSequenceAt(i);
-
-      if (nextSeq == null)
-      {
-        continue;
-      }
-
-      sr.drawSequence(nextSeq, av.alignment.findAllGroups(nextSeq),
-                      startRes, endRes,
-                      offset + ( (i - startSeq) * av.charHeight));
-
-      if (av.showSequenceFeatures)
-      {
-        fr.drawSequence(g, nextSeq, startRes, endRes,
-                        offset + ( (i - startSeq) * av.charHeight));
-      }
-
-      /// Highlight search Results once all sequences have been drawn
-      //////////////////////////////////////////////////////////
-      if (searchResults != null)
-      {
-        int[] visibleResults = searchResults.getResults(nextSeq, startRes,
-            endRes);
-        if (visibleResults != null)
-        {
-          for (int r = 0; r < visibleResults.length; r += 2)
-          {
-            sr.drawHighlightedText(nextSeq, visibleResults[r],
-                                   visibleResults[r + 1],
-                                   (visibleResults[r] - startRes) *
-                                   av.charWidth,
-                                   offset + ( (i - startSeq) * av.charHeight));
-          }
-        }
-      }
-
-      if (av.cursorMode && cursorY == i
-          && cursorX >= startRes && cursorX <= endRes)
-      {
-        sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * av.charWidth,
-                      offset + ( (i - startSeq) * av.charHeight));
-      }
-    }
-
-    if (av.getSelectionGroup() != null || av.alignment.getGroups().size() > 0)
-    {
-      drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
-    }
-
-  }
-
-  void drawGroupsBoundaries(Graphics g,
-                            int startRes, int endRes,
-                            int startSeq, int endSeq,
-                            int offset)
-  {
-    //
-    /////////////////////////////////////
-    // Now outline any areas if necessary
-    /////////////////////////////////////
-    SequenceGroup group = av.getSelectionGroup();
-
-    int sx = -1;
-    int sy = -1;
-    int ex = -1;
-    int groupIndex = -1;
-
-    if ( (group == null) && (av.alignment.getGroups().size() > 0))
-    {
-      group = (SequenceGroup) av.alignment.getGroups().elementAt(0);
-      groupIndex = 0;
-    }
-
-    if (group != null)
-    {
-      do
-      {
-        int oldY = -1;
-        int i = 0;
-        boolean inGroup = false;
-        int top = -1;
-        int bottom = -1;
-        int alHeight = av.alignment.getHeight() - 1;
-
-        for (i = startSeq; i < endSeq; i++)
-        {
-          sx = (group.getStartRes() - startRes) * av.charWidth;
-          sy = offset + ( (i - startSeq) * av.charHeight);
-          ex = ( ( (group.getEndRes() + 1) - group.getStartRes()) *
-                av.charWidth) -
-              1;
-
-          if (sx + ex < 0 || sx > imgWidth)
-          {
-            continue;
-          }
-
-          if ( (sx <= (endRes - startRes) * av.charWidth) &&
-              group.getSequences(null).
-              contains(av.alignment.getSequenceAt(i)))
-          {
-            if ( (bottom == -1) &&
-                (i >= alHeight ||
-                 !group.getSequences(null).contains(
-                     av.alignment.getSequenceAt(i + 1))))
-            {
-              bottom = sy + av.charHeight;
-            }
-
-            if (!inGroup)
-            {
-              if ( ( (top == -1) && (i == 0)) ||
-                  !group.getSequences(null).contains(
-                      av.alignment.getSequenceAt(i - 1)))
-              {
-                top = sy;
-              }
-
-              oldY = sy;
-              inGroup = true;
-
-              if (group == av.getSelectionGroup())
-              {
-                g.setColor(Color.red);
-              }
-              else
-              {
-                g.setColor(group.getOutlineColour());
-              }
-            }
-          }
-          else
-          {
-            if (inGroup)
-            {
-              if (sx >= 0 && sx < imgWidth)
-              {
-                g.drawLine(sx, oldY, sx, sy);
-              }
-
-              if (sx + ex < imgWidth)
-              {
-                g.drawLine(sx + ex, oldY, sx + ex, sy);
-              }
-
-              if (sx < 0)
-              {
-                ex += sx;
-                sx = 0;
-              }
-
-              if (sx + ex > imgWidth)
-              {
-                ex = imgWidth;
-              }
-
-              else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
-              {
-                ex = (endRes - startRes + 1) * av.charWidth;
-              }
-
-              if (top != -1)
-              {
-                g.drawLine(sx, top, sx + ex, top);
-                top = -1;
-              }
-
-              if (bottom != -1)
-              {
-                g.drawLine(sx, bottom, sx + ex, bottom);
-                bottom = -1;
-              }
-
-              inGroup = false;
-            }
-          }
-        }
-
-        if (inGroup)
-        {
-          sy = offset + ( (i - startSeq) * av.charHeight);
-          if (sx >= 0 && sx < imgWidth)
-          {
-            g.drawLine(sx, oldY, sx, sy);
-          }
-
-          if (sx + ex < imgWidth)
-          {
-            g.drawLine(sx + ex, oldY, sx + ex, sy);
-          }
-
-          if (sx < 0)
-          {
-            ex += sx;
-            sx = 0;
-          }
-
-          if (sx + ex > imgWidth)
-          {
-            ex = imgWidth;
-          }
-          else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
-          {
-            ex = (endRes - startRes + 1) * av.charWidth;
-          }
-
-          if (top != -1)
-          {
-            g.drawLine(sx, top, sx + ex, top);
-            top = -1;
-          }
-
-          if (bottom != -1)
-          {
-            g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
-            bottom = -1;
-          }
-
-          inGroup = false;
-        }
-
-        groupIndex++;
-
-        if (groupIndex >= av.alignment.getGroups().size())
-        {
-          break;
-        }
-
-        group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex);
-      }
-      while (groupIndex < av.alignment.getGroups().size());
-
-    }
-  }
-
-  public void highlightSearchResults(SearchResults results)
-  {
-    searchResults = results;
-
-    repaint();
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.appletgui;
+
+import java.awt.*;
+
+import jalview.datamodel.*;
+
+public class SeqCanvas extends Panel
+{
+  FeatureRenderer fr;
+
+  SequenceRenderer sr;
+
+  Image img;
+
+  Graphics gg;
+
+  int imgWidth;
+
+  int imgHeight;
+
+  AlignViewport av;
+
+  SearchResults searchResults = null;
+
+  boolean fastPaint = false;
+
+  int cursorX = 0;
+
+  int cursorY = 0;
+
+  public SeqCanvas(AlignViewport av)
+  {
+    this.av = av;
+    fr = new FeatureRenderer(av);
+    sr = new SequenceRenderer(av);
+    PaintRefresher.Register(this, av.getSequenceSetId());
+  }
+
+  public AlignViewport getViewport()
+  {
+    return av;
+  }
+
+  public FeatureRenderer getFeatureRenderer()
+  {
+    return fr;
+  }
+
+  public SequenceRenderer getSequenceRenderer()
+  {
+    return sr;
+  }
+
+  void drawNorthScale(Graphics g, int startx, int endx, int ypos)
+  {
+    int scalestartx = startx - startx % 10 + 10;
+
+    g.setColor(Color.black);
+
+    // NORTH SCALE
+    for (int i = scalestartx; i < endx; i += 10)
+    {
+      int value = i;
+      if (av.hasHiddenColumns)
+      {
+        value = av.getColumnSelection().adjustForHiddenColumns(value);
+      }
+
+      g.drawString(String.valueOf(value), (i - startx - 1) * av.charWidth,
+              ypos - (av.charHeight / 2));
+
+      g.drawLine(((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
+              (ypos + 2) - (av.charHeight / 2),
+              ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
+              ypos - 2);
+    }
+  }
+
+  void drawWestScale(Graphics g, int startx, int endx, int ypos)
+  {
+    FontMetrics fm = getFontMetrics(av.getFont());
+    ypos += av.charHeight;
+    if (av.hasHiddenColumns)
+    {
+      startx = av.getColumnSelection().adjustForHiddenColumns(startx);
+      endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+    }
+
+    int maxwidth = av.alignment.getWidth();
+    if (av.hasHiddenColumns)
+    {
+      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+    }
+
+    // WEST SCALE
+    for (int i = 0; i < av.alignment.getHeight(); i++)
+    {
+      SequenceI seq = av.alignment.getSequenceAt(i);
+      int index = startx;
+      int value = -1;
+
+      while (index < endx)
+      {
+        if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+        {
+          index++;
+
+          continue;
+        }
+
+        value = av.alignment.getSequenceAt(i).findPosition(index);
+
+        break;
+      }
+
+      if (value != -1)
+      {
+        int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))
+                - av.charWidth / 2;
+        g.drawString(value + "", x, (ypos + (i * av.charHeight))
+                - (av.charHeight / 5));
+      }
+    }
+  }
+
+  void drawEastScale(Graphics g, int startx, int endx, int ypos)
+  {
+    ypos += av.charHeight;
+
+    if (av.hasHiddenColumns)
+    {
+      endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+    }
+
+    SequenceI seq;
+    // EAST SCALE
+    for (int i = 0; i < av.alignment.getHeight(); i++)
+    {
+      seq = av.alignment.getSequenceAt(i);
+      int index = endx;
+      int value = -1;
+
+      while (index > startx)
+      {
+        if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+        {
+          index--;
+
+          continue;
+        }
+
+        value = seq.findPosition(index);
+
+        break;
+      }
+
+      if (value != -1)
+      {
+        g.drawString(String.valueOf(value), 0, (ypos + (i * av.charHeight))
+                - (av.charHeight / 5));
+      }
+    }
+  }
+
+  int lastsr = 0;
+
+  void fastPaint(int horizontal, int vertical)
+  {
+    if (fastPaint || gg == null)
+    {
+      return;
+    }
+
+    // Its possible on certain browsers that the call to fastpaint
+    // is faster than it can paint, so this check here catches
+    // this possibility
+    if (lastsr + horizontal != av.startRes)
+    {
+      horizontal = av.startRes - lastsr;
+    }
+
+    lastsr = av.startRes;
+
+    fastPaint = true;
+    gg.copyArea(horizontal * av.charWidth, vertical * av.charHeight,
+            imgWidth - horizontal * av.charWidth, imgHeight - vertical
+                    * av.charHeight, -horizontal * av.charWidth, -vertical
+                    * av.charHeight);
+
+    int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq, transX = 0, transY = 0;
+
+    if (horizontal > 0) // scrollbar pulled right, image to the left
+    {
+      transX = (er - sr - horizontal) * av.charWidth;
+      sr = er - horizontal;
+    }
+    else if (horizontal < 0)
+    {
+      er = sr - horizontal;
+    }
+
+    else if (vertical > 0) // scroll down
+    {
+      ss = es - vertical;
+      if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time
+      {
+        ss = av.startSeq;
+      }
+      else
+      {
+        transY = imgHeight - vertical * av.charHeight;
+      }
+    }
+    else if (vertical < 0)
+    {
+      es = ss - vertical;
+      if (es > av.endSeq)
+      {
+        es = av.endSeq;
+      }
+    }
+
+    gg.translate(transX, transY);
+
+    drawPanel(gg, sr, er, ss, es, 0);
+    gg.translate(-transX, -transY);
+
+    repaint();
+
+  }
+
+  /**
+   * Definitions of startx and endx (hopefully): SMJS This is what I'm working
+   * towards! startx is the first residue (starting at 0) to display. endx is
+   * the last residue to display (starting at 0). starty is the first sequence
+   * to display (starting at 0). endy is the last sequence to display (starting
+   * at 0). NOTE 1: The av limits are set in setFont in this class and in the
+   * adjustment listener in SeqPanel when the scrollbars move.
+   */
+  public void update(Graphics g)
+  {
+    paint(g);
+  }
+
+  public void paint(Graphics g)
+  {
+
+    if (img != null
+            && (fastPaint || (getSize().width != g.getClipBounds().width) || (getSize().height != g
+                    .getClipBounds().height)))
+    {
+      g.drawImage(img, 0, 0, this);
+      fastPaint = false;
+      return;
+    }
+
+    if (fastPaint)
+    {
+      g.drawImage(img, 0, 0, this);
+      fastPaint = false;
+      return;
+    }
+
+    // this draws the whole of the alignment
+    imgWidth = this.getSize().width;
+    imgHeight = this.getSize().height;
+
+    imgWidth -= imgWidth % av.charWidth;
+    imgHeight -= imgHeight % av.charHeight;
+
+    if (imgWidth < 1 || imgHeight < 1)
+    {
+      return;
+    }
+
+    if (img == null || imgWidth != img.getWidth(this)
+            || imgHeight != img.getHeight(this))
+    {
+      img = createImage(imgWidth, imgHeight);
+      gg = img.getGraphics();
+      gg.setFont(av.getFont());
+    }
+
+    gg.setColor(Color.white);
+    gg.fillRect(0, 0, imgWidth, imgHeight);
+
+    if (av.getWrapAlignment())
+    {
+      drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes);
+    }
+    else
+    {
+      drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);
+    }
+
+    g.drawImage(img, 0, 0, this);
+
+  }
+
+  int LABEL_WEST, LABEL_EAST;
+
+  public int getWrappedCanvasWidth(int cwidth)
+  {
+    cwidth -= cwidth % av.charWidth;
+
+    FontMetrics fm = getFontMetrics(av.getFont());
+
+    LABEL_EAST = 0;
+    LABEL_WEST = 0;
+
+    if (av.scaleRightWrapped)
+    {
+      LABEL_EAST = fm.stringWidth(getMask());
+    }
+
+    if (av.scaleLeftWrapped)
+    {
+      LABEL_WEST = fm.stringWidth(getMask());
+    }
+
+    return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
+  }
+
+  /**
+   * Generates a string of zeroes.
+   * 
+   * @return String
+   */
+  String getMask()
+  {
+    String mask = "0";
+    int maxWidth = 0;
+    int tmp;
+    for (int i = 0; i < av.alignment.getHeight(); i++)
+    {
+      tmp = av.alignment.getSequenceAt(i).getEnd();
+      if (tmp > maxWidth)
+      {
+        maxWidth = tmp;
+      }
+    }
+
+    for (int i = maxWidth; i > 0; i /= 10)
+    {
+      mask += "0";
+    }
+    return mask;
+  }
+
+  public void drawWrappedPanel(Graphics g, int canvasWidth,
+          int canvasHeight, int startRes)
+  {
+    AlignmentI al = av.getAlignment();
+
+    FontMetrics fm = getFontMetrics(av.getFont());
+
+    if (av.scaleRightWrapped)
+    {
+      LABEL_EAST = fm.stringWidth(getMask());
+    }
+
+    if (av.scaleLeftWrapped)
+    {
+      LABEL_WEST = fm.stringWidth(getMask());
+    }
+
+    int hgap = av.charHeight;
+    if (av.scaleAboveWrapped)
+    {
+      hgap += av.charHeight;
+    }
+
+    int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
+    int cHeight = av.getAlignment().getHeight() * av.charHeight;
+
+    av.setWrappedWidth(cWidth);
+
+    av.endRes = av.startRes + cWidth;
+
+    int endx;
+    int ypos = hgap;
+
+    int maxwidth = av.alignment.getWidth() - 1;
+
+    if (av.hasHiddenColumns)
+    {
+      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+    }
+
+    while ((ypos <= canvasHeight) && (startRes < maxwidth))
+    {
+      endx = startRes + cWidth - 1;
+
+      if (endx > maxwidth)
+      {
+        endx = maxwidth;
+      }
+
+      g.setColor(Color.black);
+
+      if (av.scaleLeftWrapped)
+      {
+        drawWestScale(g, startRes, endx, ypos);
+      }
+
+      if (av.scaleRightWrapped)
+      {
+        g.translate(canvasWidth - LABEL_EAST, 0);
+        drawEastScale(g, startRes, endx, ypos);
+        g.translate(-(canvasWidth - LABEL_EAST), 0);
+      }
+
+      g.translate(LABEL_WEST, 0);
+
+      if (av.scaleAboveWrapped)
+      {
+        drawNorthScale(g, startRes, endx, ypos);
+      }
+      if (av.hasHiddenColumns && av.showHiddenMarkers)
+      {
+        g.setColor(Color.blue);
+        int res;
+        for (int i = 0; i < av.getColumnSelection().getHiddenColumns()
+                .size(); i++)
+        {
+          res = av.getColumnSelection().findHiddenRegionPosition(i)
+                  - startRes;
+
+          if (res < 0 || res > endx - startRes)
+          {
+            continue;
+          }
+
+          gg.fillPolygon(new int[]
+          { res * av.charWidth - av.charHeight / 4,
+              res * av.charWidth + av.charHeight / 4, res * av.charWidth },
+                  new int[]
+                  { ypos - (av.charHeight / 2), ypos - (av.charHeight / 2),
+                      ypos - (av.charHeight / 2) + 8 }, 3);
+
+        }
+      }
+
+      if (g.getClip() == null)
+      {
+        g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);
+      }
+
+      drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
+      g.setClip(null);
+
+      if (av.showAnnotation)
+      {
+        g.translate(0, cHeight + ypos + 4);
+        if (annotations == null)
+        {
+          annotations = new AnnotationPanel(av);
+        }
+
+        annotations.drawComponent(g, startRes, endx + 1);
+        g.translate(0, -cHeight - ypos - 4);
+      }
+      g.translate(-LABEL_WEST, 0);
+
+      ypos += cHeight + getAnnotationHeight() + hgap;
+
+      startRes += cWidth;
+    }
+
+  }
+
+  AnnotationPanel annotations;
+
+  int getAnnotationHeight()
+  {
+    if (!av.showAnnotation)
+    {
+      return 0;
+    }
+
+    if (annotations == null)
+    {
+      annotations = new AnnotationPanel(av);
+    }
+
+    return annotations.adjustPanelHeight();
+  }
+
+  void drawPanel(Graphics g1, int startRes, int endRes, int startSeq,
+          int endSeq, int offset)
+  {
+    if (!av.hasHiddenColumns)
+    {
+      draw(g1, startRes, endRes, startSeq, endSeq, offset);
+    }
+    else
+    {
+      java.util.Vector regions = av.getColumnSelection().getHiddenColumns();
+
+      int screenY = 0;
+      int blockStart = startRes;
+      int blockEnd = endRes;
+
+      for (int i = 0; i < regions.size(); i++)
+      {
+        int[] region = (int[]) regions.elementAt(i);
+        int hideStart = region[0];
+        int hideEnd = region[1];
+
+        if (hideStart <= blockStart)
+        {
+          blockStart += (hideEnd - hideStart) + 1;
+          continue;
+        }
+
+        blockEnd = hideStart - 1;
+
+        g1.translate(screenY * av.charWidth, 0);
+
+        draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
+
+        if (av.getShowHiddenMarkers())
+        {
+          g1.setColor(Color.blue);
+          g1
+                  .drawLine((blockEnd - blockStart + 1) * av.charWidth - 1,
+                          0 + offset, (blockEnd - blockStart + 1)
+                                  * av.charWidth - 1, (endSeq - startSeq)
+                                  * av.charHeight + offset);
+        }
+
+        g1.translate(-screenY * av.charWidth, 0);
+        screenY += blockEnd - blockStart + 1;
+        blockStart = hideEnd + 1;
+      }
+
+      if (screenY <= (endRes - startRes))
+      {
+        blockEnd = blockStart + (endRes - startRes) - screenY;
+        g1.translate(screenY * av.charWidth, 0);
+        draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
+
+        g1.translate(-screenY * av.charWidth, 0);
+      }
+    }
+
+  }
+
+  // int startRes, int endRes, int startSeq, int endSeq, int x, int y,
+  // int x1, int x2, int y1, int y2, int startx, int starty,
+  void draw(Graphics g, int startRes, int endRes, int startSeq, int endSeq,
+          int offset)
+  {
+    g.setFont(av.getFont());
+    sr.prepare(g, av.renderGaps);
+
+    SequenceI nextSeq;
+
+    // / First draw the sequences
+    // ///////////////////////////
+    for (int i = startSeq; i < endSeq; i++)
+    {
+      nextSeq = av.alignment.getSequenceAt(i);
+
+      if (nextSeq == null)
+      {
+        continue;
+      }
+
+      sr.drawSequence(nextSeq, av.alignment.findAllGroups(nextSeq),
+              startRes, endRes, offset + ((i - startSeq) * av.charHeight));
+
+      if (av.showSequenceFeatures)
+      {
+        fr.drawSequence(g, nextSeq, startRes, endRes, offset
+                + ((i - startSeq) * av.charHeight));
+      }
+
+      // / Highlight search Results once all sequences have been drawn
+      // ////////////////////////////////////////////////////////
+      if (searchResults != null)
+      {
+        int[] visibleResults = searchResults.getResults(nextSeq, startRes,
+                endRes);
+        if (visibleResults != null)
+        {
+          for (int r = 0; r < visibleResults.length; r += 2)
+          {
+            sr.drawHighlightedText(nextSeq, visibleResults[r],
+                    visibleResults[r + 1], (visibleResults[r] - startRes)
+                            * av.charWidth, offset
+                            + ((i - startSeq) * av.charHeight));
+          }
+        }
+      }
+
+      if (av.cursorMode && cursorY == i && cursorX >= startRes
+              && cursorX <= endRes)
+      {
+        sr.drawCursor(nextSeq, cursorX,
+                (cursorX - startRes) * av.charWidth, offset
+                        + ((i - startSeq) * av.charHeight));
+      }
+    }
+
+    if (av.getSelectionGroup() != null
+            || av.alignment.getGroups().size() > 0)
+    {
+      drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
+    }
+
+  }
+
+  void drawGroupsBoundaries(Graphics g, int startRes, int endRes,
+          int startSeq, int endSeq, int offset)
+  {
+    //
+    // ///////////////////////////////////
+    // Now outline any areas if necessary
+    // ///////////////////////////////////
+    SequenceGroup group = av.getSelectionGroup();
+
+    int sx = -1;
+    int sy = -1;
+    int ex = -1;
+    int groupIndex = -1;
+
+    if ((group == null) && (av.alignment.getGroups().size() > 0))
+    {
+      group = (SequenceGroup) av.alignment.getGroups().elementAt(0);
+      groupIndex = 0;
+    }
+
+    if (group != null)
+    {
+      do
+      {
+        int oldY = -1;
+        int i = 0;
+        boolean inGroup = false;
+        int top = -1;
+        int bottom = -1;
+        int alHeight = av.alignment.getHeight() - 1;
+
+        for (i = startSeq; i < endSeq; i++)
+        {
+          sx = (group.getStartRes() - startRes) * av.charWidth;
+          sy = offset + ((i - startSeq) * av.charHeight);
+          ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) - 1;
+
+          if (sx + ex < 0 || sx > imgWidth)
+          {
+            continue;
+          }
+
+          if ((sx <= (endRes - startRes) * av.charWidth)
+                  && group.getSequences(null).contains(
+                          av.alignment.getSequenceAt(i)))
+          {
+            if ((bottom == -1)
+                    && (i >= alHeight || !group.getSequences(null)
+                            .contains(av.alignment.getSequenceAt(i + 1))))
+            {
+              bottom = sy + av.charHeight;
+            }
+
+            if (!inGroup)
+            {
+              if (((top == -1) && (i == 0))
+                      || !group.getSequences(null).contains(
+                              av.alignment.getSequenceAt(i - 1)))
+              {
+                top = sy;
+              }
+
+              oldY = sy;
+              inGroup = true;
+
+              if (group == av.getSelectionGroup())
+              {
+                g.setColor(Color.red);
+              }
+              else
+              {
+                g.setColor(group.getOutlineColour());
+              }
+            }
+          }
+          else
+          {
+            if (inGroup)
+            {
+              if (sx >= 0 && sx < imgWidth)
+              {
+                g.drawLine(sx, oldY, sx, sy);
+              }
+
+              if (sx + ex < imgWidth)
+              {
+                g.drawLine(sx + ex, oldY, sx + ex, sy);
+              }
+
+              if (sx < 0)
+              {
+                ex += sx;
+                sx = 0;
+              }
+
+              if (sx + ex > imgWidth)
+              {
+                ex = imgWidth;
+              }
+
+              else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
+              {
+                ex = (endRes - startRes + 1) * av.charWidth;
+              }
+
+              if (top != -1)
+              {
+                g.drawLine(sx, top, sx + ex, top);
+                top = -1;
+              }
+
+              if (bottom != -1)
+              {
+                g.drawLine(sx, bottom, sx + ex, bottom);
+                bottom = -1;
+              }
+
+              inGroup = false;
+            }
+          }
+        }
+
+        if (inGroup)
+        {
+          sy = offset + ((i - startSeq) * av.charHeight);
+          if (sx >= 0 && sx < imgWidth)
+          {
+            g.drawLine(sx, oldY, sx, sy);
+          }
+
+          if (sx + ex < imgWidth)
+          {
+            g.drawLine(sx + ex, oldY, sx + ex, sy);
+          }
+
+          if (sx < 0)
+          {
+            ex += sx;
+            sx = 0;
+          }
+
+          if (sx + ex > imgWidth)
+          {
+            ex = imgWidth;
+          }
+          else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
+          {
+            ex = (endRes - startRes + 1) * av.charWidth;
+          }
+
+          if (top != -1)
+          {
+            g.drawLine(sx, top, sx + ex, top);
+            top = -1;
+          }
+
+          if (bottom != -1)
+          {
+            g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
+            bottom = -1;
+          }
+
+          inGroup = false;
+        }
+
+        groupIndex++;
+
+        if (groupIndex >= av.alignment.getGroups().size())
+        {
+          break;
+        }
+
+        group = (SequenceGroup) av.alignment.getGroups().elementAt(
+                groupIndex);
+      } while (groupIndex < av.alignment.getGroups().size());
+
+    }
+  }
+
+  public void highlightSearchResults(SearchResults results)
+  {
+    searchResults = results;
+
+    repaint();
+  }
+
+}
diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 158f0ab..bf392e9 100755
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.appletgui;
 
 import java.util.*;
@@ -30,44 +29,56 @@ import jalview.schemes.*;
 import jalview.structure.SequenceListener;
 import jalview.structure.StructureSelectionManager;
 
-public class SeqPanel
-    extends Panel implements MouseMotionListener, MouseListener, SequenceListener
+public class SeqPanel extends Panel implements MouseMotionListener,
+        MouseListener, SequenceListener
 {
 
   public SeqCanvas seqCanvas;
+
   public AlignmentPanel ap;
 
   protected int lastres;
+
   protected int startseq;
 
   protected AlignViewport av;
 
-  // if character is inserted or deleted, we will need to recalculate the conservation
+  // if character is inserted or deleted, we will need to recalculate the
+  // conservation
   boolean seqEditOccurred = false;
 
   ScrollThread scrollThread = null;
+
   boolean mouseDragging = false;
+
   boolean editingSeqs = false;
+
   boolean groupEditing = false;
 
   int oldSeq = -1;
+
   boolean changeEndSeq = false;
+
   boolean changeStartSeq = false;
+
   boolean changeEndRes = false;
+
   boolean changeStartRes = false;
+
   SequenceGroup stretchGroup = null;
 
   StringBuffer keyboardNo1;
+
   StringBuffer keyboardNo2;
 
   boolean mouseWheelPressed = false;
+
   Point lastMousePress;
 
   EditCommand editCommand;
 
   StructureSelectionManager ssm;
 
-
   public SeqPanel(AlignViewport avp, AlignmentPanel p)
   {
     this.av = avp;
@@ -91,8 +102,8 @@ public class SeqPanel
     if (editCommand != null && editCommand.getSize() > 0)
     {
       ap.alignFrame.addHistoryItem(editCommand);
-      av.firePropertyChange("alignment", null,
-                            av.getAlignment().getSequences());
+      av.firePropertyChange("alignment", null, av.getAlignment()
+              .getSequences());
     }
 
     startseq = -1;
@@ -132,12 +143,10 @@ public class SeqPanel
 
   void setCursorPosition()
   {
-    SequenceI sequence =
-        (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
+    SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
+            seqCanvas.cursorY);
 
-    seqCanvas.cursorX = sequence.findIndex(
-        getKeyboardNo1() - 1
-        );
+    seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1() - 1);
     scrollToVisible();
   }
 
@@ -151,14 +160,13 @@ public class SeqPanel
       int maxWidth = av.alignment.getWidth();
 
       while (!av.colSel.isVisible(seqCanvas.cursorX)
-             && seqCanvas.cursorX < maxWidth
-             && seqCanvas.cursorX > 0)
+              && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
       {
         seqCanvas.cursorX += dx;
       }
 
       if (seqCanvas.cursorX >= maxWidth
-          || !av.colSel.isVisible(seqCanvas.cursorX))
+              || !av.colSel.isVisible(seqCanvas.cursorX))
       {
         seqCanvas.cursorX = original;
       }
@@ -201,7 +209,8 @@ public class SeqPanel
       {
         ap.scrollUp(false);
       }
-      while (seqCanvas.cursorX < av.colSel.adjustForHiddenColumns(av.startRes))
+      while (seqCanvas.cursorX < av.colSel
+              .adjustForHiddenColumns(av.startRes))
       {
 
         if (!ap.scrollRight(false))
@@ -209,7 +218,8 @@ public class SeqPanel
           break;
         }
       }
-      while (seqCanvas.cursorX > av.colSel.adjustForHiddenColumns(av.endRes))
+      while (seqCanvas.cursorX > av.colSel
+              .adjustForHiddenColumns(av.endRes))
       {
         if (!ap.scrollRight(true))
         {
@@ -218,20 +228,20 @@ public class SeqPanel
       }
     }
     setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
-                     seqCanvas.cursorX, seqCanvas.cursorY);
+            seqCanvas.cursorX, seqCanvas.cursorY);
 
     seqCanvas.repaint();
   }
 
   void setSelectionAreaAtCursor(boolean topLeft)
   {
-    SequenceI sequence =
-        (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
+    SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
+            seqCanvas.cursorY);
 
     if (av.getSelectionGroup() != null)
     {
       SequenceGroup sg = av.selectionGroup;
-      //Find the top and bottom of this group
+      // Find the top and bottom of this group
       int min = av.alignment.getHeight(), max = 0;
       for (int i = 0; i < sg.getSize(); i++)
       {
@@ -356,17 +366,16 @@ public class SeqPanel
     }
   }
 
-
   void setStatusMessage(SequenceI sequence, int res, int seq)
   {
-    StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
-                                         sequence.getName());
+    StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: "
+            + sequence.getName());
 
     Object obj = null;
     if (av.alignment.isNucleotide())
     {
-      obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
-                                                 "");
+      obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
+              + "");
       if (obj != null)
       {
         text.append(" Nucleotide: ");
@@ -386,8 +395,7 @@ public class SeqPanel
 
       if (obj != "")
       {
-        text.append(obj + " (" + sequence.findPosition(res) +
-                    ")");
+        text.append(obj + " (" + sequence.findPosition(res) + ")");
       }
     }
 
@@ -399,18 +407,16 @@ public class SeqPanel
   {
     lastMousePress = evt.getPoint();
 
-    //For now, ignore the mouseWheel font resizing on Macs
-    //As the Button2_mask always seems to be true
-    if ( (evt.getModifiers() & InputEvent.BUTTON2_MASK) ==
-        InputEvent.BUTTON2_MASK && !av.MAC)
+    // For now, ignore the mouseWheel font resizing on Macs
+    // As the Button2_mask always seems to be true
+    if ((evt.getModifiers() & InputEvent.BUTTON2_MASK) == InputEvent.BUTTON2_MASK
+            && !av.MAC)
     {
       mouseWheelPressed = true;
       return;
     }
 
-    if (evt.isShiftDown()
-        || evt.isControlDown()
-        || evt.isAltDown())
+    if (evt.isShiftDown() || evt.isControlDown() || evt.isAltDown())
     {
       if (evt.isControlDown() || evt.isAltDown())
       {
@@ -432,8 +438,8 @@ public class SeqPanel
       return;
     }
 
-    if ( (seq < av.getAlignment().getHeight()) &&
-        (res < av.getAlignment().getSequenceAt(seq).getLength()))
+    if ((seq < av.getAlignment().getHeight())
+            && (res < av.getAlignment().getSequenceAt(seq).getLength()))
     {
       startseq = seq;
       lastres = res;
@@ -453,30 +459,26 @@ public class SeqPanel
     if (evt.getClickCount() > 1)
     {
       if (av.getSelectionGroup().getSize() == 1
-          && av.getSelectionGroup().getEndRes()
-          - av.getSelectionGroup().getStartRes() < 2)
+              && av.getSelectionGroup().getEndRes()
+                      - av.getSelectionGroup().getStartRes() < 2)
       {
         av.setSelectionGroup(null);
       }
 
-      SequenceFeature[] features = findFeaturesAtRes(
-          sequence,
-          sequence.findPosition(findRes(evt))
-          );
+      SequenceFeature[] features = findFeaturesAtRes(sequence, sequence
+              .findPosition(findRes(evt)));
 
       if (features != null && features.length > 0)
       {
         SearchResults highlight = new SearchResults();
-        highlight.addResult(sequence,
-                            features[0].getBegin(),
-                            features[0].getEnd());
+        highlight.addResult(sequence, features[0].getBegin(), features[0]
+                .getEnd());
         seqCanvas.highlightSearchResults(highlight);
       }
       if (features != null && features.length > 0)
       {
-        seqCanvas.getFeatureRenderer().amendFeatures(
-            new SequenceI[]
-            {sequence}, features, false, ap);
+        seqCanvas.getFeatureRenderer().amendFeatures(new SequenceI[]
+        { sequence }, features, false, ap);
 
         seqCanvas.highlightSearchResults(null);
       }
@@ -500,7 +502,9 @@ public class SeqPanel
   }
 
   int startWrapBlock = -1;
+
   int wrappedBlock = -1;
+
   int findRes(MouseEvent evt)
   {
     int res = 0;
@@ -515,8 +519,8 @@ public class SeqPanel
         hgap += av.charHeight;
       }
 
-      int cHeight = av.getAlignment().getHeight() * av.charHeight
-          + hgap + seqCanvas.getAnnotationHeight();
+      int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+              + seqCanvas.getAnnotationHeight();
 
       int y = evt.getY();
       y -= hgap;
@@ -551,8 +555,9 @@ public class SeqPanel
   int findSeq(MouseEvent evt)
   {
     final int sqnum = findAlRow(evt);
-    return (sqnum<0) ? 0 : sqnum;
+    return (sqnum < 0) ? 0 : sqnum;
   }
+
   /**
    * 
    * @param evt
@@ -571,13 +576,13 @@ public class SeqPanel
         hgap += av.charHeight;
       }
 
-      int cHeight = av.getAlignment().getHeight() * av.charHeight
-          + hgap + seqCanvas.getAnnotationHeight();
+      int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+              + seqCanvas.getAnnotationHeight();
 
       y -= hgap;
 
-      seq = Math.min( (y % cHeight) / av.getCharHeight(),
-                     av.alignment.getHeight() - 1);
+      seq = Math.min((y % cHeight) / av.getCharHeight(), av.alignment
+              .getHeight() - 1);
       if (seq < 0)
       {
         seq = -1;
@@ -585,8 +590,8 @@ public class SeqPanel
     }
     else
     {
-      seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(),
-                     av.alignment.getHeight() - 1);
+      seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(),
+              av.alignment.getHeight() - 1);
       if (seq < 0)
       {
         seq = -1;
@@ -596,18 +601,16 @@ public class SeqPanel
     return seq;
   }
 
-
-
   public void doMousePressed(MouseEvent evt)
   {
 
     int seq = findSeq(evt);
     int res = findRes(evt);
 
-    if (seq < av.getAlignment().getHeight() &&
-        res < av.getAlignment().getSequenceAt(seq).getLength())
+    if (seq < av.getAlignment().getHeight()
+            && res < av.getAlignment().getSequenceAt(seq).getLength())
     {
-      //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
+      // char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
       // Find the residue's position in the sequence (res is the position
       // in the alignment
 
@@ -623,18 +626,17 @@ public class SeqPanel
     return;
   }
 
-
   String lastMessage;
+
   public void mouseOverSequence(SequenceI sequence, int index, int pos)
   {
-    String tmp = sequence.hashCode()+index+"";
+    String tmp = sequence.hashCode() + index + "";
     if (lastMessage == null || !lastMessage.equals(tmp))
       ssm.mouseOverSequence(sequence, index, pos);
 
     lastMessage = tmp;
   }
 
-
   public void highlightSequence(SearchResults results)
   {
     seqCanvas.highlightSearchResults(results);
@@ -643,7 +645,7 @@ public class SeqPanel
   public void updateColours(SequenceI seq, int index)
   {
     System.out.println("update the seqPanel colours");
-    //repaint();
+    // repaint();
   }
 
   public void mouseMoved(MouseEvent evt)
@@ -674,15 +676,14 @@ public class SeqPanel
     if (ssm != null)
       mouseOverSequence(sequence, res, respos);
 
-
-    StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
-                                         sequence.getName());
+    StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: "
+            + sequence.getName());
 
     Object obj = null;
     if (av.alignment.isNucleotide())
     {
-      obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
-                                                 "");
+      obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
+              + "");
       if (obj != null)
       {
         text.append(" Nucleotide: ");
@@ -715,8 +716,8 @@ public class SeqPanel
       {
         if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
         {
-          if (!groups[g].getName().startsWith("JTreeGroup") &&
-              !groups[g].getName().startsWith("JGroup"))
+          if (!groups[g].getName().startsWith("JTreeGroup")
+                  && !groups[g].getName().startsWith("JGroup"))
           {
             tooltipText.append(groups[g].getName() + " ");
           }
@@ -730,33 +731,33 @@ public class SeqPanel
     }
 
     // use aa to see if the mouse pointer is on a
-    SequenceFeature [] allFeatures = findFeaturesAtRes(sequence,
-                                               sequence.findPosition(res));
+    SequenceFeature[] allFeatures = findFeaturesAtRes(sequence, sequence
+            .findPosition(res));
 
-      int index = 0;
-      while (index < allFeatures.length)
-      {
-        SequenceFeature sf = allFeatures[index];
+    int index = 0;
+    while (index < allFeatures.length)
+    {
+      SequenceFeature sf = allFeatures[index];
 
-        tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end);
+      tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end);
 
-        if (sf.getDescription() != null)
-        {
-          tooltipText.append(" " + sf.getDescription());
-        }
+      if (sf.getDescription() != null)
+      {
+        tooltipText.append(" " + sf.getDescription());
+      }
 
-        if (sf.getValue("status") != null)
+      if (sf.getValue("status") != null)
+      {
+        String status = sf.getValue("status").toString();
+        if (status.length() > 0)
         {
-          String status = sf.getValue("status").toString();
-          if (status.length() > 0)
-          {
-            tooltipText.append(" (" + sf.getValue("status") + ")");
-          }
+          tooltipText.append(" (" + sf.getValue("status") + ")");
         }
-        tooltipText.append("\n");
-
-        index++;
       }
+      tooltipText.append("\n");
+
+      index++;
+    }
 
     if (tooltip == null)
     {
@@ -777,22 +778,21 @@ public class SeqPanel
       for (int i = 0; i < features.length; i++)
       {
         if (av.featuresDisplayed == null
-            || !av.featuresDisplayed.containsKey(features[i].getType()))
+                || !av.featuresDisplayed.containsKey(features[i].getType()))
         {
           continue;
         }
 
-
-
         if (features[i].featureGroup != null
-           && seqCanvas.fr.featureGroups!=null
-            && seqCanvas.fr.featureGroups.containsKey(features[i].featureGroup)
-            && !((Boolean)seqCanvas.fr.featureGroups.get(features[i].featureGroup)).booleanValue())
+                && seqCanvas.fr.featureGroups != null
+                && seqCanvas.fr.featureGroups
+                        .containsKey(features[i].featureGroup)
+                && !((Boolean) seqCanvas.fr.featureGroups
+                        .get(features[i].featureGroup)).booleanValue())
           continue;
 
-
-        if ( (features[i].getBegin() <= res) &&
-            (features[i].getEnd() >= res))
+        if ((features[i].getBegin() <= res)
+                && (features[i].getEnd() >= res))
         {
           tmp.addElement(features[i]);
         }
@@ -805,7 +805,6 @@ public class SeqPanel
     return features;
   }
 
-
   Tooltip tooltip;
 
   public void mouseDragged(MouseEvent evt)
@@ -814,9 +813,9 @@ public class SeqPanel
     {
       int oldWidth = av.charWidth;
 
-      //Which is bigger, left-right or up-down?
-      if (Math.abs(evt.getY() - lastMousePress.y)
-          > Math.abs(evt.getX() - lastMousePress.x))
+      // Which is bigger, left-right or up-down?
+      if (Math.abs(evt.getY() - lastMousePress.y) > Math.abs(evt.getX()
+              - lastMousePress.x))
       {
         int fontSize = av.font.getSize();
 
@@ -834,7 +833,9 @@ public class SeqPanel
           fontSize = 1;
         }
 
-        av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
+        av
+                .setFont(new Font(av.font.getName(), av.font.getStyle(),
+                        fontSize));
         av.charWidth = oldWidth;
       }
       else
@@ -879,12 +880,12 @@ public class SeqPanel
       res = 0;
     }
 
-    if ( (lastres == -1) || (lastres == res))
+    if ((lastres == -1) || (lastres == res))
     {
       return;
     }
 
-    if ( (res < av.getAlignment().getWidth()) && (res < lastres))
+    if ((res < av.getAlignment().getWidth()) && (res < lastres))
     {
       // dragLeft, delete gap
       editSequence(false, res);
@@ -914,7 +915,7 @@ public class SeqPanel
     if (!groupEditing && av.hasHiddenRows)
     {
       if (av.hiddenRepSequences != null
-          && av.hiddenRepSequences.containsKey(seq))
+              && av.hiddenRepSequences.containsKey(seq))
       {
         sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
         groupEditing = true;
@@ -956,18 +957,19 @@ public class SeqPanel
     message.append(Math.abs(startres - lastres) + " gaps.");
     ap.alignFrame.statusBar.setText(message.toString());
 
-    //Are we editing within a selection group?
+    // Are we editing within a selection group?
     if (groupEditing
-        || (sg != null && sg.getSequences(av.hiddenRepSequences).contains(seq)))
+            || (sg != null && sg.getSequences(av.hiddenRepSequences)
+                    .contains(seq)))
     {
       fixedColumns = true;
 
-      //sg might be null as the user may only see 1 sequence,
-      //but the sequence represents a group
+      // sg might be null as the user may only see 1 sequence,
+      // but the sequence represents a group
       if (sg == null)
       {
         if (av.hiddenRepSequences == null
-            || !av.hiddenRepSequences.containsKey(seq))
+                || !av.hiddenRepSequences.containsKey(seq))
         {
           endEditing();
           return;
@@ -979,10 +981,10 @@ public class SeqPanel
       fixedLeft = sg.getStartRes();
       fixedRight = sg.getEndRes();
 
-      if ( (startres < fixedLeft && lastres >= fixedLeft)
-          || (startres >= fixedLeft && lastres < fixedLeft)
-          || (startres > fixedRight && lastres <= fixedRight)
-          || (startres <= fixedRight && lastres > fixedRight))
+      if ((startres < fixedLeft && lastres >= fixedLeft)
+              || (startres >= fixedLeft && lastres < fixedLeft)
+              || (startres > fixedRight && lastres <= fixedRight)
+              || (startres <= fixedRight && lastres > fixedRight))
       {
         endEditing();
         return;
@@ -1006,15 +1008,15 @@ public class SeqPanel
       int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
       int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
 
-      if ( (insertGap && startres > y1 && lastres < y1)
-          || (!insertGap && startres < y2 && lastres > y2))
+      if ((insertGap && startres > y1 && lastres < y1)
+              || (!insertGap && startres < y2 && lastres > y2))
       {
         endEditing();
         return;
       }
 
-      //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
-      //Selection spans a hidden region
+      // System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
+      // Selection spans a hidden region
       if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
       {
         if (startres >= y2)
@@ -1041,12 +1043,10 @@ public class SeqPanel
       // drag to right
       if (insertGap)
       {
-        //If the user has selected the whole sequence, and is dragging to
+        // If the user has selected the whole sequence, and is dragging to
         // the right, we can still extend the alignment and selectionGroup
-        if (sg.getStartRes() == 0
-            && sg.getEndRes() == fixedRight
-            && sg.getEndRes() == av.alignment.getWidth() - 1
-            )
+        if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
+                && sg.getEndRes() == av.alignment.getWidth() - 1)
         {
           sg.setEndRes(av.alignment.getWidth() + startres - lastres);
           fixedRight = sg.getEndRes();
@@ -1056,9 +1056,7 @@ public class SeqPanel
         // Find the next gap before the end
         // of the visible region boundary
         boolean blank = false;
-        for (fixedRight = fixedRight;
-             fixedRight > lastres;
-             fixedRight--)
+        for (fixedRight = fixedRight; fixedRight > lastres; fixedRight--)
         {
           blank = true;
 
@@ -1066,8 +1064,8 @@ public class SeqPanel
           {
             for (int j = 0; j < startres - lastres; j++)
             {
-              if (!jalview.util.Comparison.isGap(
-                  groupSeqs[g].getCharAt(fixedRight - j)))
+              if (!jalview.util.Comparison.isGap(groupSeqs[g]
+                      .getCharAt(fixedRight - j)))
               {
                 blank = false;
                 break;
@@ -1084,9 +1082,8 @@ public class SeqPanel
         {
           if (sg.getSize() == av.alignment.getHeight())
           {
-            if ( (av.hasHiddenColumns
-                  &&
-                  startres < av.getColumnSelection().getHiddenBoundaryRight(startres)))
+            if ((av.hasHiddenColumns && startres < av.getColumnSelection()
+                    .getHiddenBoundaryRight(startres)))
             {
               endEditing();
               return;
@@ -1101,8 +1098,8 @@ public class SeqPanel
                 alWidth = hwidth;
               }
             }
-            //We can still insert gaps if the selectionGroup
-            //contains all the sequences
+            // We can still insert gaps if the selectionGroup
+            // contains all the sequences
             sg.setEndRes(sg.getEndRes() + startres - lastres);
             fixedRight = alWidth + startres - lastres;
           }
@@ -1117,7 +1114,7 @@ public class SeqPanel
       // drag to left
       else if (!insertGap)
       {
-        /// Are we able to delete?
+        // / Are we able to delete?
         // ie are all columns blank?
 
         for (g = 0; g < groupSize; g++)
@@ -1129,8 +1126,7 @@ public class SeqPanel
               continue;
             }
 
-            if (!jalview.util.Comparison.isGap(
-                groupSeqs[g].getCharAt(j)))
+            if (!jalview.util.Comparison.isGap(groupSeqs[g].getCharAt(j)))
             {
               // Not a gap, block edit not valid
               endEditing();
@@ -1152,11 +1148,8 @@ public class SeqPanel
         }
         else
         {
-          editCommand.appendEdit(EditCommand.INSERT_GAP,
-                                 groupSeqs,
-                                 startres, startres - lastres,
-                                 av.alignment,
-                                 true);
+          editCommand.appendEdit(EditCommand.INSERT_GAP, groupSeqs,
+                  startres, startres - lastres, av.alignment, true);
         }
       }
       else
@@ -1171,16 +1164,14 @@ public class SeqPanel
         }
         else
         {
-          editCommand.appendEdit(EditCommand.DELETE_GAP,
-                                 groupSeqs,
-                                 startres, lastres - startres,
-                                 av.alignment,
-                                 true);
+          editCommand.appendEdit(EditCommand.DELETE_GAP, groupSeqs,
+                  startres, lastres - startres, av.alignment, true);
         }
 
       }
     }
-    else /////Editing a single sequence///////////
+    else
+    // ///Editing a single sequence///////////
     {
       if (insertGap)
       {
@@ -1190,17 +1181,13 @@ public class SeqPanel
           for (int j = lastres; j < startres; j++)
           {
             insertChar(j, new SequenceI[]
-                       {seq}, fixedRight);
+            { seq }, fixedRight);
           }
         }
         else
         {
-          editCommand.appendEdit(EditCommand.INSERT_GAP,
-                                 new SequenceI[]
-                                 {seq},
-                                 lastres, startres - lastres,
-                                 av.alignment,
-                                 true);
+          editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[]
+          { seq }, lastres, startres - lastres, av.alignment, true);
         }
       }
       else
@@ -1216,12 +1203,12 @@ public class SeqPanel
               break;
             }
             deleteChar(startres, new SequenceI[]
-                       {seq}, fixedRight);
+            { seq }, fixedRight);
           }
         }
         else
         {
-          //could be a keyboard edit trying to delete none gaps
+          // could be a keyboard edit trying to delete none gaps
           int max = 0;
           for (int m = startres; m < lastres; m++)
           {
@@ -1234,12 +1221,8 @@ public class SeqPanel
 
           if (max > 0)
           {
-            editCommand.appendEdit(EditCommand.DELETE_GAP,
-                                   new SequenceI[]
-                                   {seq},
-                                   startres, max,
-                                   av.alignment,
-                                   true);
+            editCommand.appendEdit(EditCommand.DELETE_GAP, new SequenceI[]
+            { seq }, startres, max, av.alignment, true);
           }
         }
       }
@@ -1254,14 +1237,14 @@ public class SeqPanel
     int blankColumn = fixedColumn;
     for (int s = 0; s < seq.length; s++)
     {
-      //Find the next gap before the end of the visible region boundary
-      //If lastCol > j, theres a boundary after the gap insertion
+      // Find the next gap before the end of the visible region boundary
+      // If lastCol > j, theres a boundary after the gap insertion
 
       for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
       {
         if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
         {
-          //Theres a space, so break and insert the gap
+          // Theres a space, so break and insert the gap
           break;
         }
       }
@@ -1274,32 +1257,27 @@ public class SeqPanel
       }
     }
 
-    editCommand.appendEdit(EditCommand.DELETE_GAP,
-                           seq,
-                           blankColumn, 1, av.alignment, true);
+    editCommand.appendEdit(EditCommand.DELETE_GAP, seq, blankColumn, 1,
+            av.alignment, true);
 
-    editCommand.appendEdit(EditCommand.INSERT_GAP,
-                           seq,
-                           j, 1, av.alignment,
-                           true);
+    editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1, av.alignment,
+            true);
 
   }
 
   void deleteChar(int j, SequenceI[] seq, int fixedColumn)
   {
 
-    editCommand.appendEdit(EditCommand.DELETE_GAP,
-                           seq,
-                           j, 1, av.alignment, true);
+    editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1, av.alignment,
+            true);
 
-    editCommand.appendEdit(EditCommand.INSERT_GAP,
-                           seq,
-                           fixedColumn, 1, av.alignment, true);
+    editCommand.appendEdit(EditCommand.INSERT_GAP, seq, fixedColumn, 1,
+            av.alignment, true);
   }
 
-//////////////////////////////////////////
-/////Everything below this is for defining the boundary of the rubberband
-//////////////////////////////////////////
+  // ////////////////////////////////////////
+  // ///Everything below this is for defining the boundary of the rubberband
+  // ////////////////////////////////////////
   public void doMousePressedDefineMode(MouseEvent evt)
   {
     if (scrollThread != null)
@@ -1330,8 +1308,8 @@ public class SeqPanel
     if (stretchGroup == null)
     {
       stretchGroup = av.alignment.findGroup(sequence);
-      if (stretchGroup != null && res > stretchGroup.getStartRes() &&
-          res < stretchGroup.getEndRes())
+      if (stretchGroup != null && res > stretchGroup.getStartRes()
+              && res < stretchGroup.getEndRes())
       {
         av.setSelectionGroup(stretchGroup);
       }
@@ -1342,8 +1320,8 @@ public class SeqPanel
     }
 
     else if (!stretchGroup.getSequences(null).contains(sequence)
-             || stretchGroup.getStartRes() > res
-             || stretchGroup.getEndRes() < res)
+            || stretchGroup.getStartRes() > res
+            || stretchGroup.getEndRes() < res)
     {
       stretchGroup = null;
 
@@ -1353,8 +1331,8 @@ public class SeqPanel
       {
         for (int i = 0; i < allGroups.length; i++)
         {
-          if (allGroups[i].getStartRes() <= res &&
-              allGroups[i].getEndRes() >= res)
+          if (allGroups[i].getStartRes() <= res
+                  && allGroups[i].getEndRes() >= res)
           {
             stretchGroup = allGroups[i];
             break;
@@ -1365,11 +1343,10 @@ public class SeqPanel
     }
 
     // DETECT RIGHT MOUSE BUTTON IN AWT
-    if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==
-        InputEvent.BUTTON3_MASK)
+    if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
     {
-      SequenceFeature [] allFeatures = findFeaturesAtRes(sequence,
-                                               sequence.findPosition(res));
+      SequenceFeature[] allFeatures = findFeaturesAtRes(sequence, sequence
+              .findPosition(res));
 
       Vector links = null;
       if (allFeatures != null)
@@ -1378,10 +1355,13 @@ public class SeqPanel
         {
           if (allFeatures[i].links != null)
           {
-            links = new Vector();
+            if (links==null)
+            { 
+              links = new Vector();
+            }
             for (int j = 0; j < allFeatures[i].links.size(); j++)
             {
-              links.addElement(allFeatures[i].links.elementAt(j));
+            links.addElement(allFeatures[i].links.elementAt(j));
             }
           }
         }
@@ -1400,7 +1380,7 @@ public class SeqPanel
       return;
     }
 
-    //Only if left mouse button do we want to change group sizes
+    // Only if left mouse button do we want to change group sizes
 
     if (stretchGroup == null)
     {
@@ -1415,12 +1395,12 @@ public class SeqPanel
       if (av.getConservationSelected())
       {
         SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
-                                          "Background");
+                "Background");
       }
       if (av.getAbovePIDThreshold())
       {
         SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
-                                       "Background");
+                "Background");
       }
 
     }
@@ -1437,29 +1417,29 @@ public class SeqPanel
     {
       if (stretchGroup.cs instanceof ClustalxColourScheme)
       {
-        ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(
-            stretchGroup.getSequences(av.hiddenRepSequences),
-            stretchGroup.getWidth());
+        ((ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup
+                .getSequences(av.hiddenRepSequences), stretchGroup
+                .getWidth());
       }
 
       if (stretchGroup.cs instanceof Blosum62ColourScheme
-          || stretchGroup.cs instanceof PIDColourScheme
-          || stretchGroup.cs.conservationApplied()
-          || stretchGroup.cs.getThreshold() > 0)
+              || stretchGroup.cs instanceof PIDColourScheme
+              || stretchGroup.cs.conservationApplied()
+              || stretchGroup.cs.getThreshold() > 0)
       {
         stretchGroup.recalcConservation();
       }
 
       if (stretchGroup.cs.conservationApplied())
       {
-        SliderPanel.setConservationSlider(ap, stretchGroup.cs,
-                                          stretchGroup.getName());
+        SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup
+                .getName());
         stretchGroup.recalcConservation();
       }
       else
       {
-        SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
-                                       stretchGroup.getName());
+        SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup
+                .getName());
       }
     }
     changeEndRes = false;
@@ -1538,7 +1518,7 @@ public class SeqPanel
       dragDirection = -1;
     }
 
-    while ( (y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
+    while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
     {
       // This routine ensures we don't skip any sequences, as the
       // selection is quite slow.
@@ -1573,8 +1553,8 @@ public class SeqPanel
       oldSeq = -1;
     }
 
-    if (res > av.endRes || res < av.startRes
-        || y < av.startSeq || y > av.endSeq)
+    if (res > av.endRes || res < av.startRes || y < av.startSeq
+            || y > av.endSeq)
     {
       mouseExited(evt);
     }
@@ -1639,11 +1619,12 @@ public class SeqPanel
   }
 
   // this class allows scrolling off the bottom of the visible alignment
-  class ScrollThread
-      extends Thread
+  class ScrollThread extends Thread
   {
     MouseEvent evt;
+
     boolean running = false;
+
     public ScrollThread()
     {
       start();
@@ -1673,8 +1654,8 @@ public class SeqPanel
             running = ap.scrollUp(true);
           }
 
-          if (mouseDragging && evt.getY() >= getSize().height &&
-              av.alignment.getHeight() > av.getEndSeq())
+          if (mouseDragging && evt.getY() >= getSize().height
+                  && av.alignment.getHeight() > av.getEndSeq())
           {
             running = ap.scrollUp(false);
           }
@@ -1693,9 +1674,9 @@ public class SeqPanel
         try
         {
           Thread.sleep(75);
+        } catch (Exception ex)
+        {
         }
-        catch (Exception ex)
-        {}
       }
     }
   }
diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index daf971d..c41c35f 100755
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -1,333 +1,340 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.appletgui;
-
-import java.awt.*;
-
-import jalview.datamodel.*;
-import jalview.schemes.*;
-
-public class SequenceRenderer
-{
-  AlignViewport av;
-  FontMetrics fm;
-  boolean renderGaps = true;
-  SequenceGroup currentSequenceGroup = null;
-  SequenceGroup[] allGroups = null;
-  Color resBoxColour;
-  Graphics graphics;
-  boolean forOverview = false;
-
-  public SequenceRenderer(AlignViewport av)
-  {
-    this.av = av;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param b DOCUMENT ME!
-   */
-  public void prepare(Graphics g, boolean renderGaps)
-  {
-    graphics = g;
-    fm = g.getFontMetrics();
-
-    this.renderGaps = renderGaps;
-  }
-
-  public Color getResidueBoxColour(SequenceI seq, int i)
-  {
-    allGroups = av.alignment.findAllGroups(seq);
-
-    if (inCurrentSequenceGroup(i))
-    {
-      if (currentSequenceGroup.getDisplayBoxes())
-      {
-        getBoxColour(currentSequenceGroup.cs, seq, i);
-      }
-    }
-    else if (av.getShowBoxes())
-    {
-      getBoxColour(av.globalColourScheme, seq, i);
-    }
-
-    return resBoxColour;
-  }
-
-  void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
-  {
-    if (cs != null)
-    {
-      resBoxColour = cs.findColour(seq.getCharAt(i), i);
-    }
-    else if (forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
-    {
-      resBoxColour = Color.lightGray;
-    }
-    else
-    {
-      resBoxColour = Color.white;
-    }
-
-  }
-
-  public Color findSequenceColour(SequenceI seq, int i)
-  {
-    allGroups = av.alignment.findAllGroups(seq);
-    drawBoxes(seq, i, i, 0);
-    return resBoxColour;
-  }
-
-  public void drawSequence(SequenceI seq, SequenceGroup[] sg,
-                           int start, int end, int y1)
-  {
-    if (seq == null)
-    {
-      return;
-    }
-
-    allGroups = sg;
-
-    drawBoxes(seq, start, end, y1);
-
-    if (av.validCharWidth)
-    {
-      drawText(seq, start, end, y1);
-    }
-  }
-
-  public void drawBoxes(SequenceI seq, int start, int end, int y1)
-  {
-    int i = start;
-    int length = seq.getLength();
-
-    int curStart = -1;
-    int curWidth = av.charWidth;
-
-    Color tempColour = null;
-    while (i <= end)
-    {
-      resBoxColour = Color.white;
-      if (i < length)
-      {
-        if (inCurrentSequenceGroup(i))
-        {
-          if (currentSequenceGroup.getDisplayBoxes())
-          {
-            getBoxColour(currentSequenceGroup.cs, seq, i);
-          }
-        }
-        else if (av.getShowBoxes())
-        {
-          getBoxColour(av.getGlobalColourScheme(), seq, i);
-        }
-      }
-
-      if (resBoxColour != tempColour)
-      {
-        if (tempColour != null)
-        {
-          graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,
-                            av.charHeight);
-        }
-        graphics.setColor(resBoxColour);
-
-        curStart = i;
-        curWidth = av.charWidth;
-        tempColour = resBoxColour;
-
-      }
-      else
-      {
-        curWidth += av.charWidth;
-      }
-
-      i++;
-    }
-
-    graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,
-                      av.charHeight);
-  }
-
-  public void drawText(SequenceI seq, int start, int end, int y1)
-  {
-    Font boldFont = null;
-    boolean bold = false;
-    if (av.upperCasebold)
-    {
-      boldFont = new Font(av.getFont().getName(), Font.BOLD, av.charHeight);
-
-      graphics.setFont(av.getFont());
-    }
-
-    y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady
-
-    int charOffset = 0;
-
-    // Need to find the sequence position here.
-    if (end + 1 >= seq.getLength())
-    {
-      end = seq.getLength() - 1;
-    }
-
-    char s = ' ';
-
-    for (int i = start; i <= end; i++)
-    {
-      graphics.setColor(Color.black);
-
-      s = seq.getCharAt(i);
-      if (!renderGaps && jalview.util.Comparison.isGap(s))
-      {
-        continue;
-      }
-
-      if (inCurrentSequenceGroup(i))
-      {
-        if (!currentSequenceGroup.getDisplayText())
-        {
-          continue;
-        }
-
-        if (currentSequenceGroup.getColourText())
-        {
-          getBoxColour(currentSequenceGroup.cs, seq, i);
-          graphics.setColor(resBoxColour.darker());
-        }
-      }
-      else
-      {
-        if (!av.getShowText())
-        {
-          continue;
-        }
-
-        if (av.getColourText())
-        {
-          getBoxColour(av.getGlobalColourScheme(), seq, i);
-          if (av.getShowBoxes())
-          {
-            graphics.setColor(resBoxColour.darker());
-          }
-          else
-          {
-            graphics.setColor(resBoxColour);
-          }
-        }
-      }
-
-      if (av.upperCasebold)
-      {
-        fm = graphics.getFontMetrics();
-        if ('A' <= s && s <= 'Z')
-        {
-          if (!bold)
-          {
-
-            graphics.setFont(boldFont);
-          }
-          bold = true;
-        }
-        else if (bold)
-        {
-          graphics.setFont(av.font);
-          bold = false;
-        }
-
-      }
-
-      charOffset = (av.charWidth - fm.charWidth(s)) / 2;
-      graphics.drawString(String.valueOf(s),
-                          charOffset + av.charWidth * (i - start),
-                          y1);
-    }
-
-  }
-
-  boolean inCurrentSequenceGroup(int res)
-  {
-    if (allGroups == null)
-    {
-      return false;
-    }
-
-    for (int i = 0; i < allGroups.length; i++)
-    {
-      if (allGroups[i].getStartRes() <= res && allGroups[i].getEndRes() >= res)
-      {
-        currentSequenceGroup = allGroups[i];
-        return true;
-      }
-    }
-
-    return false;
-  }
-
-  public void drawHighlightedText(SequenceI seq, int start, int end, int x1,
-                                  int y1)
-  {
-    int pady = av.charHeight / 5;
-    int charOffset = 0;
-    graphics.setColor(Color.black);
-    graphics.fillRect(x1, y1, av.charWidth * (end - start + 1), av.charHeight);
-    graphics.setColor(Color.white);
-
-    char s = '~';
-    // Need to find the sequence position here.
-    if (av.validCharWidth)
-    {
-      for (int i = start; i <= end; i++)
-      {
-        if (i < seq.getLength())
-        {
-          s = seq.getCharAt(i);
-        }
-
-        charOffset = (av.charWidth - fm.charWidth(s)) / 2;
-        graphics.drawString(String.valueOf(s),
-                            charOffset + x1 + av.charWidth * (i - start),
-                            y1 + av.charHeight - pady);
-      }
-    }
-  }
-
-  public void drawCursor(SequenceI seq, int res, int x1, int y1)
-  {
-    int pady = av.charHeight / 5;
-    int charOffset = 0;
-    graphics.setColor(Color.black);
-    graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
-    graphics.setColor(Color.white);
-
-    graphics.setColor(Color.white);
-
-    char s = seq.getCharAt(res);
-    if (av.validCharWidth)
-    {
-
-      charOffset = (av.charWidth - fm.charWidth(s)) / 2;
-      graphics.drawString(String.valueOf(s),
-                          charOffset + x1,
-                          (y1 + av.charHeight) - pady);
-    }
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.appletgui;
+
+import java.awt.*;
+
+import jalview.datamodel.*;
+import jalview.schemes.*;
+
+public class SequenceRenderer
+{
+  AlignViewport av;
+
+  FontMetrics fm;
+
+  boolean renderGaps = true;
+
+  SequenceGroup currentSequenceGroup = null;
+
+  SequenceGroup[] allGroups = null;
+
+  Color resBoxColour;
+
+  Graphics graphics;
+
+  boolean forOverview = false;
+
+  public SequenceRenderer(AlignViewport av)
+  {
+    this.av = av;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param b
+   *                DOCUMENT ME!
+   */
+  public void prepare(Graphics g, boolean renderGaps)
+  {
+    graphics = g;
+    fm = g.getFontMetrics();
+
+    this.renderGaps = renderGaps;
+  }
+
+  public Color getResidueBoxColour(SequenceI seq, int i)
+  {
+    allGroups = av.alignment.findAllGroups(seq);
+
+    if (inCurrentSequenceGroup(i))
+    {
+      if (currentSequenceGroup.getDisplayBoxes())
+      {
+        getBoxColour(currentSequenceGroup.cs, seq, i);
+      }
+    }
+    else if (av.getShowBoxes())
+    {
+      getBoxColour(av.globalColourScheme, seq, i);
+    }
+
+    return resBoxColour;
+  }
+
+  void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
+  {
+    if (cs != null)
+    {
+      resBoxColour = cs.findColour(seq.getCharAt(i), i);
+    }
+    else if (forOverview
+            && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
+    {
+      resBoxColour = Color.lightGray;
+    }
+    else
+    {
+      resBoxColour = Color.white;
+    }
+
+  }
+
+  public Color findSequenceColour(SequenceI seq, int i)
+  {
+    allGroups = av.alignment.findAllGroups(seq);
+    drawBoxes(seq, i, i, 0);
+    return resBoxColour;
+  }
+
+  public void drawSequence(SequenceI seq, SequenceGroup[] sg, int start,
+          int end, int y1)
+  {
+    if (seq == null)
+    {
+      return;
+    }
+
+    allGroups = sg;
+
+    drawBoxes(seq, start, end, y1);
+
+    if (av.validCharWidth)
+    {
+      drawText(seq, start, end, y1);
+    }
+  }
+
+  public void drawBoxes(SequenceI seq, int start, int end, int y1)
+  {
+    int i = start;
+    int length = seq.getLength();
+
+    int curStart = -1;
+    int curWidth = av.charWidth;
+
+    Color tempColour = null;
+    while (i <= end)
+    {
+      resBoxColour = Color.white;
+      if (i < length)
+      {
+        if (inCurrentSequenceGroup(i))
+        {
+          if (currentSequenceGroup.getDisplayBoxes())
+          {
+            getBoxColour(currentSequenceGroup.cs, seq, i);
+          }
+        }
+        else if (av.getShowBoxes())
+        {
+          getBoxColour(av.getGlobalColourScheme(), seq, i);
+        }
+      }
+
+      if (resBoxColour != tempColour)
+      {
+        if (tempColour != null)
+        {
+          graphics.fillRect(av.charWidth * (curStart - start), y1,
+                  curWidth, av.charHeight);
+        }
+        graphics.setColor(resBoxColour);
+
+        curStart = i;
+        curWidth = av.charWidth;
+        tempColour = resBoxColour;
+
+      }
+      else
+      {
+        curWidth += av.charWidth;
+      }
+
+      i++;
+    }
+
+    graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,
+            av.charHeight);
+  }
+
+  public void drawText(SequenceI seq, int start, int end, int y1)
+  {
+    Font boldFont = null;
+    boolean bold = false;
+    if (av.upperCasebold)
+    {
+      boldFont = new Font(av.getFont().getName(), Font.BOLD, av.charHeight);
+
+      graphics.setFont(av.getFont());
+    }
+
+    y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady
+
+    int charOffset = 0;
+
+    // Need to find the sequence position here.
+    if (end + 1 >= seq.getLength())
+    {
+      end = seq.getLength() - 1;
+    }
+
+    char s = ' ';
+
+    for (int i = start; i <= end; i++)
+    {
+      graphics.setColor(Color.black);
+
+      s = seq.getCharAt(i);
+      if (!renderGaps && jalview.util.Comparison.isGap(s))
+      {
+        continue;
+      }
+
+      if (inCurrentSequenceGroup(i))
+      {
+        if (!currentSequenceGroup.getDisplayText())
+        {
+          continue;
+        }
+
+        if (currentSequenceGroup.getColourText())
+        {
+          getBoxColour(currentSequenceGroup.cs, seq, i);
+          graphics.setColor(resBoxColour.darker());
+        }
+      }
+      else
+      {
+        if (!av.getShowText())
+        {
+          continue;
+        }
+
+        if (av.getColourText())
+        {
+          getBoxColour(av.getGlobalColourScheme(), seq, i);
+          if (av.getShowBoxes())
+          {
+            graphics.setColor(resBoxColour.darker());
+          }
+          else
+          {
+            graphics.setColor(resBoxColour);
+          }
+        }
+      }
+
+      if (av.upperCasebold)
+      {
+        fm = graphics.getFontMetrics();
+        if ('A' <= s && s <= 'Z')
+        {
+          if (!bold)
+          {
+
+            graphics.setFont(boldFont);
+          }
+          bold = true;
+        }
+        else if (bold)
+        {
+          graphics.setFont(av.font);
+          bold = false;
+        }
+
+      }
+
+      charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+      graphics.drawString(String.valueOf(s), charOffset + av.charWidth
+              * (i - start), y1);
+    }
+
+  }
+
+  boolean inCurrentSequenceGroup(int res)
+  {
+    if (allGroups == null)
+    {
+      return false;
+    }
+
+    for (int i = 0; i < allGroups.length; i++)
+    {
+      if (allGroups[i].getStartRes() <= res
+              && allGroups[i].getEndRes() >= res)
+      {
+        currentSequenceGroup = allGroups[i];
+        return true;
+      }
+    }
+
+    return false;
+  }
+
+  public void drawHighlightedText(SequenceI seq, int start, int end,
+          int x1, int y1)
+  {
+    int pady = av.charHeight / 5;
+    int charOffset = 0;
+    graphics.setColor(Color.black);
+    graphics.fillRect(x1, y1, av.charWidth * (end - start + 1),
+            av.charHeight);
+    graphics.setColor(Color.white);
+
+    char s = '~';
+    // Need to find the sequence position here.
+    if (av.validCharWidth)
+    {
+      for (int i = start; i <= end; i++)
+      {
+        if (i < seq.getLength())
+        {
+          s = seq.getCharAt(i);
+        }
+
+        charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+        graphics.drawString(String.valueOf(s), charOffset + x1
+                + av.charWidth * (i - start), y1 + av.charHeight - pady);
+      }
+    }
+  }
+
+  public void drawCursor(SequenceI seq, int res, int x1, int y1)
+  {
+    int pady = av.charHeight / 5;
+    int charOffset = 0;
+    graphics.setColor(Color.black);
+    graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
+    graphics.setColor(Color.white);
+
+    graphics.setColor(Color.white);
+
+    char s = seq.getCharAt(res);
+    if (av.validCharWidth)
+    {
+
+      charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+      graphics.drawString(String.valueOf(s), charOffset + x1,
+              (y1 + av.charHeight) - pady);
+    }
+  }
+
+}
diff --git a/src/jalview/appletgui/SliderPanel.java b/src/jalview/appletgui/SliderPanel.java
index 8507331..a05bbf0 100755
--- a/src/jalview/appletgui/SliderPanel.java
+++ b/src/jalview/appletgui/SliderPanel.java
@@ -1,363 +1,377 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.appletgui;
-
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
-import jalview.schemes.*;
-
-public class SliderPanel
-    extends Panel implements ActionListener,
-    AdjustmentListener,
-    MouseListener
-{
-  AlignmentPanel ap;
-  boolean forConservation = true;
-  ColourSchemeI cs;
-
-  static Frame conservationSlider;
-  static Frame PIDSlider;
-
-  public static int setConservationSlider(AlignmentPanel ap, ColourSchemeI cs,
-                                          String source)
-  {
-    SliderPanel sp = null;
-
-    if (conservationSlider == null)
-    {
-      sp = new SliderPanel(ap, cs.getConservationInc(), true, cs);
-      conservationSlider = new Frame();
-      conservationSlider.add(sp);
-    }
-    else
-    {
-      sp = (SliderPanel) conservationSlider.getComponent(0);
-      sp.cs = cs;
-    }
-
-    conservationSlider.setTitle("Conservation Colour Increment  (" + source +
-                                ")");
-    if (ap.av.alignment.getGroups() != null)
-    {
-      sp.setAllGroupsCheckEnabled(true);
-    }
-    else
-    {
-      sp.setAllGroupsCheckEnabled(false);
-    }
-
-    return sp.getValue();
-  }
-
-  public static void showConservationSlider()
-  {
-    try
-    {
-      PIDSlider.setVisible(false);
-      PIDSlider = null;
-    }
-    catch (Exception ex)
-    {}
-
-    if (!conservationSlider.isVisible())
-    {
-      jalview.bin.JalviewLite.addFrame(conservationSlider,
-                                       conservationSlider.getTitle(), 420, 100);
-      conservationSlider.addWindowListener(new WindowAdapter()
-      {
-        public void windowClosing(WindowEvent e)
-        {
-          conservationSlider = null;
-        }
-      });
-
-    }
-
-  }
-
-  public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs,
-                                       String source)
-  {
-    SliderPanel pid = null;
-    if (PIDSlider == null)
-    {
-      pid = new SliderPanel(ap, 50, false, cs);
-      PIDSlider = new Frame();
-      PIDSlider.add(pid);
-    }
-    else
-    {
-      pid = (SliderPanel) PIDSlider.getComponent(0);
-      pid.cs = cs;
-    }
-    PIDSlider.setTitle("Percentage Identity Threshold (" + source + ")");
-
-    if (ap.av.alignment.getGroups() != null)
-    {
-      pid.setAllGroupsCheckEnabled(true);
-    }
-    else
-    {
-      pid.setAllGroupsCheckEnabled(false);
-    }
-
-    return pid.getValue();
-
-  }
-
-  public static void showPIDSlider()
-  {
-    try
-    {
-      conservationSlider.setVisible(false);
-      conservationSlider = null;
-    }
-    catch (Exception ex)
-    {}
-
-    if (!PIDSlider.isVisible())
-    {
-      jalview.bin.JalviewLite.addFrame(PIDSlider, PIDSlider.getTitle(), 420,
-                                       100);
-      PIDSlider.addWindowListener(new WindowAdapter()
-      {
-        public void windowClosing(WindowEvent e)
-        {
-          PIDSlider = null;
-        }
-      });
-    }
-
-  }
-
-  public SliderPanel(AlignmentPanel ap, int value, boolean forConserve,
-                     ColourSchemeI cs)
-  {
-    try
-    {
-      jbInit();
-    }
-    catch (Exception e)
-    {
-      e.printStackTrace();
-    }
-    this.ap = ap;
-    this.cs = cs;
-    forConservation = forConserve;
-    undoButton.setVisible(false);
-    applyButton.setVisible(false);
-    if (forConservation)
-    {
-      label.setText("Modify conservation visibility");
-      slider.setMinimum(0);
-      slider.setMaximum(50 + slider.getVisibleAmount());
-      slider.setUnitIncrement(1);
-    }
-    else
-    {
-      label.setText("Colour residues above % occurence");
-      slider.setMinimum(0);
-      slider.setMaximum(100 + slider.getVisibleAmount());
-      slider.setBlockIncrement(1);
-    }
-
-    slider.addAdjustmentListener(this);
-    slider.addMouseListener(this);
-
-    slider.setValue(value);
-    valueField.setText(value + "");
-  }
-
-  public void valueChanged(int i)
-  {
-    if (cs == null)
-    {
-      return;
-    }
-
-    ColourSchemeI toChange = null;
-    Vector allGroups = null;
-    int groupIndex = 0;
-
-    if (allGroupsCheck.getState())
-    {
-      allGroups = ap.av.alignment.getGroups();
-      groupIndex = allGroups.size() - 1;
-    }
-    else
-    {
-      toChange = cs;
-    }
-
-    while (groupIndex > -1)
-    {
-      if (allGroups != null)
-      {
-        toChange = ( (SequenceGroup) allGroups.elementAt(groupIndex)).cs;
-      }
-
-      if (forConservation)
-      {
-        toChange.setConservationInc(i);
-      }
-      else
-      {
-        toChange.setThreshold(i, ap.av.getIgnoreGapsConsensus());
-      }
-
-      groupIndex--;
-    }
-
-    ap.seqPanel.seqCanvas.repaint();
-
-  }
-
-  public void setAllGroupsCheckEnabled(boolean b)
-  {
-    allGroupsCheck.setEnabled(b);
-  }
-
-  public void actionPerformed(ActionEvent evt)
-  {
-    if (evt.getSource() == applyButton)
-    {
-      applyButton_actionPerformed();
-    }
-    else if (evt.getSource() == undoButton)
-    {
-      undoButton_actionPerformed();
-    }
-    else if (evt.getSource() == valueField)
-    {
-      valueField_actionPerformed();
-    }
-  }
-
-  public void adjustmentValueChanged(AdjustmentEvent evt)
-  {
-    valueField.setText(slider.getValue() + "");
-    valueChanged(slider.getValue());
-  }
-
-  public void valueField_actionPerformed()
-  {
-    try
-    {
-      int i = Integer.parseInt(valueField.getText());
-      slider.setValue(i);
-    }
-    catch (Exception ex)
-    {
-      valueField.setText(slider.getValue() + "");
-    }
-  }
-
-  public void setValue(int value)
-  {
-    slider.setValue(value);
-  }
-
-  public int getValue()
-  {
-    return Integer.parseInt(valueField.getText());
-  }
-
-  // this is used for conservation colours, PID colours and redundancy threshold
-  protected Scrollbar slider = new Scrollbar();
-  protected TextField valueField = new TextField();
-  protected Label label = new Label();
-  Panel jPanel1 = new Panel();
-  Panel jPanel2 = new Panel();
-  protected Button applyButton = new Button();
-  protected Button undoButton = new Button();
-  FlowLayout flowLayout1 = new FlowLayout();
-  protected Checkbox allGroupsCheck = new Checkbox();
-  BorderLayout borderLayout1 = new BorderLayout();
-  BorderLayout borderLayout2 = new BorderLayout();
-  FlowLayout flowLayout2 = new FlowLayout();
-
-  private void jbInit()
-      throws Exception
-  {
-    this.setLayout(borderLayout2);
-
-    // slider.setMajorTickSpacing(10);
-    //  slider.setMinorTickSpacing(1);
-    //  slider.setPaintTicks(true);
-    slider.setBackground(Color.white);
-    slider.setFont(new java.awt.Font("Verdana", 0, 11));
-    slider.setOrientation(0);
-    valueField.setFont(new java.awt.Font("Verdana", 0, 11));
-    valueField.setText("      ");
-    valueField.addActionListener(this);
-    label.setFont(new java.awt.Font("Verdana", 0, 11));
-    label.setText("set this label text");
-    jPanel1.setLayout(borderLayout1);
-    jPanel2.setLayout(flowLayout1);
-    applyButton.setFont(new java.awt.Font("Verdana", 0, 11));
-    applyButton.setLabel("Apply");
-    applyButton.addActionListener(this);
-    undoButton.setEnabled(false);
-    undoButton.setFont(new java.awt.Font("Verdana", 0, 11));
-    undoButton.setLabel("Undo");
-    undoButton.addActionListener(this);
-    allGroupsCheck.setEnabled(false);
-    allGroupsCheck.setFont(new java.awt.Font("Verdana", 0, 11));
-    allGroupsCheck.setLabel("Apply threshold to all groups");
-    allGroupsCheck.setName("Apply to all Groups");
-    this.setBackground(Color.white);
-    this.setForeground(Color.black);
-    jPanel2.add(label, null);
-    jPanel2.add(applyButton, null);
-    jPanel2.add(undoButton, null);
-    jPanel2.add(allGroupsCheck);
-    jPanel1.add(valueField, java.awt.BorderLayout.EAST);
-    jPanel1.add(slider, java.awt.BorderLayout.CENTER);
-    this.add(jPanel1, java.awt.BorderLayout.SOUTH);
-    this.add(jPanel2, java.awt.BorderLayout.CENTER);
-  }
-
-  protected void applyButton_actionPerformed()
-  {}
-
-  protected void undoButton_actionPerformed()
-  {}
-
-  public void mousePressed(MouseEvent evt)
-  {}
-
-  public void mouseReleased(MouseEvent evt)
-  {
-      ap.paintAlignment(true);
-  }
-
-  public void mouseClicked(MouseEvent evt)
-  {}
-
-  public void mouseEntered(MouseEvent evt)
-  {}
-
-  public void mouseExited(MouseEvent evt)
-  {}
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.appletgui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import jalview.datamodel.*;
+import jalview.schemes.*;
+
+public class SliderPanel extends Panel implements ActionListener,
+        AdjustmentListener, MouseListener
+{
+  AlignmentPanel ap;
+
+  boolean forConservation = true;
+
+  ColourSchemeI cs;
+
+  static Frame conservationSlider;
+
+  static Frame PIDSlider;
+
+  public static int setConservationSlider(AlignmentPanel ap,
+          ColourSchemeI cs, String source)
+  {
+    SliderPanel sp = null;
+
+    if (conservationSlider == null)
+    {
+      sp = new SliderPanel(ap, cs.getConservationInc(), true, cs);
+      conservationSlider = new Frame();
+      conservationSlider.add(sp);
+    }
+    else
+    {
+      sp = (SliderPanel) conservationSlider.getComponent(0);
+      sp.cs = cs;
+    }
+
+    conservationSlider.setTitle("Conservation Colour Increment  (" + source
+            + ")");
+    if (ap.av.alignment.getGroups() != null)
+    {
+      sp.setAllGroupsCheckEnabled(true);
+    }
+    else
+    {
+      sp.setAllGroupsCheckEnabled(false);
+    }
+
+    return sp.getValue();
+  }
+
+  public static void showConservationSlider()
+  {
+    try
+    {
+      PIDSlider.setVisible(false);
+      PIDSlider = null;
+    } catch (Exception ex)
+    {
+    }
+
+    if (!conservationSlider.isVisible())
+    {
+      jalview.bin.JalviewLite.addFrame(conservationSlider,
+              conservationSlider.getTitle(), 420, 100);
+      conservationSlider.addWindowListener(new WindowAdapter()
+      {
+        public void windowClosing(WindowEvent e)
+        {
+          conservationSlider = null;
+        }
+      });
+
+    }
+
+  }
+
+  public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs,
+          String source)
+  {
+    SliderPanel pid = null;
+    if (PIDSlider == null)
+    {
+      pid = new SliderPanel(ap, 50, false, cs);
+      PIDSlider = new Frame();
+      PIDSlider.add(pid);
+    }
+    else
+    {
+      pid = (SliderPanel) PIDSlider.getComponent(0);
+      pid.cs = cs;
+    }
+    PIDSlider.setTitle("Percentage Identity Threshold (" + source + ")");
+
+    if (ap.av.alignment.getGroups() != null)
+    {
+      pid.setAllGroupsCheckEnabled(true);
+    }
+    else
+    {
+      pid.setAllGroupsCheckEnabled(false);
+    }
+
+    return pid.getValue();
+
+  }
+
+  public static void showPIDSlider()
+  {
+    try
+    {
+      conservationSlider.setVisible(false);
+      conservationSlider = null;
+    } catch (Exception ex)
+    {
+    }
+
+    if (!PIDSlider.isVisible())
+    {
+      jalview.bin.JalviewLite.addFrame(PIDSlider, PIDSlider.getTitle(),
+              420, 100);
+      PIDSlider.addWindowListener(new WindowAdapter()
+      {
+        public void windowClosing(WindowEvent e)
+        {
+          PIDSlider = null;
+        }
+      });
+    }
+
+  }
+
+  public SliderPanel(AlignmentPanel ap, int value, boolean forConserve,
+          ColourSchemeI cs)
+  {
+    try
+    {
+      jbInit();
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+    this.ap = ap;
+    this.cs = cs;
+    forConservation = forConserve;
+    undoButton.setVisible(false);
+    applyButton.setVisible(false);
+    if (forConservation)
+    {
+      label.setText("Modify conservation visibility");
+      slider.setMinimum(0);
+      slider.setMaximum(50 + slider.getVisibleAmount());
+      slider.setUnitIncrement(1);
+    }
+    else
+    {
+      label.setText("Colour residues above % occurence");
+      slider.setMinimum(0);
+      slider.setMaximum(100 + slider.getVisibleAmount());
+      slider.setBlockIncrement(1);
+    }
+
+    slider.addAdjustmentListener(this);
+    slider.addMouseListener(this);
+
+    slider.setValue(value);
+    valueField.setText(value + "");
+  }
+
+  public void valueChanged(int i)
+  {
+    if (cs == null)
+    {
+      return;
+    }
+
+    ColourSchemeI toChange = null;
+    Vector allGroups = null;
+    int groupIndex = 0;
+
+    if (allGroupsCheck.getState())
+    {
+      allGroups = ap.av.alignment.getGroups();
+      groupIndex = allGroups.size() - 1;
+    }
+    else
+    {
+      toChange = cs;
+    }
+
+    while (groupIndex > -1)
+    {
+      if (allGroups != null)
+      {
+        toChange = ((SequenceGroup) allGroups.elementAt(groupIndex)).cs;
+      }
+
+      if (forConservation)
+      {
+        toChange.setConservationInc(i);
+      }
+      else
+      {
+        toChange.setThreshold(i, ap.av.getIgnoreGapsConsensus());
+      }
+
+      groupIndex--;
+    }
+
+    ap.seqPanel.seqCanvas.repaint();
+
+  }
+
+  public void setAllGroupsCheckEnabled(boolean b)
+  {
+    allGroupsCheck.setEnabled(b);
+  }
+
+  public void actionPerformed(ActionEvent evt)
+  {
+    if (evt.getSource() == applyButton)
+    {
+      applyButton_actionPerformed();
+    }
+    else if (evt.getSource() == undoButton)
+    {
+      undoButton_actionPerformed();
+    }
+    else if (evt.getSource() == valueField)
+    {
+      valueField_actionPerformed();
+    }
+  }
+
+  public void adjustmentValueChanged(AdjustmentEvent evt)
+  {
+    valueField.setText(slider.getValue() + "");
+    valueChanged(slider.getValue());
+  }
+
+  public void valueField_actionPerformed()
+  {
+    try
+    {
+      int i = Integer.parseInt(valueField.getText());
+      slider.setValue(i);
+    } catch (Exception ex)
+    {
+      valueField.setText(slider.getValue() + "");
+    }
+  }
+
+  public void setValue(int value)
+  {
+    slider.setValue(value);
+  }
+
+  public int getValue()
+  {
+    return Integer.parseInt(valueField.getText());
+  }
+
+  // this is used for conservation colours, PID colours and redundancy threshold
+  protected Scrollbar slider = new Scrollbar();
+
+  protected TextField valueField = new TextField();
+
+  protected Label label = new Label();
+
+  Panel jPanel1 = new Panel();
+
+  Panel jPanel2 = new Panel();
+
+  protected Button applyButton = new Button();
+
+  protected Button undoButton = new Button();
+
+  FlowLayout flowLayout1 = new FlowLayout();
+
+  protected Checkbox allGroupsCheck = new Checkbox();
+
+  BorderLayout borderLayout1 = new BorderLayout();
+
+  BorderLayout borderLayout2 = new BorderLayout();
+
+  FlowLayout flowLayout2 = new FlowLayout();
+
+  private void jbInit() throws Exception
+  {
+    this.setLayout(borderLayout2);
+
+    // slider.setMajorTickSpacing(10);
+    // slider.setMinorTickSpacing(1);
+    // slider.setPaintTicks(true);
+    slider.setBackground(Color.white);
+    slider.setFont(new java.awt.Font("Verdana", 0, 11));
+    slider.setOrientation(0);
+    valueField.setFont(new java.awt.Font("Verdana", 0, 11));
+    valueField.setText("      ");
+    valueField.addActionListener(this);
+    label.setFont(new java.awt.Font("Verdana", 0, 11));
+    label.setText("set this label text");
+    jPanel1.setLayout(borderLayout1);
+    jPanel2.setLayout(flowLayout1);
+    applyButton.setFont(new java.awt.Font("Verdana", 0, 11));
+    applyButton.setLabel("Apply");
+    applyButton.addActionListener(this);
+    undoButton.setEnabled(false);
+    undoButton.setFont(new java.awt.Font("Verdana", 0, 11));
+    undoButton.setLabel("Undo");
+    undoButton.addActionListener(this);
+    allGroupsCheck.setEnabled(false);
+    allGroupsCheck.setFont(new java.awt.Font("Verdana", 0, 11));
+    allGroupsCheck.setLabel("Apply threshold to all groups");
+    allGroupsCheck.setName("Apply to all Groups");
+    this.setBackground(Color.white);
+    this.setForeground(Color.black);
+    jPanel2.add(label, null);
+    jPanel2.add(applyButton, null);
+    jPanel2.add(undoButton, null);
+    jPanel2.add(allGroupsCheck);
+    jPanel1.add(valueField, java.awt.BorderLayout.EAST);
+    jPanel1.add(slider, java.awt.BorderLayout.CENTER);
+    this.add(jPanel1, java.awt.BorderLayout.SOUTH);
+    this.add(jPanel2, java.awt.BorderLayout.CENTER);
+  }
+
+  protected void applyButton_actionPerformed()
+  {
+  }
+
+  protected void undoButton_actionPerformed()
+  {
+  }
+
+  public void mousePressed(MouseEvent evt)
+  {
+  }
+
+  public void mouseReleased(MouseEvent evt)
+  {
+    ap.paintAlignment(true);
+  }
+
+  public void mouseClicked(MouseEvent evt)
+  {
+  }
+
+  public void mouseEntered(MouseEvent evt)
+  {
+  }
+
+  public void mouseExited(MouseEvent evt)
+  {
+  }
+}
diff --git a/src/jalview/appletgui/Tooltip.java b/src/jalview/appletgui/Tooltip.java
index 7de5193..0bbe98b 100755
--- a/src/jalview/appletgui/Tooltip.java
+++ b/src/jalview/appletgui/Tooltip.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.appletgui;
 
 import java.applet.*;
@@ -25,21 +24,25 @@ import java.util.*;
 import java.awt.*;
 import java.awt.event.*;
 
-public class Tooltip
-    extends Canvas implements MouseListener,
-    MouseMotionListener
+public class Tooltip extends Canvas implements MouseListener,
+        MouseMotionListener
 {
   private String[] tip;
+
   private String lastTip = "";
+
   private boolean setPosition = false;
+
   protected Component owner;
 
   private Container mainContainer;
+
   private LayoutManager mainLayout;
 
   private boolean shown;
 
   private final int VERTICAL_OFFSET = 20;
+
   private final int HORIZONTAL_ENLARGE = 10;
 
   int fontHeight = 0;
@@ -77,15 +80,15 @@ public class Tooltip
       {
         if (lindex > 0)
         {
-          g.drawString(tip[i].substring(0, lindex), 3, (i + 1) * fontHeight - 3);
+          g.drawString(tip[i].substring(0, lindex), 3, (i + 1) * fontHeight
+                  - 3);
           x += fm.stringWidth(tip[i].substring(0, lindex) + 3);
         }
         g.drawImage(linkImage, x, i * fontHeight + 1, this);
         if (lindex + 6 < tip[i].length())
         {
-          g.drawString(tip[i].substring(lindex + 6),
-                       x + linkImage.getWidth(this),
-                       (i + 1) * fontHeight - 3);
+          g.drawString(tip[i].substring(lindex + 6), x
+                  + linkImage.getWidth(this), (i + 1) * fontHeight - 3);
         }
       }
       else
@@ -128,8 +131,7 @@ public class Tooltip
       index++;
     }
 
-    setSize(longestLine + HORIZONTAL_ENLARGE,
-            fontHeight * this.tip.length);
+    setSize(longestLine + HORIZONTAL_ENLARGE, fontHeight * this.tip.length);
 
     repaint();
 
@@ -137,21 +139,21 @@ public class Tooltip
 
   void setTipLocation(MouseEvent evt)
   {
-    if(mainContainer==null || owner==null)
+    if (mainContainer == null || owner == null)
     {
       return;
     }
-    setLocation( (owner.getLocationOnScreen().x
-                  - mainContainer.getLocationOnScreen().x) + evt.getX(),
-                (owner.getLocationOnScreen().y -
-                 mainContainer.getLocationOnScreen().y
-                 + VERTICAL_OFFSET) + evt.getY());
+    setLocation((owner.getLocationOnScreen().x - mainContainer
+            .getLocationOnScreen().x)
+            + evt.getX(), (owner.getLocationOnScreen().y
+            - mainContainer.getLocationOnScreen().y + VERTICAL_OFFSET)
+            + evt.getY());
 
     // correction, whole tool tip must be visible
     if (mainContainer.getSize().width < (getLocation().x + getSize().width))
     {
       setLocation(mainContainer.getSize().width - getSize().width,
-                  getLocation().y);
+              getLocation().y);
     }
   }
 
@@ -171,7 +173,7 @@ public class Tooltip
     Container parent = owner.getParent();
     while (true)
     {
-      if ( (parent instanceof Applet) || (parent instanceof Frame))
+      if ((parent instanceof Applet) || (parent instanceof Frame))
       {
         mainContainer = parent;
         break;
@@ -200,10 +202,12 @@ public class Tooltip
   }
 
   public void mouseReleased(MouseEvent me)
-  {}
+  {
+  }
 
   public void mouseClicked(MouseEvent me)
-  {}
+  {
+  }
 
   public void mouseMoved(MouseEvent me)
   {
@@ -224,5 +228,6 @@ public class Tooltip
   }
 
   public void mouseDragged(MouseEvent me)
-  {}
+  {
+  }
 }
diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 425c7a9..8c445f0 100755
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.appletgui;
 
 import java.util.*;
@@ -29,28 +28,39 @@ import jalview.datamodel.*;
 import jalview.schemes.*;
 import jalview.util.*;
 
-public class TreeCanvas
-    extends Panel implements MouseListener, MouseMotionListener
+public class TreeCanvas extends Panel implements MouseListener,
+        MouseMotionListener
 {
   NJTree tree;
+
   ScrollPane scrollPane;
+
   AlignViewport av;
+
   public static final String PLACEHOLDER = " * ";
+
   Font font;
+
   boolean fitToWindow = true;
+
   boolean showDistances = false;
+
   boolean showBootstrap = false;
+
   boolean markPlaceholders = false;
 
   int offx = 20;
+
   int offy;
 
   float threshold;
 
   String longestName;
+
   int labelLength = -1;
 
   Hashtable nameHash = new Hashtable();
+
   Hashtable nodeHash = new Hashtable();
 
   SequenceNode highlightNode;
@@ -99,19 +109,19 @@ public class TreeCanvas
         has_placeholders = true;
       }
 
-      if (longestName.length() < ( (Sequence) lf.element()).getName()
-          .length())
+      if (longestName.length() < ((Sequence) lf.element()).getName()
+              .length())
       {
-        longestName = TreeCanvas.PLACEHOLDER +
-            ( (Sequence) lf.element()).getName();
+        longestName = TreeCanvas.PLACEHOLDER
+                + ((Sequence) lf.element()).getName();
       }
     }
 
     setMarkPlaceholders(has_placeholders);
   }
 
-  public void drawNode(Graphics g, SequenceNode node, float chunk, float scale,
-                       int width, int offx, int offy)
+  public void drawNode(Graphics g, SequenceNode node, float chunk,
+          float scale, int width, int offx, int offy)
   {
     if (node == null)
     {
@@ -125,14 +135,14 @@ public class TreeCanvas
       float height = node.height;
       float dist = node.dist;
 
-      int xstart = (int) ( (height - dist) * scale) + offx;
+      int xstart = (int) ((height - dist) * scale) + offx;
       int xend = (int) (height * scale) + offx;
 
       int ypos = (int) (node.ycount * chunk) + offy;
 
       if (node.element() instanceof SequenceI)
       {
-        SequenceI seq = (SequenceI) ( (SequenceNode) node).element();
+        SequenceI seq = (SequenceI) ((SequenceNode) node).element();
 
         if (av.getSequenceColour(seq) == Color.white)
         {
@@ -160,8 +170,8 @@ public class TreeCanvas
       if (showBootstrap)
       {
         int btstrap = node.getBootstrap();
-        if (btstrap>-1)
-        { 
+        if (btstrap > -1)
+        {
           if (showDistances)
           {
             nodeLabel = nodeLabel + " : ";
@@ -174,21 +184,23 @@ public class TreeCanvas
         g.drawString(nodeLabel, xstart + 2, ypos - 2);
       }
 
-      String name = (markPlaceholders && node.isPlaceholder()) ?
-          (PLACEHOLDER + node.getName()) : node.getName();
+      String name = (markPlaceholders && node.isPlaceholder()) ? (PLACEHOLDER + node
+              .getName())
+              : node.getName();
       FontMetrics fm = g.getFontMetrics(font);
       int charWidth = fm.stringWidth(name) + 3;
       int charHeight = fm.getHeight();
 
       Rectangle rect = new Rectangle(xend + 10, ypos - charHeight,
-                                     charWidth, charHeight);
+              charWidth, charHeight);
 
-      nameHash.put( (SequenceI) node.element(), rect);
+      nameHash.put((SequenceI) node.element(), rect);
 
       // Colour selected leaves differently
       SequenceGroup selected = av.getSelectionGroup();
-      if (selected != null &&
-          selected.getSequences(null).contains( (SequenceI) node.element()))
+      if (selected != null
+              && selected.getSequences(null).contains(
+                      (SequenceI) node.element()))
       {
         g.setColor(Color.gray);
 
@@ -200,17 +212,19 @@ public class TreeCanvas
     }
     else
     {
-      drawNode(g, (SequenceNode) node.left(), chunk, scale, width, offx, offy);
-      drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx, offy);
+      drawNode(g, (SequenceNode) node.left(), chunk, scale, width, offx,
+              offy);
+      drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx,
+              offy);
 
       float height = node.height;
       float dist = node.dist;
 
-      int xstart = (int) ( (height - dist) * scale) + offx;
+      int xstart = (int) ((height - dist) * scale) + offx;
       int xend = (int) (height * scale) + offx;
       int ypos = (int) (node.ycount * chunk) + offy;
 
-      g.setColor( ( (SequenceNode) node).color.darker());
+      g.setColor(((SequenceNode) node).color.darker());
 
       // Draw horizontal line
       g.drawLine(xstart, ypos, xend, ypos);
@@ -223,14 +237,16 @@ public class TreeCanvas
         g.fillRect(xend - 2, ypos - 2, 4, 4);
       }
 
-      int ystart = (int) ( ( (SequenceNode) node.left()).ycount * chunk) + offy;
-      int yend = (int) ( ( (SequenceNode) node.right()).ycount * chunk) + offy;
+      int ystart = (int) (((SequenceNode) node.left()).ycount * chunk)
+              + offy;
+      int yend = (int) (((SequenceNode) node.right()).ycount * chunk)
+              + offy;
 
       Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);
       nodeHash.put(node, pos);
 
-      g.drawLine( (int) (height * scale) + offx, ystart,
-                 (int) (height * scale) + offx, yend);
+      g.drawLine((int) (height * scale) + offx, ystart,
+              (int) (height * scale) + offx, yend);
 
       String nodeLabel = "";
 
@@ -242,8 +258,8 @@ public class TreeCanvas
       if (showBootstrap)
       {
         int btstrap = node.getBootstrap();
-        if (btstrap>-1)
-        { 
+        if (btstrap > -1)
+        {
           if (showDistances)
           {
             nodeLabel = nodeLabel + " : ";
@@ -269,8 +285,8 @@ public class TreeCanvas
       Object ob = keys.nextElement();
       Rectangle rect = (Rectangle) nameHash.get(ob);
 
-      if (x >= rect.x && x <= (rect.x + rect.width) &&
-          y >= rect.y && y <= (rect.y + rect.height))
+      if (x >= rect.x && x <= (rect.x + rect.width) && y >= rect.y
+              && y <= (rect.y + rect.height))
       {
         return ob;
       }
@@ -282,8 +298,8 @@ public class TreeCanvas
       Object ob = keys.nextElement();
       Rectangle rect = (Rectangle) nodeHash.get(ob);
 
-      if (x >= rect.x && x <= (rect.x + rect.width) &&
-          y >= rect.y && y <= (rect.y + rect.height))
+      if (x >= rect.x && x <= (rect.x + rect.width) && y >= rect.y
+              && y <= (rect.y + rect.height))
       {
         return ob;
       }
@@ -299,12 +315,11 @@ public class TreeCanvas
 
     SequenceNode top = tree.getTopNode();
 
-    float wscale = (float) (width * .8 - offx * 2) / tree.getMaxHeight()
-        ;
+    float wscale = (float) (width * .8 - offx * 2) / tree.getMaxHeight();
     if (top.count == 0)
     {
-      top.count = ( (SequenceNode) top.left()).count +
-          ( (SequenceNode) top.right()).count;
+      top.count = ((SequenceNode) top.left()).count
+              + ((SequenceNode) top.right()).count;
     }
     float chunk = (float) (height - offy) / top.count;
 
@@ -312,7 +327,7 @@ public class TreeCanvas
   }
 
   public void pickNode(Rectangle pickBox, SequenceNode node, float chunk,
-                       float scale, int width, int offx, int offy)
+          float scale, int width, int offx, int offy)
   {
     if (node == null)
     {
@@ -322,9 +337,9 @@ public class TreeCanvas
     if (node.left() == null && node.right() == null)
     {
       float height = node.height;
-      //float dist = node.dist;
+      // float dist = node.dist;
 
-      //int xstart = (int) ( (height - dist) * scale) + offx;
+      // int xstart = (int) ( (height - dist) * scale) + offx;
       int xend = (int) (height * scale) + offx;
 
       int ypos = (int) (node.ycount * chunk) + offy;
@@ -344,10 +359,10 @@ public class TreeCanvas
     }
     else
     {
-      pickNode(pickBox, (SequenceNode) node.left(), chunk, scale, width, offx,
-               offy);
-      pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width, offx,
-               offy);
+      pickNode(pickBox, (SequenceNode) node.left(), chunk, scale, width,
+              offx, offy);
+      pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width,
+              offx, offy);
     }
   }
 
@@ -364,14 +379,14 @@ public class TreeCanvas
 
       if (node.element() instanceof SequenceI)
       {
-        av.setSequenceColour( (SequenceI) node.element(), c);
+        av.setSequenceColour((SequenceI) node.element(), c);
       }
     }
     else
     {
       node.color = c;
-      setColor( (SequenceNode) node.left(), c);
-      setColor( (SequenceNode) node.right(), c);
+      setColor((SequenceNode) node.left(), c);
+      setColor((SequenceNode) node.right(), c);
     }
   }
 
@@ -421,16 +436,20 @@ public class TreeCanvas
     g.setColor(Color.white);
     g.fillRect(0, 0, width, height);
 
-    labelLength = g.getFontMetrics(font).stringWidth(longestName) + 20; //20 allows for scrollbar
+    labelLength = g.getFontMetrics(font).stringWidth(longestName) + 20; // 20
+                                                                        // allows
+                                                                        // for
+                                                                        // scrollbar
 
-    float wscale = (float) (width - labelLength - offx * 2) / tree.getMaxHeight();
+    float wscale = (float) (width - labelLength - offx * 2)
+            / tree.getMaxHeight();
 
     SequenceNode top = tree.getTopNode();
 
     if (top.count == 0)
     {
-      top.count = ( (SequenceNode) top.left()).count +
-          ( (SequenceNode) top.right()).count;
+      top.count = ((SequenceNode) top.left()).count
+              + ((SequenceNode) top.right()).count;
     }
     float chunk = (float) (height - offy) / top.count;
 
@@ -447,8 +466,8 @@ public class TreeCanvas
         g.setColor(Color.gray);
       }
 
-      int x = (int) (threshold *
-                     (float) (getSize().width - labelLength - 2 * offx) + offx);
+      int x = (int) (threshold
+              * (float) (getSize().width - labelLength - 2 * offx) + offx);
 
       g.drawLine(x, 0, x, getSize().height);
     }
@@ -456,13 +475,16 @@ public class TreeCanvas
   }
 
   public void mouseReleased(MouseEvent e)
-  {}
+  {
+  }
 
   public void mouseEntered(MouseEvent e)
-  {}
+  {
+  }
 
   public void mouseExited(MouseEvent e)
-  {}
+  {
+  }
 
   public void mouseClicked(MouseEvent evt)
   {
@@ -481,8 +503,8 @@ public class TreeCanvas
 
         for (int i = 0; i < leaves.size(); i++)
         {
-          SequenceI seq =
-              (SequenceI) ( (SequenceNode) leaves.elementAt(i)).element();
+          SequenceI seq = (SequenceI) ((SequenceNode) leaves.elementAt(i))
+                  .element();
           treeSelectionChanged(seq);
         }
       }
@@ -493,7 +515,8 @@ public class TreeCanvas
   }
 
   public void mouseDragged(MouseEvent ect)
-  {}
+  {
+  }
 
   public void mouseMoved(MouseEvent evt)
   {
@@ -527,19 +550,19 @@ public class TreeCanvas
 
     if (ob instanceof SequenceI)
     {
-      treeSelectionChanged( (Sequence) ob);
+      treeSelectionChanged((Sequence) ob);
       PaintRefresher.Refresh(this, av.getSequenceSetId());
       repaint();
       return;
     }
-    else if (! (ob instanceof SequenceNode))
+    else if (!(ob instanceof SequenceNode))
     {
       // Find threshold
 
       if (tree.getMaxHeight() != 0)
       {
-        threshold = (float) (x - offx) /
-            (float) (getSize().width - labelLength - 2 * offx);
+        threshold = (float) (x - offx)
+                / (float) (getSize().width - labelLength - 2 * offx);
 
         tree.getGroups().removeAllElements();
         tree.groupNodes(tree.getTopNode(), threshold);
@@ -564,18 +587,18 @@ public class TreeCanvas
     for (int i = 0; i < tree.getGroups().size(); i++)
     {
 
-      Color col = new Color( (int) (Math.random() * 255),
-                            (int) (Math.random() * 255),
-                            (int) (Math.random() * 255));
-      setColor( (SequenceNode) tree.getGroups().elementAt(i), col.brighter());
+      Color col = new Color((int) (Math.random() * 255), (int) (Math
+              .random() * 255), (int) (Math.random() * 255));
+      setColor((SequenceNode) tree.getGroups().elementAt(i), col.brighter());
 
-      Vector l = tree.findLeaves( (SequenceNode) tree.getGroups().elementAt(
-          i), new Vector());
+      Vector l = tree.findLeaves((SequenceNode) tree.getGroups().elementAt(
+              i), new Vector());
 
       Vector sequences = new Vector();
       for (int j = 0; j < l.size(); j++)
       {
-        SequenceI s1 = (SequenceI) ( (SequenceNode) l.elementAt(j)).element();
+        SequenceI s1 = (SequenceI) ((SequenceNode) l.elementAt(j))
+                .element();
         if (!sequences.contains(s1))
         {
           sequences.addElement(s1);
@@ -588,38 +611,32 @@ public class TreeCanvas
       {
         if (av.getGlobalColourScheme() instanceof UserColourScheme)
         {
-          cs = new UserColourScheme(
-              ( (UserColourScheme) av.getGlobalColourScheme()).getColours());
+          cs = new UserColourScheme(((UserColourScheme) av
+                  .getGlobalColourScheme()).getColours());
 
         }
         else
         {
-          cs = ColourSchemeProperty.getColour(sequences,
-                                              av.alignment.getWidth(),
-                                              ColourSchemeProperty.
-                                              getColourName(
-                                                  av.getGlobalColourScheme()));
+          cs = ColourSchemeProperty.getColour(sequences, av.alignment
+                  .getWidth(), ColourSchemeProperty.getColourName(av
+                  .getGlobalColourScheme()));
         }
 
-        cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
-                        av.getIgnoreGapsConsensus());
+        cs.setThreshold(av.getGlobalColourScheme().getThreshold(), av
+                .getIgnoreGapsConsensus());
       }
 
-      SequenceGroup sg = new SequenceGroup(sequences, "",
-                                           cs, true, true,
-                                           false, 0,
-                                           av.alignment.getWidth() - 1);
+      SequenceGroup sg = new SequenceGroup(sequences, "", cs, true, true,
+              false, 0, av.alignment.getWidth() - 1);
 
       sg.setName("JTreeGroup:" + sg.hashCode());
       sg.setIdColour(col);
       if (av.getGlobalColourScheme() != null
-          && av.getGlobalColourScheme().conservationApplied())
+              && av.getGlobalColourScheme().conservationApplied())
       {
         Conservation c = new Conservation("Group",
-                                          ResidueProperties.propHash, 3,
-                                          sg.getSequences(null),
-                                          sg.getStartRes(),
-                                          sg.getEndRes());
+                ResidueProperties.propHash, 3, sg.getSequences(null), sg
+                        .getStartRes(), sg.getEndRes());
 
         c.calculate();
         c.verdict(false, av.ConsPercGaps);
diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index 6ab01aa..d6c0069 100755
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.appletgui;
 
 import java.awt.*;
@@ -27,16 +26,23 @@ import jalview.analysis.*;
 import jalview.datamodel.*;
 import jalview.io.*;
 
-public class TreePanel
-    extends EmbmenuFrame implements ActionListener, ItemListener
+public class TreePanel extends EmbmenuFrame implements ActionListener,
+        ItemListener
 {
   SequenceI[] seq;
+
   String type;
+
   String pwtype;
+
   int start;
+
   int end;
+
   TreeCanvas treeCanvas;
+
   NJTree tree;
+
   AlignViewport av;
 
   public NJTree getTree()
@@ -46,13 +52,19 @@ public class TreePanel
 
   /**
    * Creates a new TreePanel object.
-   *
-   * @param av DOCUMENT ME!
-   * @param seqVector DOCUMENT ME!
-   * @param type DOCUMENT ME!
-   * @param pwtype DOCUMENT ME!
-   * @param s DOCUMENT ME!
-   * @param e DOCUMENT ME!
+   * 
+   * @param av
+   *                DOCUMENT ME!
+   * @param seqVector
+   *                DOCUMENT ME!
+   * @param type
+   *                DOCUMENT ME!
+   * @param pwtype
+   *                DOCUMENT ME!
+   * @param s
+   *                DOCUMENT ME!
+   * @param e
+   *                DOCUMENT ME!
    */
   public TreePanel(AlignViewport av, String type, String pwtype)
   {
@@ -60,8 +72,7 @@ public class TreePanel
     {
       jbInit();
       this.setMenuBar(jMenuBar1);
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       ex.printStackTrace();
     }
@@ -71,73 +82,78 @@ public class TreePanel
 
   /**
    * Creates a new TreePanel object.
-   *
-   * @param av DOCUMENT ME!
-   * @param seqVector DOCUMENT ME!
-   * @param newtree DOCUMENT ME!
-   * @param type DOCUMENT ME!
-   * @param pwtype DOCUMENT ME!
+   * 
+   * @param av
+   *                DOCUMENT ME!
+   * @param seqVector
+   *                DOCUMENT ME!
+   * @param newtree
+   *                DOCUMENT ME!
+   * @param type
+   *                DOCUMENT ME!
+   * @param pwtype
+   *                DOCUMENT ME!
    */
-  public TreePanel(AlignViewport av,
-                   String type,
-                   String pwtype,
-                   NewickFile newtree)
+  public TreePanel(AlignViewport av, String type, String pwtype,
+          NewickFile newtree)
   {
     try
     {
       jbInit();
       this.setMenuBar(jMenuBar1);
-    }
-    catch (Exception e)
+    } catch (Exception e)
     {
       e.printStackTrace();
     }
 
     initTreePanel(av, type, pwtype, newtree);
   }
-  void initTreePanel(AlignViewport av,
-                     String type,
-                     String pwtype,
-                     NewickFile newTree)
+
+  void initTreePanel(AlignViewport av, String type, String pwtype,
+          NewickFile newTree)
   {
 
     this.av = av;
     this.type = type;
     this.pwtype = pwtype;
 
-
     treeCanvas = new TreeCanvas(av, scrollPane);
     TreeLoader tl = new TreeLoader(newTree);
     tl.start();
     embedMenuIfNeeded(treeCanvas);
     scrollPane.add(treeCanvas, BorderLayout.CENTER);
   }
+
   void showOriginalData()
   {
-    // decide if av alignment is sufficiently different to original data to warrant a new window to be created
-    // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)
+    // decide if av alignment is sufficiently different to original data to
+    // warrant a new window to be created
+    // create new alignmnt window with hidden regions (unhiding hidden regions
+    // yields unaligned seqs)
     // or create a selection box around columns in alignment view
     // test Alignment(SeqCigar[])
     if (tree.seqData != null)
     {
       char gc = '-';
-      try {
+      try
+      {
         // we try to get the associated view's gap character
         // but this may fail if the view was closed...
-        gc = av.
-        getGapCharacter();
-      } catch (Exception ex) {};
-      Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(gc);
+        gc = av.getGapCharacter();
+      } catch (Exception ex)
+      {
+      }
+      ;
+      Object[] alAndColsel = tree.seqData
+              .getAlignmentAndColumnSelection(gc);
 
       if (alAndColsel != null && alAndColsel[0] != null)
       {
-        Alignment al = new Alignment( (SequenceI[]) alAndColsel[0]);
-        AlignFrame af = new AlignFrame(al,
-                                       av.applet,
-                                       "Original Data for Tree",
-                                       false);
+        Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
+        AlignFrame af = new AlignFrame(al, av.applet,
+                "Original Data for Tree", false);
 
-        af.viewport.setHiddenColumns( (ColumnSelection) alAndColsel[1]);
+        af.viewport.setHiddenColumns((ColumnSelection) alAndColsel[1]);
       }
     }
     else
@@ -146,10 +162,10 @@ public class TreePanel
     }
   }
 
-  class TreeLoader
-      extends Thread
+  class TreeLoader extends Thread
   {
     NewickFile newtree;
+
     jalview.datamodel.AlignmentView odata = null;
 
     public TreeLoader(NewickFile newtree)
@@ -163,12 +179,12 @@ public class TreePanel
       {
         if (odata == null)
         {
-          tree = new NJTree(av.alignment.getSequencesArray(),
-                            newtree);
+          tree = new NJTree(av.alignment.getSequencesArray(), newtree);
         }
         else
         {
-          tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);
+          tree = new NJTree(av.alignment.getSequencesArray(), odata,
+                  newtree);
         }
 
       }
@@ -176,7 +192,8 @@ public class TreePanel
       {
         int start, end;
         SequenceI[] seqs;
-        AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup() != null);
+        AlignmentView seqStrings = av.getAlignmentView(av
+                .getSelectionGroup() != null);
         if (av.getSelectionGroup() == null)
         {
           start = 0;
@@ -254,7 +271,8 @@ public class TreePanel
 
   public void newickOutput_actionPerformed()
   {
-    jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
+    jalview.io.NewickFile fout = new jalview.io.NewickFile(tree
+            .getTopNode());
     String output = fout.print(false, true);
     CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
     cap.setText(output);
@@ -285,20 +303,30 @@ public class TreePanel
   }
 
   BorderLayout borderLayout1 = new BorderLayout();
+
   protected ScrollPane scrollPane = new ScrollPane();
+
   MenuBar jMenuBar1 = new MenuBar();
+
   Menu jMenu2 = new Menu();
+
   protected MenuItem fontSize = new MenuItem();
+
   protected CheckboxMenuItem bootstrapMenu = new CheckboxMenuItem();
+
   protected CheckboxMenuItem distanceMenu = new CheckboxMenuItem();
+
   protected CheckboxMenuItem placeholdersMenu = new CheckboxMenuItem();
+
   protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem();
+
   Menu fileMenu = new Menu();
+
   MenuItem newickOutput = new MenuItem();
+
   MenuItem inputData = new MenuItem();
 
-  private void jbInit()
-      throws Exception
+  private void jbInit() throws Exception
   {
     setLayout(borderLayout1);
     this.setBackground(Color.white);
diff --git a/src/jalview/appletgui/UserDefinedColours.java b/src/jalview/appletgui/UserDefinedColours.java
index 6e14146..0f30539 100755
--- a/src/jalview/appletgui/UserDefinedColours.java
+++ b/src/jalview/appletgui/UserDefinedColours.java
@@ -1,589 +1,606 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.appletgui;
-
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
-import jalview.schemes.*;
-
-public class UserDefinedColours
-    extends Panel implements ActionListener, AdjustmentListener
-{
-
-  AlignmentPanel ap;
-  SequenceGroup seqGroup;
-  Button selectedButton;
-  Vector oldColours = new Vector();
-  ColourSchemeI oldColourScheme;
-  Frame frame;
-  MCview.AppletPDBCanvas pdbcanvas;
-  AppletJmol jmol;
-
-  Dialog dialog;
-  Object caller;
-  String originalLabel;
-  Color originalColour;
-
-  int R = 0, G = 0, B = 0;
-
-  public ColourSchemeI loadDefaultColours()
-  {
-    // NOT IMPLEMENTED YET IN APPLET VERSION
-    return null;
-  }
-
-  public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
-  {
-    this.ap = ap;
-    seqGroup = sg;
-
-    if (seqGroup != null)
-    {
-      oldColourScheme = seqGroup.cs;
-    }
-    else
-    {
-      oldColourScheme = ap.av.getGlobalColourScheme();
-    }
-
-    init();
-  }
-
-  public UserDefinedColours(MCview.AppletPDBCanvas pdb)
-  {
-    this.pdbcanvas = pdb;
-    init();
-  }
-
-  public UserDefinedColours(AppletJmol jmol)
-  {
-    this.jmol = jmol;
-    init();
-  }
-
-  public UserDefinedColours(FeatureRenderer fr, Frame alignframe)
-  {
-    caller = fr;
-    originalColour = fr.colourPanel.getBackground();
-    originalLabel = "Feature Colour";
-    setForDialog("Select Feature Colour", alignframe);
-    setTargetColour(fr.colourPanel.getBackground());
-    dialog.setVisible(true);
-  }
-
-  public UserDefinedColours(Component caller,
-                            Color col1,
-                            Frame alignframe)
-  {
-    this.caller = caller;
-    originalColour = col1;
-    originalLabel = "Select Colour";
-    setForDialog("Select Colour", alignframe);
-    setTargetColour(col1);
-    dialog.setVisible(true);
-  }
-
-
-  public UserDefinedColours(Object caller,
-                            String label,
-                            Color colour)
-  {
-    this.caller = caller;
-    originalColour = colour;
-    originalLabel = label;
-    init();
-    remove(buttonPanel);
-
-    setTargetColour(colour);
-
-    okcancelPanel.setBounds(new Rectangle(0, 113, 400, 35));
-    frame.setTitle("User Defined Colours - " + label);
-    frame.setSize(420, 200);
-  }
-
-  void setForDialog(String title, Frame alignframe)
-  {
-    init();
-    frame.setVisible(false);
-    remove(buttonPanel);
-    dialog = new Dialog(alignframe, title, true);
-
-    dialog.add(this);
-    this.setSize(400,123);
-    okcancelPanel.setBounds(new Rectangle(0, 123, 400, 35));
-    int height = 160 + alignframe.getInsets().top + getInsets().bottom;
-    int width = 400;
-
-    dialog.setBounds(alignframe.getBounds().x
-              + (alignframe.getSize().width - width) / 2,
-              alignframe.getBounds().y
-              + (alignframe.getSize().height - height) / 2,
-              width, height);
-
-  }
-
-  public void actionPerformed(ActionEvent evt)
-  {
-    if (evt.getSource() == okButton)
-    {
-      okButton_actionPerformed();
-    }
-    else if (evt.getSource() == applyButton)
-    {
-      applyButton_actionPerformed();
-    }
-    else if (evt.getSource() == cancelButton)
-    {
-      cancelButton_actionPerformed();
-    }
-    else if (evt.getSource() == rText)
-    {
-      rText_actionPerformed();
-    }
-    else if (evt.getSource() == gText)
-    {
-      gText_actionPerformed();
-    }
-    else if (evt.getSource() == bText)
-    {
-      bText_actionPerformed();
-    }
-  }
-
-  public void adjustmentValueChanged(AdjustmentEvent evt)
-  {
-    if (evt.getSource() == rScroller)
-    {
-      rScroller_adjustmentValueChanged();
-    }
-    else if (evt.getSource() == gScroller)
-    {
-      gScroller_adjustmentValueChanged();
-    }
-    else if (evt.getSource() == bScroller)
-    {
-      bScroller_adjustmentValueChanged();
-    }
-  }
-
-  void init()
-  {
-    try
-    {
-      jbInit();
-    }
-    catch (Exception e)
-    {
-      e.printStackTrace();
-    }
-    frame = new Frame();
-    frame.add(this);
-    jalview.bin.JalviewLite.addFrame(frame, "User defined colours", 420, 345);
-
-    if (seqGroup != null)
-    {
-      frame.setTitle(frame.getTitle() + " (" + seqGroup.getName() + ")");
-    }
-
-    for (int i = 0; i < 20; i++)
-    {
-      makeButton(ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i]) +
-                 "", ResidueProperties.aa[i]);
-    }
-
-    makeButton("B", "B");
-    makeButton("Z", "Z");
-    makeButton("X", "X");
-    makeButton("Gap", "'.','-',' '");
-
-    validate();
-  }
-
-  protected void rText_actionPerformed()
-  {
-    try
-    {
-      int i = Integer.parseInt(rText.getText());
-      rScroller.setValue(i);
-      rScroller_adjustmentValueChanged();
-    }
-    catch (NumberFormatException ex)
-    {}
-  }
-
-  protected void gText_actionPerformed()
-  {
-    try
-    {
-      int i = Integer.parseInt(gText.getText());
-      gScroller.setValue(i);
-      gScroller_adjustmentValueChanged();
-    }
-    catch (NumberFormatException ex)
-    {}
-
-  }
-
-  protected void bText_actionPerformed()
-  {
-    try
-    {
-      int i = Integer.parseInt(bText.getText());
-      bScroller.setValue(i);
-      bScroller_adjustmentValueChanged();
-    }
-    catch (NumberFormatException ex)
-    {}
-
-  }
-
-  protected void rScroller_adjustmentValueChanged()
-  {
-    R = rScroller.getValue();
-    rText.setText(R + "");
-    colourChanged();
-  }
-
-  protected void gScroller_adjustmentValueChanged()
-  {
-    G = gScroller.getValue();
-    gText.setText(G + "");
-    colourChanged();
-  }
-
-  protected void bScroller_adjustmentValueChanged()
-  {
-    B = bScroller.getValue();
-    bText.setText(B + "");
-    colourChanged();
-  }
-
-  public void colourChanged()
-  {
-    Color col = new Color(R, G, B);
-    target.setBackground(col);
-    target.repaint();
-
-    if (selectedButton != null)
-    {
-      selectedButton.setBackground(col);
-      selectedButton.repaint();
-    }
-  }
-
-  void setTargetColour(Color col)
-  {
-    R = col.getRed();
-    G = col.getGreen();
-    B = col.getBlue();
-
-    rScroller.setValue(R);
-    gScroller.setValue(G);
-    bScroller.setValue(B);
-    rText.setText(R + "");
-    gText.setText(G + "");
-    bText.setText(B + "");
-    colourChanged();
-  }
-
-  public void colourButtonPressed(MouseEvent e)
-  {
-    selectedButton = (Button) e.getSource();
-    setTargetColour(selectedButton.getBackground());
-  }
-
-  void makeButton(String label, String aa)
-  {
-    final Button button = new Button();
-    Color col = Color.white;
-
-    try
-    {
-      col = oldColourScheme.findColour(aa.charAt(0), -1);
-    }
-    catch (Exception ex)
-    {}
-
-    button.setBackground(col);
-    oldColours.addElement(col);
-    button.setLabel(label);
-    button.setForeground(col.darker().darker().darker());
-    button.setFont(new java.awt.Font("Verdana", 1, 10));
-    button.addMouseListener(new java.awt.event.MouseAdapter()
-    {
-      public void mousePressed(MouseEvent e)
-      {
-        colourButtonPressed(e);
-      }
-    });
-
-    buttonPanel.add(button, null);
-  }
-
-  protected void okButton_actionPerformed()
-  {
-    applyButton_actionPerformed();
-    if (dialog != null)
-      dialog.setVisible(false);
-
-    frame.setVisible(false);
-  }
-
-  public Color getColor()
-  {
-    return new Color(R, G, B);
-  }
-
-  protected void applyButton_actionPerformed()
-  {
-    if (caller != null)
-    {
-      if (caller instanceof FeatureSettings)
-      {
-        ( (FeatureSettings) caller).setUserColour
-            (originalLabel, getColor());
-      }
-      else if (caller instanceof AnnotationColourChooser)
-      {
-        if (originalLabel.equals("Min Colour"))
-        {
-          ( (AnnotationColourChooser) caller).minColour_actionPerformed
-              (getColor());
-        }
-        else
-        {
-          ( (AnnotationColourChooser) caller).maxColour_actionPerformed
-              (getColor());
-        }
-      }
-      else if(caller instanceof FeatureRenderer)
-      {
-        ((FeatureRenderer)caller).colourPanel.setBackground(getColor());
-      }
-
-      return;
-    }
-
-    Color[] newColours = new Color[24];
-    for (int i = 0; i < 24; i++)
-    {
-      Button button = (Button) buttonPanel.getComponent(i);
-      newColours[i] = button.getBackground();
-    }
-
-    UserColourScheme ucs = new UserColourScheme(newColours);
-    if (ap != null)
-    {
-      ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
-    }
-
-    if (ap != null)
-    {
-      if (seqGroup != null)
-      {
-        seqGroup.cs = ucs;
-      }
-      else
-      {
-        ap.av.setGlobalColourScheme(ucs);
-      }
-      ap.seqPanel.seqCanvas.img = null;
-      ap.paintAlignment(true);
-    }
-    else if(jmol!=null)
-    {
-      jmol.setJalviewColourScheme(ucs);
-    }
-    else if (pdbcanvas != null)
-    {
-      pdbcanvas.setColours(ucs);
-    }
-  }
-
-  protected void cancelButton_actionPerformed()
-  {
-    if (caller != null)
-    {
-      if (caller instanceof FeatureSettings)
-      {
-        ( (FeatureSettings) caller).setUserColour
-            (originalLabel, originalColour);
-      }
-      else if (caller instanceof AnnotationColourChooser)
-      {
-        if (originalLabel.equals("Min Colour"))
-        {
-          ( (AnnotationColourChooser) caller).minColour_actionPerformed
-              (originalColour);
-        }
-        else
-        {
-          ( (AnnotationColourChooser) caller).maxColour_actionPerformed
-              (originalColour);
-        }
-      }
-      else if (caller instanceof FeatureRenderer)
-      {
-        ( (FeatureRenderer) caller).colourPanel.setBackground(originalColour);
-
-      }
-
-      if(dialog!=null)
-        dialog.setVisible(false);
-
-      frame.setVisible(false);
-      return;
-    }
-
-    Color[] newColours = new Color[24];
-    for (int i = 0; i < 24; i++)
-    {
-      newColours[i] = (Color) oldColours.elementAt(i);
-      buttonPanel.getComponent(i).setBackground(newColours[i]);
-    }
-
-    UserColourScheme ucs = new UserColourScheme(newColours);
-
-    if (ap != null)
-    {
-      if (seqGroup != null)
-      {
-        seqGroup.cs = ucs;
-      }
-      else
-      {
-        ap.av.setGlobalColourScheme(ucs);
-      }
-      ap.paintAlignment(true);
-    }
-    else if(jmol !=null)
-    {
-      jmol.setJalviewColourScheme(ucs);
-    }
-    else if (pdbcanvas != null)
-    {
-      pdbcanvas.pdb.setColours(ucs);
-    }
-
-    frame.setVisible(false);
-  }
-
-  protected Panel buttonPanel = new Panel();
-  protected GridLayout gridLayout = new GridLayout();
-  Panel okcancelPanel = new Panel();
-  protected Button okButton = new Button();
-  protected Button applyButton = new Button();
-  protected Button cancelButton = new Button();
-  protected Scrollbar rScroller = new Scrollbar();
-  Label label1 = new Label();
-  protected TextField rText = new TextField();
-  Label label4 = new Label();
-  protected Scrollbar gScroller = new Scrollbar();
-  protected TextField gText = new TextField();
-  Label label5 = new Label();
-  protected Scrollbar bScroller = new Scrollbar();
-  protected TextField bText = new TextField();
-  protected Panel target = new Panel();
-
-  private void jbInit()
-      throws Exception
-  {
-    this.setLayout(null);
-    buttonPanel.setLayout(gridLayout);
-    gridLayout.setColumns(6);
-    gridLayout.setRows(4);
-    okButton.setFont(new java.awt.Font("Verdana", 0, 11));
-    okButton.setLabel("OK");
-    okButton.addActionListener(this);
-    applyButton.setFont(new java.awt.Font("Verdana", 0, 11));
-    applyButton.setLabel("Apply");
-    applyButton.addActionListener(this);
-    cancelButton.setFont(new java.awt.Font("Verdana", 0, 11));
-    cancelButton.setLabel("Cancel");
-    cancelButton.addActionListener(this);
-    this.setBackground(new Color(212, 208, 223));
-    okcancelPanel.setBounds(new Rectangle(0, 265, 400, 35));
-    buttonPanel.setBounds(new Rectangle(0, 123, 400, 142));
-    rScroller.setMaximum(256);
-    rScroller.setMinimum(0);
-    rScroller.setOrientation(0);
-    rScroller.setUnitIncrement(1);
-    rScroller.setVisibleAmount(1);
-    rScroller.setBounds(new Rectangle(36, 27, 119, 19));
-    rScroller.addAdjustmentListener(this);
-    label1.setAlignment(Label.RIGHT);
-    label1.setText("R");
-    label1.setBounds(new Rectangle(19, 30, 16, 15));
-    rText.setFont(new java.awt.Font("Dialog", Font.PLAIN, 10));
-    rText.setText("0        ");
-    rText.setBounds(new Rectangle(156, 27, 53, 19));
-    rText.addActionListener(this);
-    label4.setAlignment(Label.RIGHT);
-    label4.setText("G");
-    label4.setBounds(new Rectangle(15, 56, 20, 15));
-    gScroller.setMaximum(256);
-    gScroller.setMinimum(0);
-    gScroller.setOrientation(0);
-    gScroller.setUnitIncrement(1);
-    gScroller.setVisibleAmount(1);
-    gScroller.setBounds(new Rectangle(35, 52, 120, 20));
-    gScroller.addAdjustmentListener(this);
-    gText.setFont(new java.awt.Font("Dialog", Font.PLAIN, 10));
-    gText.setText("0        ");
-    gText.setBounds(new Rectangle(156, 52, 53, 20));
-    gText.addActionListener(this);
-    label5.setAlignment(Label.RIGHT);
-    label5.setText("B");
-    label5.setBounds(new Rectangle(14, 82, 20, 15));
-    bScroller.setMaximum(256);
-    bScroller.setMinimum(0);
-    bScroller.setOrientation(0);
-    bScroller.setUnitIncrement(1);
-    bScroller.setVisibleAmount(1);
-    bScroller.setBounds(new Rectangle(35, 78, 120, 20));
-    bScroller.addAdjustmentListener(this);
-    bText.setFont(new java.awt.Font("Dialog", Font.PLAIN, 10));
-    bText.setText("0        ");
-    bText.setBounds(new Rectangle(157, 78, 52, 20));
-    bText.addActionListener(this);
-    target.setBackground(Color.black);
-    target.setBounds(new Rectangle(229, 26, 134, 79));
-    this.add(okcancelPanel, null);
-    okcancelPanel.add(okButton, null);
-    okcancelPanel.add(applyButton, null);
-    okcancelPanel.add(cancelButton, null);
-    this.add(buttonPanel, null);
-    this.add(target, null);
-    this.add(gScroller);
-    this.add(rScroller);
-    this.add(bScroller);
-    this.add(label5);
-    this.add(label4);
-    this.add(label1);
-    this.add(gText);
-    this.add(rText);
-    this.add(bText);
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.appletgui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import jalview.datamodel.*;
+import jalview.schemes.*;
+
+public class UserDefinedColours extends Panel implements ActionListener,
+        AdjustmentListener
+{
+
+  AlignmentPanel ap;
+
+  SequenceGroup seqGroup;
+
+  Button selectedButton;
+
+  Vector oldColours = new Vector();
+
+  ColourSchemeI oldColourScheme;
+
+  Frame frame;
+
+  MCview.AppletPDBCanvas pdbcanvas;
+
+  AppletJmol jmol;
+
+  Dialog dialog;
+
+  Object caller;
+
+  String originalLabel;
+
+  Color originalColour;
+
+  int R = 0, G = 0, B = 0;
+
+  public ColourSchemeI loadDefaultColours()
+  {
+    // NOT IMPLEMENTED YET IN APPLET VERSION
+    return null;
+  }
+
+  public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
+  {
+    this.ap = ap;
+    seqGroup = sg;
+
+    if (seqGroup != null)
+    {
+      oldColourScheme = seqGroup.cs;
+    }
+    else
+    {
+      oldColourScheme = ap.av.getGlobalColourScheme();
+    }
+
+    init();
+  }
+
+  public UserDefinedColours(MCview.AppletPDBCanvas pdb)
+  {
+    this.pdbcanvas = pdb;
+    init();
+  }
+
+  public UserDefinedColours(AppletJmol jmol)
+  {
+    this.jmol = jmol;
+    init();
+  }
+
+  public UserDefinedColours(FeatureRenderer fr, Frame alignframe)
+  {
+    caller = fr;
+    originalColour = fr.colourPanel.getBackground();
+    originalLabel = "Feature Colour";
+    setForDialog("Select Feature Colour", alignframe);
+    setTargetColour(fr.colourPanel.getBackground());
+    dialog.setVisible(true);
+  }
+
+  public UserDefinedColours(Component caller, Color col1, Frame alignframe)
+  {
+    this.caller = caller;
+    originalColour = col1;
+    originalLabel = "Select Colour";
+    setForDialog("Select Colour", alignframe);
+    setTargetColour(col1);
+    dialog.setVisible(true);
+  }
+
+  public UserDefinedColours(Object caller, String label, Color colour)
+  {
+    this.caller = caller;
+    originalColour = colour;
+    originalLabel = label;
+    init();
+    remove(buttonPanel);
+
+    setTargetColour(colour);
+
+    okcancelPanel.setBounds(new Rectangle(0, 113, 400, 35));
+    frame.setTitle("User Defined Colours - " + label);
+    frame.setSize(420, 200);
+  }
+
+  void setForDialog(String title, Frame alignframe)
+  {
+    init();
+    frame.setVisible(false);
+    remove(buttonPanel);
+    dialog = new Dialog(alignframe, title, true);
+
+    dialog.add(this);
+    this.setSize(400, 123);
+    okcancelPanel.setBounds(new Rectangle(0, 123, 400, 35));
+    int height = 160 + alignframe.getInsets().top + getInsets().bottom;
+    int width = 400;
+
+    dialog.setBounds(alignframe.getBounds().x
+            + (alignframe.getSize().width - width) / 2, alignframe
+            .getBounds().y
+            + (alignframe.getSize().height - height) / 2, width, height);
+
+  }
+
+  public void actionPerformed(ActionEvent evt)
+  {
+    if (evt.getSource() == okButton)
+    {
+      okButton_actionPerformed();
+    }
+    else if (evt.getSource() == applyButton)
+    {
+      applyButton_actionPerformed();
+    }
+    else if (evt.getSource() == cancelButton)
+    {
+      cancelButton_actionPerformed();
+    }
+    else if (evt.getSource() == rText)
+    {
+      rText_actionPerformed();
+    }
+    else if (evt.getSource() == gText)
+    {
+      gText_actionPerformed();
+    }
+    else if (evt.getSource() == bText)
+    {
+      bText_actionPerformed();
+    }
+  }
+
+  public void adjustmentValueChanged(AdjustmentEvent evt)
+  {
+    if (evt.getSource() == rScroller)
+    {
+      rScroller_adjustmentValueChanged();
+    }
+    else if (evt.getSource() == gScroller)
+    {
+      gScroller_adjustmentValueChanged();
+    }
+    else if (evt.getSource() == bScroller)
+    {
+      bScroller_adjustmentValueChanged();
+    }
+  }
+
+  void init()
+  {
+    try
+    {
+      jbInit();
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+    frame = new Frame();
+    frame.add(this);
+    jalview.bin.JalviewLite.addFrame(frame, "User defined colours", 420,
+            345);
+
+    if (seqGroup != null)
+    {
+      frame.setTitle(frame.getTitle() + " (" + seqGroup.getName() + ")");
+    }
+
+    for (int i = 0; i < 20; i++)
+    {
+      makeButton(ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i])
+              + "", ResidueProperties.aa[i]);
+    }
+
+    makeButton("B", "B");
+    makeButton("Z", "Z");
+    makeButton("X", "X");
+    makeButton("Gap", "'.','-',' '");
+
+    validate();
+  }
+
+  protected void rText_actionPerformed()
+  {
+    try
+    {
+      int i = Integer.parseInt(rText.getText());
+      rScroller.setValue(i);
+      rScroller_adjustmentValueChanged();
+    } catch (NumberFormatException ex)
+    {
+    }
+  }
+
+  protected void gText_actionPerformed()
+  {
+    try
+    {
+      int i = Integer.parseInt(gText.getText());
+      gScroller.setValue(i);
+      gScroller_adjustmentValueChanged();
+    } catch (NumberFormatException ex)
+    {
+    }
+
+  }
+
+  protected void bText_actionPerformed()
+  {
+    try
+    {
+      int i = Integer.parseInt(bText.getText());
+      bScroller.setValue(i);
+      bScroller_adjustmentValueChanged();
+    } catch (NumberFormatException ex)
+    {
+    }
+
+  }
+
+  protected void rScroller_adjustmentValueChanged()
+  {
+    R = rScroller.getValue();
+    rText.setText(R + "");
+    colourChanged();
+  }
+
+  protected void gScroller_adjustmentValueChanged()
+  {
+    G = gScroller.getValue();
+    gText.setText(G + "");
+    colourChanged();
+  }
+
+  protected void bScroller_adjustmentValueChanged()
+  {
+    B = bScroller.getValue();
+    bText.setText(B + "");
+    colourChanged();
+  }
+
+  public void colourChanged()
+  {
+    Color col = new Color(R, G, B);
+    target.setBackground(col);
+    target.repaint();
+
+    if (selectedButton != null)
+    {
+      selectedButton.setBackground(col);
+      selectedButton.repaint();
+    }
+  }
+
+  void setTargetColour(Color col)
+  {
+    R = col.getRed();
+    G = col.getGreen();
+    B = col.getBlue();
+
+    rScroller.setValue(R);
+    gScroller.setValue(G);
+    bScroller.setValue(B);
+    rText.setText(R + "");
+    gText.setText(G + "");
+    bText.setText(B + "");
+    colourChanged();
+  }
+
+  public void colourButtonPressed(MouseEvent e)
+  {
+    selectedButton = (Button) e.getSource();
+    setTargetColour(selectedButton.getBackground());
+  }
+
+  void makeButton(String label, String aa)
+  {
+    final Button button = new Button();
+    Color col = Color.white;
+
+    try
+    {
+      col = oldColourScheme.findColour(aa.charAt(0), -1);
+    } catch (Exception ex)
+    {
+    }
+
+    button.setBackground(col);
+    oldColours.addElement(col);
+    button.setLabel(label);
+    button.setForeground(col.darker().darker().darker());
+    button.setFont(new java.awt.Font("Verdana", 1, 10));
+    button.addMouseListener(new java.awt.event.MouseAdapter()
+    {
+      public void mousePressed(MouseEvent e)
+      {
+        colourButtonPressed(e);
+      }
+    });
+
+    buttonPanel.add(button, null);
+  }
+
+  protected void okButton_actionPerformed()
+  {
+    applyButton_actionPerformed();
+    if (dialog != null)
+      dialog.setVisible(false);
+
+    frame.setVisible(false);
+  }
+
+  public Color getColor()
+  {
+    return new Color(R, G, B);
+  }
+
+  protected void applyButton_actionPerformed()
+  {
+    if (caller != null)
+    {
+      if (caller instanceof FeatureSettings)
+      {
+        ((FeatureSettings) caller).setUserColour(originalLabel, getColor());
+      }
+      else if (caller instanceof AnnotationColourChooser)
+      {
+        if (originalLabel.equals("Min Colour"))
+        {
+          ((AnnotationColourChooser) caller)
+                  .minColour_actionPerformed(getColor());
+        }
+        else
+        {
+          ((AnnotationColourChooser) caller)
+                  .maxColour_actionPerformed(getColor());
+        }
+      }
+      else if (caller instanceof FeatureRenderer)
+      {
+        ((FeatureRenderer) caller).colourPanel.setBackground(getColor());
+      }
+
+      return;
+    }
+
+    Color[] newColours = new Color[24];
+    for (int i = 0; i < 24; i++)
+    {
+      Button button = (Button) buttonPanel.getComponent(i);
+      newColours[i] = button.getBackground();
+    }
+
+    UserColourScheme ucs = new UserColourScheme(newColours);
+    if (ap != null)
+    {
+      ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+    }
+
+    if (ap != null)
+    {
+      if (seqGroup != null)
+      {
+        seqGroup.cs = ucs;
+      }
+      else
+      {
+        ap.av.setGlobalColourScheme(ucs);
+      }
+      ap.seqPanel.seqCanvas.img = null;
+      ap.paintAlignment(true);
+    }
+    else if (jmol != null)
+    {
+      jmol.setJalviewColourScheme(ucs);
+    }
+    else if (pdbcanvas != null)
+    {
+      pdbcanvas.setColours(ucs);
+    }
+  }
+
+  protected void cancelButton_actionPerformed()
+  {
+    if (caller != null)
+    {
+      if (caller instanceof FeatureSettings)
+      {
+        ((FeatureSettings) caller).setUserColour(originalLabel,
+                originalColour);
+      }
+      else if (caller instanceof AnnotationColourChooser)
+      {
+        if (originalLabel.equals("Min Colour"))
+        {
+          ((AnnotationColourChooser) caller)
+                  .minColour_actionPerformed(originalColour);
+        }
+        else
+        {
+          ((AnnotationColourChooser) caller)
+                  .maxColour_actionPerformed(originalColour);
+        }
+      }
+      else if (caller instanceof FeatureRenderer)
+      {
+        ((FeatureRenderer) caller).colourPanel
+                .setBackground(originalColour);
+
+      }
+
+      if (dialog != null)
+        dialog.setVisible(false);
+
+      frame.setVisible(false);
+      return;
+    }
+
+    Color[] newColours = new Color[24];
+    for (int i = 0; i < 24; i++)
+    {
+      newColours[i] = (Color) oldColours.elementAt(i);
+      buttonPanel.getComponent(i).setBackground(newColours[i]);
+    }
+
+    UserColourScheme ucs = new UserColourScheme(newColours);
+
+    if (ap != null)
+    {
+      if (seqGroup != null)
+      {
+        seqGroup.cs = ucs;
+      }
+      else
+      {
+        ap.av.setGlobalColourScheme(ucs);
+      }
+      ap.paintAlignment(true);
+    }
+    else if (jmol != null)
+    {
+      jmol.setJalviewColourScheme(ucs);
+    }
+    else if (pdbcanvas != null)
+    {
+      pdbcanvas.pdb.setColours(ucs);
+    }
+
+    frame.setVisible(false);
+  }
+
+  protected Panel buttonPanel = new Panel();
+
+  protected GridLayout gridLayout = new GridLayout();
+
+  Panel okcancelPanel = new Panel();
+
+  protected Button okButton = new Button();
+
+  protected Button applyButton = new Button();
+
+  protected Button cancelButton = new Button();
+
+  protected Scrollbar rScroller = new Scrollbar();
+
+  Label label1 = new Label();
+
+  protected TextField rText = new TextField();
+
+  Label label4 = new Label();
+
+  protected Scrollbar gScroller = new Scrollbar();
+
+  protected TextField gText = new TextField();
+
+  Label label5 = new Label();
+
+  protected Scrollbar bScroller = new Scrollbar();
+
+  protected TextField bText = new TextField();
+
+  protected Panel target = new Panel();
+
+  private void jbInit() throws Exception
+  {
+    this.setLayout(null);
+    buttonPanel.setLayout(gridLayout);
+    gridLayout.setColumns(6);
+    gridLayout.setRows(4);
+    okButton.setFont(new java.awt.Font("Verdana", 0, 11));
+    okButton.setLabel("OK");
+    okButton.addActionListener(this);
+    applyButton.setFont(new java.awt.Font("Verdana", 0, 11));
+    applyButton.setLabel("Apply");
+    applyButton.addActionListener(this);
+    cancelButton.setFont(new java.awt.Font("Verdana", 0, 11));
+    cancelButton.setLabel("Cancel");
+    cancelButton.addActionListener(this);
+    this.setBackground(new Color(212, 208, 223));
+    okcancelPanel.setBounds(new Rectangle(0, 265, 400, 35));
+    buttonPanel.setBounds(new Rectangle(0, 123, 400, 142));
+    rScroller.setMaximum(256);
+    rScroller.setMinimum(0);
+    rScroller.setOrientation(0);
+    rScroller.setUnitIncrement(1);
+    rScroller.setVisibleAmount(1);
+    rScroller.setBounds(new Rectangle(36, 27, 119, 19));
+    rScroller.addAdjustmentListener(this);
+    label1.setAlignment(Label.RIGHT);
+    label1.setText("R");
+    label1.setBounds(new Rectangle(19, 30, 16, 15));
+    rText.setFont(new java.awt.Font("Dialog", Font.PLAIN, 10));
+    rText.setText("0        ");
+    rText.setBounds(new Rectangle(156, 27, 53, 19));
+    rText.addActionListener(this);
+    label4.setAlignment(Label.RIGHT);
+    label4.setText("G");
+    label4.setBounds(new Rectangle(15, 56, 20, 15));
+    gScroller.setMaximum(256);
+    gScroller.setMinimum(0);
+    gScroller.setOrientation(0);
+    gScroller.setUnitIncrement(1);
+    gScroller.setVisibleAmount(1);
+    gScroller.setBounds(new Rectangle(35, 52, 120, 20));
+    gScroller.addAdjustmentListener(this);
+    gText.setFont(new java.awt.Font("Dialog", Font.PLAIN, 10));
+    gText.setText("0        ");
+    gText.setBounds(new Rectangle(156, 52, 53, 20));
+    gText.addActionListener(this);
+    label5.setAlignment(Label.RIGHT);
+    label5.setText("B");
+    label5.setBounds(new Rectangle(14, 82, 20, 15));
+    bScroller.setMaximum(256);
+    bScroller.setMinimum(0);
+    bScroller.setOrientation(0);
+    bScroller.setUnitIncrement(1);
+    bScroller.setVisibleAmount(1);
+    bScroller.setBounds(new Rectangle(35, 78, 120, 20));
+    bScroller.addAdjustmentListener(this);
+    bText.setFont(new java.awt.Font("Dialog", Font.PLAIN, 10));
+    bText.setText("0        ");
+    bText.setBounds(new Rectangle(157, 78, 52, 20));
+    bText.addActionListener(this);
+    target.setBackground(Color.black);
+    target.setBounds(new Rectangle(229, 26, 134, 79));
+    this.add(okcancelPanel, null);
+    okcancelPanel.add(okButton, null);
+    okcancelPanel.add(applyButton, null);
+    okcancelPanel.add(cancelButton, null);
+    this.add(buttonPanel, null);
+    this.add(target, null);
+    this.add(gScroller);
+    this.add(rScroller);
+    this.add(bScroller);
+    this.add(label5);
+    this.add(label4);
+    this.add(label1);
+    this.add(gText);
+    this.add(rText);
+    this.add(bText);
+  }
+
+}
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 0744cd9..e5f7f7b 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -24,73 +24,89 @@ import java.util.*;
 import org.apache.log4j.*;
 
 /**
- * Stores and retrieves Jalview Application Properties
- * Lists and fields within list entries are separated by '|' symbols unless otherwise stated
- * (|) clauses are alternative values for a tag.
- * <br><br>Current properties include:
- * <ul>
- * <br>logs.Axis.Level - one of the stringified Levels for log4j controlling the logging level for axis (used for web services)
- * <br>
- * </li><li>logs.Castor.Level - one of the stringified Levels for log4j controlling the logging level for castor (used for serialization)
+ * Stores and retrieves Jalview Application Properties Lists and fields within
+ * list entries are separated by '|' symbols unless otherwise stated (|) clauses
+ * are alternative values for a tag. <br>
  * <br>
- * </li><li>logs.Jalview.Level - Cache.log stringified level.
+ * Current properties include:
+ * <ul>
  * <br>
- * </li><li>DISCOVERY_START - Boolean - controls if discovery services are queried on startup
- * </li><li>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
- * </li><li>SCREEN_WIDTH
- * </li><li>SCREEN_HEIGHT
- * </li><li>SCREEN_Y=285
- * </li><li>SCREEN_X=371
- * </li><li>SHOW_FULLSCREEN boolean
- * </li><li>FONT_NAME java font name for alignment text display
- * </li><li>FONT_SIZE size of displayed alignment text
- * </li><li>FONT_STYLE style of font displayed (sequence labels are always italic)
- * </li><li>GAP_SYMBOL character to treat as gap symbol (usually -,.,' ')
- * </li><li>LAST_DIRECTORY last directory for browsing alignment
- * </li><li>USER_DEFINED_COLOURS list of user defined colour scheme files
- * </li><li>SHOW_FULL_ID show id with '/start-end' numbers appended
- * </li><li>SHOW_IDENTITY show percentage identity annotation
- * </li><li>SHOW_QUALITY show alignment quality annotation
- * </li><li>SHOW_ANNOTATIONS show alignment annotation rows
- * </li><li>SHOW_CONSERVATION show alignment conservation annotation
- * </li><li>CENTRE_COLUMN_LABELS centre the labels at each column in a displayed annotation row 
- * </li><li>DEFAULT_COLOUR default colour scheme to apply for a new alignment
- * </li><li>DEFAULT_FILE_FORMAT file format used to save 
- * </li><li>STARTUP_FILE file loaded on startup (may be a fully qualified url)
- * </li><li>SHOW_STARTUP_FILE flag to control loading of startup file
- * </li><li>VERSION the version of the jalview build
- * </li><li>BUILD_DATE date of this build
- * </li><li>LATEST_VERSION the latest jalview version advertised on the www.jalview.org
- * </li><li>PIR_MODELLER boolean indicating if PIR files are written with MODELLER descriptions
- * </li><li>(FASTA,MSF,PILEUP,CLUSTAL,BLC,PIR,PFAM)_JVSUFFIX boolean for adding jv suffix to file
- * </li><li>RECENT_URL list of recently retrieved URLs
- * </li><li>RECENT_FILE list of recently opened files
- * </li><li>USE_PROXY flag for whether a http proxy is to be used
- * </li><li>PROXY_SERVER the proxy
- * </li><li>PROXY_PORT
- * </li><li>NOQUESTIONNAIRES true to prevent jalview from checking the questionnaire service
- * </li><li>QUESTIONNAIRE last questionnaire:responder id string from questionnaire service
- * </li><li>DAS_LOCAL_SOURCE list of local das sources
- * </li><li>SHOW_OVERVIEW boolean for overview window display
- * </li><li>ANTI_ALIAS boolean for smooth fonts
- * </li><li>RIGHT_ALIGN_IDS boolean
- * </li><li>AUTO_CALC_CONSENSUS boolean for automatic recalculation of consensus
- * </li><li>PAD_GAPS boolean
- * </li><li>ID_ITALICS boolean 
- * </li><li>SHOW_JV_SUFFIX
- * </li><li>WRAP_ALIGNMENT
- * </li><li>EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering style check
- * </li><li>SORT_ALIGNMENT (No sort|Id|Pairwise Identity)
- * </li><li>SEQUENCE_LINKS list of name|URL pairs for opening a url with $SEQUENCE_ID$
- * </li><li>DAS_REGISTRY_URL the registry to query
- * </li><li>DEFAULT_BROWSER for unix
- * </li><li>DAS_ACTIVE_SOURCE list of active sources
- * </li><li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop (false) 
- * </li><li> 
+ * logs.Axis.Level - one of the stringified Levels for log4j controlling the
+ * logging level for axis (used for web services) <br>
+ * </li>
+ * <li>logs.Castor.Level - one of the stringified Levels for log4j controlling
+ * the logging level for castor (used for serialization) <br>
+ * </li>
+ * <li>logs.Jalview.Level - Cache.log stringified level. <br>
+ * </li>
+ * <li>DISCOVERY_START - Boolean - controls if discovery services are queried
+ * on startup </li>
+ * <li>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
  * </li>
+ * <li>SCREEN_WIDTH </li>
+ * <li>SCREEN_HEIGHT </li>
+ * <li>SCREEN_Y=285 </li>
+ * <li>SCREEN_X=371 </li>
+ * <li>SHOW_FULLSCREEN boolean </li>
+ * <li>FONT_NAME java font name for alignment text display </li>
+ * <li>FONT_SIZE size of displayed alignment text </li>
+ * <li>FONT_STYLE style of font displayed (sequence labels are always italic)
+ * </li>
+ * <li>GAP_SYMBOL character to treat as gap symbol (usually -,.,' ') </li>
+ * <li>LAST_DIRECTORY last directory for browsing alignment </li>
+ * <li>USER_DEFINED_COLOURS list of user defined colour scheme files </li>
+ * <li>SHOW_FULL_ID show id with '/start-end' numbers appended </li>
+ * <li>SHOW_IDENTITY show percentage identity annotation </li>
+ * <li>SHOW_QUALITY show alignment quality annotation </li>
+ * <li>SHOW_ANNOTATIONS show alignment annotation rows </li>
+ * <li>SHOW_CONSERVATION show alignment conservation annotation </li>
+ * <li>CENTRE_COLUMN_LABELS centre the labels at each column in a displayed
+ * annotation row </li>
+ * <li>DEFAULT_COLOUR default colour scheme to apply for a new alignment </li>
+ * <li>DEFAULT_FILE_FORMAT file format used to save </li>
+ * <li>STARTUP_FILE file loaded on startup (may be a fully qualified url) </li>
+ * <li>SHOW_STARTUP_FILE flag to control loading of startup file </li>
+ * <li>VERSION the version of the jalview build </li>
+ * <li>BUILD_DATE date of this build </li>
+ * <li>LATEST_VERSION the latest jalview version advertised on the
+ * www.jalview.org </li>
+ * <li>PIR_MODELLER boolean indicating if PIR files are written with MODELLER
+ * descriptions </li>
+ * <li>(FASTA,MSF,PILEUP,CLUSTAL,BLC,PIR,PFAM)_JVSUFFIX boolean for adding jv
+ * suffix to file </li>
+ * <li>RECENT_URL list of recently retrieved URLs </li>
+ * <li>RECENT_FILE list of recently opened files </li>
+ * <li>USE_PROXY flag for whether a http proxy is to be used </li>
+ * <li>PROXY_SERVER the proxy </li>
+ * <li>PROXY_PORT </li>
+ * <li>NOQUESTIONNAIRES true to prevent jalview from checking the questionnaire
+ * service </li>
+ * <li>QUESTIONNAIRE last questionnaire:responder id string from questionnaire
+ * service </li>
+ * <li>DAS_LOCAL_SOURCE list of local das sources </li>
+ * <li>SHOW_OVERVIEW boolean for overview window display </li>
+ * <li>ANTI_ALIAS boolean for smooth fonts </li>
+ * <li>RIGHT_ALIGN_IDS boolean </li>
+ * <li>AUTO_CALC_CONSENSUS boolean for automatic recalculation of consensus
+ * </li>
+ * <li>PAD_GAPS boolean </li>
+ * <li>ID_ITALICS boolean </li>
+ * <li>SHOW_JV_SUFFIX </li>
+ * <li>WRAP_ALIGNMENT </li>
+ * <li>EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering
+ * style check </li>
+ * <li>SORT_ALIGNMENT (No sort|Id|Pairwise Identity) </li>
+ * <li>SEQUENCE_LINKS list of name|URL pairs for opening a url with
+ * $SEQUENCE_ID$ </li>
+ * <li>DAS_REGISTRY_URL the registry to query </li>
+ * <li>DEFAULT_BROWSER for unix </li>
+ * <li>DAS_ACTIVE_SOURCE list of active sources </li>
+ * <li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
+ * (false) </li>
+ * <li> </li>
  * 
  * </ul>
-
+ * 
  * @author $author$
  * @version $Revision$
  */
@@ -100,14 +116,17 @@ public class Cache
    * property giving log4j level for CASTOR loggers
    */
   public static final String CASTORLOGLEVEL = "logs.Castor.level";
+
   /**
    * property giving log4j level for AXIS loggers
    */
   public static final String AXISLOGLEVEL = "logs.Axis.level";
+
   /**
    * property giving log4j level for Jalview Log
    */
   public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
+
   public static final String DAS_LOCAL_SOURCE = "DAS_LOCAL_SOURCE";
 
   /**
@@ -118,7 +137,7 @@ public class Cache
   /** Jalview Properties */
   public static Properties applicationProperties = new Properties();
 
-  /** Default file is  ~/.jalview_properties */
+  /** Default file is ~/.jalview_properties */
   static String propertiesFile;
 
   public static void initLogger()
@@ -126,33 +145,32 @@ public class Cache
     try
     {
       ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
-      "System.err");
+              "System.err");
       ap.setName("JalviewLogger");
-      org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for log output
+      org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for
+                                                                // log output
       Logger laxis = Logger.getLogger("org.apache.axis");
       Logger lcastor = Logger.getLogger("org.exolab.castor");
       jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
 
       laxis.setLevel(Level.toLevel(Cache.getDefault("logs.Axis.Level",
-          Level.INFO.toString())));
+              Level.INFO.toString())));
       lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
-          Level.INFO.toString())));
+              Level.INFO.toString())));
       lcastor = Logger.getLogger("org.exolab.castor.xml");
       lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
               Level.INFO.toString())));
-      //lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
-      //lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
-      //        Level.INFO.toString())));
+      // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
+      // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
+      // Level.INFO.toString())));
       jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault(
-          "logs.Jalview.level",
-          Level.INFO.toString())));
-      //laxis.addAppender(ap);
-      //lcastor.addAppender(ap);
-      //jalview.bin.Cache.log.addAppender(ap);
+              "logs.Jalview.level", Level.INFO.toString())));
+      // laxis.addAppender(ap);
+      // lcastor.addAppender(ap);
+      // jalview.bin.Cache.log.addAppender(ap);
       // Tell the user that debug is enabled
       jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       System.err.println("Problems initializing the log4j system\n");
       ex.printStackTrace(System.err);
@@ -165,8 +183,8 @@ public class Cache
     propertiesFile = propsFile;
     if (propsFile == null)
     {
-      propertiesFile = System.getProperty("user.home") + File.separatorChar +
-          ".jalview_properties";
+      propertiesFile = System.getProperty("user.home") + File.separatorChar
+              + ".jalview_properties";
     }
 
     try
@@ -176,17 +194,19 @@ public class Cache
       applicationProperties.remove("LATEST_VERSION");
       applicationProperties.remove("VERSION");
       fis.close();
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       System.out.println("Error reading properties file: " + ex);
     }
 
     if (getDefault("USE_PROXY", false))
     {
-      System.out.println("Using proxyServer: " + getDefault("PROXY_SERVER", null) +
-                         " proxyPort: " + getDefault("PROXY_PORT", null));
-      System.setProperty("http.proxyHost", getDefault("PROXY_SERVER", null));
+      System.out.println("Using proxyServer: "
+              + getDefault("PROXY_SERVER", null) + " proxyPort: "
+              + getDefault("PROXY_PORT", null));
+      System
+              .setProperty("http.proxyHost", getDefault("PROXY_SERVER",
+                      null));
       System.setProperty("http.proxyPort", getDefault("PROXY_PORT", null));
     }
 
@@ -195,20 +215,16 @@ public class Cache
     // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
     try
     {
-      String buildDetails = "jar:"
-          .concat(
-              Cache.class.getProtectionDomain().getCodeSource().getLocation().
-              toString()
-              .concat("!/.build_properties")
-          );
+      String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
+              .getCodeSource().getLocation().toString().concat(
+                      "!/.build_properties"));
 
       java.net.URL localJarFileURL = new java.net.URL(buildDetails);
 
       InputStream in = localJarFileURL.openStream();
       applicationProperties.load(in);
       in.close();
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       System.out.println("Error reading build details: " + ex);
       applicationProperties.remove("VERSION");
@@ -228,32 +244,34 @@ public class Cache
 
     // jnlpVersion will be null if we're using InstallAnywhere
     // Dont do this check if running in headless mode
-    if (jnlpVersion == null && (
-        System.getProperty("java.awt.headless") == null
-        || System.getProperty("java.awt.headless").equals("false")))
+    if (jnlpVersion == null
+            && (System.getProperty("java.awt.headless") == null || System
+                    .getProperty("java.awt.headless").equals("false")))
     {
 
-      class VersionChecker
-          extends Thread
+      class VersionChecker extends Thread
       {
         public void run()
         {
-          String orgtimeout = System.getProperty("sun.net.client.defaultConnectTimeout");
-          if (orgtimeout==null)
+          String orgtimeout = System
+                  .getProperty("sun.net.client.defaultConnectTimeout");
+          if (orgtimeout == null)
           {
-            orgtimeout="30";
-            System.out.println("# INFO: Setting default net timeout to "+orgtimeout+" seconds.");
+            orgtimeout = "30";
+            System.out.println("# INFO: Setting default net timeout to "
+                    + orgtimeout + " seconds.");
           }
           String jnlpVersion = null;
           try
           {
-            System.setProperty("sun.net.client.defaultConnectTimeout", "5000");
+            System.setProperty("sun.net.client.defaultConnectTimeout",
+                    "5000");
             java.net.URL url = new java.net.URL(
-                "http://www.jalview.org/webstart/jalview.jnlp");
-            BufferedReader in = new BufferedReader(new InputStreamReader(url.
-                openStream()));
+                    "http://www.jalview.org/webstart/jalview.jnlp");
+            BufferedReader in = new BufferedReader(new InputStreamReader(
+                    url.openStream()));
             String line = null;
-            while ( (line = in.readLine()) != null)
+            while ((line = in.readLine()) != null)
             {
               if (line.indexOf("jalview.version") == -1)
               {
@@ -265,14 +283,15 @@ public class Cache
               jnlpVersion = line;
               break;
             }
-          }
-          catch (Exception ex)
+          } catch (Exception ex)
           {
-            System.out.println("Non-fatal exceptions when checking version at www.jalview.org :");
+            System.out
+                    .println("Non-fatal exceptions when checking version at www.jalview.org :");
             System.out.println(ex);
             jnlpVersion = getProperty("VERSION");
           }
-          System.setProperty("sun.net.client.defaultConnectTimeout", orgtimeout);
+          System.setProperty("sun.net.client.defaultConnectTimeout",
+                  orgtimeout);
 
           setProperty("LATEST_VERSION", jnlpVersion);
         }
@@ -295,18 +314,20 @@ public class Cache
 
     setProperty("VERSION", codeVersion);
 
-    //LOAD USERDEFINED COLOURS
-    jalview.gui.UserDefinedColours.initUserColourSchemes(getProperty(
-        "USER_DEFINED_COLOURS"));
-    jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER", false);
+    // LOAD USERDEFINED COLOURS
+    jalview.gui.UserDefinedColours
+            .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
+    jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
+            false);
   }
 
   /**
-   * Gets Jalview application property of given key. Returns null
-   * if key not found
-   *
-   * @param key Name of property
-   *
+   * Gets Jalview application property of given key. Returns null if key not
+   * found
+   * 
+   * @param key
+   *                Name of property
+   * 
    * @return Property value
    */
   public static String getProperty(String key)
@@ -314,8 +335,9 @@ public class Cache
     return applicationProperties.getProperty(key);
   }
 
-  /** These methods are used when checking if the saved preference
-   * is different to the default setting
+  /**
+   * These methods are used when checking if the saved preference is different
+   * to the default setting
    */
 
   public static boolean getDefault(String property, boolean def)
@@ -329,8 +351,9 @@ public class Cache
     return def;
   }
 
-  /** These methods are used when checking if the saved preference
-   * is different to the default setting
+  /**
+   * These methods are used when checking if the saved preference is different
+   * to the default setting
    */
   public static String getDefault(String property, String def)
   {
@@ -345,10 +368,12 @@ public class Cache
 
   /**
    * Stores property in the file "HOME_DIR/.jalview_properties"
-   *
-   * @param key Name of object
-   * @param obj String value of property
-   *
+   * 
+   * @param key
+   *                Name of object
+   * @param obj
+   *                String value of property
+   * 
    * @return String value of property
    */
   public static String setProperty(String key, String obj)
@@ -359,11 +384,10 @@ public class Cache
       applicationProperties.setProperty(key, obj);
       applicationProperties.store(out, "---JalviewX Properties File---");
       out.close();
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
-      System.out.println("Error setting property: " + key + " " + obj + "\n" +
-                         ex);
+      System.out.println("Error setting property: " + key + " " + obj
+              + "\n" + ex);
     }
     return obj;
   }
@@ -375,8 +399,7 @@ public class Cache
       FileOutputStream out = new FileOutputStream(propertiesFile);
       applicationProperties.store(out, "---JalviewX Properties File---");
       out.close();
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       System.out.println("Error saving properties: " + ex);
     }
@@ -386,8 +409,10 @@ public class Cache
    * internal vamsas class discovery state
    */
   private static int vamsasJarsArePresent = -1;
+
   /**
    * Searches for vamsas client classes on class path.
+   * 
    * @return true if vamsas client is present on classpath
    */
   public static boolean vamsasJarsPresent()
@@ -397,21 +422,20 @@ public class Cache
       try
       {
         if (jalview.jbgui.GDesktop.class.getClassLoader().loadClass(
-            "uk.ac.vamsas.client.VorbaId") != null)
+                "uk.ac.vamsas.client.VorbaId") != null)
         {
-          jalview.bin.Cache.log.debug(
-              "Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
+          jalview.bin.Cache.log
+                  .debug("Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
           vamsasJarsArePresent = 1;
           Logger lvclient = Logger.getLogger("uk.ac.vamsas");
-          lvclient.setLevel(Level.toLevel(Cache.getDefault("logs.Vamsas.Level",
-              Level.INFO.toString())));
+          lvclient.setLevel(Level.toLevel(Cache.getDefault(
+                  "logs.Vamsas.Level", Level.INFO.toString())));
 
           lvclient.addAppender(log.getAppender("JalviewLogger"));
           // Tell the user that debug is enabled
           lvclient.debug("Jalview Vamsas Client Debugging Output Follows.");
         }
-      }
-      catch (Exception e)
+      } catch (Exception e)
       {
         vamsasJarsArePresent = 0;
         jalview.bin.Cache.log.debug("Vamsas Classes are not present");
@@ -419,12 +443,15 @@ public class Cache
     }
     return (vamsasJarsArePresent > 0);
   }
+
   /**
    * internal vamsas class discovery state
    */
   private static int groovyJarsArePresent = -1;
+
   /**
    * Searches for vamsas client classes on class path.
+   * 
    * @return true if vamsas client is present on classpath
    */
   public static boolean groovyJarsPresent()
@@ -434,21 +461,20 @@ public class Cache
       try
       {
         if (Cache.class.getClassLoader().loadClass(
-            "groovy.lang.GroovyObject") != null)
+                "groovy.lang.GroovyObject") != null)
         {
-          jalview.bin.Cache.log.debug(
-              "Found Groovy (groovy.lang.GroovyObject can be loaded)");
+          jalview.bin.Cache.log
+                  .debug("Found Groovy (groovy.lang.GroovyObject can be loaded)");
           groovyJarsArePresent = 1;
           Logger lgclient = Logger.getLogger("groovy");
-          lgclient.setLevel(Level.toLevel(Cache.getDefault("logs.Groovy.Level",
-              Level.INFO.toString())));
+          lgclient.setLevel(Level.toLevel(Cache.getDefault(
+                  "logs.Groovy.Level", Level.INFO.toString())));
 
           lgclient.addAppender(log.getAppender("JalviewLogger"));
           // Tell the user that debug is enabled
           lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
         }
-      }
-      catch (Exception e)
+      } catch (Exception e)
       {
         groovyJarsArePresent = 0;
         jalview.bin.Cache.log.debug("Groovy Classes are not present");
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 4f383a0..36f4ff6 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -166,9 +166,11 @@ public class Jalview
 
     String file = null, protocol = null, format = null, data = null;
     jalview.io.FileLoader fileLoader = new jalview.io.FileLoader();
-    Vector getFeatures = null; // vector of das source nicknames to fetch features from
+    Vector getFeatures = null; // vector of das source nicknames to fetch
+                                // features from
     // loading is done.
-    String groovyscript = null; // script to execute after all loading is completed one way or another
+    String groovyscript = null; // script to execute after all loading is
+                                // completed one way or another
     // extract groovy argument and execute if necessary
     groovyscript = aparser.getValue("groovy");
     file = aparser.getValue("open");
@@ -268,31 +270,36 @@ public class Jalview
         }
       }
       getFeatures = checkDasArguments(aparser);
-      if (af != null && getFeatures!=null)
+      if (af != null && getFeatures != null)
       {
-        startFeatureFetching(getFeatures); 
+        startFeatureFetching(getFeatures);
         // need to block until fetching is complete.
         while (af.operationInProgress())
         {
           // wait around until fetching is finished.
-          try {
+          try
+          {
             Thread.sleep(10);
           } catch (Exception e)
           {
-            
+
           }
         }
       }
-      if (groovyscript!=null)
+      if (groovyscript != null)
       {
-        // Execute the groovy script after we've  done all the rendering stuff
+        // Execute the groovy script after we've done all the rendering stuff
         // and before any images or figures are generated.
         if (jalview.bin.Cache.groovyJarsPresent())
         {
-          System.out.println("Executing script "+groovyscript);
+          System.out.println("Executing script " + groovyscript);
           executeGroovyScript(groovyscript, desktop);
-        } else {
-          System.err.println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "+groovyscript);
+        }
+        else
+        {
+          System.err
+                  .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
+                          + groovyscript);
         }
         groovyscript = null;
       }
@@ -372,128 +379,156 @@ public class Jalview
       // extract groovy arguments before anything else.
     }
     // Once all loading is done. Retrieve features.
-    if (getFeatures!=null)
+    if (getFeatures != null)
     {
-      if (startUpAlframe!=null)
+      if (startUpAlframe != null)
       {
         startFeatureFetching(getFeatures);
       }
     }
-    if (groovyscript!=null)
+    if (groovyscript != null)
     {
       if (jalview.bin.Cache.groovyJarsPresent())
       {
-        System.out.println("Executing script "+groovyscript);
+        System.out.println("Executing script " + groovyscript);
         executeGroovyScript(groovyscript, desktop);
-      } else {
-        System.err.println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "+groovyscript);
+      }
+      else
+      {
+        System.err
+                .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
+                        + groovyscript);
       }
     }
 
     // Once all other stuff is done, execute any groovy scripts (in order)
   }
+
   /**
    * Locate the given string as a file and pass it to the groovy interpreter.
-   * @param groovyscript the script to execute
-   * @param jalviewContext the Jalview Desktop object passed in to the groovy binding as the 'Jalview' object.
+   * 
+   * @param groovyscript
+   *                the script to execute
+   * @param jalviewContext
+   *                the Jalview Desktop object passed in to the groovy binding
+   *                as the 'Jalview' object.
    */
-  private static void executeGroovyScript(String groovyscript, Object jalviewContext)
+  private static void executeGroovyScript(String groovyscript,
+          Object jalviewContext)
   {
-    if (jalviewContext==null)
+    if (jalviewContext == null)
     {
-      System.err.println("Sorry. Groovy support is currently only available when running with the Jalview GUI enabled.");
+      System.err
+              .println("Sorry. Groovy support is currently only available when running with the Jalview GUI enabled.");
     }
     File sfile = null;
     if (groovyscript.trim().equals("STDIN"))
     {
       // read from stdin into a tempfile and execute it
-      try {
+      try
+      {
         sfile = File.createTempFile("jalview", "groovy");
-        PrintWriter outfile = new PrintWriter(new OutputStreamWriter(new FileOutputStream(sfile)));
-        BufferedReader br = new BufferedReader(new java.io.InputStreamReader(System.in));
-        String line=null;
-        while ((line=br.readLine())!=null)
+        PrintWriter outfile = new PrintWriter(new OutputStreamWriter(
+                new FileOutputStream(sfile)));
+        BufferedReader br = new BufferedReader(
+                new java.io.InputStreamReader(System.in));
+        String line = null;
+        while ((line = br.readLine()) != null)
         {
-          outfile.write(line+"\n");
+          outfile.write(line + "\n");
         }
         br.close();
         outfile.flush();
         outfile.close();
-        
+
       } catch (Exception ex)
       {
-        System.err.println("Failed to read from STDIN into tempfile "+((sfile==null) ? "(tempfile wasn't created)" : sfile.toString()));
+        System.err.println("Failed to read from STDIN into tempfile "
+                + ((sfile == null) ? "(tempfile wasn't created)" : sfile
+                        .toString()));
         ex.printStackTrace();
         return;
       }
-    } else {
+    }
+    else
+    {
       sfile = new File(groovyscript);
     }
     if (!sfile.exists())
     {
-      System.err.println("File '"+groovyscript+"' does not exist.");
+      System.err.println("File '" + groovyscript + "' does not exist.");
       return;
     }
     if (!sfile.canRead())
     {
-      System.err.println("File '"+groovyscript+"' cannot be read.");
+      System.err.println("File '" + groovyscript + "' cannot be read.");
       return;
     }
-    if (sfile.length()<1)
+    if (sfile.length() < 1)
     {
-      System.err.println("File '"+groovyscript+"' is empty.");
+      System.err.println("File '" + groovyscript + "' is empty.");
       return;
     }
     boolean success = false;
-    try {
-      /* The following code performs the GroovyScriptEngine invocation using reflection,
-       * and is equivalent to this fragment from the embedding groovy documentation on 
-       * the groovy site:
-       * <code>
-         import groovy.lang.Binding;
-         import groovy.util.GroovyScriptEngine;
-        
-         String[] roots = new String[] { "/my/groovy/script/path" };
-         GroovyScriptEngine gse = new GroovyScriptEngine(roots);
-         Binding binding = new Binding();
-         binding.setVariable("input", "world");
-         gse.run("hello.groovy", binding);
-         * </code>
-         */
-        ClassLoader cl = jalviewContext.getClass().getClassLoader();
-        Class   gbindingc = cl.loadClass("groovy.lang.Binding");
-        Constructor gbcons = gbindingc.getConstructor(null);
-        Object gbinding = gbcons.newInstance(null);
-        java.lang.reflect.Method setvar = gbindingc.getMethod("setVariable", new Class[] { String.class, Object.class} );
-        setvar.invoke(gbinding, new Object[] { "Jalview", jalviewContext});
-        Class gsec = cl.loadClass("groovy.util.GroovyScriptEngine");
-        Constructor gseccons = gsec.getConstructor(new Class[] { URL[].class } ); // String[].class });
-        Object gse = gseccons.newInstance(new Object[] { new URL[] { sfile.toURL() } }); // .toString() } });
-        java.lang.reflect.Method run = gsec.getMethod("run", new Class[]{ String.class, gbindingc });
-        run.invoke(gse, new Object[] { sfile.getName(), gbinding });
-        success = true;
+    try
+    {
+      /*
+       * The following code performs the GroovyScriptEngine invocation using
+       * reflection, and is equivalent to this fragment from the embedding
+       * groovy documentation on the groovy site: <code> import
+       * groovy.lang.Binding; import groovy.util.GroovyScriptEngine;
+       * 
+       * String[] roots = new String[] { "/my/groovy/script/path" };
+       * GroovyScriptEngine gse = new GroovyScriptEngine(roots); Binding binding =
+       * new Binding(); binding.setVariable("input", "world");
+       * gse.run("hello.groovy", binding); </code>
+       */
+      ClassLoader cl = jalviewContext.getClass().getClassLoader();
+      Class gbindingc = cl.loadClass("groovy.lang.Binding");
+      Constructor gbcons = gbindingc.getConstructor(null);
+      Object gbinding = gbcons.newInstance(null);
+      java.lang.reflect.Method setvar = gbindingc.getMethod("setVariable",
+              new Class[]
+              { String.class, Object.class });
+      setvar.invoke(gbinding, new Object[]
+      { "Jalview", jalviewContext });
+      Class gsec = cl.loadClass("groovy.util.GroovyScriptEngine");
+      Constructor gseccons = gsec.getConstructor(new Class[]
+      { URL[].class }); // String[].class });
+      Object gse = gseccons.newInstance(new Object[]
+      { new URL[]
+      { sfile.toURL() } }); // .toString() } });
+      java.lang.reflect.Method run = gsec.getMethod("run", new Class[]
+      { String.class, gbindingc });
+      run.invoke(gse, new Object[]
+      { sfile.getName(), gbinding });
+      success = true;
     } catch (Exception e)
     {
-      System.err.println("Exception Whilst trying to execute file "+sfile+" as a groovy script.");
+      System.err.println("Exception Whilst trying to execute file " + sfile
+              + " as a groovy script.");
       e.printStackTrace(System.err);
-      
+
     }
     if (success && groovyscript.equals("STDIN"))
     {
-      // delete temp file that we made - but only if it was successfully executed
+      // delete temp file that we made - but only if it was successfully
+      // executed
       sfile.delete();
     }
   }
+
   /**
    * Check commandline for any das server definitions or any fetchfrom switches
+   * 
    * @return vector of DAS source nicknames to retrieve from
    */
   private static Vector checkDasArguments(ArgsParser aparser)
   {
-    Vector source=null;
+    Vector source = null;
     String data;
     String locsources = Cache.getProperty(Cache.DAS_LOCAL_SOURCE);
-    while ((data = aparser.getValue("dasserver"))!=null)
+    while ((data = aparser.getValue("dasserver")) != null)
     {
       String nickname = null;
       String url = null;
@@ -509,32 +544,35 @@ public class Jalview
         {
           nickname = url;
         }
-        if (locsources==null)
+        if (locsources == null)
+        {
+          locsources = "";
+        }
+        else
         {
-          locsources="";
-        } else {
-          locsources+="\t";
+          locsources += "\t";
         }
-        locsources=locsources+nickname+"|"+url;
+        locsources = locsources + nickname + "|" + url;
         System.err
                 .println("NOTE! dasserver parameter not yet really supported (got args of "
                         + nickname + "|" + url);
-        if (source==null)
+        if (source == null)
         {
           source = new Vector();
         }
         source.addElement(nickname);
       }
     } // loop until no more server entries are found.
-    if (locsources!=null && locsources.indexOf('|')>-1)
+    if (locsources != null && locsources.indexOf('|') > -1)
     {
-      Cache.log.debug("Setting local source list in properties file to:\n"+locsources);
+      Cache.log.debug("Setting local source list in properties file to:\n"
+              + locsources);
       Cache.setProperty(Cache.DAS_LOCAL_SOURCE, locsources);
     }
-    while ((data = aparser.getValue("fetchfrom"))!=null)
+    while ((data = aparser.getValue("fetchfrom")) != null)
     {
-      System.out.println("adding source '"+data+"'");
-      if (source==null)
+      System.out.println("adding source '" + data + "'");
+      if (source == null)
       {
         source = new Vector();
       }
@@ -542,24 +580,27 @@ public class Jalview
     }
     return source;
   }
+
   /**
    * start a feature fetcher for every alignment frame
+   * 
    * @param dasSources
    */
   private static void startFeatureFetching(final Vector dasSources)
   {
     AlignFrame afs[] = Desktop.getAlignframes();
-    if (afs==null || afs.length==0)
+    if (afs == null || afs.length == 0)
     {
       return;
     }
-    for (int i = 0; i<afs.length; i++)
+    for (int i = 0; i < afs.length; i++)
     {
       final AlignFrame af = afs[i];
-      SwingUtilities.invokeLater(new Runnable() {
+      SwingUtilities.invokeLater(new Runnable()
+      {
 
         public void run()
-        { 
+        {
           af.featureSettings_actionPerformed(null);
           af.featureSettings.fetchDasFeatures(dasSources);
         }
@@ -581,11 +622,12 @@ public class Jalview
 
 /**
  * Notes: this argParser does not distinguish between parameter switches,
- * parameter values and argument text. If an argument happens to be identical
- * to a parameter, it will be taken as such (even though it didn't have a '-' prefixing it).
+ * parameter values and argument text. If an argument happens to be identical to
+ * a parameter, it will be taken as such (even though it didn't have a '-'
+ * prefixing it).
  * 
  * @author Andrew Waterhouse and JBP documented.
- *
+ * 
  */
 class ArgsParser
 {
@@ -604,8 +646,10 @@ class ArgsParser
       vargs.addElement(arg);
     }
   }
+
   /**
    * check for and remove first occurence of arg+parameter in arglist.
+   * 
    * @param arg
    * @return return the argument following the given arg if arg was in list.
    */
@@ -621,8 +665,10 @@ class ArgsParser
     }
     return ret;
   }
+
   /**
    * check for and remove first occurence of arg in arglist.
+   * 
    * @param arg
    * @return true if arg was present in argslist.
    */
diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 393476d..cb8f4f7 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -327,7 +327,7 @@ public class JalviewLite extends Applet
      * if true disable the check for jmol
      */
     String chkforJmol = getParameter("nojmol");
-    if (chkforJmol!=null)
+    if (chkforJmol != null)
     {
       checkForJmol = !chkforJmol.equals("true");
     }
@@ -559,11 +559,14 @@ public class JalviewLite extends Applet
         } catch (java.lang.ClassNotFoundException ex)
         {
         }
-      } else {
-        jmolAvailable=false;
+      }
+      else
+      {
+        jmolAvailable = false;
         if (debug)
         {
-          System.err.println("Skipping Jmol check. Will use MCView (probably)");
+          System.err
+                  .println("Skipping Jmol check. Will use MCView (probably)");
         }
       }
     }
@@ -747,13 +750,13 @@ public class JalviewLite extends Applet
                     param, protocol);
             JnetAnnotationMaker.add_annotation(predictions,
                     currentAlignFrame.viewport.getAlignment(), 0, false); // false==do
-                                                                          // not
-                                                                          // add
-                                                                          // sequence
-                                                                          // profile
-                                                                          // from
-                                                                          // concise
-                                                                          // output
+            // not
+            // add
+            // sequence
+            // profile
+            // from
+            // concise
+            // output
             currentAlignFrame.alignPanel.fontChanged();
             currentAlignFrame.alignPanel.setScrollValues(0, 0);
           } catch (Exception ex)
@@ -829,14 +832,16 @@ public class JalviewLite extends Applet
             }
             param = setProtocolState(param);
 
-            if (!jmolAvailable
-                    && protocol == AppletFormatAdapter.CLASSLOADER)
+            if (// !jmolAvailable
+            // &&
+            protocol == AppletFormatAdapter.CLASSLOADER)
             {
-              // TODO: pass PDB file in classloader on to Jmol
+              // TODO: verify this Re:
+              // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
               // This exception preserves the current behaviour where, even if
               // the local pdb file was identified in the class loader
               protocol = AppletFormatAdapter.URL; // this is probably NOT
-                                                  // CORRECT!
+              // CORRECT!
               param = addProtocol(param); // 
             }
 
@@ -971,7 +976,8 @@ public class JalviewLite extends Applet
    * separator used for separatorList
    */
   protected String separator = "|"; // this is a safe(ish) separator - tabs
-                                    // don't work for firefox
+
+  // don't work for firefox
 
   /**
    * parse the string into a list
@@ -1119,7 +1125,7 @@ public class JalviewLite extends Applet
           boolean state)
   {
     boolean st = state;// !(state==null || state.equals("") ||
-                        // state.toLowerCase().equals("false"));
+    // state.toLowerCase().equals("false"));
     alf.setFeatureGroupState(separatorListToArray(groups), st);
   }
 
diff --git a/src/jalview/binding/Alignment.java b/src/jalview/binding/Alignment.java
index 5b107b5..96812e3 100755
--- a/src/jalview/binding/Alignment.java
+++ b/src/jalview/binding/Alignment.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,151 +30,166 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Alignment implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _annotation.
-     */
-    private jalview.binding.Annotation _annotation;
-
-    /**
-     * Field _sequenceSet.
-     */
-    private jalview.binding.SequenceSet _sequenceSet;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Alignment() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'annotation'.
-     * 
-     * @return the value of field 'Annotation'.
-     */
-    public jalview.binding.Annotation getAnnotation(
-    ) {
-        return this._annotation;
-    }
-
-    /**
-     * Returns the value of field 'sequenceSet'.
-     * 
-     * @return the value of field 'SequenceSet'.
-     */
-    public jalview.binding.SequenceSet getSequenceSet(
-    ) {
-        return this._sequenceSet;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'annotation'.
-     * 
-     * @param annotation the value of field 'annotation'.
-     */
-    public void setAnnotation(
-            final jalview.binding.Annotation annotation) {
-        this._annotation = annotation;
-    }
-
-    /**
-     * Sets the value of field 'sequenceSet'.
-     * 
-     * @param sequenceSet the value of field 'sequenceSet'.
-     */
-    public void setSequenceSet(
-            final jalview.binding.SequenceSet sequenceSet) {
-        this._sequenceSet = sequenceSet;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.Alignment
-     */
-    public static jalview.binding.Alignment unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.Alignment) Unmarshaller.unmarshal(jalview.binding.Alignment.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class Alignment implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _annotation.
+   */
+  private jalview.binding.Annotation _annotation;
+
+  /**
+   * Field _sequenceSet.
+   */
+  private jalview.binding.SequenceSet _sequenceSet;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Alignment()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Returns the value of field 'annotation'.
+   * 
+   * @return the value of field 'Annotation'.
+   */
+  public jalview.binding.Annotation getAnnotation()
+  {
+    return this._annotation;
+  }
+
+  /**
+   * Returns the value of field 'sequenceSet'.
+   * 
+   * @return the value of field 'SequenceSet'.
+   */
+  public jalview.binding.SequenceSet getSequenceSet()
+  {
+    return this._sequenceSet;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'annotation'.
+   * 
+   * @param annotation
+   *                the value of field 'annotation'.
+   */
+  public void setAnnotation(final jalview.binding.Annotation annotation)
+  {
+    this._annotation = annotation;
+  }
+
+  /**
+   * Sets the value of field 'sequenceSet'.
+   * 
+   * @param sequenceSet
+   *                the value of field 'sequenceSet'.
+   */
+  public void setSequenceSet(final jalview.binding.SequenceSet sequenceSet)
+  {
+    this._sequenceSet = sequenceSet;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.binding.Alignment
+   */
+  public static jalview.binding.Alignment unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.Alignment) Unmarshaller.unmarshal(
+            jalview.binding.Alignment.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/Annotation.java b/src/jalview/binding/Annotation.java
index 108d3ad..ec3e248 100755
--- a/src/jalview/binding/Annotation.java
+++ b/src/jalview/binding/Annotation.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,414 +30,445 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Annotation implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _graph.
-     */
-    private boolean _graph;
-
-    /**
-     * keeps track of state for field: _graph
-     */
-    private boolean _has_graph;
-
-    /**
-     * Field _graphType.
-     */
-    private int _graphType;
-
-    /**
-     * keeps track of state for field: _graphType
-     */
-    private boolean _has_graphType;
-
-    /**
-     * Field _annotationElementList.
-     */
-    private java.util.Vector _annotationElementList;
-
-    /**
-     * Field _label.
-     */
-    private java.lang.String _label;
-
-    /**
-     * Field _description.
-     */
-    private java.lang.String _description;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Annotation() {
-        super();
-        this._annotationElementList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vAnnotationElement
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addAnnotationElement(
-            final jalview.binding.AnnotationElement vAnnotationElement)
-    throws java.lang.IndexOutOfBoundsException {
-        this._annotationElementList.addElement(vAnnotationElement);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vAnnotationElement
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addAnnotationElement(
-            final int index,
-            final jalview.binding.AnnotationElement vAnnotationElement)
-    throws java.lang.IndexOutOfBoundsException {
-        this._annotationElementList.add(index, vAnnotationElement);
-    }
-
-    /**
-     */
-    public void deleteGraph(
-    ) {
-        this._has_graph= false;
-    }
-
-    /**
-     */
-    public void deleteGraphType(
-    ) {
-        this._has_graphType= false;
-    }
-
-    /**
-     * Method enumerateAnnotationElement.
-     * 
-     * @return an Enumeration over all
-     * jalview.binding.AnnotationElement elements
-     */
-    public java.util.Enumeration enumerateAnnotationElement(
-    ) {
-        return this._annotationElementList.elements();
-    }
-
-    /**
-     * Method getAnnotationElement.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the jalview.binding.AnnotationElement
-     * at the given index
-     */
-    public jalview.binding.AnnotationElement getAnnotationElement(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._annotationElementList.size()) {
-            throw new IndexOutOfBoundsException("getAnnotationElement: Index value '" + index + "' not in range [0.." + (this._annotationElementList.size() - 1) + "]");
-        }
-        
-        return (jalview.binding.AnnotationElement) _annotationElementList.get(index);
-    }
-
-    /**
-     * Method getAnnotationElement.Returns the contents of the
-     * collection in an Array.  <p>Note:  Just in case the
-     * collection contents are changing in another thread, we pass
-     * a 0-length Array of the correct type into the API call. 
-     * This way we <i>know</i> that the Array returned is of
-     * exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.binding.AnnotationElement[] getAnnotationElement(
-    ) {
-        jalview.binding.AnnotationElement[] array = new jalview.binding.AnnotationElement[0];
-        return (jalview.binding.AnnotationElement[]) this._annotationElementList.toArray(array);
-    }
-
-    /**
-     * Method getAnnotationElementCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getAnnotationElementCount(
-    ) {
-        return this._annotationElementList.size();
-    }
-
-    /**
-     * Returns the value of field 'description'.
-     * 
-     * @return the value of field 'Description'.
-     */
-    public java.lang.String getDescription(
-    ) {
-        return this._description;
+public class Annotation implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _graph.
+   */
+  private boolean _graph;
+
+  /**
+   * keeps track of state for field: _graph
+   */
+  private boolean _has_graph;
+
+  /**
+   * Field _graphType.
+   */
+  private int _graphType;
+
+  /**
+   * keeps track of state for field: _graphType
+   */
+  private boolean _has_graphType;
+
+  /**
+   * Field _annotationElementList.
+   */
+  private java.util.Vector _annotationElementList;
+
+  /**
+   * Field _label.
+   */
+  private java.lang.String _label;
+
+  /**
+   * Field _description.
+   */
+  private java.lang.String _description;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Annotation()
+  {
+    super();
+    this._annotationElementList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vAnnotationElement
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addAnnotationElement(
+          final jalview.binding.AnnotationElement vAnnotationElement)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._annotationElementList.addElement(vAnnotationElement);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAnnotationElement
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addAnnotationElement(final int index,
+          final jalview.binding.AnnotationElement vAnnotationElement)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._annotationElementList.add(index, vAnnotationElement);
+  }
+
+  /**
+   */
+  public void deleteGraph()
+  {
+    this._has_graph = false;
+  }
+
+  /**
+   */
+  public void deleteGraphType()
+  {
+    this._has_graphType = false;
+  }
+
+  /**
+   * Method enumerateAnnotationElement.
+   * 
+   * @return an Enumeration over all jalview.binding.AnnotationElement elements
+   */
+  public java.util.Enumeration enumerateAnnotationElement()
+  {
+    return this._annotationElementList.elements();
+  }
+
+  /**
+   * Method getAnnotationElement.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.binding.AnnotationElement at the given
+   *         index
+   */
+  public jalview.binding.AnnotationElement getAnnotationElement(
+          final int index) throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._annotationElementList.size())
+    {
+      throw new IndexOutOfBoundsException(
+              "getAnnotationElement: Index value '" + index
+                      + "' not in range [0.."
+                      + (this._annotationElementList.size() - 1) + "]");
     }
 
-    /**
-     * Returns the value of field 'graph'.
-     * 
-     * @return the value of field 'Graph'.
-     */
-    public boolean getGraph(
-    ) {
-        return this._graph;
+    return (jalview.binding.AnnotationElement) _annotationElementList
+            .get(index);
+  }
+
+  /**
+   * Method getAnnotationElement.Returns the contents of the collection in an
+   * Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.binding.AnnotationElement[] getAnnotationElement()
+  {
+    jalview.binding.AnnotationElement[] array = new jalview.binding.AnnotationElement[0];
+    return (jalview.binding.AnnotationElement[]) this._annotationElementList
+            .toArray(array);
+  }
+
+  /**
+   * Method getAnnotationElementCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getAnnotationElementCount()
+  {
+    return this._annotationElementList.size();
+  }
+
+  /**
+   * Returns the value of field 'description'.
+   * 
+   * @return the value of field 'Description'.
+   */
+  public java.lang.String getDescription()
+  {
+    return this._description;
+  }
+
+  /**
+   * Returns the value of field 'graph'.
+   * 
+   * @return the value of field 'Graph'.
+   */
+  public boolean getGraph()
+  {
+    return this._graph;
+  }
+
+  /**
+   * Returns the value of field 'graphType'.
+   * 
+   * @return the value of field 'GraphType'.
+   */
+  public int getGraphType()
+  {
+    return this._graphType;
+  }
+
+  /**
+   * Returns the value of field 'label'.
+   * 
+   * @return the value of field 'Label'.
+   */
+  public java.lang.String getLabel()
+  {
+    return this._label;
+  }
+
+  /**
+   * Method hasGraph.
+   * 
+   * @return true if at least one Graph has been added
+   */
+  public boolean hasGraph()
+  {
+    return this._has_graph;
+  }
+
+  /**
+   * Method hasGraphType.
+   * 
+   * @return true if at least one GraphType has been added
+   */
+  public boolean hasGraphType()
+  {
+    return this._has_graphType;
+  }
+
+  /**
+   * Returns the value of field 'graph'.
+   * 
+   * @return the value of field 'Graph'.
+   */
+  public boolean isGraph()
+  {
+    return this._graph;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
-
-    /**
-     * Returns the value of field 'graphType'.
-     * 
-     * @return the value of field 'GraphType'.
-     */
-    public int getGraphType(
-    ) {
-        return this._graphType;
-    }
-
-    /**
-     * Returns the value of field 'label'.
-     * 
-     * @return the value of field 'Label'.
-     */
-    public java.lang.String getLabel(
-    ) {
-        return this._label;
-    }
-
-    /**
-     * Method hasGraph.
-     * 
-     * @return true if at least one Graph has been added
-     */
-    public boolean hasGraph(
-    ) {
-        return this._has_graph;
-    }
-
-    /**
-     * Method hasGraphType.
-     * 
-     * @return true if at least one GraphType has been added
-     */
-    public boolean hasGraphType(
-    ) {
-        return this._has_graphType;
-    }
-
-    /**
-     * Returns the value of field 'graph'.
-     * 
-     * @return the value of field 'Graph'.
-     */
-    public boolean isGraph(
-    ) {
-        return this._graph;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     */
-    public void removeAllAnnotationElement(
-    ) {
-        this._annotationElementList.clear();
-    }
-
-    /**
-     * Method removeAnnotationElement.
-     * 
-     * @param vAnnotationElement
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeAnnotationElement(
-            final jalview.binding.AnnotationElement vAnnotationElement) {
-        boolean removed = _annotationElementList.remove(vAnnotationElement);
-        return removed;
-    }
-
-    /**
-     * Method removeAnnotationElementAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.binding.AnnotationElement removeAnnotationElementAt(
-            final int index) {
-        java.lang.Object obj = this._annotationElementList.remove(index);
-        return (jalview.binding.AnnotationElement) obj;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vAnnotationElement
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setAnnotationElement(
-            final int index,
-            final jalview.binding.AnnotationElement vAnnotationElement)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._annotationElementList.size()) {
-            throw new IndexOutOfBoundsException("setAnnotationElement: Index value '" + index + "' not in range [0.." + (this._annotationElementList.size() - 1) + "]");
-        }
-        
-        this._annotationElementList.set(index, vAnnotationElement);
-    }
-
-    /**
-     * 
-     * 
-     * @param vAnnotationElementArray
-     */
-    public void setAnnotationElement(
-            final jalview.binding.AnnotationElement[] vAnnotationElementArray) {
-        //-- copy array
-        _annotationElementList.clear();
-        
-        for (int i = 0; i < vAnnotationElementArray.length; i++) {
-                this._annotationElementList.add(vAnnotationElementArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of field 'description'.
-     * 
-     * @param description the value of field 'description'.
-     */
-    public void setDescription(
-            final java.lang.String description) {
-        this._description = description;
-    }
-
-    /**
-     * Sets the value of field 'graph'.
-     * 
-     * @param graph the value of field 'graph'.
-     */
-    public void setGraph(
-            final boolean graph) {
-        this._graph = graph;
-        this._has_graph = true;
-    }
-
-    /**
-     * Sets the value of field 'graphType'.
-     * 
-     * @param graphType the value of field 'graphType'.
-     */
-    public void setGraphType(
-            final int graphType) {
-        this._graphType = graphType;
-        this._has_graphType = true;
-    }
-
-    /**
-     * Sets the value of field 'label'.
-     * 
-     * @param label the value of field 'label'.
-     */
-    public void setLabel(
-            final java.lang.String label) {
-        this._label = label;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.Annotation
-     */
-    public static jalview.binding.Annotation unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.Annotation) Unmarshaller.unmarshal(jalview.binding.Annotation.class, reader);
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   */
+  public void removeAllAnnotationElement()
+  {
+    this._annotationElementList.clear();
+  }
+
+  /**
+   * Method removeAnnotationElement.
+   * 
+   * @param vAnnotationElement
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeAnnotationElement(
+          final jalview.binding.AnnotationElement vAnnotationElement)
+  {
+    boolean removed = _annotationElementList.remove(vAnnotationElement);
+    return removed;
+  }
+
+  /**
+   * Method removeAnnotationElementAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.binding.AnnotationElement removeAnnotationElementAt(
+          final int index)
+  {
+    java.lang.Object obj = this._annotationElementList.remove(index);
+    return (jalview.binding.AnnotationElement) obj;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAnnotationElement
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setAnnotationElement(final int index,
+          final jalview.binding.AnnotationElement vAnnotationElement)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._annotationElementList.size())
+    {
+      throw new IndexOutOfBoundsException(
+              "setAnnotationElement: Index value '" + index
+                      + "' not in range [0.."
+                      + (this._annotationElementList.size() - 1) + "]");
     }
 
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+    this._annotationElementList.set(index, vAnnotationElement);
+  }
+
+  /**
+   * 
+   * 
+   * @param vAnnotationElementArray
+   */
+  public void setAnnotationElement(
+          final jalview.binding.AnnotationElement[] vAnnotationElementArray)
+  {
+    // -- copy array
+    _annotationElementList.clear();
+
+    for (int i = 0; i < vAnnotationElementArray.length; i++)
+    {
+      this._annotationElementList.add(vAnnotationElementArray[i]);
     }
+  }
+
+  /**
+   * Sets the value of field 'description'.
+   * 
+   * @param description
+   *                the value of field 'description'.
+   */
+  public void setDescription(final java.lang.String description)
+  {
+    this._description = description;
+  }
+
+  /**
+   * Sets the value of field 'graph'.
+   * 
+   * @param graph
+   *                the value of field 'graph'.
+   */
+  public void setGraph(final boolean graph)
+  {
+    this._graph = graph;
+    this._has_graph = true;
+  }
+
+  /**
+   * Sets the value of field 'graphType'.
+   * 
+   * @param graphType
+   *                the value of field 'graphType'.
+   */
+  public void setGraphType(final int graphType)
+  {
+    this._graphType = graphType;
+    this._has_graphType = true;
+  }
+
+  /**
+   * Sets the value of field 'label'.
+   * 
+   * @param label
+   *                the value of field 'label'.
+   */
+  public void setLabel(final java.lang.String label)
+  {
+    this._label = label;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.binding.Annotation
+   */
+  public static jalview.binding.Annotation unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.Annotation) Unmarshaller.unmarshal(
+            jalview.binding.Annotation.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/AnnotationElement.java b/src/jalview/binding/AnnotationElement.java
index d133fe0..160141c 100755
--- a/src/jalview/binding/AnnotationElement.java
+++ b/src/jalview/binding/AnnotationElement.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,273 +30,291 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class AnnotationElement implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _position.
-     */
-    private int _position;
-
-    /**
-     * keeps track of state for field: _position
-     */
-    private boolean _has_position;
-
-    /**
-     * Field _displayCharacter.
-     */
-    private java.lang.String _displayCharacter;
-
-    /**
-     * Field _description.
-     */
-    private java.lang.String _description;
-
-    /**
-     * Field _secondaryStructure.
-     */
-    private java.lang.String _secondaryStructure;
-
-    /**
-     * Field _value.
-     */
-    private float _value;
-
-    /**
-     * keeps track of state for field: _value
-     */
-    private boolean _has_value;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public AnnotationElement() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     */
-    public void deletePosition(
-    ) {
-        this._has_position= false;
-    }
-
-    /**
-     */
-    public void deleteValue(
-    ) {
-        this._has_value= false;
-    }
-
-    /**
-     * Returns the value of field 'description'.
-     * 
-     * @return the value of field 'Description'.
-     */
-    public java.lang.String getDescription(
-    ) {
-        return this._description;
-    }
-
-    /**
-     * Returns the value of field 'displayCharacter'.
-     * 
-     * @return the value of field 'DisplayCharacter'.
-     */
-    public java.lang.String getDisplayCharacter(
-    ) {
-        return this._displayCharacter;
-    }
-
-    /**
-     * Returns the value of field 'position'.
-     * 
-     * @return the value of field 'Position'.
-     */
-    public int getPosition(
-    ) {
-        return this._position;
-    }
-
-    /**
-     * Returns the value of field 'secondaryStructure'.
-     * 
-     * @return the value of field 'SecondaryStructure'.
-     */
-    public java.lang.String getSecondaryStructure(
-    ) {
-        return this._secondaryStructure;
-    }
-
-    /**
-     * Returns the value of field 'value'.
-     * 
-     * @return the value of field 'Value'.
-     */
-    public float getValue(
-    ) {
-        return this._value;
-    }
-
-    /**
-     * Method hasPosition.
-     * 
-     * @return true if at least one Position has been added
-     */
-    public boolean hasPosition(
-    ) {
-        return this._has_position;
-    }
-
-    /**
-     * Method hasValue.
-     * 
-     * @return true if at least one Value has been added
-     */
-    public boolean hasValue(
-    ) {
-        return this._has_value;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'description'.
-     * 
-     * @param description the value of field 'description'.
-     */
-    public void setDescription(
-            final java.lang.String description) {
-        this._description = description;
-    }
-
-    /**
-     * Sets the value of field 'displayCharacter'.
-     * 
-     * @param displayCharacter the value of field 'displayCharacter'
-     */
-    public void setDisplayCharacter(
-            final java.lang.String displayCharacter) {
-        this._displayCharacter = displayCharacter;
-    }
-
-    /**
-     * Sets the value of field 'position'.
-     * 
-     * @param position the value of field 'position'.
-     */
-    public void setPosition(
-            final int position) {
-        this._position = position;
-        this._has_position = true;
-    }
-
-    /**
-     * Sets the value of field 'secondaryStructure'.
-     * 
-     * @param secondaryStructure the value of field
-     * 'secondaryStructure'.
-     */
-    public void setSecondaryStructure(
-            final java.lang.String secondaryStructure) {
-        this._secondaryStructure = secondaryStructure;
-    }
-
-    /**
-     * Sets the value of field 'value'.
-     * 
-     * @param value the value of field 'value'.
-     */
-    public void setValue(
-            final float value) {
-        this._value = value;
-        this._has_value = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.AnnotationElement
-     */
-    public static jalview.binding.AnnotationElement unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.AnnotationElement) Unmarshaller.unmarshal(jalview.binding.AnnotationElement.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class AnnotationElement implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _position.
+   */
+  private int _position;
+
+  /**
+   * keeps track of state for field: _position
+   */
+  private boolean _has_position;
+
+  /**
+   * Field _displayCharacter.
+   */
+  private java.lang.String _displayCharacter;
+
+  /**
+   * Field _description.
+   */
+  private java.lang.String _description;
+
+  /**
+   * Field _secondaryStructure.
+   */
+  private java.lang.String _secondaryStructure;
+
+  /**
+   * Field _value.
+   */
+  private float _value;
+
+  /**
+   * keeps track of state for field: _value
+   */
+  private boolean _has_value;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public AnnotationElement()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   */
+  public void deletePosition()
+  {
+    this._has_position = false;
+  }
+
+  /**
+   */
+  public void deleteValue()
+  {
+    this._has_value = false;
+  }
+
+  /**
+   * Returns the value of field 'description'.
+   * 
+   * @return the value of field 'Description'.
+   */
+  public java.lang.String getDescription()
+  {
+    return this._description;
+  }
+
+  /**
+   * Returns the value of field 'displayCharacter'.
+   * 
+   * @return the value of field 'DisplayCharacter'.
+   */
+  public java.lang.String getDisplayCharacter()
+  {
+    return this._displayCharacter;
+  }
+
+  /**
+   * Returns the value of field 'position'.
+   * 
+   * @return the value of field 'Position'.
+   */
+  public int getPosition()
+  {
+    return this._position;
+  }
+
+  /**
+   * Returns the value of field 'secondaryStructure'.
+   * 
+   * @return the value of field 'SecondaryStructure'.
+   */
+  public java.lang.String getSecondaryStructure()
+  {
+    return this._secondaryStructure;
+  }
+
+  /**
+   * Returns the value of field 'value'.
+   * 
+   * @return the value of field 'Value'.
+   */
+  public float getValue()
+  {
+    return this._value;
+  }
+
+  /**
+   * Method hasPosition.
+   * 
+   * @return true if at least one Position has been added
+   */
+  public boolean hasPosition()
+  {
+    return this._has_position;
+  }
+
+  /**
+   * Method hasValue.
+   * 
+   * @return true if at least one Value has been added
+   */
+  public boolean hasValue()
+  {
+    return this._has_value;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'description'.
+   * 
+   * @param description
+   *                the value of field 'description'.
+   */
+  public void setDescription(final java.lang.String description)
+  {
+    this._description = description;
+  }
+
+  /**
+   * Sets the value of field 'displayCharacter'.
+   * 
+   * @param displayCharacter
+   *                the value of field 'displayCharacter'
+   */
+  public void setDisplayCharacter(final java.lang.String displayCharacter)
+  {
+    this._displayCharacter = displayCharacter;
+  }
+
+  /**
+   * Sets the value of field 'position'.
+   * 
+   * @param position
+   *                the value of field 'position'.
+   */
+  public void setPosition(final int position)
+  {
+    this._position = position;
+    this._has_position = true;
+  }
+
+  /**
+   * Sets the value of field 'secondaryStructure'.
+   * 
+   * @param secondaryStructure
+   *                the value of field 'secondaryStructure'.
+   */
+  public void setSecondaryStructure(
+          final java.lang.String secondaryStructure)
+  {
+    this._secondaryStructure = secondaryStructure;
+  }
+
+  /**
+   * Sets the value of field 'value'.
+   * 
+   * @param value
+   *                the value of field 'value'.
+   */
+  public void setValue(final float value)
+  {
+    this._value = value;
+    this._has_value = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.binding.AnnotationElement
+   */
+  public static jalview.binding.AnnotationElement unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.AnnotationElement) Unmarshaller.unmarshal(
+            jalview.binding.AnnotationElement.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/Colour.java b/src/jalview/binding/Colour.java
index 488ff98..60d0291 100755
--- a/src/jalview/binding/Colour.java
+++ b/src/jalview/binding/Colour.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,151 +30,165 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Colour implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _name.
-     */
-    private java.lang.String _name;
-
-    /**
-     * Field _RGB.
-     */
-    private java.lang.String _RGB;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Colour() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'name'.
-     * 
-     * @return the value of field 'Name'.
-     */
-    public java.lang.String getName(
-    ) {
-        return this._name;
-    }
-
-    /**
-     * Returns the value of field 'RGB'.
-     * 
-     * @return the value of field 'RGB'.
-     */
-    public java.lang.String getRGB(
-    ) {
-        return this._RGB;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'name'.
-     * 
-     * @param name the value of field 'name'.
-     */
-    public void setName(
-            final java.lang.String name) {
-        this._name = name;
-    }
-
-    /**
-     * Sets the value of field 'RGB'.
-     * 
-     * @param RGB the value of field 'RGB'.
-     */
-    public void setRGB(
-            final java.lang.String RGB) {
-        this._RGB = RGB;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.Colour
-     */
-    public static jalview.binding.Colour unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.Colour) Unmarshaller.unmarshal(jalview.binding.Colour.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class Colour implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _name.
+   */
+  private java.lang.String _name;
+
+  /**
+   * Field _RGB.
+   */
+  private java.lang.String _RGB;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Colour()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Returns the value of field 'name'.
+   * 
+   * @return the value of field 'Name'.
+   */
+  public java.lang.String getName()
+  {
+    return this._name;
+  }
+
+  /**
+   * Returns the value of field 'RGB'.
+   * 
+   * @return the value of field 'RGB'.
+   */
+  public java.lang.String getRGB()
+  {
+    return this._RGB;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'name'.
+   * 
+   * @param name
+   *                the value of field 'name'.
+   */
+  public void setName(final java.lang.String name)
+  {
+    this._name = name;
+  }
+
+  /**
+   * Sets the value of field 'RGB'.
+   * 
+   * @param RGB
+   *                the value of field 'RGB'.
+   */
+  public void setRGB(final java.lang.String RGB)
+  {
+    this._RGB = RGB;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.binding.Colour
+   */
+  public static jalview.binding.Colour unmarshal(final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.Colour) Unmarshaller.unmarshal(
+            jalview.binding.Colour.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/Feature.java b/src/jalview/binding/Feature.java
index d429df3..509d0e6 100755
--- a/src/jalview/binding/Feature.java
+++ b/src/jalview/binding/Feature.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,272 +30,290 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Feature implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _begin.
-     */
-    private int _begin;
-
-    /**
-     * keeps track of state for field: _begin
-     */
-    private boolean _has_begin;
-
-    /**
-     * Field _end.
-     */
-    private int _end;
-
-    /**
-     * keeps track of state for field: _end
-     */
-    private boolean _has_end;
-
-    /**
-     * Field _type.
-     */
-    private java.lang.String _type;
-
-    /**
-     * Field _description.
-     */
-    private java.lang.String _description;
-
-    /**
-     * Field _status.
-     */
-    private java.lang.String _status;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Feature() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     */
-    public void deleteBegin(
-    ) {
-        this._has_begin= false;
-    }
-
-    /**
-     */
-    public void deleteEnd(
-    ) {
-        this._has_end= false;
-    }
-
-    /**
-     * Returns the value of field 'begin'.
-     * 
-     * @return the value of field 'Begin'.
-     */
-    public int getBegin(
-    ) {
-        return this._begin;
-    }
-
-    /**
-     * Returns the value of field 'description'.
-     * 
-     * @return the value of field 'Description'.
-     */
-    public java.lang.String getDescription(
-    ) {
-        return this._description;
-    }
-
-    /**
-     * Returns the value of field 'end'.
-     * 
-     * @return the value of field 'End'.
-     */
-    public int getEnd(
-    ) {
-        return this._end;
-    }
-
-    /**
-     * Returns the value of field 'status'.
-     * 
-     * @return the value of field 'Status'.
-     */
-    public java.lang.String getStatus(
-    ) {
-        return this._status;
-    }
-
-    /**
-     * Returns the value of field 'type'.
-     * 
-     * @return the value of field 'Type'.
-     */
-    public java.lang.String getType(
-    ) {
-        return this._type;
-    }
-
-    /**
-     * Method hasBegin.
-     * 
-     * @return true if at least one Begin has been added
-     */
-    public boolean hasBegin(
-    ) {
-        return this._has_begin;
-    }
-
-    /**
-     * Method hasEnd.
-     * 
-     * @return true if at least one End has been added
-     */
-    public boolean hasEnd(
-    ) {
-        return this._has_end;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'begin'.
-     * 
-     * @param begin the value of field 'begin'.
-     */
-    public void setBegin(
-            final int begin) {
-        this._begin = begin;
-        this._has_begin = true;
-    }
-
-    /**
-     * Sets the value of field 'description'.
-     * 
-     * @param description the value of field 'description'.
-     */
-    public void setDescription(
-            final java.lang.String description) {
-        this._description = description;
-    }
-
-    /**
-     * Sets the value of field 'end'.
-     * 
-     * @param end the value of field 'end'.
-     */
-    public void setEnd(
-            final int end) {
-        this._end = end;
-        this._has_end = true;
-    }
-
-    /**
-     * Sets the value of field 'status'.
-     * 
-     * @param status the value of field 'status'.
-     */
-    public void setStatus(
-            final java.lang.String status) {
-        this._status = status;
-    }
-
-    /**
-     * Sets the value of field 'type'.
-     * 
-     * @param type the value of field 'type'.
-     */
-    public void setType(
-            final java.lang.String type) {
-        this._type = type;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.Feature
-     */
-    public static jalview.binding.Feature unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.Feature) Unmarshaller.unmarshal(jalview.binding.Feature.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class Feature implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _begin.
+   */
+  private int _begin;
+
+  /**
+   * keeps track of state for field: _begin
+   */
+  private boolean _has_begin;
+
+  /**
+   * Field _end.
+   */
+  private int _end;
+
+  /**
+   * keeps track of state for field: _end
+   */
+  private boolean _has_end;
+
+  /**
+   * Field _type.
+   */
+  private java.lang.String _type;
+
+  /**
+   * Field _description.
+   */
+  private java.lang.String _description;
+
+  /**
+   * Field _status.
+   */
+  private java.lang.String _status;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Feature()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   */
+  public void deleteBegin()
+  {
+    this._has_begin = false;
+  }
+
+  /**
+   */
+  public void deleteEnd()
+  {
+    this._has_end = false;
+  }
+
+  /**
+   * Returns the value of field 'begin'.
+   * 
+   * @return the value of field 'Begin'.
+   */
+  public int getBegin()
+  {
+    return this._begin;
+  }
+
+  /**
+   * Returns the value of field 'description'.
+   * 
+   * @return the value of field 'Description'.
+   */
+  public java.lang.String getDescription()
+  {
+    return this._description;
+  }
+
+  /**
+   * Returns the value of field 'end'.
+   * 
+   * @return the value of field 'End'.
+   */
+  public int getEnd()
+  {
+    return this._end;
+  }
+
+  /**
+   * Returns the value of field 'status'.
+   * 
+   * @return the value of field 'Status'.
+   */
+  public java.lang.String getStatus()
+  {
+    return this._status;
+  }
+
+  /**
+   * Returns the value of field 'type'.
+   * 
+   * @return the value of field 'Type'.
+   */
+  public java.lang.String getType()
+  {
+    return this._type;
+  }
+
+  /**
+   * Method hasBegin.
+   * 
+   * @return true if at least one Begin has been added
+   */
+  public boolean hasBegin()
+  {
+    return this._has_begin;
+  }
+
+  /**
+   * Method hasEnd.
+   * 
+   * @return true if at least one End has been added
+   */
+  public boolean hasEnd()
+  {
+    return this._has_end;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'begin'.
+   * 
+   * @param begin
+   *                the value of field 'begin'.
+   */
+  public void setBegin(final int begin)
+  {
+    this._begin = begin;
+    this._has_begin = true;
+  }
+
+  /**
+   * Sets the value of field 'description'.
+   * 
+   * @param description
+   *                the value of field 'description'.
+   */
+  public void setDescription(final java.lang.String description)
+  {
+    this._description = description;
+  }
+
+  /**
+   * Sets the value of field 'end'.
+   * 
+   * @param end
+   *                the value of field 'end'.
+   */
+  public void setEnd(final int end)
+  {
+    this._end = end;
+    this._has_end = true;
+  }
+
+  /**
+   * Sets the value of field 'status'.
+   * 
+   * @param status
+   *                the value of field 'status'.
+   */
+  public void setStatus(final java.lang.String status)
+  {
+    this._status = status;
+  }
+
+  /**
+   * Sets the value of field 'type'.
+   * 
+   * @param type
+   *                the value of field 'type'.
+   */
+  public void setType(final java.lang.String type)
+  {
+    this._type = type;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.binding.Feature
+   */
+  public static jalview.binding.Feature unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.Feature) Unmarshaller.unmarshal(
+            jalview.binding.Feature.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/FeatureSettings.java b/src/jalview/binding/FeatureSettings.java
index f3d06be..b6c3640 100755
--- a/src/jalview/binding/FeatureSettings.java
+++ b/src/jalview/binding/FeatureSettings.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,257 +30,275 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class FeatureSettings implements java.io.Serializable {
+public class FeatureSettings implements java.io.Serializable
+{
 
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
 
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
+  /**
+   * Field _settingList.
+   */
+  private java.util.Vector _settingList;
 
-    /**
-     * Field _settingList.
-     */
-    private java.util.Vector _settingList;
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
 
+  public FeatureSettings()
+  {
+    super();
+    this._settingList = new java.util.Vector();
+  }
 
-      //----------------/
-     //- Constructors -/
-    //----------------/
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    public FeatureSettings() {
-        super();
-        this._settingList = new java.util.Vector();
-    }
+  /**
+   * 
+   * 
+   * @param vSetting
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addSetting(final jalview.binding.Setting vSetting)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._settingList.addElement(vSetting);
+  }
 
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSetting
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addSetting(final int index,
+          final jalview.binding.Setting vSetting)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._settingList.add(index, vSetting);
+  }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+  /**
+   * Method enumerateSetting.
+   * 
+   * @return an Enumeration over all jalview.binding.Setting elements
+   */
+  public java.util.Enumeration enumerateSetting()
+  {
+    return this._settingList.elements();
+  }
 
-    /**
-     * 
-     * 
-     * @param vSetting
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSetting(
-            final jalview.binding.Setting vSetting)
-    throws java.lang.IndexOutOfBoundsException {
-        this._settingList.addElement(vSetting);
+  /**
+   * Method getSetting.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.binding.Setting at the given index
+   */
+  public jalview.binding.Setting getSetting(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._settingList.size())
+    {
+      throw new IndexOutOfBoundsException("getSetting: Index value '"
+              + index + "' not in range [0.."
+              + (this._settingList.size() - 1) + "]");
     }
 
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSetting
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSetting(
-            final int index,
-            final jalview.binding.Setting vSetting)
-    throws java.lang.IndexOutOfBoundsException {
-        this._settingList.add(index, vSetting);
-    }
+    return (jalview.binding.Setting) _settingList.get(index);
+  }
 
-    /**
-     * Method enumerateSetting.
-     * 
-     * @return an Enumeration over all jalview.binding.Setting
-     * elements
-     */
-    public java.util.Enumeration enumerateSetting(
-    ) {
-        return this._settingList.elements();
-    }
+  /**
+   * Method getSetting.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.binding.Setting[] getSetting()
+  {
+    jalview.binding.Setting[] array = new jalview.binding.Setting[0];
+    return (jalview.binding.Setting[]) this._settingList.toArray(array);
+  }
 
-    /**
-     * Method getSetting.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the jalview.binding.Setting at the
-     * given index
-     */
-    public jalview.binding.Setting getSetting(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._settingList.size()) {
-            throw new IndexOutOfBoundsException("getSetting: Index value '" + index + "' not in range [0.." + (this._settingList.size() - 1) + "]");
-        }
-        
-        return (jalview.binding.Setting) _settingList.get(index);
-    }
+  /**
+   * Method getSettingCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getSettingCount()
+  {
+    return this._settingList.size();
+  }
 
-    /**
-     * Method getSetting.Returns the contents of the collection in
-     * an Array.  <p>Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we <i>know</i>
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.binding.Setting[] getSetting(
-    ) {
-        jalview.binding.Setting[] array = new jalview.binding.Setting[0];
-        return (jalview.binding.Setting[]) this._settingList.toArray(array);
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
 
-    /**
-     * Method getSettingCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getSettingCount(
-    ) {
-        return this._settingList.size();
-    }
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
 
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
 
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
+  /**
+   */
+  public void removeAllSetting()
+  {
+    this._settingList.clear();
+  }
 
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
+  /**
+   * Method removeSetting.
+   * 
+   * @param vSetting
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeSetting(final jalview.binding.Setting vSetting)
+  {
+    boolean removed = _settingList.remove(vSetting);
+    return removed;
+  }
 
-    /**
-     */
-    public void removeAllSetting(
-    ) {
-        this._settingList.clear();
-    }
+  /**
+   * Method removeSettingAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.binding.Setting removeSettingAt(final int index)
+  {
+    java.lang.Object obj = this._settingList.remove(index);
+    return (jalview.binding.Setting) obj;
+  }
 
-    /**
-     * Method removeSetting.
-     * 
-     * @param vSetting
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeSetting(
-            final jalview.binding.Setting vSetting) {
-        boolean removed = _settingList.remove(vSetting);
-        return removed;
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSetting
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setSetting(final int index,
+          final jalview.binding.Setting vSetting)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._settingList.size())
+    {
+      throw new IndexOutOfBoundsException("setSetting: Index value '"
+              + index + "' not in range [0.."
+              + (this._settingList.size() - 1) + "]");
     }
 
-    /**
-     * Method removeSettingAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.binding.Setting removeSettingAt(
-            final int index) {
-        java.lang.Object obj = this._settingList.remove(index);
-        return (jalview.binding.Setting) obj;
-    }
+    this._settingList.set(index, vSetting);
+  }
 
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSetting
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setSetting(
-            final int index,
-            final jalview.binding.Setting vSetting)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._settingList.size()) {
-            throw new IndexOutOfBoundsException("setSetting: Index value '" + index + "' not in range [0.." + (this._settingList.size() - 1) + "]");
-        }
-        
-        this._settingList.set(index, vSetting);
-    }
+  /**
+   * 
+   * 
+   * @param vSettingArray
+   */
+  public void setSetting(final jalview.binding.Setting[] vSettingArray)
+  {
+    // -- copy array
+    _settingList.clear();
 
-    /**
-     * 
-     * 
-     * @param vSettingArray
-     */
-    public void setSetting(
-            final jalview.binding.Setting[] vSettingArray) {
-        //-- copy array
-        _settingList.clear();
-        
-        for (int i = 0; i < vSettingArray.length; i++) {
-                this._settingList.add(vSettingArray[i]);
-        }
+    for (int i = 0; i < vSettingArray.length; i++)
+    {
+      this._settingList.add(vSettingArray[i]);
     }
+  }
 
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.FeatureSettings
-     */
-    public static jalview.binding.FeatureSettings unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.FeatureSettings) Unmarshaller.unmarshal(jalview.binding.FeatureSettings.class, reader);
-    }
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.binding.FeatureSettings
+   */
+  public static jalview.binding.FeatureSettings unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.FeatureSettings) Unmarshaller.unmarshal(
+            jalview.binding.FeatureSettings.class, reader);
+  }
 
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/Features.java b/src/jalview/binding/Features.java
index e50ae7c..8adfa03 100755
--- a/src/jalview/binding/Features.java
+++ b/src/jalview/binding/Features.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,98 +30,110 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Features extends Feature 
-implements java.io.Serializable
+public class Features extends Feature implements java.io.Serializable
 {
 
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
 
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Features() {
-        super();
-    }
+  public Features()
+  {
+    super();
+  }
 
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
 
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
 
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
 
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.Feature
-     */
-    public static jalview.binding.Feature unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.Feature) Unmarshaller.unmarshal(jalview.binding.Features.class, reader);
-    }
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.binding.Feature
+   */
+  public static jalview.binding.Feature unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.Feature) Unmarshaller.unmarshal(
+            jalview.binding.Features.class, reader);
+  }
 
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/JGroup.java b/src/jalview/binding/JGroup.java
index 862eebd..a0117ee 100755
--- a/src/jalview/binding/JGroup.java
+++ b/src/jalview/binding/JGroup.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,721 +30,746 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class JGroup implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _start.
-     */
-    private int _start;
-
-    /**
-     * keeps track of state for field: _start
-     */
-    private boolean _has_start;
-
-    /**
-     * Field _end.
-     */
-    private int _end;
-
-    /**
-     * keeps track of state for field: _end
-     */
-    private boolean _has_end;
-
-    /**
-     * Field _name.
-     */
-    private java.lang.String _name;
-
-    /**
-     * Field _colour.
-     */
-    private java.lang.String _colour;
-
-    /**
-     * Field _consThreshold.
-     */
-    private int _consThreshold;
-
-    /**
-     * keeps track of state for field: _consThreshold
-     */
-    private boolean _has_consThreshold;
-
-    /**
-     * Field _pidThreshold.
-     */
-    private int _pidThreshold;
-
-    /**
-     * keeps track of state for field: _pidThreshold
-     */
-    private boolean _has_pidThreshold;
-
-    /**
-     * Field _outlineColour.
-     */
-    private int _outlineColour;
-
-    /**
-     * keeps track of state for field: _outlineColour
-     */
-    private boolean _has_outlineColour;
-
-    /**
-     * Field _displayBoxes.
-     */
-    private boolean _displayBoxes;
-
-    /**
-     * keeps track of state for field: _displayBoxes
-     */
-    private boolean _has_displayBoxes;
-
-    /**
-     * Field _displayText.
-     */
-    private boolean _displayText;
-
-    /**
-     * keeps track of state for field: _displayText
-     */
-    private boolean _has_displayText;
-
-    /**
-     * Field _colourText.
-     */
-    private boolean _colourText;
-
-    /**
-     * keeps track of state for field: _colourText
-     */
-    private boolean _has_colourText;
-
-    /**
-     * Field _seqList.
-     */
-    private java.util.Vector _seqList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JGroup() {
-        super();
-        this._seqList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vSeq
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSeq(
-            final int vSeq)
-    throws java.lang.IndexOutOfBoundsException {
-        this._seqList.addElement(new java.lang.Integer(vSeq));
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSeq
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSeq(
-            final int index,
-            final int vSeq)
-    throws java.lang.IndexOutOfBoundsException {
-        this._seqList.add(index, new java.lang.Integer(vSeq));
-    }
-
-    /**
-     */
-    public void deleteColourText(
-    ) {
-        this._has_colourText= false;
-    }
-
-    /**
-     */
-    public void deleteConsThreshold(
-    ) {
-        this._has_consThreshold= false;
-    }
-
-    /**
-     */
-    public void deleteDisplayBoxes(
-    ) {
-        this._has_displayBoxes= false;
-    }
-
-    /**
-     */
-    public void deleteDisplayText(
-    ) {
-        this._has_displayText= false;
-    }
-
-    /**
-     */
-    public void deleteEnd(
-    ) {
-        this._has_end= false;
-    }
-
-    /**
-     */
-    public void deleteOutlineColour(
-    ) {
-        this._has_outlineColour= false;
-    }
-
-    /**
-     */
-    public void deletePidThreshold(
-    ) {
-        this._has_pidThreshold= false;
-    }
-
-    /**
-     */
-    public void deleteStart(
-    ) {
-        this._has_start= false;
-    }
-
-    /**
-     * Method enumerateSeq.
-     * 
-     * @return an Enumeration over all int elements
-     */
-    public java.util.Enumeration enumerateSeq(
-    ) {
-        return this._seqList.elements();
-    }
-
-    /**
-     * Returns the value of field 'colour'.
-     * 
-     * @return the value of field 'Colour'.
-     */
-    public java.lang.String getColour(
-    ) {
-        return this._colour;
-    }
-
-    /**
-     * Returns the value of field 'colourText'.
-     * 
-     * @return the value of field 'ColourText'.
-     */
-    public boolean getColourText(
-    ) {
-        return this._colourText;
-    }
-
-    /**
-     * Returns the value of field 'consThreshold'.
-     * 
-     * @return the value of field 'ConsThreshold'.
-     */
-    public int getConsThreshold(
-    ) {
-        return this._consThreshold;
-    }
-
-    /**
-     * Returns the value of field 'displayBoxes'.
-     * 
-     * @return the value of field 'DisplayBoxes'.
-     */
-    public boolean getDisplayBoxes(
-    ) {
-        return this._displayBoxes;
-    }
-
-    /**
-     * Returns the value of field 'displayText'.
-     * 
-     * @return the value of field 'DisplayText'.
-     */
-    public boolean getDisplayText(
-    ) {
-        return this._displayText;
-    }
-
-    /**
-     * Returns the value of field 'end'.
-     * 
-     * @return the value of field 'End'.
-     */
-    public int getEnd(
-    ) {
-        return this._end;
-    }
-
-    /**
-     * Returns the value of field 'name'.
-     * 
-     * @return the value of field 'Name'.
-     */
-    public java.lang.String getName(
-    ) {
-        return this._name;
-    }
-
-    /**
-     * Returns the value of field 'outlineColour'.
-     * 
-     * @return the value of field 'OutlineColour'.
-     */
-    public int getOutlineColour(
-    ) {
-        return this._outlineColour;
-    }
-
-    /**
-     * Returns the value of field 'pidThreshold'.
-     * 
-     * @return the value of field 'PidThreshold'.
-     */
-    public int getPidThreshold(
-    ) {
-        return this._pidThreshold;
-    }
-
-    /**
-     * Method getSeq.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the int at the given index
-     */
-    public int getSeq(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._seqList.size()) {
-            throw new IndexOutOfBoundsException("getSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");
-        }
-        
-        return ((java.lang.Integer) _seqList.get(index)).intValue();
-    }
-
-    /**
-     * Method getSeq.Returns the contents of the collection in an
-     * Array.  
-     * 
-     * @return this collection as an Array
-     */
-    public int[] getSeq(
-    ) {
-        int size = this._seqList.size();
-        int[] array = new int[size];
-        java.util.Iterator iter = _seqList.iterator();
-        for (int index = 0; index < size; index++) {
-            array[index] = ((java.lang.Integer) iter.next()).intValue();
-        }
-        return array;
-    }
-
-    /**
-     * Method getSeqCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getSeqCount(
-    ) {
-        return this._seqList.size();
-    }
-
-    /**
-     * Returns the value of field 'start'.
-     * 
-     * @return the value of field 'Start'.
-     */
-    public int getStart(
-    ) {
-        return this._start;
-    }
-
-    /**
-     * Method hasColourText.
-     * 
-     * @return true if at least one ColourText has been added
-     */
-    public boolean hasColourText(
-    ) {
-        return this._has_colourText;
-    }
-
-    /**
-     * Method hasConsThreshold.
-     * 
-     * @return true if at least one ConsThreshold has been added
-     */
-    public boolean hasConsThreshold(
-    ) {
-        return this._has_consThreshold;
-    }
-
-    /**
-     * Method hasDisplayBoxes.
-     * 
-     * @return true if at least one DisplayBoxes has been added
-     */
-    public boolean hasDisplayBoxes(
-    ) {
-        return this._has_displayBoxes;
-    }
-
-    /**
-     * Method hasDisplayText.
-     * 
-     * @return true if at least one DisplayText has been added
-     */
-    public boolean hasDisplayText(
-    ) {
-        return this._has_displayText;
-    }
-
-    /**
-     * Method hasEnd.
-     * 
-     * @return true if at least one End has been added
-     */
-    public boolean hasEnd(
-    ) {
-        return this._has_end;
-    }
-
-    /**
-     * Method hasOutlineColour.
-     * 
-     * @return true if at least one OutlineColour has been added
-     */
-    public boolean hasOutlineColour(
-    ) {
-        return this._has_outlineColour;
-    }
-
-    /**
-     * Method hasPidThreshold.
-     * 
-     * @return true if at least one PidThreshold has been added
-     */
-    public boolean hasPidThreshold(
-    ) {
-        return this._has_pidThreshold;
-    }
-
-    /**
-     * Method hasStart.
-     * 
-     * @return true if at least one Start has been added
-     */
-    public boolean hasStart(
-    ) {
-        return this._has_start;
-    }
-
-    /**
-     * Returns the value of field 'colourText'.
-     * 
-     * @return the value of field 'ColourText'.
-     */
-    public boolean isColourText(
-    ) {
-        return this._colourText;
-    }
-
-    /**
-     * Returns the value of field 'displayBoxes'.
-     * 
-     * @return the value of field 'DisplayBoxes'.
-     */
-    public boolean isDisplayBoxes(
-    ) {
-        return this._displayBoxes;
-    }
-
-    /**
-     * Returns the value of field 'displayText'.
-     * 
-     * @return the value of field 'DisplayText'.
-     */
-    public boolean isDisplayText(
-    ) {
-        return this._displayText;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     */
-    public void removeAllSeq(
-    ) {
-        this._seqList.clear();
-    }
-
-    /**
-     * Method removeSeq.
-     * 
-     * @param vSeq
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeSeq(
-            final int vSeq) {
-        boolean removed = _seqList.remove(new java.lang.Integer(vSeq));
-        return removed;
-    }
-
-    /**
-     * Method removeSeqAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public int removeSeqAt(
-            final int index) {
-        java.lang.Object obj = this._seqList.remove(index);
-        return ((java.lang.Integer) obj).intValue();
-    }
-
-    /**
-     * Sets the value of field 'colour'.
-     * 
-     * @param colour the value of field 'colour'.
-     */
-    public void setColour(
-            final java.lang.String colour) {
-        this._colour = colour;
-    }
-
-    /**
-     * Sets the value of field 'colourText'.
-     * 
-     * @param colourText the value of field 'colourText'.
-     */
-    public void setColourText(
-            final boolean colourText) {
-        this._colourText = colourText;
-        this._has_colourText = true;
-    }
-
-    /**
-     * Sets the value of field 'consThreshold'.
-     * 
-     * @param consThreshold the value of field 'consThreshold'.
-     */
-    public void setConsThreshold(
-            final int consThreshold) {
-        this._consThreshold = consThreshold;
-        this._has_consThreshold = true;
-    }
-
-    /**
-     * Sets the value of field 'displayBoxes'.
-     * 
-     * @param displayBoxes the value of field 'displayBoxes'.
-     */
-    public void setDisplayBoxes(
-            final boolean displayBoxes) {
-        this._displayBoxes = displayBoxes;
-        this._has_displayBoxes = true;
-    }
-
-    /**
-     * Sets the value of field 'displayText'.
-     * 
-     * @param displayText the value of field 'displayText'.
-     */
-    public void setDisplayText(
-            final boolean displayText) {
-        this._displayText = displayText;
-        this._has_displayText = true;
-    }
-
-    /**
-     * Sets the value of field 'end'.
-     * 
-     * @param end the value of field 'end'.
-     */
-    public void setEnd(
-            final int end) {
-        this._end = end;
-        this._has_end = true;
-    }
-
-    /**
-     * Sets the value of field 'name'.
-     * 
-     * @param name the value of field 'name'.
-     */
-    public void setName(
-            final java.lang.String name) {
-        this._name = name;
-    }
-
-    /**
-     * Sets the value of field 'outlineColour'.
-     * 
-     * @param outlineColour the value of field 'outlineColour'.
-     */
-    public void setOutlineColour(
-            final int outlineColour) {
-        this._outlineColour = outlineColour;
-        this._has_outlineColour = true;
-    }
-
-    /**
-     * Sets the value of field 'pidThreshold'.
-     * 
-     * @param pidThreshold the value of field 'pidThreshold'.
-     */
-    public void setPidThreshold(
-            final int pidThreshold) {
-        this._pidThreshold = pidThreshold;
-        this._has_pidThreshold = true;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSeq
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setSeq(
-            final int index,
-            final int vSeq)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._seqList.size()) {
-            throw new IndexOutOfBoundsException("setSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");
-        }
-        
-        this._seqList.set(index, new java.lang.Integer(vSeq));
-    }
-
-    /**
-     * 
-     * 
-     * @param vSeqArray
-     */
-    public void setSeq(
-            final int[] vSeqArray) {
-        //-- copy array
-        _seqList.clear();
-        
-        for (int i = 0; i < vSeqArray.length; i++) {
-                this._seqList.add(new java.lang.Integer(vSeqArray[i]));
-        }
-    }
-
-    /**
-     * Sets the value of field 'start'.
-     * 
-     * @param start the value of field 'start'.
-     */
-    public void setStart(
-            final int start) {
-        this._start = start;
-        this._has_start = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.JGroup
-     */
-    public static jalview.binding.JGroup unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.JGroup) Unmarshaller.unmarshal(jalview.binding.JGroup.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+public class JGroup implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _start.
+   */
+  private int _start;
+
+  /**
+   * keeps track of state for field: _start
+   */
+  private boolean _has_start;
+
+  /**
+   * Field _end.
+   */
+  private int _end;
+
+  /**
+   * keeps track of state for field: _end
+   */
+  private boolean _has_end;
+
+  /**
+   * Field _name.
+   */
+  private java.lang.String _name;
+
+  /**
+   * Field _colour.
+   */
+  private java.lang.String _colour;
+
+  /**
+   * Field _consThreshold.
+   */
+  private int _consThreshold;
+
+  /**
+   * keeps track of state for field: _consThreshold
+   */
+  private boolean _has_consThreshold;
+
+  /**
+   * Field _pidThreshold.
+   */
+  private int _pidThreshold;
+
+  /**
+   * keeps track of state for field: _pidThreshold
+   */
+  private boolean _has_pidThreshold;
+
+  /**
+   * Field _outlineColour.
+   */
+  private int _outlineColour;
+
+  /**
+   * keeps track of state for field: _outlineColour
+   */
+  private boolean _has_outlineColour;
+
+  /**
+   * Field _displayBoxes.
+   */
+  private boolean _displayBoxes;
+
+  /**
+   * keeps track of state for field: _displayBoxes
+   */
+  private boolean _has_displayBoxes;
+
+  /**
+   * Field _displayText.
+   */
+  private boolean _displayText;
+
+  /**
+   * keeps track of state for field: _displayText
+   */
+  private boolean _has_displayText;
+
+  /**
+   * Field _colourText.
+   */
+  private boolean _colourText;
+
+  /**
+   * keeps track of state for field: _colourText
+   */
+  private boolean _has_colourText;
+
+  /**
+   * Field _seqList.
+   */
+  private java.util.Vector _seqList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public JGroup()
+  {
+    super();
+    this._seqList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vSeq
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addSeq(final int vSeq)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._seqList.addElement(new java.lang.Integer(vSeq));
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSeq
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addSeq(final int index, final int vSeq)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._seqList.add(index, new java.lang.Integer(vSeq));
+  }
+
+  /**
+   */
+  public void deleteColourText()
+  {
+    this._has_colourText = false;
+  }
+
+  /**
+   */
+  public void deleteConsThreshold()
+  {
+    this._has_consThreshold = false;
+  }
+
+  /**
+   */
+  public void deleteDisplayBoxes()
+  {
+    this._has_displayBoxes = false;
+  }
+
+  /**
+   */
+  public void deleteDisplayText()
+  {
+    this._has_displayText = false;
+  }
+
+  /**
+   */
+  public void deleteEnd()
+  {
+    this._has_end = false;
+  }
+
+  /**
+   */
+  public void deleteOutlineColour()
+  {
+    this._has_outlineColour = false;
+  }
+
+  /**
+   */
+  public void deletePidThreshold()
+  {
+    this._has_pidThreshold = false;
+  }
+
+  /**
+   */
+  public void deleteStart()
+  {
+    this._has_start = false;
+  }
+
+  /**
+   * Method enumerateSeq.
+   * 
+   * @return an Enumeration over all int elements
+   */
+  public java.util.Enumeration enumerateSeq()
+  {
+    return this._seqList.elements();
+  }
+
+  /**
+   * Returns the value of field 'colour'.
+   * 
+   * @return the value of field 'Colour'.
+   */
+  public java.lang.String getColour()
+  {
+    return this._colour;
+  }
+
+  /**
+   * Returns the value of field 'colourText'.
+   * 
+   * @return the value of field 'ColourText'.
+   */
+  public boolean getColourText()
+  {
+    return this._colourText;
+  }
+
+  /**
+   * Returns the value of field 'consThreshold'.
+   * 
+   * @return the value of field 'ConsThreshold'.
+   */
+  public int getConsThreshold()
+  {
+    return this._consThreshold;
+  }
+
+  /**
+   * Returns the value of field 'displayBoxes'.
+   * 
+   * @return the value of field 'DisplayBoxes'.
+   */
+  public boolean getDisplayBoxes()
+  {
+    return this._displayBoxes;
+  }
+
+  /**
+   * Returns the value of field 'displayText'.
+   * 
+   * @return the value of field 'DisplayText'.
+   */
+  public boolean getDisplayText()
+  {
+    return this._displayText;
+  }
+
+  /**
+   * Returns the value of field 'end'.
+   * 
+   * @return the value of field 'End'.
+   */
+  public int getEnd()
+  {
+    return this._end;
+  }
+
+  /**
+   * Returns the value of field 'name'.
+   * 
+   * @return the value of field 'Name'.
+   */
+  public java.lang.String getName()
+  {
+    return this._name;
+  }
+
+  /**
+   * Returns the value of field 'outlineColour'.
+   * 
+   * @return the value of field 'OutlineColour'.
+   */
+  public int getOutlineColour()
+  {
+    return this._outlineColour;
+  }
+
+  /**
+   * Returns the value of field 'pidThreshold'.
+   * 
+   * @return the value of field 'PidThreshold'.
+   */
+  public int getPidThreshold()
+  {
+    return this._pidThreshold;
+  }
+
+  /**
+   * Method getSeq.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the int at the given index
+   */
+  public int getSeq(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._seqList.size())
+    {
+      throw new IndexOutOfBoundsException("getSeq: Index value '" + index
+              + "' not in range [0.." + (this._seqList.size() - 1) + "]");
+    }
+
+    return ((java.lang.Integer) _seqList.get(index)).intValue();
+  }
+
+  /**
+   * Method getSeq.Returns the contents of the collection in an Array.
+   * 
+   * @return this collection as an Array
+   */
+  public int[] getSeq()
+  {
+    int size = this._seqList.size();
+    int[] array = new int[size];
+    java.util.Iterator iter = _seqList.iterator();
+    for (int index = 0; index < size; index++)
+    {
+      array[index] = ((java.lang.Integer) iter.next()).intValue();
+    }
+    return array;
+  }
+
+  /**
+   * Method getSeqCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getSeqCount()
+  {
+    return this._seqList.size();
+  }
+
+  /**
+   * Returns the value of field 'start'.
+   * 
+   * @return the value of field 'Start'.
+   */
+  public int getStart()
+  {
+    return this._start;
+  }
+
+  /**
+   * Method hasColourText.
+   * 
+   * @return true if at least one ColourText has been added
+   */
+  public boolean hasColourText()
+  {
+    return this._has_colourText;
+  }
+
+  /**
+   * Method hasConsThreshold.
+   * 
+   * @return true if at least one ConsThreshold has been added
+   */
+  public boolean hasConsThreshold()
+  {
+    return this._has_consThreshold;
+  }
+
+  /**
+   * Method hasDisplayBoxes.
+   * 
+   * @return true if at least one DisplayBoxes has been added
+   */
+  public boolean hasDisplayBoxes()
+  {
+    return this._has_displayBoxes;
+  }
+
+  /**
+   * Method hasDisplayText.
+   * 
+   * @return true if at least one DisplayText has been added
+   */
+  public boolean hasDisplayText()
+  {
+    return this._has_displayText;
+  }
+
+  /**
+   * Method hasEnd.
+   * 
+   * @return true if at least one End has been added
+   */
+  public boolean hasEnd()
+  {
+    return this._has_end;
+  }
+
+  /**
+   * Method hasOutlineColour.
+   * 
+   * @return true if at least one OutlineColour has been added
+   */
+  public boolean hasOutlineColour()
+  {
+    return this._has_outlineColour;
+  }
+
+  /**
+   * Method hasPidThreshold.
+   * 
+   * @return true if at least one PidThreshold has been added
+   */
+  public boolean hasPidThreshold()
+  {
+    return this._has_pidThreshold;
+  }
+
+  /**
+   * Method hasStart.
+   * 
+   * @return true if at least one Start has been added
+   */
+  public boolean hasStart()
+  {
+    return this._has_start;
+  }
+
+  /**
+   * Returns the value of field 'colourText'.
+   * 
+   * @return the value of field 'ColourText'.
+   */
+  public boolean isColourText()
+  {
+    return this._colourText;
+  }
+
+  /**
+   * Returns the value of field 'displayBoxes'.
+   * 
+   * @return the value of field 'DisplayBoxes'.
+   */
+  public boolean isDisplayBoxes()
+  {
+    return this._displayBoxes;
+  }
+
+  /**
+   * Returns the value of field 'displayText'.
+   * 
+   * @return the value of field 'DisplayText'.
+   */
+  public boolean isDisplayText()
+  {
+    return this._displayText;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   */
+  public void removeAllSeq()
+  {
+    this._seqList.clear();
+  }
+
+  /**
+   * Method removeSeq.
+   * 
+   * @param vSeq
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeSeq(final int vSeq)
+  {
+    boolean removed = _seqList.remove(new java.lang.Integer(vSeq));
+    return removed;
+  }
+
+  /**
+   * Method removeSeqAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public int removeSeqAt(final int index)
+  {
+    java.lang.Object obj = this._seqList.remove(index);
+    return ((java.lang.Integer) obj).intValue();
+  }
+
+  /**
+   * Sets the value of field 'colour'.
+   * 
+   * @param colour
+   *                the value of field 'colour'.
+   */
+  public void setColour(final java.lang.String colour)
+  {
+    this._colour = colour;
+  }
+
+  /**
+   * Sets the value of field 'colourText'.
+   * 
+   * @param colourText
+   *                the value of field 'colourText'.
+   */
+  public void setColourText(final boolean colourText)
+  {
+    this._colourText = colourText;
+    this._has_colourText = true;
+  }
+
+  /**
+   * Sets the value of field 'consThreshold'.
+   * 
+   * @param consThreshold
+   *                the value of field 'consThreshold'.
+   */
+  public void setConsThreshold(final int consThreshold)
+  {
+    this._consThreshold = consThreshold;
+    this._has_consThreshold = true;
+  }
+
+  /**
+   * Sets the value of field 'displayBoxes'.
+   * 
+   * @param displayBoxes
+   *                the value of field 'displayBoxes'.
+   */
+  public void setDisplayBoxes(final boolean displayBoxes)
+  {
+    this._displayBoxes = displayBoxes;
+    this._has_displayBoxes = true;
+  }
+
+  /**
+   * Sets the value of field 'displayText'.
+   * 
+   * @param displayText
+   *                the value of field 'displayText'.
+   */
+  public void setDisplayText(final boolean displayText)
+  {
+    this._displayText = displayText;
+    this._has_displayText = true;
+  }
+
+  /**
+   * Sets the value of field 'end'.
+   * 
+   * @param end
+   *                the value of field 'end'.
+   */
+  public void setEnd(final int end)
+  {
+    this._end = end;
+    this._has_end = true;
+  }
+
+  /**
+   * Sets the value of field 'name'.
+   * 
+   * @param name
+   *                the value of field 'name'.
+   */
+  public void setName(final java.lang.String name)
+  {
+    this._name = name;
+  }
+
+  /**
+   * Sets the value of field 'outlineColour'.
+   * 
+   * @param outlineColour
+   *                the value of field 'outlineColour'.
+   */
+  public void setOutlineColour(final int outlineColour)
+  {
+    this._outlineColour = outlineColour;
+    this._has_outlineColour = true;
+  }
+
+  /**
+   * Sets the value of field 'pidThreshold'.
+   * 
+   * @param pidThreshold
+   *                the value of field 'pidThreshold'.
+   */
+  public void setPidThreshold(final int pidThreshold)
+  {
+    this._pidThreshold = pidThreshold;
+    this._has_pidThreshold = true;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSeq
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setSeq(final int index, final int vSeq)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._seqList.size())
+    {
+      throw new IndexOutOfBoundsException("setSeq: Index value '" + index
+              + "' not in range [0.." + (this._seqList.size() - 1) + "]");
+    }
+
+    this._seqList.set(index, new java.lang.Integer(vSeq));
+  }
+
+  /**
+   * 
+   * 
+   * @param vSeqArray
+   */
+  public void setSeq(final int[] vSeqArray)
+  {
+    // -- copy array
+    _seqList.clear();
+
+    for (int i = 0; i < vSeqArray.length; i++)
+    {
+      this._seqList.add(new java.lang.Integer(vSeqArray[i]));
+    }
+  }
+
+  /**
+   * Sets the value of field 'start'.
+   * 
+   * @param start
+   *                the value of field 'start'.
+   */
+  public void setStart(final int start)
+  {
+    this._start = start;
+    this._has_start = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.binding.JGroup
+   */
+  public static jalview.binding.JGroup unmarshal(final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.JGroup) Unmarshaller.unmarshal(
+            jalview.binding.JGroup.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/JSeq.java b/src/jalview/binding/JSeq.java
index 14b1f2f..19ef2ae 100755
--- a/src/jalview/binding/JSeq.java
+++ b/src/jalview/binding/JSeq.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,605 +30,631 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class JSeq implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _colour.
-     */
-    private int _colour;
-
-    /**
-     * keeps track of state for field: _colour
-     */
-    private boolean _has_colour;
-
-    /**
-     * Field _start.
-     */
-    private int _start;
-
-    /**
-     * keeps track of state for field: _start
-     */
-    private boolean _has_start;
-
-    /**
-     * Field _end.
-     */
-    private int _end;
-
-    /**
-     * keeps track of state for field: _end
-     */
-    private boolean _has_end;
-
-    /**
-     * Field _id.
-     */
-    private int _id;
-
-    /**
-     * keeps track of state for field: _id
-     */
-    private boolean _has_id;
-
-    /**
-     * Field _featuresList.
-     */
-    private java.util.Vector _featuresList;
-
-    /**
-     * Field _pdbidsList.
-     */
-    private java.util.Vector _pdbidsList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JSeq() {
-        super();
-        this._featuresList = new java.util.Vector();
-        this._pdbidsList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vFeatures
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addFeatures(
-            final jalview.binding.Features vFeatures)
-    throws java.lang.IndexOutOfBoundsException {
-        this._featuresList.addElement(vFeatures);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vFeatures
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addFeatures(
-            final int index,
-            final jalview.binding.Features vFeatures)
-    throws java.lang.IndexOutOfBoundsException {
-        this._featuresList.add(index, vFeatures);
-    }
-
-    /**
-     * 
-     * 
-     * @param vPdbids
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addPdbids(
-            final jalview.binding.Pdbids vPdbids)
-    throws java.lang.IndexOutOfBoundsException {
-        this._pdbidsList.addElement(vPdbids);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vPdbids
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addPdbids(
-            final int index,
-            final jalview.binding.Pdbids vPdbids)
-    throws java.lang.IndexOutOfBoundsException {
-        this._pdbidsList.add(index, vPdbids);
-    }
-
-    /**
-     */
-    public void deleteColour(
-    ) {
-        this._has_colour= false;
-    }
-
-    /**
-     */
-    public void deleteEnd(
-    ) {
-        this._has_end= false;
-    }
-
-    /**
-     */
-    public void deleteId(
-    ) {
-        this._has_id= false;
-    }
-
-    /**
-     */
-    public void deleteStart(
-    ) {
-        this._has_start= false;
-    }
-
-    /**
-     * Method enumerateFeatures.
-     * 
-     * @return an Enumeration over all jalview.binding.Features
-     * elements
-     */
-    public java.util.Enumeration enumerateFeatures(
-    ) {
-        return this._featuresList.elements();
-    }
-
-    /**
-     * Method enumeratePdbids.
-     * 
-     * @return an Enumeration over all jalview.binding.Pdbids
-     * elements
-     */
-    public java.util.Enumeration enumeratePdbids(
-    ) {
-        return this._pdbidsList.elements();
-    }
-
-    /**
-     * Returns the value of field 'colour'.
-     * 
-     * @return the value of field 'Colour'.
-     */
-    public int getColour(
-    ) {
-        return this._colour;
-    }
-
-    /**
-     * Returns the value of field 'end'.
-     * 
-     * @return the value of field 'End'.
-     */
-    public int getEnd(
-    ) {
-        return this._end;
-    }
-
-    /**
-     * Method getFeatures.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the jalview.binding.Features at the
-     * given index
-     */
-    public jalview.binding.Features getFeatures(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._featuresList.size()) {
-            throw new IndexOutOfBoundsException("getFeatures: Index value '" + index + "' not in range [0.." + (this._featuresList.size() - 1) + "]");
-        }
-        
-        return (jalview.binding.Features) _featuresList.get(index);
-    }
-
-    /**
-     * Method getFeatures.Returns the contents of the collection in
-     * an Array.  <p>Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we <i>know</i>
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.binding.Features[] getFeatures(
-    ) {
-        jalview.binding.Features[] array = new jalview.binding.Features[0];
-        return (jalview.binding.Features[]) this._featuresList.toArray(array);
-    }
-
-    /**
-     * Method getFeaturesCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getFeaturesCount(
-    ) {
-        return this._featuresList.size();
-    }
-
-    /**
-     * Returns the value of field 'id'.
-     * 
-     * @return the value of field 'Id'.
-     */
-    public int getId(
-    ) {
-        return this._id;
-    }
-
-    /**
-     * Method getPdbids.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the jalview.binding.Pdbids at the given
-     * index
-     */
-    public jalview.binding.Pdbids getPdbids(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._pdbidsList.size()) {
-            throw new IndexOutOfBoundsException("getPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]");
-        }
-        
-        return (jalview.binding.Pdbids) _pdbidsList.get(index);
-    }
-
-    /**
-     * Method getPdbids.Returns the contents of the collection in
-     * an Array.  <p>Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we <i>know</i>
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.binding.Pdbids[] getPdbids(
-    ) {
-        jalview.binding.Pdbids[] array = new jalview.binding.Pdbids[0];
-        return (jalview.binding.Pdbids[]) this._pdbidsList.toArray(array);
-    }
-
-    /**
-     * Method getPdbidsCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getPdbidsCount(
-    ) {
-        return this._pdbidsList.size();
-    }
-
-    /**
-     * Returns the value of field 'start'.
-     * 
-     * @return the value of field 'Start'.
-     */
-    public int getStart(
-    ) {
-        return this._start;
-    }
-
-    /**
-     * Method hasColour.
-     * 
-     * @return true if at least one Colour has been added
-     */
-    public boolean hasColour(
-    ) {
-        return this._has_colour;
-    }
-
-    /**
-     * Method hasEnd.
-     * 
-     * @return true if at least one End has been added
-     */
-    public boolean hasEnd(
-    ) {
-        return this._has_end;
-    }
-
-    /**
-     * Method hasId.
-     * 
-     * @return true if at least one Id has been added
-     */
-    public boolean hasId(
-    ) {
-        return this._has_id;
-    }
-
-    /**
-     * Method hasStart.
-     * 
-     * @return true if at least one Start has been added
-     */
-    public boolean hasStart(
-    ) {
-        return this._has_start;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     */
-    public void removeAllFeatures(
-    ) {
-        this._featuresList.clear();
-    }
-
-    /**
-     */
-    public void removeAllPdbids(
-    ) {
-        this._pdbidsList.clear();
-    }
-
-    /**
-     * Method removeFeatures.
-     * 
-     * @param vFeatures
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeFeatures(
-            final jalview.binding.Features vFeatures) {
-        boolean removed = _featuresList.remove(vFeatures);
-        return removed;
-    }
-
-    /**
-     * Method removeFeaturesAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.binding.Features removeFeaturesAt(
-            final int index) {
-        java.lang.Object obj = this._featuresList.remove(index);
-        return (jalview.binding.Features) obj;
-    }
-
-    /**
-     * Method removePdbids.
-     * 
-     * @param vPdbids
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removePdbids(
-            final jalview.binding.Pdbids vPdbids) {
-        boolean removed = _pdbidsList.remove(vPdbids);
-        return removed;
-    }
-
-    /**
-     * Method removePdbidsAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.binding.Pdbids removePdbidsAt(
-            final int index) {
-        java.lang.Object obj = this._pdbidsList.remove(index);
-        return (jalview.binding.Pdbids) obj;
-    }
-
-    /**
-     * Sets the value of field 'colour'.
-     * 
-     * @param colour the value of field 'colour'.
-     */
-    public void setColour(
-            final int colour) {
-        this._colour = colour;
-        this._has_colour = true;
-    }
-
-    /**
-     * Sets the value of field 'end'.
-     * 
-     * @param end the value of field 'end'.
-     */
-    public void setEnd(
-            final int end) {
-        this._end = end;
-        this._has_end = true;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vFeatures
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setFeatures(
-            final int index,
-            final jalview.binding.Features vFeatures)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._featuresList.size()) {
-            throw new IndexOutOfBoundsException("setFeatures: Index value '" + index + "' not in range [0.." + (this._featuresList.size() - 1) + "]");
-        }
-        
-        this._featuresList.set(index, vFeatures);
-    }
-
-    /**
-     * 
-     * 
-     * @param vFeaturesArray
-     */
-    public void setFeatures(
-            final jalview.binding.Features[] vFeaturesArray) {
-        //-- copy array
-        _featuresList.clear();
-        
-        for (int i = 0; i < vFeaturesArray.length; i++) {
-                this._featuresList.add(vFeaturesArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of field 'id'.
-     * 
-     * @param id the value of field 'id'.
-     */
-    public void setId(
-            final int id) {
-        this._id = id;
-        this._has_id = true;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vPdbids
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setPdbids(
-            final int index,
-            final jalview.binding.Pdbids vPdbids)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._pdbidsList.size()) {
-            throw new IndexOutOfBoundsException("setPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]");
-        }
-        
-        this._pdbidsList.set(index, vPdbids);
-    }
-
-    /**
-     * 
-     * 
-     * @param vPdbidsArray
-     */
-    public void setPdbids(
-            final jalview.binding.Pdbids[] vPdbidsArray) {
-        //-- copy array
-        _pdbidsList.clear();
-        
-        for (int i = 0; i < vPdbidsArray.length; i++) {
-                this._pdbidsList.add(vPdbidsArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of field 'start'.
-     * 
-     * @param start the value of field 'start'.
-     */
-    public void setStart(
-            final int start) {
-        this._start = start;
-        this._has_start = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.JSeq
-     */
-    public static jalview.binding.JSeq unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.JSeq) Unmarshaller.unmarshal(jalview.binding.JSeq.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+public class JSeq implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _colour.
+   */
+  private int _colour;
+
+  /**
+   * keeps track of state for field: _colour
+   */
+  private boolean _has_colour;
+
+  /**
+   * Field _start.
+   */
+  private int _start;
+
+  /**
+   * keeps track of state for field: _start
+   */
+  private boolean _has_start;
+
+  /**
+   * Field _end.
+   */
+  private int _end;
+
+  /**
+   * keeps track of state for field: _end
+   */
+  private boolean _has_end;
+
+  /**
+   * Field _id.
+   */
+  private int _id;
+
+  /**
+   * keeps track of state for field: _id
+   */
+  private boolean _has_id;
+
+  /**
+   * Field _featuresList.
+   */
+  private java.util.Vector _featuresList;
+
+  /**
+   * Field _pdbidsList.
+   */
+  private java.util.Vector _pdbidsList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public JSeq()
+  {
+    super();
+    this._featuresList = new java.util.Vector();
+    this._pdbidsList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vFeatures
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addFeatures(final jalview.binding.Features vFeatures)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._featuresList.addElement(vFeatures);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vFeatures
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addFeatures(final int index,
+          final jalview.binding.Features vFeatures)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._featuresList.add(index, vFeatures);
+  }
+
+  /**
+   * 
+   * 
+   * @param vPdbids
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addPdbids(final jalview.binding.Pdbids vPdbids)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._pdbidsList.addElement(vPdbids);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vPdbids
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addPdbids(final int index,
+          final jalview.binding.Pdbids vPdbids)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._pdbidsList.add(index, vPdbids);
+  }
+
+  /**
+   */
+  public void deleteColour()
+  {
+    this._has_colour = false;
+  }
+
+  /**
+   */
+  public void deleteEnd()
+  {
+    this._has_end = false;
+  }
+
+  /**
+   */
+  public void deleteId()
+  {
+    this._has_id = false;
+  }
+
+  /**
+   */
+  public void deleteStart()
+  {
+    this._has_start = false;
+  }
+
+  /**
+   * Method enumerateFeatures.
+   * 
+   * @return an Enumeration over all jalview.binding.Features elements
+   */
+  public java.util.Enumeration enumerateFeatures()
+  {
+    return this._featuresList.elements();
+  }
+
+  /**
+   * Method enumeratePdbids.
+   * 
+   * @return an Enumeration over all jalview.binding.Pdbids elements
+   */
+  public java.util.Enumeration enumeratePdbids()
+  {
+    return this._pdbidsList.elements();
+  }
+
+  /**
+   * Returns the value of field 'colour'.
+   * 
+   * @return the value of field 'Colour'.
+   */
+  public int getColour()
+  {
+    return this._colour;
+  }
+
+  /**
+   * Returns the value of field 'end'.
+   * 
+   * @return the value of field 'End'.
+   */
+  public int getEnd()
+  {
+    return this._end;
+  }
+
+  /**
+   * Method getFeatures.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.binding.Features at the given index
+   */
+  public jalview.binding.Features getFeatures(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._featuresList.size())
+    {
+      throw new IndexOutOfBoundsException("getFeatures: Index value '"
+              + index + "' not in range [0.."
+              + (this._featuresList.size() - 1) + "]");
+    }
+
+    return (jalview.binding.Features) _featuresList.get(index);
+  }
+
+  /**
+   * Method getFeatures.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.binding.Features[] getFeatures()
+  {
+    jalview.binding.Features[] array = new jalview.binding.Features[0];
+    return (jalview.binding.Features[]) this._featuresList.toArray(array);
+  }
+
+  /**
+   * Method getFeaturesCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getFeaturesCount()
+  {
+    return this._featuresList.size();
+  }
+
+  /**
+   * Returns the value of field 'id'.
+   * 
+   * @return the value of field 'Id'.
+   */
+  public int getId()
+  {
+    return this._id;
+  }
+
+  /**
+   * Method getPdbids.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.binding.Pdbids at the given index
+   */
+  public jalview.binding.Pdbids getPdbids(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._pdbidsList.size())
+    {
+      throw new IndexOutOfBoundsException("getPdbids: Index value '"
+              + index + "' not in range [0.."
+              + (this._pdbidsList.size() - 1) + "]");
+    }
+
+    return (jalview.binding.Pdbids) _pdbidsList.get(index);
+  }
+
+  /**
+   * Method getPdbids.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.binding.Pdbids[] getPdbids()
+  {
+    jalview.binding.Pdbids[] array = new jalview.binding.Pdbids[0];
+    return (jalview.binding.Pdbids[]) this._pdbidsList.toArray(array);
+  }
+
+  /**
+   * Method getPdbidsCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getPdbidsCount()
+  {
+    return this._pdbidsList.size();
+  }
+
+  /**
+   * Returns the value of field 'start'.
+   * 
+   * @return the value of field 'Start'.
+   */
+  public int getStart()
+  {
+    return this._start;
+  }
+
+  /**
+   * Method hasColour.
+   * 
+   * @return true if at least one Colour has been added
+   */
+  public boolean hasColour()
+  {
+    return this._has_colour;
+  }
+
+  /**
+   * Method hasEnd.
+   * 
+   * @return true if at least one End has been added
+   */
+  public boolean hasEnd()
+  {
+    return this._has_end;
+  }
+
+  /**
+   * Method hasId.
+   * 
+   * @return true if at least one Id has been added
+   */
+  public boolean hasId()
+  {
+    return this._has_id;
+  }
+
+  /**
+   * Method hasStart.
+   * 
+   * @return true if at least one Start has been added
+   */
+  public boolean hasStart()
+  {
+    return this._has_start;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   */
+  public void removeAllFeatures()
+  {
+    this._featuresList.clear();
+  }
+
+  /**
+   */
+  public void removeAllPdbids()
+  {
+    this._pdbidsList.clear();
+  }
+
+  /**
+   * Method removeFeatures.
+   * 
+   * @param vFeatures
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeFeatures(final jalview.binding.Features vFeatures)
+  {
+    boolean removed = _featuresList.remove(vFeatures);
+    return removed;
+  }
+
+  /**
+   * Method removeFeaturesAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.binding.Features removeFeaturesAt(final int index)
+  {
+    java.lang.Object obj = this._featuresList.remove(index);
+    return (jalview.binding.Features) obj;
+  }
+
+  /**
+   * Method removePdbids.
+   * 
+   * @param vPdbids
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removePdbids(final jalview.binding.Pdbids vPdbids)
+  {
+    boolean removed = _pdbidsList.remove(vPdbids);
+    return removed;
+  }
+
+  /**
+   * Method removePdbidsAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.binding.Pdbids removePdbidsAt(final int index)
+  {
+    java.lang.Object obj = this._pdbidsList.remove(index);
+    return (jalview.binding.Pdbids) obj;
+  }
+
+  /**
+   * Sets the value of field 'colour'.
+   * 
+   * @param colour
+   *                the value of field 'colour'.
+   */
+  public void setColour(final int colour)
+  {
+    this._colour = colour;
+    this._has_colour = true;
+  }
+
+  /**
+   * Sets the value of field 'end'.
+   * 
+   * @param end
+   *                the value of field 'end'.
+   */
+  public void setEnd(final int end)
+  {
+    this._end = end;
+    this._has_end = true;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vFeatures
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setFeatures(final int index,
+          final jalview.binding.Features vFeatures)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._featuresList.size())
+    {
+      throw new IndexOutOfBoundsException("setFeatures: Index value '"
+              + index + "' not in range [0.."
+              + (this._featuresList.size() - 1) + "]");
+    }
+
+    this._featuresList.set(index, vFeatures);
+  }
+
+  /**
+   * 
+   * 
+   * @param vFeaturesArray
+   */
+  public void setFeatures(final jalview.binding.Features[] vFeaturesArray)
+  {
+    // -- copy array
+    _featuresList.clear();
+
+    for (int i = 0; i < vFeaturesArray.length; i++)
+    {
+      this._featuresList.add(vFeaturesArray[i]);
+    }
+  }
+
+  /**
+   * Sets the value of field 'id'.
+   * 
+   * @param id
+   *                the value of field 'id'.
+   */
+  public void setId(final int id)
+  {
+    this._id = id;
+    this._has_id = true;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vPdbids
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setPdbids(final int index,
+          final jalview.binding.Pdbids vPdbids)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._pdbidsList.size())
+    {
+      throw new IndexOutOfBoundsException("setPdbids: Index value '"
+              + index + "' not in range [0.."
+              + (this._pdbidsList.size() - 1) + "]");
+    }
+
+    this._pdbidsList.set(index, vPdbids);
+  }
+
+  /**
+   * 
+   * 
+   * @param vPdbidsArray
+   */
+  public void setPdbids(final jalview.binding.Pdbids[] vPdbidsArray)
+  {
+    // -- copy array
+    _pdbidsList.clear();
+
+    for (int i = 0; i < vPdbidsArray.length; i++)
+    {
+      this._pdbidsList.add(vPdbidsArray[i]);
+    }
+  }
+
+  /**
+   * Sets the value of field 'start'.
+   * 
+   * @param start
+   *                the value of field 'start'.
+   */
+  public void setStart(final int start)
+  {
+    this._start = start;
+    this._has_start = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.binding.JSeq
+   */
+  public static jalview.binding.JSeq unmarshal(final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.JSeq) Unmarshaller.unmarshal(
+            jalview.binding.JSeq.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/JalviewModel.java b/src/jalview/binding/JalviewModel.java
index 21f8be9..eae870d 100755
--- a/src/jalview/binding/JalviewModel.java
+++ b/src/jalview/binding/JalviewModel.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,202 +30,219 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class JalviewModel implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _creationDate.
-     */
-    private java.util.Date _creationDate;
-
-    /**
-     * Field _version.
-     */
-    private java.lang.String _version;
-
-    /**
-     * Field _vamsasModel.
-     */
-    private jalview.binding.VamsasModel _vamsasModel;
-
-    /**
-     * Field _jalviewModelSequence.
-     */
-    private jalview.binding.JalviewModelSequence _jalviewModelSequence;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JalviewModel() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'creationDate'.
-     * 
-     * @return the value of field 'CreationDate'.
-     */
-    public java.util.Date getCreationDate(
-    ) {
-        return this._creationDate;
-    }
-
-    /**
-     * Returns the value of field 'jalviewModelSequence'.
-     * 
-     * @return the value of field 'JalviewModelSequence'.
-     */
-    public jalview.binding.JalviewModelSequence getJalviewModelSequence(
-    ) {
-        return this._jalviewModelSequence;
-    }
-
-    /**
-     * Returns the value of field 'vamsasModel'.
-     * 
-     * @return the value of field 'VamsasModel'.
-     */
-    public jalview.binding.VamsasModel getVamsasModel(
-    ) {
-        return this._vamsasModel;
-    }
-
-    /**
-     * Returns the value of field 'version'.
-     * 
-     * @return the value of field 'Version'.
-     */
-    public java.lang.String getVersion(
-    ) {
-        return this._version;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'creationDate'.
-     * 
-     * @param creationDate the value of field 'creationDate'.
-     */
-    public void setCreationDate(
-            final java.util.Date creationDate) {
-        this._creationDate = creationDate;
-    }
-
-    /**
-     * Sets the value of field 'jalviewModelSequence'.
-     * 
-     * @param jalviewModelSequence the value of field
-     * 'jalviewModelSequence'.
-     */
-    public void setJalviewModelSequence(
-            final jalview.binding.JalviewModelSequence jalviewModelSequence) {
-        this._jalviewModelSequence = jalviewModelSequence;
-    }
-
-    /**
-     * Sets the value of field 'vamsasModel'.
-     * 
-     * @param vamsasModel the value of field 'vamsasModel'.
-     */
-    public void setVamsasModel(
-            final jalview.binding.VamsasModel vamsasModel) {
-        this._vamsasModel = vamsasModel;
-    }
-
-    /**
-     * Sets the value of field 'version'.
-     * 
-     * @param version the value of field 'version'.
-     */
-    public void setVersion(
-            final java.lang.String version) {
-        this._version = version;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.JalviewModel
-     */
-    public static jalview.binding.JalviewModel unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.JalviewModel) Unmarshaller.unmarshal(jalview.binding.JalviewModel.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class JalviewModel implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _creationDate.
+   */
+  private java.util.Date _creationDate;
+
+  /**
+   * Field _version.
+   */
+  private java.lang.String _version;
+
+  /**
+   * Field _vamsasModel.
+   */
+  private jalview.binding.VamsasModel _vamsasModel;
+
+  /**
+   * Field _jalviewModelSequence.
+   */
+  private jalview.binding.JalviewModelSequence _jalviewModelSequence;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public JalviewModel()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Returns the value of field 'creationDate'.
+   * 
+   * @return the value of field 'CreationDate'.
+   */
+  public java.util.Date getCreationDate()
+  {
+    return this._creationDate;
+  }
+
+  /**
+   * Returns the value of field 'jalviewModelSequence'.
+   * 
+   * @return the value of field 'JalviewModelSequence'.
+   */
+  public jalview.binding.JalviewModelSequence getJalviewModelSequence()
+  {
+    return this._jalviewModelSequence;
+  }
+
+  /**
+   * Returns the value of field 'vamsasModel'.
+   * 
+   * @return the value of field 'VamsasModel'.
+   */
+  public jalview.binding.VamsasModel getVamsasModel()
+  {
+    return this._vamsasModel;
+  }
+
+  /**
+   * Returns the value of field 'version'.
+   * 
+   * @return the value of field 'Version'.
+   */
+  public java.lang.String getVersion()
+  {
+    return this._version;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'creationDate'.
+   * 
+   * @param creationDate
+   *                the value of field 'creationDate'.
+   */
+  public void setCreationDate(final java.util.Date creationDate)
+  {
+    this._creationDate = creationDate;
+  }
+
+  /**
+   * Sets the value of field 'jalviewModelSequence'.
+   * 
+   * @param jalviewModelSequence
+   *                the value of field 'jalviewModelSequence'.
+   */
+  public void setJalviewModelSequence(
+          final jalview.binding.JalviewModelSequence jalviewModelSequence)
+  {
+    this._jalviewModelSequence = jalviewModelSequence;
+  }
+
+  /**
+   * Sets the value of field 'vamsasModel'.
+   * 
+   * @param vamsasModel
+   *                the value of field 'vamsasModel'.
+   */
+  public void setVamsasModel(final jalview.binding.VamsasModel vamsasModel)
+  {
+    this._vamsasModel = vamsasModel;
+  }
+
+  /**
+   * Sets the value of field 'version'.
+   * 
+   * @param version
+   *                the value of field 'version'.
+   */
+  public void setVersion(final java.lang.String version)
+  {
+    this._version = version;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.binding.JalviewModel
+   */
+  public static jalview.binding.JalviewModel unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.JalviewModel) Unmarshaller.unmarshal(
+            jalview.binding.JalviewModel.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/JalviewModelSequence.java b/src/jalview/binding/JalviewModelSequence.java
index 5ebcee6..2a247c0 100755
--- a/src/jalview/binding/JalviewModelSequence.java
+++ b/src/jalview/binding/JalviewModelSequence.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,904 +30,941 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class JalviewModelSequence implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _JSeqList.
-     */
-    private java.util.Vector _JSeqList;
-
-    /**
-     * Field _JGroupList.
-     */
-    private java.util.Vector _JGroupList;
-
-    /**
-     * Field _viewportList.
-     */
-    private java.util.Vector _viewportList;
-
-    /**
-     * Field _userColoursList.
-     */
-    private java.util.Vector _userColoursList;
-
-    /**
-     * Field _treeList.
-     */
-    private java.util.Vector _treeList;
-
-    /**
-     * Field _featureSettings.
-     */
-    private jalview.binding.FeatureSettings _featureSettings;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JalviewModelSequence() {
-        super();
-        this._JSeqList = new java.util.Vector();
-        this._JGroupList = new java.util.Vector();
-        this._viewportList = new java.util.Vector();
-        this._userColoursList = new java.util.Vector();
-        this._treeList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vJGroup
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addJGroup(
-            final jalview.binding.JGroup vJGroup)
-    throws java.lang.IndexOutOfBoundsException {
-        this._JGroupList.addElement(vJGroup);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vJGroup
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addJGroup(
-            final int index,
-            final jalview.binding.JGroup vJGroup)
-    throws java.lang.IndexOutOfBoundsException {
-        this._JGroupList.add(index, vJGroup);
-    }
-
-    /**
-     * 
-     * 
-     * @param vJSeq
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addJSeq(
-            final jalview.binding.JSeq vJSeq)
-    throws java.lang.IndexOutOfBoundsException {
-        this._JSeqList.addElement(vJSeq);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vJSeq
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addJSeq(
-            final int index,
-            final jalview.binding.JSeq vJSeq)
-    throws java.lang.IndexOutOfBoundsException {
-        this._JSeqList.add(index, vJSeq);
-    }
-
-    /**
-     * 
-     * 
-     * @param vTree
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addTree(
-            final jalview.binding.Tree vTree)
-    throws java.lang.IndexOutOfBoundsException {
-        this._treeList.addElement(vTree);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vTree
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addTree(
-            final int index,
-            final jalview.binding.Tree vTree)
-    throws java.lang.IndexOutOfBoundsException {
-        this._treeList.add(index, vTree);
-    }
-
-    /**
-     * 
-     * 
-     * @param vUserColours
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addUserColours(
-            final jalview.binding.UserColours vUserColours)
-    throws java.lang.IndexOutOfBoundsException {
-        this._userColoursList.addElement(vUserColours);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vUserColours
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addUserColours(
-            final int index,
-            final jalview.binding.UserColours vUserColours)
-    throws java.lang.IndexOutOfBoundsException {
-        this._userColoursList.add(index, vUserColours);
-    }
-
-    /**
-     * 
-     * 
-     * @param vViewport
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addViewport(
-            final jalview.binding.Viewport vViewport)
-    throws java.lang.IndexOutOfBoundsException {
-        this._viewportList.addElement(vViewport);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vViewport
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addViewport(
-            final int index,
-            final jalview.binding.Viewport vViewport)
-    throws java.lang.IndexOutOfBoundsException {
-        this._viewportList.add(index, vViewport);
-    }
-
-    /**
-     * Method enumerateJGroup.
-     * 
-     * @return an Enumeration over all jalview.binding.JGroup
-     * elements
-     */
-    public java.util.Enumeration enumerateJGroup(
-    ) {
-        return this._JGroupList.elements();
-    }
-
-    /**
-     * Method enumerateJSeq.
-     * 
-     * @return an Enumeration over all jalview.binding.JSeq elements
-     */
-    public java.util.Enumeration enumerateJSeq(
-    ) {
-        return this._JSeqList.elements();
-    }
-
-    /**
-     * Method enumerateTree.
-     * 
-     * @return an Enumeration over all jalview.binding.Tree elements
-     */
-    public java.util.Enumeration enumerateTree(
-    ) {
-        return this._treeList.elements();
-    }
-
-    /**
-     * Method enumerateUserColours.
-     * 
-     * @return an Enumeration over all jalview.binding.UserColours
-     * elements
-     */
-    public java.util.Enumeration enumerateUserColours(
-    ) {
-        return this._userColoursList.elements();
-    }
-
-    /**
-     * Method enumerateViewport.
-     * 
-     * @return an Enumeration over all jalview.binding.Viewport
-     * elements
-     */
-    public java.util.Enumeration enumerateViewport(
-    ) {
-        return this._viewportList.elements();
-    }
-
-    /**
-     * Returns the value of field 'featureSettings'.
-     * 
-     * @return the value of field 'FeatureSettings'.
-     */
-    public jalview.binding.FeatureSettings getFeatureSettings(
-    ) {
-        return this._featureSettings;
-    }
-
-    /**
-     * Method getJGroup.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the jalview.binding.JGroup at the given
-     * index
-     */
-    public jalview.binding.JGroup getJGroup(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._JGroupList.size()) {
-            throw new IndexOutOfBoundsException("getJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]");
-        }
-        
-        return (jalview.binding.JGroup) _JGroupList.get(index);
-    }
-
-    /**
-     * Method getJGroup.Returns the contents of the collection in
-     * an Array.  <p>Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we <i>know</i>
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.binding.JGroup[] getJGroup(
-    ) {
-        jalview.binding.JGroup[] array = new jalview.binding.JGroup[0];
-        return (jalview.binding.JGroup[]) this._JGroupList.toArray(array);
-    }
-
-    /**
-     * Method getJGroupCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getJGroupCount(
-    ) {
-        return this._JGroupList.size();
-    }
-
-    /**
-     * Method getJSeq.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the jalview.binding.JSeq at the given
-     * index
-     */
-    public jalview.binding.JSeq getJSeq(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._JSeqList.size()) {
-            throw new IndexOutOfBoundsException("getJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
-        }
-        
-        return (jalview.binding.JSeq) _JSeqList.get(index);
-    }
-
-    /**
-     * Method getJSeq.Returns the contents of the collection in an
-     * Array.  <p>Note:  Just in case the collection contents are
-     * changing in another thread, we pass a 0-length Array of the
-     * correct type into the API call.  This way we <i>know</i>
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.binding.JSeq[] getJSeq(
-    ) {
-        jalview.binding.JSeq[] array = new jalview.binding.JSeq[0];
-        return (jalview.binding.JSeq[]) this._JSeqList.toArray(array);
-    }
-
-    /**
-     * Method getJSeqCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getJSeqCount(
-    ) {
-        return this._JSeqList.size();
-    }
-
-    /**
-     * Method getTree.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the jalview.binding.Tree at the given
-     * index
-     */
-    public jalview.binding.Tree getTree(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._treeList.size()) {
-            throw new IndexOutOfBoundsException("getTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
-        }
-        
-        return (jalview.binding.Tree) _treeList.get(index);
-    }
-
-    /**
-     * Method getTree.Returns the contents of the collection in an
-     * Array.  <p>Note:  Just in case the collection contents are
-     * changing in another thread, we pass a 0-length Array of the
-     * correct type into the API call.  This way we <i>know</i>
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.binding.Tree[] getTree(
-    ) {
-        jalview.binding.Tree[] array = new jalview.binding.Tree[0];
-        return (jalview.binding.Tree[]) this._treeList.toArray(array);
-    }
-
-    /**
-     * Method getTreeCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getTreeCount(
-    ) {
-        return this._treeList.size();
-    }
-
-    /**
-     * Method getUserColours.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the jalview.binding.UserColours at the
-     * given index
-     */
-    public jalview.binding.UserColours getUserColours(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._userColoursList.size()) {
-            throw new IndexOutOfBoundsException("getUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]");
-        }
-        
-        return (jalview.binding.UserColours) _userColoursList.get(index);
-    }
-
-    /**
-     * Method getUserColours.Returns the contents of the collection
-     * in an Array.  <p>Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we <i>know</i>
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.binding.UserColours[] getUserColours(
-    ) {
-        jalview.binding.UserColours[] array = new jalview.binding.UserColours[0];
-        return (jalview.binding.UserColours[]) this._userColoursList.toArray(array);
-    }
-
-    /**
-     * Method getUserColoursCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getUserColoursCount(
-    ) {
-        return this._userColoursList.size();
-    }
-
-    /**
-     * Method getViewport.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the jalview.binding.Viewport at the
-     * given index
-     */
-    public jalview.binding.Viewport getViewport(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._viewportList.size()) {
-            throw new IndexOutOfBoundsException("getViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]");
-        }
-        
-        return (jalview.binding.Viewport) _viewportList.get(index);
-    }
-
-    /**
-     * Method getViewport.Returns the contents of the collection in
-     * an Array.  <p>Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we <i>know</i>
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.binding.Viewport[] getViewport(
-    ) {
-        jalview.binding.Viewport[] array = new jalview.binding.Viewport[0];
-        return (jalview.binding.Viewport[]) this._viewportList.toArray(array);
-    }
-
-    /**
-     * Method getViewportCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getViewportCount(
-    ) {
-        return this._viewportList.size();
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     */
-    public void removeAllJGroup(
-    ) {
-        this._JGroupList.clear();
-    }
-
-    /**
-     */
-    public void removeAllJSeq(
-    ) {
-        this._JSeqList.clear();
-    }
-
-    /**
-     */
-    public void removeAllTree(
-    ) {
-        this._treeList.clear();
-    }
-
-    /**
-     */
-    public void removeAllUserColours(
-    ) {
-        this._userColoursList.clear();
-    }
-
-    /**
-     */
-    public void removeAllViewport(
-    ) {
-        this._viewportList.clear();
-    }
-
-    /**
-     * Method removeJGroup.
-     * 
-     * @param vJGroup
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeJGroup(
-            final jalview.binding.JGroup vJGroup) {
-        boolean removed = _JGroupList.remove(vJGroup);
-        return removed;
-    }
-
-    /**
-     * Method removeJGroupAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.binding.JGroup removeJGroupAt(
-            final int index) {
-        java.lang.Object obj = this._JGroupList.remove(index);
-        return (jalview.binding.JGroup) obj;
-    }
-
-    /**
-     * Method removeJSeq.
-     * 
-     * @param vJSeq
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeJSeq(
-            final jalview.binding.JSeq vJSeq) {
-        boolean removed = _JSeqList.remove(vJSeq);
-        return removed;
-    }
-
-    /**
-     * Method removeJSeqAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.binding.JSeq removeJSeqAt(
-            final int index) {
-        java.lang.Object obj = this._JSeqList.remove(index);
-        return (jalview.binding.JSeq) obj;
-    }
-
-    /**
-     * Method removeTree.
-     * 
-     * @param vTree
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeTree(
-            final jalview.binding.Tree vTree) {
-        boolean removed = _treeList.remove(vTree);
-        return removed;
-    }
-
-    /**
-     * Method removeTreeAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.binding.Tree removeTreeAt(
-            final int index) {
-        java.lang.Object obj = this._treeList.remove(index);
-        return (jalview.binding.Tree) obj;
-    }
-
-    /**
-     * Method removeUserColours.
-     * 
-     * @param vUserColours
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeUserColours(
-            final jalview.binding.UserColours vUserColours) {
-        boolean removed = _userColoursList.remove(vUserColours);
-        return removed;
-    }
-
-    /**
-     * Method removeUserColoursAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.binding.UserColours removeUserColoursAt(
-            final int index) {
-        java.lang.Object obj = this._userColoursList.remove(index);
-        return (jalview.binding.UserColours) obj;
-    }
-
-    /**
-     * Method removeViewport.
-     * 
-     * @param vViewport
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeViewport(
-            final jalview.binding.Viewport vViewport) {
-        boolean removed = _viewportList.remove(vViewport);
-        return removed;
-    }
-
-    /**
-     * Method removeViewportAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.binding.Viewport removeViewportAt(
-            final int index) {
-        java.lang.Object obj = this._viewportList.remove(index);
-        return (jalview.binding.Viewport) obj;
-    }
-
-    /**
-     * Sets the value of field 'featureSettings'.
-     * 
-     * @param featureSettings the value of field 'featureSettings'.
-     */
-    public void setFeatureSettings(
-            final jalview.binding.FeatureSettings featureSettings) {
-        this._featureSettings = featureSettings;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vJGroup
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setJGroup(
-            final int index,
-            final jalview.binding.JGroup vJGroup)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._JGroupList.size()) {
-            throw new IndexOutOfBoundsException("setJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]");
-        }
-        
-        this._JGroupList.set(index, vJGroup);
-    }
-
-    /**
-     * 
-     * 
-     * @param vJGroupArray
-     */
-    public void setJGroup(
-            final jalview.binding.JGroup[] vJGroupArray) {
-        //-- copy array
-        _JGroupList.clear();
-        
-        for (int i = 0; i < vJGroupArray.length; i++) {
-                this._JGroupList.add(vJGroupArray[i]);
-        }
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vJSeq
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setJSeq(
-            final int index,
-            final jalview.binding.JSeq vJSeq)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._JSeqList.size()) {
-            throw new IndexOutOfBoundsException("setJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
-        }
-        
-        this._JSeqList.set(index, vJSeq);
-    }
-
-    /**
-     * 
-     * 
-     * @param vJSeqArray
-     */
-    public void setJSeq(
-            final jalview.binding.JSeq[] vJSeqArray) {
-        //-- copy array
-        _JSeqList.clear();
-        
-        for (int i = 0; i < vJSeqArray.length; i++) {
-                this._JSeqList.add(vJSeqArray[i]);
-        }
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vTree
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setTree(
-            final int index,
-            final jalview.binding.Tree vTree)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._treeList.size()) {
-            throw new IndexOutOfBoundsException("setTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
-        }
-        
-        this._treeList.set(index, vTree);
-    }
-
-    /**
-     * 
-     * 
-     * @param vTreeArray
-     */
-    public void setTree(
-            final jalview.binding.Tree[] vTreeArray) {
-        //-- copy array
-        _treeList.clear();
-        
-        for (int i = 0; i < vTreeArray.length; i++) {
-                this._treeList.add(vTreeArray[i]);
-        }
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vUserColours
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setUserColours(
-            final int index,
-            final jalview.binding.UserColours vUserColours)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._userColoursList.size()) {
-            throw new IndexOutOfBoundsException("setUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]");
-        }
-        
-        this._userColoursList.set(index, vUserColours);
-    }
-
-    /**
-     * 
-     * 
-     * @param vUserColoursArray
-     */
-    public void setUserColours(
-            final jalview.binding.UserColours[] vUserColoursArray) {
-        //-- copy array
-        _userColoursList.clear();
-        
-        for (int i = 0; i < vUserColoursArray.length; i++) {
-                this._userColoursList.add(vUserColoursArray[i]);
-        }
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vViewport
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setViewport(
-            final int index,
-            final jalview.binding.Viewport vViewport)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._viewportList.size()) {
-            throw new IndexOutOfBoundsException("setViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]");
-        }
-        
-        this._viewportList.set(index, vViewport);
-    }
-
-    /**
-     * 
-     * 
-     * @param vViewportArray
-     */
-    public void setViewport(
-            final jalview.binding.Viewport[] vViewportArray) {
-        //-- copy array
-        _viewportList.clear();
-        
-        for (int i = 0; i < vViewportArray.length; i++) {
-                this._viewportList.add(vViewportArray[i]);
-        }
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.JalviewModelSequence
-     */
-    public static jalview.binding.JalviewModelSequence unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.JalviewModelSequence) Unmarshaller.unmarshal(jalview.binding.JalviewModelSequence.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+public class JalviewModelSequence implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _JSeqList.
+   */
+  private java.util.Vector _JSeqList;
+
+  /**
+   * Field _JGroupList.
+   */
+  private java.util.Vector _JGroupList;
+
+  /**
+   * Field _viewportList.
+   */
+  private java.util.Vector _viewportList;
+
+  /**
+   * Field _userColoursList.
+   */
+  private java.util.Vector _userColoursList;
+
+  /**
+   * Field _treeList.
+   */
+  private java.util.Vector _treeList;
+
+  /**
+   * Field _featureSettings.
+   */
+  private jalview.binding.FeatureSettings _featureSettings;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public JalviewModelSequence()
+  {
+    super();
+    this._JSeqList = new java.util.Vector();
+    this._JGroupList = new java.util.Vector();
+    this._viewportList = new java.util.Vector();
+    this._userColoursList = new java.util.Vector();
+    this._treeList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vJGroup
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addJGroup(final jalview.binding.JGroup vJGroup)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._JGroupList.addElement(vJGroup);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vJGroup
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addJGroup(final int index,
+          final jalview.binding.JGroup vJGroup)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._JGroupList.add(index, vJGroup);
+  }
+
+  /**
+   * 
+   * 
+   * @param vJSeq
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addJSeq(final jalview.binding.JSeq vJSeq)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._JSeqList.addElement(vJSeq);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vJSeq
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addJSeq(final int index, final jalview.binding.JSeq vJSeq)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._JSeqList.add(index, vJSeq);
+  }
+
+  /**
+   * 
+   * 
+   * @param vTree
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addTree(final jalview.binding.Tree vTree)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._treeList.addElement(vTree);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vTree
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addTree(final int index, final jalview.binding.Tree vTree)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._treeList.add(index, vTree);
+  }
+
+  /**
+   * 
+   * 
+   * @param vUserColours
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addUserColours(final jalview.binding.UserColours vUserColours)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._userColoursList.addElement(vUserColours);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vUserColours
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addUserColours(final int index,
+          final jalview.binding.UserColours vUserColours)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._userColoursList.add(index, vUserColours);
+  }
+
+  /**
+   * 
+   * 
+   * @param vViewport
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addViewport(final jalview.binding.Viewport vViewport)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._viewportList.addElement(vViewport);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vViewport
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addViewport(final int index,
+          final jalview.binding.Viewport vViewport)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._viewportList.add(index, vViewport);
+  }
+
+  /**
+   * Method enumerateJGroup.
+   * 
+   * @return an Enumeration over all jalview.binding.JGroup elements
+   */
+  public java.util.Enumeration enumerateJGroup()
+  {
+    return this._JGroupList.elements();
+  }
+
+  /**
+   * Method enumerateJSeq.
+   * 
+   * @return an Enumeration over all jalview.binding.JSeq elements
+   */
+  public java.util.Enumeration enumerateJSeq()
+  {
+    return this._JSeqList.elements();
+  }
+
+  /**
+   * Method enumerateTree.
+   * 
+   * @return an Enumeration over all jalview.binding.Tree elements
+   */
+  public java.util.Enumeration enumerateTree()
+  {
+    return this._treeList.elements();
+  }
+
+  /**
+   * Method enumerateUserColours.
+   * 
+   * @return an Enumeration over all jalview.binding.UserColours elements
+   */
+  public java.util.Enumeration enumerateUserColours()
+  {
+    return this._userColoursList.elements();
+  }
+
+  /**
+   * Method enumerateViewport.
+   * 
+   * @return an Enumeration over all jalview.binding.Viewport elements
+   */
+  public java.util.Enumeration enumerateViewport()
+  {
+    return this._viewportList.elements();
+  }
+
+  /**
+   * Returns the value of field 'featureSettings'.
+   * 
+   * @return the value of field 'FeatureSettings'.
+   */
+  public jalview.binding.FeatureSettings getFeatureSettings()
+  {
+    return this._featureSettings;
+  }
+
+  /**
+   * Method getJGroup.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.binding.JGroup at the given index
+   */
+  public jalview.binding.JGroup getJGroup(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._JGroupList.size())
+    {
+      throw new IndexOutOfBoundsException("getJGroup: Index value '"
+              + index + "' not in range [0.."
+              + (this._JGroupList.size() - 1) + "]");
+    }
+
+    return (jalview.binding.JGroup) _JGroupList.get(index);
+  }
+
+  /**
+   * Method getJGroup.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.binding.JGroup[] getJGroup()
+  {
+    jalview.binding.JGroup[] array = new jalview.binding.JGroup[0];
+    return (jalview.binding.JGroup[]) this._JGroupList.toArray(array);
+  }
+
+  /**
+   * Method getJGroupCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getJGroupCount()
+  {
+    return this._JGroupList.size();
+  }
+
+  /**
+   * Method getJSeq.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.binding.JSeq at the given index
+   */
+  public jalview.binding.JSeq getJSeq(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._JSeqList.size())
+    {
+      throw new IndexOutOfBoundsException("getJSeq: Index value '" + index
+              + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
+    }
+
+    return (jalview.binding.JSeq) _JSeqList.get(index);
+  }
+
+  /**
+   * Method getJSeq.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.binding.JSeq[] getJSeq()
+  {
+    jalview.binding.JSeq[] array = new jalview.binding.JSeq[0];
+    return (jalview.binding.JSeq[]) this._JSeqList.toArray(array);
+  }
+
+  /**
+   * Method getJSeqCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getJSeqCount()
+  {
+    return this._JSeqList.size();
+  }
+
+  /**
+   * Method getTree.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.binding.Tree at the given index
+   */
+  public jalview.binding.Tree getTree(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._treeList.size())
+    {
+      throw new IndexOutOfBoundsException("getTree: Index value '" + index
+              + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+    }
+
+    return (jalview.binding.Tree) _treeList.get(index);
+  }
+
+  /**
+   * Method getTree.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.binding.Tree[] getTree()
+  {
+    jalview.binding.Tree[] array = new jalview.binding.Tree[0];
+    return (jalview.binding.Tree[]) this._treeList.toArray(array);
+  }
+
+  /**
+   * Method getTreeCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getTreeCount()
+  {
+    return this._treeList.size();
+  }
+
+  /**
+   * Method getUserColours.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.binding.UserColours at the given index
+   */
+  public jalview.binding.UserColours getUserColours(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._userColoursList.size())
+    {
+      throw new IndexOutOfBoundsException("getUserColours: Index value '"
+              + index + "' not in range [0.."
+              + (this._userColoursList.size() - 1) + "]");
+    }
+
+    return (jalview.binding.UserColours) _userColoursList.get(index);
+  }
+
+  /**
+   * Method getUserColours.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.binding.UserColours[] getUserColours()
+  {
+    jalview.binding.UserColours[] array = new jalview.binding.UserColours[0];
+    return (jalview.binding.UserColours[]) this._userColoursList
+            .toArray(array);
+  }
+
+  /**
+   * Method getUserColoursCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getUserColoursCount()
+  {
+    return this._userColoursList.size();
+  }
+
+  /**
+   * Method getViewport.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.binding.Viewport at the given index
+   */
+  public jalview.binding.Viewport getViewport(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._viewportList.size())
+    {
+      throw new IndexOutOfBoundsException("getViewport: Index value '"
+              + index + "' not in range [0.."
+              + (this._viewportList.size() - 1) + "]");
+    }
+
+    return (jalview.binding.Viewport) _viewportList.get(index);
+  }
+
+  /**
+   * Method getViewport.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.binding.Viewport[] getViewport()
+  {
+    jalview.binding.Viewport[] array = new jalview.binding.Viewport[0];
+    return (jalview.binding.Viewport[]) this._viewportList.toArray(array);
+  }
+
+  /**
+   * Method getViewportCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getViewportCount()
+  {
+    return this._viewportList.size();
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   */
+  public void removeAllJGroup()
+  {
+    this._JGroupList.clear();
+  }
+
+  /**
+   */
+  public void removeAllJSeq()
+  {
+    this._JSeqList.clear();
+  }
+
+  /**
+   */
+  public void removeAllTree()
+  {
+    this._treeList.clear();
+  }
+
+  /**
+   */
+  public void removeAllUserColours()
+  {
+    this._userColoursList.clear();
+  }
+
+  /**
+   */
+  public void removeAllViewport()
+  {
+    this._viewportList.clear();
+  }
+
+  /**
+   * Method removeJGroup.
+   * 
+   * @param vJGroup
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeJGroup(final jalview.binding.JGroup vJGroup)
+  {
+    boolean removed = _JGroupList.remove(vJGroup);
+    return removed;
+  }
+
+  /**
+   * Method removeJGroupAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.binding.JGroup removeJGroupAt(final int index)
+  {
+    java.lang.Object obj = this._JGroupList.remove(index);
+    return (jalview.binding.JGroup) obj;
+  }
+
+  /**
+   * Method removeJSeq.
+   * 
+   * @param vJSeq
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeJSeq(final jalview.binding.JSeq vJSeq)
+  {
+    boolean removed = _JSeqList.remove(vJSeq);
+    return removed;
+  }
+
+  /**
+   * Method removeJSeqAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.binding.JSeq removeJSeqAt(final int index)
+  {
+    java.lang.Object obj = this._JSeqList.remove(index);
+    return (jalview.binding.JSeq) obj;
+  }
+
+  /**
+   * Method removeTree.
+   * 
+   * @param vTree
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeTree(final jalview.binding.Tree vTree)
+  {
+    boolean removed = _treeList.remove(vTree);
+    return removed;
+  }
+
+  /**
+   * Method removeTreeAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.binding.Tree removeTreeAt(final int index)
+  {
+    java.lang.Object obj = this._treeList.remove(index);
+    return (jalview.binding.Tree) obj;
+  }
+
+  /**
+   * Method removeUserColours.
+   * 
+   * @param vUserColours
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeUserColours(
+          final jalview.binding.UserColours vUserColours)
+  {
+    boolean removed = _userColoursList.remove(vUserColours);
+    return removed;
+  }
+
+  /**
+   * Method removeUserColoursAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.binding.UserColours removeUserColoursAt(final int index)
+  {
+    java.lang.Object obj = this._userColoursList.remove(index);
+    return (jalview.binding.UserColours) obj;
+  }
+
+  /**
+   * Method removeViewport.
+   * 
+   * @param vViewport
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeViewport(final jalview.binding.Viewport vViewport)
+  {
+    boolean removed = _viewportList.remove(vViewport);
+    return removed;
+  }
+
+  /**
+   * Method removeViewportAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.binding.Viewport removeViewportAt(final int index)
+  {
+    java.lang.Object obj = this._viewportList.remove(index);
+    return (jalview.binding.Viewport) obj;
+  }
+
+  /**
+   * Sets the value of field 'featureSettings'.
+   * 
+   * @param featureSettings
+   *                the value of field 'featureSettings'.
+   */
+  public void setFeatureSettings(
+          final jalview.binding.FeatureSettings featureSettings)
+  {
+    this._featureSettings = featureSettings;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vJGroup
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setJGroup(final int index,
+          final jalview.binding.JGroup vJGroup)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._JGroupList.size())
+    {
+      throw new IndexOutOfBoundsException("setJGroup: Index value '"
+              + index + "' not in range [0.."
+              + (this._JGroupList.size() - 1) + "]");
+    }
+
+    this._JGroupList.set(index, vJGroup);
+  }
+
+  /**
+   * 
+   * 
+   * @param vJGroupArray
+   */
+  public void setJGroup(final jalview.binding.JGroup[] vJGroupArray)
+  {
+    // -- copy array
+    _JGroupList.clear();
+
+    for (int i = 0; i < vJGroupArray.length; i++)
+    {
+      this._JGroupList.add(vJGroupArray[i]);
+    }
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vJSeq
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setJSeq(final int index, final jalview.binding.JSeq vJSeq)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._JSeqList.size())
+    {
+      throw new IndexOutOfBoundsException("setJSeq: Index value '" + index
+              + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
+    }
+
+    this._JSeqList.set(index, vJSeq);
+  }
+
+  /**
+   * 
+   * 
+   * @param vJSeqArray
+   */
+  public void setJSeq(final jalview.binding.JSeq[] vJSeqArray)
+  {
+    // -- copy array
+    _JSeqList.clear();
+
+    for (int i = 0; i < vJSeqArray.length; i++)
+    {
+      this._JSeqList.add(vJSeqArray[i]);
+    }
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vTree
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setTree(final int index, final jalview.binding.Tree vTree)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._treeList.size())
+    {
+      throw new IndexOutOfBoundsException("setTree: Index value '" + index
+              + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+    }
+
+    this._treeList.set(index, vTree);
+  }
+
+  /**
+   * 
+   * 
+   * @param vTreeArray
+   */
+  public void setTree(final jalview.binding.Tree[] vTreeArray)
+  {
+    // -- copy array
+    _treeList.clear();
+
+    for (int i = 0; i < vTreeArray.length; i++)
+    {
+      this._treeList.add(vTreeArray[i]);
+    }
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vUserColours
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setUserColours(final int index,
+          final jalview.binding.UserColours vUserColours)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._userColoursList.size())
+    {
+      throw new IndexOutOfBoundsException("setUserColours: Index value '"
+              + index + "' not in range [0.."
+              + (this._userColoursList.size() - 1) + "]");
+    }
+
+    this._userColoursList.set(index, vUserColours);
+  }
+
+  /**
+   * 
+   * 
+   * @param vUserColoursArray
+   */
+  public void setUserColours(
+          final jalview.binding.UserColours[] vUserColoursArray)
+  {
+    // -- copy array
+    _userColoursList.clear();
+
+    for (int i = 0; i < vUserColoursArray.length; i++)
+    {
+      this._userColoursList.add(vUserColoursArray[i]);
+    }
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vViewport
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setViewport(final int index,
+          final jalview.binding.Viewport vViewport)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._viewportList.size())
+    {
+      throw new IndexOutOfBoundsException("setViewport: Index value '"
+              + index + "' not in range [0.."
+              + (this._viewportList.size() - 1) + "]");
+    }
+
+    this._viewportList.set(index, vViewport);
+  }
+
+  /**
+   * 
+   * 
+   * @param vViewportArray
+   */
+  public void setViewport(final jalview.binding.Viewport[] vViewportArray)
+  {
+    // -- copy array
+    _viewportList.clear();
+
+    for (int i = 0; i < vViewportArray.length; i++)
+    {
+      this._viewportList.add(vViewportArray[i]);
+    }
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.binding.JalviewModelSequence
+   */
+  public static jalview.binding.JalviewModelSequence unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.JalviewModelSequence) Unmarshaller.unmarshal(
+            jalview.binding.JalviewModelSequence.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/JalviewUserColours.java b/src/jalview/binding/JalviewUserColours.java
index b5d0335..822392e 100755
--- a/src/jalview/binding/JalviewUserColours.java
+++ b/src/jalview/binding/JalviewUserColours.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,280 +30,299 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class JalviewUserColours implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _schemeName.
-     */
-    private java.lang.String _schemeName;
-
-    /**
-     * Field _colourList.
-     */
-    private java.util.Vector _colourList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JalviewUserColours() {
-        super();
-        this._colourList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vColour
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addColour(
-            final Colour vColour)
-    throws java.lang.IndexOutOfBoundsException {
-        this._colourList.addElement(vColour);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vColour
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addColour(
-            final int index,
-            final Colour vColour)
-    throws java.lang.IndexOutOfBoundsException {
-        this._colourList.add(index, vColour);
-    }
-
-    /**
-     * Method enumerateColour.
-     * 
-     * @return an Enumeration over all Colour elements
-     */
-    public java.util.Enumeration enumerateColour(
-    ) {
-        return this._colourList.elements();
-    }
-
-    /**
-     * Method getColour.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the Colour at the given index
-     */
-    public Colour getColour(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._colourList.size()) {
-            throw new IndexOutOfBoundsException("getColour: Index value '" + index + "' not in range [0.." + (this._colourList.size() - 1) + "]");
-        }
-        
-        return (Colour) _colourList.get(index);
-    }
-
-    /**
-     * Method getColour.Returns the contents of the collection in
-     * an Array.  <p>Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we <i>know</i>
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public Colour[] getColour(
-    ) {
-        Colour[] array = new Colour[0];
-        return (Colour[]) this._colourList.toArray(array);
-    }
-
-    /**
-     * Method getColourCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getColourCount(
-    ) {
-        return this._colourList.size();
-    }
-
-    /**
-     * Returns the value of field 'schemeName'.
-     * 
-     * @return the value of field 'SchemeName'.
-     */
-    public java.lang.String getSchemeName(
-    ) {
-        return this._schemeName;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
+public class JalviewUserColours implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _schemeName.
+   */
+  private java.lang.String _schemeName;
+
+  /**
+   * Field _colourList.
+   */
+  private java.util.Vector _colourList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public JalviewUserColours()
+  {
+    super();
+    this._colourList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vColour
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addColour(final Colour vColour)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._colourList.addElement(vColour);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vColour
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addColour(final int index, final Colour vColour)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._colourList.add(index, vColour);
+  }
+
+  /**
+   * Method enumerateColour.
+   * 
+   * @return an Enumeration over all Colour elements
+   */
+  public java.util.Enumeration enumerateColour()
+  {
+    return this._colourList.elements();
+  }
+
+  /**
+   * Method getColour.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the Colour at the given index
+   */
+  public Colour getColour(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._colourList.size())
+    {
+      throw new IndexOutOfBoundsException("getColour: Index value '"
+              + index + "' not in range [0.."
+              + (this._colourList.size() - 1) + "]");
     }
 
-    /**
-     */
-    public void removeAllColour(
-    ) {
-        this._colourList.clear();
+    return (Colour) _colourList.get(index);
+  }
+
+  /**
+   * Method getColour.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public Colour[] getColour()
+  {
+    Colour[] array = new Colour[0];
+    return (Colour[]) this._colourList.toArray(array);
+  }
+
+  /**
+   * Method getColourCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getColourCount()
+  {
+    return this._colourList.size();
+  }
+
+  /**
+   * Returns the value of field 'schemeName'.
+   * 
+   * @return the value of field 'SchemeName'.
+   */
+  public java.lang.String getSchemeName()
+  {
+    return this._schemeName;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
-
-    /**
-     * Method removeColour.
-     * 
-     * @param vColour
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeColour(
-            final Colour vColour) {
-        boolean removed = _colourList.remove(vColour);
-        return removed;
-    }
-
-    /**
-     * Method removeColourAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public Colour removeColourAt(
-            final int index) {
-        java.lang.Object obj = this._colourList.remove(index);
-        return (Colour) obj;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vColour
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setColour(
-            final int index,
-            final Colour vColour)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._colourList.size()) {
-            throw new IndexOutOfBoundsException("setColour: Index value '" + index + "' not in range [0.." + (this._colourList.size() - 1) + "]");
-        }
-        
-        this._colourList.set(index, vColour);
-    }
-
-    /**
-     * 
-     * 
-     * @param vColourArray
-     */
-    public void setColour(
-            final Colour[] vColourArray) {
-        //-- copy array
-        _colourList.clear();
-        
-        for (int i = 0; i < vColourArray.length; i++) {
-                this._colourList.add(vColourArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of field 'schemeName'.
-     * 
-     * @param schemeName the value of field 'schemeName'.
-     */
-    public void setSchemeName(
-            final java.lang.String schemeName) {
-        this._schemeName = schemeName;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.JalviewUserColours
-     */
-    public static jalview.binding.JalviewUserColours unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(jalview.binding.JalviewUserColours.class, reader);
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   */
+  public void removeAllColour()
+  {
+    this._colourList.clear();
+  }
+
+  /**
+   * Method removeColour.
+   * 
+   * @param vColour
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeColour(final Colour vColour)
+  {
+    boolean removed = _colourList.remove(vColour);
+    return removed;
+  }
+
+  /**
+   * Method removeColourAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public Colour removeColourAt(final int index)
+  {
+    java.lang.Object obj = this._colourList.remove(index);
+    return (Colour) obj;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vColour
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setColour(final int index, final Colour vColour)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._colourList.size())
+    {
+      throw new IndexOutOfBoundsException("setColour: Index value '"
+              + index + "' not in range [0.."
+              + (this._colourList.size() - 1) + "]");
     }
 
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+    this._colourList.set(index, vColour);
+  }
+
+  /**
+   * 
+   * 
+   * @param vColourArray
+   */
+  public void setColour(final Colour[] vColourArray)
+  {
+    // -- copy array
+    _colourList.clear();
+
+    for (int i = 0; i < vColourArray.length; i++)
+    {
+      this._colourList.add(vColourArray[i]);
     }
+  }
+
+  /**
+   * Sets the value of field 'schemeName'.
+   * 
+   * @param schemeName
+   *                the value of field 'schemeName'.
+   */
+  public void setSchemeName(final java.lang.String schemeName)
+  {
+    this._schemeName = schemeName;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.binding.JalviewUserColours
+   */
+  public static jalview.binding.JalviewUserColours unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(
+            jalview.binding.JalviewUserColours.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/Pdbentry.java b/src/jalview/binding/Pdbentry.java
index cac4cf6..53a2484 100755
--- a/src/jalview/binding/Pdbentry.java
+++ b/src/jalview/binding/Pdbentry.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,308 +30,330 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Pdbentry implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _id.
-     */
-    private java.lang.String _id;
-
-    /**
-     * Field _type.
-     */
-    private java.lang.String _type;
-
-    /**
-     * Field _items.
-     */
-    private java.util.Vector _items;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Pdbentry() {
-        super();
-        this._items = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vPdbentryItem
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addPdbentryItem(
-            final jalview.binding.PdbentryItem vPdbentryItem)
-    throws java.lang.IndexOutOfBoundsException {
-        this._items.addElement(vPdbentryItem);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vPdbentryItem
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addPdbentryItem(
-            final int index,
-            final jalview.binding.PdbentryItem vPdbentryItem)
-    throws java.lang.IndexOutOfBoundsException {
-        this._items.add(index, vPdbentryItem);
-    }
-
-    /**
-     * Method enumeratePdbentryItem.
-     * 
-     * @return an Enumeration over all jalview.binding.PdbentryItem
-     * elements
-     */
-    public java.util.Enumeration enumeratePdbentryItem(
-    ) {
-        return this._items.elements();
-    }
-
-    /**
-     * Returns the value of field 'id'.
-     * 
-     * @return the value of field 'Id'.
-     */
-    public java.lang.String getId(
-    ) {
-        return this._id;
-    }
-
-    /**
-     * Method getPdbentryItem.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the jalview.binding.PdbentryItem at the
-     * given index
-     */
-    public jalview.binding.PdbentryItem getPdbentryItem(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._items.size()) {
-            throw new IndexOutOfBoundsException("getPdbentryItem: Index value '" + index + "' not in range [0.." + (this._items.size() - 1) + "]");
-        }
-        
-        return (jalview.binding.PdbentryItem) _items.get(index);
-    }
-
-    /**
-     * Method getPdbentryItem.Returns the contents of the
-     * collection in an Array.  <p>Note:  Just in case the
-     * collection contents are changing in another thread, we pass
-     * a 0-length Array of the correct type into the API call. 
-     * This way we <i>know</i> that the Array returned is of
-     * exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.binding.PdbentryItem[] getPdbentryItem(
-    ) {
-        jalview.binding.PdbentryItem[] array = new jalview.binding.PdbentryItem[0];
-        return (jalview.binding.PdbentryItem[]) this._items.toArray(array);
-    }
-
-    /**
-     * Method getPdbentryItemCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getPdbentryItemCount(
-    ) {
-        return this._items.size();
-    }
-
-    /**
-     * Returns the value of field 'type'.
-     * 
-     * @return the value of field 'Type'.
-     */
-    public java.lang.String getType(
-    ) {
-        return this._type;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     */
-    public void removeAllPdbentryItem(
-    ) {
-        this._items.clear();
-    }
-
-    /**
-     * Method removePdbentryItem.
-     * 
-     * @param vPdbentryItem
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removePdbentryItem(
-            final jalview.binding.PdbentryItem vPdbentryItem) {
-        boolean removed = _items.remove(vPdbentryItem);
-        return removed;
-    }
-
-    /**
-     * Method removePdbentryItemAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.binding.PdbentryItem removePdbentryItemAt(
-            final int index) {
-        java.lang.Object obj = this._items.remove(index);
-        return (jalview.binding.PdbentryItem) obj;
-    }
-
-    /**
-     * Sets the value of field 'id'.
-     * 
-     * @param id the value of field 'id'.
-     */
-    public void setId(
-            final java.lang.String id) {
-        this._id = id;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vPdbentryItem
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setPdbentryItem(
-            final int index,
-            final jalview.binding.PdbentryItem vPdbentryItem)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._items.size()) {
-            throw new IndexOutOfBoundsException("setPdbentryItem: Index value '" + index + "' not in range [0.." + (this._items.size() - 1) + "]");
-        }
-        
-        this._items.set(index, vPdbentryItem);
+public class Pdbentry implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _id.
+   */
+  private java.lang.String _id;
+
+  /**
+   * Field _type.
+   */
+  private java.lang.String _type;
+
+  /**
+   * Field _items.
+   */
+  private java.util.Vector _items;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Pdbentry()
+  {
+    super();
+    this._items = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vPdbentryItem
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addPdbentryItem(
+          final jalview.binding.PdbentryItem vPdbentryItem)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._items.addElement(vPdbentryItem);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vPdbentryItem
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addPdbentryItem(final int index,
+          final jalview.binding.PdbentryItem vPdbentryItem)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._items.add(index, vPdbentryItem);
+  }
+
+  /**
+   * Method enumeratePdbentryItem.
+   * 
+   * @return an Enumeration over all jalview.binding.PdbentryItem elements
+   */
+  public java.util.Enumeration enumeratePdbentryItem()
+  {
+    return this._items.elements();
+  }
+
+  /**
+   * Returns the value of field 'id'.
+   * 
+   * @return the value of field 'Id'.
+   */
+  public java.lang.String getId()
+  {
+    return this._id;
+  }
+
+  /**
+   * Method getPdbentryItem.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.binding.PdbentryItem at the given index
+   */
+  public jalview.binding.PdbentryItem getPdbentryItem(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._items.size())
+    {
+      throw new IndexOutOfBoundsException("getPdbentryItem: Index value '"
+              + index + "' not in range [0.." + (this._items.size() - 1)
+              + "]");
     }
 
-    /**
-     * 
-     * 
-     * @param vPdbentryItemArray
-     */
-    public void setPdbentryItem(
-            final jalview.binding.PdbentryItem[] vPdbentryItemArray) {
-        //-- copy array
-        _items.clear();
-        
-        for (int i = 0; i < vPdbentryItemArray.length; i++) {
-                this._items.add(vPdbentryItemArray[i]);
-        }
+    return (jalview.binding.PdbentryItem) _items.get(index);
+  }
+
+  /**
+   * Method getPdbentryItem.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.binding.PdbentryItem[] getPdbentryItem()
+  {
+    jalview.binding.PdbentryItem[] array = new jalview.binding.PdbentryItem[0];
+    return (jalview.binding.PdbentryItem[]) this._items.toArray(array);
+  }
+
+  /**
+   * Method getPdbentryItemCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getPdbentryItemCount()
+  {
+    return this._items.size();
+  }
+
+  /**
+   * Returns the value of field 'type'.
+   * 
+   * @return the value of field 'Type'.
+   */
+  public java.lang.String getType()
+  {
+    return this._type;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
-
-    /**
-     * Sets the value of field 'type'.
-     * 
-     * @param type the value of field 'type'.
-     */
-    public void setType(
-            final java.lang.String type) {
-        this._type = type;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.Pdbentry
-     */
-    public static jalview.binding.Pdbentry unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.Pdbentry) Unmarshaller.unmarshal(jalview.binding.Pdbentry.class, reader);
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   */
+  public void removeAllPdbentryItem()
+  {
+    this._items.clear();
+  }
+
+  /**
+   * Method removePdbentryItem.
+   * 
+   * @param vPdbentryItem
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removePdbentryItem(
+          final jalview.binding.PdbentryItem vPdbentryItem)
+  {
+    boolean removed = _items.remove(vPdbentryItem);
+    return removed;
+  }
+
+  /**
+   * Method removePdbentryItemAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.binding.PdbentryItem removePdbentryItemAt(final int index)
+  {
+    java.lang.Object obj = this._items.remove(index);
+    return (jalview.binding.PdbentryItem) obj;
+  }
+
+  /**
+   * Sets the value of field 'id'.
+   * 
+   * @param id
+   *                the value of field 'id'.
+   */
+  public void setId(final java.lang.String id)
+  {
+    this._id = id;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vPdbentryItem
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setPdbentryItem(final int index,
+          final jalview.binding.PdbentryItem vPdbentryItem)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._items.size())
+    {
+      throw new IndexOutOfBoundsException("setPdbentryItem: Index value '"
+              + index + "' not in range [0.." + (this._items.size() - 1)
+              + "]");
     }
 
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+    this._items.set(index, vPdbentryItem);
+  }
+
+  /**
+   * 
+   * 
+   * @param vPdbentryItemArray
+   */
+  public void setPdbentryItem(
+          final jalview.binding.PdbentryItem[] vPdbentryItemArray)
+  {
+    // -- copy array
+    _items.clear();
+
+    for (int i = 0; i < vPdbentryItemArray.length; i++)
+    {
+      this._items.add(vPdbentryItemArray[i]);
     }
+  }
+
+  /**
+   * Sets the value of field 'type'.
+   * 
+   * @param type
+   *                the value of field 'type'.
+   */
+  public void setType(final java.lang.String type)
+  {
+    this._type = type;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.binding.Pdbentry
+   */
+  public static jalview.binding.Pdbentry unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.Pdbentry) Unmarshaller.unmarshal(
+            jalview.binding.Pdbentry.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/PdbentryItem.java b/src/jalview/binding/PdbentryItem.java
index 83bc40a..dc2314b 100755
--- a/src/jalview/binding/PdbentryItem.java
+++ b/src/jalview/binding/PdbentryItem.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.binding;
 
 /**
@@ -12,181 +23,185 @@ package jalview.binding;
  * 
  * @version $Revision$ $Date$
  */
-public class PdbentryItem implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _propertyList.
-     */
-    private java.util.Vector _propertyList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public PdbentryItem() {
-        super();
-        this._propertyList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vProperty
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addProperty(
-            final jalview.binding.Property vProperty)
-    throws java.lang.IndexOutOfBoundsException {
-        this._propertyList.addElement(vProperty);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vProperty
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addProperty(
-            final int index,
-            final jalview.binding.Property vProperty)
-    throws java.lang.IndexOutOfBoundsException {
-        this._propertyList.add(index, vProperty);
-    }
-
-    /**
-     * Method enumerateProperty.
-     * 
-     * @return an Enumeration over all jalview.binding.Property
-     * elements
-     */
-    public java.util.Enumeration enumerateProperty(
-    ) {
-        return this._propertyList.elements();
-    }
-
-    /**
-     * Method getProperty.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the jalview.binding.Property at the
-     * given index
-     */
-    public jalview.binding.Property getProperty(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._propertyList.size()) {
-            throw new IndexOutOfBoundsException("getProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
-        }
-        
-        return (jalview.binding.Property) _propertyList.get(index);
-    }
-
-    /**
-     * Method getProperty.Returns the contents of the collection in
-     * an Array.  <p>Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we <i>know</i>
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.binding.Property[] getProperty(
-    ) {
-        jalview.binding.Property[] array = new jalview.binding.Property[0];
-        return (jalview.binding.Property[]) this._propertyList.toArray(array);
-    }
-
-    /**
-     * Method getPropertyCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getPropertyCount(
-    ) {
-        return this._propertyList.size();
-    }
-
-    /**
-     */
-    public void removeAllProperty(
-    ) {
-        this._propertyList.clear();
-    }
-
-    /**
-     * Method removeProperty.
-     * 
-     * @param vProperty
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeProperty(
-            final jalview.binding.Property vProperty) {
-        boolean removed = _propertyList.remove(vProperty);
-        return removed;
-    }
-
-    /**
-     * Method removePropertyAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.binding.Property removePropertyAt(
-            final int index) {
-        java.lang.Object obj = this._propertyList.remove(index);
-        return (jalview.binding.Property) obj;
+public class PdbentryItem implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _propertyList.
+   */
+  private java.util.Vector _propertyList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public PdbentryItem()
+  {
+    super();
+    this._propertyList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vProperty
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addProperty(final jalview.binding.Property vProperty)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._propertyList.addElement(vProperty);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vProperty
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addProperty(final int index,
+          final jalview.binding.Property vProperty)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._propertyList.add(index, vProperty);
+  }
+
+  /**
+   * Method enumerateProperty.
+   * 
+   * @return an Enumeration over all jalview.binding.Property elements
+   */
+  public java.util.Enumeration enumerateProperty()
+  {
+    return this._propertyList.elements();
+  }
+
+  /**
+   * Method getProperty.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.binding.Property at the given index
+   */
+  public jalview.binding.Property getProperty(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._propertyList.size())
+    {
+      throw new IndexOutOfBoundsException("getProperty: Index value '"
+              + index + "' not in range [0.."
+              + (this._propertyList.size() - 1) + "]");
     }
 
-    /**
-     * 
-     * 
-     * @param index
-     * @param vProperty
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setProperty(
-            final int index,
-            final jalview.binding.Property vProperty)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._propertyList.size()) {
-            throw new IndexOutOfBoundsException("setProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
-        }
-        
-        this._propertyList.set(index, vProperty);
+    return (jalview.binding.Property) _propertyList.get(index);
+  }
+
+  /**
+   * Method getProperty.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.binding.Property[] getProperty()
+  {
+    jalview.binding.Property[] array = new jalview.binding.Property[0];
+    return (jalview.binding.Property[]) this._propertyList.toArray(array);
+  }
+
+  /**
+   * Method getPropertyCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getPropertyCount()
+  {
+    return this._propertyList.size();
+  }
+
+  /**
+   */
+  public void removeAllProperty()
+  {
+    this._propertyList.clear();
+  }
+
+  /**
+   * Method removeProperty.
+   * 
+   * @param vProperty
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeProperty(final jalview.binding.Property vProperty)
+  {
+    boolean removed = _propertyList.remove(vProperty);
+    return removed;
+  }
+
+  /**
+   * Method removePropertyAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.binding.Property removePropertyAt(final int index)
+  {
+    java.lang.Object obj = this._propertyList.remove(index);
+    return (jalview.binding.Property) obj;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vProperty
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setProperty(final int index,
+          final jalview.binding.Property vProperty)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._propertyList.size())
+    {
+      throw new IndexOutOfBoundsException("setProperty: Index value '"
+              + index + "' not in range [0.."
+              + (this._propertyList.size() - 1) + "]");
     }
 
-    /**
-     * 
-     * 
-     * @param vPropertyArray
-     */
-    public void setProperty(
-            final jalview.binding.Property[] vPropertyArray) {
-        //-- copy array
-        _propertyList.clear();
-        
-        for (int i = 0; i < vPropertyArray.length; i++) {
-                this._propertyList.add(vPropertyArray[i]);
-        }
+    this._propertyList.set(index, vProperty);
+  }
+
+  /**
+   * 
+   * 
+   * @param vPropertyArray
+   */
+  public void setProperty(final jalview.binding.Property[] vPropertyArray)
+  {
+    // -- copy array
+    _propertyList.clear();
+
+    for (int i = 0; i < vPropertyArray.length; i++)
+    {
+      this._propertyList.add(vPropertyArray[i]);
     }
+  }
 
 }
diff --git a/src/jalview/binding/Pdbids.java b/src/jalview/binding/Pdbids.java
index b4745a2..9713859 100755
--- a/src/jalview/binding/Pdbids.java
+++ b/src/jalview/binding/Pdbids.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,98 +30,110 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Pdbids extends Pdbentry 
-implements java.io.Serializable
+public class Pdbids extends Pdbentry implements java.io.Serializable
 {
 
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
 
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Pdbids() {
-        super();
-    }
+  public Pdbids()
+  {
+    super();
+  }
 
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
 
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
 
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
 
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.Pdbentry
-     */
-    public static jalview.binding.Pdbentry unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.Pdbentry) Unmarshaller.unmarshal(jalview.binding.Pdbids.class, reader);
-    }
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.binding.Pdbentry
+   */
+  public static jalview.binding.Pdbentry unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.Pdbentry) Unmarshaller.unmarshal(
+            jalview.binding.Pdbids.class, reader);
+  }
 
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/Property.java b/src/jalview/binding/Property.java
index f1114f7..4ab620a 100755
--- a/src/jalview/binding/Property.java
+++ b/src/jalview/binding/Property.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,151 +30,166 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Property implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _name.
-     */
-    private java.lang.String _name;
-
-    /**
-     * Field _value.
-     */
-    private java.lang.String _value;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Property() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'name'.
-     * 
-     * @return the value of field 'Name'.
-     */
-    public java.lang.String getName(
-    ) {
-        return this._name;
-    }
-
-    /**
-     * Returns the value of field 'value'.
-     * 
-     * @return the value of field 'Value'.
-     */
-    public java.lang.String getValue(
-    ) {
-        return this._value;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'name'.
-     * 
-     * @param name the value of field 'name'.
-     */
-    public void setName(
-            final java.lang.String name) {
-        this._name = name;
-    }
-
-    /**
-     * Sets the value of field 'value'.
-     * 
-     * @param value the value of field 'value'.
-     */
-    public void setValue(
-            final java.lang.String value) {
-        this._value = value;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.Property
-     */
-    public static jalview.binding.Property unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.Property) Unmarshaller.unmarshal(jalview.binding.Property.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class Property implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _name.
+   */
+  private java.lang.String _name;
+
+  /**
+   * Field _value.
+   */
+  private java.lang.String _value;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Property()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Returns the value of field 'name'.
+   * 
+   * @return the value of field 'Name'.
+   */
+  public java.lang.String getName()
+  {
+    return this._name;
+  }
+
+  /**
+   * Returns the value of field 'value'.
+   * 
+   * @return the value of field 'Value'.
+   */
+  public java.lang.String getValue()
+  {
+    return this._value;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'name'.
+   * 
+   * @param name
+   *                the value of field 'name'.
+   */
+  public void setName(final java.lang.String name)
+  {
+    this._name = name;
+  }
+
+  /**
+   * Sets the value of field 'value'.
+   * 
+   * @param value
+   *                the value of field 'value'.
+   */
+  public void setValue(final java.lang.String value)
+  {
+    this._value = value;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.binding.Property
+   */
+  public static jalview.binding.Property unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.Property) Unmarshaller.unmarshal(
+            jalview.binding.Property.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/Sequence.java b/src/jalview/binding/Sequence.java
index 9c8cbc2..bd895f6 100755
--- a/src/jalview/binding/Sequence.java
+++ b/src/jalview/binding/Sequence.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,98 +30,110 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Sequence extends SequenceType 
-implements java.io.Serializable
+public class Sequence extends SequenceType implements java.io.Serializable
 {
 
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
 
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Sequence() {
-        super();
-    }
+  public Sequence()
+  {
+    super();
+  }
 
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
 
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
 
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
 
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.SequenceType
-     */
-    public static jalview.binding.SequenceType unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.SequenceType) Unmarshaller.unmarshal(jalview.binding.Sequence.class, reader);
-    }
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.binding.SequenceType
+   */
+  public static jalview.binding.SequenceType unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.SequenceType) Unmarshaller.unmarshal(
+            jalview.binding.Sequence.class, reader);
+  }
 
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/SequenceSet.java b/src/jalview/binding/SequenceSet.java
index 13a9020..e348f9a 100755
--- a/src/jalview/binding/SequenceSet.java
+++ b/src/jalview/binding/SequenceSet.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,496 +30,524 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class SequenceSet implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _gapChar.
-     */
-    private java.lang.String _gapChar;
-
-    /**
-     * Field _aligned.
-     */
-    private boolean _aligned;
-
-    /**
-     * keeps track of state for field: _aligned
-     */
-    private boolean _has_aligned;
-
-    /**
-     * Field _sequenceList.
-     */
-    private java.util.Vector _sequenceList;
-
-    /**
-     * Field _annotationList.
-     */
-    private java.util.Vector _annotationList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public SequenceSet() {
-        super();
-        this._sequenceList = new java.util.Vector();
-        this._annotationList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vAnnotation
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addAnnotation(
-            final jalview.binding.Annotation vAnnotation)
-    throws java.lang.IndexOutOfBoundsException {
-        this._annotationList.addElement(vAnnotation);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vAnnotation
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addAnnotation(
-            final int index,
-            final jalview.binding.Annotation vAnnotation)
-    throws java.lang.IndexOutOfBoundsException {
-        this._annotationList.add(index, vAnnotation);
-    }
-
-    /**
-     * 
-     * 
-     * @param vSequence
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSequence(
-            final jalview.binding.Sequence vSequence)
-    throws java.lang.IndexOutOfBoundsException {
-        this._sequenceList.addElement(vSequence);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSequence
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSequence(
-            final int index,
-            final jalview.binding.Sequence vSequence)
-    throws java.lang.IndexOutOfBoundsException {
-        this._sequenceList.add(index, vSequence);
-    }
-
-    /**
-     */
-    public void deleteAligned(
-    ) {
-        this._has_aligned= false;
-    }
-
-    /**
-     * Method enumerateAnnotation.
-     * 
-     * @return an Enumeration over all jalview.binding.Annotation
-     * elements
-     */
-    public java.util.Enumeration enumerateAnnotation(
-    ) {
-        return this._annotationList.elements();
-    }
-
-    /**
-     * Method enumerateSequence.
-     * 
-     * @return an Enumeration over all jalview.binding.Sequence
-     * elements
-     */
-    public java.util.Enumeration enumerateSequence(
-    ) {
-        return this._sequenceList.elements();
-    }
-
-    /**
-     * Returns the value of field 'aligned'.
-     * 
-     * @return the value of field 'Aligned'.
-     */
-    public boolean getAligned(
-    ) {
-        return this._aligned;
-    }
-
-    /**
-     * Method getAnnotation.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the jalview.binding.Annotation at the
-     * given index
-     */
-    public jalview.binding.Annotation getAnnotation(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._annotationList.size()) {
-            throw new IndexOutOfBoundsException("getAnnotation: Index value '" + index + "' not in range [0.." + (this._annotationList.size() - 1) + "]");
-        }
-        
-        return (jalview.binding.Annotation) _annotationList.get(index);
-    }
-
-    /**
-     * Method getAnnotation.Returns the contents of the collection
-     * in an Array.  <p>Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we <i>know</i>
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.binding.Annotation[] getAnnotation(
-    ) {
-        jalview.binding.Annotation[] array = new jalview.binding.Annotation[0];
-        return (jalview.binding.Annotation[]) this._annotationList.toArray(array);
-    }
-
-    /**
-     * Method getAnnotationCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getAnnotationCount(
-    ) {
-        return this._annotationList.size();
-    }
-
-    /**
-     * Returns the value of field 'gapChar'.
-     * 
-     * @return the value of field 'GapChar'.
-     */
-    public java.lang.String getGapChar(
-    ) {
-        return this._gapChar;
-    }
-
-    /**
-     * Method getSequence.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the jalview.binding.Sequence at the
-     * given index
-     */
-    public jalview.binding.Sequence getSequence(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._sequenceList.size()) {
-            throw new IndexOutOfBoundsException("getSequence: Index value '" + index + "' not in range [0.." + (this._sequenceList.size() - 1) + "]");
-        }
-        
-        return (jalview.binding.Sequence) _sequenceList.get(index);
-    }
-
-    /**
-     * Method getSequence.Returns the contents of the collection in
-     * an Array.  <p>Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we <i>know</i>
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.binding.Sequence[] getSequence(
-    ) {
-        jalview.binding.Sequence[] array = new jalview.binding.Sequence[0];
-        return (jalview.binding.Sequence[]) this._sequenceList.toArray(array);
-    }
-
-    /**
-     * Method getSequenceCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getSequenceCount(
-    ) {
-        return this._sequenceList.size();
-    }
-
-    /**
-     * Method hasAligned.
-     * 
-     * @return true if at least one Aligned has been added
-     */
-    public boolean hasAligned(
-    ) {
-        return this._has_aligned;
-    }
-
-    /**
-     * Returns the value of field 'aligned'.
-     * 
-     * @return the value of field 'Aligned'.
-     */
-    public boolean isAligned(
-    ) {
-        return this._aligned;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     */
-    public void removeAllAnnotation(
-    ) {
-        this._annotationList.clear();
-    }
-
-    /**
-     */
-    public void removeAllSequence(
-    ) {
-        this._sequenceList.clear();
-    }
-
-    /**
-     * Method removeAnnotation.
-     * 
-     * @param vAnnotation
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeAnnotation(
-            final jalview.binding.Annotation vAnnotation) {
-        boolean removed = _annotationList.remove(vAnnotation);
-        return removed;
-    }
-
-    /**
-     * Method removeAnnotationAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.binding.Annotation removeAnnotationAt(
-            final int index) {
-        java.lang.Object obj = this._annotationList.remove(index);
-        return (jalview.binding.Annotation) obj;
-    }
-
-    /**
-     * Method removeSequence.
-     * 
-     * @param vSequence
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeSequence(
-            final jalview.binding.Sequence vSequence) {
-        boolean removed = _sequenceList.remove(vSequence);
-        return removed;
-    }
-
-    /**
-     * Method removeSequenceAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.binding.Sequence removeSequenceAt(
-            final int index) {
-        java.lang.Object obj = this._sequenceList.remove(index);
-        return (jalview.binding.Sequence) obj;
-    }
-
-    /**
-     * Sets the value of field 'aligned'.
-     * 
-     * @param aligned the value of field 'aligned'.
-     */
-    public void setAligned(
-            final boolean aligned) {
-        this._aligned = aligned;
-        this._has_aligned = true;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vAnnotation
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setAnnotation(
-            final int index,
-            final jalview.binding.Annotation vAnnotation)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._annotationList.size()) {
-            throw new IndexOutOfBoundsException("setAnnotation: Index value '" + index + "' not in range [0.." + (this._annotationList.size() - 1) + "]");
-        }
-        
-        this._annotationList.set(index, vAnnotation);
-    }
-
-    /**
-     * 
-     * 
-     * @param vAnnotationArray
-     */
-    public void setAnnotation(
-            final jalview.binding.Annotation[] vAnnotationArray) {
-        //-- copy array
-        _annotationList.clear();
-        
-        for (int i = 0; i < vAnnotationArray.length; i++) {
-                this._annotationList.add(vAnnotationArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of field 'gapChar'.
-     * 
-     * @param gapChar the value of field 'gapChar'.
-     */
-    public void setGapChar(
-            final java.lang.String gapChar) {
-        this._gapChar = gapChar;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSequence
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setSequence(
-            final int index,
-            final jalview.binding.Sequence vSequence)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._sequenceList.size()) {
-            throw new IndexOutOfBoundsException("setSequence: Index value '" + index + "' not in range [0.." + (this._sequenceList.size() - 1) + "]");
-        }
-        
-        this._sequenceList.set(index, vSequence);
-    }
-
-    /**
-     * 
-     * 
-     * @param vSequenceArray
-     */
-    public void setSequence(
-            final jalview.binding.Sequence[] vSequenceArray) {
-        //-- copy array
-        _sequenceList.clear();
-        
-        for (int i = 0; i < vSequenceArray.length; i++) {
-                this._sequenceList.add(vSequenceArray[i]);
-        }
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.SequenceSet
-     */
-    public static jalview.binding.SequenceSet unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.SequenceSet) Unmarshaller.unmarshal(jalview.binding.SequenceSet.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+public class SequenceSet implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _gapChar.
+   */
+  private java.lang.String _gapChar;
+
+  /**
+   * Field _aligned.
+   */
+  private boolean _aligned;
+
+  /**
+   * keeps track of state for field: _aligned
+   */
+  private boolean _has_aligned;
+
+  /**
+   * Field _sequenceList.
+   */
+  private java.util.Vector _sequenceList;
+
+  /**
+   * Field _annotationList.
+   */
+  private java.util.Vector _annotationList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public SequenceSet()
+  {
+    super();
+    this._sequenceList = new java.util.Vector();
+    this._annotationList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vAnnotation
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addAnnotation(final jalview.binding.Annotation vAnnotation)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._annotationList.addElement(vAnnotation);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAnnotation
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addAnnotation(final int index,
+          final jalview.binding.Annotation vAnnotation)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._annotationList.add(index, vAnnotation);
+  }
+
+  /**
+   * 
+   * 
+   * @param vSequence
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addSequence(final jalview.binding.Sequence vSequence)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._sequenceList.addElement(vSequence);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSequence
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addSequence(final int index,
+          final jalview.binding.Sequence vSequence)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._sequenceList.add(index, vSequence);
+  }
+
+  /**
+   */
+  public void deleteAligned()
+  {
+    this._has_aligned = false;
+  }
+
+  /**
+   * Method enumerateAnnotation.
+   * 
+   * @return an Enumeration over all jalview.binding.Annotation elements
+   */
+  public java.util.Enumeration enumerateAnnotation()
+  {
+    return this._annotationList.elements();
+  }
+
+  /**
+   * Method enumerateSequence.
+   * 
+   * @return an Enumeration over all jalview.binding.Sequence elements
+   */
+  public java.util.Enumeration enumerateSequence()
+  {
+    return this._sequenceList.elements();
+  }
+
+  /**
+   * Returns the value of field 'aligned'.
+   * 
+   * @return the value of field 'Aligned'.
+   */
+  public boolean getAligned()
+  {
+    return this._aligned;
+  }
+
+  /**
+   * Method getAnnotation.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.binding.Annotation at the given index
+   */
+  public jalview.binding.Annotation getAnnotation(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._annotationList.size())
+    {
+      throw new IndexOutOfBoundsException("getAnnotation: Index value '"
+              + index + "' not in range [0.."
+              + (this._annotationList.size() - 1) + "]");
+    }
+
+    return (jalview.binding.Annotation) _annotationList.get(index);
+  }
+
+  /**
+   * Method getAnnotation.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.binding.Annotation[] getAnnotation()
+  {
+    jalview.binding.Annotation[] array = new jalview.binding.Annotation[0];
+    return (jalview.binding.Annotation[]) this._annotationList
+            .toArray(array);
+  }
+
+  /**
+   * Method getAnnotationCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getAnnotationCount()
+  {
+    return this._annotationList.size();
+  }
+
+  /**
+   * Returns the value of field 'gapChar'.
+   * 
+   * @return the value of field 'GapChar'.
+   */
+  public java.lang.String getGapChar()
+  {
+    return this._gapChar;
+  }
+
+  /**
+   * Method getSequence.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.binding.Sequence at the given index
+   */
+  public jalview.binding.Sequence getSequence(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._sequenceList.size())
+    {
+      throw new IndexOutOfBoundsException("getSequence: Index value '"
+              + index + "' not in range [0.."
+              + (this._sequenceList.size() - 1) + "]");
+    }
+
+    return (jalview.binding.Sequence) _sequenceList.get(index);
+  }
+
+  /**
+   * Method getSequence.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.binding.Sequence[] getSequence()
+  {
+    jalview.binding.Sequence[] array = new jalview.binding.Sequence[0];
+    return (jalview.binding.Sequence[]) this._sequenceList.toArray(array);
+  }
+
+  /**
+   * Method getSequenceCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getSequenceCount()
+  {
+    return this._sequenceList.size();
+  }
+
+  /**
+   * Method hasAligned.
+   * 
+   * @return true if at least one Aligned has been added
+   */
+  public boolean hasAligned()
+  {
+    return this._has_aligned;
+  }
+
+  /**
+   * Returns the value of field 'aligned'.
+   * 
+   * @return the value of field 'Aligned'.
+   */
+  public boolean isAligned()
+  {
+    return this._aligned;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   */
+  public void removeAllAnnotation()
+  {
+    this._annotationList.clear();
+  }
+
+  /**
+   */
+  public void removeAllSequence()
+  {
+    this._sequenceList.clear();
+  }
+
+  /**
+   * Method removeAnnotation.
+   * 
+   * @param vAnnotation
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeAnnotation(
+          final jalview.binding.Annotation vAnnotation)
+  {
+    boolean removed = _annotationList.remove(vAnnotation);
+    return removed;
+  }
+
+  /**
+   * Method removeAnnotationAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.binding.Annotation removeAnnotationAt(final int index)
+  {
+    java.lang.Object obj = this._annotationList.remove(index);
+    return (jalview.binding.Annotation) obj;
+  }
+
+  /**
+   * Method removeSequence.
+   * 
+   * @param vSequence
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeSequence(final jalview.binding.Sequence vSequence)
+  {
+    boolean removed = _sequenceList.remove(vSequence);
+    return removed;
+  }
+
+  /**
+   * Method removeSequenceAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.binding.Sequence removeSequenceAt(final int index)
+  {
+    java.lang.Object obj = this._sequenceList.remove(index);
+    return (jalview.binding.Sequence) obj;
+  }
+
+  /**
+   * Sets the value of field 'aligned'.
+   * 
+   * @param aligned
+   *                the value of field 'aligned'.
+   */
+  public void setAligned(final boolean aligned)
+  {
+    this._aligned = aligned;
+    this._has_aligned = true;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAnnotation
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setAnnotation(final int index,
+          final jalview.binding.Annotation vAnnotation)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._annotationList.size())
+    {
+      throw new IndexOutOfBoundsException("setAnnotation: Index value '"
+              + index + "' not in range [0.."
+              + (this._annotationList.size() - 1) + "]");
+    }
+
+    this._annotationList.set(index, vAnnotation);
+  }
+
+  /**
+   * 
+   * 
+   * @param vAnnotationArray
+   */
+  public void setAnnotation(
+          final jalview.binding.Annotation[] vAnnotationArray)
+  {
+    // -- copy array
+    _annotationList.clear();
+
+    for (int i = 0; i < vAnnotationArray.length; i++)
+    {
+      this._annotationList.add(vAnnotationArray[i]);
+    }
+  }
+
+  /**
+   * Sets the value of field 'gapChar'.
+   * 
+   * @param gapChar
+   *                the value of field 'gapChar'.
+   */
+  public void setGapChar(final java.lang.String gapChar)
+  {
+    this._gapChar = gapChar;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSequence
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setSequence(final int index,
+          final jalview.binding.Sequence vSequence)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._sequenceList.size())
+    {
+      throw new IndexOutOfBoundsException("setSequence: Index value '"
+              + index + "' not in range [0.."
+              + (this._sequenceList.size() - 1) + "]");
+    }
+
+    this._sequenceList.set(index, vSequence);
+  }
+
+  /**
+   * 
+   * 
+   * @param vSequenceArray
+   */
+  public void setSequence(final jalview.binding.Sequence[] vSequenceArray)
+  {
+    // -- copy array
+    _sequenceList.clear();
+
+    for (int i = 0; i < vSequenceArray.length; i++)
+    {
+      this._sequenceList.add(vSequenceArray[i]);
+    }
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.binding.SequenceSet
+   */
+  public static jalview.binding.SequenceSet unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.SequenceSet) Unmarshaller.unmarshal(
+            jalview.binding.SequenceSet.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/SequenceType.java b/src/jalview/binding/SequenceType.java
index 1bb2a62..a6bf64e 100755
--- a/src/jalview/binding/SequenceType.java
+++ b/src/jalview/binding/SequenceType.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,176 +30,192 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class SequenceType implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _id.
-     */
-    private java.lang.String _id;
-
-    /**
-     * Field _sequence.
-     */
-    private java.lang.String _sequence;
-
-    /**
-     * Field _name.
-     */
-    private java.lang.String _name;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public SequenceType() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'id'.
-     * 
-     * @return the value of field 'Id'.
-     */
-    public java.lang.String getId(
-    ) {
-        return this._id;
-    }
-
-    /**
-     * Returns the value of field 'name'.
-     * 
-     * @return the value of field 'Name'.
-     */
-    public java.lang.String getName(
-    ) {
-        return this._name;
-    }
-
-    /**
-     * Returns the value of field 'sequence'.
-     * 
-     * @return the value of field 'Sequence'.
-     */
-    public java.lang.String getSequence(
-    ) {
-        return this._sequence;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'id'.
-     * 
-     * @param id the value of field 'id'.
-     */
-    public void setId(
-            final java.lang.String id) {
-        this._id = id;
-    }
-
-    /**
-     * Sets the value of field 'name'.
-     * 
-     * @param name the value of field 'name'.
-     */
-    public void setName(
-            final java.lang.String name) {
-        this._name = name;
-    }
-
-    /**
-     * Sets the value of field 'sequence'.
-     * 
-     * @param sequence the value of field 'sequence'.
-     */
-    public void setSequence(
-            final java.lang.String sequence) {
-        this._sequence = sequence;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.SequenceType
-     */
-    public static jalview.binding.SequenceType unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.SequenceType) Unmarshaller.unmarshal(jalview.binding.SequenceType.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class SequenceType implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _id.
+   */
+  private java.lang.String _id;
+
+  /**
+   * Field _sequence.
+   */
+  private java.lang.String _sequence;
+
+  /**
+   * Field _name.
+   */
+  private java.lang.String _name;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public SequenceType()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Returns the value of field 'id'.
+   * 
+   * @return the value of field 'Id'.
+   */
+  public java.lang.String getId()
+  {
+    return this._id;
+  }
+
+  /**
+   * Returns the value of field 'name'.
+   * 
+   * @return the value of field 'Name'.
+   */
+  public java.lang.String getName()
+  {
+    return this._name;
+  }
+
+  /**
+   * Returns the value of field 'sequence'.
+   * 
+   * @return the value of field 'Sequence'.
+   */
+  public java.lang.String getSequence()
+  {
+    return this._sequence;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'id'.
+   * 
+   * @param id
+   *                the value of field 'id'.
+   */
+  public void setId(final java.lang.String id)
+  {
+    this._id = id;
+  }
+
+  /**
+   * Sets the value of field 'name'.
+   * 
+   * @param name
+   *                the value of field 'name'.
+   */
+  public void setName(final java.lang.String name)
+  {
+    this._name = name;
+  }
+
+  /**
+   * Sets the value of field 'sequence'.
+   * 
+   * @param sequence
+   *                the value of field 'sequence'.
+   */
+  public void setSequence(final java.lang.String sequence)
+  {
+    this._sequence = sequence;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.binding.SequenceType
+   */
+  public static jalview.binding.SequenceType unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.SequenceType) Unmarshaller.unmarshal(
+            jalview.binding.SequenceType.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/Setting.java b/src/jalview/binding/Setting.java
index 9cd84b4..3f05e27 100755
--- a/src/jalview/binding/Setting.java
+++ b/src/jalview/binding/Setting.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,232 +30,248 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Setting implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _type.
-     */
-    private java.lang.String _type;
-
-    /**
-     * Field _colour.
-     */
-    private int _colour;
-
-    /**
-     * keeps track of state for field: _colour
-     */
-    private boolean _has_colour;
-
-    /**
-     * Field _display.
-     */
-    private boolean _display;
-
-    /**
-     * keeps track of state for field: _display
-     */
-    private boolean _has_display;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Setting() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     */
-    public void deleteColour(
-    ) {
-        this._has_colour= false;
-    }
-
-    /**
-     */
-    public void deleteDisplay(
-    ) {
-        this._has_display= false;
-    }
-
-    /**
-     * Returns the value of field 'colour'.
-     * 
-     * @return the value of field 'Colour'.
-     */
-    public int getColour(
-    ) {
-        return this._colour;
-    }
-
-    /**
-     * Returns the value of field 'display'.
-     * 
-     * @return the value of field 'Display'.
-     */
-    public boolean getDisplay(
-    ) {
-        return this._display;
-    }
-
-    /**
-     * Returns the value of field 'type'.
-     * 
-     * @return the value of field 'Type'.
-     */
-    public java.lang.String getType(
-    ) {
-        return this._type;
-    }
-
-    /**
-     * Method hasColour.
-     * 
-     * @return true if at least one Colour has been added
-     */
-    public boolean hasColour(
-    ) {
-        return this._has_colour;
-    }
-
-    /**
-     * Method hasDisplay.
-     * 
-     * @return true if at least one Display has been added
-     */
-    public boolean hasDisplay(
-    ) {
-        return this._has_display;
-    }
-
-    /**
-     * Returns the value of field 'display'.
-     * 
-     * @return the value of field 'Display'.
-     */
-    public boolean isDisplay(
-    ) {
-        return this._display;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'colour'.
-     * 
-     * @param colour the value of field 'colour'.
-     */
-    public void setColour(
-            final int colour) {
-        this._colour = colour;
-        this._has_colour = true;
-    }
-
-    /**
-     * Sets the value of field 'display'.
-     * 
-     * @param display the value of field 'display'.
-     */
-    public void setDisplay(
-            final boolean display) {
-        this._display = display;
-        this._has_display = true;
-    }
-
-    /**
-     * Sets the value of field 'type'.
-     * 
-     * @param type the value of field 'type'.
-     */
-    public void setType(
-            final java.lang.String type) {
-        this._type = type;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.Setting
-     */
-    public static jalview.binding.Setting unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.Setting) Unmarshaller.unmarshal(jalview.binding.Setting.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class Setting implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _type.
+   */
+  private java.lang.String _type;
+
+  /**
+   * Field _colour.
+   */
+  private int _colour;
+
+  /**
+   * keeps track of state for field: _colour
+   */
+  private boolean _has_colour;
+
+  /**
+   * Field _display.
+   */
+  private boolean _display;
+
+  /**
+   * keeps track of state for field: _display
+   */
+  private boolean _has_display;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Setting()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   */
+  public void deleteColour()
+  {
+    this._has_colour = false;
+  }
+
+  /**
+   */
+  public void deleteDisplay()
+  {
+    this._has_display = false;
+  }
+
+  /**
+   * Returns the value of field 'colour'.
+   * 
+   * @return the value of field 'Colour'.
+   */
+  public int getColour()
+  {
+    return this._colour;
+  }
+
+  /**
+   * Returns the value of field 'display'.
+   * 
+   * @return the value of field 'Display'.
+   */
+  public boolean getDisplay()
+  {
+    return this._display;
+  }
+
+  /**
+   * Returns the value of field 'type'.
+   * 
+   * @return the value of field 'Type'.
+   */
+  public java.lang.String getType()
+  {
+    return this._type;
+  }
+
+  /**
+   * Method hasColour.
+   * 
+   * @return true if at least one Colour has been added
+   */
+  public boolean hasColour()
+  {
+    return this._has_colour;
+  }
+
+  /**
+   * Method hasDisplay.
+   * 
+   * @return true if at least one Display has been added
+   */
+  public boolean hasDisplay()
+  {
+    return this._has_display;
+  }
+
+  /**
+   * Returns the value of field 'display'.
+   * 
+   * @return the value of field 'Display'.
+   */
+  public boolean isDisplay()
+  {
+    return this._display;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'colour'.
+   * 
+   * @param colour
+   *                the value of field 'colour'.
+   */
+  public void setColour(final int colour)
+  {
+    this._colour = colour;
+    this._has_colour = true;
+  }
+
+  /**
+   * Sets the value of field 'display'.
+   * 
+   * @param display
+   *                the value of field 'display'.
+   */
+  public void setDisplay(final boolean display)
+  {
+    this._display = display;
+    this._has_display = true;
+  }
+
+  /**
+   * Sets the value of field 'type'.
+   * 
+   * @param type
+   *                the value of field 'type'.
+   */
+  public void setType(final java.lang.String type)
+  {
+    this._type = type;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.binding.Setting
+   */
+  public static jalview.binding.Setting unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.Setting) Unmarshaller.unmarshal(
+            jalview.binding.Setting.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/Tree.java b/src/jalview/binding/Tree.java
index 5f138d0..f7679f1 100755
--- a/src/jalview/binding/Tree.java
+++ b/src/jalview/binding/Tree.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,802 +30,829 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Tree implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _width.
-     */
-    private int _width;
-
-    /**
-     * keeps track of state for field: _width
-     */
-    private boolean _has_width;
-
-    /**
-     * Field _height.
-     */
-    private int _height;
-
-    /**
-     * keeps track of state for field: _height
-     */
-    private boolean _has_height;
-
-    /**
-     * Field _xpos.
-     */
-    private int _xpos;
-
-    /**
-     * keeps track of state for field: _xpos
-     */
-    private boolean _has_xpos;
-
-    /**
-     * Field _ypos.
-     */
-    private int _ypos;
-
-    /**
-     * keeps track of state for field: _ypos
-     */
-    private boolean _has_ypos;
-
-    /**
-     * Field _fontName.
-     */
-    private java.lang.String _fontName;
-
-    /**
-     * Field _fontSize.
-     */
-    private int _fontSize;
-
-    /**
-     * keeps track of state for field: _fontSize
-     */
-    private boolean _has_fontSize;
-
-    /**
-     * Field _fontStyle.
-     */
-    private int _fontStyle;
-
-    /**
-     * keeps track of state for field: _fontStyle
-     */
-    private boolean _has_fontStyle;
-
-    /**
-     * Field _threshold.
-     */
-    private float _threshold;
-
-    /**
-     * keeps track of state for field: _threshold
-     */
-    private boolean _has_threshold;
-
-    /**
-     * Field _showBootstrap.
-     */
-    private boolean _showBootstrap;
-
-    /**
-     * keeps track of state for field: _showBootstrap
-     */
-    private boolean _has_showBootstrap;
-
-    /**
-     * Field _showDistances.
-     */
-    private boolean _showDistances;
-
-    /**
-     * keeps track of state for field: _showDistances
-     */
-    private boolean _has_showDistances;
-
-    /**
-     * Field _markUnlinked.
-     */
-    private boolean _markUnlinked;
-
-    /**
-     * keeps track of state for field: _markUnlinked
-     */
-    private boolean _has_markUnlinked;
-
-    /**
-     * Field _fitToWindow.
-     */
-    private boolean _fitToWindow;
-
-    /**
-     * keeps track of state for field: _fitToWindow
-     */
-    private boolean _has_fitToWindow;
-
-    /**
-     * Field _currentTree.
-     */
-    private boolean _currentTree;
-
-    /**
-     * keeps track of state for field: _currentTree
-     */
-    private boolean _has_currentTree;
-
-    /**
-     * Field _title.
-     */
-    private java.lang.String _title;
-
-    /**
-     * Field _newick.
-     */
-    private java.lang.String _newick;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Tree() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     */
-    public void deleteCurrentTree(
-    ) {
-        this._has_currentTree= false;
-    }
-
-    /**
-     */
-    public void deleteFitToWindow(
-    ) {
-        this._has_fitToWindow= false;
-    }
-
-    /**
-     */
-    public void deleteFontSize(
-    ) {
-        this._has_fontSize= false;
-    }
-
-    /**
-     */
-    public void deleteFontStyle(
-    ) {
-        this._has_fontStyle= false;
-    }
-
-    /**
-     */
-    public void deleteHeight(
-    ) {
-        this._has_height= false;
-    }
-
-    /**
-     */
-    public void deleteMarkUnlinked(
-    ) {
-        this._has_markUnlinked= false;
-    }
-
-    /**
-     */
-    public void deleteShowBootstrap(
-    ) {
-        this._has_showBootstrap= false;
-    }
-
-    /**
-     */
-    public void deleteShowDistances(
-    ) {
-        this._has_showDistances= false;
-    }
-
-    /**
-     */
-    public void deleteThreshold(
-    ) {
-        this._has_threshold= false;
-    }
-
-    /**
-     */
-    public void deleteWidth(
-    ) {
-        this._has_width= false;
-    }
-
-    /**
-     */
-    public void deleteXpos(
-    ) {
-        this._has_xpos= false;
-    }
-
-    /**
-     */
-    public void deleteYpos(
-    ) {
-        this._has_ypos= false;
-    }
-
-    /**
-     * Returns the value of field 'currentTree'.
-     * 
-     * @return the value of field 'CurrentTree'.
-     */
-    public boolean getCurrentTree(
-    ) {
-        return this._currentTree;
-    }
-
-    /**
-     * Returns the value of field 'fitToWindow'.
-     * 
-     * @return the value of field 'FitToWindow'.
-     */
-    public boolean getFitToWindow(
-    ) {
-        return this._fitToWindow;
-    }
-
-    /**
-     * Returns the value of field 'fontName'.
-     * 
-     * @return the value of field 'FontName'.
-     */
-    public java.lang.String getFontName(
-    ) {
-        return this._fontName;
-    }
-
-    /**
-     * Returns the value of field 'fontSize'.
-     * 
-     * @return the value of field 'FontSize'.
-     */
-    public int getFontSize(
-    ) {
-        return this._fontSize;
-    }
-
-    /**
-     * Returns the value of field 'fontStyle'.
-     * 
-     * @return the value of field 'FontStyle'.
-     */
-    public int getFontStyle(
-    ) {
-        return this._fontStyle;
-    }
-
-    /**
-     * Returns the value of field 'height'.
-     * 
-     * @return the value of field 'Height'.
-     */
-    public int getHeight(
-    ) {
-        return this._height;
-    }
-
-    /**
-     * Returns the value of field 'markUnlinked'.
-     * 
-     * @return the value of field 'MarkUnlinked'.
-     */
-    public boolean getMarkUnlinked(
-    ) {
-        return this._markUnlinked;
-    }
-
-    /**
-     * Returns the value of field 'newick'.
-     * 
-     * @return the value of field 'Newick'.
-     */
-    public java.lang.String getNewick(
-    ) {
-        return this._newick;
-    }
-
-    /**
-     * Returns the value of field 'showBootstrap'.
-     * 
-     * @return the value of field 'ShowBootstrap'.
-     */
-    public boolean getShowBootstrap(
-    ) {
-        return this._showBootstrap;
-    }
-
-    /**
-     * Returns the value of field 'showDistances'.
-     * 
-     * @return the value of field 'ShowDistances'.
-     */
-    public boolean getShowDistances(
-    ) {
-        return this._showDistances;
-    }
-
-    /**
-     * Returns the value of field 'threshold'.
-     * 
-     * @return the value of field 'Threshold'.
-     */
-    public float getThreshold(
-    ) {
-        return this._threshold;
-    }
-
-    /**
-     * Returns the value of field 'title'.
-     * 
-     * @return the value of field 'Title'.
-     */
-    public java.lang.String getTitle(
-    ) {
-        return this._title;
-    }
-
-    /**
-     * Returns the value of field 'width'.
-     * 
-     * @return the value of field 'Width'.
-     */
-    public int getWidth(
-    ) {
-        return this._width;
-    }
-
-    /**
-     * Returns the value of field 'xpos'.
-     * 
-     * @return the value of field 'Xpos'.
-     */
-    public int getXpos(
-    ) {
-        return this._xpos;
-    }
-
-    /**
-     * Returns the value of field 'ypos'.
-     * 
-     * @return the value of field 'Ypos'.
-     */
-    public int getYpos(
-    ) {
-        return this._ypos;
-    }
-
-    /**
-     * Method hasCurrentTree.
-     * 
-     * @return true if at least one CurrentTree has been added
-     */
-    public boolean hasCurrentTree(
-    ) {
-        return this._has_currentTree;
-    }
-
-    /**
-     * Method hasFitToWindow.
-     * 
-     * @return true if at least one FitToWindow has been added
-     */
-    public boolean hasFitToWindow(
-    ) {
-        return this._has_fitToWindow;
-    }
-
-    /**
-     * Method hasFontSize.
-     * 
-     * @return true if at least one FontSize has been added
-     */
-    public boolean hasFontSize(
-    ) {
-        return this._has_fontSize;
-    }
-
-    /**
-     * Method hasFontStyle.
-     * 
-     * @return true if at least one FontStyle has been added
-     */
-    public boolean hasFontStyle(
-    ) {
-        return this._has_fontStyle;
-    }
-
-    /**
-     * Method hasHeight.
-     * 
-     * @return true if at least one Height has been added
-     */
-    public boolean hasHeight(
-    ) {
-        return this._has_height;
-    }
-
-    /**
-     * Method hasMarkUnlinked.
-     * 
-     * @return true if at least one MarkUnlinked has been added
-     */
-    public boolean hasMarkUnlinked(
-    ) {
-        return this._has_markUnlinked;
-    }
-
-    /**
-     * Method hasShowBootstrap.
-     * 
-     * @return true if at least one ShowBootstrap has been added
-     */
-    public boolean hasShowBootstrap(
-    ) {
-        return this._has_showBootstrap;
-    }
-
-    /**
-     * Method hasShowDistances.
-     * 
-     * @return true if at least one ShowDistances has been added
-     */
-    public boolean hasShowDistances(
-    ) {
-        return this._has_showDistances;
-    }
-
-    /**
-     * Method hasThreshold.
-     * 
-     * @return true if at least one Threshold has been added
-     */
-    public boolean hasThreshold(
-    ) {
-        return this._has_threshold;
-    }
-
-    /**
-     * Method hasWidth.
-     * 
-     * @return true if at least one Width has been added
-     */
-    public boolean hasWidth(
-    ) {
-        return this._has_width;
-    }
-
-    /**
-     * Method hasXpos.
-     * 
-     * @return true if at least one Xpos has been added
-     */
-    public boolean hasXpos(
-    ) {
-        return this._has_xpos;
-    }
-
-    /**
-     * Method hasYpos.
-     * 
-     * @return true if at least one Ypos has been added
-     */
-    public boolean hasYpos(
-    ) {
-        return this._has_ypos;
-    }
-
-    /**
-     * Returns the value of field 'currentTree'.
-     * 
-     * @return the value of field 'CurrentTree'.
-     */
-    public boolean isCurrentTree(
-    ) {
-        return this._currentTree;
-    }
-
-    /**
-     * Returns the value of field 'fitToWindow'.
-     * 
-     * @return the value of field 'FitToWindow'.
-     */
-    public boolean isFitToWindow(
-    ) {
-        return this._fitToWindow;
-    }
-
-    /**
-     * Returns the value of field 'markUnlinked'.
-     * 
-     * @return the value of field 'MarkUnlinked'.
-     */
-    public boolean isMarkUnlinked(
-    ) {
-        return this._markUnlinked;
-    }
-
-    /**
-     * Returns the value of field 'showBootstrap'.
-     * 
-     * @return the value of field 'ShowBootstrap'.
-     */
-    public boolean isShowBootstrap(
-    ) {
-        return this._showBootstrap;
-    }
-
-    /**
-     * Returns the value of field 'showDistances'.
-     * 
-     * @return the value of field 'ShowDistances'.
-     */
-    public boolean isShowDistances(
-    ) {
-        return this._showDistances;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'currentTree'.
-     * 
-     * @param currentTree the value of field 'currentTree'.
-     */
-    public void setCurrentTree(
-            final boolean currentTree) {
-        this._currentTree = currentTree;
-        this._has_currentTree = true;
-    }
-
-    /**
-     * Sets the value of field 'fitToWindow'.
-     * 
-     * @param fitToWindow the value of field 'fitToWindow'.
-     */
-    public void setFitToWindow(
-            final boolean fitToWindow) {
-        this._fitToWindow = fitToWindow;
-        this._has_fitToWindow = true;
-    }
-
-    /**
-     * Sets the value of field 'fontName'.
-     * 
-     * @param fontName the value of field 'fontName'.
-     */
-    public void setFontName(
-            final java.lang.String fontName) {
-        this._fontName = fontName;
-    }
-
-    /**
-     * Sets the value of field 'fontSize'.
-     * 
-     * @param fontSize the value of field 'fontSize'.
-     */
-    public void setFontSize(
-            final int fontSize) {
-        this._fontSize = fontSize;
-        this._has_fontSize = true;
-    }
-
-    /**
-     * Sets the value of field 'fontStyle'.
-     * 
-     * @param fontStyle the value of field 'fontStyle'.
-     */
-    public void setFontStyle(
-            final int fontStyle) {
-        this._fontStyle = fontStyle;
-        this._has_fontStyle = true;
-    }
-
-    /**
-     * Sets the value of field 'height'.
-     * 
-     * @param height the value of field 'height'.
-     */
-    public void setHeight(
-            final int height) {
-        this._height = height;
-        this._has_height = true;
-    }
-
-    /**
-     * Sets the value of field 'markUnlinked'.
-     * 
-     * @param markUnlinked the value of field 'markUnlinked'.
-     */
-    public void setMarkUnlinked(
-            final boolean markUnlinked) {
-        this._markUnlinked = markUnlinked;
-        this._has_markUnlinked = true;
-    }
-
-    /**
-     * Sets the value of field 'newick'.
-     * 
-     * @param newick the value of field 'newick'.
-     */
-    public void setNewick(
-            final java.lang.String newick) {
-        this._newick = newick;
-    }
-
-    /**
-     * Sets the value of field 'showBootstrap'.
-     * 
-     * @param showBootstrap the value of field 'showBootstrap'.
-     */
-    public void setShowBootstrap(
-            final boolean showBootstrap) {
-        this._showBootstrap = showBootstrap;
-        this._has_showBootstrap = true;
-    }
-
-    /**
-     * Sets the value of field 'showDistances'.
-     * 
-     * @param showDistances the value of field 'showDistances'.
-     */
-    public void setShowDistances(
-            final boolean showDistances) {
-        this._showDistances = showDistances;
-        this._has_showDistances = true;
-    }
-
-    /**
-     * Sets the value of field 'threshold'.
-     * 
-     * @param threshold the value of field 'threshold'.
-     */
-    public void setThreshold(
-            final float threshold) {
-        this._threshold = threshold;
-        this._has_threshold = true;
-    }
-
-    /**
-     * Sets the value of field 'title'.
-     * 
-     * @param title the value of field 'title'.
-     */
-    public void setTitle(
-            final java.lang.String title) {
-        this._title = title;
-    }
-
-    /**
-     * Sets the value of field 'width'.
-     * 
-     * @param width the value of field 'width'.
-     */
-    public void setWidth(
-            final int width) {
-        this._width = width;
-        this._has_width = true;
-    }
-
-    /**
-     * Sets the value of field 'xpos'.
-     * 
-     * @param xpos the value of field 'xpos'.
-     */
-    public void setXpos(
-            final int xpos) {
-        this._xpos = xpos;
-        this._has_xpos = true;
-    }
-
-    /**
-     * Sets the value of field 'ypos'.
-     * 
-     * @param ypos the value of field 'ypos'.
-     */
-    public void setYpos(
-            final int ypos) {
-        this._ypos = ypos;
-        this._has_ypos = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.Tree
-     */
-    public static jalview.binding.Tree unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.Tree) Unmarshaller.unmarshal(jalview.binding.Tree.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+public class Tree implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _width.
+   */
+  private int _width;
+
+  /**
+   * keeps track of state for field: _width
+   */
+  private boolean _has_width;
+
+  /**
+   * Field _height.
+   */
+  private int _height;
+
+  /**
+   * keeps track of state for field: _height
+   */
+  private boolean _has_height;
+
+  /**
+   * Field _xpos.
+   */
+  private int _xpos;
+
+  /**
+   * keeps track of state for field: _xpos
+   */
+  private boolean _has_xpos;
+
+  /**
+   * Field _ypos.
+   */
+  private int _ypos;
+
+  /**
+   * keeps track of state for field: _ypos
+   */
+  private boolean _has_ypos;
+
+  /**
+   * Field _fontName.
+   */
+  private java.lang.String _fontName;
+
+  /**
+   * Field _fontSize.
+   */
+  private int _fontSize;
+
+  /**
+   * keeps track of state for field: _fontSize
+   */
+  private boolean _has_fontSize;
+
+  /**
+   * Field _fontStyle.
+   */
+  private int _fontStyle;
+
+  /**
+   * keeps track of state for field: _fontStyle
+   */
+  private boolean _has_fontStyle;
+
+  /**
+   * Field _threshold.
+   */
+  private float _threshold;
+
+  /**
+   * keeps track of state for field: _threshold
+   */
+  private boolean _has_threshold;
+
+  /**
+   * Field _showBootstrap.
+   */
+  private boolean _showBootstrap;
+
+  /**
+   * keeps track of state for field: _showBootstrap
+   */
+  private boolean _has_showBootstrap;
+
+  /**
+   * Field _showDistances.
+   */
+  private boolean _showDistances;
+
+  /**
+   * keeps track of state for field: _showDistances
+   */
+  private boolean _has_showDistances;
+
+  /**
+   * Field _markUnlinked.
+   */
+  private boolean _markUnlinked;
+
+  /**
+   * keeps track of state for field: _markUnlinked
+   */
+  private boolean _has_markUnlinked;
+
+  /**
+   * Field _fitToWindow.
+   */
+  private boolean _fitToWindow;
+
+  /**
+   * keeps track of state for field: _fitToWindow
+   */
+  private boolean _has_fitToWindow;
+
+  /**
+   * Field _currentTree.
+   */
+  private boolean _currentTree;
+
+  /**
+   * keeps track of state for field: _currentTree
+   */
+  private boolean _has_currentTree;
+
+  /**
+   * Field _title.
+   */
+  private java.lang.String _title;
+
+  /**
+   * Field _newick.
+   */
+  private java.lang.String _newick;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Tree()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   */
+  public void deleteCurrentTree()
+  {
+    this._has_currentTree = false;
+  }
+
+  /**
+   */
+  public void deleteFitToWindow()
+  {
+    this._has_fitToWindow = false;
+  }
+
+  /**
+   */
+  public void deleteFontSize()
+  {
+    this._has_fontSize = false;
+  }
+
+  /**
+   */
+  public void deleteFontStyle()
+  {
+    this._has_fontStyle = false;
+  }
+
+  /**
+   */
+  public void deleteHeight()
+  {
+    this._has_height = false;
+  }
+
+  /**
+   */
+  public void deleteMarkUnlinked()
+  {
+    this._has_markUnlinked = false;
+  }
+
+  /**
+   */
+  public void deleteShowBootstrap()
+  {
+    this._has_showBootstrap = false;
+  }
+
+  /**
+   */
+  public void deleteShowDistances()
+  {
+    this._has_showDistances = false;
+  }
+
+  /**
+   */
+  public void deleteThreshold()
+  {
+    this._has_threshold = false;
+  }
+
+  /**
+   */
+  public void deleteWidth()
+  {
+    this._has_width = false;
+  }
+
+  /**
+   */
+  public void deleteXpos()
+  {
+    this._has_xpos = false;
+  }
+
+  /**
+   */
+  public void deleteYpos()
+  {
+    this._has_ypos = false;
+  }
+
+  /**
+   * Returns the value of field 'currentTree'.
+   * 
+   * @return the value of field 'CurrentTree'.
+   */
+  public boolean getCurrentTree()
+  {
+    return this._currentTree;
+  }
+
+  /**
+   * Returns the value of field 'fitToWindow'.
+   * 
+   * @return the value of field 'FitToWindow'.
+   */
+  public boolean getFitToWindow()
+  {
+    return this._fitToWindow;
+  }
+
+  /**
+   * Returns the value of field 'fontName'.
+   * 
+   * @return the value of field 'FontName'.
+   */
+  public java.lang.String getFontName()
+  {
+    return this._fontName;
+  }
+
+  /**
+   * Returns the value of field 'fontSize'.
+   * 
+   * @return the value of field 'FontSize'.
+   */
+  public int getFontSize()
+  {
+    return this._fontSize;
+  }
+
+  /**
+   * Returns the value of field 'fontStyle'.
+   * 
+   * @return the value of field 'FontStyle'.
+   */
+  public int getFontStyle()
+  {
+    return this._fontStyle;
+  }
+
+  /**
+   * Returns the value of field 'height'.
+   * 
+   * @return the value of field 'Height'.
+   */
+  public int getHeight()
+  {
+    return this._height;
+  }
+
+  /**
+   * Returns the value of field 'markUnlinked'.
+   * 
+   * @return the value of field 'MarkUnlinked'.
+   */
+  public boolean getMarkUnlinked()
+  {
+    return this._markUnlinked;
+  }
+
+  /**
+   * Returns the value of field 'newick'.
+   * 
+   * @return the value of field 'Newick'.
+   */
+  public java.lang.String getNewick()
+  {
+    return this._newick;
+  }
+
+  /**
+   * Returns the value of field 'showBootstrap'.
+   * 
+   * @return the value of field 'ShowBootstrap'.
+   */
+  public boolean getShowBootstrap()
+  {
+    return this._showBootstrap;
+  }
+
+  /**
+   * Returns the value of field 'showDistances'.
+   * 
+   * @return the value of field 'ShowDistances'.
+   */
+  public boolean getShowDistances()
+  {
+    return this._showDistances;
+  }
+
+  /**
+   * Returns the value of field 'threshold'.
+   * 
+   * @return the value of field 'Threshold'.
+   */
+  public float getThreshold()
+  {
+    return this._threshold;
+  }
+
+  /**
+   * Returns the value of field 'title'.
+   * 
+   * @return the value of field 'Title'.
+   */
+  public java.lang.String getTitle()
+  {
+    return this._title;
+  }
+
+  /**
+   * Returns the value of field 'width'.
+   * 
+   * @return the value of field 'Width'.
+   */
+  public int getWidth()
+  {
+    return this._width;
+  }
+
+  /**
+   * Returns the value of field 'xpos'.
+   * 
+   * @return the value of field 'Xpos'.
+   */
+  public int getXpos()
+  {
+    return this._xpos;
+  }
+
+  /**
+   * Returns the value of field 'ypos'.
+   * 
+   * @return the value of field 'Ypos'.
+   */
+  public int getYpos()
+  {
+    return this._ypos;
+  }
+
+  /**
+   * Method hasCurrentTree.
+   * 
+   * @return true if at least one CurrentTree has been added
+   */
+  public boolean hasCurrentTree()
+  {
+    return this._has_currentTree;
+  }
+
+  /**
+   * Method hasFitToWindow.
+   * 
+   * @return true if at least one FitToWindow has been added
+   */
+  public boolean hasFitToWindow()
+  {
+    return this._has_fitToWindow;
+  }
+
+  /**
+   * Method hasFontSize.
+   * 
+   * @return true if at least one FontSize has been added
+   */
+  public boolean hasFontSize()
+  {
+    return this._has_fontSize;
+  }
+
+  /**
+   * Method hasFontStyle.
+   * 
+   * @return true if at least one FontStyle has been added
+   */
+  public boolean hasFontStyle()
+  {
+    return this._has_fontStyle;
+  }
+
+  /**
+   * Method hasHeight.
+   * 
+   * @return true if at least one Height has been added
+   */
+  public boolean hasHeight()
+  {
+    return this._has_height;
+  }
+
+  /**
+   * Method hasMarkUnlinked.
+   * 
+   * @return true if at least one MarkUnlinked has been added
+   */
+  public boolean hasMarkUnlinked()
+  {
+    return this._has_markUnlinked;
+  }
+
+  /**
+   * Method hasShowBootstrap.
+   * 
+   * @return true if at least one ShowBootstrap has been added
+   */
+  public boolean hasShowBootstrap()
+  {
+    return this._has_showBootstrap;
+  }
+
+  /**
+   * Method hasShowDistances.
+   * 
+   * @return true if at least one ShowDistances has been added
+   */
+  public boolean hasShowDistances()
+  {
+    return this._has_showDistances;
+  }
+
+  /**
+   * Method hasThreshold.
+   * 
+   * @return true if at least one Threshold has been added
+   */
+  public boolean hasThreshold()
+  {
+    return this._has_threshold;
+  }
+
+  /**
+   * Method hasWidth.
+   * 
+   * @return true if at least one Width has been added
+   */
+  public boolean hasWidth()
+  {
+    return this._has_width;
+  }
+
+  /**
+   * Method hasXpos.
+   * 
+   * @return true if at least one Xpos has been added
+   */
+  public boolean hasXpos()
+  {
+    return this._has_xpos;
+  }
+
+  /**
+   * Method hasYpos.
+   * 
+   * @return true if at least one Ypos has been added
+   */
+  public boolean hasYpos()
+  {
+    return this._has_ypos;
+  }
+
+  /**
+   * Returns the value of field 'currentTree'.
+   * 
+   * @return the value of field 'CurrentTree'.
+   */
+  public boolean isCurrentTree()
+  {
+    return this._currentTree;
+  }
+
+  /**
+   * Returns the value of field 'fitToWindow'.
+   * 
+   * @return the value of field 'FitToWindow'.
+   */
+  public boolean isFitToWindow()
+  {
+    return this._fitToWindow;
+  }
+
+  /**
+   * Returns the value of field 'markUnlinked'.
+   * 
+   * @return the value of field 'MarkUnlinked'.
+   */
+  public boolean isMarkUnlinked()
+  {
+    return this._markUnlinked;
+  }
+
+  /**
+   * Returns the value of field 'showBootstrap'.
+   * 
+   * @return the value of field 'ShowBootstrap'.
+   */
+  public boolean isShowBootstrap()
+  {
+    return this._showBootstrap;
+  }
+
+  /**
+   * Returns the value of field 'showDistances'.
+   * 
+   * @return the value of field 'ShowDistances'.
+   */
+  public boolean isShowDistances()
+  {
+    return this._showDistances;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'currentTree'.
+   * 
+   * @param currentTree
+   *                the value of field 'currentTree'.
+   */
+  public void setCurrentTree(final boolean currentTree)
+  {
+    this._currentTree = currentTree;
+    this._has_currentTree = true;
+  }
+
+  /**
+   * Sets the value of field 'fitToWindow'.
+   * 
+   * @param fitToWindow
+   *                the value of field 'fitToWindow'.
+   */
+  public void setFitToWindow(final boolean fitToWindow)
+  {
+    this._fitToWindow = fitToWindow;
+    this._has_fitToWindow = true;
+  }
+
+  /**
+   * Sets the value of field 'fontName'.
+   * 
+   * @param fontName
+   *                the value of field 'fontName'.
+   */
+  public void setFontName(final java.lang.String fontName)
+  {
+    this._fontName = fontName;
+  }
+
+  /**
+   * Sets the value of field 'fontSize'.
+   * 
+   * @param fontSize
+   *                the value of field 'fontSize'.
+   */
+  public void setFontSize(final int fontSize)
+  {
+    this._fontSize = fontSize;
+    this._has_fontSize = true;
+  }
+
+  /**
+   * Sets the value of field 'fontStyle'.
+   * 
+   * @param fontStyle
+   *                the value of field 'fontStyle'.
+   */
+  public void setFontStyle(final int fontStyle)
+  {
+    this._fontStyle = fontStyle;
+    this._has_fontStyle = true;
+  }
+
+  /**
+   * Sets the value of field 'height'.
+   * 
+   * @param height
+   *                the value of field 'height'.
+   */
+  public void setHeight(final int height)
+  {
+    this._height = height;
+    this._has_height = true;
+  }
+
+  /**
+   * Sets the value of field 'markUnlinked'.
+   * 
+   * @param markUnlinked
+   *                the value of field 'markUnlinked'.
+   */
+  public void setMarkUnlinked(final boolean markUnlinked)
+  {
+    this._markUnlinked = markUnlinked;
+    this._has_markUnlinked = true;
+  }
+
+  /**
+   * Sets the value of field 'newick'.
+   * 
+   * @param newick
+   *                the value of field 'newick'.
+   */
+  public void setNewick(final java.lang.String newick)
+  {
+    this._newick = newick;
+  }
+
+  /**
+   * Sets the value of field 'showBootstrap'.
+   * 
+   * @param showBootstrap
+   *                the value of field 'showBootstrap'.
+   */
+  public void setShowBootstrap(final boolean showBootstrap)
+  {
+    this._showBootstrap = showBootstrap;
+    this._has_showBootstrap = true;
+  }
+
+  /**
+   * Sets the value of field 'showDistances'.
+   * 
+   * @param showDistances
+   *                the value of field 'showDistances'.
+   */
+  public void setShowDistances(final boolean showDistances)
+  {
+    this._showDistances = showDistances;
+    this._has_showDistances = true;
+  }
+
+  /**
+   * Sets the value of field 'threshold'.
+   * 
+   * @param threshold
+   *                the value of field 'threshold'.
+   */
+  public void setThreshold(final float threshold)
+  {
+    this._threshold = threshold;
+    this._has_threshold = true;
+  }
+
+  /**
+   * Sets the value of field 'title'.
+   * 
+   * @param title
+   *                the value of field 'title'.
+   */
+  public void setTitle(final java.lang.String title)
+  {
+    this._title = title;
+  }
+
+  /**
+   * Sets the value of field 'width'.
+   * 
+   * @param width
+   *                the value of field 'width'.
+   */
+  public void setWidth(final int width)
+  {
+    this._width = width;
+    this._has_width = true;
+  }
+
+  /**
+   * Sets the value of field 'xpos'.
+   * 
+   * @param xpos
+   *                the value of field 'xpos'.
+   */
+  public void setXpos(final int xpos)
+  {
+    this._xpos = xpos;
+    this._has_xpos = true;
+  }
+
+  /**
+   * Sets the value of field 'ypos'.
+   * 
+   * @param ypos
+   *                the value of field 'ypos'.
+   */
+  public void setYpos(final int ypos)
+  {
+    this._ypos = ypos;
+    this._has_ypos = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.binding.Tree
+   */
+  public static jalview.binding.Tree unmarshal(final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.Tree) Unmarshaller.unmarshal(
+            jalview.binding.Tree.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/UserColourScheme.java b/src/jalview/binding/UserColourScheme.java
index 24c97ff..2002137 100755
--- a/src/jalview/binding/UserColourScheme.java
+++ b/src/jalview/binding/UserColourScheme.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,98 +30,111 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class UserColourScheme extends JalviewUserColours 
-implements java.io.Serializable
+public class UserColourScheme extends JalviewUserColours implements
+        java.io.Serializable
 {
 
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
 
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public UserColourScheme() {
-        super();
-    }
+  public UserColourScheme()
+  {
+    super();
+  }
 
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
 
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
 
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
 
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.JalviewUserColours
-     */
-    public static jalview.binding.JalviewUserColours unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(jalview.binding.UserColourScheme.class, reader);
-    }
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.binding.JalviewUserColours
+   */
+  public static jalview.binding.JalviewUserColours unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(
+            jalview.binding.UserColourScheme.class, reader);
+  }
 
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/UserColours.java b/src/jalview/binding/UserColours.java
index bdefe05..467904a 100755
--- a/src/jalview/binding/UserColours.java
+++ b/src/jalview/binding/UserColours.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,151 +30,167 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class UserColours implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _id.
-     */
-    private java.lang.String _id;
-
-    /**
-     * Field _userColourScheme.
-     */
-    private jalview.binding.UserColourScheme _userColourScheme;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public UserColours() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'id'.
-     * 
-     * @return the value of field 'Id'.
-     */
-    public java.lang.String getId(
-    ) {
-        return this._id;
-    }
-
-    /**
-     * Returns the value of field 'userColourScheme'.
-     * 
-     * @return the value of field 'UserColourScheme'.
-     */
-    public jalview.binding.UserColourScheme getUserColourScheme(
-    ) {
-        return this._userColourScheme;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'id'.
-     * 
-     * @param id the value of field 'id'.
-     */
-    public void setId(
-            final java.lang.String id) {
-        this._id = id;
-    }
-
-    /**
-     * Sets the value of field 'userColourScheme'.
-     * 
-     * @param userColourScheme the value of field 'userColourScheme'
-     */
-    public void setUserColourScheme(
-            final jalview.binding.UserColourScheme userColourScheme) {
-        this._userColourScheme = userColourScheme;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.UserColours
-     */
-    public static jalview.binding.UserColours unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.UserColours) Unmarshaller.unmarshal(jalview.binding.UserColours.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class UserColours implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _id.
+   */
+  private java.lang.String _id;
+
+  /**
+   * Field _userColourScheme.
+   */
+  private jalview.binding.UserColourScheme _userColourScheme;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public UserColours()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Returns the value of field 'id'.
+   * 
+   * @return the value of field 'Id'.
+   */
+  public java.lang.String getId()
+  {
+    return this._id;
+  }
+
+  /**
+   * Returns the value of field 'userColourScheme'.
+   * 
+   * @return the value of field 'UserColourScheme'.
+   */
+  public jalview.binding.UserColourScheme getUserColourScheme()
+  {
+    return this._userColourScheme;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'id'.
+   * 
+   * @param id
+   *                the value of field 'id'.
+   */
+  public void setId(final java.lang.String id)
+  {
+    this._id = id;
+  }
+
+  /**
+   * Sets the value of field 'userColourScheme'.
+   * 
+   * @param userColourScheme
+   *                the value of field 'userColourScheme'
+   */
+  public void setUserColourScheme(
+          final jalview.binding.UserColourScheme userColourScheme)
+  {
+    this._userColourScheme = userColourScheme;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.binding.UserColours
+   */
+  public static jalview.binding.UserColours unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.UserColours) Unmarshaller.unmarshal(
+            jalview.binding.UserColours.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/VAMSAS.java b/src/jalview/binding/VAMSAS.java
index 1c92bd3..b886fb9 100755
--- a/src/jalview/binding/VAMSAS.java
+++ b/src/jalview/binding/VAMSAS.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,563 +30,588 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class VAMSAS implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _alignmentList.
-     */
-    private java.util.Vector _alignmentList;
-
-    /**
-     * Field _treeList.
-     */
-    private java.util.Vector _treeList;
-
-    /**
-     * Field _sequenceSetList.
-     */
-    private java.util.Vector _sequenceSetList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public VAMSAS() {
-        super();
-        this._alignmentList = new java.util.Vector();
-        this._treeList = new java.util.Vector();
-        this._sequenceSetList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vAlignment
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addAlignment(
-            final Alignment vAlignment)
-    throws java.lang.IndexOutOfBoundsException {
-        this._alignmentList.addElement(vAlignment);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vAlignment
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addAlignment(
-            final int index,
-            final Alignment vAlignment)
-    throws java.lang.IndexOutOfBoundsException {
-        this._alignmentList.add(index, vAlignment);
-    }
-
-    /**
-     * 
-     * 
-     * @param vSequenceSet
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSequenceSet(
-            final SequenceSet vSequenceSet)
-    throws java.lang.IndexOutOfBoundsException {
-        this._sequenceSetList.addElement(vSequenceSet);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSequenceSet
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSequenceSet(
-            final int index,
-            final SequenceSet vSequenceSet)
-    throws java.lang.IndexOutOfBoundsException {
-        this._sequenceSetList.add(index, vSequenceSet);
-    }
-
-    /**
-     * 
-     * 
-     * @param vTree
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addTree(
-            final java.lang.String vTree)
-    throws java.lang.IndexOutOfBoundsException {
-        this._treeList.addElement(vTree);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vTree
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addTree(
-            final int index,
-            final java.lang.String vTree)
-    throws java.lang.IndexOutOfBoundsException {
-        this._treeList.add(index, vTree);
-    }
-
-    /**
-     * Method enumerateAlignment.
-     * 
-     * @return an Enumeration over all Alignment elements
-     */
-    public java.util.Enumeration enumerateAlignment(
-    ) {
-        return this._alignmentList.elements();
-    }
-
-    /**
-     * Method enumerateSequenceSet.
-     * 
-     * @return an Enumeration over all SequenceSet elements
-     */
-    public java.util.Enumeration enumerateSequenceSet(
-    ) {
-        return this._sequenceSetList.elements();
-    }
-
-    /**
-     * Method enumerateTree.
-     * 
-     * @return an Enumeration over all java.lang.String elements
-     */
-    public java.util.Enumeration enumerateTree(
-    ) {
-        return this._treeList.elements();
-    }
-
-    /**
-     * Method getAlignment.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the Alignment at the given index
-     */
-    public Alignment getAlignment(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._alignmentList.size()) {
-            throw new IndexOutOfBoundsException("getAlignment: Index value '" + index + "' not in range [0.." + (this._alignmentList.size() - 1) + "]");
-        }
-        
-        return (Alignment) _alignmentList.get(index);
-    }
-
-    /**
-     * Method getAlignment.Returns the contents of the collection
-     * in an Array.  <p>Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we <i>know</i>
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public Alignment[] getAlignment(
-    ) {
-        Alignment[] array = new Alignment[0];
-        return (Alignment[]) this._alignmentList.toArray(array);
-    }
-
-    /**
-     * Method getAlignmentCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getAlignmentCount(
-    ) {
-        return this._alignmentList.size();
-    }
-
-    /**
-     * Method getSequenceSet.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the SequenceSet at the given index
-     */
-    public SequenceSet getSequenceSet(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._sequenceSetList.size()) {
-            throw new IndexOutOfBoundsException("getSequenceSet: Index value '" + index + "' not in range [0.." + (this._sequenceSetList.size() - 1) + "]");
-        }
-        
-        return (SequenceSet) _sequenceSetList.get(index);
-    }
-
-    /**
-     * Method getSequenceSet.Returns the contents of the collection
-     * in an Array.  <p>Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we <i>know</i>
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public SequenceSet[] getSequenceSet(
-    ) {
-        SequenceSet[] array = new SequenceSet[0];
-        return (SequenceSet[]) this._sequenceSetList.toArray(array);
-    }
-
-    /**
-     * Method getSequenceSetCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getSequenceSetCount(
-    ) {
-        return this._sequenceSetList.size();
-    }
-
-    /**
-     * Method getTree.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the java.lang.String at the given index
-     */
-    public java.lang.String getTree(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._treeList.size()) {
-            throw new IndexOutOfBoundsException("getTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
-        }
-        
-        return (java.lang.String) _treeList.get(index);
-    }
-
-    /**
-     * Method getTree.Returns the contents of the collection in an
-     * Array.  <p>Note:  Just in case the collection contents are
-     * changing in another thread, we pass a 0-length Array of the
-     * correct type into the API call.  This way we <i>know</i>
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public java.lang.String[] getTree(
-    ) {
-        java.lang.String[] array = new java.lang.String[0];
-        return (java.lang.String[]) this._treeList.toArray(array);
-    }
-
-    /**
-     * Method getTreeCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getTreeCount(
-    ) {
-        return this._treeList.size();
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Method removeAlignment.
-     * 
-     * @param vAlignment
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeAlignment(
-            final Alignment vAlignment) {
-        boolean removed = _alignmentList.remove(vAlignment);
-        return removed;
-    }
-
-    /**
-     * Method removeAlignmentAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public Alignment removeAlignmentAt(
-            final int index) {
-        java.lang.Object obj = this._alignmentList.remove(index);
-        return (Alignment) obj;
-    }
-
-    /**
-     */
-    public void removeAllAlignment(
-    ) {
-        this._alignmentList.clear();
-    }
-
-    /**
-     */
-    public void removeAllSequenceSet(
-    ) {
-        this._sequenceSetList.clear();
-    }
-
-    /**
-     */
-    public void removeAllTree(
-    ) {
-        this._treeList.clear();
-    }
-
-    /**
-     * Method removeSequenceSet.
-     * 
-     * @param vSequenceSet
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeSequenceSet(
-            final SequenceSet vSequenceSet) {
-        boolean removed = _sequenceSetList.remove(vSequenceSet);
-        return removed;
-    }
-
-    /**
-     * Method removeSequenceSetAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public SequenceSet removeSequenceSetAt(
-            final int index) {
-        java.lang.Object obj = this._sequenceSetList.remove(index);
-        return (SequenceSet) obj;
-    }
-
-    /**
-     * Method removeTree.
-     * 
-     * @param vTree
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeTree(
-            final java.lang.String vTree) {
-        boolean removed = _treeList.remove(vTree);
-        return removed;
-    }
-
-    /**
-     * Method removeTreeAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public java.lang.String removeTreeAt(
-            final int index) {
-        java.lang.Object obj = this._treeList.remove(index);
-        return (java.lang.String) obj;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vAlignment
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setAlignment(
-            final int index,
-            final Alignment vAlignment)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._alignmentList.size()) {
-            throw new IndexOutOfBoundsException("setAlignment: Index value '" + index + "' not in range [0.." + (this._alignmentList.size() - 1) + "]");
-        }
-        
-        this._alignmentList.set(index, vAlignment);
-    }
-
-    /**
-     * 
-     * 
-     * @param vAlignmentArray
-     */
-    public void setAlignment(
-            final Alignment[] vAlignmentArray) {
-        //-- copy array
-        _alignmentList.clear();
-        
-        for (int i = 0; i < vAlignmentArray.length; i++) {
-                this._alignmentList.add(vAlignmentArray[i]);
-        }
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSequenceSet
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setSequenceSet(
-            final int index,
-            final SequenceSet vSequenceSet)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._sequenceSetList.size()) {
-            throw new IndexOutOfBoundsException("setSequenceSet: Index value '" + index + "' not in range [0.." + (this._sequenceSetList.size() - 1) + "]");
-        }
-        
-        this._sequenceSetList.set(index, vSequenceSet);
-    }
-
-    /**
-     * 
-     * 
-     * @param vSequenceSetArray
-     */
-    public void setSequenceSet(
-            final SequenceSet[] vSequenceSetArray) {
-        //-- copy array
-        _sequenceSetList.clear();
-        
-        for (int i = 0; i < vSequenceSetArray.length; i++) {
-                this._sequenceSetList.add(vSequenceSetArray[i]);
-        }
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vTree
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setTree(
-            final int index,
-            final java.lang.String vTree)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._treeList.size()) {
-            throw new IndexOutOfBoundsException("setTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
-        }
-        
-        this._treeList.set(index, vTree);
-    }
-
-    /**
-     * 
-     * 
-     * @param vTreeArray
-     */
-    public void setTree(
-            final java.lang.String[] vTreeArray) {
-        //-- copy array
-        _treeList.clear();
-        
-        for (int i = 0; i < vTreeArray.length; i++) {
-                this._treeList.add(vTreeArray[i]);
-        }
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.VAMSAS
-     */
-    public static jalview.binding.VAMSAS unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(jalview.binding.VAMSAS.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+public class VAMSAS implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _alignmentList.
+   */
+  private java.util.Vector _alignmentList;
+
+  /**
+   * Field _treeList.
+   */
+  private java.util.Vector _treeList;
+
+  /**
+   * Field _sequenceSetList.
+   */
+  private java.util.Vector _sequenceSetList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public VAMSAS()
+  {
+    super();
+    this._alignmentList = new java.util.Vector();
+    this._treeList = new java.util.Vector();
+    this._sequenceSetList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vAlignment
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addAlignment(final Alignment vAlignment)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._alignmentList.addElement(vAlignment);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAlignment
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addAlignment(final int index, final Alignment vAlignment)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._alignmentList.add(index, vAlignment);
+  }
+
+  /**
+   * 
+   * 
+   * @param vSequenceSet
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addSequenceSet(final SequenceSet vSequenceSet)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._sequenceSetList.addElement(vSequenceSet);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSequenceSet
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addSequenceSet(final int index, final SequenceSet vSequenceSet)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._sequenceSetList.add(index, vSequenceSet);
+  }
+
+  /**
+   * 
+   * 
+   * @param vTree
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addTree(final java.lang.String vTree)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._treeList.addElement(vTree);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vTree
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addTree(final int index, final java.lang.String vTree)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._treeList.add(index, vTree);
+  }
+
+  /**
+   * Method enumerateAlignment.
+   * 
+   * @return an Enumeration over all Alignment elements
+   */
+  public java.util.Enumeration enumerateAlignment()
+  {
+    return this._alignmentList.elements();
+  }
+
+  /**
+   * Method enumerateSequenceSet.
+   * 
+   * @return an Enumeration over all SequenceSet elements
+   */
+  public java.util.Enumeration enumerateSequenceSet()
+  {
+    return this._sequenceSetList.elements();
+  }
+
+  /**
+   * Method enumerateTree.
+   * 
+   * @return an Enumeration over all java.lang.String elements
+   */
+  public java.util.Enumeration enumerateTree()
+  {
+    return this._treeList.elements();
+  }
+
+  /**
+   * Method getAlignment.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the Alignment at the given index
+   */
+  public Alignment getAlignment(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._alignmentList.size())
+    {
+      throw new IndexOutOfBoundsException("getAlignment: Index value '"
+              + index + "' not in range [0.."
+              + (this._alignmentList.size() - 1) + "]");
+    }
+
+    return (Alignment) _alignmentList.get(index);
+  }
+
+  /**
+   * Method getAlignment.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public Alignment[] getAlignment()
+  {
+    Alignment[] array = new Alignment[0];
+    return (Alignment[]) this._alignmentList.toArray(array);
+  }
+
+  /**
+   * Method getAlignmentCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getAlignmentCount()
+  {
+    return this._alignmentList.size();
+  }
+
+  /**
+   * Method getSequenceSet.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the SequenceSet at the given index
+   */
+  public SequenceSet getSequenceSet(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._sequenceSetList.size())
+    {
+      throw new IndexOutOfBoundsException("getSequenceSet: Index value '"
+              + index + "' not in range [0.."
+              + (this._sequenceSetList.size() - 1) + "]");
+    }
+
+    return (SequenceSet) _sequenceSetList.get(index);
+  }
+
+  /**
+   * Method getSequenceSet.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public SequenceSet[] getSequenceSet()
+  {
+    SequenceSet[] array = new SequenceSet[0];
+    return (SequenceSet[]) this._sequenceSetList.toArray(array);
+  }
+
+  /**
+   * Method getSequenceSetCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getSequenceSetCount()
+  {
+    return this._sequenceSetList.size();
+  }
+
+  /**
+   * Method getTree.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the java.lang.String at the given index
+   */
+  public java.lang.String getTree(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._treeList.size())
+    {
+      throw new IndexOutOfBoundsException("getTree: Index value '" + index
+              + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+    }
+
+    return (java.lang.String) _treeList.get(index);
+  }
+
+  /**
+   * Method getTree.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public java.lang.String[] getTree()
+  {
+    java.lang.String[] array = new java.lang.String[0];
+    return (java.lang.String[]) this._treeList.toArray(array);
+  }
+
+  /**
+   * Method getTreeCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getTreeCount()
+  {
+    return this._treeList.size();
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Method removeAlignment.
+   * 
+   * @param vAlignment
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeAlignment(final Alignment vAlignment)
+  {
+    boolean removed = _alignmentList.remove(vAlignment);
+    return removed;
+  }
+
+  /**
+   * Method removeAlignmentAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public Alignment removeAlignmentAt(final int index)
+  {
+    java.lang.Object obj = this._alignmentList.remove(index);
+    return (Alignment) obj;
+  }
+
+  /**
+   */
+  public void removeAllAlignment()
+  {
+    this._alignmentList.clear();
+  }
+
+  /**
+   */
+  public void removeAllSequenceSet()
+  {
+    this._sequenceSetList.clear();
+  }
+
+  /**
+   */
+  public void removeAllTree()
+  {
+    this._treeList.clear();
+  }
+
+  /**
+   * Method removeSequenceSet.
+   * 
+   * @param vSequenceSet
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeSequenceSet(final SequenceSet vSequenceSet)
+  {
+    boolean removed = _sequenceSetList.remove(vSequenceSet);
+    return removed;
+  }
+
+  /**
+   * Method removeSequenceSetAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public SequenceSet removeSequenceSetAt(final int index)
+  {
+    java.lang.Object obj = this._sequenceSetList.remove(index);
+    return (SequenceSet) obj;
+  }
+
+  /**
+   * Method removeTree.
+   * 
+   * @param vTree
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeTree(final java.lang.String vTree)
+  {
+    boolean removed = _treeList.remove(vTree);
+    return removed;
+  }
+
+  /**
+   * Method removeTreeAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public java.lang.String removeTreeAt(final int index)
+  {
+    java.lang.Object obj = this._treeList.remove(index);
+    return (java.lang.String) obj;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAlignment
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setAlignment(final int index, final Alignment vAlignment)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._alignmentList.size())
+    {
+      throw new IndexOutOfBoundsException("setAlignment: Index value '"
+              + index + "' not in range [0.."
+              + (this._alignmentList.size() - 1) + "]");
+    }
+
+    this._alignmentList.set(index, vAlignment);
+  }
+
+  /**
+   * 
+   * 
+   * @param vAlignmentArray
+   */
+  public void setAlignment(final Alignment[] vAlignmentArray)
+  {
+    // -- copy array
+    _alignmentList.clear();
+
+    for (int i = 0; i < vAlignmentArray.length; i++)
+    {
+      this._alignmentList.add(vAlignmentArray[i]);
+    }
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSequenceSet
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setSequenceSet(final int index, final SequenceSet vSequenceSet)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._sequenceSetList.size())
+    {
+      throw new IndexOutOfBoundsException("setSequenceSet: Index value '"
+              + index + "' not in range [0.."
+              + (this._sequenceSetList.size() - 1) + "]");
+    }
+
+    this._sequenceSetList.set(index, vSequenceSet);
+  }
+
+  /**
+   * 
+   * 
+   * @param vSequenceSetArray
+   */
+  public void setSequenceSet(final SequenceSet[] vSequenceSetArray)
+  {
+    // -- copy array
+    _sequenceSetList.clear();
+
+    for (int i = 0; i < vSequenceSetArray.length; i++)
+    {
+      this._sequenceSetList.add(vSequenceSetArray[i]);
+    }
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vTree
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setTree(final int index, final java.lang.String vTree)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._treeList.size())
+    {
+      throw new IndexOutOfBoundsException("setTree: Index value '" + index
+              + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+    }
+
+    this._treeList.set(index, vTree);
+  }
+
+  /**
+   * 
+   * 
+   * @param vTreeArray
+   */
+  public void setTree(final java.lang.String[] vTreeArray)
+  {
+    // -- copy array
+    _treeList.clear();
+
+    for (int i = 0; i < vTreeArray.length; i++)
+    {
+      this._treeList.add(vTreeArray[i]);
+    }
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.binding.VAMSAS
+   */
+  public static jalview.binding.VAMSAS unmarshal(final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(
+            jalview.binding.VAMSAS.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/VamsasModel.java b/src/jalview/binding/VamsasModel.java
index 5fda35e..f44a964 100755
--- a/src/jalview/binding/VamsasModel.java
+++ b/src/jalview/binding/VamsasModel.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,98 +30,109 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class VamsasModel extends VAMSAS 
-implements java.io.Serializable
+public class VamsasModel extends VAMSAS implements java.io.Serializable
 {
 
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
 
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public VamsasModel() {
-        super();
-    }
+  public VamsasModel()
+  {
+    super();
+  }
 
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
 
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
 
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
 
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.VAMSAS
-     */
-    public static jalview.binding.VAMSAS unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(jalview.binding.VamsasModel.class, reader);
-    }
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.binding.VAMSAS
+   */
+  public static jalview.binding.VAMSAS unmarshal(final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(
+            jalview.binding.VamsasModel.class, reader);
+  }
 
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/Viewport.java b/src/jalview/binding/Viewport.java
index 643c323..95b8adf 100755
--- a/src/jalview/binding/Viewport.java
+++ b/src/jalview/binding/Viewport.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,1414 +30,1449 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Viewport implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _conservationSelected.
-     */
-    private boolean _conservationSelected;
-
-    /**
-     * keeps track of state for field: _conservationSelected
-     */
-    private boolean _has_conservationSelected;
-
-    /**
-     * Field _pidSelected.
-     */
-    private boolean _pidSelected;
-
-    /**
-     * keeps track of state for field: _pidSelected
-     */
-    private boolean _has_pidSelected;
-
-    /**
-     * Field _bgColour.
-     */
-    private java.lang.String _bgColour;
-
-    /**
-     * Field _consThreshold.
-     */
-    private int _consThreshold;
-
-    /**
-     * keeps track of state for field: _consThreshold
-     */
-    private boolean _has_consThreshold;
-
-    /**
-     * Field _pidThreshold.
-     */
-    private int _pidThreshold;
-
-    /**
-     * keeps track of state for field: _pidThreshold
-     */
-    private boolean _has_pidThreshold;
-
-    /**
-     * Field _title.
-     */
-    private java.lang.String _title;
-
-    /**
-     * Field _showFullId.
-     */
-    private boolean _showFullId;
-
-    /**
-     * keeps track of state for field: _showFullId
-     */
-    private boolean _has_showFullId;
-
-    /**
-     * Field _showText.
-     */
-    private boolean _showText;
-
-    /**
-     * keeps track of state for field: _showText
-     */
-    private boolean _has_showText;
-
-    /**
-     * Field _showColourText.
-     */
-    private boolean _showColourText;
-
-    /**
-     * keeps track of state for field: _showColourText
-     */
-    private boolean _has_showColourText;
-
-    /**
-     * Field _showBoxes.
-     */
-    private boolean _showBoxes;
-
-    /**
-     * keeps track of state for field: _showBoxes
-     */
-    private boolean _has_showBoxes;
-
-    /**
-     * Field _wrapAlignment.
-     */
-    private boolean _wrapAlignment;
-
-    /**
-     * keeps track of state for field: _wrapAlignment
-     */
-    private boolean _has_wrapAlignment;
-
-    /**
-     * Field _renderGaps.
-     */
-    private boolean _renderGaps;
-
-    /**
-     * keeps track of state for field: _renderGaps
-     */
-    private boolean _has_renderGaps;
-
-    /**
-     * Field _showSequenceFeatures.
-     */
-    private boolean _showSequenceFeatures;
-
-    /**
-     * keeps track of state for field: _showSequenceFeatures
-     */
-    private boolean _has_showSequenceFeatures;
-
-    /**
-     * Field _showAnnotation.
-     */
-    private boolean _showAnnotation;
-
-    /**
-     * keeps track of state for field: _showAnnotation
-     */
-    private boolean _has_showAnnotation;
-
-    /**
-     * Field _showConservation.
-     */
-    private boolean _showConservation;
-
-    /**
-     * keeps track of state for field: _showConservation
-     */
-    private boolean _has_showConservation;
-
-    /**
-     * Field _showQuality.
-     */
-    private boolean _showQuality;
-
-    /**
-     * keeps track of state for field: _showQuality
-     */
-    private boolean _has_showQuality;
-
-    /**
-     * Field _showIdentity.
-     */
-    private boolean _showIdentity;
-
-    /**
-     * keeps track of state for field: _showIdentity
-     */
-    private boolean _has_showIdentity;
-
-    /**
-     * Field _xpos.
-     */
-    private int _xpos;
-
-    /**
-     * keeps track of state for field: _xpos
-     */
-    private boolean _has_xpos;
-
-    /**
-     * Field _ypos.
-     */
-    private int _ypos;
-
-    /**
-     * keeps track of state for field: _ypos
-     */
-    private boolean _has_ypos;
-
-    /**
-     * Field _width.
-     */
-    private int _width;
-
-    /**
-     * keeps track of state for field: _width
-     */
-    private boolean _has_width;
-
-    /**
-     * Field _height.
-     */
-    private int _height;
-
-    /**
-     * keeps track of state for field: _height
-     */
-    private boolean _has_height;
-
-    /**
-     * Field _startRes.
-     */
-    private int _startRes;
-
-    /**
-     * keeps track of state for field: _startRes
-     */
-    private boolean _has_startRes;
-
-    /**
-     * Field _startSeq.
-     */
-    private int _startSeq;
-
-    /**
-     * keeps track of state for field: _startSeq
-     */
-    private boolean _has_startSeq;
-
-    /**
-     * Field _fontName.
-     */
-    private java.lang.String _fontName;
-
-    /**
-     * Field _fontSize.
-     */
-    private int _fontSize;
-
-    /**
-     * keeps track of state for field: _fontSize
-     */
-    private boolean _has_fontSize;
-
-    /**
-     * Field _fontStyle.
-     */
-    private int _fontStyle;
-
-    /**
-     * keeps track of state for field: _fontStyle
-     */
-    private boolean _has_fontStyle;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Viewport() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     */
-    public void deleteConsThreshold(
-    ) {
-        this._has_consThreshold= false;
-    }
-
-    /**
-     */
-    public void deleteConservationSelected(
-    ) {
-        this._has_conservationSelected= false;
-    }
-
-    /**
-     */
-    public void deleteFontSize(
-    ) {
-        this._has_fontSize= false;
-    }
-
-    /**
-     */
-    public void deleteFontStyle(
-    ) {
-        this._has_fontStyle= false;
-    }
-
-    /**
-     */
-    public void deleteHeight(
-    ) {
-        this._has_height= false;
-    }
-
-    /**
-     */
-    public void deletePidSelected(
-    ) {
-        this._has_pidSelected= false;
-    }
-
-    /**
-     */
-    public void deletePidThreshold(
-    ) {
-        this._has_pidThreshold= false;
-    }
-
-    /**
-     */
-    public void deleteRenderGaps(
-    ) {
-        this._has_renderGaps= false;
-    }
-
-    /**
-     */
-    public void deleteShowAnnotation(
-    ) {
-        this._has_showAnnotation= false;
-    }
-
-    /**
-     */
-    public void deleteShowBoxes(
-    ) {
-        this._has_showBoxes= false;
-    }
-
-    /**
-     */
-    public void deleteShowColourText(
-    ) {
-        this._has_showColourText= false;
-    }
-
-    /**
-     */
-    public void deleteShowConservation(
-    ) {
-        this._has_showConservation= false;
-    }
-
-    /**
-     */
-    public void deleteShowFullId(
-    ) {
-        this._has_showFullId= false;
-    }
-
-    /**
-     */
-    public void deleteShowIdentity(
-    ) {
-        this._has_showIdentity= false;
-    }
-
-    /**
-     */
-    public void deleteShowQuality(
-    ) {
-        this._has_showQuality= false;
-    }
-
-    /**
-     */
-    public void deleteShowSequenceFeatures(
-    ) {
-        this._has_showSequenceFeatures= false;
-    }
-
-    /**
-     */
-    public void deleteShowText(
-    ) {
-        this._has_showText= false;
-    }
-
-    /**
-     */
-    public void deleteStartRes(
-    ) {
-        this._has_startRes= false;
-    }
-
-    /**
-     */
-    public void deleteStartSeq(
-    ) {
-        this._has_startSeq= false;
-    }
-
-    /**
-     */
-    public void deleteWidth(
-    ) {
-        this._has_width= false;
-    }
-
-    /**
-     */
-    public void deleteWrapAlignment(
-    ) {
-        this._has_wrapAlignment= false;
-    }
-
-    /**
-     */
-    public void deleteXpos(
-    ) {
-        this._has_xpos= false;
-    }
-
-    /**
-     */
-    public void deleteYpos(
-    ) {
-        this._has_ypos= false;
-    }
-
-    /**
-     * Returns the value of field 'bgColour'.
-     * 
-     * @return the value of field 'BgColour'.
-     */
-    public java.lang.String getBgColour(
-    ) {
-        return this._bgColour;
-    }
-
-    /**
-     * Returns the value of field 'consThreshold'.
-     * 
-     * @return the value of field 'ConsThreshold'.
-     */
-    public int getConsThreshold(
-    ) {
-        return this._consThreshold;
-    }
-
-    /**
-     * Returns the value of field 'conservationSelected'.
-     * 
-     * @return the value of field 'ConservationSelected'.
-     */
-    public boolean getConservationSelected(
-    ) {
-        return this._conservationSelected;
-    }
-
-    /**
-     * Returns the value of field 'fontName'.
-     * 
-     * @return the value of field 'FontName'.
-     */
-    public java.lang.String getFontName(
-    ) {
-        return this._fontName;
-    }
-
-    /**
-     * Returns the value of field 'fontSize'.
-     * 
-     * @return the value of field 'FontSize'.
-     */
-    public int getFontSize(
-    ) {
-        return this._fontSize;
-    }
-
-    /**
-     * Returns the value of field 'fontStyle'.
-     * 
-     * @return the value of field 'FontStyle'.
-     */
-    public int getFontStyle(
-    ) {
-        return this._fontStyle;
-    }
-
-    /**
-     * Returns the value of field 'height'.
-     * 
-     * @return the value of field 'Height'.
-     */
-    public int getHeight(
-    ) {
-        return this._height;
-    }
-
-    /**
-     * Returns the value of field 'pidSelected'.
-     * 
-     * @return the value of field 'PidSelected'.
-     */
-    public boolean getPidSelected(
-    ) {
-        return this._pidSelected;
-    }
-
-    /**
-     * Returns the value of field 'pidThreshold'.
-     * 
-     * @return the value of field 'PidThreshold'.
-     */
-    public int getPidThreshold(
-    ) {
-        return this._pidThreshold;
-    }
-
-    /**
-     * Returns the value of field 'renderGaps'.
-     * 
-     * @return the value of field 'RenderGaps'.
-     */
-    public boolean getRenderGaps(
-    ) {
-        return this._renderGaps;
-    }
-
-    /**
-     * Returns the value of field 'showAnnotation'.
-     * 
-     * @return the value of field 'ShowAnnotation'.
-     */
-    public boolean getShowAnnotation(
-    ) {
-        return this._showAnnotation;
-    }
-
-    /**
-     * Returns the value of field 'showBoxes'.
-     * 
-     * @return the value of field 'ShowBoxes'.
-     */
-    public boolean getShowBoxes(
-    ) {
-        return this._showBoxes;
-    }
-
-    /**
-     * Returns the value of field 'showColourText'.
-     * 
-     * @return the value of field 'ShowColourText'.
-     */
-    public boolean getShowColourText(
-    ) {
-        return this._showColourText;
-    }
-
-    /**
-     * Returns the value of field 'showConservation'.
-     * 
-     * @return the value of field 'ShowConservation'.
-     */
-    public boolean getShowConservation(
-    ) {
-        return this._showConservation;
-    }
-
-    /**
-     * Returns the value of field 'showFullId'.
-     * 
-     * @return the value of field 'ShowFullId'.
-     */
-    public boolean getShowFullId(
-    ) {
-        return this._showFullId;
-    }
-
-    /**
-     * Returns the value of field 'showIdentity'.
-     * 
-     * @return the value of field 'ShowIdentity'.
-     */
-    public boolean getShowIdentity(
-    ) {
-        return this._showIdentity;
-    }
-
-    /**
-     * Returns the value of field 'showQuality'.
-     * 
-     * @return the value of field 'ShowQuality'.
-     */
-    public boolean getShowQuality(
-    ) {
-        return this._showQuality;
-    }
-
-    /**
-     * Returns the value of field 'showSequenceFeatures'.
-     * 
-     * @return the value of field 'ShowSequenceFeatures'.
-     */
-    public boolean getShowSequenceFeatures(
-    ) {
-        return this._showSequenceFeatures;
-    }
-
-    /**
-     * Returns the value of field 'showText'.
-     * 
-     * @return the value of field 'ShowText'.
-     */
-    public boolean getShowText(
-    ) {
-        return this._showText;
-    }
-
-    /**
-     * Returns the value of field 'startRes'.
-     * 
-     * @return the value of field 'StartRes'.
-     */
-    public int getStartRes(
-    ) {
-        return this._startRes;
-    }
-
-    /**
-     * Returns the value of field 'startSeq'.
-     * 
-     * @return the value of field 'StartSeq'.
-     */
-    public int getStartSeq(
-    ) {
-        return this._startSeq;
-    }
-
-    /**
-     * Returns the value of field 'title'.
-     * 
-     * @return the value of field 'Title'.
-     */
-    public java.lang.String getTitle(
-    ) {
-        return this._title;
-    }
-
-    /**
-     * Returns the value of field 'width'.
-     * 
-     * @return the value of field 'Width'.
-     */
-    public int getWidth(
-    ) {
-        return this._width;
-    }
-
-    /**
-     * Returns the value of field 'wrapAlignment'.
-     * 
-     * @return the value of field 'WrapAlignment'.
-     */
-    public boolean getWrapAlignment(
-    ) {
-        return this._wrapAlignment;
-    }
-
-    /**
-     * Returns the value of field 'xpos'.
-     * 
-     * @return the value of field 'Xpos'.
-     */
-    public int getXpos(
-    ) {
-        return this._xpos;
-    }
-
-    /**
-     * Returns the value of field 'ypos'.
-     * 
-     * @return the value of field 'Ypos'.
-     */
-    public int getYpos(
-    ) {
-        return this._ypos;
-    }
-
-    /**
-     * Method hasConsThreshold.
-     * 
-     * @return true if at least one ConsThreshold has been added
-     */
-    public boolean hasConsThreshold(
-    ) {
-        return this._has_consThreshold;
-    }
-
-    /**
-     * Method hasConservationSelected.
-     * 
-     * @return true if at least one ConservationSelected has been
-     * added
-     */
-    public boolean hasConservationSelected(
-    ) {
-        return this._has_conservationSelected;
-    }
-
-    /**
-     * Method hasFontSize.
-     * 
-     * @return true if at least one FontSize has been added
-     */
-    public boolean hasFontSize(
-    ) {
-        return this._has_fontSize;
-    }
-
-    /**
-     * Method hasFontStyle.
-     * 
-     * @return true if at least one FontStyle has been added
-     */
-    public boolean hasFontStyle(
-    ) {
-        return this._has_fontStyle;
-    }
-
-    /**
-     * Method hasHeight.
-     * 
-     * @return true if at least one Height has been added
-     */
-    public boolean hasHeight(
-    ) {
-        return this._has_height;
-    }
-
-    /**
-     * Method hasPidSelected.
-     * 
-     * @return true if at least one PidSelected has been added
-     */
-    public boolean hasPidSelected(
-    ) {
-        return this._has_pidSelected;
-    }
-
-    /**
-     * Method hasPidThreshold.
-     * 
-     * @return true if at least one PidThreshold has been added
-     */
-    public boolean hasPidThreshold(
-    ) {
-        return this._has_pidThreshold;
-    }
-
-    /**
-     * Method hasRenderGaps.
-     * 
-     * @return true if at least one RenderGaps has been added
-     */
-    public boolean hasRenderGaps(
-    ) {
-        return this._has_renderGaps;
-    }
-
-    /**
-     * Method hasShowAnnotation.
-     * 
-     * @return true if at least one ShowAnnotation has been added
-     */
-    public boolean hasShowAnnotation(
-    ) {
-        return this._has_showAnnotation;
-    }
-
-    /**
-     * Method hasShowBoxes.
-     * 
-     * @return true if at least one ShowBoxes has been added
-     */
-    public boolean hasShowBoxes(
-    ) {
-        return this._has_showBoxes;
-    }
-
-    /**
-     * Method hasShowColourText.
-     * 
-     * @return true if at least one ShowColourText has been added
-     */
-    public boolean hasShowColourText(
-    ) {
-        return this._has_showColourText;
-    }
-
-    /**
-     * Method hasShowConservation.
-     * 
-     * @return true if at least one ShowConservation has been added
-     */
-    public boolean hasShowConservation(
-    ) {
-        return this._has_showConservation;
-    }
-
-    /**
-     * Method hasShowFullId.
-     * 
-     * @return true if at least one ShowFullId has been added
-     */
-    public boolean hasShowFullId(
-    ) {
-        return this._has_showFullId;
-    }
-
-    /**
-     * Method hasShowIdentity.
-     * 
-     * @return true if at least one ShowIdentity has been added
-     */
-    public boolean hasShowIdentity(
-    ) {
-        return this._has_showIdentity;
-    }
-
-    /**
-     * Method hasShowQuality.
-     * 
-     * @return true if at least one ShowQuality has been added
-     */
-    public boolean hasShowQuality(
-    ) {
-        return this._has_showQuality;
-    }
-
-    /**
-     * Method hasShowSequenceFeatures.
-     * 
-     * @return true if at least one ShowSequenceFeatures has been
-     * added
-     */
-    public boolean hasShowSequenceFeatures(
-    ) {
-        return this._has_showSequenceFeatures;
-    }
-
-    /**
-     * Method hasShowText.
-     * 
-     * @return true if at least one ShowText has been added
-     */
-    public boolean hasShowText(
-    ) {
-        return this._has_showText;
-    }
-
-    /**
-     * Method hasStartRes.
-     * 
-     * @return true if at least one StartRes has been added
-     */
-    public boolean hasStartRes(
-    ) {
-        return this._has_startRes;
-    }
-
-    /**
-     * Method hasStartSeq.
-     * 
-     * @return true if at least one StartSeq has been added
-     */
-    public boolean hasStartSeq(
-    ) {
-        return this._has_startSeq;
-    }
-
-    /**
-     * Method hasWidth.
-     * 
-     * @return true if at least one Width has been added
-     */
-    public boolean hasWidth(
-    ) {
-        return this._has_width;
-    }
-
-    /**
-     * Method hasWrapAlignment.
-     * 
-     * @return true if at least one WrapAlignment has been added
-     */
-    public boolean hasWrapAlignment(
-    ) {
-        return this._has_wrapAlignment;
-    }
-
-    /**
-     * Method hasXpos.
-     * 
-     * @return true if at least one Xpos has been added
-     */
-    public boolean hasXpos(
-    ) {
-        return this._has_xpos;
-    }
-
-    /**
-     * Method hasYpos.
-     * 
-     * @return true if at least one Ypos has been added
-     */
-    public boolean hasYpos(
-    ) {
-        return this._has_ypos;
-    }
-
-    /**
-     * Returns the value of field 'conservationSelected'.
-     * 
-     * @return the value of field 'ConservationSelected'.
-     */
-    public boolean isConservationSelected(
-    ) {
-        return this._conservationSelected;
-    }
-
-    /**
-     * Returns the value of field 'pidSelected'.
-     * 
-     * @return the value of field 'PidSelected'.
-     */
-    public boolean isPidSelected(
-    ) {
-        return this._pidSelected;
-    }
-
-    /**
-     * Returns the value of field 'renderGaps'.
-     * 
-     * @return the value of field 'RenderGaps'.
-     */
-    public boolean isRenderGaps(
-    ) {
-        return this._renderGaps;
-    }
-
-    /**
-     * Returns the value of field 'showAnnotation'.
-     * 
-     * @return the value of field 'ShowAnnotation'.
-     */
-    public boolean isShowAnnotation(
-    ) {
-        return this._showAnnotation;
-    }
-
-    /**
-     * Returns the value of field 'showBoxes'.
-     * 
-     * @return the value of field 'ShowBoxes'.
-     */
-    public boolean isShowBoxes(
-    ) {
-        return this._showBoxes;
-    }
-
-    /**
-     * Returns the value of field 'showColourText'.
-     * 
-     * @return the value of field 'ShowColourText'.
-     */
-    public boolean isShowColourText(
-    ) {
-        return this._showColourText;
-    }
-
-    /**
-     * Returns the value of field 'showConservation'.
-     * 
-     * @return the value of field 'ShowConservation'.
-     */
-    public boolean isShowConservation(
-    ) {
-        return this._showConservation;
-    }
-
-    /**
-     * Returns the value of field 'showFullId'.
-     * 
-     * @return the value of field 'ShowFullId'.
-     */
-    public boolean isShowFullId(
-    ) {
-        return this._showFullId;
-    }
-
-    /**
-     * Returns the value of field 'showIdentity'.
-     * 
-     * @return the value of field 'ShowIdentity'.
-     */
-    public boolean isShowIdentity(
-    ) {
-        return this._showIdentity;
-    }
-
-    /**
-     * Returns the value of field 'showQuality'.
-     * 
-     * @return the value of field 'ShowQuality'.
-     */
-    public boolean isShowQuality(
-    ) {
-        return this._showQuality;
-    }
-
-    /**
-     * Returns the value of field 'showSequenceFeatures'.
-     * 
-     * @return the value of field 'ShowSequenceFeatures'.
-     */
-    public boolean isShowSequenceFeatures(
-    ) {
-        return this._showSequenceFeatures;
-    }
-
-    /**
-     * Returns the value of field 'showText'.
-     * 
-     * @return the value of field 'ShowText'.
-     */
-    public boolean isShowText(
-    ) {
-        return this._showText;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * Returns the value of field 'wrapAlignment'.
-     * 
-     * @return the value of field 'WrapAlignment'.
-     */
-    public boolean isWrapAlignment(
-    ) {
-        return this._wrapAlignment;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'bgColour'.
-     * 
-     * @param bgColour the value of field 'bgColour'.
-     */
-    public void setBgColour(
-            final java.lang.String bgColour) {
-        this._bgColour = bgColour;
-    }
-
-    /**
-     * Sets the value of field 'consThreshold'.
-     * 
-     * @param consThreshold the value of field 'consThreshold'.
-     */
-    public void setConsThreshold(
-            final int consThreshold) {
-        this._consThreshold = consThreshold;
-        this._has_consThreshold = true;
-    }
-
-    /**
-     * Sets the value of field 'conservationSelected'.
-     * 
-     * @param conservationSelected the value of field
-     * 'conservationSelected'.
-     */
-    public void setConservationSelected(
-            final boolean conservationSelected) {
-        this._conservationSelected = conservationSelected;
-        this._has_conservationSelected = true;
-    }
-
-    /**
-     * Sets the value of field 'fontName'.
-     * 
-     * @param fontName the value of field 'fontName'.
-     */
-    public void setFontName(
-            final java.lang.String fontName) {
-        this._fontName = fontName;
-    }
-
-    /**
-     * Sets the value of field 'fontSize'.
-     * 
-     * @param fontSize the value of field 'fontSize'.
-     */
-    public void setFontSize(
-            final int fontSize) {
-        this._fontSize = fontSize;
-        this._has_fontSize = true;
-    }
-
-    /**
-     * Sets the value of field 'fontStyle'.
-     * 
-     * @param fontStyle the value of field 'fontStyle'.
-     */
-    public void setFontStyle(
-            final int fontStyle) {
-        this._fontStyle = fontStyle;
-        this._has_fontStyle = true;
-    }
-
-    /**
-     * Sets the value of field 'height'.
-     * 
-     * @param height the value of field 'height'.
-     */
-    public void setHeight(
-            final int height) {
-        this._height = height;
-        this._has_height = true;
-    }
-
-    /**
-     * Sets the value of field 'pidSelected'.
-     * 
-     * @param pidSelected the value of field 'pidSelected'.
-     */
-    public void setPidSelected(
-            final boolean pidSelected) {
-        this._pidSelected = pidSelected;
-        this._has_pidSelected = true;
-    }
-
-    /**
-     * Sets the value of field 'pidThreshold'.
-     * 
-     * @param pidThreshold the value of field 'pidThreshold'.
-     */
-    public void setPidThreshold(
-            final int pidThreshold) {
-        this._pidThreshold = pidThreshold;
-        this._has_pidThreshold = true;
-    }
-
-    /**
-     * Sets the value of field 'renderGaps'.
-     * 
-     * @param renderGaps the value of field 'renderGaps'.
-     */
-    public void setRenderGaps(
-            final boolean renderGaps) {
-        this._renderGaps = renderGaps;
-        this._has_renderGaps = true;
-    }
-
-    /**
-     * Sets the value of field 'showAnnotation'.
-     * 
-     * @param showAnnotation the value of field 'showAnnotation'.
-     */
-    public void setShowAnnotation(
-            final boolean showAnnotation) {
-        this._showAnnotation = showAnnotation;
-        this._has_showAnnotation = true;
-    }
-
-    /**
-     * Sets the value of field 'showBoxes'.
-     * 
-     * @param showBoxes the value of field 'showBoxes'.
-     */
-    public void setShowBoxes(
-            final boolean showBoxes) {
-        this._showBoxes = showBoxes;
-        this._has_showBoxes = true;
-    }
-
-    /**
-     * Sets the value of field 'showColourText'.
-     * 
-     * @param showColourText the value of field 'showColourText'.
-     */
-    public void setShowColourText(
-            final boolean showColourText) {
-        this._showColourText = showColourText;
-        this._has_showColourText = true;
-    }
-
-    /**
-     * Sets the value of field 'showConservation'.
-     * 
-     * @param showConservation the value of field 'showConservation'
-     */
-    public void setShowConservation(
-            final boolean showConservation) {
-        this._showConservation = showConservation;
-        this._has_showConservation = true;
-    }
-
-    /**
-     * Sets the value of field 'showFullId'.
-     * 
-     * @param showFullId the value of field 'showFullId'.
-     */
-    public void setShowFullId(
-            final boolean showFullId) {
-        this._showFullId = showFullId;
-        this._has_showFullId = true;
-    }
-
-    /**
-     * Sets the value of field 'showIdentity'.
-     * 
-     * @param showIdentity the value of field 'showIdentity'.
-     */
-    public void setShowIdentity(
-            final boolean showIdentity) {
-        this._showIdentity = showIdentity;
-        this._has_showIdentity = true;
-    }
-
-    /**
-     * Sets the value of field 'showQuality'.
-     * 
-     * @param showQuality the value of field 'showQuality'.
-     */
-    public void setShowQuality(
-            final boolean showQuality) {
-        this._showQuality = showQuality;
-        this._has_showQuality = true;
-    }
-
-    /**
-     * Sets the value of field 'showSequenceFeatures'.
-     * 
-     * @param showSequenceFeatures the value of field
-     * 'showSequenceFeatures'.
-     */
-    public void setShowSequenceFeatures(
-            final boolean showSequenceFeatures) {
-        this._showSequenceFeatures = showSequenceFeatures;
-        this._has_showSequenceFeatures = true;
-    }
-
-    /**
-     * Sets the value of field 'showText'.
-     * 
-     * @param showText the value of field 'showText'.
-     */
-    public void setShowText(
-            final boolean showText) {
-        this._showText = showText;
-        this._has_showText = true;
-    }
-
-    /**
-     * Sets the value of field 'startRes'.
-     * 
-     * @param startRes the value of field 'startRes'.
-     */
-    public void setStartRes(
-            final int startRes) {
-        this._startRes = startRes;
-        this._has_startRes = true;
-    }
-
-    /**
-     * Sets the value of field 'startSeq'.
-     * 
-     * @param startSeq the value of field 'startSeq'.
-     */
-    public void setStartSeq(
-            final int startSeq) {
-        this._startSeq = startSeq;
-        this._has_startSeq = true;
-    }
-
-    /**
-     * Sets the value of field 'title'.
-     * 
-     * @param title the value of field 'title'.
-     */
-    public void setTitle(
-            final java.lang.String title) {
-        this._title = title;
-    }
-
-    /**
-     * Sets the value of field 'width'.
-     * 
-     * @param width the value of field 'width'.
-     */
-    public void setWidth(
-            final int width) {
-        this._width = width;
-        this._has_width = true;
-    }
-
-    /**
-     * Sets the value of field 'wrapAlignment'.
-     * 
-     * @param wrapAlignment the value of field 'wrapAlignment'.
-     */
-    public void setWrapAlignment(
-            final boolean wrapAlignment) {
-        this._wrapAlignment = wrapAlignment;
-        this._has_wrapAlignment = true;
-    }
-
-    /**
-     * Sets the value of field 'xpos'.
-     * 
-     * @param xpos the value of field 'xpos'.
-     */
-    public void setXpos(
-            final int xpos) {
-        this._xpos = xpos;
-        this._has_xpos = true;
-    }
-
-    /**
-     * Sets the value of field 'ypos'.
-     * 
-     * @param ypos the value of field 'ypos'.
-     */
-    public void setYpos(
-            final int ypos) {
-        this._ypos = ypos;
-        this._has_ypos = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.Viewport
-     */
-    public static jalview.binding.Viewport unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.Viewport) Unmarshaller.unmarshal(jalview.binding.Viewport.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+public class Viewport implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _conservationSelected.
+   */
+  private boolean _conservationSelected;
+
+  /**
+   * keeps track of state for field: _conservationSelected
+   */
+  private boolean _has_conservationSelected;
+
+  /**
+   * Field _pidSelected.
+   */
+  private boolean _pidSelected;
+
+  /**
+   * keeps track of state for field: _pidSelected
+   */
+  private boolean _has_pidSelected;
+
+  /**
+   * Field _bgColour.
+   */
+  private java.lang.String _bgColour;
+
+  /**
+   * Field _consThreshold.
+   */
+  private int _consThreshold;
+
+  /**
+   * keeps track of state for field: _consThreshold
+   */
+  private boolean _has_consThreshold;
+
+  /**
+   * Field _pidThreshold.
+   */
+  private int _pidThreshold;
+
+  /**
+   * keeps track of state for field: _pidThreshold
+   */
+  private boolean _has_pidThreshold;
+
+  /**
+   * Field _title.
+   */
+  private java.lang.String _title;
+
+  /**
+   * Field _showFullId.
+   */
+  private boolean _showFullId;
+
+  /**
+   * keeps track of state for field: _showFullId
+   */
+  private boolean _has_showFullId;
+
+  /**
+   * Field _showText.
+   */
+  private boolean _showText;
+
+  /**
+   * keeps track of state for field: _showText
+   */
+  private boolean _has_showText;
+
+  /**
+   * Field _showColourText.
+   */
+  private boolean _showColourText;
+
+  /**
+   * keeps track of state for field: _showColourText
+   */
+  private boolean _has_showColourText;
+
+  /**
+   * Field _showBoxes.
+   */
+  private boolean _showBoxes;
+
+  /**
+   * keeps track of state for field: _showBoxes
+   */
+  private boolean _has_showBoxes;
+
+  /**
+   * Field _wrapAlignment.
+   */
+  private boolean _wrapAlignment;
+
+  /**
+   * keeps track of state for field: _wrapAlignment
+   */
+  private boolean _has_wrapAlignment;
+
+  /**
+   * Field _renderGaps.
+   */
+  private boolean _renderGaps;
+
+  /**
+   * keeps track of state for field: _renderGaps
+   */
+  private boolean _has_renderGaps;
+
+  /**
+   * Field _showSequenceFeatures.
+   */
+  private boolean _showSequenceFeatures;
+
+  /**
+   * keeps track of state for field: _showSequenceFeatures
+   */
+  private boolean _has_showSequenceFeatures;
+
+  /**
+   * Field _showAnnotation.
+   */
+  private boolean _showAnnotation;
+
+  /**
+   * keeps track of state for field: _showAnnotation
+   */
+  private boolean _has_showAnnotation;
+
+  /**
+   * Field _showConservation.
+   */
+  private boolean _showConservation;
+
+  /**
+   * keeps track of state for field: _showConservation
+   */
+  private boolean _has_showConservation;
+
+  /**
+   * Field _showQuality.
+   */
+  private boolean _showQuality;
+
+  /**
+   * keeps track of state for field: _showQuality
+   */
+  private boolean _has_showQuality;
+
+  /**
+   * Field _showIdentity.
+   */
+  private boolean _showIdentity;
+
+  /**
+   * keeps track of state for field: _showIdentity
+   */
+  private boolean _has_showIdentity;
+
+  /**
+   * Field _xpos.
+   */
+  private int _xpos;
+
+  /**
+   * keeps track of state for field: _xpos
+   */
+  private boolean _has_xpos;
+
+  /**
+   * Field _ypos.
+   */
+  private int _ypos;
+
+  /**
+   * keeps track of state for field: _ypos
+   */
+  private boolean _has_ypos;
+
+  /**
+   * Field _width.
+   */
+  private int _width;
+
+  /**
+   * keeps track of state for field: _width
+   */
+  private boolean _has_width;
+
+  /**
+   * Field _height.
+   */
+  private int _height;
+
+  /**
+   * keeps track of state for field: _height
+   */
+  private boolean _has_height;
+
+  /**
+   * Field _startRes.
+   */
+  private int _startRes;
+
+  /**
+   * keeps track of state for field: _startRes
+   */
+  private boolean _has_startRes;
+
+  /**
+   * Field _startSeq.
+   */
+  private int _startSeq;
+
+  /**
+   * keeps track of state for field: _startSeq
+   */
+  private boolean _has_startSeq;
+
+  /**
+   * Field _fontName.
+   */
+  private java.lang.String _fontName;
+
+  /**
+   * Field _fontSize.
+   */
+  private int _fontSize;
+
+  /**
+   * keeps track of state for field: _fontSize
+   */
+  private boolean _has_fontSize;
+
+  /**
+   * Field _fontStyle.
+   */
+  private int _fontStyle;
+
+  /**
+   * keeps track of state for field: _fontStyle
+   */
+  private boolean _has_fontStyle;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Viewport()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   */
+  public void deleteConsThreshold()
+  {
+    this._has_consThreshold = false;
+  }
+
+  /**
+   */
+  public void deleteConservationSelected()
+  {
+    this._has_conservationSelected = false;
+  }
+
+  /**
+   */
+  public void deleteFontSize()
+  {
+    this._has_fontSize = false;
+  }
+
+  /**
+   */
+  public void deleteFontStyle()
+  {
+    this._has_fontStyle = false;
+  }
+
+  /**
+   */
+  public void deleteHeight()
+  {
+    this._has_height = false;
+  }
+
+  /**
+   */
+  public void deletePidSelected()
+  {
+    this._has_pidSelected = false;
+  }
+
+  /**
+   */
+  public void deletePidThreshold()
+  {
+    this._has_pidThreshold = false;
+  }
+
+  /**
+   */
+  public void deleteRenderGaps()
+  {
+    this._has_renderGaps = false;
+  }
+
+  /**
+   */
+  public void deleteShowAnnotation()
+  {
+    this._has_showAnnotation = false;
+  }
+
+  /**
+   */
+  public void deleteShowBoxes()
+  {
+    this._has_showBoxes = false;
+  }
+
+  /**
+   */
+  public void deleteShowColourText()
+  {
+    this._has_showColourText = false;
+  }
+
+  /**
+   */
+  public void deleteShowConservation()
+  {
+    this._has_showConservation = false;
+  }
+
+  /**
+   */
+  public void deleteShowFullId()
+  {
+    this._has_showFullId = false;
+  }
+
+  /**
+   */
+  public void deleteShowIdentity()
+  {
+    this._has_showIdentity = false;
+  }
+
+  /**
+   */
+  public void deleteShowQuality()
+  {
+    this._has_showQuality = false;
+  }
+
+  /**
+   */
+  public void deleteShowSequenceFeatures()
+  {
+    this._has_showSequenceFeatures = false;
+  }
+
+  /**
+   */
+  public void deleteShowText()
+  {
+    this._has_showText = false;
+  }
+
+  /**
+   */
+  public void deleteStartRes()
+  {
+    this._has_startRes = false;
+  }
+
+  /**
+   */
+  public void deleteStartSeq()
+  {
+    this._has_startSeq = false;
+  }
+
+  /**
+   */
+  public void deleteWidth()
+  {
+    this._has_width = false;
+  }
+
+  /**
+   */
+  public void deleteWrapAlignment()
+  {
+    this._has_wrapAlignment = false;
+  }
+
+  /**
+   */
+  public void deleteXpos()
+  {
+    this._has_xpos = false;
+  }
+
+  /**
+   */
+  public void deleteYpos()
+  {
+    this._has_ypos = false;
+  }
+
+  /**
+   * Returns the value of field 'bgColour'.
+   * 
+   * @return the value of field 'BgColour'.
+   */
+  public java.lang.String getBgColour()
+  {
+    return this._bgColour;
+  }
+
+  /**
+   * Returns the value of field 'consThreshold'.
+   * 
+   * @return the value of field 'ConsThreshold'.
+   */
+  public int getConsThreshold()
+  {
+    return this._consThreshold;
+  }
+
+  /**
+   * Returns the value of field 'conservationSelected'.
+   * 
+   * @return the value of field 'ConservationSelected'.
+   */
+  public boolean getConservationSelected()
+  {
+    return this._conservationSelected;
+  }
+
+  /**
+   * Returns the value of field 'fontName'.
+   * 
+   * @return the value of field 'FontName'.
+   */
+  public java.lang.String getFontName()
+  {
+    return this._fontName;
+  }
+
+  /**
+   * Returns the value of field 'fontSize'.
+   * 
+   * @return the value of field 'FontSize'.
+   */
+  public int getFontSize()
+  {
+    return this._fontSize;
+  }
+
+  /**
+   * Returns the value of field 'fontStyle'.
+   * 
+   * @return the value of field 'FontStyle'.
+   */
+  public int getFontStyle()
+  {
+    return this._fontStyle;
+  }
+
+  /**
+   * Returns the value of field 'height'.
+   * 
+   * @return the value of field 'Height'.
+   */
+  public int getHeight()
+  {
+    return this._height;
+  }
+
+  /**
+   * Returns the value of field 'pidSelected'.
+   * 
+   * @return the value of field 'PidSelected'.
+   */
+  public boolean getPidSelected()
+  {
+    return this._pidSelected;
+  }
+
+  /**
+   * Returns the value of field 'pidThreshold'.
+   * 
+   * @return the value of field 'PidThreshold'.
+   */
+  public int getPidThreshold()
+  {
+    return this._pidThreshold;
+  }
+
+  /**
+   * Returns the value of field 'renderGaps'.
+   * 
+   * @return the value of field 'RenderGaps'.
+   */
+  public boolean getRenderGaps()
+  {
+    return this._renderGaps;
+  }
+
+  /**
+   * Returns the value of field 'showAnnotation'.
+   * 
+   * @return the value of field 'ShowAnnotation'.
+   */
+  public boolean getShowAnnotation()
+  {
+    return this._showAnnotation;
+  }
+
+  /**
+   * Returns the value of field 'showBoxes'.
+   * 
+   * @return the value of field 'ShowBoxes'.
+   */
+  public boolean getShowBoxes()
+  {
+    return this._showBoxes;
+  }
+
+  /**
+   * Returns the value of field 'showColourText'.
+   * 
+   * @return the value of field 'ShowColourText'.
+   */
+  public boolean getShowColourText()
+  {
+    return this._showColourText;
+  }
+
+  /**
+   * Returns the value of field 'showConservation'.
+   * 
+   * @return the value of field 'ShowConservation'.
+   */
+  public boolean getShowConservation()
+  {
+    return this._showConservation;
+  }
+
+  /**
+   * Returns the value of field 'showFullId'.
+   * 
+   * @return the value of field 'ShowFullId'.
+   */
+  public boolean getShowFullId()
+  {
+    return this._showFullId;
+  }
+
+  /**
+   * Returns the value of field 'showIdentity'.
+   * 
+   * @return the value of field 'ShowIdentity'.
+   */
+  public boolean getShowIdentity()
+  {
+    return this._showIdentity;
+  }
+
+  /**
+   * Returns the value of field 'showQuality'.
+   * 
+   * @return the value of field 'ShowQuality'.
+   */
+  public boolean getShowQuality()
+  {
+    return this._showQuality;
+  }
+
+  /**
+   * Returns the value of field 'showSequenceFeatures'.
+   * 
+   * @return the value of field 'ShowSequenceFeatures'.
+   */
+  public boolean getShowSequenceFeatures()
+  {
+    return this._showSequenceFeatures;
+  }
+
+  /**
+   * Returns the value of field 'showText'.
+   * 
+   * @return the value of field 'ShowText'.
+   */
+  public boolean getShowText()
+  {
+    return this._showText;
+  }
+
+  /**
+   * Returns the value of field 'startRes'.
+   * 
+   * @return the value of field 'StartRes'.
+   */
+  public int getStartRes()
+  {
+    return this._startRes;
+  }
+
+  /**
+   * Returns the value of field 'startSeq'.
+   * 
+   * @return the value of field 'StartSeq'.
+   */
+  public int getStartSeq()
+  {
+    return this._startSeq;
+  }
+
+  /**
+   * Returns the value of field 'title'.
+   * 
+   * @return the value of field 'Title'.
+   */
+  public java.lang.String getTitle()
+  {
+    return this._title;
+  }
+
+  /**
+   * Returns the value of field 'width'.
+   * 
+   * @return the value of field 'Width'.
+   */
+  public int getWidth()
+  {
+    return this._width;
+  }
+
+  /**
+   * Returns the value of field 'wrapAlignment'.
+   * 
+   * @return the value of field 'WrapAlignment'.
+   */
+  public boolean getWrapAlignment()
+  {
+    return this._wrapAlignment;
+  }
+
+  /**
+   * Returns the value of field 'xpos'.
+   * 
+   * @return the value of field 'Xpos'.
+   */
+  public int getXpos()
+  {
+    return this._xpos;
+  }
+
+  /**
+   * Returns the value of field 'ypos'.
+   * 
+   * @return the value of field 'Ypos'.
+   */
+  public int getYpos()
+  {
+    return this._ypos;
+  }
+
+  /**
+   * Method hasConsThreshold.
+   * 
+   * @return true if at least one ConsThreshold has been added
+   */
+  public boolean hasConsThreshold()
+  {
+    return this._has_consThreshold;
+  }
+
+  /**
+   * Method hasConservationSelected.
+   * 
+   * @return true if at least one ConservationSelected has been added
+   */
+  public boolean hasConservationSelected()
+  {
+    return this._has_conservationSelected;
+  }
+
+  /**
+   * Method hasFontSize.
+   * 
+   * @return true if at least one FontSize has been added
+   */
+  public boolean hasFontSize()
+  {
+    return this._has_fontSize;
+  }
+
+  /**
+   * Method hasFontStyle.
+   * 
+   * @return true if at least one FontStyle has been added
+   */
+  public boolean hasFontStyle()
+  {
+    return this._has_fontStyle;
+  }
+
+  /**
+   * Method hasHeight.
+   * 
+   * @return true if at least one Height has been added
+   */
+  public boolean hasHeight()
+  {
+    return this._has_height;
+  }
+
+  /**
+   * Method hasPidSelected.
+   * 
+   * @return true if at least one PidSelected has been added
+   */
+  public boolean hasPidSelected()
+  {
+    return this._has_pidSelected;
+  }
+
+  /**
+   * Method hasPidThreshold.
+   * 
+   * @return true if at least one PidThreshold has been added
+   */
+  public boolean hasPidThreshold()
+  {
+    return this._has_pidThreshold;
+  }
+
+  /**
+   * Method hasRenderGaps.
+   * 
+   * @return true if at least one RenderGaps has been added
+   */
+  public boolean hasRenderGaps()
+  {
+    return this._has_renderGaps;
+  }
+
+  /**
+   * Method hasShowAnnotation.
+   * 
+   * @return true if at least one ShowAnnotation has been added
+   */
+  public boolean hasShowAnnotation()
+  {
+    return this._has_showAnnotation;
+  }
+
+  /**
+   * Method hasShowBoxes.
+   * 
+   * @return true if at least one ShowBoxes has been added
+   */
+  public boolean hasShowBoxes()
+  {
+    return this._has_showBoxes;
+  }
+
+  /**
+   * Method hasShowColourText.
+   * 
+   * @return true if at least one ShowColourText has been added
+   */
+  public boolean hasShowColourText()
+  {
+    return this._has_showColourText;
+  }
+
+  /**
+   * Method hasShowConservation.
+   * 
+   * @return true if at least one ShowConservation has been added
+   */
+  public boolean hasShowConservation()
+  {
+    return this._has_showConservation;
+  }
+
+  /**
+   * Method hasShowFullId.
+   * 
+   * @return true if at least one ShowFullId has been added
+   */
+  public boolean hasShowFullId()
+  {
+    return this._has_showFullId;
+  }
+
+  /**
+   * Method hasShowIdentity.
+   * 
+   * @return true if at least one ShowIdentity has been added
+   */
+  public boolean hasShowIdentity()
+  {
+    return this._has_showIdentity;
+  }
+
+  /**
+   * Method hasShowQuality.
+   * 
+   * @return true if at least one ShowQuality has been added
+   */
+  public boolean hasShowQuality()
+  {
+    return this._has_showQuality;
+  }
+
+  /**
+   * Method hasShowSequenceFeatures.
+   * 
+   * @return true if at least one ShowSequenceFeatures has been added
+   */
+  public boolean hasShowSequenceFeatures()
+  {
+    return this._has_showSequenceFeatures;
+  }
+
+  /**
+   * Method hasShowText.
+   * 
+   * @return true if at least one ShowText has been added
+   */
+  public boolean hasShowText()
+  {
+    return this._has_showText;
+  }
+
+  /**
+   * Method hasStartRes.
+   * 
+   * @return true if at least one StartRes has been added
+   */
+  public boolean hasStartRes()
+  {
+    return this._has_startRes;
+  }
+
+  /**
+   * Method hasStartSeq.
+   * 
+   * @return true if at least one StartSeq has been added
+   */
+  public boolean hasStartSeq()
+  {
+    return this._has_startSeq;
+  }
+
+  /**
+   * Method hasWidth.
+   * 
+   * @return true if at least one Width has been added
+   */
+  public boolean hasWidth()
+  {
+    return this._has_width;
+  }
+
+  /**
+   * Method hasWrapAlignment.
+   * 
+   * @return true if at least one WrapAlignment has been added
+   */
+  public boolean hasWrapAlignment()
+  {
+    return this._has_wrapAlignment;
+  }
+
+  /**
+   * Method hasXpos.
+   * 
+   * @return true if at least one Xpos has been added
+   */
+  public boolean hasXpos()
+  {
+    return this._has_xpos;
+  }
+
+  /**
+   * Method hasYpos.
+   * 
+   * @return true if at least one Ypos has been added
+   */
+  public boolean hasYpos()
+  {
+    return this._has_ypos;
+  }
+
+  /**
+   * Returns the value of field 'conservationSelected'.
+   * 
+   * @return the value of field 'ConservationSelected'.
+   */
+  public boolean isConservationSelected()
+  {
+    return this._conservationSelected;
+  }
+
+  /**
+   * Returns the value of field 'pidSelected'.
+   * 
+   * @return the value of field 'PidSelected'.
+   */
+  public boolean isPidSelected()
+  {
+    return this._pidSelected;
+  }
+
+  /**
+   * Returns the value of field 'renderGaps'.
+   * 
+   * @return the value of field 'RenderGaps'.
+   */
+  public boolean isRenderGaps()
+  {
+    return this._renderGaps;
+  }
+
+  /**
+   * Returns the value of field 'showAnnotation'.
+   * 
+   * @return the value of field 'ShowAnnotation'.
+   */
+  public boolean isShowAnnotation()
+  {
+    return this._showAnnotation;
+  }
+
+  /**
+   * Returns the value of field 'showBoxes'.
+   * 
+   * @return the value of field 'ShowBoxes'.
+   */
+  public boolean isShowBoxes()
+  {
+    return this._showBoxes;
+  }
+
+  /**
+   * Returns the value of field 'showColourText'.
+   * 
+   * @return the value of field 'ShowColourText'.
+   */
+  public boolean isShowColourText()
+  {
+    return this._showColourText;
+  }
+
+  /**
+   * Returns the value of field 'showConservation'.
+   * 
+   * @return the value of field 'ShowConservation'.
+   */
+  public boolean isShowConservation()
+  {
+    return this._showConservation;
+  }
+
+  /**
+   * Returns the value of field 'showFullId'.
+   * 
+   * @return the value of field 'ShowFullId'.
+   */
+  public boolean isShowFullId()
+  {
+    return this._showFullId;
+  }
+
+  /**
+   * Returns the value of field 'showIdentity'.
+   * 
+   * @return the value of field 'ShowIdentity'.
+   */
+  public boolean isShowIdentity()
+  {
+    return this._showIdentity;
+  }
+
+  /**
+   * Returns the value of field 'showQuality'.
+   * 
+   * @return the value of field 'ShowQuality'.
+   */
+  public boolean isShowQuality()
+  {
+    return this._showQuality;
+  }
+
+  /**
+   * Returns the value of field 'showSequenceFeatures'.
+   * 
+   * @return the value of field 'ShowSequenceFeatures'.
+   */
+  public boolean isShowSequenceFeatures()
+  {
+    return this._showSequenceFeatures;
+  }
+
+  /**
+   * Returns the value of field 'showText'.
+   * 
+   * @return the value of field 'ShowText'.
+   */
+  public boolean isShowText()
+  {
+    return this._showText;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * Returns the value of field 'wrapAlignment'.
+   * 
+   * @return the value of field 'WrapAlignment'.
+   */
+  public boolean isWrapAlignment()
+  {
+    return this._wrapAlignment;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'bgColour'.
+   * 
+   * @param bgColour
+   *                the value of field 'bgColour'.
+   */
+  public void setBgColour(final java.lang.String bgColour)
+  {
+    this._bgColour = bgColour;
+  }
+
+  /**
+   * Sets the value of field 'consThreshold'.
+   * 
+   * @param consThreshold
+   *                the value of field 'consThreshold'.
+   */
+  public void setConsThreshold(final int consThreshold)
+  {
+    this._consThreshold = consThreshold;
+    this._has_consThreshold = true;
+  }
+
+  /**
+   * Sets the value of field 'conservationSelected'.
+   * 
+   * @param conservationSelected
+   *                the value of field 'conservationSelected'.
+   */
+  public void setConservationSelected(final boolean conservationSelected)
+  {
+    this._conservationSelected = conservationSelected;
+    this._has_conservationSelected = true;
+  }
+
+  /**
+   * Sets the value of field 'fontName'.
+   * 
+   * @param fontName
+   *                the value of field 'fontName'.
+   */
+  public void setFontName(final java.lang.String fontName)
+  {
+    this._fontName = fontName;
+  }
+
+  /**
+   * Sets the value of field 'fontSize'.
+   * 
+   * @param fontSize
+   *                the value of field 'fontSize'.
+   */
+  public void setFontSize(final int fontSize)
+  {
+    this._fontSize = fontSize;
+    this._has_fontSize = true;
+  }
+
+  /**
+   * Sets the value of field 'fontStyle'.
+   * 
+   * @param fontStyle
+   *                the value of field 'fontStyle'.
+   */
+  public void setFontStyle(final int fontStyle)
+  {
+    this._fontStyle = fontStyle;
+    this._has_fontStyle = true;
+  }
+
+  /**
+   * Sets the value of field 'height'.
+   * 
+   * @param height
+   *                the value of field 'height'.
+   */
+  public void setHeight(final int height)
+  {
+    this._height = height;
+    this._has_height = true;
+  }
+
+  /**
+   * Sets the value of field 'pidSelected'.
+   * 
+   * @param pidSelected
+   *                the value of field 'pidSelected'.
+   */
+  public void setPidSelected(final boolean pidSelected)
+  {
+    this._pidSelected = pidSelected;
+    this._has_pidSelected = true;
+  }
+
+  /**
+   * Sets the value of field 'pidThreshold'.
+   * 
+   * @param pidThreshold
+   *                the value of field 'pidThreshold'.
+   */
+  public void setPidThreshold(final int pidThreshold)
+  {
+    this._pidThreshold = pidThreshold;
+    this._has_pidThreshold = true;
+  }
+
+  /**
+   * Sets the value of field 'renderGaps'.
+   * 
+   * @param renderGaps
+   *                the value of field 'renderGaps'.
+   */
+  public void setRenderGaps(final boolean renderGaps)
+  {
+    this._renderGaps = renderGaps;
+    this._has_renderGaps = true;
+  }
+
+  /**
+   * Sets the value of field 'showAnnotation'.
+   * 
+   * @param showAnnotation
+   *                the value of field 'showAnnotation'.
+   */
+  public void setShowAnnotation(final boolean showAnnotation)
+  {
+    this._showAnnotation = showAnnotation;
+    this._has_showAnnotation = true;
+  }
+
+  /**
+   * Sets the value of field 'showBoxes'.
+   * 
+   * @param showBoxes
+   *                the value of field 'showBoxes'.
+   */
+  public void setShowBoxes(final boolean showBoxes)
+  {
+    this._showBoxes = showBoxes;
+    this._has_showBoxes = true;
+  }
+
+  /**
+   * Sets the value of field 'showColourText'.
+   * 
+   * @param showColourText
+   *                the value of field 'showColourText'.
+   */
+  public void setShowColourText(final boolean showColourText)
+  {
+    this._showColourText = showColourText;
+    this._has_showColourText = true;
+  }
+
+  /**
+   * Sets the value of field 'showConservation'.
+   * 
+   * @param showConservation
+   *                the value of field 'showConservation'
+   */
+  public void setShowConservation(final boolean showConservation)
+  {
+    this._showConservation = showConservation;
+    this._has_showConservation = true;
+  }
+
+  /**
+   * Sets the value of field 'showFullId'.
+   * 
+   * @param showFullId
+   *                the value of field 'showFullId'.
+   */
+  public void setShowFullId(final boolean showFullId)
+  {
+    this._showFullId = showFullId;
+    this._has_showFullId = true;
+  }
+
+  /**
+   * Sets the value of field 'showIdentity'.
+   * 
+   * @param showIdentity
+   *                the value of field 'showIdentity'.
+   */
+  public void setShowIdentity(final boolean showIdentity)
+  {
+    this._showIdentity = showIdentity;
+    this._has_showIdentity = true;
+  }
+
+  /**
+   * Sets the value of field 'showQuality'.
+   * 
+   * @param showQuality
+   *                the value of field 'showQuality'.
+   */
+  public void setShowQuality(final boolean showQuality)
+  {
+    this._showQuality = showQuality;
+    this._has_showQuality = true;
+  }
+
+  /**
+   * Sets the value of field 'showSequenceFeatures'.
+   * 
+   * @param showSequenceFeatures
+   *                the value of field 'showSequenceFeatures'.
+   */
+  public void setShowSequenceFeatures(final boolean showSequenceFeatures)
+  {
+    this._showSequenceFeatures = showSequenceFeatures;
+    this._has_showSequenceFeatures = true;
+  }
+
+  /**
+   * Sets the value of field 'showText'.
+   * 
+   * @param showText
+   *                the value of field 'showText'.
+   */
+  public void setShowText(final boolean showText)
+  {
+    this._showText = showText;
+    this._has_showText = true;
+  }
+
+  /**
+   * Sets the value of field 'startRes'.
+   * 
+   * @param startRes
+   *                the value of field 'startRes'.
+   */
+  public void setStartRes(final int startRes)
+  {
+    this._startRes = startRes;
+    this._has_startRes = true;
+  }
+
+  /**
+   * Sets the value of field 'startSeq'.
+   * 
+   * @param startSeq
+   *                the value of field 'startSeq'.
+   */
+  public void setStartSeq(final int startSeq)
+  {
+    this._startSeq = startSeq;
+    this._has_startSeq = true;
+  }
+
+  /**
+   * Sets the value of field 'title'.
+   * 
+   * @param title
+   *                the value of field 'title'.
+   */
+  public void setTitle(final java.lang.String title)
+  {
+    this._title = title;
+  }
+
+  /**
+   * Sets the value of field 'width'.
+   * 
+   * @param width
+   *                the value of field 'width'.
+   */
+  public void setWidth(final int width)
+  {
+    this._width = width;
+    this._has_width = true;
+  }
+
+  /**
+   * Sets the value of field 'wrapAlignment'.
+   * 
+   * @param wrapAlignment
+   *                the value of field 'wrapAlignment'.
+   */
+  public void setWrapAlignment(final boolean wrapAlignment)
+  {
+    this._wrapAlignment = wrapAlignment;
+    this._has_wrapAlignment = true;
+  }
+
+  /**
+   * Sets the value of field 'xpos'.
+   * 
+   * @param xpos
+   *                the value of field 'xpos'.
+   */
+  public void setXpos(final int xpos)
+  {
+    this._xpos = xpos;
+    this._has_xpos = true;
+  }
+
+  /**
+   * Sets the value of field 'ypos'.
+   * 
+   * @param ypos
+   *                the value of field 'ypos'.
+   */
+  public void setYpos(final int ypos)
+  {
+    this._ypos = ypos;
+    this._has_ypos = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.binding.Viewport
+   */
+  public static jalview.binding.Viewport unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.Viewport) Unmarshaller.unmarshal(
+            jalview.binding.Viewport.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/commands/ChangeCaseCommand.java b/src/jalview/commands/ChangeCaseCommand.java
index 976be92..7a74e08 100644
--- a/src/jalview/commands/ChangeCaseCommand.java
+++ b/src/jalview/commands/ChangeCaseCommand.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -20,20 +20,24 @@ package jalview.commands;
 
 import jalview.datamodel.*;
 
-public class ChangeCaseCommand
-    implements CommandI
+public class ChangeCaseCommand implements CommandI
 {
   String description;
+
   public static int TO_LOWER = 0;
+
   public static int TO_UPPER = 1;
+
   public static int TOGGLE_CASE = 2;
+
   int caseChange = -1;
+
   SequenceI[] seqs;
+
   int[][] regions;
-  public ChangeCaseCommand(String description,
-                           SequenceI[] seqs,
-                           int[][] regions,
-                           int caseChange)
+
+  public ChangeCaseCommand(String description, SequenceI[] seqs,
+          int[][] regions, int caseChange)
   {
     this.description = description;
     this.seqs = seqs;
@@ -89,19 +93,20 @@ public class ChangeCaseCommand
           newSeq.append(sequence.substring(0, start));
         }
 
-        if ( (caseChange == TO_UPPER && doCommand)
-            || (caseChange == TO_LOWER && !doCommand))
+        if ((caseChange == TO_UPPER && doCommand)
+                || (caseChange == TO_LOWER && !doCommand))
         {
           newSeq.append(sequence.substring(start, end).toUpperCase());
         }
 
-        else if ( (caseChange == TO_LOWER && doCommand)
-                 || (caseChange == TO_UPPER && !doCommand))
+        else if ((caseChange == TO_LOWER && doCommand)
+                || (caseChange == TO_UPPER && !doCommand))
         {
           newSeq.append(sequence.substring(start, end).toLowerCase());
         }
 
-        else //TOGGLE CASE
+        else
+        // TOGGLE CASE
         {
           for (int c = start; c < end; c++)
           {
diff --git a/src/jalview/commands/CommandI.java b/src/jalview/commands/CommandI.java
index 97675e7..9fe508b 100644
--- a/src/jalview/commands/CommandI.java
+++ b/src/jalview/commands/CommandI.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index e859e3e..85e6ad5 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -23,27 +23,37 @@ import java.util.*;
 import jalview.datamodel.*;
 
 /**
- *
- * <p>Title: EditCommmand</p>
- *
- * <p>Description: Essential information for performing
- * undo and redo for cut/paste insert/delete gap
- * which can be stored in the HistoryList </p>
- *
- * <p>Copyright: Copyright (c) 2006</p>
- *
- * <p>Company: Dundee University</p>
- *
+ * 
+ * <p>
+ * Title: EditCommmand
+ * </p>
+ * 
+ * <p>
+ * Description: Essential information for performing undo and redo for cut/paste
+ * insert/delete gap which can be stored in the HistoryList
+ * </p>
+ * 
+ * <p>
+ * Copyright: Copyright (c) 2006
+ * </p>
+ * 
+ * <p>
+ * Company: Dundee University
+ * </p>
+ * 
  * @author not attributable
  * @version 1.0
  */
-public class EditCommand
-    implements CommandI
+public class EditCommand implements CommandI
 {
   public static final int INSERT_GAP = 0;
+
   public static final int DELETE_GAP = 1;
+
   public static final int CUT = 2;
+
   public static final int PASTE = 3;
+
   public static final int REPLACE = 4;
 
   Edit[] edits;
@@ -51,44 +61,35 @@ public class EditCommand
   String description;
 
   public EditCommand()
-  {}
+  {
+  }
 
   public EditCommand(String description)
   {
     this.description = description;
   }
 
-  public EditCommand(String description,
-                     int command,
-                     SequenceI[] seqs,
-                     int position,
-                     int number,
-                     AlignmentI al)
+  public EditCommand(String description, int command, SequenceI[] seqs,
+          int position, int number, AlignmentI al)
   {
     this.description = description;
     if (command == CUT || command == PASTE)
     {
       edits = new Edit[]
-          {
-          new Edit(command, seqs, position, number, al)};
+      { new Edit(command, seqs, position, number, al) };
     }
 
     performEdit(0, null);
   }
 
-  public EditCommand(String description,
-                     int command,
-                     String replace,
-                     SequenceI[] seqs,
-                     int position,
-                     int number,
-                     AlignmentI al)
+  public EditCommand(String description, int command, String replace,
+          SequenceI[] seqs, int position, int number, AlignmentI al)
   {
     this.description = description;
     if (command == REPLACE)
     {
       edits = new Edit[]
-          { new Edit(command, seqs, position, number, al, replace)};
+      { new Edit(command, seqs, position, number, al, replace) };
     }
 
     performEdit(0, null);
@@ -110,9 +111,11 @@ public class EditCommand
   }
 
   /**
-   * append a new editCommand
-   * Note. this shouldn't be called if the edit is an operation affects more alignment objects than the one referenced
-   * in al (for example, cut or pasting whole sequences). Use the form with an additional AlignmentI[] views parameter.
+   * append a new editCommand Note. this shouldn't be called if the edit is an
+   * operation affects more alignment objects than the one referenced in al (for
+   * example, cut or pasting whole sequences). Use the form with an additional
+   * AlignmentI[] views parameter.
+   * 
    * @param command
    * @param seqs
    * @param position
@@ -120,17 +123,16 @@ public class EditCommand
    * @param al
    * @param performEdit
    */
-  final public void appendEdit(int command,
-          SequenceI[] seqs,
-          int position,
-          int number,
-          AlignmentI al,
-          boolean performEdit)
+  final public void appendEdit(int command, SequenceI[] seqs, int position,
+          int number, AlignmentI al, boolean performEdit)
   {
     appendEdit(command, seqs, position, number, al, performEdit, null);
   }
+
   /**
-   * append a new edit command with a set of alignment views that may be operated on
+   * append a new edit command with a set of alignment views that may be
+   * operated on
+   * 
    * @param command
    * @param seqs
    * @param position
@@ -139,14 +141,11 @@ public class EditCommand
    * @param performEdit
    * @param views
    */
-  final public void appendEdit(int command,
-                               SequenceI[] seqs,
-                               int position,
-                               int number,
-                               AlignmentI al,
-                               boolean performEdit, AlignmentI[] views)
+  final public void appendEdit(int command, SequenceI[] seqs, int position,
+          int number, AlignmentI al, boolean performEdit, AlignmentI[] views)
   {
-    Edit edit = new Edit(command, seqs, position, number, al.getGapCharacter());
+    Edit edit = new Edit(command, seqs, position, number, al
+            .getGapCharacter());
     if (al.getHeight() == seqs.length)
     {
       edit.al = al;
@@ -163,8 +162,7 @@ public class EditCommand
     else
     {
       edits = new Edit[]
-          {
-          edit};
+      { edit };
     }
 
     if (performEdit)
@@ -178,30 +176,30 @@ public class EditCommand
     int eSize = edits.length;
     for (int e = commandIndex; e < eSize; e++)
     {
-      switch(edits[e].command)
+      switch (edits[e].command)
       {
-        case INSERT_GAP:
+      case INSERT_GAP:
         insertGap(edits[e]);
-          break;
-        case DELETE_GAP:
+        break;
+      case DELETE_GAP:
         deleteGap(edits[e]);
-          break;
-        case CUT:
+        break;
+      case CUT:
         cut(edits[e], views);
-          break;
-        case PASTE:
+        break;
+      case PASTE:
         paste(edits[e], views);
-          break;
-        case REPLACE:
-          replace(edits[e]);
-          break;
+        break;
+      case REPLACE:
+        replace(edits[e]);
+        break;
       }
     }
   }
 
   final public void doCommand(AlignmentI[] views)
   {
-    performEdit(0,views);
+    performEdit(0, views);
   }
 
   final public void undoCommand(AlignmentI[] views)
@@ -211,21 +209,21 @@ public class EditCommand
     {
       switch (edits[e].command)
       {
-        case INSERT_GAP:
+      case INSERT_GAP:
         deleteGap(edits[e]);
-          break;
-        case DELETE_GAP:
+        break;
+      case DELETE_GAP:
         insertGap(edits[e]);
-          break;
-        case CUT:
+        break;
+      case CUT:
         paste(edits[e], views);
-          break;
-        case PASTE:
+        break;
+      case PASTE:
         cut(edits[e], views);
-          break;
-        case REPLACE:
-          replace(edits[e]);
-          break;
+        break;
+      case REPLACE:
+        replace(edits[e]);
+        break;
       }
     }
   }
@@ -235,9 +233,8 @@ public class EditCommand
 
     for (int s = 0; s < command.seqs.length; s++)
     {
-      command.seqs[s].insertCharAt(command.position,
-                                   command.number,
-                                   command.gapChar);
+      command.seqs[s].insertCharAt(command.position, command.number,
+              command.gapChar);
     }
 
     adjustAnnotations(command, true, false, null);
@@ -247,8 +244,8 @@ public class EditCommand
   {
     for (int s = 0; s < command.seqs.length; s++)
     {
-      command.seqs[s].deleteChars(command.position,
-                                  command.position + command.number);
+      command.seqs[s].deleteChars(command.position, command.position
+              + command.number);
     }
 
     adjustAnnotations(command, false, false, null);
@@ -256,7 +253,7 @@ public class EditCommand
 
   void cut(Edit command, AlignmentI[] views)
   {
-    boolean seqDeleted=false;
+    boolean seqDeleted = false;
     command.string = new char[command.seqs.length][];
 
     for (int i = 0; i < command.seqs.length; i++)
@@ -264,35 +261,35 @@ public class EditCommand
       if (command.seqs[i].getLength() > command.position)
       {
         command.string[i] = command.seqs[i].getSequence(command.position,
-            command.position + command.number);
+                command.position + command.number);
         SequenceI oldds = command.seqs[i].getDatasetSequence();
-        if (command.oldds!=null && command.oldds[i]!=null)
+        if (command.oldds != null && command.oldds[i] != null)
         {
           // we are redoing an undone cut.
           command.seqs[i].setDatasetSequence(null);
         }
-        command.seqs[i].deleteChars(command.position,
-                command.position + command.number);
-        if (command.oldds!=null && command.oldds[i]!=null)
+        command.seqs[i].deleteChars(command.position, command.position
+                + command.number);
+        if (command.oldds != null && command.oldds[i] != null)
         {
           // oldds entry contains the cut dataset sequence.
           command.seqs[i].setDatasetSequence(command.oldds[i]);
           command.oldds[i] = oldds;
-        } else {
+        }
+        else
+        {
           // modify the oldds if necessary
-          if (oldds!=command.seqs[i].getDatasetSequence()
-            || command.seqs[i].getSequenceFeatures() != null)
+          if (oldds != command.seqs[i].getDatasetSequence()
+                  || command.seqs[i].getSequenceFeatures() != null)
           {
-            if (command.oldds==null)
+            if (command.oldds == null)
             {
               command.oldds = new SequenceI[command.seqs.length];
             }
             command.oldds[i] = oldds;
-            adjustFeatures(command, i,
-                    command.seqs[i].findPosition(command.position),
-                    command.seqs[i].findPosition(command.position +
-                            command.number),
-                            false);
+            adjustFeatures(command, i, command.seqs[i]
+                    .findPosition(command.position), command.seqs[i]
+                    .findPosition(command.position + command.number), false);
           }
         }
       }
@@ -300,7 +297,7 @@ public class EditCommand
       if (command.seqs[i].getLength() < 1)
       {
         command.al.deleteSequence(command.seqs[i]);
-        seqDeleted=true;
+        seqDeleted = true;
       }
     }
 
@@ -312,14 +309,14 @@ public class EditCommand
     StringBuffer tmp;
     boolean newDSNeeded;
     boolean newDSWasNeeded;
-    int newstart,newend;
-    boolean seqWasDeleted=false;
+    int newstart, newend;
+    boolean seqWasDeleted = false;
     int start = 0, end = 0;
 
     for (int i = 0; i < command.seqs.length; i++)
     {
       newDSNeeded = false;
-      newDSWasNeeded = command.oldds!=null && command.oldds[i]!=null;
+      newDSWasNeeded = command.oldds != null && command.oldds[i] != null;
       if (command.seqs[i].getLength() < 1)
       {
         // ie this sequence was deleted, we need to
@@ -327,27 +324,28 @@ public class EditCommand
         if (command.alIndex[i] < command.al.getHeight())
         {
           command.al.getSequences().insertElementAt(command.seqs[i],
-              command.alIndex[i]);
+                  command.alIndex[i]);
         }
         else
         {
           command.al.addSequence(command.seqs[i]);
         }
-        seqWasDeleted=true;
+        seqWasDeleted = true;
       }
       newstart = command.seqs[i].getStart();
       newend = command.seqs[i].getEnd();
 
       tmp = new StringBuffer();
       tmp.append(command.seqs[i].getSequence());
-      //Undo of a delete does not replace original dataset sequence on to alignment sequence.
-      
+      // Undo of a delete does not replace original dataset sequence on to
+      // alignment sequence.
+
       if (command.string != null && command.string[i] != null)
       {
         if (command.position >= tmp.length())
         {
-          //This occurs if padding is on, and residues
-          //are removed from end of alignment
+          // This occurs if padding is on, and residues
+          // are removed from end of alignment
           int length = command.position - tmp.length();
           while (length > 0)
           {
@@ -358,17 +356,16 @@ public class EditCommand
         tmp.insert(command.position, command.string[i]);
         for (int s = 0; s < command.string[i].length; s++)
         {
-          if (jalview.schemes.ResidueProperties.aaIndex[command.string[i][s]] !=
-              23)
+          if (jalview.schemes.ResidueProperties.aaIndex[command.string[i][s]] != 23)
           {
             if (!newDSNeeded)
             {
               newDSNeeded = true;
               start = command.seqs[i].findPosition(command.position);
-              end = command.seqs[i].findPosition(command.position +
-                                               command.number);
+              end = command.seqs[i].findPosition(command.position
+                      + command.number);
             }
-            if (command.seqs[i].getStart()==start)
+            if (command.seqs[i].getStart() == start)
               newstart--;
             else
               newend++;
@@ -383,28 +380,28 @@ public class EditCommand
       if (newDSNeeded)
       {
         if (command.seqs[i].getDatasetSequence() != null)
-        { 
+        {
           SequenceI ds;
           if (newDSWasNeeded)
           {
             ds = command.oldds[i];
-          } else {
+          }
+          else
+          {
             // make a new DS sequence
             // use new ds mechanism here
-            ds= new Sequence(command.seqs[i].getName(),
-                                     jalview.analysis.AlignSeq.extractGaps(
-                                         jalview.util.Comparison.GapChars,
-                                         command.seqs[i].getSequenceAsString()
-                                     ),
-                                     command.seqs[i].getStart(),
-                                     command.seqs[i].getEnd());
+            ds = new Sequence(command.seqs[i].getName(),
+                    jalview.analysis.AlignSeq.extractGaps(
+                            jalview.util.Comparison.GapChars,
+                            command.seqs[i].getSequenceAsString()),
+                    command.seqs[i].getStart(), command.seqs[i].getEnd());
             ds.setDescription(command.seqs[i].getDescription());
           }
-          if (command.oldds==null)
+          if (command.oldds == null)
           {
             command.oldds = new SequenceI[command.seqs.length];
           }
-          command.oldds[i]=command.seqs[i].getDatasetSequence();
+          command.oldds[i] = command.seqs[i].getDatasetSequence();
           command.seqs[i].setDatasetSequence(ds);
         }
         adjustFeatures(command, i, start, end, true);
@@ -421,30 +418,23 @@ public class EditCommand
     String oldstring;
     int start = command.position;
     int end = command.number;
-    // TODO TUTORIAL - Fix for replacement with different length of sequence (or whole sequence)
-    // TODO Jalview 2.4 bugfix change to an aggregate command - original sequence string is cut, new string is pasted in.
+    // TODO TUTORIAL - Fix for replacement with different length of sequence (or
+    // whole sequence)
+    // TODO Jalview 2.4 bugfix change to an aggregate command - original
+    // sequence string is cut, new string is pasted in.
     command.number = start + command.string[0].length;
     for (int i = 0; i < command.seqs.length; i++)
     {
-      /**  cut
-       *     addHistoryItem(new EditCommand("Cut Sequences",
-                                      EditCommand.CUT,
-                                      cut,
-                                      sg.getStartRes(),
-                                      sg.getEndRes()-sg.getStartRes()+1,
-                                      viewport.alignment));
-
+      /**
+       * cut addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT,
+       * cut, sg.getStartRes(), sg.getEndRes()-sg.getStartRes()+1,
+       * viewport.alignment));
+       * 
        */
-      /** then
-       *        addHistoryItem(new EditCommand(
-               "Add sequences",
-               EditCommand.PASTE,
-               sequences,
-               0,
-               alignment.getWidth(),
-               alignment)
-              );
-
+      /**
+       * then addHistoryItem(new EditCommand( "Add sequences",
+       * EditCommand.PASTE, sequences, 0, alignment.getWidth(), alignment) );
+       * 
        */
       oldstring = command.seqs[i].getSequenceAsString();
       tmp = new StringBuffer(oldstring.substring(0, start));
@@ -457,7 +447,8 @@ public class EditCommand
     }
   }
 
-  final void adjustAnnotations(Edit command, boolean insert, boolean modifyVisibility, AlignmentI[] views)
+  final void adjustAnnotations(Edit command, boolean insert,
+          boolean modifyVisibility, AlignmentI[] views)
   {
     AlignmentAnnotation[] annotations = null;
 
@@ -479,28 +470,31 @@ public class EditCommand
         if (modifyVisibility)
         {
           // Rows are only removed or added to sequence object.
-          if (!insert) {
+          if (!insert)
+          {
             // remove rows
             tmp = command.seqs[s].getAnnotation();
-            if (tmp!=null) {
-              int alen=tmp.length;
-              for (int aa =0; aa<tmp.length; aa++)
+            if (tmp != null)
+            {
+              int alen = tmp.length;
+              for (int aa = 0; aa < tmp.length; aa++)
               {
                 if (!command.al.deleteAnnotation(tmp[aa]))
                 {
-                  // strip out annotation not in the current al (will be put back on insert in all views)
+                  // strip out annotation not in the current al (will be put
+                  // back on insert in all views)
                   tmp[aa] = null;
                   alen--;
                 }
               }
               command.seqs[s].setAlignmentAnnotation(null);
-              if (alen!=tmp.length)
+              if (alen != tmp.length)
               {
                 // save the non-null annotation references only
                 AlignmentAnnotation[] saved = new AlignmentAnnotation[alen];
-                for (int aa=0,aapos=0;aa<tmp.length;aa++)
+                for (int aa = 0, aapos = 0; aa < tmp.length; aa++)
                 {
-                  if (tmp[aa]!=null)
+                  if (tmp[aa] != null)
                   {
                     saved[aapos++] = tmp[aa];
                     tmp[aa] = null;
@@ -509,56 +503,68 @@ public class EditCommand
                 tmp = saved;
                 command.deletedAnnotationRows.put(command.seqs[s], saved);
                 // and then remove any annotation in the other views
-                for (int alview=0; views!=null && alview<views.length; alview++)
+                for (int alview = 0; views != null && alview < views.length; alview++)
                 {
-                  if (views[alview]!=command.al)
+                  if (views[alview] != command.al)
                   {
-                    AlignmentAnnotation[] toremove = views[alview].getAlignmentAnnotation();
-                    if (toremove==null || toremove.length==0)
+                    AlignmentAnnotation[] toremove = views[alview]
+                            .getAlignmentAnnotation();
+                    if (toremove == null || toremove.length == 0)
                     {
                       continue;
                     }
-                    // remove any alignment annotation on this sequence that's on that alignment view.
-                    for (int aa = 0; aa<toremove.length; aa++)
+                    // remove any alignment annotation on this sequence that's
+                    // on that alignment view.
+                    for (int aa = 0; aa < toremove.length; aa++)
                     {
-                      if (toremove[aa].sequenceRef==command.seqs[s])
+                      if (toremove[aa].sequenceRef == command.seqs[s])
                       {
                         views[alview].deleteAnnotation(toremove[aa]);
                       }
                     }
                   }
                 }
-              } else {
+              }
+              else
+              {
                 // save all the annotation
                 command.deletedAnnotationRows.put(command.seqs[s], tmp);
               }
             }
-          } else {
+          }
+          else
+          {
             // recover rows
-            if (command.deletedAnnotationRows!=null && command.deletedAnnotationRows.containsKey(command.seqs[s]))
+            if (command.deletedAnnotationRows != null
+                    && command.deletedAnnotationRows
+                            .containsKey(command.seqs[s]))
             {
-              AlignmentAnnotation[] revealed = (AlignmentAnnotation[]) command.deletedAnnotationRows.get(command.seqs[s]);
+              AlignmentAnnotation[] revealed = (AlignmentAnnotation[]) command.deletedAnnotationRows
+                      .get(command.seqs[s]);
               command.seqs[s].setAlignmentAnnotation(revealed);
-              if (revealed!=null) {
-                for (int aa =0; aa<revealed.length; aa++)
+              if (revealed != null)
+              {
+                for (int aa = 0; aa < revealed.length; aa++)
                 {
                   // iterate through al adding original annotation
                   command.al.addAnnotation(revealed[aa]);
                 }
-                for (int aa =0; aa<revealed.length; aa++)
+                for (int aa = 0; aa < revealed.length; aa++)
                 {
                   command.al.setAnnotationIndex(revealed[aa], aa);
                 }
-                // and then duplicate added annotation on every other alignment view
-                for (int vnum=0; views!=null && vnum<views.length; vnum++)
+                // and then duplicate added annotation on every other alignment
+                // view
+                for (int vnum = 0; views != null && vnum < views.length; vnum++)
                 {
-                  if (views[vnum]!=command.al)
+                  if (views[vnum] != command.al)
                   {
-                    int avwidth = views[vnum].getWidth()+1;
+                    int avwidth = views[vnum].getWidth() + 1;
                     // duplicate in this view
-                    for (int a=0; a<revealed.length; a++)
+                    for (int a = 0; a < revealed.length; a++)
                     {
-                      AlignmentAnnotation newann = new AlignmentAnnotation(revealed[a]);
+                      AlignmentAnnotation newann = new AlignmentAnnotation(
+                              revealed[a]);
                       command.seqs[s].addAlignmentAnnotation(newann);
                       newann.padAnnotation(avwidth);
                       views[vnum].addAnnotation(newann);
@@ -583,14 +589,13 @@ public class EditCommand
         }
         else
         {
-          tmp = new AlignmentAnnotation
-              [aSize + command.seqs[s].getAnnotation().length];
+          tmp = new AlignmentAnnotation[aSize
+                  + command.seqs[s].getAnnotation().length];
 
           System.arraycopy(annotations, 0, tmp, 0, aSize);
 
-          System.arraycopy(command.seqs[s].getAnnotation(),
-                           0, tmp, aSize,
-                           command.seqs[s].getAnnotation().length);
+          System.arraycopy(command.seqs[s].getAnnotation(), 0, tmp, aSize,
+                  command.seqs[s].getAnnotation().length);
 
           annotations = tmp;
         }
@@ -612,7 +617,8 @@ public class EditCommand
     Annotation[] temp;
     for (int a = 0; a < annotations.length; a++)
     {
-      if (annotations[a].autoCalculated || annotations[a].annotations == null)
+      if (annotations[a].autoCalculated
+              || annotations[a].annotations == null)
       {
         continue;
       }
@@ -623,12 +629,10 @@ public class EditCommand
       if (insert)
       {
         temp = new Annotation[aSize + command.number];
-        if(annotations[a].padGaps)
+        if (annotations[a].padGaps)
           for (int aa = 0; aa < temp.length; aa++)
           {
-            temp[aa] = new Annotation(
-                command.gapChar+"",
-                null, ' ', 0);
+            temp[aa] = new Annotation(command.gapChar + "", null, ' ', 0);
           }
       }
       else
@@ -656,52 +660,44 @@ public class EditCommand
         temp = new Annotation[tSize];
       }
 
-
       if (insert)
       {
         if (command.position < annotations[a].annotations.length)
         {
-          System.arraycopy(annotations[a].annotations,
-                           0, temp, 0, command.position);
+          System.arraycopy(annotations[a].annotations, 0, temp, 0,
+                  command.position);
 
           if (command.deletedAnnotations != null
-              &&
-              command.deletedAnnotations.containsKey(annotations[a].
-              annotationId))
+                  && command.deletedAnnotations
+                          .containsKey(annotations[a].annotationId))
           {
-            Annotation[] restore = (Annotation[])
-                command.deletedAnnotations.get(annotations[a].annotationId);
+            Annotation[] restore = (Annotation[]) command.deletedAnnotations
+                    .get(annotations[a].annotationId);
 
-            System.arraycopy(restore,
-                             0,
-                             temp,
-                             command.position,
-                             command.number);
+            System.arraycopy(restore, 0, temp, command.position,
+                    command.number);
 
           }
 
-          System.arraycopy(annotations[a].annotations,
-                           command.position, temp,
-                           command.position + command.number,
-                           aSize - command.position);
+          System.arraycopy(annotations[a].annotations, command.position,
+                  temp, command.position + command.number, aSize
+                          - command.position);
         }
         else
         {
           if (command.deletedAnnotations != null
-              &&
-              command.deletedAnnotations.containsKey(annotations[a].
-              annotationId))
+                  && command.deletedAnnotations
+                          .containsKey(annotations[a].annotationId))
           {
-            Annotation[] restore = (Annotation[])
-                command.deletedAnnotations.get(annotations[a].annotationId);
-
-            temp = new Annotation[annotations[a].annotations.length +
-                restore.length];
-            System.arraycopy(annotations[a].annotations,
-                             0, temp, 0,
-                             annotations[a].annotations.length);
+            Annotation[] restore = (Annotation[]) command.deletedAnnotations
+                    .get(annotations[a].annotationId);
+
+            temp = new Annotation[annotations[a].annotations.length
+                    + restore.length];
+            System.arraycopy(annotations[a].annotations, 0, temp, 0,
+                    annotations[a].annotations.length);
             System.arraycopy(restore, 0, temp,
-                             annotations[a].annotations.length, restore.length);
+                    annotations[a].annotations.length, restore.length);
           }
           else
           {
@@ -713,15 +709,18 @@ public class EditCommand
       {
         if (tSize != aSize || command.position < 2)
         {
-          int copylen = Math.min(command.position, annotations[a].annotations.length);
-          if (copylen>0)
-            System.arraycopy(annotations[a].annotations,
-                           0, temp, 0, copylen); //command.position);
+          int copylen = Math.min(command.position,
+                  annotations[a].annotations.length);
+          if (copylen > 0)
+            System.arraycopy(annotations[a].annotations, 0, temp, 0,
+                    copylen); // command.position);
 
           Annotation[] deleted = new Annotation[command.number];
-          if (copylen>=command.position) {
-            copylen = Math.min(command.number, annotations[a].annotations.length-command.position);
-            if (copylen>0)
+          if (copylen >= command.position)
+          {
+            copylen = Math.min(command.number,
+                    annotations[a].annotations.length - command.position);
+            if (copylen > 0)
             {
               System.arraycopy(annotations[a].annotations,
                       command.position, deleted, 0, copylen); // command.number);
@@ -729,12 +728,14 @@ public class EditCommand
           }
 
           command.deletedAnnotations.put(annotations[a].annotationId,
-                                         deleted);
-          if (annotations[a].annotations.length>command.position+command.number) {
-            System.arraycopy(annotations[a].annotations,
-                           command.position + command.number,
-                           temp, command.position,
-                           annotations[a].annotations.length - command.position - command.number); // aSize
+                  deleted);
+          if (annotations[a].annotations.length > command.position
+                  + command.number)
+          {
+            System.arraycopy(annotations[a].annotations, command.position
+                    + command.number, temp, command.position,
+                    annotations[a].annotations.length - command.position
+                            - command.number); // aSize
           }
         }
         else
@@ -744,17 +745,16 @@ public class EditCommand
           if (dSize > 0)
           {
             Annotation[] deleted = new Annotation[command.number];
-            System.arraycopy(annotations[a].annotations,
-                             command.position, deleted, 0, dSize);
+            System.arraycopy(annotations[a].annotations, command.position,
+                    deleted, 0, dSize);
 
             command.deletedAnnotations.put(annotations[a].annotationId,
-                                           deleted);
+                    deleted);
 
             tSize = Math.min(annotations[a].annotations.length,
-                             command.position);
+                    command.position);
             temp = new Annotation[tSize];
-            System.arraycopy(annotations[a].annotations,
-                             0, temp, 0, tSize);
+            System.arraycopy(annotations[a].annotations, 0, temp, 0, tSize);
           }
           else
           {
@@ -768,7 +768,7 @@ public class EditCommand
   }
 
   final void adjustFeatures(Edit command, int index, int i, int j,
-                            boolean insert)
+          boolean insert)
   {
     SequenceI seq = command.seqs[index];
     SequenceI sequence = seq.getDatasetSequence();
@@ -780,11 +780,11 @@ public class EditCommand
     if (insert)
     {
       if (command.editedFeatures != null
-          && command.editedFeatures.containsKey(seq))
+              && command.editedFeatures.containsKey(seq))
       {
-        sequence.setSequenceFeatures(
-            (SequenceFeature[]) command.editedFeatures.get(seq)
-            );
+        sequence
+                .setSequenceFeatures((SequenceFeature[]) command.editedFeatures
+                        .get(seq));
       }
 
       return;
@@ -849,23 +849,31 @@ public class EditCommand
   class Edit
   {
     public SequenceI[] oldds;
+
     boolean fullAlignmentHeight = false;
+
     Hashtable deletedAnnotationRows;
+
     Hashtable deletedAnnotations;
+
     Hashtable editedFeatures;
+
     AlignmentI al;
+
     int command;
+
     char[][] string;
+
     SequenceI[] seqs;
+
     int[] alIndex;
+
     int position, number;
+
     char gapChar;
 
-    Edit(int command,
-         SequenceI[] seqs,
-         int position,
-         int number,
-         char gapChar)
+    Edit(int command, SequenceI[] seqs, int position, int number,
+            char gapChar)
     {
       this.command = command;
       this.seqs = seqs;
@@ -874,11 +882,8 @@ public class EditCommand
       this.gapChar = gapChar;
     }
 
-    Edit(int command,
-         SequenceI[] seqs,
-         int position,
-         int number,
-         AlignmentI al)
+    Edit(int command, SequenceI[] seqs, int position, int number,
+            AlignmentI al)
     {
       this.gapChar = al.getGapCharacter();
       this.command = command;
@@ -896,12 +901,8 @@ public class EditCommand
       fullAlignmentHeight = (al.getHeight() == seqs.length);
     }
 
-    Edit(int command,
-         SequenceI[] seqs,
-         int position,
-         int number,
-         AlignmentI al,
-         String replace)
+    Edit(int command, SequenceI[] seqs, int position, int number,
+            AlignmentI al, String replace)
     {
       this.command = command;
       this.seqs = seqs;
diff --git a/src/jalview/commands/OrderCommand.java b/src/jalview/commands/OrderCommand.java
index b331690..6ea28ee 100644
--- a/src/jalview/commands/OrderCommand.java
+++ b/src/jalview/commands/OrderCommand.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -21,17 +21,17 @@ package jalview.commands;
 import jalview.analysis.*;
 import jalview.datamodel.*;
 
-public class OrderCommand
-    implements CommandI
+public class OrderCommand implements CommandI
 {
   String description;
+
   SequenceI[] seqs;
+
   SequenceI[] seqs2;
+
   AlignmentI al;
 
-  public OrderCommand(String description,
-                      SequenceI[] seqs,
-                      AlignmentI al)
+  public OrderCommand(String description, SequenceI[] seqs, AlignmentI al)
   {
     this.description = description;
     this.seqs = seqs;
diff --git a/src/jalview/commands/RemoveGapColCommand.java b/src/jalview/commands/RemoveGapColCommand.java
index a874f71..c5e12f5 100644
--- a/src/jalview/commands/RemoveGapColCommand.java
+++ b/src/jalview/commands/RemoveGapColCommand.java
@@ -1,33 +1,50 @@
-package jalview.commands;
-
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
+package jalview.commands;
+
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer Copyright (C) 2007 AM
+ * Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU General Public License as published by the Free Software
+ * Foundation; either version 2 of the License, or (at your option) any later
+ * version.
+ * 
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+ * details.
+ * 
+ * You should have received a copy of the GNU General Public License along with
+ * this program; if not, write to the Free Software Foundation, Inc., 51
+ * Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
 
 import jalview.datamodel.*;
 
-public class RemoveGapColCommand
-    extends EditCommand
+public class RemoveGapColCommand extends EditCommand
 {
   int columnsDeleted;
-  public RemoveGapColCommand(String description,
-                             SequenceI[] seqs,
-                             int start, int end, AlignmentI al)
+
+  public RemoveGapColCommand(String description, SequenceI[] seqs,
+          int start, int end, AlignmentI al)
   {
     this.description = description;
 
@@ -67,11 +84,8 @@ public class RemoveGapColCommand
 
       if (!delete && startCol > -1)
       {
-        this.appendEdit(DELETE_GAP, seqs,
-                        startCol - columnsDeleted,
-                        endCol - startCol,
-                        al,
-                        false,null);
+        this.appendEdit(DELETE_GAP, seqs, startCol - columnsDeleted, endCol
+                - startCol, al, false, null);
 
         columnsDeleted += (endCol - startCol);
         startCol = -1;
@@ -81,25 +95,22 @@ public class RemoveGapColCommand
 
     if (delete && startCol > -1)
     {
-      //This is for empty columns at the
-      //end of the alignment
+      // This is for empty columns at the
+      // end of the alignment
 
-      this.appendEdit(DELETE_GAP, seqs,
-                      startCol - columnsDeleted,
-                      end - startCol + 1,
-                      al,
-                      false,null);
+      this.appendEdit(DELETE_GAP, seqs, startCol - columnsDeleted, end
+              - startCol + 1, al, false, null);
 
       columnsDeleted += (end - startCol + 1);
     }
 
-    performEdit(0,null);
+    performEdit(0, null);
   }
 
   public int getSize()
   {
-    //We're interested in the number of columns deleted,
-    //Not the number of sequence edits.
+    // We're interested in the number of columns deleted,
+    // Not the number of sequence edits.
     return columnsDeleted;
   }
 
diff --git a/src/jalview/commands/RemoveGapsCommand.java b/src/jalview/commands/RemoveGapsCommand.java
index 5639fa5..d2bd486 100644
--- a/src/jalview/commands/RemoveGapsCommand.java
+++ b/src/jalview/commands/RemoveGapsCommand.java
@@ -1,31 +1,48 @@
-package jalview.commands;
-
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
+package jalview.commands;
+
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer Copyright (C) 2007 AM
+ * Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU General Public License as published by the Free Software
+ * Foundation; either version 2 of the License, or (at your option) any later
+ * version.
+ * 
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+ * details.
+ * 
+ * You should have received a copy of the GNU General Public License along with
+ * this program; if not, write to the Free Software Foundation, Inc., 51
+ * Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
 
 import jalview.datamodel.*;
 
-public class RemoveGapsCommand
-    extends EditCommand
+public class RemoveGapsCommand extends EditCommand
 {
-  public RemoveGapsCommand(String description,
-                           SequenceI[] seqs, AlignmentI al)
+  public RemoveGapsCommand(String description, SequenceI[] seqs,
+          AlignmentI al)
   {
     this.description = description;
     int width = 0;
@@ -40,9 +57,8 @@ public class RemoveGapsCommand
     findGaps(seqs, 0, width, al);
   }
 
-  public RemoveGapsCommand(String description,
-                           SequenceI[] seqs,
-                           int start, int end, AlignmentI al)
+  public RemoveGapsCommand(String description, SequenceI[] seqs, int start,
+          int end, AlignmentI al)
   {
     this.description = description;
     findGaps(seqs, start, end, al);
@@ -91,11 +107,8 @@ public class RemoveGapsCommand
         if (!delete && startCol > -1)
         {
           this.appendEdit(DELETE_GAP, new SequenceI[]
-                          {seqs[s]},
-                          start + startCol - deletedCols,
-                          endCol - startCol,
-                          al,
-                          false,null);
+          { seqs[s] }, start + startCol - deletedCols, endCol - startCol,
+                  al, false, null);
 
           deletedCols += (endCol - startCol);
           startCol = -1;
@@ -105,16 +118,13 @@ public class RemoveGapsCommand
       if (delete && startCol > -1)
       {
         this.appendEdit(DELETE_GAP, new SequenceI[]
-                        {seqs[s]},
-                        start + startCol - deletedCols,
-                        jSize - startCol,
-                        al,
-                        false,null);
+        { seqs[s] }, start + startCol - deletedCols, jSize - startCol, al,
+                false, null);
       }
 
     }
 
-    performEdit(0,null);
+    performEdit(0, null);
   }
 
 }
diff --git a/src/jalview/commands/SlideSequencesCommand.java b/src/jalview/commands/SlideSequencesCommand.java
index 9b9c99e..c8a5533 100644
--- a/src/jalview/commands/SlideSequencesCommand.java
+++ b/src/jalview/commands/SlideSequencesCommand.java
@@ -1,23 +1,21 @@
-
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/
-
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.commands;
 
 import jalview.datamodel.*;
@@ -26,11 +24,8 @@ public class SlideSequencesCommand extends EditCommand
 {
   boolean gapsInsertedBegin = false;
 
-  public SlideSequencesCommand(String description,
-                               SequenceI[] seqsLeft,
-                               SequenceI[] seqsRight,
-                               int slideSize,
-                               char gapChar)
+  public SlideSequencesCommand(String description, SequenceI[] seqsLeft,
+          SequenceI[] seqsRight, int slideSize, char gapChar)
   {
     this.description = description;
 
@@ -49,12 +44,12 @@ public class SlideSequencesCommand extends EditCommand
 
     if (!gapsInsertedBegin)
       edits = new Edit[]
-          {  new Edit(DELETE_GAP, seqsLeft, 0, slideSize, gapChar)};
+      { new Edit(DELETE_GAP, seqsLeft, 0, slideSize, gapChar) };
     else
       edits = new Edit[]
-          {  new Edit(INSERT_GAP, seqsRight, 0, slideSize, gapChar)};
+      { new Edit(INSERT_GAP, seqsRight, 0, slideSize, gapChar) };
 
-    performEdit(0,null);
+    performEdit(0, null);
   }
 
   public boolean getGapsInsertedBegin()
@@ -66,7 +61,7 @@ public class SlideSequencesCommand extends EditCommand
   {
     boolean same = false;
 
-    if(command.edits[0].seqs.length==edits[0].seqs.length)
+    if (command.edits[0].seqs.length == edits[0].seqs.length)
     {
       same = true;
       for (int i = 0; i < command.edits[0].seqs.length; i++)
@@ -78,7 +73,7 @@ public class SlideSequencesCommand extends EditCommand
       }
     }
 
-    if(same)
+    if (same)
     {
       Edit[] temp = new Edit[command.edits.length + 1];
       System.arraycopy(command.edits, 0, temp, 0, command.edits.length);
@@ -89,5 +84,3 @@ public class SlideSequencesCommand extends EditCommand
     return same;
   }
 }
-
-
diff --git a/src/jalview/commands/TrimRegionCommand.java b/src/jalview/commands/TrimRegionCommand.java
index 4110bd1..30f813f 100644
--- a/src/jalview/commands/TrimRegionCommand.java
+++ b/src/jalview/commands/TrimRegionCommand.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -23,10 +23,10 @@ import java.util.*;
 import jalview.datamodel.*;
 import jalview.util.*;
 
-public class TrimRegionCommand
-    extends EditCommand
+public class TrimRegionCommand extends EditCommand
 {
   public static String TRIM_LEFT = "TrimLeft";
+
   public static String TRIM_RIGHT = "TrimRight";
 
   public ColumnSelection colSel = null;
@@ -41,13 +41,9 @@ public class TrimRegionCommand
 
   int columnsDeleted;
 
-  public TrimRegionCommand(String description,
-                           String command,
-                           SequenceI[] seqs,
-                           int column,
-                           AlignmentI al,
-                           ColumnSelection colSel,
-                           SequenceGroup selectedRegion)
+  public TrimRegionCommand(String description, String command,
+          SequenceI[] seqs, int column, AlignmentI al,
+          ColumnSelection colSel, SequenceGroup selectedRegion)
   {
     this.description = description;
     this.selectionGroup = selectedRegion;
@@ -62,8 +58,7 @@ public class TrimRegionCommand
       columnsDeleted = column;
 
       edits = new Edit[]
-          {
-          new Edit(CUT, seqs, 0, column, al)};
+      { new Edit(CUT, seqs, 0, column, al) };
     }
     else if (command.equalsIgnoreCase(TRIM_RIGHT))
     {
@@ -76,12 +71,11 @@ public class TrimRegionCommand
       columnsDeleted = width - 1;
 
       edits = new Edit[]
-          {
-          new Edit(CUT, seqs, column + 1, width, al)};
+      { new Edit(CUT, seqs, column + 1, width, al) };
     }
 
-    //We need to keep a record of the sequence start
-    //in order to restore the state after a redo
+    // We need to keep a record of the sequence start
+    // in order to restore the state after a redo
     int i, isize = edits[0].seqs.length;
     start = new int[isize];
     for (i = 0; i < isize; i++)
@@ -89,7 +83,7 @@ public class TrimRegionCommand
       start[i] = edits[0].seqs[i].getStart();
     }
 
-    performEdit(0,null);
+    performEdit(0, null);
   }
 
   void cut(Edit command)
@@ -99,13 +93,13 @@ public class TrimRegionCommand
     {
       if (command.position == 0)
       {
-        //This is a TRIM_LEFT command
+        // This is a TRIM_LEFT command
         column = command.seqs[j].findPosition(command.number);
         command.seqs[j].setStart(column);
       }
       else
       {
-        //This is a TRIM_RIGHT command
+        // This is a TRIM_RIGHT command
         column = command.seqs[j].findPosition(command.position) - 1;
         command.seqs[j].setEnd(column);
       }
@@ -124,7 +118,7 @@ public class TrimRegionCommand
     else
     {
       deletedHiddenColumns = colSel.compensateForEdit(command.position,
-          command.number);
+              command.number);
       if (selectionGroup != null)
       {
         selectionGroup.adjustForRemoveRight(command.position);
@@ -144,8 +138,8 @@ public class TrimRegionCommand
       }
       else
       {
-        column = command.seqs[j]
-            .findPosition(command.number + command.position) - 1;
+        column = command.seqs[j].findPosition(command.number
+                + command.position) - 1;
         command.seqs[j].setEnd(column);
       }
     }
@@ -155,7 +149,7 @@ public class TrimRegionCommand
       colSel.compensateForEdit(0, -command.number);
       if (selectionGroup != null)
       {
-        selectionGroup.adjustForRemoveLeft( -command.number);
+        selectionGroup.adjustForRemoveLeft(-command.number);
       }
     }
 
diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index 6c6c26e..3b59249 100644
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.datamodel;
 
 import java.util.Enumeration;
@@ -13,25 +31,29 @@ import jalview.util.MapList;
 public class AlignedCodonFrame
 {
   /**
-   * array of nucleotide positions for aligned codons at column of aligned proteins.
+   * array of nucleotide positions for aligned codons at column of aligned
+   * proteins.
    */
   public int[][] codons = null;
+
   /**
-   * width of protein sequence alignement
-   * implicit assertion that codons.length >= aaWidth
+   * width of protein sequence alignement implicit assertion that codons.length >=
+   * aaWidth
    */
-  public int aaWidth=0;
+  public int aaWidth = 0;
+
   /**
    * initialise codon frame with a nominal alignment width
+   * 
    * @param aWidth
    */
   public AlignedCodonFrame(int aWidth)
   {
-    if (aWidth<=0)
-   {
-      codons=null;
+    if (aWidth <= 0)
+    {
+      codons = null;
       return;
-   }
+    }
     codons = new int[aWidth][];
     for (int res = 0; res < aWidth; res++)
       codons[res] = null;
@@ -39,6 +61,7 @@ public class AlignedCodonFrame
 
   /**
    * ensure that codons array is at least as wide as aslen residues
+   * 
    * @param aslen
    * @return (possibly newly expanded) codon array
    */
@@ -57,29 +80,37 @@ public class AlignedCodonFrame
     }
     return codons;
   }
+
   /**
-   * @return width of aligned translated amino acid residues 
+   * @return width of aligned translated amino acid residues
    */
   public int getaaWidth()
   {
     return aaWidth;
   }
+
   /**
-   * TODO: not an ideal solution - we reference the aligned amino acid sequences in order to make insertions on them
-   * Better would be dnaAlignment and aaAlignment reference....
+   * TODO: not an ideal solution - we reference the aligned amino acid sequences
+   * in order to make insertions on them Better would be dnaAlignment and
+   * aaAlignment reference....
    */
-  Vector a_aaSeqs=new Vector();
+  Vector a_aaSeqs = new Vector();
+
   /**
-   * increase aaWidth by one and insert a new aligned codon position space at aspos.
+   * increase aaWidth by one and insert a new aligned codon position space at
+   * aspos.
+   * 
    * @param aspos
    */
   public void insertAAGap(int aspos, char gapCharacter)
-  {            
-    // this aa appears before the aligned codons at aspos - so shift them in each pair of mapped sequences
+  {
+    // this aa appears before the aligned codons at aspos - so shift them in
+    // each pair of mapped sequences
     aaWidth++;
-    if (a_aaSeqs!=null)
+    if (a_aaSeqs != null)
     {
-      // we actually have to modify the aligned sequences here, so use the a_aaSeqs vector
+      // we actually have to modify the aligned sequences here, so use the
+      // a_aaSeqs vector
       Enumeration sq = a_aaSeqs.elements();
       while (sq.hasMoreElements())
       {
@@ -87,11 +118,11 @@ public class AlignedCodonFrame
       }
     }
     checkCodonFrameWidth(aspos);
-    if (aspos<aaWidth)
+    if (aspos < aaWidth)
     {
       aaWidth++;
-      System.arraycopy(codons, aspos, codons, aspos+1, aaWidth-aspos);
-      codons[aspos]=null; // clear so new codon position can be marked.
+      System.arraycopy(codons, aspos, codons, aspos + 1, aaWidth - aspos);
+      codons[aspos] = null; // clear so new codon position can be marked.
     }
   }
 
@@ -99,80 +130,90 @@ public class AlignedCodonFrame
   {
     aaWidth = aapos;
   }
+
   /**
    * tied array of na Sequence objects.
    */
-  SequenceI[] dnaSeqs=null;
+  SequenceI[] dnaSeqs = null;
+
   /**
-   * tied array of Mappings to protein sequence Objects and 
-     SequenceI[] aaSeqs=null;
-   * MapLists where eac maps from the corresponding dnaSeqs element to corresponding aaSeqs element  
+   * tied array of Mappings to protein sequence Objects and SequenceI[]
+   * aaSeqs=null; MapLists where eac maps from the corresponding dnaSeqs element
+   * to corresponding aaSeqs element
    */
-  Mapping[] dnaToProt=null;
+  Mapping[] dnaToProt = null;
+
   /**
-   * add a mapping between the dataset sequences for the associated dna and protein sequence objects
+   * add a mapping between the dataset sequences for the associated dna and
+   * protein sequence objects
+   * 
    * @param dnaseq
    * @param aaseq
    * @param map
    */
   public void addMap(SequenceI dnaseq, SequenceI aaseq, MapList map)
-  { 
-    int nlen=1;
-    if (dnaSeqs!=null)
+  {
+    int nlen = 1;
+    if (dnaSeqs != null)
     {
-      nlen = dnaSeqs.length+1;
+      nlen = dnaSeqs.length + 1;
     }
     SequenceI[] ndna = new SequenceI[nlen];
     Mapping[] ndtp = new Mapping[nlen];
-    if (dnaSeqs!=null)
+    if (dnaSeqs != null)
     {
-      System.arraycopy(dnaSeqs,0,ndna, 0, dnaSeqs.length);
-      System.arraycopy(dnaToProt,0,ndtp, 0, dnaSeqs.length);
+      System.arraycopy(dnaSeqs, 0, ndna, 0, dnaSeqs.length);
+      System.arraycopy(dnaToProt, 0, ndtp, 0, dnaSeqs.length);
     }
     dnaSeqs = ndna;
     dnaToProt = ndtp;
     nlen--;
-    dnaSeqs[nlen] = (dnaseq.getDatasetSequence()==null) ? dnaseq : dnaseq.getDatasetSequence();
+    dnaSeqs[nlen] = (dnaseq.getDatasetSequence() == null) ? dnaseq : dnaseq
+            .getDatasetSequence();
     Mapping mp = new Mapping(map);
     // JBPNote DEBUG! THIS !
-    //dnaseq.transferAnnotation(aaseq, mp);
-    //aaseq.transferAnnotation(dnaseq, new Mapping(map.getInverse()));
-    mp.to = (aaseq.getDatasetSequence()==null) ? aaseq : aaseq.getDatasetSequence();
+    // dnaseq.transferAnnotation(aaseq, mp);
+    // aaseq.transferAnnotation(dnaseq, new Mapping(map.getInverse()));
+    mp.to = (aaseq.getDatasetSequence() == null) ? aaseq : aaseq
+            .getDatasetSequence();
     a_aaSeqs.addElement(aaseq);
     dnaToProt[nlen] = mp;
   }
 
-
   public SequenceI[] getdnaSeqs()
   {
     return dnaSeqs;
   }
+
   public SequenceI[] getAaSeqs()
   {
-    if (dnaToProt==null)
+    if (dnaToProt == null)
       return null;
     SequenceI[] sqs = new SequenceI[dnaToProt.length];
-    for (int sz=0; sz<dnaToProt.length; sz++)
+    for (int sz = 0; sz < dnaToProt.length; sz++)
     {
-      sqs[sz]  = dnaToProt[sz].to;
+      sqs[sz] = dnaToProt[sz].to;
     }
     return sqs;
   }
+
   public MapList[] getdnaToProt()
   {
-    if (dnaToProt==null)
+    if (dnaToProt == null)
       return null;
     MapList[] sqs = new MapList[dnaToProt.length];
-    for (int sz=0; sz<dnaToProt.length; sz++)
+    for (int sz = 0; sz < dnaToProt.length; sz++)
     {
-      sqs[sz]  = dnaToProt[sz].map;
+      sqs[sz] = dnaToProt[sz].map;
     }
     return sqs;
   }
+
   public Mapping[] getProtMappings()
   {
     return dnaToProt;
   }
+
   /**
    * 
    * @param sequenceRef
@@ -180,18 +221,19 @@ public class AlignedCodonFrame
    */
   public SequenceI getAaForDnaSeq(SequenceI dnaSeqRef)
   {
-    if (dnaSeqs==null)
+    if (dnaSeqs == null)
     {
       return null;
     }
     SequenceI dnads = dnaSeqRef.getDatasetSequence();
-    for (int ds=0;ds<dnaSeqs.length; ds++)
+    for (int ds = 0; ds < dnaSeqs.length; ds++)
     {
-      if (dnaSeqs[ds]==dnaSeqRef || dnaSeqs[ds]==dnads)
+      if (dnaSeqs[ds] == dnaSeqRef || dnaSeqs[ds] == dnads)
         return dnaToProt[ds].to;
     }
     return null;
   }
+
   /**
    * 
    * @param sequenceRef
@@ -199,69 +241,79 @@ public class AlignedCodonFrame
    */
   public SequenceI getDnaForAaSeq(SequenceI aaSeqRef)
   {
-    if (dnaToProt==null)
+    if (dnaToProt == null)
     {
       return null;
     }
     SequenceI aads = aaSeqRef.getDatasetSequence();
-    for (int as=0;as<dnaToProt.length; as++)
+    for (int as = 0; as < dnaToProt.length; as++)
     {
-      if (dnaToProt[as].to==aaSeqRef || dnaToProt[as].to==aads)
+      if (dnaToProt[as].to == aaSeqRef || dnaToProt[as].to == aads)
         return dnaSeqs[as];
     }
     return null;
   }
+
   /**
    * test to see if codon frame involves seq in any way
-   * @param seq a nucleotide or protein sequence
-   * @return true if a mapping exists to or from this sequence to any translated sequence
+   * 
+   * @param seq
+   *                a nucleotide or protein sequence
+   * @return true if a mapping exists to or from this sequence to any translated
+   *         sequence
    */
   public boolean involvesSequence(SequenceI seq)
   {
-    return getAaForDnaSeq(seq)!=null || getDnaForAaSeq(seq)!=null;
+    return getAaForDnaSeq(seq) != null || getDnaForAaSeq(seq) != null;
   }
+
   /**
-   * Add search results for regions in other sequences that translate or are translated from a particular position in seq 
+   * Add search results for regions in other sequences that translate or are
+   * translated from a particular position in seq
+   * 
    * @param seq
-   * @param index position in seq
-   * @param results where highlighted regions go
+   * @param index
+   *                position in seq
+   * @param results
+   *                where highlighted regions go
    */
-  public void markMappedRegion(SequenceI seq, int index, SearchResults results)
+  public void markMappedRegion(SequenceI seq, int index,
+          SearchResults results)
   {
-    if (dnaToProt==null)
+    if (dnaToProt == null)
     {
       return;
     }
     int[] codon;
     SequenceI ds = seq.getDatasetSequence();
-    for (int mi = 0; mi<dnaToProt.length; mi++)
+    for (int mi = 0; mi < dnaToProt.length; mi++)
     {
-      if (dnaSeqs[mi]==seq || dnaSeqs[mi]==ds)
+      if (dnaSeqs[mi] == seq || dnaSeqs[mi] == ds)
       {
         // DEBUG System.err.println("dna pos "+index);
-        codon = dnaToProt[mi].map.locateInTo(index,index);
-        if (codon!=null)
+        codon = dnaToProt[mi].map.locateInTo(index, index);
+        if (codon != null)
         {
-          for (int i=0; i<codon.length; i+=2)
-            {
-              results.addResult(dnaToProt[mi].to, codon[i], codon[i+1]);
-            }
+          for (int i = 0; i < codon.length; i += 2)
+          {
+            results.addResult(dnaToProt[mi].to, codon[i], codon[i + 1]);
+          }
         }
-      } else
-        if (dnaToProt[mi].to==seq || dnaToProt[mi].to==ds)
+      }
+      else if (dnaToProt[mi].to == seq || dnaToProt[mi].to == ds)
+      {
+        // DEBUG System.err.println("aa pos "+index);
         {
-          // DEBUG System.err.println("aa pos "+index);
+          codon = dnaToProt[mi].map.locateInFrom(index, index);
+          if (codon != null)
           {
-            codon = dnaToProt[mi].map.locateInFrom(index, index);
-            if (codon!=null)
+            for (int i = 0; i < codon.length; i += 2)
             {
-            for (int i=0; i<codon.length; i+=2)
-              {
-                results.addResult(dnaSeqs[mi], codon[i], codon[i+1]);
-              }
+              results.addResult(dnaSeqs[mi], codon[i], codon[i + 1]);
+            }
           }
         }
-        }
+      }
     }
   }
 }
diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index a88fa9e..1312e22 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -22,17 +22,23 @@ import java.util.*;
 
 import jalview.analysis.*;
 
-/** Data structure to hold and manipulate a multiple sequence alignment
+/**
+ * Data structure to hold and manipulate a multiple sequence alignment
  */
-public class Alignment
-    implements AlignmentI
+public class Alignment implements AlignmentI
 {
   protected Alignment dataset;
+
   protected Vector sequences;
+
   protected Vector groups = new Vector();
+
   protected char gapCharacter = '-';
+
   protected int type = NUCLEOTIDE;
+
   public static final int PROTEIN = 0;
+
   public static final int NUCLEOTIDE = 1;
 
   /** DOCUMENT ME!! */
@@ -64,8 +70,9 @@ public class Alignment
 
   }
 
-  /** Make an alignment from an array of Sequences.
-   *
+  /**
+   * Make an alignment from an array of Sequences.
+   * 
    * @param sequences
    */
   public Alignment(SequenceI[] seqs)
@@ -75,20 +82,25 @@ public class Alignment
 
   /**
    * Make a new alignment from an array of SeqCigars
-   * @param seqs SeqCigar[]
+   * 
+   * @param seqs
+   *                SeqCigar[]
    */
   public Alignment(SeqCigar[] alseqs)
   {
-    SequenceI[] seqs = SeqCigar.createAlignmentSequences(alseqs, gapCharacter,
-        new ColumnSelection(), null);
+    SequenceI[] seqs = SeqCigar.createAlignmentSequences(alseqs,
+            gapCharacter, new ColumnSelection(), null);
     initAlignment(seqs);
   }
 
   /**
-   * Make a new alignment from an CigarArray
-   * JBPNote - can only do this when compactAlignment does not contain hidden regions.
-   * JBPNote - must also check that compactAlignment resolves to a set of SeqCigars - or construct them appropriately.
-   * @param compactAlignment CigarArray
+   * Make a new alignment from an CigarArray JBPNote - can only do this when
+   * compactAlignment does not contain hidden regions. JBPNote - must also check
+   * that compactAlignment resolves to a set of SeqCigars - or construct them
+   * appropriately.
+   * 
+   * @param compactAlignment
+   *                CigarArray
    */
   public static AlignmentI createAlignment(CigarArray compactAlignment)
   {
@@ -98,7 +110,7 @@ public class Alignment
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public Vector getSequences()
@@ -108,7 +120,7 @@ public class Alignment
 
   public SequenceI[] getSequencesArray()
   {
-    if (sequences==null)
+    if (sequences == null)
       return null;
     SequenceI[] reply = new SequenceI[sequences.size()];
     for (int i = 0; i < sequences.size(); i++)
@@ -120,9 +132,10 @@ public class Alignment
 
   /**
    * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
-   *
+   * 
+   * @param i
+   *                DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   public SequenceI getSequenceAt(int i)
@@ -135,8 +148,9 @@ public class Alignment
     return null;
   }
 
-  /** Adds a sequence to the alignment.  Recalculates maxLength and size.
-   *
+  /**
+   * Adds a sequence to the alignment. Recalculates maxLength and size.
+   * 
    * @param snew
    */
   public void addSequence(SequenceI snew)
@@ -156,17 +170,22 @@ public class Alignment
         snew = adding;
       }
     }
-    if (sequences==null) {
-      initAlignment(new SequenceI[] { snew });
-    } else {
+    if (sequences == null)
+    {
+      initAlignment(new SequenceI[]
+      { snew });
+    }
+    else
+    {
       sequences.addElement(snew);
     }
-    if (hiddenSequences!=null)
+    if (hiddenSequences != null)
       hiddenSequences.adjustHeightSequenceAdded();
   }
 
-  /** Adds a sequence to the alignment.  Recalculates maxLength and size.
-   *
+  /**
+   * Adds a sequence to the alignment. Recalculates maxLength and size.
+   * 
    * @param snew
    */
   public void setSequenceAt(int i, SequenceI snew)
@@ -179,7 +198,7 @@ public class Alignment
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public Vector getGroups()
@@ -189,7 +208,7 @@ public class Alignment
 
   public void finalize()
   {
-    if(getDataset()!=null)
+    if (getDataset() != null)
       getDataset().removeAlignmentRef();
 
     dataset = null;
@@ -200,11 +219,12 @@ public class Alignment
   }
 
   /**
-   * decrement the alignmentRefs counter by one and call finalize if it goes to zero.
+   * decrement the alignmentRefs counter by one and call finalize if it goes to
+   * zero.
    */
   private void removeAlignmentRef()
   {
-    if (--alignmentRefs==0)
+    if (--alignmentRefs == 0)
     {
       finalize();
     }
@@ -212,8 +232,9 @@ public class Alignment
 
   /**
    * DOCUMENT ME!
-   *
-   * @param s DOCUMENT ME!
+   * 
+   * @param s
+   *                DOCUMENT ME!
    */
   public void deleteSequence(SequenceI s)
   {
@@ -222,8 +243,9 @@ public class Alignment
 
   /**
    * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
+   * 
+   * @param i
+   *                DOCUMENT ME!
    */
   public void deleteSequence(int i)
   {
@@ -252,9 +274,10 @@ public class Alignment
 
   /**
    * DOCUMENT ME!
-   *
-   * @param s DOCUMENT ME!
-   *
+   * 
+   * @param s
+   *                DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   public SequenceGroup[] findAllGroups(SequenceI s)
@@ -336,33 +359,38 @@ public class Alignment
   /**    */
   public SequenceI findName(String name)
   {
-    return findName(name,false);
+    return findName(name, false);
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.datamodel.AlignmentI#findName(java.lang.String, boolean)
    */
   public SequenceI findName(String token, boolean b)
   {
     return findName(null, token, b);
   }
-  
-  /* (non-Javadoc)
-   * @see jalview.datamodel.AlignmentI#findName(SequenceI, java.lang.String, boolean)
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.AlignmentI#findName(SequenceI, java.lang.String,
+   *      boolean)
    */
   public SequenceI findName(SequenceI startAfter, String token, boolean b)
   {
-  
+
     int i = 0;
-    SequenceI sq=null;
-    String sqname=null;
-    if (startAfter!=null)
+    SequenceI sq = null;
+    String sqname = null;
+    if (startAfter != null)
     {
       // try to find the sequence in the alignment
-      boolean matched=false;
-      while (i<sequences.size())
+      boolean matched = false;
+      while (i < sequences.size())
       {
-        if (getSequenceAt(i++)==startAfter)
+        if (getSequenceAt(i++) == startAfter)
         {
           matched = true;
           break;
@@ -370,7 +398,7 @@ public class Alignment
       }
       if (!matched)
       {
-        i=0;
+        i = 0;
       }
     }
     while (i < sequences.size())
@@ -378,7 +406,7 @@ public class Alignment
       sq = getSequenceAt(i);
       sqname = sq.getName();
       if (sqname.equals(token) // exact match
-          || (b && // allow imperfect matches - case varies 
+              || (b && // allow imperfect matches - case varies
               (sqname.equalsIgnoreCase(token))))
       {
         return getSequenceAt(i);
@@ -389,6 +417,7 @@ public class Alignment
 
     return null;
   }
+
   public SequenceI[] findSequenceMatch(String name)
   {
     Vector matches = new Vector();
@@ -433,7 +462,7 @@ public class Alignment
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public int getHeight()
@@ -443,7 +472,7 @@ public class Alignment
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public int getWidth()
@@ -463,8 +492,9 @@ public class Alignment
 
   /**
    * DOCUMENT ME!
-   *
-   * @param gc DOCUMENT ME!
+   * 
+   * @param gc
+   *                DOCUMENT ME!
    */
   public void setGapCharacter(char gc)
   {
@@ -473,17 +503,14 @@ public class Alignment
     for (int i = 0; i < sequences.size(); i++)
     {
       Sequence seq = (Sequence) sequences.elementAt(i);
-      seq.setSequence(seq.getSequenceAsString()
-                      .replace('.', gc)
-                      .replace('-', gc)
-                      .replace(' ', gc)
-          );
+      seq.setSequence(seq.getSequenceAsString().replace('.', gc).replace(
+              '-', gc).replace(' ', gc));
     }
   }
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public char getGapCharacter()
@@ -493,7 +520,7 @@ public class Alignment
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public boolean isAligned()
@@ -510,7 +537,10 @@ public class Alignment
 
     return true;
   }
-  /* (non-Javadoc)
+
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.datamodel.AlignmentI#deleteAnnotation(jalview.datamodel.AlignmentAnnotation)
    */
   public boolean deleteAnnotation(AlignmentAnnotation aa)
@@ -529,24 +559,24 @@ public class Alignment
 
     AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize - 1];
 
-    boolean swap=false;
+    boolean swap = false;
     int tIndex = 0;
 
     for (int i = 0; i < aSize; i++)
     {
       if (annotations[i] == aa)
       {
-        swap=true;
+        swap = true;
         continue;
       }
-      if (tIndex<temp.length)
+      if (tIndex < temp.length)
         temp[tIndex++] = annotations[i];
     }
 
     if (swap)
     {
       annotations = temp;
-      if(aa.sequenceRef!=null)
+      if (aa.sequenceRef != null)
         aa.sequenceRef.removeAlignmentAnnotation(aa);
     }
     return swap;
@@ -554,8 +584,9 @@ public class Alignment
 
   /**
    * DOCUMENT ME!
-   *
-   * @param aa DOCUMENT ME!
+   * 
+   * @param aa
+   *                DOCUMENT ME!
    */
   public void addAnnotation(AlignmentAnnotation aa)
   {
@@ -616,7 +647,7 @@ public class Alignment
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public AlignmentAnnotation[] getAlignmentAnnotation()
@@ -678,10 +709,12 @@ public class Alignment
     }
     dataset.addAlignmentRef();
   }
+
   /**
    * reference count for number of alignments referencing this one.
    */
-  int alignmentRefs=0;
+  int alignmentRefs = 0;
+
   /**
    * increase reference count to this alignment.
    */
@@ -699,7 +732,7 @@ public class Alignment
   {
     boolean modified = false;
 
-    //Remove excess gaps from the end of alignment
+    // Remove excess gaps from the end of alignment
     int maxLength = -1;
 
     SequenceI current;
@@ -708,8 +741,8 @@ public class Alignment
       current = getSequenceAt(i);
       for (int j = current.getLength(); j > maxLength; j--)
       {
-        if (j > maxLength && !jalview.util.Comparison.isGap(
-            current.getCharAt(j)))
+        if (j > maxLength
+                && !jalview.util.Comparison.isGap(current.getCharAt(j)))
         {
           maxLength = j;
           break;
@@ -720,16 +753,14 @@ public class Alignment
     maxLength++;
 
     int cLength;
-    for (int i = 0; i < sequences.size();
-         i++)
+    for (int i = 0; i < sequences.size(); i++)
     {
       current = getSequenceAt(i);
       cLength = current.getLength();
 
       if (cLength < maxLength)
       {
-        current.insertCharAt(cLength,
-                             maxLength - cLength, gapCharacter);
+        current.insertCharAt(cLength, maxLength - cLength, gapCharacter);
         modified = true;
       }
       else if (current.getLength() > maxLength)
@@ -750,7 +781,7 @@ public class Alignment
     SeqCigar alseqs[] = new SeqCigar[sequences.size()];
     for (int i = 0; i < sequences.size(); i++)
     {
-      alseqs[i] = new SeqCigar( (SequenceI) sequences.elementAt(i));
+      alseqs[i] = new SeqCigar((SequenceI) sequences.elementAt(i));
     }
     CigarArray cal = new CigarArray(alseqs);
     cal.addOperation(CigarArray.M, getWidth());
@@ -759,15 +790,15 @@ public class Alignment
 
   public void setProperty(Object key, Object value)
   {
-    if(alignmentProperties==null)
+    if (alignmentProperties == null)
       alignmentProperties = new Hashtable();
 
-    alignmentProperties.put(key,value);
+    alignmentProperties.put(key, value);
   }
 
   public Object getProperty(Object key)
   {
-    if(alignmentProperties!=null)
+    if (alignmentProperties != null)
       return alignmentProperties.get(key);
     else
       return null;
@@ -777,26 +808,33 @@ public class Alignment
   {
     return alignmentProperties;
   }
-  AlignedCodonFrame[] codonFrameList=null;
-  /* (non-Javadoc)
+
+  AlignedCodonFrame[] codonFrameList = null;
+
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame)
    */
   public void addCodonFrame(AlignedCodonFrame codons)
   {
-    if (codons==null)
+    if (codons == null)
       return;
-    if (codonFrameList==null)
+    if (codonFrameList == null)
     {
-      codonFrameList = new AlignedCodonFrame[] { codons };
+      codonFrameList = new AlignedCodonFrame[]
+      { codons };
       return;
     }
-    AlignedCodonFrame[] t = new AlignedCodonFrame[codonFrameList.length+1];
+    AlignedCodonFrame[] t = new AlignedCodonFrame[codonFrameList.length + 1];
     System.arraycopy(codonFrameList, 0, t, 0, codonFrameList.length);
     t[codonFrameList.length] = codons;
     codonFrameList = t;
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.datamodel.AlignmentI#getCodonFrame(int)
    */
   public AlignedCodonFrame getCodonFrame(int index)
@@ -804,27 +842,31 @@ public class Alignment
     return codonFrameList[index];
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
    */
   public AlignedCodonFrame[] getCodonFrame(SequenceI seq)
   {
-    if (seq==null || codonFrameList==null)
+    if (seq == null || codonFrameList == null)
       return null;
-    Vector cframes=new Vector();
-    for (int f=0;f<codonFrameList.length; f++)
+    Vector cframes = new Vector();
+    for (int f = 0; f < codonFrameList.length; f++)
     {
       if (codonFrameList[f].involvesSequence(seq))
         cframes.addElement(codonFrameList[f]);
     }
-    if (cframes.size()==0)
+    if (cframes.size() == 0)
       return null;
     AlignedCodonFrame[] cfr = new AlignedCodonFrame[cframes.size()];
     cframes.copyInto(cfr);
     return cfr;
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.datamodel.AlignmentI#getCodonFrames()
    */
   public AlignedCodonFrame[] getCodonFrames()
@@ -832,23 +874,26 @@ public class Alignment
     return codonFrameList;
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.AlignedCodonFrame)
    */
   public boolean removeCodonFrame(AlignedCodonFrame codons)
   {
-    if (codons==null || codonFrameList==null)
+    if (codons == null || codonFrameList == null)
       return false;
-    boolean removed=false;
-    int i=0,iSize=codonFrameList.length;
-    while (i<iSize)
+    boolean removed = false;
+    int i = 0, iSize = codonFrameList.length;
+    while (i < iSize)
     {
-      if (codonFrameList[i]==codons)
+      if (codonFrameList[i] == codons)
       {
-        removed=true;
-        if (i+1<iSize)
+        removed = true;
+        if (i + 1 < iSize)
         {
-          System.arraycopy(codonFrameList,i+1,codonFrameList, i, iSize-i-1);
+          System.arraycopy(codonFrameList, i + 1, codonFrameList, i, iSize
+                  - i - 1);
         }
         iSize--;
       }
diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index f2864db..381a054 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -23,14 +23,16 @@ import java.util.Hashtable;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
 public class AlignmentAnnotation
 {
-  /** If true, this annotations is calculated every edit,
-   * eg consensus, quality or conservation graphs */
+  /**
+   * If true, this annotations is calculated every edit, eg consensus, quality
+   * or conservation graphs
+   */
   public boolean autoCalculated = false;
 
   public String annotationId;
@@ -57,11 +59,12 @@ public class AlignmentAnnotation
   /**
    * Score associated with label and description.
    */
-  public double score= Double.NaN;
+  public double score = Double.NaN;
+
   /**
    * flag indicating if annotation has a score.
    */
-  public boolean hasScore=false;
+  public boolean hasScore = false;
 
   public GraphLine threshold;
 
@@ -98,7 +101,6 @@ public class AlignmentAnnotation
 
   public boolean belowAlignment = true;
 
-
   public static int getGraphValueFromString(String string)
   {
     if (string.equalsIgnoreCase("BAR_GRAPH"))
@@ -117,13 +119,16 @@ public class AlignmentAnnotation
 
   /**
    * Creates a new AlignmentAnnotation object.
-   *
-   * @param label short label shown under sequence labels
-   * @param description text displayed on mouseover
-   * @param annotations set of positional annotation elements
+   * 
+   * @param label
+   *                short label shown under sequence labels
+   * @param description
+   *                text displayed on mouseover
+   * @param annotations
+   *                set of positional annotation elements
    */
   public AlignmentAnnotation(String label, String description,
-                             Annotation[] annotations)
+          Annotation[] annotations)
   {
     // always editable?
     editable = true;
@@ -131,44 +136,48 @@ public class AlignmentAnnotation
     this.description = description;
     this.annotations = annotations;
 
-     validateRangeAndDisplay();
+    validateRangeAndDisplay();
   }
 
   void areLabelsSecondaryStructure()
   {
     boolean nonSSLabel = false;
-    char firstChar=0;
+    char firstChar = 0;
     for (int i = 0; i < annotations.length; i++)
     {
       if (annotations[i] == null)
       {
         continue;
       }
-      if (annotations[i].secondaryStructure == 'H' ||
-          annotations[i].secondaryStructure == 'E')
+      if (annotations[i].secondaryStructure == 'H'
+              || annotations[i].secondaryStructure == 'E')
       {
-          hasIcons = true;
+        hasIcons = true;
       }
 
-      if(annotations[i].displayCharacter==null)
+      if (annotations[i].displayCharacter == null)
       {
         continue;
       }
       if (annotations[i].displayCharacter.length() == 1)
-      {      
+      {
         firstChar = annotations[i].displayCharacter.charAt(0);
-        // check to see if it looks like a sequence or is secondary structure labelling.
+        // check to see if it looks like a sequence or is secondary structure
+        // labelling.
         if (
-                // Uncomment to only catch case where displayCharacter==secondary Structure 
-              // to correctly redisplay SS annotation imported from Stockholm, exported to JalviewXML and read back in again.
-          // && annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
-          firstChar!='H'
-          && firstChar!='E'
-          && firstChar!='-'
-          && firstChar!='-' && firstChar<jalview.schemes.ResidueProperties.aaIndex.length)
+        // Uncomment to only catch case where displayCharacter==secondary
+        // Structure
+        // to correctly redisplay SS annotation imported from Stockholm,
+        // exported to JalviewXML and read back in again.
+        // &&
+        // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
+        firstChar != 'H'
+                && firstChar != 'E'
+                && firstChar != '-'
+                && firstChar != '-'
+                && firstChar < jalview.schemes.ResidueProperties.aaIndex.length)
         {
-          if (jalview.schemes.ResidueProperties.aaIndex
-                  [firstChar] < 23)
+          if (jalview.schemes.ResidueProperties.aaIndex[firstChar] < 23)
           {
             nonSSLabel = true;
           }
@@ -186,10 +195,11 @@ public class AlignmentAnnotation
       hasIcons = false;
       for (int j = 0; j < annotations.length; j++)
       {
-        if (annotations[j] != null && annotations[j].secondaryStructure != ' ')
+        if (annotations[j] != null
+                && annotations[j].secondaryStructure != ' ')
         {
-          annotations[j].displayCharacter
-              = String.valueOf(annotations[j].secondaryStructure);
+          annotations[j].displayCharacter = String
+                  .valueOf(annotations[j].secondaryStructure);
           annotations[j].secondaryStructure = ' ';
         }
 
@@ -198,22 +208,28 @@ public class AlignmentAnnotation
 
     annotationId = this.hashCode() + "";
   }
+
   /**
    * Creates a new AlignmentAnnotation object.
-   *
-   * @param label DOCUMENT ME!
-   * @param description DOCUMENT ME!
-   * @param annotations DOCUMENT ME!
-   * @param min DOCUMENT ME!
-   * @param max DOCUMENT ME!
-   * @param winLength DOCUMENT ME!
+   * 
+   * @param label
+   *                DOCUMENT ME!
+   * @param description
+   *                DOCUMENT ME!
+   * @param annotations
+   *                DOCUMENT ME!
+   * @param min
+   *                DOCUMENT ME!
+   * @param max
+   *                DOCUMENT ME!
+   * @param winLength
+   *                DOCUMENT ME!
    */
   public AlignmentAnnotation(String label, String description,
-                             Annotation[] annotations, float min, float max,
-                             int graphType)
+          Annotation[] annotations, float min, float max, int graphType)
   {
     // graphs are not editable
-    editable = graphType==0;
+    editable = graphType == 0;
 
     this.label = label;
     this.description = description;
@@ -223,18 +239,17 @@ public class AlignmentAnnotation
     graphMax = max;
     validateRangeAndDisplay();
   }
+
   /**
-   * checks graphMin and graphMax,
-   * secondary structure symbols,
-   * sets graphType appropriately,
-   * sets null labels to the empty string
-   * if appropriate.
+   * checks graphMin and graphMax, secondary structure symbols, sets graphType
+   * appropriately, sets null labels to the empty string if appropriate.
    */
-  private void validateRangeAndDisplay() {
+  private void validateRangeAndDisplay()
+  {
 
-    if (annotations==null)
+    if (annotations == null)
     {
-      visible=false; // try to prevent renderer from displaying.
+      visible = false; // try to prevent renderer from displaying.
       return; // this is a non-annotation row annotation - ie a sequence score.
     }
 
@@ -253,9 +268,8 @@ public class AlignmentAnnotation
           continue;
         }
 
-        if (drawValues
-            && annotations[i].displayCharacter!=null
-            && annotations[i].displayCharacter.length() > 1)
+        if (drawValues && annotations[i].displayCharacter != null
+                && annotations[i].displayCharacter.length() > 1)
         {
           drawValues = false;
         }
@@ -290,8 +304,9 @@ public class AlignmentAnnotation
   }
 
   /**
-   * Copy constructor
-   * creates a new independent annotation row with the same associated sequenceRef
+   * Copy constructor creates a new independent annotation row with the same
+   * associated sequenceRef
+   * 
    * @param annotation
    */
   public AlignmentAnnotation(AlignmentAnnotation annotation)
@@ -316,39 +331,47 @@ public class AlignmentAnnotation
     {
       this.score = annotation.score;
     }
-    if (threshold!=null) {
+    if (threshold != null)
+    {
       threshold = new GraphLine(annotation.threshold);
     }
-    if (annotation.annotations!=null) {
+    if (annotation.annotations != null)
+    {
       Annotation[] ann = annotation.annotations;
       this.annotations = new Annotation[ann.length];
-      for (int i=0; i<ann.length; i++) {
+      for (int i = 0; i < ann.length; i++)
+      {
         annotations[i] = new Annotation(ann[i]);
-      };
-      if (annotation.sequenceRef!=null) {
+      }
+      ;
+      if (annotation.sequenceRef != null)
+      {
         this.sequenceRef = annotation.sequenceRef;
-        if (annotation.sequenceMapping!=null)
+        if (annotation.sequenceMapping != null)
         {
-          Integer p=null;
+          Integer p = null;
           sequenceMapping = new Hashtable();
-          Enumeration pos=annotation.sequenceMapping.keys();
-          while (pos.hasMoreElements()) {
+          Enumeration pos = annotation.sequenceMapping.keys();
+          while (pos.hasMoreElements())
+          {
             // could optimise this!
             p = (Integer) pos.nextElement();
             Annotation a = (Annotation) annotation.sequenceMapping.get(p);
-            if (a==null)
+            if (a == null)
             {
               continue;
             }
-            for (int i=0; i<ann.length; i++)
+            for (int i = 0; i < ann.length; i++)
             {
-              if (ann[i]==a)
+              if (ann[i] == a)
               {
                 sequenceMapping.put(p, annotations[i]);
               }
             }
           }
-        } else {
+        }
+        else
+        {
           this.sequenceMapping = null;
         }
       }
@@ -359,41 +382,44 @@ public class AlignmentAnnotation
   /**
    * clip the annotation to the columns given by startRes and endRes (inclusive)
    * and prune any existing sequenceMapping to just those columns.
+   * 
    * @param startRes
    * @param endRes
    */
   public void restrict(int startRes, int endRes)
   {
-    if (annotations==null)
+    if (annotations == null)
     {
       // non-positional
       return;
     }
-    if (startRes<0)
-      startRes=0;
-    if (startRes>=annotations.length)
-      startRes = annotations.length-1;
-    if (endRes>=annotations.length)
-      endRes = annotations.length-1;
-    if (annotations==null)
+    if (startRes < 0)
+      startRes = 0;
+    if (startRes >= annotations.length)
+      startRes = annotations.length - 1;
+    if (endRes >= annotations.length)
+      endRes = annotations.length - 1;
+    if (annotations == null)
       return;
-    Annotation[] temp = new Annotation[endRes-startRes+1];
-    if (startRes<annotations.length)
+    Annotation[] temp = new Annotation[endRes - startRes + 1];
+    if (startRes < annotations.length)
     {
-      System.arraycopy(annotations, startRes, temp, 0, endRes-startRes+1);
+      System.arraycopy(annotations, startRes, temp, 0, endRes - startRes
+              + 1);
     }
-    if (sequenceRef!=null) {
+    if (sequenceRef != null)
+    {
       // Clip the mapping, if it exists.
       int spos = sequenceRef.findPosition(startRes);
       int epos = sequenceRef.findPosition(endRes);
-      if (sequenceMapping!=null)
+      if (sequenceMapping != null)
       {
         Hashtable newmapping = new Hashtable();
         Enumeration e = sequenceMapping.keys();
         while (e.hasMoreElements())
         {
           Integer pos = (Integer) e.nextElement();
-          if (pos.intValue()>=spos && pos.intValue()<=epos)
+          if (pos.intValue() >= spos && pos.intValue() <= epos)
           {
             newmapping.put(pos, sequenceMapping.get(pos));
           }
@@ -402,32 +428,37 @@ public class AlignmentAnnotation
         sequenceMapping = newmapping;
       }
     }
-    annotations=temp;
+    annotations = temp;
   }
+
   /**
    * set the annotation row to be at least length Annotations
-   * @param length minimum number of columns required in the annotation row
+   * 
+   * @param length
+   *                minimum number of columns required in the annotation row
    * @return false if the annotation row is greater than length
    */
-  public boolean padAnnotation(int length) {
-    if (annotations==null)
+  public boolean padAnnotation(int length)
+  {
+    if (annotations == null)
     {
-      return true; // annotation row is correct - null == not visible and undefined length
+      return true; // annotation row is correct - null == not visible and
+                    // undefined length
     }
-    if (annotations.length<length)
+    if (annotations.length < length)
     {
       Annotation[] na = new Annotation[length];
       System.arraycopy(annotations, 0, na, 0, annotations.length);
       annotations = na;
       return true;
     }
-    return annotations.length>length;
+    return annotations.length > length;
 
   }
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public String toString()
@@ -484,22 +515,24 @@ public class AlignmentAnnotation
   }
 
   /**
-   * Attach the annotation to seqRef, starting from startRes position. If alreadyMapped is true then the indices of the annotation[] array are sequence positions rather than alignment column positions.
+   * Attach the annotation to seqRef, starting from startRes position. If
+   * alreadyMapped is true then the indices of the annotation[] array are
+   * sequence positions rather than alignment column positions.
+   * 
    * @param seqRef
    * @param startRes
    * @param alreadyMapped
    */
-  public void createSequenceMapping(SequenceI seqRef,
-                                    int startRes,
-                                    boolean alreadyMapped)
+  public void createSequenceMapping(SequenceI seqRef, int startRes,
+          boolean alreadyMapped)
   {
 
     if (seqRef == null)
     {
       return;
     }
-    sequenceRef=seqRef;
-    if (annotations==null)
+    sequenceRef = seqRef;
+    if (annotations == null)
     {
       return;
     }
@@ -528,10 +561,10 @@ public class AlignmentAnnotation
 
   public void adjustForAlignment()
   {
-    if (sequenceRef==null)
+    if (sequenceRef == null)
       return;
 
-    if (annotations==null)
+    if (annotations == null)
     {
       return;
     }
@@ -540,7 +573,7 @@ public class AlignmentAnnotation
 
     if (aSize == 0)
     {
-      //Its been deleted
+      // Its been deleted
       return;
     }
 
@@ -561,20 +594,27 @@ public class AlignmentAnnotation
 
     annotations = temp;
   }
+
   /**
-   * remove any null entries in annotation row and return the
-   * number of non-null annotation elements.
+   * remove any null entries in annotation row and return the number of non-null
+   * annotation elements.
+   * 
    * @return
    */
-  public int compactAnnotationArray() {
-    int i=0,iSize=annotations.length;
-    while (i<iSize)
+  public int compactAnnotationArray()
+  {
+    int i = 0, iSize = annotations.length;
+    while (i < iSize)
     {
-      if (annotations[i]==null) {
-        if (i+1<iSize)
-          System.arraycopy(annotations, i+1, annotations, i, iSize-i-1);
+      if (annotations[i] == null)
+      {
+        if (i + 1 < iSize)
+          System.arraycopy(annotations, i + 1, annotations, i, iSize - i
+                  - 1);
         iSize--;
-      } else {
+      }
+      else
+      {
         i++;
       }
     }
@@ -587,10 +627,12 @@ public class AlignmentAnnotation
 
   /**
    * Associate this annotion with the aligned residues of a particular sequence.
-   * sequenceMapping will be updated in the following way:
-   *   null sequenceI - existing mapping will be discarded but annotations left in mapped positions.
-   *   valid sequenceI not equal to current sequenceRef: mapping is discarded and rebuilt assuming 1:1 correspondence
-   *   TODO: overload with parameter to specify correspondence between current and new sequenceRef
+   * sequenceMapping will be updated in the following way: null sequenceI -
+   * existing mapping will be discarded but annotations left in mapped
+   * positions. valid sequenceI not equal to current sequenceRef: mapping is
+   * discarded and rebuilt assuming 1:1 correspondence TODO: overload with
+   * parameter to specify correspondence between current and new sequenceRef
+   * 
    * @param sequenceI
    */
   public void setSequenceRef(SequenceI sequenceI)
@@ -599,7 +641,10 @@ public class AlignmentAnnotation
     {
       if (sequenceRef != null)
       {
-        if (sequenceRef != sequenceI && !sequenceRef.equals(sequenceI) && sequenceRef.getDatasetSequence()!=sequenceI.getDatasetSequence())
+        if (sequenceRef != sequenceI
+                && !sequenceRef.equals(sequenceI)
+                && sequenceRef.getDatasetSequence() != sequenceI
+                        .getDatasetSequence())
         {
           // if sequenceRef isn't intersecting with sequenceI
           // throw away old mapping and reconstruct.
@@ -642,23 +687,27 @@ public class AlignmentAnnotation
   }
 
   /**
-   * @param score the score to set
+   * @param score
+   *                the score to set
    */
   public void setScore(double score)
   {
-    hasScore=true;
+    hasScore = true;
     this.score = score;
   }
+
   /**
-   *
+   * 
    * @return true if annotation has an associated score
    */
   public boolean hasScore()
   {
     return hasScore || !Double.isNaN(score);
   }
+
   /**
    * Score only annotation
+   * 
    * @param label
    * @param description
    * @param score
@@ -668,8 +717,10 @@ public class AlignmentAnnotation
     this(label, description, null);
     setScore(score);
   }
+
   /**
    * copy constructor with edit based on the hidden columns marked in colSel
+   * 
    * @param alignmentAnnotation
    * @param colSel
    */
@@ -677,7 +728,7 @@ public class AlignmentAnnotation
           ColumnSelection colSel)
   {
     this(alignmentAnnotation);
-    if (annotations==null)
+    if (annotations == null)
     {
       return;
     }
@@ -687,29 +738,33 @@ public class AlignmentAnnotation
   public void setPadGaps(boolean padgaps, char gapchar)
   {
     this.padGaps = padgaps;
-    if(padgaps)
+    if (padgaps)
     {
       hasText = true;
-      for(int i=0; i<annotations.length; i++)
+      for (int i = 0; i < annotations.length; i++)
       {
-        if(annotations[i]==null)
-          annotations[i] = new Annotation(String.valueOf(gapchar),null,' ',0f);
-        else if(annotations[i].displayCharacter==null ||annotations[i].displayCharacter.equals(" "))
-          annotations[i].displayCharacter=String.valueOf(gapchar);
+        if (annotations[i] == null)
+          annotations[i] = new Annotation(String.valueOf(gapchar), null,
+                  ' ', 0f);
+        else if (annotations[i].displayCharacter == null
+                || annotations[i].displayCharacter.equals(" "))
+          annotations[i].displayCharacter = String.valueOf(gapchar);
       }
     }
   }
 
   /**
    * format description string for display
+   * 
    * @param seqname
-   * @return Get the annotation description string optionally prefixed by associated sequence name (if any) 
+   * @return Get the annotation description string optionally prefixed by
+   *         associated sequence name (if any)
    */
   public String getDescription(boolean seqname)
   {
-    if (seqname && this.sequenceRef!=null)
+    if (seqname && this.sequenceRef != null)
     {
-      return sequenceRef.getName()+" : "+description;
+      return sequenceRef.getName() + " : " + description;
     }
     return description;
   }
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index f89602f..b4075a0 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -20,88 +20,96 @@ package jalview.datamodel;
 
 import java.util.*;
 
-/** Data structure to hold and manipulate a multiple sequence alignment
+/**
+ * Data structure to hold and manipulate a multiple sequence alignment
  */
 public interface AlignmentI
 {
   /**
-   *  Calculates the number of sequences in an alignment
-   *
+   * Calculates the number of sequences in an alignment
+   * 
    * @return Number of sequences in alignment
    */
   public int getHeight();
 
   /**
    * Calculates the maximum width of the alignment, including gaps.
-   *
+   * 
    * @return Greatest sequence length within alignment.
    */
   public int getWidth();
 
   /**
    * Calculates if this set of sequences is all the same length
-   *
+   * 
    * @return true if all sequences in alignment are the same length
    */
   public boolean isAligned();
 
   /**
    * Gets sequences as a Vector
-   *
+   * 
    * @return All sequences in alignment.
    */
   public Vector getSequences();
 
   /**
    * Gets sequences as a SequenceI[]
-   *
+   * 
    * @return All sequences in alignment.
    */
   public SequenceI[] getSequencesArray();
 
   /**
    * Find a specific sequence in this alignment.
-   *
-   * @param i Index of required sequence.
-   *
+   * 
+   * @param i
+   *                Index of required sequence.
+   * 
    * @return SequenceI at given index.
    */
   public SequenceI getSequenceAt(int i);
 
   /**
    * Add a new sequence to this alignment.
-   *
-   * @param seq New sequence will be added at end of alignment.
+   * 
+   * @param seq
+   *                New sequence will be added at end of alignment.
    */
   public void addSequence(SequenceI seq);
 
   /**
    * Used to set a particular index of the alignment with the given sequence.
-   *
-   * @param i Index of sequence to be updated.
-   * @param seq New sequence to be inserted.
+   * 
+   * @param i
+   *                Index of sequence to be updated.
+   * @param seq
+   *                New sequence to be inserted.
    */
   public void setSequenceAt(int i, SequenceI seq);
 
   /**
    * Deletes a sequence from the alignment
-   *
-   * @param s Sequence to be deleted.
+   * 
+   * @param s
+   *                Sequence to be deleted.
    */
   public void deleteSequence(SequenceI s);
 
   /**
    * Deletes a sequence from the alignment.
-   *
-   * @param i Index of sequence to be deleted.
+   * 
+   * @param i
+   *                Index of sequence to be deleted.
    */
   public void deleteSequence(int i);
 
   /**
    * Finds sequence in alignment using sequence name as query.
-   *
-   * @param name Id of sequence to search for.
-   *
+   * 
+   * @param name
+   *                Id of sequence to search for.
+   * 
    * @return Sequence matching query, if found. If not found returns null.
    */
   public SequenceI findName(String name);
@@ -110,54 +118,58 @@ public interface AlignmentI
 
   /**
    * Finds index of a given sequence in the alignment.
-   *
-   * @param s Sequence to look for.
-   *
+   * 
+   * @param s
+   *                Sequence to look for.
+   * 
    * @return Index of sequence within the alignment.
    */
   public int findIndex(SequenceI s);
 
   /**
    * Finds group that given sequence is part of.
-   *
-   * @param s Sequence in alignment.
-   *
-   * @return First group found for sequence. WARNING :
-   * Sequences may be members of several groups. This method is incomplete.
+   * 
+   * @param s
+   *                Sequence in alignment.
+   * 
+   * @return First group found for sequence. WARNING : Sequences may be members
+   *         of several groups. This method is incomplete.
    */
   public SequenceGroup findGroup(SequenceI s);
 
   /**
    * Finds all groups that a given sequence is part of.
-   *
-   * @param s Sequence in alignment.
-   *
+   * 
+   * @param s
+   *                Sequence in alignment.
+   * 
    * @return All groups containing given sequence.
    */
   public SequenceGroup[] findAllGroups(SequenceI s);
 
   /**
    * Adds a new SequenceGroup to this alignment.
-   *
-   * @param sg New group to be added.
+   * 
+   * @param sg
+   *                New group to be added.
    */
   public void addGroup(SequenceGroup sg);
 
   /**
    * Deletes a specific SequenceGroup
-   *
-   * @param g Group will be deleted from alignment.
+   * 
+   * @param g
+   *                Group will be deleted from alignment.
    */
   public void deleteGroup(SequenceGroup g);
 
   /**
    * Get all the groups associated with this alignment.
-   *
+   * 
    * @return All groups as a Vector.
    */
   public Vector getGroups();
 
-
   /**
    * Deletes all groups from this alignment.
    */
@@ -165,77 +177,88 @@ public interface AlignmentI
 
   /**
    * Adds a new AlignmentAnnotation to this alignment
-   * @note Care should be taken to ensure that annotation is at
-   * least as wide as the longest sequence in the alignment
-   * for rendering purposes.
+   * 
+   * @note Care should be taken to ensure that annotation is at least as wide as
+   *       the longest sequence in the alignment for rendering purposes.
    */
   public void addAnnotation(AlignmentAnnotation aa);
+
   /**
    * moves annotation to a specified index in alignment annotation display stack
-   * @param aa the annotation object to be moved
-   * @param index the destination position
+   * 
+   * @param aa
+   *                the annotation object to be moved
+   * @param index
+   *                the destination position
    */
   public void setAnnotationIndex(AlignmentAnnotation aa, int index);
 
   /**
-   * Deletes a specific AlignmentAnnotation from the alignment,
-   * and removes its reference from any SequenceI object's annotation
-   * if and only if aa is contained within the alignment's annotation
-   * vector. Otherwise, it will do nothing.
+   * Deletes a specific AlignmentAnnotation from the alignment, and removes its
+   * reference from any SequenceI object's annotation if and only if aa is
+   * contained within the alignment's annotation vector. Otherwise, it will do
+   * nothing.
    * 
-   * @param aa the annotation to delete
+   * @param aa
+   *                the annotation to delete
    * @return true if annotation was deleted from this alignment.
    */
   public boolean deleteAnnotation(AlignmentAnnotation aa);
 
   /**
    * Get the annotation associated with this alignment
-   *
+   * 
    * @return array of AlignmentAnnotation objects
    */
   public AlignmentAnnotation[] getAlignmentAnnotation();
 
   /**
    * Change the gap character used in this alignment to 'gc'
-   *
-   * @param gc the new gap character.
+   * 
+   * @param gc
+   *                the new gap character.
    */
   public void setGapCharacter(char gc);
 
   /**
    * Get the gap character used in this alignment
-   *
+   * 
    * @return gap character
    */
   public char getGapCharacter();
 
   /**
    * Test for all nucleotide alignment
-   *
+   * 
    * @return true if alignment is nucleotide sequence
    */
   public boolean isNucleotide();
 
   /**
    * Set alignment to be a nucleotide sequence
-   *
+   * 
    */
   public void setNucleotide(boolean b);
 
   /**
    * Get the associated dataset for the alignment.
-   * @return Alignment containing dataset sequences or null of this is a dataset.
+   * 
+   * @return Alignment containing dataset sequences or null of this is a
+   *         dataset.
    */
   public Alignment getDataset();
 
   /**
    * Set the associated dataset for the alignment, or create one.
-   * @param dataset The dataset alignment or null to construct one.
+   * 
+   * @param dataset
+   *                The dataset alignment or null to construct one.
    */
   public void setDataset(Alignment dataset);
 
   /**
    * pads sequences with gaps (to ensure the set looks like an alignment)
+   * 
    * @return boolean true if alignment was modified
    */
   public boolean padGaps();
@@ -244,70 +267,96 @@ public interface AlignmentI
 
   /**
    * Compact representation of alignment
+   * 
    * @return CigarArray
    */
   public CigarArray getCompactAlignment();
 
   /**
-   * Set an arbitrary key value pair for an alignment.
-   * Note: both key and value objects should return a 
-   * meaningful, human readable response to .toString()
+   * Set an arbitrary key value pair for an alignment. Note: both key and value
+   * objects should return a meaningful, human readable response to .toString()
+   * 
    * @param key
    * @param value
    */
   public void setProperty(Object key, Object value);
+
   /**
-   * Get a named property from the alignment. 
+   * Get a named property from the alignment.
+   * 
    * @param key
    * @return value of property
    */
   public Object getProperty(Object key);
+
   /**
    * Get the property hashtable.
+   * 
    * @return hashtable of alignment properties (or null if none are defined)
    */
   public Hashtable getProperties();
 
   /**
    * add a reference to a frame of aligned codons for this alignment
+   * 
    * @param codons
    */
   public void addCodonFrame(AlignedCodonFrame codons);
+
   /**
    * remove a particular codon frame reference from this alignment
+   * 
    * @param codons
    * @return true if codon frame was removed.
    */
   public boolean removeCodonFrame(AlignedCodonFrame codons);
+
   /**
    * get all codon frames associated with this alignment
+   * 
    * @return
    */
   public AlignedCodonFrame[] getCodonFrames();
+
   /**
    * get a particular codon frame
+   * 
    * @param index
    * @return
    */
   public AlignedCodonFrame getCodonFrame(int index);
+
   /**
    * get codon frames involving sequenceI
    */
   public AlignedCodonFrame[] getCodonFrame(SequenceI seq);
+
   /**
    * find sequence with given name in alignment
-   * @param token name to find
-   * @param b true implies that case insensitive matching will <em>also</em> be tried 
+   * 
+   * @param token
+   *                name to find
+   * @param b
+   *                true implies that case insensitive matching will
+   *                <em>also</em> be tried
    * @return matched sequence or null
    */
   public SequenceI findName(String token, boolean b);
+
   /**
-   * find next sequence with given name in alignment starting after a given sequence
-   * @param startAfter the sequence after which the search will be started (usually the result of the last call to findName) 
-   * @param token name to find
-   * @param b true implies that case insensitive matching will <em>also</em> be tried 
+   * find next sequence with given name in alignment starting after a given
+   * sequence
+   * 
+   * @param startAfter
+   *                the sequence after which the search will be started (usually
+   *                the result of the last call to findName)
+   * @param token
+   *                name to find
+   * @param b
+   *                true implies that case insensitive matching will
+   *                <em>also</em> be tried
    * @return matched sequence or null
    */
   public SequenceI findName(SequenceI startAfter, String token, boolean b);
-  
+
 }
diff --git a/src/jalview/datamodel/AlignmentOrder.java b/src/jalview/datamodel/AlignmentOrder.java
index b149749..f807890 100755
--- a/src/jalview/datamodel/AlignmentOrder.java
+++ b/src/jalview/datamodel/AlignmentOrder.java
@@ -1,316 +1,349 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.datamodel;
-
-import java.util.*;
-
-/**
- * <p>Title: </p>
- *
- * <p>Description: </p>
- *
- * <p>Copyright: Copyright (c) 2004</p>
- *
- * <p>Company: Dundee University</p>
- *
- * @author not attributable
- * @version 1.0
- */
-public class AlignmentOrder
-{
-  // JBPNote : this method would return a vector containing all sequences in seqset
-  // with those also contained in order at the beginning of the vector in the order
-  // given by order. AlignmentSorter.vectorSubsetToArray already does this, but that method
-  // should be here for completeness.
-
-  /*  public Vector getOrder(AlignmentI seqset)
-     {
-       Vector perm = new Vector(seqset.getHeight());
-       for (i=0, o = 0, n=seqset.getHeight(), p = Order.size(); i<n; i++)
-    perm.setElement(i,...).
-       return Order;
-     }
-   */
-
-  /** DOCUMENT ME!! */
-  public static final int FILE = 0;
-
-  /** DOCUMENT ME!! */
-  public static final int MSA = 1;
-
-  /** DOCUMENT ME!! */
-  public static final int USER = 2;
-  private int Type = 0;
-  private String Name;
-  private Vector Order = null;
-
-  /**
-   * Creates a new AlignmentOrder object.
-   */
-  public AlignmentOrder()
-  {
-  }
-
-  /**
-   * AlignmentOrder
-   *
-   * @param anOrder Vector
-   */
-  public AlignmentOrder(Vector anOrder)
-  {
-    Order = anOrder;
-  }
-
-  /**
-   * AlignmentOrder
-   *
-   * @param orderFrom AlignmentI
-   */
-  public AlignmentOrder(AlignmentI orderFrom)
-  {
-    Order = new Vector();
-
-    for (int i = 0, ns = orderFrom.getHeight(); i < ns; i++)
-    {
-      Order.addElement(orderFrom.getSequenceAt(i));
-    }
-  }
-
-  /**
-   * Creates a new AlignmentOrder object.
-   *
-   * @param orderFrom DOCUMENT ME!
-   */
-  public AlignmentOrder(SequenceI[] orderFrom)
-  {
-    Order = new Vector();
-
-    for (int i = 0, ns = orderFrom.length; i < ns; i++)
-    {
-      Order.addElement(orderFrom[i]);
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param Type DOCUMENT ME!
-   */
-  public void setType(int Type)
-  {
-    this.Type = Type;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public int getType()
-  {
-    return Type;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param Name DOCUMENT ME!
-   */
-  public void setName(String Name)
-  {
-    this.Name = Name;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public String getName()
-  {
-    return Name;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param Order DOCUMENT ME!
-   */
-  public void setOrder(Vector Order)
-  {
-    this.Order = Order;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Vector getOrder()
-  {
-    return Order;
-  }
-
-  /**
-   * replaces oldref with newref in the alignment order.
-   * @param oldref
-   * @param newref
-   * @return true if oldref was contained in order and replaced with newref
-   */
-  public boolean updateSequence(SequenceI oldref, SequenceI newref)
-  {
-    int found = Order.indexOf(oldref);
-    if (found > -1)
-    {
-      Order.setElementAt(newref, found);
-    }
-    return found > -1;
-  }
-
-  /**
-   * Exact equivalence of two AlignmentOrders
-   * @param o
-   * @return true if o orders the same sequenceI objects in the same way
-   */
-  public boolean equals(AlignmentOrder o)
-  {
-    return equals(o, true);
-  }
-
-  /**
-   * Exact equivalence of two AlignmentOrders
-   *  // TODO: Weak SequenceI equivalence - will throw Error at moment
-   * @param o
-   * @param identity - false - use weak equivalence (refers to same or different parts of same sequence)
-   * @return true if o orders equivalent sequenceI objects in the same way
-   */
-  public boolean equals(AlignmentOrder o, boolean identity)
-  {
-    if (o != this)
-    {
-      if (o == null)
-      {
-        return false;
-      }
-      if (Order != null && o.Order != null && Order.size() == o.Order.size())
-      {
-        if (!identity)
-        {
-          throw new Error("Weak sequenceI equivalence not yet implemented.");
-        }
-        else
-        {
-          for (int i = 0, j = o.Order.size(); i < j; i++)
-          {
-            if (Order.elementAt(i) != o.Order.elementAt(i))
-            {
-              return false;
-            }
-          }
-        }
-      }
-      else
-      {
-        return false;
-      }
-    }
-    return true;
-  }
-
-  /**
-   * Consistency test for alignmentOrders
-   * @param o
-   * @return true if o contains or is contained by this and the common SequenceI objects are ordered in the same way
-   */
-  public boolean isConsistent(AlignmentOrder o)
-  {
-    return isConsistent(o, true);
-  }
-
-  /**
-   * Consistency test for alignmentOrders
-   * @param o
-   *  // TODO: Weak SequenceI equivalence - will throw Error at moment
-   * @param identity - false - use weak equivalence (refers to same or different parts of same sequence)
-   * @return true if o contains or is contained by this and the common SequenceI objects are ordered in the same way
-   */
-  public boolean isConsistent(AlignmentOrder o, boolean identity)
-  {
-    if (o != this)
-    {
-      if (o == null)
-      {
-        return false;
-      }
-      if (Order != null && o.Order != null)
-      {
-        Vector c, s;
-        if (o.Order.size() > Order.size())
-        {
-          c = o.Order;
-          s = Order;
-        }
-        else
-        {
-          c = Order;
-          s = o.Order;
-        }
-        if (!identity)
-        {
-          throw new Error("Weak sequenceI equivalence not yet implemented.");
-        }
-        else
-        {
-          // test if c contains s and order in s is conserved in c
-          int last = -1;
-          for (int i = 0, j = s.size(); i < j; i++)
-          {
-            int pos = c.indexOf(s.elementAt(i)); // JBPNote - optimize by incremental position search
-            if (pos > last)
-            {
-              last = pos;
-            }
-            else
-            {
-              return false;
-            }
-          }
-        }
-      }
-      else
-      {
-        return false;
-      }
-    }
-    return true;
-  }
-  /**
-   * AlignmentOrder
-   *
-   * @param orderThis AlignmentI
-   * @param byThat AlignmentI
-   */
-
-  /* public AlignmentOrder(AlignmentI orderThis, AlignmentI byThat)
-   {
-     // Vector is an ordering of this alignment using the order of sequence objects in byThat,
-     // where ids and unaligned sequences must match
-
-   } */
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.datamodel;
+
+import java.util.*;
+
+/**
+ * <p>
+ * Title:
+ * </p>
+ * 
+ * <p>
+ * Description:
+ * </p>
+ * 
+ * <p>
+ * Copyright: Copyright (c) 2004
+ * </p>
+ * 
+ * <p>
+ * Company: Dundee University
+ * </p>
+ * 
+ * @author not attributable
+ * @version 1.0
+ */
+public class AlignmentOrder
+{
+  // JBPNote : this method would return a vector containing all sequences in
+  // seqset
+  // with those also contained in order at the beginning of the vector in the
+  // order
+  // given by order. AlignmentSorter.vectorSubsetToArray already does this, but
+  // that method
+  // should be here for completeness.
+
+  /*
+   * public Vector getOrder(AlignmentI seqset) { Vector perm = new
+   * Vector(seqset.getHeight()); for (i=0, o = 0, n=seqset.getHeight(), p =
+   * Order.size(); i<n; i++) perm.setElement(i,...). return Order; }
+   */
+
+  /** DOCUMENT ME!! */
+  public static final int FILE = 0;
+
+  /** DOCUMENT ME!! */
+  public static final int MSA = 1;
+
+  /** DOCUMENT ME!! */
+  public static final int USER = 2;
+
+  private int Type = 0;
+
+  private String Name;
+
+  private Vector Order = null;
+
+  /**
+   * Creates a new AlignmentOrder object.
+   */
+  public AlignmentOrder()
+  {
+  }
+
+  /**
+   * AlignmentOrder
+   * 
+   * @param anOrder
+   *                Vector
+   */
+  public AlignmentOrder(Vector anOrder)
+  {
+    Order = anOrder;
+  }
+
+  /**
+   * AlignmentOrder
+   * 
+   * @param orderFrom
+   *                AlignmentI
+   */
+  public AlignmentOrder(AlignmentI orderFrom)
+  {
+    Order = new Vector();
+
+    for (int i = 0, ns = orderFrom.getHeight(); i < ns; i++)
+    {
+      Order.addElement(orderFrom.getSequenceAt(i));
+    }
+  }
+
+  /**
+   * Creates a new AlignmentOrder object.
+   * 
+   * @param orderFrom
+   *                DOCUMENT ME!
+   */
+  public AlignmentOrder(SequenceI[] orderFrom)
+  {
+    Order = new Vector();
+
+    for (int i = 0, ns = orderFrom.length; i < ns; i++)
+    {
+      Order.addElement(orderFrom[i]);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param Type
+   *                DOCUMENT ME!
+   */
+  public void setType(int Type)
+  {
+    this.Type = Type;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public int getType()
+  {
+    return Type;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param Name
+   *                DOCUMENT ME!
+   */
+  public void setName(String Name)
+  {
+    this.Name = Name;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public String getName()
+  {
+    return Name;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param Order
+   *                DOCUMENT ME!
+   */
+  public void setOrder(Vector Order)
+  {
+    this.Order = Order;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public Vector getOrder()
+  {
+    return Order;
+  }
+
+  /**
+   * replaces oldref with newref in the alignment order.
+   * 
+   * @param oldref
+   * @param newref
+   * @return true if oldref was contained in order and replaced with newref
+   */
+  public boolean updateSequence(SequenceI oldref, SequenceI newref)
+  {
+    int found = Order.indexOf(oldref);
+    if (found > -1)
+    {
+      Order.setElementAt(newref, found);
+    }
+    return found > -1;
+  }
+
+  /**
+   * Exact equivalence of two AlignmentOrders
+   * 
+   * @param o
+   * @return true if o orders the same sequenceI objects in the same way
+   */
+  public boolean equals(AlignmentOrder o)
+  {
+    return equals(o, true);
+  }
+
+  /**
+   * Exact equivalence of two AlignmentOrders // TODO: Weak SequenceI
+   * equivalence - will throw Error at moment
+   * 
+   * @param o
+   * @param identity -
+   *                false - use weak equivalence (refers to same or different
+   *                parts of same sequence)
+   * @return true if o orders equivalent sequenceI objects in the same way
+   */
+  public boolean equals(AlignmentOrder o, boolean identity)
+  {
+    if (o != this)
+    {
+      if (o == null)
+      {
+        return false;
+      }
+      if (Order != null && o.Order != null
+              && Order.size() == o.Order.size())
+      {
+        if (!identity)
+        {
+          throw new Error("Weak sequenceI equivalence not yet implemented.");
+        }
+        else
+        {
+          for (int i = 0, j = o.Order.size(); i < j; i++)
+          {
+            if (Order.elementAt(i) != o.Order.elementAt(i))
+            {
+              return false;
+            }
+          }
+        }
+      }
+      else
+      {
+        return false;
+      }
+    }
+    return true;
+  }
+
+  /**
+   * Consistency test for alignmentOrders
+   * 
+   * @param o
+   * @return true if o contains or is contained by this and the common SequenceI
+   *         objects are ordered in the same way
+   */
+  public boolean isConsistent(AlignmentOrder o)
+  {
+    return isConsistent(o, true);
+  }
+
+  /**
+   * Consistency test for alignmentOrders
+   * 
+   * @param o //
+   *                TODO: Weak SequenceI equivalence - will throw Error at
+   *                moment
+   * @param identity -
+   *                false - use weak equivalence (refers to same or different
+   *                parts of same sequence)
+   * @return true if o contains or is contained by this and the common SequenceI
+   *         objects are ordered in the same way
+   */
+  public boolean isConsistent(AlignmentOrder o, boolean identity)
+  {
+    if (o != this)
+    {
+      if (o == null)
+      {
+        return false;
+      }
+      if (Order != null && o.Order != null)
+      {
+        Vector c, s;
+        if (o.Order.size() > Order.size())
+        {
+          c = o.Order;
+          s = Order;
+        }
+        else
+        {
+          c = Order;
+          s = o.Order;
+        }
+        if (!identity)
+        {
+          throw new Error("Weak sequenceI equivalence not yet implemented.");
+        }
+        else
+        {
+          // test if c contains s and order in s is conserved in c
+          int last = -1;
+          for (int i = 0, j = s.size(); i < j; i++)
+          {
+            int pos = c.indexOf(s.elementAt(i)); // JBPNote - optimize by
+                                                  // incremental position search
+            if (pos > last)
+            {
+              last = pos;
+            }
+            else
+            {
+              return false;
+            }
+          }
+        }
+      }
+      else
+      {
+        return false;
+      }
+    }
+    return true;
+  }
+  /**
+   * AlignmentOrder
+   * 
+   * @param orderThis
+   *                AlignmentI
+   * @param byThat
+   *                AlignmentI
+   */
+
+  /*
+   * public AlignmentOrder(AlignmentI orderThis, AlignmentI byThat) { // Vector
+   * is an ordering of this alignment using the order of sequence objects in
+   * byThat, // where ids and unaligned sequences must match
+   *  }
+   */
+}
diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index 79e0ba2..0884ea4 100644
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -1,510 +1,543 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.datamodel;
-
-/**
- * <p>Title: </p>
- *
- * <p>Description: </p>
- *
- * <p>Copyright: Copyright (c) 2004</p>
- *
- * <p>Company: Dundee University</p>
- *
- * @author not attributable
- * @version 1.0
- */
-public class AlignmentView
-{
-  /**
-   * Transient object compactly representing a 'view' of an alignment - with discontinuities marked.
-   */
-  private SeqCigar[] sequences = null;
-  private int[] contigs = null;
-  private int width = 0;
-  private int firstCol = 0;
-  public AlignmentView(CigarArray seqcigararray)
-  {
-    if (!seqcigararray.isSeqCigarArray())
-    {
-      throw new Error("Implementation Error - can only make an alignment view from a CigarArray of sequences.");
-    }
-    //contigs = seqcigararray.applyDeletions();
-    contigs = seqcigararray.getDeletedRegions();
-    sequences = seqcigararray.getSeqCigarArray();
-    width = seqcigararray.getWidth(); // visible width
-  }
-
-  /**
-   * Create an alignmentView where the first column corresponds with the 'firstcol' column of some reference alignment
-   * @param sdata
-   * @param firstcol
-   */
-  public AlignmentView(CigarArray sdata, int firstcol)
-  {
-    this(sdata);
-    firstCol = firstcol;
-  }
-
-  public void setSequences(SeqCigar[] sequences)
-  {
-    this.sequences = sequences;
-  }
-
-  public void setContigs(int[] contigs)
-  {
-    this.contigs = contigs;
-  }
-
-  public SeqCigar[] getSequences()
-  {
-    return sequences;
-  }
-
-  /**
-   * @see CigarArray.getDeletedRegions
-   * @return int[] { vis_start, sym_start, length }
-   */
-  public int[] getContigs()
-  {
-    return contigs;
-  }
-
-  /**
-   * get the full alignment and a columnselection object marking the hidden regions
-   * @param gapCharacter char
-   * @return Object[] { SequenceI[], ColumnSelection}
-   */
-  public Object[] getAlignmentAndColumnSelection(char gapCharacter)
-  {
-    ColumnSelection colsel = new ColumnSelection();
-
-    return new Object[]
-        {
-        SeqCigar.createAlignmentSequences(sequences, gapCharacter, colsel,
-                                          contigs), colsel};
-  }
-
-  /**
-   * getSequenceStrings
-   *
-   * @param c char
-   * @return String[]
-   */
-  public String[] getSequenceStrings(char c)
-  {
-    String[] seqs = new String[sequences.length];
-    for (int n = 0; n < sequences.length; n++)
-    {
-      String fullseq = sequences[n].getSequenceString(c);
-      if (contigs != null)
-      {
-        seqs[n] = "";
-        int p = 0;
-        for (int h = 0; h < contigs.length; h += 3)
-        {
-          seqs[n] += fullseq.substring(p, contigs[h + 1]);
-          p = contigs[h + 1] + contigs[h + 2];
-        }
-        seqs[n] += fullseq.substring(p);
-      }
-      else
-      {
-        seqs[n] = fullseq;
-      }
-    }
-    return seqs;
-  }
-
-  /**
-   *
-   * @return visible number of columns in alignment view
-   */
-  public int getWidth()
-  {
-    return width;
-  }
-
-  protected void setWidth(int width)
-  {
-    this.width = width;
-  }
-
-  /**
-   * get the contiguous subalignments in an alignment view.
-   * @param gapCharacter char
-   * @return SequenceI[][]
-   */
-  public SequenceI[][] getVisibleContigs(char gapCharacter)
-  {
-    SequenceI[][] smsa;
-    int njobs = 1;
-    if (sequences == null || width <= 0)
-    {
-      return null;
-    }
-    if (contigs != null && contigs.length > 0)
-    {
-      int start = 0;
-      njobs = 0;
-      int fwidth = width;
-      for (int contig = 0; contig < contigs.length; contig += 3)
-      {
-        if ( (contigs[contig + 1] - start) > 0)
-        {
-          njobs++;
-        }
-        fwidth += contigs[contig + 2]; // end up with full region width (including hidden regions)
-        start = contigs[contig + 1] + contigs[contig + 2];
-      }
-      if (start < fwidth)
-      {
-        njobs++;
-      }
-      smsa = new SequenceI[njobs][];
-      start = 0;
-      int j = 0;
-      for (int contig = 0; contig < contigs.length; contig += 3)
-      {
-        if (contigs[contig + 1] - start > 0)
-        {
-          SequenceI mseq[] = new SequenceI[sequences.length];
-          for (int s = 0; s < mseq.length; s++)
-          {
-            mseq[s] = sequences[s].getSeq(gapCharacter).getSubSequence(start,
-                contigs[contig + 1]);
-          }
-          smsa[j] = mseq;
-          j++;
-        }
-        start = contigs[contig + 1] + contigs[contig + 2];
-      }
-      if (start < fwidth)
-      {
-        SequenceI mseq[] = new SequenceI[sequences.length];
-        for (int s = 0; s < mseq.length; s++)
-        {
-          mseq[s] = sequences[s].getSeq(gapCharacter).getSubSequence(start,
-              fwidth + 1);
-        }
-        smsa[j] = mseq;
-        j++;
-      }
-    }
-    else
-    {
-      smsa = new SequenceI[1][];
-      smsa[0] = new SequenceI[sequences.length];
-      for (int s = 0; s < sequences.length; s++)
-      {
-        smsa[0][s] = sequences[s].getSeq(gapCharacter);
-      }
-    }
-    return smsa;
-  }
-
-  /**
-   * return full msa and hidden regions with visible blocks replaced with new sub alignments
-   * @param nvismsa SequenceI[][]
-   * @param orders AlignmentOrder[] corresponding to each SequenceI[] block.
-   * @return Object[]
-   */
-  public Object[] getUpdatedView(SequenceI[][] nvismsa, AlignmentOrder[] orders,
-                                 char gapCharacter)
-  {
-    if (sequences == null || width <= 0)
-    {
-      throw new Error("empty view cannot be updated.");
-    }
-    if (nvismsa == null)
-    {
-      throw new Error(
-          "nvismsa==null. use getAlignmentAndColumnSelection() instead.");
-    }
-    if (contigs != null && contigs.length > 0)
-    {
-      SequenceI[] alignment = new SequenceI[sequences.length];
-      ColumnSelection columnselection = new ColumnSelection();
-      if (contigs != null && contigs.length > 0)
-      {
-        int start = 0;
-        int nwidth = 0;
-        int owidth = width;
-        int j = 0;
-        for (int contig = 0; contig < contigs.length; contig += 3)
-        {
-          owidth += contigs[contig + 2]; // recover final column width
-          if (contigs[contig + 1] - start > 0)
-          {
-            int swidth = 0; // subalignment width
-            if (nvismsa[j] != null)
-            {
-              SequenceI mseq[] = nvismsa[j];
-              AlignmentOrder order = (orders == null) ? null : orders[j];
-              j++;
-              if (mseq.length != sequences.length)
-              {
-                throw new Error(
-                    "Mismatch between number of sequences in block " + j + " (" +
-                    mseq.length + ") and the original view (" +
-                    sequences.length + ")");
-              }
-              swidth = mseq[0].getLength(); // JBPNote: could ensure padded here.
-              for (int s = 0; s < mseq.length; s++)
-              {
-                if (alignment[s] == null)
-                {
-                  alignment[s] = mseq[s];
-                }
-                else
-                {
-                  alignment[s].setSequence(alignment[s].getSequenceAsString() +
-                                           mseq[s].getSequenceAsString());
-                  if (mseq[s].getStart() <= mseq[s].getEnd())
-                  {
-                    alignment[s].setEnd(mseq[s].getEnd());
-                  }
-                  if (order != null)
-                  {
-                    order.updateSequence(mseq[s], alignment[s]);
-                  }
-                }
-              }
-            }
-            else
-            {
-              // recover original alignment block or place gaps
-              if (true)
-              {
-                // recover input data
-                for (int s = 0; s < sequences.length; s++)
-                {
-                  SequenceI oseq = sequences[s].getSeq(gapCharacter).
-                      getSubSequence(start,
-                                     contigs[contig + 1]);
-                  if (swidth < oseq.getLength())
-                  {
-                    swidth = oseq.getLength();
-                  }
-                  if (alignment[s] == null)
-                  {
-                    alignment[s] = oseq;
-                  }
-                  else
-                  {
-                    alignment[s].setSequence(alignment[s].getSequenceAsString() +
-                                             oseq.getSequenceAsString());
-                    if (oseq.getEnd() >= oseq.getStart())
-                    {
-                      alignment[s].setEnd(oseq.getEnd());
-                    }
-                  }
-                }
-
-              }
-              j++;
-            }
-            nwidth += swidth;
-          }
-          // advance to begining of visible region
-          start = contigs[contig + 1] + contigs[contig + 2];
-          // add hidden segment to right of next region
-          for (int s = 0; s < sequences.length; s++)
-          {
-            SequenceI hseq = sequences[s].getSeq(gapCharacter).getSubSequence(
-                contigs[contig +
-                1], start);
-            if (alignment[s] == null)
-            {
-              alignment[s] = hseq;
-            }
-            else
-            {
-              alignment[s].setSequence(alignment[s].getSequenceAsString() +
-                                       hseq.getSequenceAsString());
-              if (hseq.getEnd() >= hseq.getStart())
-              {
-                alignment[s].setEnd(hseq.getEnd());
-              }
-            }
-          }
-          // mark hidden segment as hidden in the new alignment
-          columnselection.hideColumns(nwidth, nwidth + contigs[contig + 2] - 1);
-          nwidth += contigs[contig + 2];
-        }
-        // Do final segment - if it exists
-        if (j < nvismsa.length)
-        {
-          int swidth = 0;
-          if (nvismsa[j] != null)
-          {
-            SequenceI mseq[] = nvismsa[j];
-            AlignmentOrder order = (orders != null) ? orders[j] : null;
-            swidth = mseq[0].getLength();
-            for (int s = 0; s < mseq.length; s++)
-            {
-              if (alignment[s] == null)
-              {
-                alignment[s] = mseq[s];
-              }
-              else
-              {
-                alignment[s].setSequence(alignment[s].getSequenceAsString() +
-                                         mseq[s].getSequenceAsString());
-                if (mseq[s].getEnd() >= mseq[s].getStart())
-                {
-                  alignment[s].setEnd(mseq[s].getEnd());
-                }
-                if (order != null)
-                {
-                  order.updateSequence(mseq[s], alignment[s]);
-                }
-              }
-            }
-          }
-          else
-          {
-            if (start < owidth)
-            {
-              // recover input data or place gaps
-              if (true)
-              {
-                // recover input data
-                for (int s = 0; s < sequences.length; s++)
-                {
-                  SequenceI oseq = sequences[s].getSeq(gapCharacter).
-                      getSubSequence(start,
-                                     owidth + 1);
-                  if (swidth < oseq.getLength())
-                  {
-                    swidth = oseq.getLength();
-                  }
-                  if (alignment[s] == null)
-                  {
-                    alignment[s] = oseq;
-                  }
-                  else
-                  {
-                    alignment[s].setSequence(alignment[s].getSequenceAsString() +
-                                             oseq.getSequenceAsString());
-                    if (oseq.getEnd() >= oseq.getStart())
-                    {
-                      alignment[s].setEnd(oseq.getEnd());
-                    }
-                  }
-                }
-                nwidth += swidth;
-              }
-              else
-              {
-                // place gaps.
-                throw new Error("Padding not yet implemented.");
-              }
-            }
-          }
-        }
-      }
-      return new Object[]
-          {
-          alignment, columnselection};
-    }
-    else
-    {
-      if (nvismsa.length != 1)
-      {
-        throw new Error("Mismatch between visible blocks to update and number of contigs in view (contigs=0,blocks=" +
-                        nvismsa.length);
-      }
-      if (nvismsa[0] != null)
-      {
-        return new Object[]
-            {
-            nvismsa[0], new ColumnSelection()};
-      }
-      else
-      {
-        return getAlignmentAndColumnSelection(gapCharacter);
-      }
-    }
-  }
-
-  /**
-   * returns simple array of start end positions of visible range on alignment.
-   * vis_start and vis_end are inclusive - use SequenceI.getSubSequence(vis_start, vis_end+1) to recover visible sequence from underlying alignment.
-   * @return int[] { start_i, end_i } for 1<i<n visible regions.
-   */
-  public int[] getVisibleContigs()
-  {
-    if (contigs != null && contigs.length > 0)
-    {
-      int start = 0;
-      int nvis = 0;
-      int fwidth = width;
-      for (int contig = 0; contig < contigs.length; contig += 3)
-      {
-        if ( (contigs[contig + 1] - start) > 0)
-        {
-          nvis++;
-        }
-        fwidth += contigs[contig + 2]; // end up with full region width (including hidden regions)
-        start = contigs[contig + 1] + contigs[contig + 2];
-      }
-      if (start < fwidth)
-      {
-        nvis++;
-      }
-      int viscontigs[] = new int[nvis * 2];
-      nvis = 0;
-      start = 0;
-      for (int contig = 0; contig < contigs.length; contig += 3)
-      {
-        if ( (contigs[contig + 1] - start) > 0)
-        {
-          viscontigs[nvis] = start;
-          viscontigs[nvis + 1] = contigs[contig + 1] - 1; // end is inclusive
-          nvis += 2;
-        }
-        start = contigs[contig + 1] + contigs[contig + 2];
-      }
-      if (start < fwidth)
-      {
-        viscontigs[nvis] = start;
-        viscontigs[nvis + 1] = fwidth; // end is inclusive
-        nvis += 2;
-      }
-      return viscontigs;
-    }
-    else
-    {
-      return new int[]
-          {
-          0, width};
-    }
-  }
-
-  /**
-   *
-   * @return position of first visible column of AlignmentView within its parent's alignment reference frame
-   */
-  public int getAlignmentOrigin()
-  {
-    // TODO Auto-generated method stub
-    return firstCol;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.datamodel;
+
+/**
+ * <p>
+ * Title:
+ * </p>
+ * 
+ * <p>
+ * Description:
+ * </p>
+ * 
+ * <p>
+ * Copyright: Copyright (c) 2004
+ * </p>
+ * 
+ * <p>
+ * Company: Dundee University
+ * </p>
+ * 
+ * @author not attributable
+ * @version 1.0
+ */
+public class AlignmentView
+{
+  /**
+   * Transient object compactly representing a 'view' of an alignment - with
+   * discontinuities marked.
+   */
+  private SeqCigar[] sequences = null;
+
+  private int[] contigs = null;
+
+  private int width = 0;
+
+  private int firstCol = 0;
+
+  public AlignmentView(CigarArray seqcigararray)
+  {
+    if (!seqcigararray.isSeqCigarArray())
+    {
+      throw new Error(
+              "Implementation Error - can only make an alignment view from a CigarArray of sequences.");
+    }
+    // contigs = seqcigararray.applyDeletions();
+    contigs = seqcigararray.getDeletedRegions();
+    sequences = seqcigararray.getSeqCigarArray();
+    width = seqcigararray.getWidth(); // visible width
+  }
+
+  /**
+   * Create an alignmentView where the first column corresponds with the
+   * 'firstcol' column of some reference alignment
+   * 
+   * @param sdata
+   * @param firstcol
+   */
+  public AlignmentView(CigarArray sdata, int firstcol)
+  {
+    this(sdata);
+    firstCol = firstcol;
+  }
+
+  public void setSequences(SeqCigar[] sequences)
+  {
+    this.sequences = sequences;
+  }
+
+  public void setContigs(int[] contigs)
+  {
+    this.contigs = contigs;
+  }
+
+  public SeqCigar[] getSequences()
+  {
+    return sequences;
+  }
+
+  /**
+   * @see CigarArray.getDeletedRegions
+   * @return int[] { vis_start, sym_start, length }
+   */
+  public int[] getContigs()
+  {
+    return contigs;
+  }
+
+  /**
+   * get the full alignment and a columnselection object marking the hidden
+   * regions
+   * 
+   * @param gapCharacter
+   *                char
+   * @return Object[] { SequenceI[], ColumnSelection}
+   */
+  public Object[] getAlignmentAndColumnSelection(char gapCharacter)
+  {
+    ColumnSelection colsel = new ColumnSelection();
+
+    return new Object[]
+    {
+        SeqCigar.createAlignmentSequences(sequences, gapCharacter, colsel,
+                contigs), colsel };
+  }
+
+  /**
+   * getSequenceStrings
+   * 
+   * @param c
+   *                char
+   * @return String[]
+   */
+  public String[] getSequenceStrings(char c)
+  {
+    String[] seqs = new String[sequences.length];
+    for (int n = 0; n < sequences.length; n++)
+    {
+      String fullseq = sequences[n].getSequenceString(c);
+      if (contigs != null)
+      {
+        seqs[n] = "";
+        int p = 0;
+        for (int h = 0; h < contigs.length; h += 3)
+        {
+          seqs[n] += fullseq.substring(p, contigs[h + 1]);
+          p = contigs[h + 1] + contigs[h + 2];
+        }
+        seqs[n] += fullseq.substring(p);
+      }
+      else
+      {
+        seqs[n] = fullseq;
+      }
+    }
+    return seqs;
+  }
+
+  /**
+   * 
+   * @return visible number of columns in alignment view
+   */
+  public int getWidth()
+  {
+    return width;
+  }
+
+  protected void setWidth(int width)
+  {
+    this.width = width;
+  }
+
+  /**
+   * get the contiguous subalignments in an alignment view.
+   * 
+   * @param gapCharacter
+   *                char
+   * @return SequenceI[][]
+   */
+  public SequenceI[][] getVisibleContigs(char gapCharacter)
+  {
+    SequenceI[][] smsa;
+    int njobs = 1;
+    if (sequences == null || width <= 0)
+    {
+      return null;
+    }
+    if (contigs != null && contigs.length > 0)
+    {
+      int start = 0;
+      njobs = 0;
+      int fwidth = width;
+      for (int contig = 0; contig < contigs.length; contig += 3)
+      {
+        if ((contigs[contig + 1] - start) > 0)
+        {
+          njobs++;
+        }
+        fwidth += contigs[contig + 2]; // end up with full region width
+                                        // (including hidden regions)
+        start = contigs[contig + 1] + contigs[contig + 2];
+      }
+      if (start < fwidth)
+      {
+        njobs++;
+      }
+      smsa = new SequenceI[njobs][];
+      start = 0;
+      int j = 0;
+      for (int contig = 0; contig < contigs.length; contig += 3)
+      {
+        if (contigs[contig + 1] - start > 0)
+        {
+          SequenceI mseq[] = new SequenceI[sequences.length];
+          for (int s = 0; s < mseq.length; s++)
+          {
+            mseq[s] = sequences[s].getSeq(gapCharacter).getSubSequence(
+                    start, contigs[contig + 1]);
+          }
+          smsa[j] = mseq;
+          j++;
+        }
+        start = contigs[contig + 1] + contigs[contig + 2];
+      }
+      if (start < fwidth)
+      {
+        SequenceI mseq[] = new SequenceI[sequences.length];
+        for (int s = 0; s < mseq.length; s++)
+        {
+          mseq[s] = sequences[s].getSeq(gapCharacter).getSubSequence(start,
+                  fwidth + 1);
+        }
+        smsa[j] = mseq;
+        j++;
+      }
+    }
+    else
+    {
+      smsa = new SequenceI[1][];
+      smsa[0] = new SequenceI[sequences.length];
+      for (int s = 0; s < sequences.length; s++)
+      {
+        smsa[0][s] = sequences[s].getSeq(gapCharacter);
+      }
+    }
+    return smsa;
+  }
+
+  /**
+   * return full msa and hidden regions with visible blocks replaced with new
+   * sub alignments
+   * 
+   * @param nvismsa
+   *                SequenceI[][]
+   * @param orders
+   *                AlignmentOrder[] corresponding to each SequenceI[] block.
+   * @return Object[]
+   */
+  public Object[] getUpdatedView(SequenceI[][] nvismsa,
+          AlignmentOrder[] orders, char gapCharacter)
+  {
+    if (sequences == null || width <= 0)
+    {
+      throw new Error("empty view cannot be updated.");
+    }
+    if (nvismsa == null)
+    {
+      throw new Error(
+              "nvismsa==null. use getAlignmentAndColumnSelection() instead.");
+    }
+    if (contigs != null && contigs.length > 0)
+    {
+      SequenceI[] alignment = new SequenceI[sequences.length];
+      ColumnSelection columnselection = new ColumnSelection();
+      if (contigs != null && contigs.length > 0)
+      {
+        int start = 0;
+        int nwidth = 0;
+        int owidth = width;
+        int j = 0;
+        for (int contig = 0; contig < contigs.length; contig += 3)
+        {
+          owidth += contigs[contig + 2]; // recover final column width
+          if (contigs[contig + 1] - start > 0)
+          {
+            int swidth = 0; // subalignment width
+            if (nvismsa[j] != null)
+            {
+              SequenceI mseq[] = nvismsa[j];
+              AlignmentOrder order = (orders == null) ? null : orders[j];
+              j++;
+              if (mseq.length != sequences.length)
+              {
+                throw new Error(
+                        "Mismatch between number of sequences in block "
+                                + j + " (" + mseq.length
+                                + ") and the original view ("
+                                + sequences.length + ")");
+              }
+              swidth = mseq[0].getLength(); // JBPNote: could ensure padded
+                                            // here.
+              for (int s = 0; s < mseq.length; s++)
+              {
+                if (alignment[s] == null)
+                {
+                  alignment[s] = mseq[s];
+                }
+                else
+                {
+                  alignment[s].setSequence(alignment[s]
+                          .getSequenceAsString()
+                          + mseq[s].getSequenceAsString());
+                  if (mseq[s].getStart() <= mseq[s].getEnd())
+                  {
+                    alignment[s].setEnd(mseq[s].getEnd());
+                  }
+                  if (order != null)
+                  {
+                    order.updateSequence(mseq[s], alignment[s]);
+                  }
+                }
+              }
+            }
+            else
+            {
+              // recover original alignment block or place gaps
+              if (true)
+              {
+                // recover input data
+                for (int s = 0; s < sequences.length; s++)
+                {
+                  SequenceI oseq = sequences[s].getSeq(gapCharacter)
+                          .getSubSequence(start, contigs[contig + 1]);
+                  if (swidth < oseq.getLength())
+                  {
+                    swidth = oseq.getLength();
+                  }
+                  if (alignment[s] == null)
+                  {
+                    alignment[s] = oseq;
+                  }
+                  else
+                  {
+                    alignment[s].setSequence(alignment[s]
+                            .getSequenceAsString()
+                            + oseq.getSequenceAsString());
+                    if (oseq.getEnd() >= oseq.getStart())
+                    {
+                      alignment[s].setEnd(oseq.getEnd());
+                    }
+                  }
+                }
+
+              }
+              j++;
+            }
+            nwidth += swidth;
+          }
+          // advance to begining of visible region
+          start = contigs[contig + 1] + contigs[contig + 2];
+          // add hidden segment to right of next region
+          for (int s = 0; s < sequences.length; s++)
+          {
+            SequenceI hseq = sequences[s].getSeq(gapCharacter)
+                    .getSubSequence(contigs[contig + 1], start);
+            if (alignment[s] == null)
+            {
+              alignment[s] = hseq;
+            }
+            else
+            {
+              alignment[s].setSequence(alignment[s].getSequenceAsString()
+                      + hseq.getSequenceAsString());
+              if (hseq.getEnd() >= hseq.getStart())
+              {
+                alignment[s].setEnd(hseq.getEnd());
+              }
+            }
+          }
+          // mark hidden segment as hidden in the new alignment
+          columnselection.hideColumns(nwidth, nwidth + contigs[contig + 2]
+                  - 1);
+          nwidth += contigs[contig + 2];
+        }
+        // Do final segment - if it exists
+        if (j < nvismsa.length)
+        {
+          int swidth = 0;
+          if (nvismsa[j] != null)
+          {
+            SequenceI mseq[] = nvismsa[j];
+            AlignmentOrder order = (orders != null) ? orders[j] : null;
+            swidth = mseq[0].getLength();
+            for (int s = 0; s < mseq.length; s++)
+            {
+              if (alignment[s] == null)
+              {
+                alignment[s] = mseq[s];
+              }
+              else
+              {
+                alignment[s].setSequence(alignment[s].getSequenceAsString()
+                        + mseq[s].getSequenceAsString());
+                if (mseq[s].getEnd() >= mseq[s].getStart())
+                {
+                  alignment[s].setEnd(mseq[s].getEnd());
+                }
+                if (order != null)
+                {
+                  order.updateSequence(mseq[s], alignment[s]);
+                }
+              }
+            }
+          }
+          else
+          {
+            if (start < owidth)
+            {
+              // recover input data or place gaps
+              if (true)
+              {
+                // recover input data
+                for (int s = 0; s < sequences.length; s++)
+                {
+                  SequenceI oseq = sequences[s].getSeq(gapCharacter)
+                          .getSubSequence(start, owidth + 1);
+                  if (swidth < oseq.getLength())
+                  {
+                    swidth = oseq.getLength();
+                  }
+                  if (alignment[s] == null)
+                  {
+                    alignment[s] = oseq;
+                  }
+                  else
+                  {
+                    alignment[s].setSequence(alignment[s]
+                            .getSequenceAsString()
+                            + oseq.getSequenceAsString());
+                    if (oseq.getEnd() >= oseq.getStart())
+                    {
+                      alignment[s].setEnd(oseq.getEnd());
+                    }
+                  }
+                }
+                nwidth += swidth;
+              }
+              else
+              {
+                // place gaps.
+                throw new Error("Padding not yet implemented.");
+              }
+            }
+          }
+        }
+      }
+      return new Object[]
+      { alignment, columnselection };
+    }
+    else
+    {
+      if (nvismsa.length != 1)
+      {
+        throw new Error(
+                "Mismatch between visible blocks to update and number of contigs in view (contigs=0,blocks="
+                        + nvismsa.length);
+      }
+      if (nvismsa[0] != null)
+      {
+        return new Object[]
+        { nvismsa[0], new ColumnSelection() };
+      }
+      else
+      {
+        return getAlignmentAndColumnSelection(gapCharacter);
+      }
+    }
+  }
+
+  /**
+   * returns simple array of start end positions of visible range on alignment.
+   * vis_start and vis_end are inclusive - use
+   * SequenceI.getSubSequence(vis_start, vis_end+1) to recover visible sequence
+   * from underlying alignment.
+   * 
+   * @return int[] { start_i, end_i } for 1<i<n visible regions.
+   */
+  public int[] getVisibleContigs()
+  {
+    if (contigs != null && contigs.length > 0)
+    {
+      int start = 0;
+      int nvis = 0;
+      int fwidth = width;
+      for (int contig = 0; contig < contigs.length; contig += 3)
+      {
+        if ((contigs[contig + 1] - start) > 0)
+        {
+          nvis++;
+        }
+        fwidth += contigs[contig + 2]; // end up with full region width
+                                        // (including hidden regions)
+        start = contigs[contig + 1] + contigs[contig + 2];
+      }
+      if (start < fwidth)
+      {
+        nvis++;
+      }
+      int viscontigs[] = new int[nvis * 2];
+      nvis = 0;
+      start = 0;
+      for (int contig = 0; contig < contigs.length; contig += 3)
+      {
+        if ((contigs[contig + 1] - start) > 0)
+        {
+          viscontigs[nvis] = start;
+          viscontigs[nvis + 1] = contigs[contig + 1] - 1; // end is inclusive
+          nvis += 2;
+        }
+        start = contigs[contig + 1] + contigs[contig + 2];
+      }
+      if (start < fwidth)
+      {
+        viscontigs[nvis] = start;
+        viscontigs[nvis + 1] = fwidth; // end is inclusive
+        nvis += 2;
+      }
+      return viscontigs;
+    }
+    else
+    {
+      return new int[]
+      { 0, width };
+    }
+  }
+
+  /**
+   * 
+   * @return position of first visible column of AlignmentView within its
+   *         parent's alignment reference frame
+   */
+  public int getAlignmentOrigin()
+  {
+    // TODO Auto-generated method stub
+    return firstCol;
+  }
+}
diff --git a/src/jalview/datamodel/Annotation.java b/src/jalview/datamodel/Annotation.java
index 9fc69bb..348c9a4 100755
--- a/src/jalview/datamodel/Annotation.java
+++ b/src/jalview/datamodel/Annotation.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -22,7 +22,7 @@ import java.awt.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
@@ -47,11 +47,15 @@ public class Annotation
 
   /**
    * Creates a new Annotation object.
-   *
-   * @param displayChar DOCUMENT ME!
-   * @param desc DOCUMENT ME!
-   * @param ss DOCUMENT ME!
-   * @param val DOCUMENT ME!
+   * 
+   * @param displayChar
+   *                DOCUMENT ME!
+   * @param desc
+   *                DOCUMENT ME!
+   * @param ss
+   *                DOCUMENT ME!
+   * @param val
+   *                DOCUMENT ME!
    */
   public Annotation(String displayChar, String desc, char ss, float val)
   {
@@ -63,32 +67,41 @@ public class Annotation
 
   /**
    * Creates a new Annotation object.
-   *
-   * @param displayChar DOCUMENT ME!
-   * @param desc DOCUMENT ME!
-   * @param ss DOCUMENT ME!
-   * @param val DOCUMENT ME!
-   * @param colour DOCUMENT ME!
+   * 
+   * @param displayChar
+   *                DOCUMENT ME!
+   * @param desc
+   *                DOCUMENT ME!
+   * @param ss
+   *                DOCUMENT ME!
+   * @param val
+   *                DOCUMENT ME!
+   * @param colour
+   *                DOCUMENT ME!
    */
   public Annotation(String displayChar, String desc, char ss, float val,
-                    Color colour)
+          Color colour)
   {
     this(displayChar, desc, ss, val);
     this.colour = colour;
   }
+
   /**
-   * Copy constructor
-   * New annotation takes on the same (or duplicated) attributes as the given template
-   * @param that template annotation
+   * Copy constructor New annotation takes on the same (or duplicated)
+   * attributes as the given template
+   * 
+   * @param that
+   *                template annotation
    */
-  public Annotation(Annotation that) {
-    if (that==null || this==that)
+  public Annotation(Annotation that)
+  {
+    if (that == null || this == that)
     {
       return;
     }
-    if (that.displayCharacter!=null)
+    if (that.displayCharacter != null)
       displayCharacter = new String(that.displayCharacter);
-    if (that.description!=null)
+    if (that.description != null)
       description = new String(that.description);
     secondaryStructure = that.secondaryStructure;
     value = that.value;
@@ -97,7 +110,9 @@ public class Annotation
 
   /**
    * Value only annotation.
-   * @param val value at this annotation position
+   * 
+   * @param val
+   *                value at this annotation position
    */
   public Annotation(float val)
   {
diff --git a/src/jalview/datamodel/BinaryNode.java b/src/jalview/datamodel/BinaryNode.java
index a7e8254..9be34b4 100755
--- a/src/jalview/datamodel/BinaryNode.java
+++ b/src/jalview/datamodel/BinaryNode.java
@@ -1,284 +1,301 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.datamodel;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class BinaryNode
-{
-  Object element;
-  String name;
-  BinaryNode left;
-  BinaryNode right;
-  BinaryNode parent;
-
-  /** DOCUMENT ME!! */
-  public int bootstrap;
-
-  /**
-   * Creates a new BinaryNode object.
-   */
-  public BinaryNode()
-  {
-    left = right = parent = null;
-    bootstrap = 0;
-  }
-
-  /**
-   * Creates a new BinaryNode object.
-   *
-   * @param element DOCUMENT ME!
-   * @param parent DOCUMENT ME!
-   * @param name DOCUMENT ME!
-   */
-  public BinaryNode(Object element, BinaryNode parent, String name)
-  {
-    this.element = element;
-    this.parent = parent;
-    this.name = name;
-
-    left = right = null;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Object element()
-  {
-    return element;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param v DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Object setElement(Object v)
-  {
-    return element = v;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public BinaryNode left()
-  {
-    return left;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param n DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public BinaryNode setLeft(BinaryNode n)
-  {
-    return left = n;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public BinaryNode right()
-  {
-    return right;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param n DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public BinaryNode setRight(BinaryNode n)
-  {
-    return right = n;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public BinaryNode parent()
-  {
-    return parent;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param n DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public BinaryNode setParent(BinaryNode n)
-  {
-    return parent = n;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public boolean isLeaf()
-  {
-    return (left == null) && (right == null);
-  }
-
-  /**
-   * attaches FIRST and SECOND node arguments as the LEFT and RIGHT children of this node (removing any old references)
-   * a null parameter DOES NOT mean that the pointer to the corresponding child node is set to  NULL - you  should use
-   * setChild(null), or detach() for this.
-   *
-   */
-  public void SetChildren(BinaryNode leftchild, BinaryNode rightchild)
-  {
-    if (leftchild != null)
-    {
-      this.setLeft(leftchild);
-      leftchild.detach();
-      leftchild.setParent(this);
-    }
-
-    if (rightchild != null)
-    {
-      this.setRight(rightchild);
-      rightchild.detach();
-      rightchild.setParent(this);
-    }
-  }
-
-  /**
-   * Detaches the node from the binary tree, along with all its child nodes.
-   * @return BinaryNode The detached node.
-   */
-  public BinaryNode detach()
-  {
-    if (this.parent != null)
-    {
-      if (this.parent.left == this)
-      {
-        this.parent.left = null;
-      }
-      else
-      {
-        if (this.parent.right == this)
-        {
-          this.parent.right = null;
-        }
-      }
-    }
-
-    this.parent = null;
-
-    return this;
-  }
-
-  /**
-   * Traverses up through the tree until a node with a free leftchild is discovered.
-   * @return BinaryNode
-   */
-  public BinaryNode ascendLeft()
-  {
-    BinaryNode c = this;
-
-    do
-    {
-      c = c.parent();
-    }
-    while ( (c != null) && (c.left() != null) && !c.left().isLeaf());
-
-    return c;
-  }
-
-  /**
-   * Traverses up through the tree until a node with a free rightchild is discovered.
-   * Jalview builds trees by descent on the left, so this may be unused.
-   * @return BinaryNode
-   */
-  public BinaryNode ascendRight()
-  {
-    BinaryNode c = this;
-
-    do
-    {
-      c = c.parent();
-    }
-    while ( (c != null) && (c.right() != null) && !c.right().isLeaf());
-
-    return c;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param name DOCUMENT ME!
-   */
-  public void setName(String name)
-  {
-    this.name = name;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public String getName()
-  {
-    return this.name;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param boot DOCUMENT ME!
-   */
-  public void setBootstrap(int boot)
-  {
-    this.bootstrap = boot;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public int getBootstrap()
-  {
-    return bootstrap;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.datamodel;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class BinaryNode
+{
+  Object element;
+
+  String name;
+
+  BinaryNode left;
+
+  BinaryNode right;
+
+  BinaryNode parent;
+
+  /** DOCUMENT ME!! */
+  public int bootstrap;
+
+  /**
+   * Creates a new BinaryNode object.
+   */
+  public BinaryNode()
+  {
+    left = right = parent = null;
+    bootstrap = 0;
+  }
+
+  /**
+   * Creates a new BinaryNode object.
+   * 
+   * @param element
+   *                DOCUMENT ME!
+   * @param parent
+   *                DOCUMENT ME!
+   * @param name
+   *                DOCUMENT ME!
+   */
+  public BinaryNode(Object element, BinaryNode parent, String name)
+  {
+    this.element = element;
+    this.parent = parent;
+    this.name = name;
+
+    left = right = null;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public Object element()
+  {
+    return element;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param v
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public Object setElement(Object v)
+  {
+    return element = v;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public BinaryNode left()
+  {
+    return left;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param n
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public BinaryNode setLeft(BinaryNode n)
+  {
+    return left = n;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public BinaryNode right()
+  {
+    return right;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param n
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public BinaryNode setRight(BinaryNode n)
+  {
+    return right = n;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public BinaryNode parent()
+  {
+    return parent;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param n
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public BinaryNode setParent(BinaryNode n)
+  {
+    return parent = n;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public boolean isLeaf()
+  {
+    return (left == null) && (right == null);
+  }
+
+  /**
+   * attaches FIRST and SECOND node arguments as the LEFT and RIGHT children of
+   * this node (removing any old references) a null parameter DOES NOT mean that
+   * the pointer to the corresponding child node is set to NULL - you should use
+   * setChild(null), or detach() for this.
+   * 
+   */
+  public void SetChildren(BinaryNode leftchild, BinaryNode rightchild)
+  {
+    if (leftchild != null)
+    {
+      this.setLeft(leftchild);
+      leftchild.detach();
+      leftchild.setParent(this);
+    }
+
+    if (rightchild != null)
+    {
+      this.setRight(rightchild);
+      rightchild.detach();
+      rightchild.setParent(this);
+    }
+  }
+
+  /**
+   * Detaches the node from the binary tree, along with all its child nodes.
+   * 
+   * @return BinaryNode The detached node.
+   */
+  public BinaryNode detach()
+  {
+    if (this.parent != null)
+    {
+      if (this.parent.left == this)
+      {
+        this.parent.left = null;
+      }
+      else
+      {
+        if (this.parent.right == this)
+        {
+          this.parent.right = null;
+        }
+      }
+    }
+
+    this.parent = null;
+
+    return this;
+  }
+
+  /**
+   * Traverses up through the tree until a node with a free leftchild is
+   * discovered.
+   * 
+   * @return BinaryNode
+   */
+  public BinaryNode ascendLeft()
+  {
+    BinaryNode c = this;
+
+    do
+    {
+      c = c.parent();
+    } while ((c != null) && (c.left() != null) && !c.left().isLeaf());
+
+    return c;
+  }
+
+  /**
+   * Traverses up through the tree until a node with a free rightchild is
+   * discovered. Jalview builds trees by descent on the left, so this may be
+   * unused.
+   * 
+   * @return BinaryNode
+   */
+  public BinaryNode ascendRight()
+  {
+    BinaryNode c = this;
+
+    do
+    {
+      c = c.parent();
+    } while ((c != null) && (c.right() != null) && !c.right().isLeaf());
+
+    return c;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param name
+   *                DOCUMENT ME!
+   */
+  public void setName(String name)
+  {
+    this.name = name;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public String getName()
+  {
+    return this.name;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param boot
+   *                DOCUMENT ME!
+   */
+  public void setBootstrap(int boot)
+  {
+    this.bootstrap = boot;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public int getBootstrap()
+  {
+    return bootstrap;
+  }
+}
diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java
index 1cdc934..52b0ece 100755
--- a/src/jalview/datamodel/BinarySequence.java
+++ b/src/jalview/datamodel/BinarySequence.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -22,20 +22,21 @@ import jalview.schemes.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class BinarySequence
-    extends Sequence
+public class BinarySequence extends Sequence
 {
   int[] binary;
+
   double[] dbinary;
 
   /**
    * Creates a new BinarySequence object.
-   *
-   * @param s DOCUMENT ME!
+   * 
+   * @param s
+   *                DOCUMENT ME!
    */
   public BinarySequence(String s)
   {
@@ -64,8 +65,7 @@ public class BinarySequence
       try
       {
         aanum = ResidueProperties.aaIndex[getCharAt(i)];
-      }
-      catch (NullPointerException e)
+      } catch (NullPointerException e)
       {
         aanum = 20;
       }
@@ -75,18 +75,19 @@ public class BinarySequence
         aanum = 20;
       }
 
-      dbinary[ (i * nores) + aanum] = 1.0;
+      dbinary[(i * nores) + aanum] = 1.0;
     }
   }
 
   /**
    * ancode using substitution matrix given in matrix
+   * 
    * @param matrix
    */
   public void matrixEncode(ScoreMatrix matrix)
   {
-    matrixEncode(matrix.isDNA() ? ResidueProperties.nucleotideIndex :
-                 ResidueProperties.aaIndex, matrix.getMatrix());
+    matrixEncode(matrix.isDNA() ? ResidueProperties.nucleotideIndex
+            : ResidueProperties.aaIndex, matrix.getMatrix());
   }
 
   /**
@@ -104,9 +105,9 @@ public class BinarySequence
 
     int nores = 21;
 
-    //for (int i = 0; i < dbinary.length; i++) {
-    //  dbinary[i] = 0.0;
-    //}
+    // for (int i = 0; i < dbinary.length; i++) {
+    // dbinary[i] = 0.0;
+    // }
     for (int i = 0; i < getSequence().length; i++)
     {
       int aanum = 20;
@@ -114,8 +115,7 @@ public class BinarySequence
       try
       {
         aanum = aaIndex[getCharAt(i)];
-      }
-      catch (NullPointerException e)
+      } catch (NullPointerException e)
       {
         aanum = 20;
       }
@@ -129,14 +129,14 @@ public class BinarySequence
 
       for (int j = 0; j < 20; j++)
       {
-        dbinary[ (i * nores) + j] = matrix[aanum][j];
+        dbinary[(i * nores) + j] = matrix[aanum][j];
       }
     }
   }
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public String toBinaryString()
@@ -158,7 +158,7 @@ public class BinarySequence
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public double[] getDBinary()
diff --git a/src/jalview/datamodel/CigarArray.java b/src/jalview/datamodel/CigarArray.java
index c17e01e..6842f4a 100644
--- a/src/jalview/datamodel/CigarArray.java
+++ b/src/jalview/datamodel/CigarArray.java
@@ -1,36 +1,37 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
 package jalview.datamodel;
 
-public class CigarArray
-    extends CigarBase
+public class CigarArray extends CigarBase
 {
   /**
-   * Do CIGAR operations on a set of sequences from many other cigars
-   * BAD THINGS WILL HAPPEN IF A CIGARARRAY IS PASSED TO A CIGARARRAY
-   * or a CIGARCIGAR is given a CIGARARRAY to insert gaps into.
+   * Do CIGAR operations on a set of sequences from many other cigars BAD THINGS
+   * WILL HAPPEN IF A CIGARARRAY IS PASSED TO A CIGARARRAY or a CIGARCIGAR is
+   * given a CIGARARRAY to insert gaps into.
    */
   /**
    * array of subject cigars
    */
   public CigarSimple refCigars[] = null;
+
   private boolean seqcigararray = false;
+
   private CigarArray()
   {
     super();
@@ -38,6 +39,7 @@ public class CigarArray
 
   /**
    * isSeqCigarArray()
+   * 
    * @return boolean true if all refCigars resolve to a SeqCigar or a CigarCigar
    */
   public boolean isSeqCigarArray()
@@ -46,9 +48,11 @@ public class CigarArray
   }
 
   /**
-   * Apply CIGAR operations to several cigars in parallel
-   * will throw an error if any of cigar are actually CigarArrays.
-   * @param cigar Cigar[]
+   * Apply CIGAR operations to several cigars in parallel will throw an error if
+   * any of cigar are actually CigarArrays.
+   * 
+   * @param cigar
+   *                Cigar[]
    */
   public CigarArray(CigarSimple[] cigars)
   {
@@ -60,8 +64,7 @@ public class CigarArray
       for (int c = 0; c < cigars.length; c++)
       {
         refCigars[c] = cigars[c];
-        if (! ( (cigars[c] instanceof SeqCigar)
-               || cigars[c] instanceof CigarCigar))
+        if (!((cigars[c] instanceof SeqCigar) || cigars[c] instanceof CigarCigar))
         {
           seqcigararray = false;
         }
@@ -71,7 +74,8 @@ public class CigarArray
 
   /**
    * @see Cigar.getSequenceAndDeletions
-   * @param GapChar char
+   * @param GapChar
+   *                char
    * @return Object[][]
    */
   protected Object[][] getArrayofSequenceAndDeletions(char GapChar)
@@ -98,8 +102,11 @@ public class CigarArray
 
   /**
    * NOTE: this is an improper sequence string function
-   * @return String formed by newline concatenated results of applying CIGAR operations to each reference object in turn.
-   * @param GapChar char
+   * 
+   * @return String formed by newline concatenated results of applying CIGAR
+   *         operations to each reference object in turn.
+   * @param GapChar
+   *                char
    * @return '\n' separated strings (empty results included as \n\n)
    */
   public String getSequenceString(char GapChar)
@@ -114,7 +121,7 @@ public class CigarArray
     {
       if (sqanddels[c] != null)
       {
-        seqStrings.append( (String) sqanddels[c][0]);
+        seqStrings.append((String) sqanddels[c][0]);
         sqanddels[c][0] = null;
       }
       seqStrings.append('\n');
@@ -124,7 +131,9 @@ public class CigarArray
 
   /**
    * return string results of applying cigar string to all reference cigars
-   * @param GapChar char
+   * 
+   * @param GapChar
+   *                char
    * @return String[]
    */
   public String[] getSequenceStrings(char GapChar)
@@ -146,18 +155,19 @@ public class CigarArray
   /**
    * Combines the CigarArray cigar operations with the operations in each
    * reference cigar - creating a new reference cigar
+   * 
    * @return Cigar[]
-
-     public CigarBase[] getEditedCigars() {
-
-    return new CigarBase[] {};
-     }
+   * 
+   * public CigarBase[] getEditedCigars() {
+   * 
+   * return new CigarBase[] {}; }
    */
   /**
-   * applyDeletions
-   * edits underlying refCigars to propagate deleted regions, and removes deletion
-   * operations from CigarArray operation list.
-   * @return int[] position after deletion occured and range of deletion in cigarArray or null if none occured
+   * applyDeletions edits underlying refCigars to propagate deleted regions, and
+   * removes deletion operations from CigarArray operation list.
+   * 
+   * @return int[] position after deletion occured and range of deletion in
+   *         cigarArray or null if none occured
    */
   public int[] applyDeletions()
   {
@@ -188,18 +198,16 @@ public class CigarArray
         }
         int delstart = cursor, delend = cursor + range[i] - 1; // inclusive
         delpos.addElement(new int[]
-                          {vcursor + offset, range[i]}); // index of right hand column after hidden region boundary
+        { vcursor + offset, range[i] }); // index of right hand column after
+                                          // hidden region boundary
         offset += range[i] - 1; // shift in visible column coordinates
         System.arraycopy(operation, i + 1, operation, i, length - i);
         System.arraycopy(range, i + 1, range, i, length - i);
         length--;
-        /*        int dmax=0;
-         for (int s=0; s<refCigars.length; s++) {
-           int d = refCigars[s].deleteRange(delstart, delend);
-           if (d>dmax)
-             dmax=d;
-         }
-         offset+=dmax; // shift in visible column coordinates
+        /*
+         * int dmax=0; for (int s=0; s<refCigars.length; s++) { int d =
+         * refCigars[s].deleteRange(delstart, delend); if (d>dmax) dmax=d; }
+         * offset+=dmax; // shift in visible column coordinates
          */
         for (int s = 0; s < refCigars.length; s++)
         {
@@ -213,7 +221,7 @@ public class CigarArray
       int[] pos = new int[delpos.size() * 2];
       for (int k = 0, l = delpos.size(); k < l; k++)
       {
-        int[] dr = ( (int[]) delpos.elementAt(k));
+        int[] dr = ((int[]) delpos.elementAt(k));
         pos[k * 2] = dr[0];
         pos[k * 2 + 1] = dr[1];
         delpos.setElementAt(null, k);
@@ -225,8 +233,9 @@ public class CigarArray
   }
 
   /**
-   *
-   * @return SeqCigar[] or null if CigarArray is not a SeqCigarArray (ie it does not resolve to set of seqCigars)
+   * 
+   * @return SeqCigar[] or null if CigarArray is not a SeqCigarArray (ie it does
+   *         not resolve to set of seqCigars)
    */
   public SeqCigar[] getSeqCigarArray()
   {
diff --git a/src/jalview/datamodel/CigarBase.java b/src/jalview/datamodel/CigarBase.java
index d44d599..b0efe6c 100644
--- a/src/jalview/datamodel/CigarBase.java
+++ b/src/jalview/datamodel/CigarBase.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -23,9 +23,8 @@ import java.util.*;
 public abstract class CigarBase
 {
   /**
-   * Base class for compact idiosyncratic representation of gaps and aligned residues
-   * Regards to Tom Oldfield for his DynamicArray class.
-   * 17th July 2006
+   * Base class for compact idiosyncratic representation of gaps and aligned
+   * residues Regards to Tom Oldfield for his DynamicArray class. 17th July 2006
    * Not thread safe.
    */
   public CigarBase()
@@ -34,27 +33,44 @@ public abstract class CigarBase
   }
 
   protected int length = 0;
-  protected int _inc_length = 10; // extension range for addition of new operations
+
+  protected int _inc_length = 10; // extension range for addition of new
+                                  // operations
+
   protected char[] operation = null;
+
   protected int[] range = null;
+
   /**
    * Range of Hidden residues in seq (translated as deleted in seq)
    */
-  public static final char D = 'D'; /**
-  * Range of insertions to seq
-  */
- public static final char I = 'I'; /**
-  * Range of aligned residues
-  */
- public static final char M = 'M';
+  public static final char D = 'D';
+
+  /**
+   * Range of insertions to seq
+   */
+  public static final char I = 'I';
+
+  /**
+   * Range of aligned residues
+   */
+  public static final char M = 'M';
+
   static protected final char _case_shift = 'a' - 'A';
+
   /**
-   * Ugly function to get edited sequence string, start and end symbol positions and the deletion regions as an array of int pairs
-   * May return null for an empty cigar string.
-   * May return null for deletion ranges if there are none.
-   * @param reference - the symbol sequence to apply the cigar operations to (or null if no sequence)
-   * @param GapChar - the symbol to use for Insert operations
-   * @return Object[] { String, int[] {start, startcol, end, endcol}, int[][3] {start, end, col} or null} the gapped sequence, first and last residue index, and the deletion ranges on the reference sequence
+   * Ugly function to get edited sequence string, start and end symbol positions
+   * and the deletion regions as an array of int pairs May return null for an
+   * empty cigar string. May return null for deletion ranges if there are none.
+   * 
+   * @param reference -
+   *                the symbol sequence to apply the cigar operations to (or
+   *                null if no sequence)
+   * @param GapChar -
+   *                the symbol to use for Insert operations
+   * @return Object[] { String, int[] {start, startcol, end, endcol}, int[][3]
+   *         {start, end, col} or null} the gapped sequence, first and last
+   *         residue index, and the deletion ranges on the reference sequence
    */
   public Object[] getSequenceAndDeletions(String reference, char GapChar)
   {
@@ -62,8 +78,7 @@ public abstract class CigarBase
     int[][] deletions = new int[length][];
     int[][] trunc_deletions = null;
     StringBuffer sq = new StringBuffer();
-    int cursor = 0, alcursor = 0, start = 0, startpos = 0, end = 0, endpos = 0,
-        delcount = -1;
+    int cursor = 0, alcursor = 0, start = 0, startpos = 0, end = 0, endpos = 0, delcount = -1;
     boolean consecutive_del = false;
     if (length == 0)
     {
@@ -78,56 +93,55 @@ public abstract class CigarBase
     {
       switch (operation[i])
       {
-        case D:
-          if (!consecutive_del)
-          {
-            deletions[++delcount] = new int[]
-                {
-                cursor, 0, alcursor};
-          }
-          cursor += range[i];
-          deletions[delcount][1] = cursor - 1;
-          consecutive_del = true;
-          break;
-        case I:
-          consecutive_del = false;
-          for (int r = 0; r < range[i]; r++)
-          {
-            sq.append(GapChar);
-            alcursor++;
-          }
-          break;
-        case M:
-          consecutive_del = false;
-          if (modstart)
-          {
-            start = cursor;
-            startpos = alcursor;
-            modstart = false;
-          }
-          if (reference != null)
+      case D:
+        if (!consecutive_del)
+        {
+          deletions[++delcount] = new int[]
+          { cursor, 0, alcursor };
+        }
+        cursor += range[i];
+        deletions[delcount][1] = cursor - 1;
+        consecutive_del = true;
+        break;
+      case I:
+        consecutive_del = false;
+        for (int r = 0; r < range[i]; r++)
+        {
+          sq.append(GapChar);
+          alcursor++;
+        }
+        break;
+      case M:
+        consecutive_del = false;
+        if (modstart)
+        {
+          start = cursor;
+          startpos = alcursor;
+          modstart = false;
+        }
+        if (reference != null)
+        {
+          int sbend = cursor + range[i];
+          if (sbend > rlength)
           {
-            int sbend = cursor + range[i];
-            if (sbend > rlength)
+            sq.append(reference.substring(cursor, rlength));
+            while (sbend-- >= rlength)
             {
-              sq.append(reference.substring(cursor, rlength));
-              while (sbend-- >= rlength)
-              {
-                sq.append(GapChar);
-              }
-            }
-            else
-            {
-              sq.append(reference.substring(cursor, sbend));
+              sq.append(GapChar);
             }
           }
-          alcursor += range[i];
-          cursor += range[i];
-          end = cursor - 1;
-          endpos = alcursor;
-          break;
-        default:
-          throw new Error("Unknown SeqCigar operation '" + operation[i] + "'");
+          else
+          {
+            sq.append(reference.substring(cursor, sbend));
+          }
+        }
+        alcursor += range[i];
+        cursor += range[i];
+        end = cursor - 1;
+        endpos = alcursor;
+        break;
+      default:
+        throw new Error("Unknown SeqCigar operation '" + operation[i] + "'");
       }
     }
     if (++delcount > 0)
@@ -137,11 +151,8 @@ public abstract class CigarBase
     }
     deletions = null;
     return new Object[]
-        {
-        ( (reference != null) ? sq.toString() : null),
-        new int[]
-        {
-        start, startpos, end, endpos}, trunc_deletions};
+    { ((reference != null) ? sq.toString() : null), new int[]
+    { start, startpos, end, endpos }, trunc_deletions };
   }
 
   protected void compact_operations()
@@ -174,19 +185,23 @@ public abstract class CigarBase
 
   /**
    * turn a cigar string into a series of operation range pairs
-   * @param cigarString String
+   * 
+   * @param cigarString
+   *                String
    * @return object[] {char[] operation, int[] range}
-   * @throws java.lang.Exception for improperly formated cigar strings or ones with unknown operations
+   * @throws java.lang.Exception
+   *                 for improperly formated cigar strings or ones with unknown
+   *                 operations
    */
   public static Object[] parseCigarString(String cigarString)
-      throws Exception
+          throws Exception
   {
     int ops = 0;
     for (int i = 0, l = cigarString.length(); i < l; i++)
     {
       char c = cigarString.charAt(i);
-      if (c == M || c == (M - _case_shift) || c == I || c == (I - _case_shift) ||
-          c == D || c == (D - _case_shift))
+      if (c == M || c == (M - _case_shift) || c == I
+              || c == (I - _case_shift) || c == D || c == (D - _case_shift))
       {
         ops++;
       }
@@ -202,8 +217,7 @@ public abstract class CigarBase
       do
       {
         c = cigarString.charAt(j++);
-      }
-      while (c >= '0' && c <= '9' && j < l);
+      } while (c >= '0' && c <= '9' && j < l);
       if (j >= l && c >= '0' && c <= '9')
       {
         throw new Exception("Unterminated cigar string.");
@@ -213,8 +227,7 @@ public abstract class CigarBase
         String rangeint = cigarString.substring(i, j - 1);
         range[op] = Integer.parseInt(rangeint);
         i = j;
-      }
-      catch (Exception e)
+      } catch (Exception e)
       {
         throw new Error("Implementation bug in parseCigarString");
       }
@@ -222,26 +235,28 @@ public abstract class CigarBase
       {
         c -= _case_shift;
       }
-      if ( (c == M || c == I || c == D))
+      if ((c == M || c == I || c == D))
       {
         operation[op++] = c;
       }
       else
       {
-        throw new Exception("Unexpected operation '" + c +
-                            "' in cigar string (position " + i + " in '" +
-                            cigarString + "'");
+        throw new Exception("Unexpected operation '" + c
+                + "' in cigar string (position " + i + " in '"
+                + cigarString + "'");
       }
     }
     return new Object[]
-        {
-        operation, range};
+    { operation, range };
   }
 
   /**
    * add an operation to cigar string
-   * @param op char
-   * @param range int
+   * 
+   * @param op
+   *                char
+   * @param range
+   *                int
    */
   public void addOperation(char op, int range)
   {
@@ -255,7 +270,8 @@ public abstract class CigarBase
     }
     if (range <= 0)
     {
-      throw new Error("Invalid range string (must be non-zero positive number)");
+      throw new Error(
+              "Invalid range string (must be non-zero positive number)");
     }
     int lngth = 0;
     if (operation == null)
@@ -274,7 +290,7 @@ public abstract class CigarBase
       System.arraycopy(rng, 0, this.range, 0, length);
       rng = null;
     }
-    if ( (length > 0) && (operation[length - 1] == op))
+    if ((length > 0) && (operation[length - 1] == op))
     {
       length--; // modify existing operation.
     }
@@ -287,130 +303,73 @@ public abstract class CigarBase
   }
 
   /**
-   * semi-efficient insert an operation on the current cigar string set at column pos (from 1)
-   * NOTE: Insertion operations simply extend width of cigar result - affecting registration of alignment
-   * Deletion ops will shorten length of result - and affect registration of alignment
-   * Match ops will also affect length of result - affecting registration of alignment
-   * (ie "10M".insert(4,I,3)->"4M3I3M") - (replace?)
-   * (ie "10M".insert(4,D,3)->"4M3D3M") - (shortens alignment)
-   * (ie "5I5M".insert(4,I,3)->"8I5M") - real insertion
-   * (ie "5I5M".insert(4,D,3)->"4I2D3M") - shortens aligment - I's are removed, Ms changed to Ds
-   * (ie "10M".insert(4,M,3)->"13M")  - lengthens - Is changed to M, Ds changed to M.
-   * (ie "5I5M".insert(4,M,3)->"4I8M") - effectively shifts sequence left by 1 residue and extends it by 3
-   * ( "10D5M".insert(-1,M,3)->"3M7D5M")
-   * ( "10D5M".insert(0,M,3)->"7D8M")
-   * ( "10D5M".insert(1,M,3)->"10D8M")
-   *
-   * ( "1M10D5M".insert(0,M,3)->"1M10D8M")
-   * ( "1M10D5M".insert(1,M,3)->"
-   *
+   * semi-efficient insert an operation on the current cigar string set at
+   * column pos (from 1) NOTE: Insertion operations simply extend width of cigar
+   * result - affecting registration of alignment Deletion ops will shorten
+   * length of result - and affect registration of alignment Match ops will also
+   * affect length of result - affecting registration of alignment (ie
+   * "10M".insert(4,I,3)->"4M3I3M") - (replace?) (ie
+   * "10M".insert(4,D,3)->"4M3D3M") - (shortens alignment) (ie
+   * "5I5M".insert(4,I,3)->"8I5M") - real insertion (ie
+   * "5I5M".insert(4,D,3)->"4I2D3M") - shortens aligment - I's are removed, Ms
+   * changed to Ds (ie "10M".insert(4,M,3)->"13M") - lengthens - Is changed to
+   * M, Ds changed to M. (ie "5I5M".insert(4,M,3)->"4I8M") - effectively shifts
+   * sequence left by 1 residue and extends it by 3 (
+   * "10D5M".insert(-1,M,3)->"3M7D5M") ( "10D5M".insert(0,M,3)->"7D8M") (
+   * "10D5M".insert(1,M,3)->"10D8M")
+   *  ( "1M10D5M".insert(0,M,3)->"1M10D8M") ( "1M10D5M".insert(1,M,3)->"
+   * 
    * if pos is beyond width - I operations are added before the operation
-   * @param pos int -1, 0-length of visible region, or greater to append new ops (with insertions in between)
-   * @param op char
-   * @param range int
-     public void addOperationAt(int pos, char op, int range)
-     {
-   int cursor = -1; // mark the position for the current operation being edited.
-    int o = 0;
-    boolean last_d = false; // previous op was a deletion.
-    if (pos < -1)
-      throw new Error("pos<-1 is not supported.");
-    while (o<length) {
-      if (operation[o] != D)
-      {
-        if ( (cursor + this.range[o]) < pos)
-        {
-          cursor += this.range[o];
-          o++;
-          last_d=false;
-        }
-        else
-        {
-          break;
-        }
-      }
-      else {
-        last_d=true;
-        o++;
-      }
-    }
-    if (o==length) {
-      // must insert more operations before pos
-      if (pos-cursor>0)
-        addInsertion(pos-cursor);
-      // then just add the new operation. Regardless of what it is.
-      addOperation(op, range);
-    } else {
-      int diff = pos - cursor;
-
-      int e_length = length-o; // new edit operation array length.
-      // diff<0 - can only happen before first insertion or match. - affects op and all following
-      // dif==0 - only when at first position of existing op -
-      // diff>0 - must preserve some existing operations
-      int[] e_range = new int[e_length];
-      System.arraycopy(this.range, o, e_range, 0, e_length);
-      char[] e_op = new char[e_length];
-      System.arraycopy(this.operation, o, e_op, 0, e_length);
-      length = o; // can now use add_operation to extend list.
-      int e_o=0; // current operation being edited.
-      switch (op) {
-        case M:
-          switch (e_op[e_o])
-          {
-            case M:
-              if (last_d && diff <= 0)
-              {
-                // reduce D's, if possible
-                if (range<=this.range[o-1]) {
-                  this.range[o - 1] -= range;
-                } else {
-                  this.range[o-1]=0;
-                }
-                if (this.range[o-1]==0)
-                  o--; // lose this op.
-              }
-              e_range[e_o] += range; // just add more matched residues
-              break;
-            case I:
-              // change from insertion to match
-              if (last_d && diff<=0)
-              {
-                // reduce D's, if possible
-                if (range<=this.range[o-1]) {
-                  this.range[o - 1] -= range;
-                } else {
-                  this.range[o-1]=0;
-                }
-                if (this.range[o-1]==0)
-                  o--; // lose this op.
-              }
-              e_range[e_o]
-                    break;
-                default:
-                  throw new Inp
-                      }
-
-                      break;
-                case I:
-                  break;
-                case D:
-              }
-          break;
-        default:
-   throw new Error("Implementation Error: Unknown operation in addOperation!");
-      }
-      // finally, add remaining ops.
-      while (e_o<e_length) {
-        addOperation(e_op[e_o], e_range[e_o]);
-        e_o++;
-      }
-    }
-     }
-   **/
+   * 
+   * @param pos
+   *                int -1, 0-length of visible region, or greater to append new
+   *                ops (with insertions in between)
+   * @param op
+   *                char
+   * @param range
+   *                int public void addOperationAt(int pos, char op, int range) {
+   *                int cursor = -1; // mark the position for the current
+   *                operation being edited. int o = 0; boolean last_d = false; //
+   *                previous op was a deletion. if (pos < -1) throw new
+   *                Error("pos<-1 is not supported."); while (o<length) { if
+   *                (operation[o] != D) { if ( (cursor + this.range[o]) < pos) {
+   *                cursor += this.range[o]; o++; last_d=false; } else { break; } }
+   *                else { last_d=true; o++; } } if (o==length) { // must insert
+   *                more operations before pos if (pos-cursor>0)
+   *                addInsertion(pos-cursor); // then just add the new
+   *                operation. Regardless of what it is. addOperation(op,
+   *                range); } else { int diff = pos - cursor;
+   * 
+   * int e_length = length-o; // new edit operation array length. // diff<0 -
+   * can only happen before first insertion or match. - affects op and all
+   * following // dif==0 - only when at first position of existing op - //
+   * diff>0 - must preserve some existing operations int[] e_range = new
+   * int[e_length]; System.arraycopy(this.range, o, e_range, 0, e_length);
+   * char[] e_op = new char[e_length]; System.arraycopy(this.operation, o, e_op,
+   * 0, e_length); length = o; // can now use add_operation to extend list. int
+   * e_o=0; // current operation being edited. switch (op) { case M: switch
+   * (e_op[e_o]) { case M: if (last_d && diff <= 0) { // reduce D's, if possible
+   * if (range<=this.range[o-1]) { this.range[o - 1] -= range; } else {
+   * this.range[o-1]=0; } if (this.range[o-1]==0) o--; // lose this op. }
+   * e_range[e_o] += range; // just add more matched residues break; case I: //
+   * change from insertion to match if (last_d && diff<=0) { // reduce D's, if
+   * possible if (range<=this.range[o-1]) { this.range[o - 1] -= range; } else {
+   * this.range[o-1]=0; } if (this.range[o-1]==0) o--; // lose this op. }
+   * e_range[e_o] break; default: throw new Inp }
+   * 
+   * break; case I: break; case D: } break; default: throw new
+   * Error("Implementation Error: Unknown operation in addOperation!"); } //
+   * finally, add remaining ops. while (e_o<e_length) { addOperation(e_op[e_o],
+   * e_range[e_o]); e_o++; } } }
+   */
   /**
-   * Mark residues from start to end (inclusive) as deleted from the alignment, and removes any insertions.
-   * @param start int
-   * @param end int
+   * Mark residues from start to end (inclusive) as deleted from the alignment,
+   * and removes any insertions.
+   * 
+   * @param start
+   *                int
+   * @param end
+   *                int
    * @return deleted int - number of symbols marked as deleted
    */
   public int deleteRange(int start, int end)
@@ -423,7 +382,8 @@ public abstract class CigarBase
     }
     if (start < 0 || start > end)
     {
-      throw new Error("Implementation Error: deleteRange out of bounds: start must be non-negative and less than end.");
+      throw new Error(
+              "Implementation Error: deleteRange out of bounds: start must be non-negative and less than end.");
     }
     // find beginning
     int cursor = 0; // mark the position for the current operation being edited.
@@ -449,7 +409,7 @@ public abstract class CigarBase
       int remain = oldrange[o]; // number of op characters left to edit
       if (!editing)
       {
-        if ( (cursor + remain) <= start)
+        if ((cursor + remain) <= start)
         {
           addOperation(oldops[o], oldrange[o]);
           cursor += oldrange[o++];
@@ -468,37 +428,37 @@ public abstract class CigarBase
       {
         switch (oldops[o])
         {
-          case M:
-            if (rlength > remain)
-            {
-              addDeleted(remain);
-              deleted += remain;
-            }
-            else
-            {
-              deleted += rlength;
-              addDeleted(rlength);
-              if (remain - rlength > 0)
-              {
-                this.addOperation(M, remain - rlength); // add remaining back.
-              }
-              rlength = 0;
-              remain = 0;
-            }
-            break;
-          case I:
+        case M:
+          if (rlength > remain)
+          {
+            addDeleted(remain);
+            deleted += remain;
+          }
+          else
+          {
+            deleted += rlength;
+            addDeleted(rlength);
             if (remain - rlength > 0)
             {
-              // only remove some gaps
-              addInsertion(remain - rlength);
-              rlength = 0;
+              this.addOperation(M, remain - rlength); // add remaining back.
             }
-            break;
-          case D:
-            throw new Error("Implementation error."); // do nothing;
-          default:
-            throw new Error("Implementation Error! Unknown operation '" +
-                            oldops[o] + "'");
+            rlength = 0;
+            remain = 0;
+          }
+          break;
+        case I:
+          if (remain - rlength > 0)
+          {
+            // only remove some gaps
+            addInsertion(remain - rlength);
+            rlength = 0;
+          }
+          break;
+        case D:
+          throw new Error("Implementation error."); // do nothing;
+        default:
+          throw new Error("Implementation Error! Unknown operation '"
+                  + oldops[o] + "'");
         }
         rlength -= remain;
         remain = oldrange[++o]; // number of op characters left to edit
@@ -509,16 +469,17 @@ public abstract class CigarBase
     {
       addOperation(oldops[o], oldrange[o++]);
     }
-    //if (cursor<(start+1)) {
+    // if (cursor<(start+1)) {
     // ran out of ops - nothing to do here ?
     // addInsertion(start-cursor);
-    //}
+    // }
     return deleted;
   }
 
   /**
-   * Deleted regions mean that there will be discontinuous sequence numbering in the
-   * sequence returned by getSeq(char).
+   * Deleted regions mean that there will be discontinuous sequence numbering in
+   * the sequence returned by getSeq(char).
+   * 
    * @return true if there deletions
    */
   public boolean hasDeletedRegions()
@@ -535,6 +496,7 @@ public abstract class CigarBase
 
   /**
    * enumerate the ranges on seq that are marked as deleted in this cigar
+   * 
    * @return int[] { vis_start, sym_start, length }
    */
   public int[] getDeletedRegions()
@@ -549,15 +511,15 @@ public abstract class CigarBase
     {
       switch (operation[i])
       {
-        case M:
-          cursor += range[i];
-        case I:
-          vcursor += range[i];
-          break;
-        case D:
-          dr.addElement(new int[]
-                        {vcursor, cursor, range[i]});
-          cursor += range[i];
+      case M:
+        cursor += range[i];
+      case I:
+        vcursor += range[i];
+        break;
+      case D:
+        dr.addElement(new int[]
+        { vcursor, cursor, range[i] });
+        cursor += range[i];
       }
     }
     if (dr.size() == 0)
@@ -577,7 +539,9 @@ public abstract class CigarBase
 
   /**
    * sum of ranges in cigar string
-   * @return int number of residues hidden, matched, or gaps inserted into sequence
+   * 
+   * @return int number of residues hidden, matched, or gaps inserted into
+   *         sequence
    */
   public int getFullWidth()
   {
@@ -594,6 +558,7 @@ public abstract class CigarBase
 
   /**
    * Visible length of aligned sequence
+   * 
    * @return int length of including gaps and less hidden regions
    */
   public int getWidth()
@@ -614,7 +579,9 @@ public abstract class CigarBase
 
   /**
    * mark a range of inserted residues
-   * @param range int
+   * 
+   * @param range
+   *                int
    */
   public void addInsertion(int range)
   {
@@ -623,7 +590,9 @@ public abstract class CigarBase
 
   /**
    * mark the next range residues as hidden (not aligned) or deleted
-   * @param range int
+   * 
+   * @param range
+   *                int
    */
   public void addDeleted(int range)
   {
@@ -633,64 +602,30 @@ public abstract class CigarBase
   /**
    * Modifies operation list to delete columns from start to end (inclusive)
    * editing will remove insertion operations, and convert matches to deletions
-   * @param start alignment column
-   * @param end alignment column
-   * @return boolean true if residues were marked as deleted.
-     public boolean deleteRange(int start, int end)
-     {
-    boolean deleted = false;
-    int op = 0, prevop = -1, firstm = -1,
-        lastm = -1, postop = -1;
-    int width = 0; // zero'th column
-    if (length > 0)
-    {
-      // find operation bracketing start of the range
-      do
-      {
-        if (operation[op] != D)
-        {
-          width += range[prevop = op];
-        }
-        op++;
-      }
-      while (op < length && width < start);
-    }
-    if (width < start)
-    {
-      // run off end - add more operations up to deletion.
-      addInsertion(start - width);
-    }
-    else
-    {
-      // edit existing operations.
-      op = prevop;
-      width -= range[prevop];
-      int[] oldrange = range;
-      char[] oldops = operation;
-      range = new int[oldrange.length];
-      operation = new char[oldops.length];
-      if (op < length)
-      {
-        do
-        {
-          if (operation[op] != D)
-          {
-            width += range[postop = op];
-          }
-          op++;
-        }
-        while (op < length && width <= end);
-      }
-    }
-    if (deleted == true)
-    {
-      addDeleted(end - start + 1);
-    }
-    return deleted;
-     }
+   * 
+   * @param start
+   *                alignment column
+   * @param end
+   *                alignment column
+   * @return boolean true if residues were marked as deleted. public boolean
+   *         deleteRange(int start, int end) { boolean deleted = false; int op =
+   *         0, prevop = -1, firstm = -1, lastm = -1, postop = -1; int width =
+   *         0; // zero'th column if (length > 0) { // find operation bracketing
+   *         start of the range do { if (operation[op] != D) { width +=
+   *         range[prevop = op]; } op++; } while (op < length && width < start); }
+   *         if (width < start) { // run off end - add more operations up to
+   *         deletion. addInsertion(start - width); } else { // edit existing
+   *         operations. op = prevop; width -= range[prevop]; int[] oldrange =
+   *         range; char[] oldops = operation; range = new int[oldrange.length];
+   *         operation = new char[oldops.length]; if (op < length) { do { if
+   *         (operation[op] != D) { width += range[postop = op]; } op++; } while
+   *         (op < length && width <= end); } } if (deleted == true) {
+   *         addDeleted(end - start + 1); } return deleted; }
    */
   /**
-   * Return an ENSEMBL style cigar string where D may indicates excluded parts of seq
+   * Return an ENSEMBL style cigar string where D may indicates excluded parts
+   * of seq
+   * 
    * @return String of form ([0-9]+[IMD])+
    */
   public String getCigarstring()
diff --git a/src/jalview/datamodel/CigarCigar.java b/src/jalview/datamodel/CigarCigar.java
index 83cce19..f5619cf 100644
--- a/src/jalview/datamodel/CigarCigar.java
+++ b/src/jalview/datamodel/CigarCigar.java
@@ -1,59 +1,62 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.datamodel;
-
-public class CigarCigar
-    extends CigarSimple
-{
-  SeqCigar refCigar;
-  /**
-   * Apply CIGAR operations to the result of another cigar
-   * @param cigar Cigar
-   */
-  CigarCigar(SeqCigar cigar)
-  {
-    super();
-    refCigar = cigar;
-  }
-
-  /**
-   *
-   * @return String formed by applying CIGAR operations to the reference object
-   * @param GapChar char
-   * @todo Implement this jalview.datamodel.Cigar method
-   */
-  public String getSequenceString(char GapChar)
-  {
-    if (length == 0)
-    {
-      return "";
-    }
-    String refString = refCigar.getSequenceString(GapChar);
-    if (refString != null)
-    {
-      return (length == 0) ? "" :
-          (String) getSequenceAndDeletions(refString, GapChar)[0];
-    }
-    else
-    {
-      return null;
-    }
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.datamodel;
+
+public class CigarCigar extends CigarSimple
+{
+  SeqCigar refCigar;
+
+  /**
+   * Apply CIGAR operations to the result of another cigar
+   * 
+   * @param cigar
+   *                Cigar
+   */
+  CigarCigar(SeqCigar cigar)
+  {
+    super();
+    refCigar = cigar;
+  }
+
+  /**
+   * 
+   * @return String formed by applying CIGAR operations to the reference object
+   * @param GapChar
+   *                char
+   * @todo Implement this jalview.datamodel.Cigar method
+   */
+  public String getSequenceString(char GapChar)
+  {
+    if (length == 0)
+    {
+      return "";
+    }
+    String refString = refCigar.getSequenceString(GapChar);
+    if (refString != null)
+    {
+      return (length == 0) ? "" : (String) getSequenceAndDeletions(
+              refString, GapChar)[0];
+    }
+    else
+    {
+      return null;
+    }
+  }
+
+}
diff --git a/src/jalview/datamodel/CigarSimple.java b/src/jalview/datamodel/CigarSimple.java
index 3891687..4013f93 100644
--- a/src/jalview/datamodel/CigarSimple.java
+++ b/src/jalview/datamodel/CigarSimple.java
@@ -1,43 +1,53 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.datamodel;
-
-/**
- * <p>Title: </p>
- *
- * <p>Description: </p>
- *
- * <p>Copyright: Copyright (c) 2004</p>
- *
- * <p>Company: Dundee University</p>
- *
- * @author not attributable
- * @version 1.0
- */
-public abstract class CigarSimple
-    extends CigarBase
-{
-  /**
-   * Return a symbol sequence with edits (gaps, insertions and deletions) applied
-   * @param GapChar char
-   * @return String
-   */
-  public abstract String getSequenceString(char GapChar);
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.datamodel;
+
+/**
+ * <p>
+ * Title:
+ * </p>
+ * 
+ * <p>
+ * Description:
+ * </p>
+ * 
+ * <p>
+ * Copyright: Copyright (c) 2004
+ * </p>
+ * 
+ * <p>
+ * Company: Dundee University
+ * </p>
+ * 
+ * @author not attributable
+ * @version 1.0
+ */
+public abstract class CigarSimple extends CigarBase
+{
+  /**
+   * Return a symbol sequence with edits (gaps, insertions and deletions)
+   * applied
+   * 
+   * @param GapChar
+   *                char
+   * @return String
+   */
+  public abstract String getSequenceString(char GapChar);
+
+}
diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 74f4cda..ca54570 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -29,13 +29,14 @@ public class ColumnSelection
 {
   Vector selected = new Vector();
 
-  //Vector of int [] {startCol, endCol}
+  // Vector of int [] {startCol, endCol}
   Vector hiddenColumns;
 
   /**
    * Add a column to the selection
-   *
-   * @param col index of column
+   * 
+   * @param col
+   *                index of column
    */
   public void addElement(int col)
   {
@@ -56,8 +57,9 @@ public class ColumnSelection
 
   /**
    * removes col from selection
-   *
-   * @param col index of column to be removed
+   * 
+   * @param col
+   *                index of column to be removed
    */
   public void removeElement(int col)
   {
@@ -71,8 +73,11 @@ public class ColumnSelection
 
   /**
    * removes a range of columns from the selection
-   * @param start int - first column in range to be removed
-   * @param end int - last col
+   * 
+   * @param start
+   *                int - first column in range to be removed
+   * @param end
+   *                int - last col
    */
   public void removeElements(int start, int end)
   {
@@ -88,7 +93,7 @@ public class ColumnSelection
   }
 
   /**
-   *
+   * 
    * @return Vector containing selected columns as Integers
    */
   public Vector getSelected()
@@ -97,9 +102,10 @@ public class ColumnSelection
   }
 
   /**
-   *
-   * @param col index to search for in column selection
-   *
+   * 
+   * @param col
+   *                index to search for in column selection
+   * 
    * @return true if Integer(col) is in selection.
    */
   public boolean contains(int col)
@@ -109,19 +115,20 @@ public class ColumnSelection
 
   /**
    * Column number at position i in selection
-   *
-   * @param i index into selected columns
-   *
+   * 
+   * @param i
+   *                index into selected columns
+   * 
    * @return column number in alignment
    */
   public int columnAt(int i)
   {
-    return ( (Integer) selected.elementAt(i)).intValue();
+    return ((Integer) selected.elementAt(i)).intValue();
   }
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public int size()
@@ -131,7 +138,7 @@ public class ColumnSelection
 
   /**
    * rightmost selected column
-   *
+   * 
    * @return rightmost column in alignment that is selected
    */
   public int getMax()
@@ -151,7 +158,7 @@ public class ColumnSelection
 
   /**
    * Leftmost column in selection
-   *
+   * 
    * @return column index of leftmost column in selection
    */
   public int getMin()
@@ -171,9 +178,11 @@ public class ColumnSelection
 
   /**
    * propagate shift in alignment columns to column selection
-   *
-   * @param start beginning of edit
-   * @param left shift in edit (+ve for removal, or -ve for inserts)
+   * 
+   * @param start
+   *                beginning of edit
+   * @param left
+   *                shift in edit (+ve for removal, or -ve for inserts)
    */
   public Vector compensateForEdit(int start, int change)
   {
@@ -197,8 +206,7 @@ public class ColumnSelection
         int[] region = (int[]) hiddenColumns.elementAt(i);
         if (region[0] > start && start + change > region[1])
         {
-          deletedHiddenColumns.addElement(
-              hiddenColumns.elementAt(i));
+          deletedHiddenColumns.addElement(hiddenColumns.elementAt(i));
 
           hiddenColumns.removeElementAt(i);
           i--;
@@ -226,10 +234,13 @@ public class ColumnSelection
   }
 
   /**
-   * propagate shift in alignment columns to column selection
-   * special version of compensateForEdit - allowing for edits within hidden regions
-   * @param start beginning of edit
-   * @param left shift in edit (+ve for removal, or -ve for inserts)
+   * propagate shift in alignment columns to column selection special version of
+   * compensateForEdit - allowing for edits within hidden regions
+   * 
+   * @param start
+   *                beginning of edit
+   * @param left
+   *                shift in edit (+ve for removal, or -ve for inserts)
    */
   private void compensateForDelEdits(int start, int change)
   {
@@ -274,8 +285,9 @@ public class ColumnSelection
   }
 
   /**
-   * Adjust hidden column boundaries based on a series of column
-   * additions or deletions in visible regions.
+   * Adjust hidden column boundaries based on a series of column additions or
+   * deletions in visible regions.
+   * 
    * @param shiftrecord
    * @return
    */
@@ -290,7 +302,7 @@ public class ColumnSelection
         for (int i = 0, j = shifts.size(); i < j; i++)
         {
           int[] sh = (int[]) shifts.elementAt(i);
-          //compensateForEdit(shifted+sh[0], sh[1]);
+          // compensateForEdit(shifted+sh[0], sh[1]);
           compensateForDelEdits(shifted + sh[0], sh[1]);
           shifted -= sh[1];
         }
@@ -301,8 +313,9 @@ public class ColumnSelection
   }
 
   /**
-   * removes intersection of position,length ranges in deletions
-   * from the start,end regions marked in intervals.
+   * removes intersection of position,length ranges in deletions from the
+   * start,end regions marked in intervals.
+   * 
    * @param deletions
    * @param intervals
    * @return
@@ -389,7 +402,8 @@ public class ColumnSelection
         }
       }
     }
-    return pruned; // true if any interval was removed or modified by operations.
+    return pruned; // true if any interval was removed or modified by
+                    // operations.
   }
 
   private boolean pruneColumnList(Vector deletion, Vector list)
@@ -400,7 +414,7 @@ public class ColumnSelection
     int i = 0, j = list.size();
     while (i < j && s <= t)
     {
-      int c = ( (Integer) list.elementAt(i++)).intValue();
+      int c = ((Integer) list.elementAt(i++)).intValue();
       if (sr[0] <= c)
       {
         if (sr[1] + sr[0] >= c)
@@ -422,8 +436,9 @@ public class ColumnSelection
   }
 
   /**
-   * remove any hiddenColumns or selected columns and shift remaining
-   * based on a series of position, range deletions.
+   * remove any hiddenColumns or selected columns and shift remaining based on a
+   * series of position, range deletions.
+   * 
    * @param deletions
    */
   public void pruneDeletions(ShiftList deletions)
@@ -457,9 +472,11 @@ public class ColumnSelection
   }
 
   /**
-   * This Method is used to return all the HiddenColumn regions
-   * less than the given index.
-   * @param end int
+   * This Method is used to return all the HiddenColumn regions less than the
+   * given index.
+   * 
+   * @param end
+   *                int
    * @return Vector
    */
   public Vector getHiddenColumns()
@@ -469,7 +486,9 @@ public class ColumnSelection
 
   /**
    * Return absolute column index for a visible column index
-   * @param column int column index in alignment view
+   * 
+   * @param column
+   *                int column index in alignment view
    * @return alignment column index for column
    */
   public int adjustForHiddenColumns(int column)
@@ -490,9 +509,11 @@ public class ColumnSelection
   }
 
   /**
-   * Use this method to find out where a visible column is in the alignment
-   * when hidden columns exist
-   * @param hiddenColumn int
+   * Use this method to find out where a visible column is in the alignment when
+   * hidden columns exist
+   * 
+   * @param hiddenColumn
+   *                int
    * @return int
    */
   public int findColumnPosition(int hiddenColumn)
@@ -510,8 +531,7 @@ public class ColumnSelection
           result -= region[1] + 1 - region[0];
         }
         index++;
-      }
-      while (index < hiddenColumns.size());
+      } while (index < hiddenColumns.size());
 
       result -= gaps;
     }
@@ -540,8 +560,7 @@ public class ColumnSelection
         gaps += region[1] + 1 - region[0];
         result = region[1] + 1;
         index++;
-      }
-      while (index < hiddenRegion + 1);
+      } while (index < hiddenRegion + 1);
 
       result -= gaps;
     }
@@ -550,10 +569,11 @@ public class ColumnSelection
   }
 
   /**
-   * THis method returns the rightmost limit of a
-   * region of an alignment with hidden columns.
-   * In otherwords, the next hidden column.
-   * @param index int
+   * THis method returns the rightmost limit of a region of an alignment with
+   * hidden columns. In otherwords, the next hidden column.
+   * 
+   * @param index
+   *                int
    */
   public int getHiddenBoundaryRight(int alPos)
   {
@@ -569,8 +589,7 @@ public class ColumnSelection
         }
 
         index++;
-      }
-      while (index < hiddenColumns.size());
+      } while (index < hiddenColumns.size());
     }
 
     return alPos;
@@ -578,10 +597,11 @@ public class ColumnSelection
   }
 
   /**
-   * This method returns the leftmost limit of a
-   * region of an alignment with hidden columns.
-   * In otherwords, the previous hidden column.
-   * @param index int
+   * This method returns the leftmost limit of a region of an alignment with
+   * hidden columns. In otherwords, the previous hidden column.
+   * 
+   * @param index
+   *                int
    */
   public int getHiddenBoundaryLeft(int alPos)
   {
@@ -597,8 +617,7 @@ public class ColumnSelection
         }
 
         index--;
-      }
-      while (index > -1);
+      } while (index > -1);
     }
 
     return alPos;
@@ -609,7 +628,7 @@ public class ColumnSelection
   {
     while (size() > 0)
     {
-      int column = ( (Integer) getSelected().firstElement()).intValue();
+      int column = ((Integer) getSelected().firstElement()).intValue();
       hideColumns(column);
     }
 
@@ -637,7 +656,7 @@ public class ColumnSelection
       else if (end < region[0] && start < region[0])
       {
         hiddenColumns.insertElementAt(new int[]
-                                      {start, end}, i);
+        { start, end }, i);
         added = true;
         break;
       }
@@ -650,15 +669,17 @@ public class ColumnSelection
     else if (!added)
     {
       hiddenColumns.addElement(new int[]
-                               {start, end});
+      { start, end });
     }
 
   }
 
   /**
-   * This method will find a range of selected columns
-   * around the column specified
-   * @param res int
+   * This method will find a range of selected columns around the column
+   * specified
+   * 
+   * @param res
+   *                int
    */
   public void hideColumns(int col)
   {
@@ -742,6 +763,7 @@ public class ColumnSelection
 
   /**
    * Copy constructor
+   * 
    * @param copy
    */
   public ColumnSelection(ColumnSelection copy)
@@ -782,7 +804,7 @@ public class ColumnSelection
   }
 
   public String[] getVisibleSequenceStrings(int start, int end,
-                                            SequenceI[] seqs)
+          SequenceI[] seqs)
   {
     int i, iSize = seqs.length;
     String selection[] = new String[iSize];
@@ -843,9 +865,11 @@ public class ColumnSelection
 
   /**
    * return all visible segments between the given start and end boundaries
-   *
-   * @param start (first column inclusive from 0)
-   * @param end (last column - not inclusive)
+   * 
+   * @param start
+   *                (first column inclusive from 0)
+   * @param end
+   *                (last column - not inclusive)
    * @return int[] {i_start, i_end, ..} where intervals lie in start<=i_start<=i_end<end
    */
   public int[] getVisibleContigs(int start, int end)
@@ -872,7 +896,7 @@ public class ColumnSelection
         if (hideStart > vstart)
         {
           visiblecontigs.addElement(new int[]
-                                    {vstart, hideStart - 1});
+          { vstart, hideStart - 1 });
         }
         vstart = hideEnd + 1;
       }
@@ -880,7 +904,7 @@ public class ColumnSelection
       if (vstart < end)
       {
         visiblecontigs.addElement(new int[]
-                                  {vstart, end - 1});
+        { vstart, end - 1 });
       }
       int[] vcontigs = new int[visiblecontigs.size() * 2];
       for (int i = 0, j = visiblecontigs.size(); i < j; i++)
@@ -896,32 +920,40 @@ public class ColumnSelection
     else
     {
       return new int[]
-          {
-          start, end - 1};
+      { start, end - 1 };
     }
   }
 
   /**
-   * delete any columns in alignmentAnnotation that are hidden (including sequence associated annotation).
+   * delete any columns in alignmentAnnotation that are hidden (including
+   * sequence associated annotation).
+   * 
    * @param alignmentAnnotation
    */
   public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation)
   {
-    makeVisibleAnnotation(-1,-1,alignmentAnnotation);
+    makeVisibleAnnotation(-1, -1, alignmentAnnotation);
   }
+
   /**
-   * delete any columns in alignmentAnnotation that are hidden (including sequence associated annotation).
-   * @param start remove any annotation to the right of this column
-   * @param end remove any annotation to the left of this column
-   * @param alignmentAnnotation the annotation to operate on
+   * delete any columns in alignmentAnnotation that are hidden (including
+   * sequence associated annotation).
+   * 
+   * @param start
+   *                remove any annotation to the right of this column
+   * @param end
+   *                remove any annotation to the left of this column
+   * @param alignmentAnnotation
+   *                the annotation to operate on
    */
-  public void makeVisibleAnnotation(int start, int end, AlignmentAnnotation alignmentAnnotation)
+  public void makeVisibleAnnotation(int start, int end,
+          AlignmentAnnotation alignmentAnnotation)
   {
-    if (alignmentAnnotation.annotations==null)
+    if (alignmentAnnotation.annotations == null)
     {
       return;
     }
-    if (start==end && end==-1)
+    if (start == end && end == -1)
     {
       start = 0;
       end = alignmentAnnotation.annotations.length;
@@ -929,81 +961,90 @@ public class ColumnSelection
     if (hiddenColumns != null && hiddenColumns.size() > 0)
     {
       // then mangle the alignmentAnnotation annotation array
-        Vector annels = new Vector();
-        Annotation[] els = null;
-        Vector regions = getHiddenColumns();
-        int blockStart = start, blockEnd = end;
-        int[] region;
-        int hideStart, hideEnd,w=0;
-
-        for (int j = 0; j < regions.size(); j++)
-        {
-          region = (int[]) regions.elementAt(j);
-          hideStart = region[0];
-          hideEnd = region[1];
+      Vector annels = new Vector();
+      Annotation[] els = null;
+      Vector regions = getHiddenColumns();
+      int blockStart = start, blockEnd = end;
+      int[] region;
+      int hideStart, hideEnd, w = 0;
 
-          if (hideStart < start)
-          {
-            continue;
-          }
+      for (int j = 0; j < regions.size(); j++)
+      {
+        region = (int[]) regions.elementAt(j);
+        hideStart = region[0];
+        hideEnd = region[1];
 
-          blockStart = Math.min(blockStart, hideEnd + 1);
-          blockEnd = Math.min(blockEnd, hideStart);
+        if (hideStart < start)
+        {
+          continue;
+        }
 
-          if (blockStart > blockEnd)
-          {
-            break;
-          }
+        blockStart = Math.min(blockStart, hideEnd + 1);
+        blockEnd = Math.min(blockEnd, hideStart);
 
-          annels.addElement(els = new Annotation[blockEnd-blockStart]);
-          System.arraycopy(alignmentAnnotation.annotations, blockStart, els, 0, els.length);
-          w+=els.length;
-          blockStart = hideEnd + 1;
-          blockEnd = end;
+        if (blockStart > blockEnd)
+        {
+          break;
         }
 
-        if (end > blockStart)
+        annels.addElement(els = new Annotation[blockEnd - blockStart]);
+        System.arraycopy(alignmentAnnotation.annotations, blockStart, els,
+                0, els.length);
+        w += els.length;
+        blockStart = hideEnd + 1;
+        blockEnd = end;
+      }
+
+      if (end > blockStart)
+      {
+        annels.addElement(els = new Annotation[end - blockStart + 1]);
+        if (end - blockStart + 1 <= alignmentAnnotation.annotations.length)
         {
-          annels.addElement(els = new Annotation[end-blockStart+1]);
-          if (end-blockStart+1<=alignmentAnnotation.annotations.length)
-          {
-            System.arraycopy(alignmentAnnotation.annotations, blockStart, els, 0, els.length);
-          } else {
-            System.arraycopy(alignmentAnnotation.annotations, blockStart, els, 0, (end-blockStart+1));
-          }
-          w+=els.length;
+          System.arraycopy(alignmentAnnotation.annotations, blockStart,
+                  els, 0, els.length);
         }
-        if (w==0)
-          return;
-        Enumeration e = annels.elements();
-        alignmentAnnotation.annotations = new Annotation[w];
-        w=0;
-        while (e.hasMoreElements())
+        else
         {
-          Annotation[] chnk = (Annotation[]) e.nextElement();
-          System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w, chnk.length);
-          w+=chnk.length;
+          System.arraycopy(alignmentAnnotation.annotations, blockStart,
+                  els, 0, (end - blockStart + 1));
         }
-    } else {
+        w += els.length;
+      }
+      if (w == 0)
+        return;
+      Enumeration e = annels.elements();
+      alignmentAnnotation.annotations = new Annotation[w];
+      w = 0;
+      while (e.hasMoreElements())
+      {
+        Annotation[] chnk = (Annotation[]) e.nextElement();
+        System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
+                chnk.length);
+        w += chnk.length;
+      }
+    }
+    else
+    {
       alignmentAnnotation.restrict(start, end);
     }
   }
 
   /**
-   * Invert the column selection from first to end-1.
-   * leaves hiddenColumns untouched (and unselected)
+   * Invert the column selection from first to end-1. leaves hiddenColumns
+   * untouched (and unselected)
+   * 
    * @param first
    * @param end
    */
   public void invertColumnSelection(int first, int width)
   {
-    boolean hasHidden = hiddenColumns!=null && hiddenColumns.size()>0;
-    for(int i=first; i<width; i++)
-    {
-      if(contains(i))
+    boolean hasHidden = hiddenColumns != null && hiddenColumns.size() > 0;
+    for (int i = first; i < width; i++)
     {
+      if (contains(i))
+      {
         removeElement(i);
-    }
+      }
       else
       {
         if (!hasHidden || isVisible(i))
@@ -1011,6 +1052,6 @@ public class ColumnSelection
           addElement(i);
         }
       }
-    }    
+    }
   }
 }
diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index b6c3192..c9d59ec 100755
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -20,74 +20,94 @@ package jalview.datamodel;
 
 public class DBRefEntry
 {
-  String source="", version="", accessionId="";
+  String source = "", version = "", accessionId = "";
+
   /**
    * maps from associated sequence to the database sequence's coordinate system
    */
-  Mapping map=null;
-  public DBRefEntry() {
-      
+  Mapping map = null;
+
+  public DBRefEntry()
+  {
+
   }
+
   public DBRefEntry(String source, String version, String accessionId)
   {
     this(source, version, accessionId, null);
   }
+
   /**
    * 
-   * @param source canonical source (uppercase only)
-   * @param version (source dependent version string)
-   * @param accessionId (source dependent accession number string)
-   * @param map (mapping from local sequence numbering to source accession numbering)
+   * @param source
+   *                canonical source (uppercase only)
+   * @param version
+   *                (source dependent version string)
+   * @param accessionId
+   *                (source dependent accession number string)
+   * @param map
+   *                (mapping from local sequence numbering to source accession
+   *                numbering)
    */
-  public DBRefEntry(String source, String version, String accessionId, Mapping map) {
+  public DBRefEntry(String source, String version, String accessionId,
+          Mapping map)
+  {
     this.source = source.toUpperCase();
     this.version = version;
     this.accessionId = accessionId;
     this.map = map;
   }
+
   public DBRefEntry(DBRefEntry entry)
   {
-    this((entry.source==null ? "" : new String(entry.source)), 
-            (entry.version==null ? "" : new String(entry.version)),
-            (entry.accessionId==null ? "" : new String(entry.accessionId)),
-            (entry.map==null ? null : new Mapping(entry.map)));
-  }
-  public boolean equals(DBRefEntry entry) {
-      if (entry==this)
-          return true;
-      if (entry==null)
-          return false;
-      if (equalRef(entry)
-              &&
-          ((map==null && entry.map==null) || (map!=null && entry.map!=null && map.equals(entry.map)))) {
-              return true;
-          }
+    this(
+            (entry.source == null ? "" : new String(entry.source)),
+            (entry.version == null ? "" : new String(entry.version)),
+            (entry.accessionId == null ? "" : new String(entry.accessionId)),
+            (entry.map == null ? null : new Mapping(entry.map)));
+  }
+
+  public boolean equals(DBRefEntry entry)
+  {
+    if (entry == this)
+      return true;
+    if (entry == null)
       return false;
+    if (equalRef(entry)
+            && ((map == null && entry.map == null) || (map != null
+                    && entry.map != null && map.equals(entry.map))))
+    {
+      return true;
+    }
+    return false;
   }
+
   /**
    * test for similar DBRef attributes, except for the map object.
-   * @param entry 
+   * 
+   * @param entry
    * @return true if source, accession and version are equal with those of entry
    */
   public boolean equalRef(DBRefEntry entry)
   {
-    if (entry==null)
+    if (entry == null)
     {
       return false;
     }
-    if (entry==this)
+    if (entry == this)
       return true;
-    if ((source!=null && entry.source!=null && source.equalsIgnoreCase(entry.source))
-            &&
-            (accessionId!=null && entry.accessionId!=null && accessionId.equalsIgnoreCase(entry.accessionId))
-            &&
-            (version!=null && entry.version!=null && version.equalsIgnoreCase(entry.version))
-            )
+    if ((source != null && entry.source != null && source
+            .equalsIgnoreCase(entry.source))
+            && (accessionId != null && entry.accessionId != null && accessionId
+                    .equalsIgnoreCase(entry.accessionId))
+            && (version != null && entry.version != null && version
+                    .equalsIgnoreCase(entry.version)))
     {
       return true;
     }
     return false;
   }
+
   public String getSource()
   {
     return source;
@@ -102,47 +122,63 @@ public class DBRefEntry
   {
     return accessionId;
   }
-/**
- * @param accessionId the accessionId to set
- */
-public void setAccessionId(String accessionId) {
+
+  /**
+   * @param accessionId
+   *                the accessionId to set
+   */
+  public void setAccessionId(String accessionId)
+  {
     this.accessionId = accessionId;
-}
-/**
- * @param source the source to set
- */
-public void setSource(String source) {
+  }
+
+  /**
+   * @param source
+   *                the source to set
+   */
+  public void setSource(String source)
+  {
     this.source = source;
-}
-/**
- * @param version the version to set
- */
-public void setVersion(String version) {
+  }
+
+  /**
+   * @param version
+   *                the version to set
+   */
+  public void setVersion(String version)
+  {
     this.version = version;
-}
-/**
- * @return the map
- */
-public Mapping getMap() {
+  }
+
+  /**
+   * @return the map
+   */
+  public Mapping getMap()
+  {
     return map;
-}
-/**
- * @param map the map to set
- */
-public void setMap(Mapping map) {
+  }
+
+  /**
+   * @param map
+   *                the map to set
+   */
+  public void setMap(Mapping map)
+  {
     this.map = map;
-}
-public boolean hasMap()
-{
-  return map!=null;
-}
-/**
- * 
- * @return source+":"+accessionId
- */
-public String getSrcAccString()
-{
-  return ((source!=null) ? source : "")
-    + ":" + ((accessionId!=null) ? accessionId : "");
-}
+  }
+
+  public boolean hasMap()
+  {
+    return map != null;
+  }
+
+  /**
+   * 
+   * @return source+":"+accessionId
+   */
+  public String getSrcAccString()
+  {
+    return ((source != null) ? source : "") + ":"
+            + ((accessionId != null) ? accessionId : "");
+  }
 }
diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index 0552b2c..6dca74f 100755
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -1,102 +1,129 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.datamodel;
-/**
- * Defines internal constants for unambiguous annotation
- * of DbRefEntry source strings and describing the data
- * retrieved from external database sources (see jalview.ws.DbSourcProxy)
- * @author JimP
- *
- */
-public class DBRefSource
-{
-  /**
-   * UNIPROT Accession Number
-   */
-  public static String UNIPROT = "UNIPROT";
-  /**
-   * UNIPROT Entry Name
-   */
-  public static String UP_NAME = "UNIPROT_NAME";
-  /**
-   * Uniprot Knowledgebase/TrEMBL
-   * as served from EMBL protein products.
-   */
-  public static final String UNIPROTKB = "UniProtKB/TrEMBL";
-  /**
-   * PDB Entry Code
-   */
-  public static String PDB = "PDB";
-  /**
-   * EMBL ID
-   */
-  public static String EMBL = "EMBL";
-  /**
-   * EMBLCDS ID
-   */
-  public static String EMBLCDS = "EMBLCDS";
-  /**
-   * PFAM ID
-   */
-  public static String PFAM = "PFAM";
-  /**
-   * GeneDB ID
-   */
-  public static final String GENEDB = "GeneDB";
-
-  /**
-   * List of databases whose sequences might have coding regions annotated
-   */
-  public static final String[] DNACODINGDBS = { EMBL, EMBLCDS, GENEDB};
-  public static final String[] CODINGDBS = { EMBLCDS, GENEDB};
-  public static final String[] PROTEINDBS = { UNIPROT, PDB, UNIPROTKB};
-  public static final String[] PROTEINSEQ = { UNIPROT, UNIPROTKB};
-  public static final String[] PROTEINSTR = { PDB };
-  public static final String[] DOMAINDBS = { PFAM };
-  /**
-   * set of unique DBRefSource property constants.
-   * These could be used to reconstruct the above groupings
-   */
-  public static final Object SEQDB = "SQ";
-  /**
-   * database of nucleic acid sequences
-   */
-  public static final Object DNASEQDB = "NASQ";
-  /**
-   * database of amino acid sequences
-   */
-  public static final Object PROTSEQDB = "PROTSQ";
-  /**
-   * database of cDNA sequences
-   */
-  public static final Object CODINGSEQDB = "CODING";
-  /**
-   * database of na sequences with exon annotation
-   */
-  public static final Object DNACODINGSEQDB = "XONCODING";
-  /**
-   * DB returns several sequences associated with a protein domain
-   */
-  public static final Object DOMAINDB = "DOMAIN";
-  /**
-   * DB query can take multiple accession codes concatenated
-   * by a separator. Value of property indicates maximum number of accession codes to send at a time.
-   */
-  public static final Object MULTIACC = "MULTIACC";
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.datamodel;
+
+/**
+ * Defines internal constants for unambiguous annotation of DbRefEntry source
+ * strings and describing the data retrieved from external database sources (see
+ * jalview.ws.DbSourcProxy)
+ * 
+ * @author JimP
+ * 
+ */
+public class DBRefSource
+{
+  /**
+   * UNIPROT Accession Number
+   */
+  public static String UNIPROT = "UNIPROT";
+
+  /**
+   * UNIPROT Entry Name
+   */
+  public static String UP_NAME = "UNIPROT_NAME";
+
+  /**
+   * Uniprot Knowledgebase/TrEMBL as served from EMBL protein products.
+   */
+  public static final String UNIPROTKB = "UniProtKB/TrEMBL";
+
+  /**
+   * PDB Entry Code
+   */
+  public static String PDB = "PDB";
+
+  /**
+   * EMBL ID
+   */
+  public static String EMBL = "EMBL";
+
+  /**
+   * EMBLCDS ID
+   */
+  public static String EMBLCDS = "EMBLCDS";
+
+  /**
+   * PFAM ID
+   */
+  public static String PFAM = "PFAM";
+
+  /**
+   * GeneDB ID
+   */
+  public static final String GENEDB = "GeneDB";
+
+  /**
+   * List of databases whose sequences might have coding regions annotated
+   */
+  public static final String[] DNACODINGDBS =
+  { EMBL, EMBLCDS, GENEDB };
+
+  public static final String[] CODINGDBS =
+  { EMBLCDS, GENEDB };
+
+  public static final String[] PROTEINDBS =
+  { UNIPROT, PDB, UNIPROTKB };
+
+  public static final String[] PROTEINSEQ =
+  { UNIPROT, UNIPROTKB };
+
+  public static final String[] PROTEINSTR =
+  { PDB };
+
+  public static final String[] DOMAINDBS =
+  { PFAM };
+
+  /**
+   * set of unique DBRefSource property constants. These could be used to
+   * reconstruct the above groupings
+   */
+  public static final Object SEQDB = "SQ";
+
+  /**
+   * database of nucleic acid sequences
+   */
+  public static final Object DNASEQDB = "NASQ";
+
+  /**
+   * database of amino acid sequences
+   */
+  public static final Object PROTSEQDB = "PROTSQ";
+
+  /**
+   * database of cDNA sequences
+   */
+  public static final Object CODINGSEQDB = "CODING";
+
+  /**
+   * database of na sequences with exon annotation
+   */
+  public static final Object DNACODINGSEQDB = "XONCODING";
+
+  /**
+   * DB returns several sequences associated with a protein domain
+   */
+  public static final Object DOMAINDB = "DOMAIN";
+
+  /**
+   * DB query can take multiple accession codes concatenated by a separator.
+   * Value of property indicates maximum number of accession codes to send at a
+   * time.
+   */
+  public static final Object MULTIACC = "MULTIACC";
+}
diff --git a/src/jalview/datamodel/FeatureProperties.java b/src/jalview/datamodel/FeatureProperties.java
index d81a31c..d736a49 100644
--- a/src/jalview/datamodel/FeatureProperties.java
+++ b/src/jalview/datamodel/FeatureProperties.java
@@ -1,24 +1,49 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.datamodel;
 
 /**
  * A set of feature property constants used by jalview
+ * 
  * @author JimP
- *
+ * 
  */
 public class FeatureProperties
 {
 
   public static final String EXONPOS = "exon number";
+
   public static final String EXONPRODUCT = "product";
+
   /**
-   * lookup feature type for a particular database to see if its a coding region feature
+   * lookup feature type for a particular database to see if its a coding region
+   * feature
+   * 
    * @param dbrefsource
    * @param string
    * @return
    */
   public static boolean isCodingFeature(String dbrefsource, String type)
   {
-    return ((dbrefsource==null || dbrefsource.equalsIgnoreCase(DBRefSource.EMBL) || dbrefsource.equalsIgnoreCase(DBRefSource.EMBLCDS))
-            && type.equalsIgnoreCase("CDS"));
+    return ((dbrefsource == null
+            || dbrefsource.equalsIgnoreCase(DBRefSource.EMBL) || dbrefsource
+            .equalsIgnoreCase(DBRefSource.EMBLCDS)) && type
+            .equalsIgnoreCase("CDS"));
   }
 }
diff --git a/src/jalview/datamodel/GraphLine.java b/src/jalview/datamodel/GraphLine.java
index 77b7ef5..7a4aa56 100755
--- a/src/jalview/datamodel/GraphLine.java
+++ b/src/jalview/datamodel/GraphLine.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -21,8 +21,11 @@ package jalview.datamodel;
 public class GraphLine
 {
   public float value;
+
   public String label = "";
+
   public java.awt.Color colour = java.awt.Color.black;
+
   public boolean displayed = true;
 
   public GraphLine(float value, String label, java.awt.Color col)
@@ -38,8 +41,11 @@ public class GraphLine
       this.colour = col;
     }
   }
-  public GraphLine(GraphLine from) {
-    if (from!=null) {
+
+  public GraphLine(GraphLine from)
+  {
+    if (from != null)
+    {
       value = from.value;
       label = new String(from.label);
       colour = from.colour;
diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 21dcce1..22fe523 100755
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.datamodel;
 
 import java.util.*;
@@ -27,6 +26,7 @@ public class HiddenSequences
    * holds a list of hidden sequences associated with an alignment.
    */
   public SequenceI[] hiddenSequences;
+
   AlignmentI alignment;
 
   public HiddenSequences(AlignmentI al)
@@ -57,7 +57,8 @@ public class HiddenSequences
     int width = 0;
     for (int i = 0; i < hiddenSequences.length; i++)
     {
-      if (hiddenSequences[i] != null && hiddenSequences[i].getLength() > width)
+      if (hiddenSequences[i] != null
+              && hiddenSequences[i].getLength() > width)
       {
         width = hiddenSequences[i].getLength();
       }
@@ -67,8 +68,7 @@ public class HiddenSequences
   }
 
   /**
-   * Call this method if sequences are removed from the
-   * main alignment
+   * Call this method if sequences are removed from the main alignment
    */
   public void adjustHeightSequenceDeleted(int seqIndex)
   {
@@ -104,8 +104,8 @@ public class HiddenSequences
   }
 
   /**
-   * Call this method if sequences are added to or removed from the
-   * main alignment
+   * Call this method if sequences are added to or removed from the main
+   * alignment
    */
   public void adjustHeightSequenceAdded()
   {
@@ -162,9 +162,8 @@ public class HiddenSequences
   {
     Vector revealedSeqs = new Vector();
     SequenceI repSequence = alignment.getSequenceAt(alignmentIndex);
-    if (repSequence != null &&
-        hiddenReps != null
-        && hiddenReps.containsKey(repSequence))
+    if (repSequence != null && hiddenReps != null
+            && hiddenReps.containsKey(repSequence))
     {
       hiddenReps.remove(repSequence);
       revealedSeqs.addElement(repSequence);
@@ -191,7 +190,8 @@ public class HiddenSequences
         }
         else
         {
-          System.out.println(seq.getName() + " has been deleted whilst hidden");
+          System.out.println(seq.getName()
+                  + " has been deleted whilst hidden");
         }
       }
 
diff --git a/src/jalview/datamodel/Mapping.java b/src/jalview/datamodel/Mapping.java
index 835400e..c7e359b 100644
--- a/src/jalview/datamodel/Mapping.java
+++ b/src/jalview/datamodel/Mapping.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.datamodel;
 
 import java.util.Vector;
@@ -34,16 +52,16 @@ public class Mapping
    * create a new mapping from
    * 
    * @param to
-   *          the sequence being mapped
+   *                the sequence being mapped
    * @param exon
-   *          int[] {start,end,start,end} series on associated sequence
+   *                int[] {start,end,start,end} series on associated sequence
    * @param is
-   *          int[] {start,end,...} ranges on the reference frame being mapped
-   *          to
+   *                int[] {start,end,...} ranges on the reference frame being
+   *                mapped to
    * @param i
-   *          step size on associated sequence
+   *                step size on associated sequence
    * @param j
-   *          step size on mapped frame
+   *                step size on mapped frame
    */
   public Mapping(SequenceI to, int[] exon, int[] is, int i, int j)
   {
@@ -78,7 +96,7 @@ public class Mapping
 
   /**
    * @param map
-   *          the map to set
+   *                the map to set
    */
   public void setMap(MapList map)
   {
@@ -131,7 +149,7 @@ public class Mapping
    * gets boundary in direction of mapping
    * 
    * @param position
-   *          in mapped reference frame
+   *                in mapped reference frame
    * @return int{start, end} positions in associated sequence (in direction of
    *         mapped word)
    */
@@ -219,7 +237,7 @@ public class Mapping
       if (map != null)
       {
         int[] frange = map.locateInFrom(f.getBegin(), f.getEnd());
-        if (frange==null)
+        if (frange == null)
         {
           // JBPNote - this isprobably not the right thing to doJBPHack
           return null;
@@ -231,7 +249,7 @@ public class Mapping
           vf[v].setBegin(frange[i]);
           vf[v].setEnd(frange[i + 1]);
           if (frange.length > 2)
-            vf[v].setDescription(f.getDescription() + "\nPart " + (v+1));
+            vf[v].setDescription(f.getDescription() + "\nPart " + (v + 1));
         }
         return vf;
       }
@@ -347,7 +365,8 @@ public class Mapping
       for (int vc = 0; vc < viscontigs.length; vc += 2)
       {
         // find a mapped range in this visible region
-        int[] mpr = locateMappedRange(1+viscontigs[vc], viscontigs[vc + 1]-1);
+        int[] mpr = locateMappedRange(1 + viscontigs[vc],
+                viscontigs[vc + 1] - 1);
         if (mpr != null)
         {
           for (int m = 0; m < mpr.length; m += 2)
@@ -363,49 +382,58 @@ public class Mapping
           }
         }
       }
-      int[] from = new int[fromRange.size()*2];
-      int[] to = new int[toRange.size()*2];
+      int[] from = new int[fromRange.size() * 2];
+      int[] to = new int[toRange.size() * 2];
       int[] r;
-      for (int f=0,fSize=fromRange.size(); f<fSize; f++)
+      for (int f = 0, fSize = fromRange.size(); f < fSize; f++)
       {
         r = (int[]) fromRange.elementAt(f);
-        from[f*2] = r[0];
-        from[f*2+1] = r[1];
+        from[f * 2] = r[0];
+        from[f * 2 + 1] = r[1];
       }
-      for (int f=0,fSize=toRange.size(); f<fSize; f++)
+      for (int f = 0, fSize = toRange.size(); f < fSize; f++)
       {
         r = (int[]) toRange.elementAt(f);
-        to[f*2] = r[0];
-        to[f*2+1] = r[1];
+        to[f * 2] = r[0];
+        to[f * 2 + 1] = r[1];
       }
-      copy.setMap(new MapList(from, to, map.getFromRatio(), map.getToRatio()));
+      copy.setMap(new MapList(from, to, map.getFromRatio(), map
+              .getToRatio()));
     }
     return copy;
   }
+
   public static void main(String[] args)
   {
     /**
-     * trite test of the intersectVisContigs method
-     * for a simple DNA -> Protein exon map and a range of visContigs
+     * trite test of the intersectVisContigs method for a simple DNA -> Protein
+     * exon map and a range of visContigs
      */
-    MapList fk = new MapList(new int[] { 1,6,8,13,15,23}, new int[] { 1,7}, 3, 1);
+    MapList fk = new MapList(new int[]
+    { 1, 6, 8, 13, 15, 23 }, new int[]
+    { 1, 7 }, 3, 1);
     Mapping m = new Mapping(fk);
-    Mapping m_1 = m.intersectVisContigs(new int[] {fk.getFromLowest(), fk.getFromHighest()});
-    Mapping m_2 = m.intersectVisContigs(new int[] {1,7,11,20});
-    System.out.println(""+m_1.map.getFromRanges());
-    
-    
+    Mapping m_1 = m.intersectVisContigs(new int[]
+    { fk.getFromLowest(), fk.getFromHighest() });
+    Mapping m_2 = m.intersectVisContigs(new int[]
+    { 1, 7, 11, 20 });
+    System.out.println("" + m_1.map.getFromRanges());
+
   }
+
   /**
    * get the sequence being mapped to - if any
+   * 
    * @return null or a dataset sequence
    */
   public SequenceI getTo()
   {
     return to;
   }
+
   /**
    * set the dataset sequence being mapped to if any
+   * 
    * @param tto
    */
   public void setTo(SequenceI tto)
@@ -413,7 +441,9 @@ public class Mapping
     to = tto;
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see java.lang.Object#finalize()
    */
   protected void finalize() throws Throwable
@@ -422,5 +452,5 @@ public class Mapping
     to = null;
     super.finalize();
   }
-  
+
 }
diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java
index 69f0d68..446d719 100755
--- a/src/jalview/datamodel/PDBEntry.java
+++ b/src/jalview/datamodel/PDBEntry.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -23,38 +23,53 @@ import java.util.*;
 public class PDBEntry
 {
   String file;
+
   String type;
+
   String id;
+
   Hashtable properties;
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see java.lang.Object#equals(java.lang.Object)
    */
   public boolean equals(Object obj)
   {
-    if (obj==null || !(obj instanceof PDBEntry))
+    if (obj == null || !(obj instanceof PDBEntry))
     {
-        return false;
+      return false;
     }
-    if (obj==this)
+    if (obj == this)
       return true;
     PDBEntry o = (PDBEntry) obj;
-    return (file==o.file || (file!=null && o.file!=null && o.file.equals(file)))
-    && (type==o.type || (type!=null && o.type!=null && o.type.equals(type)))
-    && (id==o.id || (id!=null && o.id!=null && o.id.equalsIgnoreCase(id)))
-    && (properties==o.properties || (properties!=null && o.properties!=null && properties.equals(o.properties)));
+    return (file == o.file || (file != null && o.file != null && o.file
+            .equals(file)))
+            && (type == o.type || (type != null && o.type != null && o.type
+                    .equals(type)))
+            && (id == o.id || (id != null && o.id != null && o.id
+                    .equalsIgnoreCase(id)))
+            && (properties == o.properties || (properties != null
+                    && o.properties != null && properties
+                    .equals(o.properties)));
   }
+
   public PDBEntry()
-  {}
-  public PDBEntry(PDBEntry entry) {
+  {
+  }
+
+  public PDBEntry(PDBEntry entry)
+  {
     file = entry.file;
     type = entry.type;
     id = entry.id;
-    if (entry.properties!=null)
+    if (entry.properties != null)
     {
       properties = (Hashtable) entry.properties.clone();
     }
   }
+
   public void setFile(String file)
   {
     this.file = file;
diff --git a/src/jalview/datamodel/Provenance.java b/src/jalview/datamodel/Provenance.java
index f8afedf..bed8004 100755
--- a/src/jalview/datamodel/Provenance.java
+++ b/src/jalview/datamodel/Provenance.java
@@ -1,47 +1,48 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.datamodel;
-
-import java.util.*;
-
-public class Provenance
-{
-  Vector entries = new Vector();
-  public Provenance()
-  {
-
-  }
-
-  public ProvenanceEntry[] getEntries()
-  {
-    ProvenanceEntry[] ret = new ProvenanceEntry[entries.size()];
-    for (int i = 0; i < entries.size(); i++)
-    {
-      ret[i] = (ProvenanceEntry) entries.elementAt(i);
-    }
-    return ret;
-  }
-
-  public void addEntry(String user, String action, java.util.Date date,
-                       String id)
-  {
-    entries.addElement(new ProvenanceEntry(user, action, date, id));
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.datamodel;
+
+import java.util.*;
+
+public class Provenance
+{
+  Vector entries = new Vector();
+
+  public Provenance()
+  {
+
+  }
+
+  public ProvenanceEntry[] getEntries()
+  {
+    ProvenanceEntry[] ret = new ProvenanceEntry[entries.size()];
+    for (int i = 0; i < entries.size(); i++)
+    {
+      ret[i] = (ProvenanceEntry) entries.elementAt(i);
+    }
+    return ret;
+  }
+
+  public void addEntry(String user, String action, java.util.Date date,
+          String id)
+  {
+    entries.addElement(new ProvenanceEntry(user, action, date, id));
+  }
+
+}
diff --git a/src/jalview/datamodel/ProvenanceEntry.java b/src/jalview/datamodel/ProvenanceEntry.java
index b08dd6d..a33f203 100755
--- a/src/jalview/datamodel/ProvenanceEntry.java
+++ b/src/jalview/datamodel/ProvenanceEntry.java
@@ -1,52 +1,54 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.datamodel;
-
-public class ProvenanceEntry
-{
-  String user, action, id;
-  java.util.Date date;
-  public ProvenanceEntry(String u, String a, java.util.Date d, String i)
-  {
-    user = u;
-    action = a;
-    date = d;
-    id = i;
-  }
-
-  public String getUser()
-  {
-    return user;
-  }
-
-  public String getAction()
-  {
-    return action;
-  }
-
-  public java.util.Date getDate()
-  {
-    return date;
-  }
-
-  public String getID()
-  {
-    return id;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.datamodel;
+
+public class ProvenanceEntry
+{
+  String user, action, id;
+
+  java.util.Date date;
+
+  public ProvenanceEntry(String u, String a, java.util.Date d, String i)
+  {
+    user = u;
+    action = a;
+    date = d;
+    id = i;
+  }
+
+  public String getUser()
+  {
+    return user;
+  }
+
+  public String getAction()
+  {
+    return action;
+  }
+
+  public java.util.Date getDate()
+  {
+    return date;
+  }
+
+  public String getID()
+  {
+    return id;
+  }
+}
diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index b9176b4..e62c150 100755
--- a/src/jalview/datamodel/SearchResults.java
+++ b/src/jalview/datamodel/SearchResults.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -24,20 +24,23 @@ public class SearchResults
   Match[] matches;
 
   /**
-   * This method replaces the old search results which merely
-   * held an alignment index of search matches. This broke
-   * when sequences were moved around the alignment
-   * @param seq Sequence
-   * @param start int
-   * @param end int
+   * This method replaces the old search results which merely held an alignment
+   * index of search matches. This broke when sequences were moved around the
+   * alignment
+   * 
+   * @param seq
+   *                Sequence
+   * @param start
+   *                int
+   * @param end
+   *                int
    */
   public void addResult(SequenceI seq, int start, int end)
   {
     if (matches == null)
     {
       matches = new Match[]
-          {
-          new Match(seq, start, end)};
+      { new Match(seq, start, end) };
       return;
     }
 
@@ -56,9 +59,9 @@ public class SearchResults
   }
 
   /**
-   * This Method returns the search matches which lie between the
-   * start and end points of the sequence in question. It is
-   * optimised for returning objects for drawing on SequenceCanvas
+   * This Method returns the search matches which lie between the start and end
+   * points of the sequence in question. It is optimised for returning objects
+   * for drawing on SequenceCanvas
    */
   public int[] getResults(SequenceI sequence, int start, int end)
   {
@@ -69,25 +72,27 @@ public class SearchResults
 
     int[] result = null;
     int[] tmp = null;
-    int resultLength, matchStart=0, matchEnd=0;
+    int resultLength, matchStart = 0, matchEnd = 0;
     boolean mfound;
     for (int m = 0; m < matches.length; m++)
     {
-      mfound=false;
+      mfound = false;
       if (matches[m].sequence == sequence)
-        {
+      {
         mfound = true;
         // locate aligned position
         matchStart = sequence.findIndex(matches[m].start) - 1;
         matchEnd = sequence.findIndex(matches[m].end) - 1;
-        }
-      else if (matches[m].sequence == sequence.getDatasetSequence()) {
+      }
+      else if (matches[m].sequence == sequence.getDatasetSequence())
+      {
         mfound = true;
         // locate region in local context
         matchStart = sequence.findIndex(matches[m].start) - 1;
         matchEnd = sequence.findIndex(matches[m].end) - 1;
       }
-      if (mfound) {
+      if (mfound)
+      {
         if (matchStart <= end && matchEnd >= start)
         {
           if (matchStart < start)
@@ -103,8 +108,7 @@ public class SearchResults
           if (result == null)
           {
             result = new int[]
-                {
-                matchStart, matchEnd};
+            { matchStart, matchEnd };
           }
           else
           {
@@ -144,7 +148,9 @@ public class SearchResults
   class Match
   {
     SequenceI sequence;
+
     int start;
+
     int end;
 
     public Match(SequenceI seq, int start, int end)
diff --git a/src/jalview/datamodel/SeqCigar.java b/src/jalview/datamodel/SeqCigar.java
index 9ed0388..cc9eaa7 100644
--- a/src/jalview/datamodel/SeqCigar.java
+++ b/src/jalview/datamodel/SeqCigar.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -23,17 +23,20 @@ import java.util.Hashtable;
 import jalview.analysis.*;
 import jalview.util.*;
 
-public class SeqCigar
-    extends CigarSimple
+public class SeqCigar extends CigarSimple
 {
   /**
    * start(inclusive) and end(exclusive) of subsequence on refseq
    */
   private int start, end;
+
   private SequenceI refseq = null;
+
   private Hashtable seqProps;
+
   /**
    * Reference dataset sequence for the cigar string
+   * 
    * @return SequenceI
    */
   public SequenceI getRefSeq()
@@ -42,7 +45,7 @@ public class SeqCigar
   }
 
   /**
-   *
+   * 
    * @return int start index of cigar ops on refSeq
    */
   public int getStart()
@@ -51,7 +54,7 @@ public class SeqCigar
   }
 
   /**
-   *
+   * 
    * @return int end index (exclusive) of cigar ops on refSeq
    */
   public int getEnd()
@@ -61,17 +64,19 @@ public class SeqCigar
 
   /**
    * Returns sequence as a string with cigar operations applied to it
+   * 
    * @return String
    */
   public String getSequenceString(char GapChar)
   {
-    return (length == 0) ? "" :
-        (String) getSequenceAndDeletions(refseq.getSequenceAsString(start, end),
-                                         GapChar)[0];
+    return (length == 0) ? "" : (String) getSequenceAndDeletions(refseq
+            .getSequenceAsString(start, end), GapChar)[0];
   }
 
   /**
-   * recreates a gapped and edited version of RefSeq or null for an empty cigar string
+   * recreates a gapped and edited version of RefSeq or null for an empty cigar
+   * string
+   * 
    * @return SequenceI
    */
   public SequenceI getSeq(char GapChar)
@@ -81,30 +86,29 @@ public class SeqCigar
     {
       return null;
     }
-    Object[] edit_result = getSequenceAndDeletions(refseq.getSequenceAsString(
-        start, end),
-        GapChar);
+    Object[] edit_result = getSequenceAndDeletions(refseq
+            .getSequenceAsString(start, end), GapChar);
     if (edit_result == null)
     {
       throw new Error(
-          "Implementation Error - unexpected null from getSequenceAndDeletions");
+              "Implementation Error - unexpected null from getSequenceAndDeletions");
     }
     int bounds[] = (int[]) edit_result[1];
-    seq = new Sequence(refseq.getName(), (String) edit_result[0],
-                       refseq.getStart() + start + bounds[0],
-                       refseq.getStart() + start +
-                       ( (bounds[2] == 0) ? -1 : bounds[2]));
+    seq = new Sequence(refseq.getName(), (String) edit_result[0], refseq
+            .getStart()
+            + start + bounds[0], refseq.getStart() + start
+            + ((bounds[2] == 0) ? -1 : bounds[2]));
     seq.setDescription(refseq.getDescription());
-    int sstart = seq.getStart(),
-      send = seq.getEnd();
+    int sstart = seq.getStart(), send = seq.getEnd();
     // seq.checkValidRange(); probably not needed
-    // recover local properties if present 
-    if (seqProps!=null)
+    // recover local properties if present
+    if (seqProps != null)
     {
-      // this recovers dataset sequence reference as well as local features, names, start/end settings.
+      // this recovers dataset sequence reference as well as local features,
+      // names, start/end settings.
       SeqsetUtils.SeqCharacterUnhash(seq, seqProps);
     }
-    // ensure dataset sequence is up to date from local reference 
+    // ensure dataset sequence is up to date from local reference
     seq.setDatasetSequence(refseq);
     seq.setStart(sstart);
     seq.setEnd(send);
@@ -112,22 +116,26 @@ public class SeqCigar
   }
 
   /*
-     We don't allow this - refseq is given at construction time only
-   public void setSeq(SequenceI seq) {
-    this.seq = seq;
-     }
+   * We don't allow this - refseq is given at construction time only public void
+   * setSeq(SequenceI seq) { this.seq = seq; }
    */
   /**
-   * internal constructor - sets seq to a gapless sequence derived from seq
-   * and prepends any 'D' operations needed to get to the first residue of seq.
-   * @param seq SequenceI
-   * @param initialDeletion true to mark initial dataset sequence residues as deleted in subsequence
-   * @param _s index of first position in seq
-   * @param _e index after last position in (possibly gapped) seq
+   * internal constructor - sets seq to a gapless sequence derived from seq and
+   * prepends any 'D' operations needed to get to the first residue of seq.
+   * 
+   * @param seq
+   *                SequenceI
+   * @param initialDeletion
+   *                true to mark initial dataset sequence residues as deleted in
+   *                subsequence
+   * @param _s
+   *                index of first position in seq
+   * @param _e
+   *                index after last position in (possibly gapped) seq
    * @return true if gaps are present in seq
    */
   private boolean _setSeq(SequenceI seq, boolean initialDeletion, int _s,
-                          int _e)
+          int _e)
   {
     boolean hasgaps = false;
     if (seq == null)
@@ -147,13 +155,14 @@ public class SeqCigar
     start = seq.findPosition(_s) - seq.getStart();
     end = seq.findPosition(_e) - seq.getStart();
     int l_ungapped = end - start;
-    // Find correct sequence to reference and correct start and end - if necessary
+    // Find correct sequence to reference and correct start and end - if
+    // necessary
     SequenceI ds = seq.getDatasetSequence();
     if (ds == null)
     {
       // make a new dataset sequence
-      String ungapped = AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
-                                             new String(seq_string));
+      String ungapped = AlignSeq.extractGaps(
+              jalview.util.Comparison.GapChars, new String(seq_string));
       l_ungapped = ungapped.length();
       // check that we haven't just duplicated an ungapped sequence.
       if (l_ungapped == seq.getLength())
@@ -162,11 +171,11 @@ public class SeqCigar
       }
       else
       {
-        ds = new Sequence(seq.getName(), ungapped,
-                          seq.getStart(),
-                          seq.getStart() + ungapped.length() - 1);
+        ds = new Sequence(seq.getName(), ungapped, seq.getStart(), seq
+                .getStart()
+                + ungapped.length() - 1);
         // JBPNote: this would be consistent but may not be useful
-        //        seq.setDatasetSequence(ds);
+        // seq.setDatasetSequence(ds);
       }
     }
     // add in offset between seq and the dataset sequence
@@ -199,22 +208,28 @@ public class SeqCigar
     refseq = ds;
     // copy over local properties for the sequence instance of the refseq
     seqProps = SeqsetUtils.SeqCharacterHash(seq);
-    // Check  offsets
+    // Check offsets
     if (end > ds.getLength())
     {
-      throw new Error("SeqCigar: Possible implementation error: sequence is longer than dataset sequence");
-//      end = ds.getLength();
+      throw new Error(
+              "SeqCigar: Possible implementation error: sequence is longer than dataset sequence");
+      // end = ds.getLength();
     }
 
     return hasgaps;
   }
 
   /**
-   * directly initialise a cigar object with a sequence of range, operation pairs and a sequence to apply it to.
-   * operation and range should be relative to the seq.getStart()'th residue of the dataset seq resolved from seq.
-   * @param seq SequenceI
-   * @param operation char[]
-   * @param range int[]
+   * directly initialise a cigar object with a sequence of range, operation
+   * pairs and a sequence to apply it to. operation and range should be relative
+   * to the seq.getStart()'th residue of the dataset seq resolved from seq.
+   * 
+   * @param seq
+   *                SequenceI
+   * @param operation
+   *                char[]
+   * @param range
+   *                int[]
    */
   public SeqCigar(SequenceI seq, char operation[], int range[])
   {
@@ -225,7 +240,8 @@ public class SeqCigar
     }
     if (operation.length != range.length)
     {
-      throw new Error("Implementation Bug. Cigar Operation list!= range list");
+      throw new Error(
+              "Implementation Bug. Cigar Operation list!= range list");
     }
 
     if (operation != null)
@@ -235,16 +251,17 @@ public class SeqCigar
 
       if (_setSeq(seq, false, 0, 0))
       {
-        throw new Error("NOT YET Implemented: Constructing a Cigar object from a cigar string and a gapped sequence.");
+        throw new Error(
+                "NOT YET Implemented: Constructing a Cigar object from a cigar string and a gapped sequence.");
       }
       for (int i = this.length, j = 0; j < operation.length; i++, j++)
       {
         char op = operation[j];
         if (op != M && op != I && op != D)
         {
-          throw new Error(
-              "Implementation Bug. Cigar Operation '" + j + "' '" + op +
-              "' not one of '" + M + "', '" + I + "', or '" + D + "'.");
+          throw new Error("Implementation Bug. Cigar Operation '" + j
+                  + "' '" + op + "' not one of '" + M + "', '" + I
+                  + "', or '" + D + "'.");
         }
         this.operation[i] = op;
         this.range[i] = range[j];
@@ -258,14 +275,17 @@ public class SeqCigar
       this.length = 0;
       if (_setSeq(seq, false, 0, 0))
       {
-        throw new Error("NOT YET Implemented: Constructing a Cigar object from a cigar string and a gapped sequence.");
+        throw new Error(
+                "NOT YET Implemented: Constructing a Cigar object from a cigar string and a gapped sequence.");
       }
     }
   }
 
   /**
    * add range matched residues to cigar string
-   * @param range int
+   * 
+   * @param range
+   *                int
    */
   public void addMatch(int range)
   {
@@ -273,19 +293,23 @@ public class SeqCigar
   }
 
   /**
-   * Adds
-   * insertion and match operations based on seq to the cigar up to
-   * the endpos column of seq.
-   *
-   * @param cigar CigarBase
-   * @param seq SequenceI
-   * @param startpos int
-   * @param endpos int
-   * @param initialDeletions if true then initial deletions will be added from start of seq to startpos
+   * Adds insertion and match operations based on seq to the cigar up to the
+   * endpos column of seq.
+   * 
+   * @param cigar
+   *                CigarBase
+   * @param seq
+   *                SequenceI
+   * @param startpos
+   *                int
+   * @param endpos
+   *                int
+   * @param initialDeletions
+   *                if true then initial deletions will be added from start of
+   *                seq to startpos
    */
   protected static void addSequenceOps(CigarBase cigar, SequenceI seq,
-                                       int startpos, int endpos,
-                                       boolean initialDeletions)
+          int startpos, int endpos, boolean initialDeletions)
   {
     char op = '\0';
     int range = 0;
@@ -298,8 +322,9 @@ public class SeqCigar
 
     while (p <= endpos)
     {
-      boolean isGap = (p < res) ? jalview.util.Comparison.isGap(seq.getCharAt(p)) : true;
-      if ( (startpos <= p) && (p <= endpos))
+      boolean isGap = (p < res) ? jalview.util.Comparison.isGap(seq
+              .getCharAt(p)) : true;
+      if ((startpos <= p) && (p <= endpos))
       {
         if (isGap)
         {
@@ -349,7 +374,9 @@ public class SeqCigar
 
   /**
    * create a cigar string for given sequence
-   * @param seq SequenceI
+   * 
+   * @param seq
+   *                SequenceI
    */
   public SeqCigar(SequenceI seq)
   {
@@ -365,9 +392,13 @@ public class SeqCigar
 
   /**
    * Create Cigar from a range of gaps and residues on a sequence object
-   * @param seq SequenceI
-   * @param start int - first column in range
-   * @param end int - last column in range
+   * 
+   * @param seq
+   *                SequenceI
+   * @param start
+   *                int - first column in range
+   * @param end
+   *                int - last column in range
    */
   public SeqCigar(SequenceI seq, int start, int end)
   {
@@ -382,28 +413,35 @@ public class SeqCigar
   }
 
   /**
-   * Create a cigar object from a cigar string like '[<I|D|M><range>]+'
-   * Will fail if the given seq already contains gaps (JBPNote: future implementation will fix)
-   * @param seq SequenceI object resolvable to a dataset sequence
-   * @param cigarString String
+   * Create a cigar object from a cigar string like '[<I|D|M><range>]+' Will
+   * fail if the given seq already contains gaps (JBPNote: future implementation
+   * will fix)
+   * 
+   * @param seq
+   *                SequenceI object resolvable to a dataset sequence
+   * @param cigarString
+   *                String
    * @return Cigar
    */
   public static SeqCigar parseCigar(SequenceI seq, String cigarString)
-      throws Exception
+          throws Exception
   {
     Object[] opsandrange = parseCigarString(cigarString);
-    return new SeqCigar(seq, (char[]) opsandrange[0], (int[]) opsandrange[1]);
+    return new SeqCigar(seq, (char[]) opsandrange[0],
+            (int[]) opsandrange[1]);
   }
 
   /**
    * createAlignment
-   *
-   * @param alseqs SeqCigar[]
-   * @param gapCharacter char
+   * 
+   * @param alseqs
+   *                SeqCigar[]
+   * @param gapCharacter
+   *                char
    * @return SequenceI[]
    */
   public static SequenceI[] createAlignmentSequences(SeqCigar[] alseqs,
-      char gapCharacter, ColumnSelection colsel, int[] segments)
+          char gapCharacter, ColumnSelection colsel, int[] segments)
   {
     SequenceI[] seqs = new SequenceI[alseqs.length];
     StringBuffer[] g_seqs = new StringBuffer[alseqs.length];
@@ -411,23 +449,28 @@ public class SeqCigar
     Object[] gs_regions = new Object[alseqs.length];
     for (int i = 0; i < alseqs.length; i++)
     {
-      alseqs_string[i] = alseqs[i].getRefSeq().
-          getSequenceAsString(alseqs[i].start, alseqs[i].end);
+      alseqs_string[i] = alseqs[i].getRefSeq().getSequenceAsString(
+              alseqs[i].start, alseqs[i].end);
       gs_regions[i] = alseqs[i].getSequenceAndDeletions(alseqs_string[i],
-          gapCharacter); // gapped sequence, {start, start col, end. endcol}, hidden regions {{start, end, col}})
+              gapCharacter); // gapped sequence, {start, start col, end.
+                              // endcol}, hidden regions {{start, end, col}})
       if (gs_regions[i] == null)
       {
-        throw new Error("Implementation error: " + i +
-                        "'th sequence Cigar has no operations.");
+        throw new Error("Implementation error: " + i
+                + "'th sequence Cigar has no operations.");
       }
-      g_seqs[i] = new StringBuffer( (String) ( (Object[]) gs_regions[i])[0]); // the visible gapped sequence
+      g_seqs[i] = new StringBuffer((String) ((Object[]) gs_regions[i])[0]); // the
+                                                                            // visible
+                                                                            // gapped
+                                                                            // sequence
     }
     // Now account for insertions. (well - deletions)
-    // this is complicated because we must keep track of shifted positions in each sequence
+    // this is complicated because we must keep track of shifted positions in
+    // each sequence
     ShiftList shifts = new ShiftList();
     for (int i = 0; i < alseqs.length; i++)
     {
-      Object[] gs_region = ( (Object[]) ( (Object[]) gs_regions[i])[2]);
+      Object[] gs_region = ((Object[]) ((Object[]) gs_regions[i])[2]);
       if (gs_region != null)
 
       {
@@ -439,7 +482,9 @@ public class SeqCigar
           {
             insert[s] = gapCharacter;
           }
-          int inspos = shifts.shift(region[2]); // resolve insertion position in current alignment frame of reference
+          int inspos = shifts.shift(region[2]); // resolve insertion position in
+                                                // current alignment frame of
+                                                // reference
           for (int s = 0; s < alseqs.length; s++)
           {
             if (s != i)
@@ -449,19 +494,21 @@ public class SeqCigar
                 // prefix insertion with more gaps.
                 for (int l = inspos - g_seqs[s].length(); l > 0; l--)
                 {
-                  g_seqs[s].append(gapCharacter); // to debug - use a diffferent gap character here
+                  g_seqs[s].append(gapCharacter); // to debug - use a diffferent
+                                                  // gap character here
                 }
               }
               g_seqs[s].insert(inspos, insert);
             }
             else
             {
-              g_seqs[s].insert(inspos,
-                               alseqs_string[i].substring(region[0],
-                  region[1] + 1));
+              g_seqs[s].insert(inspos, alseqs_string[i].substring(
+                      region[0], region[1] + 1));
             }
           }
-          shifts.addShift(region[2], insert.length); // update shift in alignment frame of reference
+          shifts.addShift(region[2], insert.length); // update shift in
+                                                      // alignment frame of
+                                                      // reference
           if (segments == null)
           {
             // add a hidden column for this deletion
@@ -472,12 +519,12 @@ public class SeqCigar
     }
     for (int i = 0; i < alseqs.length; i++)
     {
-      int[] bounds = ( (int[]) ( (Object[]) gs_regions[i])[1]);
+      int[] bounds = ((int[]) ((Object[]) gs_regions[i])[1]);
       SequenceI ref = alseqs[i].getRefSeq();
-      seqs[i] = new Sequence(ref.getName(), g_seqs[i].toString(),
-                             ref.getStart() + alseqs[i].start + bounds[0],
-                             ref.getStart() + alseqs[i].start +
-                             (bounds[2] == 0 ? -1 : bounds[2]));
+      seqs[i] = new Sequence(ref.getName(), g_seqs[i].toString(), ref
+              .getStart()
+              + alseqs[i].start + bounds[0], ref.getStart()
+              + alseqs[i].start + (bounds[2] == 0 ? -1 : bounds[2]));
       seqs[i].setDatasetSequence(ref);
       seqs[i].setDescription(ref.getDescription());
     }
@@ -485,10 +532,10 @@ public class SeqCigar
     {
       for (int i = 0; i < segments.length; i += 3)
       {
-        //int start=shifts.shift(segments[i]-1)+1;
-        //int end=shifts.shift(segments[i]+segments[i+1]-1)-1;
-        colsel.hideColumns(segments[i + 1],
-                           segments[i + 1] + segments[i + 2] - 1);
+        // int start=shifts.shift(segments[i]-1)+1;
+        // int end=shifts.shift(segments[i]+segments[i+1]-1)-1;
+        colsel.hideColumns(segments[i + 1], segments[i + 1]
+                + segments[i + 2] - 1);
       }
     }
     return seqs;
@@ -498,9 +545,11 @@ public class SeqCigar
    * non rigorous testing
    */
   /**
-   *
-   * @param seq Sequence
-   * @param ex_cs_gapped String
+   * 
+   * @param seq
+   *                Sequence
+   * @param ex_cs_gapped
+   *                String
    * @return String
    */
   public static String testCigar_string(Sequence seq, String ex_cs_gapped)
@@ -509,71 +558,69 @@ public class SeqCigar
     String cs_gapped = c_sgapped.getCigarstring();
     if (!cs_gapped.equals(ex_cs_gapped))
     {
-      System.err.println("Failed getCigarstring: incorect string '" + cs_gapped +
-                         "' != " + ex_cs_gapped);
+      System.err.println("Failed getCigarstring: incorect string '"
+              + cs_gapped + "' != " + ex_cs_gapped);
     }
     return cs_gapped;
   }
 
   public static boolean testSeqRecovery(SeqCigar gen_sgapped,
-                                        SequenceI s_gapped)
+          SequenceI s_gapped)
   {
-    // this is non-rigorous - start and end  recovery is not tested.
+    // this is non-rigorous - start and end recovery is not tested.
     SequenceI gen_sgapped_s = gen_sgapped.getSeq('-');
     if (!gen_sgapped_s.getSequence().equals(s_gapped.getSequence()))
     {
-      System.err.println("Couldn't reconstruct sequence.\n" +
-                         gen_sgapped_s.getSequenceAsString() + "\n" +
-                         s_gapped.getSequenceAsString());
+      System.err.println("Couldn't reconstruct sequence.\n"
+              + gen_sgapped_s.getSequenceAsString() + "\n"
+              + s_gapped.getSequenceAsString());
       return false;
     }
     return true;
   }
 
-  public static void main(String argv[])
-      throws Exception
+  public static void main(String argv[]) throws Exception
   {
     String o_seq;
     Sequence s = new Sequence("MySeq",
-                              o_seq =
-                              "asdfktryasdtqwrtsaslldddptyipqqwaslchvhttt",
-                              39, 80);
+            o_seq = "asdfktryasdtqwrtsaslldddptyipqqwaslchvhttt", 39, 80);
     String orig_gapped;
-    Sequence s_gapped = new Sequence("MySeq",
-                                     orig_gapped =
-        "----asdf------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhttt",
-                                     39, 80);
+    Sequence s_gapped = new Sequence(
+            "MySeq",
+            orig_gapped = "----asdf------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhttt",
+            39, 80);
     String ex_cs_gapped = "4I4M6I6M3I11M4I12M4I9M";
     s_gapped.setDatasetSequence(s);
     String sub_gapped_s;
-    Sequence s_subsequence_gapped = new Sequence("MySeq",
-                                                 sub_gapped_s =
-        "------ktryas---dtqwrtsasll----dddptyipqqwa----slchvh",
-                                                 43, 77);
+    Sequence s_subsequence_gapped = new Sequence(
+            "MySeq",
+            sub_gapped_s = "------ktryas---dtqwrtsasll----dddptyipqqwa----slchvh",
+            43, 77);
 
     s_subsequence_gapped.setDatasetSequence(s);
     SeqCigar c_null = new SeqCigar(s);
     String cs_null = c_null.getCigarstring();
     if (!cs_null.equals("42M"))
     {
-      System.err.println(
-          "Failed to recover ungapped sequence cigar operations:" +
-          ( (cs_null == "") ? "empty string" : cs_null));
+      System.err
+              .println("Failed to recover ungapped sequence cigar operations:"
+                      + ((cs_null == "") ? "empty string" : cs_null));
     }
     testCigar_string(s_gapped, ex_cs_gapped);
     SeqCigar gen_sgapped = SeqCigar.parseCigar(s, ex_cs_gapped);
     if (!gen_sgapped.getCigarstring().equals(ex_cs_gapped))
     {
-      System.err.println("Failed parseCigar(" + ex_cs_gapped +
-                         ")->getCigarString()->'" + gen_sgapped.getCigarstring() +
-                         "'");
+      System.err.println("Failed parseCigar(" + ex_cs_gapped
+              + ")->getCigarString()->'" + gen_sgapped.getCigarstring()
+              + "'");
     }
     testSeqRecovery(gen_sgapped, s_gapped);
     // Test dataset resolution
     SeqCigar sub_gapped = new SeqCigar(s_subsequence_gapped);
     if (!testSeqRecovery(sub_gapped, s_subsequence_gapped))
     {
-      System.err.println("Failed recovery for subsequence of dataset sequence");
+      System.err
+              .println("Failed recovery for subsequence of dataset sequence");
     }
     // width functions
     if (sub_gapped.getWidth() != sub_gapped_s.length())
@@ -590,14 +637,13 @@ public class SeqCigar
     SeqCigar sub_se_gp = new SeqCigar(s_subsequence_gapped, 8, 48);
     if (sub_se_gp.getWidth() != 41)
     {
-      System.err.println(
-          "SeqCigar(seq, start, end) not properly clipped alignsequence.");
+      System.err
+              .println("SeqCigar(seq, start, end) not properly clipped alignsequence.");
     }
-    System.out.println("Original sequence align:\n" + sub_gapped_s +
-                       "\nReconstructed window from 8 to 48\n"
-                       + "XXXXXXXX" + sub_se_gp.getSequenceString('-') + "..."
-                       + "\nCigar String:" + sub_se_gp.getCigarstring() + "\n"
-        );
+    System.out.println("Original sequence align:\n" + sub_gapped_s
+            + "\nReconstructed window from 8 to 48\n" + "XXXXXXXX"
+            + sub_se_gp.getSequenceString('-') + "..." + "\nCigar String:"
+            + sub_se_gp.getCigarstring() + "\n");
     SequenceI ssgp = sub_se_gp.getSeq('-');
     System.out.println("\t " + ssgp.getSequenceAsString());
     for (int r = 0; r < 10; r++)
@@ -616,36 +662,34 @@ public class SeqCigar
     }
     {
       SeqCigar[] set = new SeqCigar[]
-          {
-          new SeqCigar(s), new SeqCigar(s_subsequence_gapped, 8, 48),
-          new SeqCigar(s_gapped)};
+      { new SeqCigar(s), new SeqCigar(s_subsequence_gapped, 8, 48),
+          new SeqCigar(s_gapped) };
       Alignment al = new Alignment(set);
       for (int i = 0; i < al.getHeight(); i++)
       {
-        System.out.println("" + al.getSequenceAt(i).getName() + "\t" +
-                           al.getSequenceAt(i).getStart() + "\t" +
-                           al.getSequenceAt(i).getEnd() + "\t" +
-                           al.getSequenceAt(i).getSequenceAsString());
+        System.out.println("" + al.getSequenceAt(i).getName() + "\t"
+                + al.getSequenceAt(i).getStart() + "\t"
+                + al.getSequenceAt(i).getEnd() + "\t"
+                + al.getSequenceAt(i).getSequenceAsString());
       }
     }
     {
       System.out.println("Gapped.");
       SeqCigar[] set = new SeqCigar[]
-          {
-          new SeqCigar(s), new SeqCigar(s_subsequence_gapped, 8, 48),
-          new SeqCigar(s_gapped)};
+      { new SeqCigar(s), new SeqCigar(s_subsequence_gapped, 8, 48),
+          new SeqCigar(s_gapped) };
       set[0].deleteRange(20, 25);
       Alignment al = new Alignment(set);
       for (int i = 0; i < al.getHeight(); i++)
       {
-        System.out.println("" + al.getSequenceAt(i).getName() + "\t" +
-                           al.getSequenceAt(i).getStart() + "\t" +
-                           al.getSequenceAt(i).getEnd() + "\t" +
-                           al.getSequenceAt(i).getSequenceAsString());
+        System.out.println("" + al.getSequenceAt(i).getName() + "\t"
+                + al.getSequenceAt(i).getStart() + "\t"
+                + al.getSequenceAt(i).getEnd() + "\t"
+                + al.getSequenceAt(i).getSequenceAsString());
       }
     }
-//    if (!ssgapedseq.equals("ryas---dtqqwa----slchvh"))
-//      System.err.println("Subseqgaped\n------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhryas---dtqwrtsasll--qwa----slchvh\n"+ssgapedseq+"\n"+sub_se_gp.getCigarstring());
+    // if (!ssgapedseq.equals("ryas---dtqqwa----slchvh"))
+    // System.err.println("Subseqgaped\n------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhryas---dtqwrtsasll--qwa----slchvh\n"+ssgapedseq+"\n"+sub_se_gp.getCigarstring());
   }
 
 }
diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 56a829c..eda5684 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -186,7 +186,7 @@ public class Sequence implements SequenceI
       }
     }
     setDatasetSequence(seq.getDatasetSequence());
-    if (datasetSequence==null && seq.getDBRef() != null)
+    if (datasetSequence == null && seq.getDBRef() != null)
     {
       // only copy DBRefs if we really are a dataset sequence
       DBRefEntry[] dbr = seq.getDBRef();
@@ -657,6 +657,7 @@ public class Sequence implements SequenceI
 
     return map;
   }
+
   /*
    * (non-Javadoc)
    * 
@@ -680,6 +681,7 @@ public class Sequence implements SequenceI
     }
     return map;
   }
+
   /*
    * (non-Javadoc)
    * 
@@ -738,7 +740,7 @@ public class Sequence implements SequenceI
             {
               createNewDs = true;
               newend--; // decrease end position by one for the deleted residue
-                        // and search further
+              // and search further
             }
           }
         }
@@ -820,7 +822,8 @@ public class Sequence implements SequenceI
 
   public DBRefEntry[] getDBRef()
   {
-    if (dbrefs==null && datasetSequence!=null && this!=datasetSequence)
+    if (dbrefs == null && datasetSequence != null
+            && this != datasetSequence)
     {
       return datasetSequence.getDBRef();
     }
diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 1f34b8b..0686419 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -22,18 +22,24 @@ import java.util.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
 public class SequenceFeature
 {
   public int begin;
+
   public int end;
+
   public float score;
+
   public String type;
+
   public String description;
+
   public Hashtable otherDetails;
+
   public java.util.Vector links;
 
   // Feature group can be set from a features file
@@ -41,13 +47,14 @@ public class SequenceFeature
   public String featureGroup;
 
   public SequenceFeature()
-  {}
+  {
+  }
 
   /**
-   * Constructs a duplicate feature.
-   * Note: Uses clone on the otherDetails so only shallow copies are made
-   * of additional properties and method will silently fail if unclonable
-   * objects are found in the hash.
+   * Constructs a duplicate feature. Note: Uses clone on the otherDetails so
+   * only shallow copies are made of additional properties and method will
+   * silently fail if unclonable objects are found in the hash.
+   * 
    * @param cpy
    */
   public SequenceFeature(SequenceFeature cpy)
@@ -74,8 +81,7 @@ public class SequenceFeature
         try
         {
           otherDetails = (Hashtable) cpy.otherDetails.clone();
-        }
-        catch (Exception e)
+        } catch (Exception e)
         {
           // Uncloneable objects in the otherDetails - don't complain
         }
@@ -91,11 +97,8 @@ public class SequenceFeature
     }
   }
 
-  public SequenceFeature(String type,
-                         String desc,
-                         String status,
-                         int begin, int end,
-                         String featureGroup)
+  public SequenceFeature(String type, String desc, String status,
+          int begin, int end, String featureGroup)
   {
     this.type = type;
     this.description = desc;
@@ -105,11 +108,8 @@ public class SequenceFeature
     this.featureGroup = featureGroup;
   }
 
-  public SequenceFeature(String type,
-                         String desc,
-                         int begin, int end,
-                         float score,
-                         String featureGroup)
+  public SequenceFeature(String type, String desc, int begin, int end,
+          float score, String featureGroup)
   {
     this.type = type;
     this.description = desc;
@@ -121,15 +121,13 @@ public class SequenceFeature
 
   public boolean equals(SequenceFeature sf)
   {
-    if (begin != sf.begin
-        || end != sf.end
-        || score != sf.score)
+    if (begin != sf.begin || end != sf.end || score != sf.score)
     {
       return false;
     }
 
-    if (! (type + description + featureGroup).equals
-        (sf.type + sf.description + sf.featureGroup))
+    if (!(type + description + featureGroup).equals(sf.type
+            + sf.description + sf.featureGroup))
     {
       return false;
     }
@@ -139,7 +137,7 @@ public class SequenceFeature
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public int getBegin()
@@ -154,7 +152,7 @@ public class SequenceFeature
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public int getEnd()
@@ -169,7 +167,7 @@ public class SequenceFeature
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public String getType()
@@ -184,7 +182,7 @@ public class SequenceFeature
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public String getDescription()
@@ -228,9 +226,11 @@ public class SequenceFeature
   }
 
   /**
-   * Used for getting values which are not in the
-   * basic set. eg STRAND, FRAME for GFF file
-   * @param key String
+   * Used for getting values which are not in the basic set. eg STRAND, FRAME
+   * for GFF file
+   * 
+   * @param key
+   *                String
    */
   public Object getValue(String key)
   {
@@ -245,10 +245,13 @@ public class SequenceFeature
   }
 
   /**
-   * Used for setting values which are not in the
-   * basic set. eg STRAND, FRAME for GFF file
-   * @param key   eg STRAND
-   * @param value eg +
+   * Used for setting values which are not in the basic set. eg STRAND, FRAME
+   * for GFF file
+   * 
+   * @param key
+   *                eg STRAND
+   * @param value
+   *                eg +
    */
   public void setValue(String key, Object value)
   {
@@ -264,8 +267,8 @@ public class SequenceFeature
   }
 
   /*
-   * The following methods are added to maintain
-   * the castor Uniprot mapping file for the moment.
+   * The following methods are added to maintain the castor Uniprot mapping file
+   * for the moment.
    */
   public void setStatus(String status)
   {
@@ -277,7 +280,7 @@ public class SequenceFeature
     if (otherDetails != null)
     {
       String stat = (String) otherDetails.get("status");
-      if (stat!=null)
+      if (stat != null)
         return new String(stat);
     }
     return null;
diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 6ded8bd..dd842ea 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -27,29 +27,45 @@ import jalview.schemes.*;
 
 /**
  * Collects a set contiguous ranges on a set of sequences
+ * 
  * @author $author$
  * @version $Revision$
  */
 public class SequenceGroup
 {
   String groupName;
+
   String description;
+
   Conservation conserve;
+
   Vector aaFrequency;
+
   boolean displayBoxes = true;
+
   boolean displayText = true;
+
   boolean colourText = false;
+
   private Vector sequences = new Vector();
+
   int width = -1;
 
   /** DOCUMENT ME!! */
   public ColourSchemeI cs;
+
   int startRes = 0;
+
   int endRes = 0;
+
   public Color outlineColour = Color.black;
-  public Color idColour = null; 
+
+  public Color idColour = null;
+
   public int thresholdTextColour = 0;
+
   public Color textColour = Color.black;
+
   public Color textColour2 = Color.white;
 
   /**
@@ -62,20 +78,21 @@ public class SequenceGroup
 
   /**
    * Creates a new SequenceGroup object.
-   *
-   * @param sequences 
-   * @param groupName 
-   * @param scheme 
-   * @param displayBoxes 
-   * @param displayText 
-   * @param colourText 
-   * @param start first column of group
-   * @param end last column of group
+   * 
+   * @param sequences
+   * @param groupName
+   * @param scheme
+   * @param displayBoxes
+   * @param displayText
+   * @param colourText
+   * @param start
+   *                first column of group
+   * @param end
+   *                last column of group
    */
   public SequenceGroup(Vector sequences, String groupName,
-                       ColourSchemeI scheme, boolean displayBoxes,
-                       boolean displayText,
-                       boolean colourText, int start, int end)
+          ColourSchemeI scheme, boolean displayBoxes, boolean displayText,
+          boolean colourText, int start, int end)
   {
     this.sequences = sequences;
     this.groupName = groupName;
@@ -93,13 +110,13 @@ public class SequenceGroup
     int iSize = sequences.size();
     SequenceI[] seqs = new SequenceI[iSize];
     SequenceI[] inorder = getSequencesInOrder(align);
-    
-    for (int i = 0,ipos=0; i < inorder.length; i++)
+
+    for (int i = 0, ipos = 0; i < inorder.length; i++)
     {
       SequenceI seq = inorder[i];
 
-      seqs[ipos] = seq.getSubSequence(startRes, endRes+1);
-      if (seqs[ipos]!=null)
+      seqs[ipos] = seq.getSubSequence(startRes, endRes + 1);
+      if (seqs[ipos] != null)
       {
         seqs[ipos].setDescription(seq.getDescription());
         seqs[ipos].setDBRef(seq.getDBRef());
@@ -112,18 +129,19 @@ public class SequenceGroup
         if (seq.getAnnotation() != null)
         {
           AlignmentAnnotation[] alann = align.getAlignmentAnnotation();
-          // Only copy annotation that is either a score or referenced by the alignment's annotation vector
+          // Only copy annotation that is either a score or referenced by the
+          // alignment's annotation vector
           for (int a = 0; a < seq.getAnnotation().length; a++)
           {
             AlignmentAnnotation tocopy = seq.getAnnotation()[a];
-            if (alann!=null)
+            if (alann != null)
             {
-              boolean found=false;
-              for (int pos=0;pos<alann.length; pos++)
+              boolean found = false;
+              for (int pos = 0; pos < alann.length; pos++)
               {
-                if (alann[pos]==tocopy)
-                { 
-                  found=true;
+                if (alann[pos] == tocopy)
+                {
+                  found = true;
                   break;
                 }
               }
@@ -139,11 +157,13 @@ public class SequenceGroup
           }
         }
         ipos++;
-      } else {
+      }
+      else
+      {
         iSize--;
       }
     }
-    if (iSize!=inorder.length)
+    if (iSize != inorder.length)
     {
       SequenceI[] nseqs = new SequenceI[iSize];
       System.arraycopy(seqs, 0, nseqs, 0, iSize);
@@ -154,9 +174,10 @@ public class SequenceGroup
   }
 
   /**
-   * If sequence ends in gaps, the end residue can
-   * be correctly calculated here
-   * @param seq SequenceI
+   * If sequence ends in gaps, the end residue can be correctly calculated here
+   * 
+   * @param seq
+   *                SequenceI
    * @return int
    */
   public int findEndRes(SequenceI seq)
@@ -167,7 +188,7 @@ public class SequenceGroup
     for (int j = 0; j < endRes + 1 && j < seq.getLength(); j++)
     {
       ch = seq.getCharAt(j);
-      if (!jalview.util.Comparison.isGap( (ch)))
+      if (!jalview.util.Comparison.isGap((ch)))
       {
         eres++;
       }
@@ -201,8 +222,7 @@ public class SequenceGroup
           for (int h = 0; h < hsg.getSize(); h++)
           {
             seq2 = hsg.getSequenceAt(h);
-            if (seq2 != seq
-                && !allSequences.contains(seq2))
+            if (seq2 != seq && !allSequences.contains(seq2))
             {
               allSequences.addElement(seq2);
             }
@@ -232,9 +252,10 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
-   * @param col DOCUMENT ME!
-   *
+   * 
+   * @param col
+   *                DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   public boolean adjustForRemoveLeft(int col)
@@ -265,9 +286,10 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
-   * @param col DOCUMENT ME!
-   *
+   * 
+   * @param col
+   *                DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   public boolean adjustForRemoveRight(int col)
@@ -288,7 +310,7 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public String getName()
@@ -303,8 +325,9 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
-   * @param name DOCUMENT ME!
+   * 
+   * @param name
+   *                DOCUMENT ME!
    */
   public void setName(String name)
   {
@@ -318,7 +341,7 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public Conservation getConservation()
@@ -328,8 +351,9 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
-   * @param c DOCUMENT ME!
+   * 
+   * @param c
+   *                DOCUMENT ME!
    */
   public void setConservation(Conservation c)
   {
@@ -338,9 +362,11 @@ public class SequenceGroup
 
   /**
    * Add s to this sequence group
-   *
-   * @param s alignment sequence to be added
-   * @param recalc true means Group's conservation should be recalculated
+   * 
+   * @param s
+   *                alignment sequence to be added
+   * @param recalc
+   *                true means Group's conservation should be recalculated
    */
   public void addSequence(SequenceI s, boolean recalc)
   {
@@ -367,19 +393,19 @@ public class SequenceGroup
 
     try
     {
-      cs.setConsensus(AAFrequency.calculate(sequences, startRes, endRes + 1));
+      cs.setConsensus(AAFrequency
+              .calculate(sequences, startRes, endRes + 1));
 
       if (cs instanceof ClustalxColourScheme)
       {
-        ( (ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
+        ((ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
       }
 
       if (cs.conservationApplied())
       {
         Conservation c = new Conservation(groupName,
-                                          ResidueProperties.propHash, 3,
-                                          sequences,
-                                          startRes, endRes + 1);
+                ResidueProperties.propHash, 3, sequences, startRes,
+                endRes + 1);
         c.calculate();
         c.verdict(false, 25);
 
@@ -387,13 +413,12 @@ public class SequenceGroup
 
         if (cs instanceof ClustalxColourScheme)
         {
-          ( (ClustalxColourScheme) cs).resetClustalX(sequences,
-              getWidth());
+          ((ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
         }
       }
-    }
-    catch (java.lang.OutOfMemoryError err)
+    } catch (java.lang.OutOfMemoryError err)
     {
+      // TODO: catch OOM
       System.out.println("Out of memory loading groups: " + err);
     }
 
@@ -401,9 +426,11 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
-   * @param s DOCUMENT ME!
-   * @param recalc DOCUMENT ME!
+   * 
+   * @param s
+   *                DOCUMENT ME!
+   * @param recalc
+   *                DOCUMENT ME!
    */
   public void addOrRemove(SequenceI s, boolean recalc)
   {
@@ -419,9 +446,11 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
-   * @param s DOCUMENT ME!
-   * @param recalc DOCUMENT ME!
+   * 
+   * @param s
+   *                DOCUMENT ME!
+   * @param recalc
+   *                DOCUMENT ME!
    */
   public void deleteSequence(SequenceI s, boolean recalc)
   {
@@ -435,7 +464,7 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public int getStartRes()
@@ -445,7 +474,7 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public int getEndRes()
@@ -455,8 +484,9 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
+   * 
+   * @param i
+   *                DOCUMENT ME!
    */
   public void setStartRes(int i)
   {
@@ -465,8 +495,9 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
+   * 
+   * @param i
+   *                DOCUMENT ME!
    */
   public void setEndRes(int i)
   {
@@ -475,7 +506,7 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public int getSize()
@@ -485,9 +516,10 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
-   *
+   * 
+   * @param i
+   *                DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   public SequenceI getSequenceAt(int i)
@@ -497,8 +529,9 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
-   * @param state DOCUMENT ME!
+   * 
+   * @param state
+   *                DOCUMENT ME!
    */
   public void setColourText(boolean state)
   {
@@ -507,7 +540,7 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public boolean getColourText()
@@ -517,8 +550,9 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
-   * @param state DOCUMENT ME!
+   * 
+   * @param state
+   *                DOCUMENT ME!
    */
   public void setDisplayText(boolean state)
   {
@@ -527,7 +561,7 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public boolean getDisplayText()
@@ -537,8 +571,9 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
-   * @param state DOCUMENT ME!
+   * 
+   * @param state
+   *                DOCUMENT ME!
    */
   public void setDisplayBoxes(boolean state)
   {
@@ -547,7 +582,7 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public boolean getDisplayBoxes()
@@ -557,7 +592,7 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public int getWidth()
@@ -565,7 +600,7 @@ public class SequenceGroup
     // MC This needs to get reset when characters are inserted and deleted
     if (sequences.size() > 0)
     {
-      width = ( (SequenceI) sequences.elementAt(0)).getLength();
+      width = ((SequenceI) sequences.elementAt(0)).getLength();
     }
 
     for (int i = 1; i < sequences.size(); i++)
@@ -583,8 +618,9 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
-   * @param c DOCUMENT ME!
+   * 
+   * @param c
+   *                DOCUMENT ME!
    */
   public void setOutlineColour(Color c)
   {
@@ -593,7 +629,7 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public Color getOutlineColour()
@@ -602,10 +638,11 @@ public class SequenceGroup
   }
 
   /**
-   *
+   * 
    * returns the sequences in the group ordered by the ordering given by al
-   *
-   * @param al Alignment
+   * 
+   * @param al
+   *                Alignment
    * @return SequenceI[]
    */
   public SequenceI[] getSequencesInOrder(AlignmentI al)
@@ -636,7 +673,8 @@ public class SequenceGroup
   }
 
   /**
-   * @param idColour the idColour to set
+   * @param idColour
+   *                the idColour to set
    */
   public void setIdColour(Color idColour)
   {
diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index d9ffc81..3e9c4c7 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -22,7 +22,7 @@ import java.util.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
@@ -30,8 +30,8 @@ public interface SequenceI
 {
   /**
    * Set the display name for the sequence
-   *
-   * @param name 
+   * 
+   * @param name
    */
   public void setName(String name);
 
@@ -42,47 +42,53 @@ public interface SequenceI
 
   /**
    * Set start position of first non-gapped symbol in sequence
-   *
-   * @param start new start position
+   * 
+   * @param start
+   *                new start position
    */
   public void setStart(int start);
 
   /**
    * get start position of first non-gapped residue in sequence
-   * @return 
+   * 
+   * @return
    */
   public int getStart();
 
   /**
    * get the displayed id of the sequence
-   * @return true means the id will be returned in the form DisplayName/Start-End
+   * 
+   * @return true means the id will be returned in the form
+   *         DisplayName/Start-End
    */
   public String getDisplayId(boolean jvsuffix);
 
   /**
    * set end position for last residue in sequence
-   * @param end 
+   * 
+   * @param end
    */
   public void setEnd(int end);
 
   /**
-   * get end position for last residue in sequence
-   * getEnd()>getStart() unless sequence only consists of gap characters
-   *
-   * @return 
+   * get end position for last residue in sequence getEnd()>getStart() unless
+   * sequence only consists of gap characters
+   * 
+   * @return
    */
   public int getEnd();
 
   /**
    * @return length of sequence including gaps
-
+   * 
    */
   public int getLength();
 
   /**
    * Replace the sequence with the given string
-   *
-   * @param sequence new sequence string
+   * 
+   * @param sequence
+   *                new sequence string
    */
   public void setSequence(String sequence);
 
@@ -93,154 +99,181 @@ public interface SequenceI
 
   /**
    * get a range on the seuqence as a string
-   * @param start DOCUMENT ME!
-   * @param end DOCUMENT ME!
-   *
+   * 
+   * @param start
+   *                DOCUMENT ME!
+   * @param end
+   *                DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   public String getSequenceAsString(int start, int end);
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public char[] getSequence();
 
   /**
    * get stretch of sequence characters in an array
-   *
-   * @param start absolute index into getSequence()
-   * @param end exclusive index of last position in segment to be returned.
-   *
+   * 
+   * @param start
+   *                absolute index into getSequence()
+   * @param end
+   *                exclusive index of last position in segment to be returned.
+   * 
    * @return char[max(0,end-start)];
    */
   public char[] getSequence(int start, int end);
 
   /**
    * create a new sequence object from start to end of this sequence
-   * @param start int
-   * @param end int
+   * 
+   * @param start
+   *                int
+   * @param end
+   *                int
    * @return SequenceI
    */
   public SequenceI getSubSequence(int start, int end);
 
   /**
    * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
-   *
+   * 
+   * @param i
+   *                DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   public char getCharAt(int i);
 
   /**
    * DOCUMENT ME!
-   *
-   * @param desc DOCUMENT ME!
+   * 
+   * @param desc
+   *                DOCUMENT ME!
    */
   public void setDescription(String desc);
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public String getDescription();
 
   /**
    * DOCUMENT ME!
-   *
-   * @param pos DOCUMENT ME!
-   *
+   * 
+   * @param pos
+   *                DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   public int findIndex(int pos);
 
   /**
    * Returns the sequence position for an alignment position
-   *
-   * @param i column index in alignment (from 1)
-   *
+   * 
+   * @param i
+   *                column index in alignment (from 1)
+   * 
    * @return residue number for residue (left of and) nearest ith column
    */
   public int findPosition(int i);
 
   /**
-   * Returns an int array where indices correspond to each residue in the sequence and the element value gives its position in the alignment
-   *
-   * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no residues in SequenceI object
+   * Returns an int array where indices correspond to each residue in the
+   * sequence and the element value gives its position in the alignment
+   * 
+   * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no
+   *         residues in SequenceI object
    */
   public int[] gapMap();
 
   /**
-   * Returns an int array where indices correspond to each position in
-   * sequence char array and the element value gives the result of findPosition
-   * for that index in the sequence.
+   * Returns an int array where indices correspond to each position in sequence
+   * char array and the element value gives the result of findPosition for that
+   * index in the sequence.
    * 
-   * @return int[SequenceI.getLength()] 
+   * @return int[SequenceI.getLength()]
    */
   public int[] findPositionMap();
+
   /**
-   * Delete a range of aligned sequence columns, creating a new dataset sequence if necessary
-   * and adjusting start and end positions accordingly.
-   *
-   * @param i first column in range to delete
-   * @param j last column in range to delete
+   * Delete a range of aligned sequence columns, creating a new dataset sequence
+   * if necessary and adjusting start and end positions accordingly.
+   * 
+   * @param i
+   *                first column in range to delete
+   * @param j
+   *                last column in range to delete
    */
   public void deleteChars(int i, int j);
 
   /**
    * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
-   * @param c DOCUMENT ME!
+   * 
+   * @param i
+   *                DOCUMENT ME!
+   * @param c
+   *                DOCUMENT ME!
    */
   public void insertCharAt(int i, char c);
 
   /**
    * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
-   * @param c DOCUMENT ME!
+   * 
+   * @param i
+   *                DOCUMENT ME!
+   * @param c
+   *                DOCUMENT ME!
    */
   public void insertCharAt(int i, int length, char c);
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public SequenceFeature[] getSequenceFeatures();
 
   /**
    * DOCUMENT ME!
-   *
-   * @param v DOCUMENT ME!
+   * 
+   * @param v
+   *                DOCUMENT ME!
    */
   public void setSequenceFeatures(SequenceFeature[] features);
 
   /**
    * DOCUMENT ME!
-   *
-   * @param id DOCUMENT ME!
+   * 
+   * @param id
+   *                DOCUMENT ME!
    */
   public void setPDBId(Vector ids);
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public Vector getPDBId();
 
   /**
    * add entry to the vector of PDBIds, if it isn't in the list already
+   * 
    * @param entry
    */
   public void addPDBId(PDBEntry entry);
+
   /**
-   * update the list of PDBEntrys to include any DBRefEntrys citing structural databases 
+   * update the list of PDBEntrys to include any DBRefEntrys citing structural
+   * databases
+   * 
    * @return true if PDBEntry list was modified
    */
   public boolean updatePDBIds();
@@ -254,9 +287,9 @@ public interface SequenceI
   public DBRefEntry[] getDBRef();
 
   /**
-   * add the given entry to the list of DBRefs for this sequence, 
-   * or replace a similar one if entry contains a map object 
-   * and the existing one doesnt. 
+   * add the given entry to the list of DBRefs for this sequence, or replace a
+   * similar one if entry contains a map object and the existing one doesnt.
+   * 
    * @param entry
    */
   public void addDBRef(DBRefEntry entry);
@@ -277,33 +310,43 @@ public interface SequenceI
 
   /**
    * Derive a sequence (using this one's dataset or as the dataset)
+   * 
    * @return duplicate sequence with valid dataset sequence
    */
   public SequenceI deriveSequence();
+
   /**
    * set the array of associated AlignmentAnnotation for this sequenceI
+   * 
    * @param revealed
    */
   public void setAlignmentAnnotation(AlignmentAnnotation[] annotation);
+
   /**
-   * Get one or more alignment annotations with a particular label.  
-   * @param label string which each returned annotation must have as a label.
+   * Get one or more alignment annotations with a particular label.
+   * 
+   * @param label
+   *                string which each returned annotation must have as a label.
    * @return null or array of annotations.
    */
   public AlignmentAnnotation[] getAnnotation(String label);
+
   /**
-   * create a new dataset sequence (if necessary) 
-   * for this sequence and sets this sequence to refer to it.
-   * This call will move any features or references on the sequence onto the dataset.
+   * create a new dataset sequence (if necessary) for this sequence and sets
+   * this sequence to refer to it. This call will move any features or
+   * references on the sequence onto the dataset.
+   * 
    * @return dataset sequence for this sequence
    */
   public SequenceI createDatasetSequence();
-  
+
   /**
-   * Transfer any database references or annotation from entry
-   * under a sequence mapping.
+   * Transfer any database references or annotation from entry under a sequence
+   * mapping.
+   * 
    * @param entry
-   * @param mp null or mapping from entry's numbering to local start/end
+   * @param mp
+   *                null or mapping from entry's numbering to local start/end
    */
   public void transferAnnotation(SequenceI entry, Mapping mp);
 
diff --git a/src/jalview/datamodel/SequenceNode.java b/src/jalview/datamodel/SequenceNode.java
index ca09301..ea3e515 100755
--- a/src/jalview/datamodel/SequenceNode.java
+++ b/src/jalview/datamodel/SequenceNode.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -22,12 +22,11 @@ import java.awt.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class SequenceNode
-    extends BinaryNode
+public class SequenceNode extends BinaryNode
 {
   /** DOCUMENT ME!! */
   public float dist;
@@ -46,6 +45,7 @@ public class SequenceNode
 
   /** DOCUMENT ME!! */
   public boolean dummy = false;
+
   private boolean placeholder = false;
 
   /**
@@ -58,13 +58,18 @@ public class SequenceNode
 
   /**
    * Creates a new SequenceNode object.
-   *
-   * @param val DOCUMENT ME!
-   * @param parent DOCUMENT ME!
-   * @param dist DOCUMENT ME!
-   * @param name DOCUMENT ME!
+   * 
+   * @param val
+   *                DOCUMENT ME!
+   * @param parent
+   *                DOCUMENT ME!
+   * @param dist
+   *                DOCUMENT ME!
+   * @param name
+   *                DOCUMENT ME!
    */
-  public SequenceNode(Object val, SequenceNode parent, float dist, String name)
+  public SequenceNode(Object val, SequenceNode parent, float dist,
+          String name)
   {
     super(val, parent, name);
     this.dist = dist;
@@ -72,16 +77,22 @@ public class SequenceNode
 
   /**
    * Creates a new SequenceNode object.
-   *
-   * @param val DOCUMENT ME!
-   * @param parent DOCUMENT ME!
-   * @param name DOCUMENT ME!
-   * @param dist DOCUMENT ME!
-   * @param bootstrap DOCUMENT ME!
-   * @param dummy DOCUMENT ME!
+   * 
+   * @param val
+   *                DOCUMENT ME!
+   * @param parent
+   *                DOCUMENT ME!
+   * @param name
+   *                DOCUMENT ME!
+   * @param dist
+   *                DOCUMENT ME!
+   * @param bootstrap
+   *                DOCUMENT ME!
+   * @param dummy
+   *                DOCUMENT ME!
    */
   public SequenceNode(Object val, SequenceNode parent, String name,
-                      float dist, int bootstrap, boolean dummy)
+          float dist, int bootstrap, boolean dummy)
   {
     super(val, parent, name);
     this.dist = dist;
@@ -90,15 +101,18 @@ public class SequenceNode
   }
 
   /**
-   * @param dummy true if node is created for the representation of polytomous trees
+   * @param dummy
+   *                true if node is created for the representation of polytomous
+   *                trees
    */
   public boolean isDummy()
   {
     return dummy;
   }
 
-  /* @param placeholder is true if the sequence refered to in the
-   *  element node is not actually present in the associated alignment
+  /*
+   * @param placeholder is true if the sequence refered to in the element node
+   * is not actually present in the associated alignment
    */
   public boolean isPlaceholder()
   {
@@ -107,9 +121,10 @@ public class SequenceNode
 
   /**
    * DOCUMENT ME!
-   *
-   * @param newstate DOCUMENT ME!
-   *
+   * 
+   * @param newstate
+   *                DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   public boolean setDummy(boolean newstate)
@@ -122,8 +137,9 @@ public class SequenceNode
 
   /**
    * DOCUMENT ME!
-   *
-   * @param Placeholder DOCUMENT ME!
+   * 
+   * @param Placeholder
+   *                DOCUMENT ME!
    */
   public void setPlaceholder(boolean Placeholder)
   {
@@ -132,7 +148,8 @@ public class SequenceNode
 
   /**
    * ascends the tree but doesn't stop until a non-dummy node is discovered.
-   * This will probably break if the tree is a mixture of BinaryNodes and SequenceNodes.
+   * This will probably break if the tree is a mixture of BinaryNodes and
+   * SequenceNodes.
    */
   public SequenceNode AscendTree()
   {
@@ -141,23 +158,25 @@ public class SequenceNode
     do
     {
       c = (SequenceNode) c.parent();
-    }
-    while ( (c != null) && c.dummy);
+    } while ((c != null) && c.dummy);
 
     return c;
   }
+
   /**
-   * test if this node has a name that might be a label rather than a bootstrap value
+   * test if this node has a name that might be a label rather than a bootstrap
+   * value
+   * 
    * @return true if node has a non-numeric label
    */
   public boolean isSequenceLabel()
   {
-    if (name!=null && name.length()>0)
+    if (name != null && name.length() > 0)
     {
-      for (int c=0,s=name.length(); c<s; c++)
+      for (int c = 0, s = name.length(); c < s; c++)
       {
         char q = name.charAt(c);
-        if ('0'<=q && q<='9')
+        if ('0' <= q && q <= '9')
           continue;
         return true;
       }
diff --git a/src/jalview/datamodel/SequencePoint.java b/src/jalview/datamodel/SequencePoint.java
index f105cc8..a8b0503 100755
--- a/src/jalview/datamodel/SequencePoint.java
+++ b/src/jalview/datamodel/SequencePoint.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -20,7 +20,7 @@ package jalview.datamodel;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
@@ -30,7 +30,8 @@ public class SequencePoint
   /**
    * for points with no real physical association with an alignment sequence
    */
-  public boolean isPlaceholder=false;
+  public boolean isPlaceholder = false;
+
   /**
    * Associated alignment sequence, or dummy sequence object.
    */
diff --git a/src/jalview/datamodel/UniprotEntry.java b/src/jalview/datamodel/UniprotEntry.java
index b963022..bd2c37c 100755
--- a/src/jalview/datamodel/UniprotEntry.java
+++ b/src/jalview/datamodel/UniprotEntry.java
@@ -1,93 +1,98 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.datamodel;
-
-import java.util.*;
-
-public class UniprotEntry
-{
-
-  UniprotSequence sequence;
-  Vector name;
-  Vector accession;
-  Vector feature;
-  Vector dbrefs;
-  UniprotProteinName protName;
-
-  public void setAccession(Vector items)
-  {
-    accession = items;
-  }
-
-  public void setFeature(Vector items)
-  {
-    feature = items;
-  }
-
-  public Vector getFeature()
-  {
-    return feature;
-  }
-
-  public Vector getAccession()
-  {
-    return accession;
-  }
-
-  public void setProtein(UniprotProteinName names)
-  {
-    protName = names;
-  }
-
-  public UniprotProteinName getProtein()
-  {
-    return protName;
-  }
-
-  public void setName(Vector na)
-  {
-    name = na;
-  }
-
-  public Vector getName()
-  {
-    return name;
-  }
-
-  public UniprotSequence getUniprotSequence()
-  {
-    return sequence;
-  }
-
-  public void setUniprotSequence(UniprotSequence seq)
-  {
-    sequence = seq;
-  }
-
-  public Vector getDbReference()
-  {
-    return dbrefs;
-  }
-
-  public void setDbReference(Vector dbref)
-  {
-    this.dbrefs = dbref;
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.datamodel;
+
+import java.util.*;
+
+public class UniprotEntry
+{
+
+  UniprotSequence sequence;
+
+  Vector name;
+
+  Vector accession;
+
+  Vector feature;
+
+  Vector dbrefs;
+
+  UniprotProteinName protName;
+
+  public void setAccession(Vector items)
+  {
+    accession = items;
+  }
+
+  public void setFeature(Vector items)
+  {
+    feature = items;
+  }
+
+  public Vector getFeature()
+  {
+    return feature;
+  }
+
+  public Vector getAccession()
+  {
+    return accession;
+  }
+
+  public void setProtein(UniprotProteinName names)
+  {
+    protName = names;
+  }
+
+  public UniprotProteinName getProtein()
+  {
+    return protName;
+  }
+
+  public void setName(Vector na)
+  {
+    name = na;
+  }
+
+  public Vector getName()
+  {
+    return name;
+  }
+
+  public UniprotSequence getUniprotSequence()
+  {
+    return sequence;
+  }
+
+  public void setUniprotSequence(UniprotSequence seq)
+  {
+    sequence = seq;
+  }
+
+  public Vector getDbReference()
+  {
+    return dbrefs;
+  }
+
+  public void setDbReference(Vector dbref)
+  {
+    this.dbrefs = dbref;
+  }
+
+}
diff --git a/src/jalview/datamodel/UniprotFile.java b/src/jalview/datamodel/UniprotFile.java
index b088ec2..6df0bad 100755
--- a/src/jalview/datamodel/UniprotFile.java
+++ b/src/jalview/datamodel/UniprotFile.java
@@ -1,36 +1,36 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.datamodel;
-
-import java.util.*;
-
-public class UniprotFile
-{
-  Vector _items;
-
-  public void setUniprotEntries(Vector items)
-  {
-    _items = items;
-  }
-
-  public Vector getUniprotEntries()
-  {
-    return _items;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.datamodel;
+
+import java.util.*;
+
+public class UniprotFile
+{
+  Vector _items;
+
+  public void setUniprotEntries(Vector items)
+  {
+    _items = items;
+  }
+
+  public Vector getUniprotEntries()
+  {
+    return _items;
+  }
+}
diff --git a/src/jalview/datamodel/UniprotProteinName.java b/src/jalview/datamodel/UniprotProteinName.java
index bb9a628..ebdf7d7 100755
--- a/src/jalview/datamodel/UniprotProteinName.java
+++ b/src/jalview/datamodel/UniprotProteinName.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
diff --git a/src/jalview/datamodel/UniprotSequence.java b/src/jalview/datamodel/UniprotSequence.java
index d5262e3..410f7b8 100755
--- a/src/jalview/datamodel/UniprotSequence.java
+++ b/src/jalview/datamodel/UniprotSequence.java
@@ -1,46 +1,46 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.datamodel;
-
-public class UniprotSequence
-{
-  /**
-   * internal content storage
-   */
-  private java.lang.String _content = "";
-
-  public void setContent(String seq)
-  {
-    StringBuffer sb = new StringBuffer();
-    for (int i = 0; i < seq.length(); i++)
-    {
-      if (seq.charAt(i) != ' ')
-      {
-        sb.append(seq.charAt(i));
-      }
-    }
-    _content = sb.toString();
-  }
-
-  public String getContent()
-  {
-    return _content;
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.datamodel;
+
+public class UniprotSequence
+{
+  /**
+   * internal content storage
+   */
+  private java.lang.String _content = "";
+
+  public void setContent(String seq)
+  {
+    StringBuffer sb = new StringBuffer();
+    for (int i = 0; i < seq.length(); i++)
+    {
+      if (seq.charAt(i) != ' ')
+      {
+        sb.append(seq.charAt(i));
+      }
+    }
+    _content = sb.toString();
+  }
+
+  public String getContent()
+  {
+    return _content;
+  }
+
+}
diff --git a/src/jalview/datamodel/xdb/embl/BasePosition.java b/src/jalview/datamodel/xdb/embl/BasePosition.java
index e0fe833..a3dffd1 100644
--- a/src/jalview/datamodel/xdb/embl/BasePosition.java
+++ b/src/jalview/datamodel/xdb/embl/BasePosition.java
@@ -1,30 +1,60 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.datamodel.xdb.embl;
 
-public class BasePosition {
-    String type;
-    String pos;
-    /**
-     * @return the pos
-     */
-    public String getPos() {
-        return pos;
-    }
-    /**
-     * @param pos the pos to set
-     */
-    public void setPos(String pos) {
-        this.pos = pos;
-    }
-    /**
-     * @return the type
-     */
-    public String getType() {
-        return type;
-    }
-    /**
-     * @param type the type to set
-     */
-    public void setType(String type) {
-        this.type = type;
-    }
+public class BasePosition
+{
+  String type;
+
+  String pos;
+
+  /**
+   * @return the pos
+   */
+  public String getPos()
+  {
+    return pos;
+  }
+
+  /**
+   * @param pos
+   *                the pos to set
+   */
+  public void setPos(String pos)
+  {
+    this.pos = pos;
+  }
+
+  /**
+   * @return the type
+   */
+  public String getType()
+  {
+    return type;
+  }
+
+  /**
+   * @param type
+   *                the type to set
+   */
+  public void setType(String type)
+  {
+    this.type = type;
+  }
 }
diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index d08ee0a..0cee0b4 100644
--- a/src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.datamodel.xdb.embl;
 
 import jalview.datamodel.DBRefEntry;
@@ -49,7 +67,7 @@ public class EmblEntry
 
   /**
    * @param accession
-   *          the accession to set
+   *                the accession to set
    */
   public void setAccession(String accession)
   {
@@ -66,7 +84,7 @@ public class EmblEntry
 
   /**
    * @param dbRefs
-   *          the dbRefs to set
+   *                the dbRefs to set
    */
   public void setDbRefs(Vector dbRefs)
   {
@@ -83,7 +101,7 @@ public class EmblEntry
 
   /**
    * @param desc
-   *          the desc to set
+   *                the desc to set
    */
   public void setDesc(String desc)
   {
@@ -100,7 +118,7 @@ public class EmblEntry
 
   /**
    * @param features
-   *          the features to set
+   *                the features to set
    */
   public void setFeatures(Vector features)
   {
@@ -117,7 +135,7 @@ public class EmblEntry
 
   /**
    * @param keywords
-   *          the keywords to set
+   *                the keywords to set
    */
   public void setKeywords(Vector keywords)
   {
@@ -134,7 +152,7 @@ public class EmblEntry
 
   /**
    * @param lastUpdated
-   *          the lastUpdated to set
+   *                the lastUpdated to set
    */
   public void setLastUpdated(String lastUpdated)
   {
@@ -151,7 +169,7 @@ public class EmblEntry
 
   /**
    * @param refs
-   *          the refs to set
+   *                the refs to set
    */
   public void setRefs(Vector refs)
   {
@@ -168,7 +186,7 @@ public class EmblEntry
 
   /**
    * @param releaseCreated
-   *          the releaseCreated to set
+   *                the releaseCreated to set
    */
   public void setRcreated(String releaseCreated)
   {
@@ -185,7 +203,7 @@ public class EmblEntry
 
   /**
    * @param releaseLastUpdated
-   *          the releaseLastUpdated to set
+   *                the releaseLastUpdated to set
    */
   public void setRLastUpdated(String releaseLastUpdated)
   {
@@ -202,7 +220,7 @@ public class EmblEntry
 
   /**
    * @param sequence
-   *          the sequence to set
+   *                the sequence to set
    */
   public void setSequence(EmblSequence sequence)
   {
@@ -219,7 +237,7 @@ public class EmblEntry
 
   /**
    * @param taxDivision
-   *          the taxDivision to set
+   *                the taxDivision to set
    */
   public void setTaxDivision(String taxDivision)
   {
@@ -236,7 +254,7 @@ public class EmblEntry
 
   /**
    * @param version
-   *          the version to set
+   *                the version to set
    */
   public void setVersion(String version)
   {
@@ -378,21 +396,24 @@ public class EmblEntry
    * Recover annotated sequences from EMBL file
    * 
    * @param noNa
-   *          don't return nucleic acid sequences
+   *                don't return nucleic acid sequences
    * @param sourceDb
-   *          TODO
+   *                TODO
    * @param noProtein
-   *          don't return any translated protein sequences marked in features
+   *                don't return any translated protein sequences marked in
+   *                features
    * @return dataset sequences with DBRefs and features - DNA always comes first
    */
   public jalview.datamodel.SequenceI[] getSequences(boolean noNa,
           boolean noPeptide, String sourceDb)
-  { //TODO: ensure emblEntry.getSequences behaves correctly for returning all cases of noNa and noPeptide
+  { // TODO: ensure emblEntry.getSequences behaves correctly for returning all
+    // cases of noNa and noPeptide
     Vector seqs = new Vector();
     Sequence dna = null;
     if (!noNa)
     {
-      // In theory we still need to create this if noNa is set to avoid a null pointer exception
+      // In theory we still need to create this if noNa is set to avoid a null
+      // pointer exception
       dna = new Sequence(sourceDb + "|" + accession, sequence.getSequence());
       dna.setDescription(desc);
       dna.addDBRef(new DBRefEntry(sourceDb, version, accession));
@@ -400,8 +421,8 @@ public class EmblEntry
       // TODO: transform EMBL Database refs to canonical form
       if (dbRefs != null)
         for (Iterator i = dbRefs.iterator(); i.hasNext(); dna
-        .addDBRef((DBRefEntry) i.next()))
-        ;
+                .addDBRef((DBRefEntry) i.next()))
+          ;
     }
     try
     {
@@ -435,8 +456,7 @@ public class EmblEntry
           }
         }
       }
-    } 
-    catch (Exception e)
+    } catch (Exception e)
     {
       System.err.println("EMBL Record Features parsing error!");
       System.err
@@ -459,14 +479,22 @@ public class EmblEntry
   }
 
   /**
-   * attempt to extract coding region and product from a feature and properly decorate it with annotations.
-   * @param feature coding feature
-   * @param sourceDb source database for the EMBLXML
-   * @param seqs place where sequences go
-   * @param dna parent dna sequence for this record
-   * @param noPeptide flag for generation of Peptide sequence objects
+   * attempt to extract coding region and product from a feature and properly
+   * decorate it with annotations.
+   * 
+   * @param feature
+   *                coding feature
+   * @param sourceDb
+   *                source database for the EMBLXML
+   * @param seqs
+   *                place where sequences go
+   * @param dna
+   *                parent dna sequence for this record
+   * @param noPeptide
+   *                flag for generation of Peptide sequence objects
    */
-  private void parseCodingFeature(EmblFeature feature, String sourceDb, Vector seqs, Sequence dna, boolean noPeptide)
+  private void parseCodingFeature(EmblFeature feature, String sourceDb,
+          Vector seqs, Sequence dna, boolean noPeptide)
   {
     boolean isEmblCdna = sourceDb.equals(DBRefSource.EMBLCDS);
     // extract coding region(s)
@@ -534,11 +562,11 @@ public class EmblEntry
         else
         {
           // throw anything else into the additional properties hash
-          String[] s= q.getValues();
+          String[] s = q.getValues();
           StringBuffer sb = new StringBuffer();
-          if (s!=null)
+          if (s != null)
           {
-            for (int i=0; i<s.length; i++)
+            for (int i = 0; i < s.length; i++)
             {
               sb.append(s[i]);
               sb.append("\n");
@@ -552,11 +580,13 @@ public class EmblEntry
     if (prseq != null && prname != null && prid != null)
     {
       // extract proteins.
-      product = new Sequence(prid
-              , prseq, prstart, prstart
-              + prseq.length() - 1);
-      product.setDescription(((prname.length()==0) ? "Protein Product from " + sourceDb : prname));
-      
+      product = new Sequence(prid, prseq, prstart, prstart + prseq.length()
+              - 1);
+      product
+              .setDescription(((prname.length() == 0) ? "Protein Product from "
+                      + sourceDb
+                      : prname));
+
       if (!noPeptide)
       {
         // Protein is also added to vector of sequences returned
@@ -575,17 +605,15 @@ public class EmblEntry
           // marked.
           exon = new int[]
           { dna.getStart(), dna.getEnd() };
-          map = new jalview.datamodel.Mapping(product, exon,
-                  new int[]
-                  { prstart, prstart + prseq.length() - 1 }, 3, 1);
+          map = new jalview.datamodel.Mapping(product, exon, new int[]
+          { prstart, prstart + prseq.length() - 1 }, 3, 1);
         }
         if ((prseq.length() + 1) * 3 == dna.getSequence().length)
         {
           exon = new int[]
           { dna.getStart(), dna.getEnd() - 3 };
-          map = new jalview.datamodel.Mapping(product, exon,
-                  new int[]
-                  { prstart, prstart + prseq.length() - 1 }, 3, 1);
+          map = new jalview.datamodel.Mapping(product, exon, new int[]
+          { prstart, prstart + prseq.length() - 1 }, 3, 1);
         }
       }
       else
@@ -594,25 +622,27 @@ public class EmblEntry
         {
           // TODO: Add a DbRef back to the parent EMBL sequence with the exon
           // map
-          // if given a dataset reference, search dataset for parent EMBL sequence if it exists and set its map
+          // if given a dataset reference, search dataset for parent EMBL
+          // sequence if it exists and set its map
           // make a new feature annotating the coding contig
         }
         else
         {
-          map = new jalview.datamodel.Mapping(product, exon,
-                  new int[]
-                  { prstart, prstart + prseq.length() - 1 }, 3, 1);
+          map = new jalview.datamodel.Mapping(product, exon, new int[]
+          { prstart, prstart + prseq.length() - 1 }, 3, 1);
           // reconstruct the EMBLCDS entry
           DBRefEntry pcdnaref = new DBRefEntry();
           pcdnaref.setAccessionId(prid);
           pcdnaref.setSource(DBRefSource.EMBLCDS);
           pcdnaref.setVersion(getVersion()); // same as parent EMBL version.
           jalview.util.MapList mp = new jalview.util.MapList(new int[]
-          { 1+(prstart-1)*3, 1+(prstart-1)*3 + (prseq.length()-1)*3 }, new int[] { prstart, prstart+prseq.length() - 1 }, 3, 1);
+          { 1 + (prstart - 1) * 3,
+              1 + (prstart - 1) * 3 + (prseq.length() - 1) * 3 }, new int[]
+          { prstart, prstart + prseq.length() - 1 }, 3, 1);
           pcdnaref.setMap(new Mapping(mp));
-          if (product!=null)
+          if (product != null)
             product.addDBRef(pcdnaref);
-          
+
         }
       }
       // add cds feature to dna seq - this may include the stop codon
@@ -623,8 +653,8 @@ public class EmblEntry
         sf.setEnd(exon[xint + 1]);
         sf.setType(feature.getName());
         sf.setFeatureGroup(sourceDb);
-        sf.setDescription("Exon " + (1 + (int)(xint/2)) + " for protein '"
-                + prname + "' EMBLCDS:" + prid);
+        sf.setDescription("Exon " + (1 + (int) (xint / 2))
+                + " for protein '" + prname + "' EMBLCDS:" + prid);
         sf.setValue(FeatureProperties.EXONPOS, new Integer(1 + xint));
         sf.setValue(FeatureProperties.EXONPRODUCT, prname);
         if (vals != null && vals.size() > 0)
@@ -649,23 +679,26 @@ public class EmblEntry
         ref.setSource(jalview.util.DBRefUtils.getCanonicalName(ref
                 .getSource()));
         // Hard code the kind of protein product accessions that EMBL cite
-        if (ref.getSource().equals(
-                jalview.datamodel.DBRefSource.UNIPROT))
+        if (ref.getSource().equals(jalview.datamodel.DBRefSource.UNIPROT))
         {
           ref.setMap(map);
-          if (map!=null && map.getTo()!=null)
+          if (map != null && map.getTo() != null)
           {
-            map.getTo().addDBRef(new DBRefEntry(ref.getSource(), ref.getVersion(), ref.getAccessionId())); // don't copy map over.
-            if (map.getTo().getName().indexOf(prid)==0)
+            map.getTo().addDBRef(
+                    new DBRefEntry(ref.getSource(), ref.getVersion(), ref
+                            .getAccessionId())); // don't copy map over.
+            if (map.getTo().getName().indexOf(prid) == 0)
             {
-              map.getTo().setName(jalview.datamodel.DBRefSource.UNIPROT+"|"+ref.getAccessionId());
+              map.getTo().setName(
+                      jalview.datamodel.DBRefSource.UNIPROT + "|"
+                              + ref.getAccessionId());
             }
           }
         }
         if (product != null)
         {
           DBRefEntry pref = new DBRefEntry(ref.getSource(), ref
-                .getVersion(), ref.getAccessionId());
+                  .getVersion(), ref.getAccessionId());
           pref.setMap(null); // reference is direct
           product.addDBRef(pref);
           // Add converse mapping reference
@@ -675,7 +708,7 @@ public class EmblEntry
             pref = new DBRefEntry(sourceDb, getVersion(), this
                     .getAccession());
             pref.setMap(pmap);
-            if (map.getTo()!=null)
+            if (map.getTo() != null)
             {
               map.getTo().addDBRef(pref);
             }
diff --git a/src/jalview/datamodel/xdb/embl/EmblError.java b/src/jalview/datamodel/xdb/embl/EmblError.java
index 3db5eca..ee76978 100644
--- a/src/jalview/datamodel/xdb/embl/EmblError.java
+++ b/src/jalview/datamodel/xdb/embl/EmblError.java
@@ -1,19 +1,41 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.datamodel.xdb.embl;
 
-public class EmblError {
-    String accession;
+public class EmblError
+{
+  String accession;
 
-    /**
-     * @return the accession
-     */
-    public String getAccession() {
-        return accession;
-    }
+  /**
+   * @return the accession
+   */
+  public String getAccession()
+  {
+    return accession;
+  }
 
-    /**
-     * @param accession the accession to set
-     */
-    public void setAccession(String accession) {
-        this.accession = accession;
-    }
+  /**
+   * @param accession
+   *                the accession to set
+   */
+  public void setAccession(String accession)
+  {
+    this.accession = accession;
+  }
 }
diff --git a/src/jalview/datamodel/xdb/embl/EmblFeature.java b/src/jalview/datamodel/xdb/embl/EmblFeature.java
index e2997fb..091846e 100644
--- a/src/jalview/datamodel/xdb/embl/EmblFeature.java
+++ b/src/jalview/datamodel/xdb/embl/EmblFeature.java
@@ -1,58 +1,101 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.datamodel.xdb.embl;
+
 import java.util.Hashtable;
 import java.util.Vector;
-public class EmblFeature {
-    String name;
-    Vector dbRefs;
-    Vector qualifiers;
-    Vector locations;
-    
-    /**
-     * @return the dbRefs
-     */
-    public Vector getDbRefs() {
-        return dbRefs;
-    }
-    /**
-     * @param dbRefs the dbRefs to set
-     */
-    public void setDbRefs(Vector dbRefs) {
-        this.dbRefs = dbRefs;
-    }
-    /**
-     * @return the locations
-     */
-    public Vector getLocations() {
-        return locations;
-    }
-    /**
-     * @param locations the locations to set
-     */
-    public void setLocations(Vector locations) {
-        this.locations = locations;
-    }
-    /**
-     * @return the name
-     */
-    public String getName() {
-        return name;
-    }
-    /**
-     * @param name the name to set
-     */
-    public void setName(String name) {
-        this.name = name;
-    }
-    /**
-     * @return the qualifiers
-     */
-    public Vector getQualifiers() {
-        return qualifiers;
-    }
-    /**
-     * @param qualifiers the qualifiers to set
-     */
-    public void setQualifiers(Vector qualifiers) {
-        this.qualifiers = qualifiers;
-    }
+
+public class EmblFeature
+{
+  String name;
+
+  Vector dbRefs;
+
+  Vector qualifiers;
+
+  Vector locations;
+
+  /**
+   * @return the dbRefs
+   */
+  public Vector getDbRefs()
+  {
+    return dbRefs;
+  }
+
+  /**
+   * @param dbRefs
+   *                the dbRefs to set
+   */
+  public void setDbRefs(Vector dbRefs)
+  {
+    this.dbRefs = dbRefs;
+  }
+
+  /**
+   * @return the locations
+   */
+  public Vector getLocations()
+  {
+    return locations;
+  }
+
+  /**
+   * @param locations
+   *                the locations to set
+   */
+  public void setLocations(Vector locations)
+  {
+    this.locations = locations;
+  }
+
+  /**
+   * @return the name
+   */
+  public String getName()
+  {
+    return name;
+  }
+
+  /**
+   * @param name
+   *                the name to set
+   */
+  public void setName(String name)
+  {
+    this.name = name;
+  }
+
+  /**
+   * @return the qualifiers
+   */
+  public Vector getQualifiers()
+  {
+    return qualifiers;
+  }
+
+  /**
+   * @param qualifiers
+   *                the qualifiers to set
+   */
+  public void setQualifiers(Vector qualifiers)
+  {
+    this.qualifiers = qualifiers;
+  }
 }
diff --git a/src/jalview/datamodel/xdb/embl/EmblFeatureLocElement.java b/src/jalview/datamodel/xdb/embl/EmblFeatureLocElement.java
index 09d27fe..4df9f67 100644
--- a/src/jalview/datamodel/xdb/embl/EmblFeatureLocElement.java
+++ b/src/jalview/datamodel/xdb/embl/EmblFeatureLocElement.java
@@ -1,70 +1,117 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.datamodel.xdb.embl;
 
-public class EmblFeatureLocElement {
-        String type;
-        String accession;
-        String version;
-        boolean complement;
-        BasePosition basePositions[]; 
-        /**
-         * @return the accession
-         */
-        public String getAccession() {
-            return accession;
-        }
-        /**
-         * @param accession the accession to set
-         */
-        public void setAccession(String accession) {
-            this.accession = accession;
-        }
-        /**
-         * @return the basePositions
-         */
-        public BasePosition[] getBasePositions() {
-            return basePositions;
-        }
-        /**
-         * @param basePositions the basePositions to set
-         */
-        public void setBasePositions(BasePosition[] basePositions) {
-            this.basePositions = basePositions;
-        }
-        /**
-         * @return the complement
-         */
-        public boolean isComplement() {
-            return complement;
-        }
-        /**
-         * @param complement the complement to set
-         */
-        public void setComplement(boolean complement) {
-            this.complement = complement;
-        }
-        /**
-         * @return the type
-         */
-        public String getType() {
-            return type;
-        }
-        /**
-         * @param type the type to set
-         */
-        public void setType(String type) {
-            this.type = type;
-        }
-        /**
-         * @return the version
-         */
-        public String getVersion() {
-            return version;
-        }
-        /**
-         * @param version the version to set
-         */
-        public void setVersion(String version) {
-            this.version = version;
-        }
-    }
-    
+public class EmblFeatureLocElement
+{
+  String type;
+
+  String accession;
+
+  String version;
+
+  boolean complement;
+
+  BasePosition basePositions[];
+
+  /**
+   * @return the accession
+   */
+  public String getAccession()
+  {
+    return accession;
+  }
+
+  /**
+   * @param accession
+   *                the accession to set
+   */
+  public void setAccession(String accession)
+  {
+    this.accession = accession;
+  }
+
+  /**
+   * @return the basePositions
+   */
+  public BasePosition[] getBasePositions()
+  {
+    return basePositions;
+  }
+
+  /**
+   * @param basePositions
+   *                the basePositions to set
+   */
+  public void setBasePositions(BasePosition[] basePositions)
+  {
+    this.basePositions = basePositions;
+  }
+
+  /**
+   * @return the complement
+   */
+  public boolean isComplement()
+  {
+    return complement;
+  }
+
+  /**
+   * @param complement
+   *                the complement to set
+   */
+  public void setComplement(boolean complement)
+  {
+    this.complement = complement;
+  }
+
+  /**
+   * @return the type
+   */
+  public String getType()
+  {
+    return type;
+  }
+
+  /**
+   * @param type
+   *                the type to set
+   */
+  public void setType(String type)
+  {
+    this.type = type;
+  }
+
+  /**
+   * @return the version
+   */
+  public String getVersion()
+  {
+    return version;
+  }
+
+  /**
+   * @param version
+   *                the version to set
+   */
+  public void setVersion(String version)
+  {
+    this.version = version;
+  }
+}
diff --git a/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java b/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
index 0341ec3..2444592 100644
--- a/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
+++ b/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
@@ -1,112 +1,169 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.datamodel.xdb.embl;
 
 import java.util.Enumeration;
 import java.util.Iterator;
 import java.util.Vector;
 
-public class EmblFeatureLocations {
-    Vector locElements;
-    String locationType;
-    boolean locationComplement;
-    /**
-     * @return the locationComplement
-     */
-    public boolean isLocationComplement() {
-        return locationComplement;
-    }
-    /**
-     * @param locationComplement the locationComplement to set
-     */
-    public void setLocationComplement(boolean locationComplement) {
-        this.locationComplement = locationComplement;
-    }
-    /**
-     * @return the locationType
-     */
-    public String getLocationType() {
-        return locationType;
-    }
-    /**
-     * @param locationType the locationType to set
-     */
-    public void setLocationType(String locationType) {
-        this.locationType = locationType;
-    }
-    /**
-     * @return the locElements
-     */
-    public Vector getLocElements() {
-        return locElements;
-    }
-    /**
-     * @param locElements the locElements to set
-     */
-    public void setLocElements(Vector locElements) {
-        this.locElements = locElements;
-    }
-    /**
-     * Return all location elements as start-end pairs (without accessions)  
-     * TODO: pass back complement and 'less than or more than' range information
-     * Note: do not use this since it throws away any accessionIds associated with
-     * each location!
-     * @return int[] { start1, end1, ... }
-     */
-    public int[] getElementRanges() {
-      return getElementRanges(null);
-    }
-    /**
-     * Return all location elements concerning given accession as start-end pairs  
-     * TODO: pass back complement and 'less than or more than' range information
-     * TODO: deal with multiple accessions
-     * @param accession the accession string for which locations are requested, or null for all locations
-     * @return null or int[] { start1, end1, ... }
-     */
-    
-    public int[] getElementRanges(String accession)
+public class EmblFeatureLocations
+{
+  Vector locElements;
+
+  String locationType;
+
+  boolean locationComplement;
+
+  /**
+   * @return the locationComplement
+   */
+  public boolean isLocationComplement()
+  {
+    return locationComplement;
+  }
+
+  /**
+   * @param locationComplement
+   *                the locationComplement to set
+   */
+  public void setLocationComplement(boolean locationComplement)
+  {
+    this.locationComplement = locationComplement;
+  }
+
+  /**
+   * @return the locationType
+   */
+  public String getLocationType()
+  {
+    return locationType;
+  }
+
+  /**
+   * @param locationType
+   *                the locationType to set
+   */
+  public void setLocationType(String locationType)
+  {
+    this.locationType = locationType;
+  }
+
+  /**
+   * @return the locElements
+   */
+  public Vector getLocElements()
+  {
+    return locElements;
+  }
+
+  /**
+   * @param locElements
+   *                the locElements to set
+   */
+  public void setLocElements(Vector locElements)
+  {
+    this.locElements = locElements;
+  }
+
+  /**
+   * Return all location elements as start-end pairs (without accessions) TODO:
+   * pass back complement and 'less than or more than' range information Note:
+   * do not use this since it throws away any accessionIds associated with each
+   * location!
+   * 
+   * @return int[] { start1, end1, ... }
+   */
+  public int[] getElementRanges()
+  {
+    return getElementRanges(null);
+  }
+
+  /**
+   * Return all location elements concerning given accession as start-end pairs
+   * TODO: pass back complement and 'less than or more than' range information
+   * TODO: deal with multiple accessions
+   * 
+   * @param accession
+   *                the accession string for which locations are requested, or
+   *                null for all locations
+   * @return null or int[] { start1, end1, ... }
+   */
+
+  public int[] getElementRanges(String accession)
+  {
+    int sepos = 0;
+    int[] se = new int[locElements.size() * 2];
+    if (locationType.equalsIgnoreCase("single"))
     {
-      int sepos=0;
-      int[] se = new int[locElements.size()*2];
-      if (locationType.equalsIgnoreCase("single")) {
-        for (Enumeration le=locElements.elements();le.hasMoreElements();) {
-            EmblFeatureLocElement loce = (EmblFeatureLocElement) le.nextElement();
-            if (accession==null || loce.accession!=null && accession.equals(loce.accession))
-            {
-              BasePosition bp[] = loce.getBasePositions();
-              if (bp.length==2) {
-                se[sepos++] = Integer.parseInt(bp[0].getPos());
-                se[sepos++] = Integer.parseInt(bp[1].getPos());
-              }
-            }
+      for (Enumeration le = locElements.elements(); le.hasMoreElements();)
+      {
+        EmblFeatureLocElement loce = (EmblFeatureLocElement) le
+                .nextElement();
+        if (accession == null || loce.accession != null
+                && accession.equals(loce.accession))
+        {
+          BasePosition bp[] = loce.getBasePositions();
+          if (bp.length == 2)
+          {
+            se[sepos++] = Integer.parseInt(bp[0].getPos());
+            se[sepos++] = Integer.parseInt(bp[1].getPos());
+          }
         }
-    } else 
-    if (locationType.equalsIgnoreCase("join")) {
-        for (Enumeration le=locElements.elements();le.hasMoreElements();) {
-          EmblFeatureLocElement loce = (EmblFeatureLocElement) le.nextElement();
-          if (accession==null || loce.accession!=null && accession.equals(loce.accession))
+      }
+    }
+    else if (locationType.equalsIgnoreCase("join"))
+    {
+      for (Enumeration le = locElements.elements(); le.hasMoreElements();)
+      {
+        EmblFeatureLocElement loce = (EmblFeatureLocElement) le
+                .nextElement();
+        if (accession == null || loce.accession != null
+                && accession.equals(loce.accession))
+        {
+          BasePosition bp[] = loce.getBasePositions();
+          if (bp.length == 2)
           {
-            BasePosition bp[] = loce.getBasePositions();
-            if (bp.length==2) {
-                se[sepos++] = Integer.parseInt(bp[0].getPos());
-                se[sepos++] = Integer.parseInt(bp[1].getPos());
-            }
+            se[sepos++] = Integer.parseInt(bp[0].getPos());
+            se[sepos++] = Integer.parseInt(bp[1].getPos());
           }
         }
-        return se;
-    } else
-    if (locationType!=null)
+      }
+      return se;
+    }
+    else if (locationType != null)
     {
-      if (jalview.bin.Cache.log!=null)
-        jalview.bin.Cache.log.error("EmbleFeatureLocations.getElementRanges cannot deal with locationType=='"+locationType+"'");
+      if (jalview.bin.Cache.log != null)
+        jalview.bin.Cache.log
+                .error("EmbleFeatureLocations.getElementRanges cannot deal with locationType=='"
+                        + locationType + "'");
       else
-        System.err.println("EmbleFeatureLocations.getElementRanges cannot deal with locationType=='"+locationType+"'");
+        System.err
+                .println("EmbleFeatureLocations.getElementRanges cannot deal with locationType=='"
+                        + locationType + "'");
     }
     // trim range if necessary.
-    if (se!=null && sepos!=se.length)
+    if (se != null && sepos != se.length)
     {
       int[] trimmed = new int[sepos];
-      System.arraycopy(se,0,trimmed, 0, sepos);
+      System.arraycopy(se, 0, trimmed, 0, sepos);
       se = trimmed;
     }
     return se;
-    }
-}
\ No newline at end of file
+  }
+}
diff --git a/src/jalview/datamodel/xdb/embl/EmblFile.java b/src/jalview/datamodel/xdb/embl/EmblFile.java
index 691cbad..8421aad 100644
--- a/src/jalview/datamodel/xdb/embl/EmblFile.java
+++ b/src/jalview/datamodel/xdb/embl/EmblFile.java
@@ -1,6 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.datamodel.xdb.embl;
 
-
 import java.io.File;
 import java.io.FileReader;
 import java.io.Reader;
@@ -9,93 +26,119 @@ import java.util.Vector;
 import org.exolab.castor.mapping.Mapping;
 import org.exolab.castor.xml.Unmarshaller;
 
-public class EmblFile {
-    Vector entries;
-    Vector errors;
-    /**
-     * @return the entries
-     */
-    public Vector getEntries() {
-        return entries;
-    }
-    /**
-     * @param entries the entries to set
-     */
-    public void setEntries(Vector entries) {
-        this.entries = entries;
-    }
-    /**
-     * @return the errors
-     */
-    public Vector getErrors() {
-        return errors;
-    }
-    /**
-     * @param errors the errors to set
-     */
-    public void setErrors(Vector errors) {
-        this.errors = errors;
-    }
-    /**
-     * Parse an EmblXML file into an EmblFile object
-     * @param file
-     * @return parsed EmblXML or null if exceptions were raised
-     */
-    public static EmblFile getEmblFile(File file)
+public class EmblFile
+{
+  Vector entries;
+
+  Vector errors;
+
+  /**
+   * @return the entries
+   */
+  public Vector getEntries()
+  {
+    return entries;
+  }
+
+  /**
+   * @param entries
+   *                the entries to set
+   */
+  public void setEntries(Vector entries)
+  {
+    this.entries = entries;
+  }
+
+  /**
+   * @return the errors
+   */
+  public Vector getErrors()
+  {
+    return errors;
+  }
+
+  /**
+   * @param errors
+   *                the errors to set
+   */
+  public void setErrors(Vector errors)
+  {
+    this.errors = errors;
+  }
+
+  /**
+   * Parse an EmblXML file into an EmblFile object
+   * 
+   * @param file
+   * @return parsed EmblXML or null if exceptions were raised
+   */
+  public static EmblFile getEmblFile(File file)
+  {
+    if (file == null)
+      return null;
+    try
     {
-        if (file==null)
-            return null;
-        try {
-            return EmblFile.getEmblFile(new FileReader(file));
-        }
-        catch (Exception e) {
-            System.err.println("Exception whilst reading EMBLfile from "+file);
-            e.printStackTrace(System.err);
-        }
-        return null;
+      return EmblFile.getEmblFile(new FileReader(file));
+    } catch (Exception e)
+    {
+      System.err.println("Exception whilst reading EMBLfile from " + file);
+      e.printStackTrace(System.err);
     }
-    public static EmblFile getEmblFile(Reader file) {
-        EmblFile record = new EmblFile();
-        try
-        {
-          // 1. Load the mapping information from the file
-          Mapping map = new Mapping(record.getClass().getClassLoader());
-          java.net.URL url = record.getClass().getResource("/embl_mapping.xml");
-          map.loadMapping(url);
+    return null;
+  }
 
-          // 2. Unmarshal the data
-          Unmarshaller unmar = new Unmarshaller(record);
-          try {
-              // uncomment to DEBUG EMBLFile reading 
-            if (((String)jalview.bin.Cache.getDefault(jalview.bin.Cache.CASTORLOGLEVEL, "debug")).equalsIgnoreCase("DEBUG")
-                    ) unmar.setDebug(jalview.bin.Cache.log.isDebugEnabled());
-          } catch (Exception e) {};
-          unmar.setIgnoreExtraElements(true);
-          unmar.setMapping(map);
+  public static EmblFile getEmblFile(Reader file)
+  {
+    EmblFile record = new EmblFile();
+    try
+    {
+      // 1. Load the mapping information from the file
+      Mapping map = new Mapping(record.getClass().getClassLoader());
+      java.net.URL url = record.getClass().getResource("/embl_mapping.xml");
+      map.loadMapping(url);
 
-          record = (EmblFile) unmar.unmarshal(file);
-        }
-        catch (Exception e)
-        {
-          e.printStackTrace(System.err);
-          record=null;
-        }
+      // 2. Unmarshal the data
+      Unmarshaller unmar = new Unmarshaller(record);
+      try
+      {
+        // uncomment to DEBUG EMBLFile reading
+        if (((String) jalview.bin.Cache.getDefault(
+                jalview.bin.Cache.CASTORLOGLEVEL, "debug"))
+                .equalsIgnoreCase("DEBUG"))
+          unmar.setDebug(jalview.bin.Cache.log.isDebugEnabled());
+      } catch (Exception e)
+      {
+      }
+      ;
+      unmar.setIgnoreExtraElements(true);
+      unmar.setMapping(map);
 
+      record = (EmblFile) unmar.unmarshal(file);
+    } catch (Exception e)
+    {
+      e.printStackTrace(System.err);
+      record = null;
+    }
 
-        return record;
-      }
-    public static void main(String args[]) {
-      File mf = null; 
-        if (args.length==1)
-        {
-          mf = new File(args[0]);
-        }
-        if (!mf.exists())
-        {
-          mf = new File("C:\\Documents and Settings\\JimP\\workspace-3.2\\Jalview Release\\schemas\\embleRecordV1.1.xml");    
-        }
-        EmblFile myfile = EmblFile.getEmblFile(mf);
-        if (myfile!=null && myfile.entries!=null && myfile.entries.size()>0)
-            System.out.println(myfile.entries.size()+" Records read. ("+mf+")");
-        }
+    return record;
+  }
+
+  public static void main(String args[])
+  {
+    File mf = null;
+    if (args.length == 1)
+    {
+      mf = new File(args[0]);
+    }
+    if (!mf.exists())
+    {
+      mf = new File(
+              "C:\\Documents and Settings\\JimP\\workspace-3.2\\Jalview Release\\schemas\\embleRecordV1.1.xml");
+    }
+    EmblFile myfile = EmblFile.getEmblFile(mf);
+    if (myfile != null && myfile.entries != null
+            && myfile.entries.size() > 0)
+      System.out.println(myfile.entries.size() + " Records read. (" + mf
+              + ")");
+  }
 }
diff --git a/src/jalview/datamodel/xdb/embl/EmblSequence.java b/src/jalview/datamodel/xdb/embl/EmblSequence.java
index c68bcc5..5bdae54 100644
--- a/src/jalview/datamodel/xdb/embl/EmblSequence.java
+++ b/src/jalview/datamodel/xdb/embl/EmblSequence.java
@@ -1,43 +1,79 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.datamodel.xdb.embl;
 
-public class EmblSequence {
-    String version;
-    String sequence;
-    String type;
-    /**
-     * @return the sequence
-     */
-    public String getSequence() {
-        return sequence;
-    }
-    /**
-     * @param sequence the sequence to set
-     */
-    public void setSequence(String sequence) {
-        this.sequence = sequence;
-    }
-    /**
-     * @return the type
-     */
-    public String getType() {
-        return type;
-    }
-    /**
-     * @param type the type to set
-     */
-    public void setType(String type) {
-        this.type = type;
-    }
-    /**
-     * @return the version
-     */
-    public String getVersion() {
-        return version;
-    }
-    /**
-     * @param version the version to set
-     */
-    public void setVersion(String version) {
-        this.version = version;
-    }
+public class EmblSequence
+{
+  String version;
+
+  String sequence;
+
+  String type;
+
+  /**
+   * @return the sequence
+   */
+  public String getSequence()
+  {
+    return sequence;
+  }
+
+  /**
+   * @param sequence
+   *                the sequence to set
+   */
+  public void setSequence(String sequence)
+  {
+    this.sequence = sequence;
+  }
+
+  /**
+   * @return the type
+   */
+  public String getType()
+  {
+    return type;
+  }
+
+  /**
+   * @param type
+   *                the type to set
+   */
+  public void setType(String type)
+  {
+    this.type = type;
+  }
+
+  /**
+   * @return the version
+   */
+  public String getVersion()
+  {
+    return version;
+  }
+
+  /**
+   * @param version
+   *                the version to set
+   */
+  public void setVersion(String version)
+  {
+    this.version = version;
+  }
 }
diff --git a/src/jalview/datamodel/xdb/embl/Qualifier.java b/src/jalview/datamodel/xdb/embl/Qualifier.java
index 37a0239..27806ff 100644
--- a/src/jalview/datamodel/xdb/embl/Qualifier.java
+++ b/src/jalview/datamodel/xdb/embl/Qualifier.java
@@ -1,73 +1,109 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.datamodel.xdb.embl;
 
-public class Qualifier {
-    String name;
-    String[] values;
-    String[] evidence;
-    /**
-     * @return the name
-     */
-    public String getName() {
-        return name;
-    }
-    /**
-     * @param name the name to set
-     */
-    public void setName(String name) {
-        this.name = name;
-    }
-    /**
-     * @return the values
-     */
-    public String[] getValues() {
-        return values;
-    }
-    /**
-     * @param values the values to set
-     */
-    public void setValues(String[] values) {
-        this.values = values;
-    }
-    public void addEvidence(String qevidence)
+public class Qualifier
+{
+  String name;
+
+  String[] values;
+
+  String[] evidence;
+
+  /**
+   * @return the name
+   */
+  public String getName()
+  {
+    return name;
+  }
+
+  /**
+   * @param name
+   *                the name to set
+   */
+  public void setName(String name)
+  {
+    this.name = name;
+  }
+
+  /**
+   * @return the values
+   */
+  public String[] getValues()
+  {
+    return values;
+  }
+
+  /**
+   * @param values
+   *                the values to set
+   */
+  public void setValues(String[] values)
+  {
+    this.values = values;
+  }
+
+  public void addEvidence(String qevidence)
+  {
+    if (evidence == null)
     {
-      if (evidence==null)
-      {
-        evidence = new String[1];
-      }
-      else
-      {
-        String[] temp = new String[evidence.length+1];
-        System.arraycopy(evidence,0,temp,0,evidence.length);
-        evidence = temp;
-      }
-      evidence[evidence.length-1] = qevidence;
+      evidence = new String[1];
     }
-    public void addValues(String value)
+    else
     {
-      if (values==null)
-      {
-        values = new String[1];
-      }
-      else
-      {
-        String[] temp = new String[values.length+1];
-        System.arraycopy(values,0,temp,0,values.length);
-        values = temp;
-      }
-      values[values.length-1] = value;
+      String[] temp = new String[evidence.length + 1];
+      System.arraycopy(evidence, 0, temp, 0, evidence.length);
+      evidence = temp;
     }
-    /**
-     * @return the evidence
-     */
-    public String[] getEvidence()
+    evidence[evidence.length - 1] = qevidence;
+  }
+
+  public void addValues(String value)
+  {
+    if (values == null)
     {
-      return evidence;
+      values = new String[1];
     }
-    /**
-     * @param evidence the evidence to set
-     */
-    public void setEvidence(String[] evidence)
+    else
     {
-      this.evidence = evidence;
+      String[] temp = new String[values.length + 1];
+      System.arraycopy(values, 0, temp, 0, values.length);
+      values = temp;
     }
+    values[values.length - 1] = value;
+  }
+
+  /**
+   * @return the evidence
+   */
+  public String[] getEvidence()
+  {
+    return evidence;
+  }
+
+  /**
+   * @param evidence
+   *                the evidence to set
+   */
+  public void setEvidence(String[] evidence)
+  {
+    this.evidence = evidence;
+  }
 }
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 648f94c..7adbd07 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,19 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Softwarechang
+ * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
 package jalview.gui;
@@ -40,62 +40,63 @@ import jalview.ws.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class AlignFrame
-    extends GAlignFrame implements DropTargetListener, IProgressIndicator
+public class AlignFrame extends GAlignFrame implements DropTargetListener,
+        IProgressIndicator
 {
   /** DOCUMENT ME!! */
   public static final int DEFAULT_WIDTH = 700;
 
   /** DOCUMENT ME!! */
   public static final int DEFAULT_HEIGHT = 500;
+
   public AlignmentPanel alignPanel;
 
   AlignViewport viewport;
 
   Vector alignPanels = new Vector();
 
-
-  /** 
-   * Last format used to load or save alignments in this window 
+  /**
+   * Last format used to load or save alignments in this window
    */
   String currentFileFormat = null;
+
   /**
    * Current filename for this alignment
    */
   String fileName = null;
 
-  
-
-
   /**
    * Creates a new AlignFrame object.
-   *
-   * @param al DOCUMENT ME!
+   * 
+   * @param al
+   *                DOCUMENT ME!
    */
   public AlignFrame(AlignmentI al, int width, int height)
   {
     this(al, null, width, height);
   }
 
-
   /**
    * new alignment window with hidden columns
-   * @param al AlignmentI
-   * @param hiddenColumns ColumnSelection or null
+   * 
+   * @param al
+   *                AlignmentI
+   * @param hiddenColumns
+   *                ColumnSelection or null
    */
   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
-                    int width, int height)
+          int width, int height)
   {
     this.setSize(width, height);
     viewport = new AlignViewport(al, hiddenColumns);
 
     alignPanel = new AlignmentPanel(this, viewport);
 
-    if(al.getDataset()==null)
+    if (al.getDataset() == null)
     {
       al.setDataset(null);
     }
@@ -106,8 +107,11 @@ public class AlignFrame
 
   /**
    * Make a new AlignFrame from exisiting alignmentPanels
-   * @param ap AlignmentPanel
-   * @param av AlignViewport
+   * 
+   * @param ap
+   *                AlignmentPanel
+   * @param av
+   *                AlignViewport
    */
   public AlignFrame(AlignmentPanel ap)
   {
@@ -124,12 +128,13 @@ public class AlignFrame
       BLOSUM62Colour.setEnabled(false);
       conservationMenuItem.setEnabled(false);
       modifyConservation.setEnabled(false);
-    //  PIDColour.setEnabled(false);
-    //  abovePIDThreshold.setEnabled(false);
-    //  modifyPID.setEnabled(false);
+      // PIDColour.setEnabled(false);
+      // abovePIDThreshold.setEnabled(false);
+      // modifyPID.setEnabled(false);
     }
 
-    String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
+    String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
+            "No sort");
 
     if (sortby.equals("Id"))
     {
@@ -141,279 +146,270 @@ public class AlignFrame
     }
 
     if (Desktop.desktop != null)
-   {
-     this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
-     addServiceListeners();
-     setGUINucleotide(viewport.alignment.isNucleotide());
-   }
+    {
+      this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
+      addServiceListeners();
+      setGUINucleotide(viewport.alignment.isNucleotide());
+    }
 
-   setMenusFromViewport(viewport);
-   buildSortByAnnotationScoresMenu();
-   if (viewport.wrapAlignment)
-   {
-     wrapMenuItem_actionPerformed(null);
-   }
+    setMenusFromViewport(viewport);
+    buildSortByAnnotationScoresMenu();
+    if (viewport.wrapAlignment)
+    {
+      wrapMenuItem_actionPerformed(null);
+    }
 
-    if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW",false))
+    if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
     {
       this.overviewMenuItem_actionPerformed(null);
     }
 
-   addKeyListener();
+    addKeyListener();
 
   }
+
   /**
-   * Change the filename and format for the alignment, and
-   * enable the 'reload' button functionality.
-   * @param file valid filename
-   * @param format format of file
+   * Change the filename and format for the alignment, and enable the 'reload'
+   * button functionality.
+   * 
+   * @param file
+   *                valid filename
+   * @param format
+   *                format of file
    */
   public void setFileName(String file, String format)
   {
-     fileName = file;
-     currentFileFormat = format;
-     reload.setEnabled(true);
+    fileName = file;
+    currentFileFormat = format;
+    reload.setEnabled(true);
   }
 
   void addKeyListener()
   {
-      addKeyListener(new KeyAdapter()
+    addKeyListener(new KeyAdapter()
+    {
+      public void keyPressed(KeyEvent evt)
       {
-        public void keyPressed(KeyEvent evt)
+        if (viewport.cursorMode
+                && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
+                        .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
+                        .getKeyCode() <= KeyEvent.VK_NUMPAD9))
+                && Character.isDigit(evt.getKeyChar()))
+          alignPanel.seqPanel.numberPressed(evt.getKeyChar());
+
+        switch (evt.getKeyCode())
         {
-          if (viewport.cursorMode &&
-              ( (evt.getKeyCode() >= KeyEvent.VK_0 &&
-                 evt.getKeyCode() <= KeyEvent.VK_9)
-               ||
-               (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0 &&
-                evt.getKeyCode() <= KeyEvent.VK_NUMPAD9)
-              )
-              && Character.isDigit(evt.getKeyChar()))
-            alignPanel.seqPanel.numberPressed(evt.getKeyChar());
-
-          switch (evt.getKeyCode())
-          {
 
-            case 27: // escape key
-              deselectAllSequenceMenuItem_actionPerformed(null);
+        case 27: // escape key
+          deselectAllSequenceMenuItem_actionPerformed(null);
 
-              break;
+          break;
 
-            case KeyEvent.VK_DOWN:
-             if (evt.isAltDown() || !viewport.cursorMode)
-              moveSelectedSequences(false);
-              if (viewport.cursorMode)
-                alignPanel.seqPanel.moveCursor(0, 1);
-              break;
+        case KeyEvent.VK_DOWN:
+          if (evt.isAltDown() || !viewport.cursorMode)
+            moveSelectedSequences(false);
+          if (viewport.cursorMode)
+            alignPanel.seqPanel.moveCursor(0, 1);
+          break;
 
-            case KeyEvent.VK_UP:
-            if (evt.isAltDown() || !viewport.cursorMode)
-              moveSelectedSequences(true);
-              if (viewport.cursorMode)
-                alignPanel.seqPanel.moveCursor(0, -1);
+        case KeyEvent.VK_UP:
+          if (evt.isAltDown() || !viewport.cursorMode)
+            moveSelectedSequences(true);
+          if (viewport.cursorMode)
+            alignPanel.seqPanel.moveCursor(0, -1);
 
-              break;
+          break;
 
-            case KeyEvent.VK_LEFT:
-            if (evt.isAltDown() || !viewport.cursorMode)
-              slideSequences(false,
-                             alignPanel.seqPanel.getKeyboardNo1());
-            else
-                alignPanel.seqPanel.moveCursor( -1, 0);
-
-
-              break;
-
-            case KeyEvent.VK_RIGHT:
-            if (evt.isAltDown() || !viewport.cursorMode)
-              slideSequences(true,
-                             alignPanel.seqPanel.getKeyboardNo1());
-            else
-                alignPanel.seqPanel.moveCursor(1, 0);
-              break;
+        case KeyEvent.VK_LEFT:
+          if (evt.isAltDown() || !viewport.cursorMode)
+            slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
+          else
+            alignPanel.seqPanel.moveCursor(-1, 0);
 
-            case KeyEvent.VK_SPACE:
-              if (viewport.cursorMode)
-              {
-                alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
-                                           || evt.isShiftDown()
-                                           || evt.isAltDown());
-              }
-              break;
+          break;
 
-            case KeyEvent.VK_DELETE:
-            case KeyEvent.VK_BACK_SPACE:
-              if (!viewport.cursorMode)
-              {
-                cut_actionPerformed(null);
-              }
-              else
-            {
-                alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
-                                           || evt.isShiftDown()
-                                           || evt.isAltDown());
-            }
+        case KeyEvent.VK_RIGHT:
+          if (evt.isAltDown() || !viewport.cursorMode)
+            slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
+          else
+            alignPanel.seqPanel.moveCursor(1, 0);
+          break;
 
-              break;
+        case KeyEvent.VK_SPACE:
+          if (viewport.cursorMode)
+          {
+            alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
+                    || evt.isShiftDown() || evt.isAltDown());
+          }
+          break;
 
-            case KeyEvent.VK_S:
-              if (viewport.cursorMode)
-              {
-                alignPanel.seqPanel.setCursorRow();
-              }
-              break;
-            case KeyEvent.VK_C:
-              if (viewport.cursorMode && !evt.isControlDown())
-              {
-                alignPanel.seqPanel.setCursorColumn();
-              }
-              break;
-            case KeyEvent.VK_P:
-              if (viewport.cursorMode)
-              {
-                alignPanel.seqPanel.setCursorPosition();
-              }
-              break;
+        case KeyEvent.VK_DELETE:
+        case KeyEvent.VK_BACK_SPACE:
+          if (!viewport.cursorMode)
+          {
+            cut_actionPerformed(null);
+          }
+          else
+          {
+            alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
+                    || evt.isShiftDown() || evt.isAltDown());
+          }
 
-            case KeyEvent.VK_ENTER:
-            case KeyEvent.VK_COMMA:
-              if (viewport.cursorMode)
-              {
-                alignPanel.seqPanel.setCursorRowAndColumn();
-              }
-              break;
+          break;
 
-            case KeyEvent.VK_Q:
-              if (viewport.cursorMode)
-              {
-                alignPanel.seqPanel.setSelectionAreaAtCursor(true);
-              }
-              break;
-            case KeyEvent.VK_M:
-              if (viewport.cursorMode)
-              {
-                alignPanel.seqPanel.setSelectionAreaAtCursor(false);
-              }
-              break;
+        case KeyEvent.VK_S:
+          if (viewport.cursorMode)
+          {
+            alignPanel.seqPanel.setCursorRow();
+          }
+          break;
+        case KeyEvent.VK_C:
+          if (viewport.cursorMode && !evt.isControlDown())
+          {
+            alignPanel.seqPanel.setCursorColumn();
+          }
+          break;
+        case KeyEvent.VK_P:
+          if (viewport.cursorMode)
+          {
+            alignPanel.seqPanel.setCursorPosition();
+          }
+          break;
 
-            case KeyEvent.VK_F2:
-              viewport.cursorMode = !viewport.cursorMode;
-              statusBar.setText("Keyboard editing mode is " +
-                                           (viewport.cursorMode ? "on" : "off"));
-              if (viewport.cursorMode)
-              {
-                alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
-                alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
-              }
-              alignPanel.seqPanel.seqCanvas.repaint();
-              break;
+        case KeyEvent.VK_ENTER:
+        case KeyEvent.VK_COMMA:
+          if (viewport.cursorMode)
+          {
+            alignPanel.seqPanel.setCursorRowAndColumn();
+          }
+          break;
 
-            case KeyEvent.VK_F1:
-              try
-              {
-                ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
-                java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
-                javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
+        case KeyEvent.VK_Q:
+          if (viewport.cursorMode)
+          {
+            alignPanel.seqPanel.setSelectionAreaAtCursor(true);
+          }
+          break;
+        case KeyEvent.VK_M:
+          if (viewport.cursorMode)
+          {
+            alignPanel.seqPanel.setSelectionAreaAtCursor(false);
+          }
+          break;
 
-                javax.help.HelpBroker hb = hs.createHelpBroker();
-                hb.setCurrentID("home");
-                hb.setDisplayed(true);
-              }
-              catch (Exception ex)
-              {
-                ex.printStackTrace();
-              }
-              break
-                  ;
-            case KeyEvent.VK_H:
-            {
-              boolean toggleSeqs = !evt.isControlDown();
-              boolean toggleCols = !evt.isShiftDown();
+        case KeyEvent.VK_F2:
+          viewport.cursorMode = !viewport.cursorMode;
+          statusBar.setText("Keyboard editing mode is "
+                  + (viewport.cursorMode ? "on" : "off"));
+          if (viewport.cursorMode)
+          {
+            alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
+            alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
+          }
+          alignPanel.seqPanel.seqCanvas.repaint();
+          break;
 
-              boolean hide = false;
+        case KeyEvent.VK_F1:
+          try
+          {
+            ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
+            java.net.URL url = javax.help.HelpSet.findHelpSet(cl,
+                    "help/help");
+            javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
+
+            javax.help.HelpBroker hb = hs.createHelpBroker();
+            hb.setCurrentID("home");
+            hb.setDisplayed(true);
+          } catch (Exception ex)
+          {
+            ex.printStackTrace();
+          }
+          break;
+        case KeyEvent.VK_H:
+        {
+          boolean toggleSeqs = !evt.isControlDown();
+          boolean toggleCols = !evt.isShiftDown();
 
-              SequenceGroup sg = viewport.getSelectionGroup();
-              if (toggleSeqs)
-              {
-                if (sg != null && sg.getSize() != viewport.alignment.getHeight())
-                {
-                  hideSelSequences_actionPerformed(null);
-                  hide = true;
-                }
-              else if (! (toggleCols &&
-                          viewport.colSel.getSelected().size() > 0))
-              {
-                  showAllSeqs_actionPerformed(null);
-              }
-            }
+          boolean hide = false;
 
-              if (toggleCols)
-              {
-                if (viewport.colSel.getSelected().size() > 0)
-                {
-                  hideSelColumns_actionPerformed(null);
-                  if (!toggleSeqs)
-                {
-                    viewport.selectionGroup = sg;
-                }
-              }
-                else if (!hide)
-              {
-                  showAllColumns_actionPerformed(null);
-              }
-            }
-              break;
-            }
-            case KeyEvent.VK_PAGE_UP:
-              if (viewport.wrapAlignment)
+          SequenceGroup sg = viewport.getSelectionGroup();
+          if (toggleSeqs)
+          {
+            if (sg != null
+                    && sg.getSize() != viewport.alignment.getHeight())
             {
-                alignPanel.scrollUp(true);
+              hideSelSequences_actionPerformed(null);
+              hide = true;
             }
-              else
+            else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
             {
-                alignPanel.setScrollValues(viewport.startRes,
-                                           viewport.startSeq
-                                           - viewport.endSeq + viewport.startSeq);
+              showAllSeqs_actionPerformed(null);
             }
-              break;
-            case KeyEvent.VK_PAGE_DOWN:
-              if (viewport.wrapAlignment)
+          }
+
+          if (toggleCols)
+          {
+            if (viewport.colSel.getSelected().size() > 0)
             {
-                alignPanel.scrollUp(false);
+              hideSelColumns_actionPerformed(null);
+              if (!toggleSeqs)
+              {
+                viewport.selectionGroup = sg;
+              }
             }
-              else
+            else if (!hide)
             {
-                alignPanel.setScrollValues(viewport.startRes,
-                                           viewport.startSeq
-                                           + viewport.endSeq - viewport.startSeq);
+              showAllColumns_actionPerformed(null);
             }
-              break;
           }
+          break;
         }
+        case KeyEvent.VK_PAGE_UP:
+          if (viewport.wrapAlignment)
+          {
+            alignPanel.scrollUp(true);
+          }
+          else
+          {
+            alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
+                    - viewport.endSeq + viewport.startSeq);
+          }
+          break;
+        case KeyEvent.VK_PAGE_DOWN:
+          if (viewport.wrapAlignment)
+          {
+            alignPanel.scrollUp(false);
+          }
+          else
+          {
+            alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
+                    + viewport.endSeq - viewport.startSeq);
+          }
+          break;
+        }
+      }
 
       public void keyReleased(KeyEvent evt)
       {
-        switch(evt.getKeyCode())
+        switch (evt.getKeyCode())
         {
-          case KeyEvent.VK_LEFT:
-            if (evt.isAltDown() || !viewport.cursorMode)
-              viewport.firePropertyChange("alignment", null,
-                                          viewport.getAlignment().getSequences());
-            break;
-
-          case KeyEvent.VK_RIGHT:
-            if (evt.isAltDown() || !viewport.cursorMode)
-              viewport.firePropertyChange("alignment", null,
-                                          viewport.getAlignment().getSequences());
-            break;
+        case KeyEvent.VK_LEFT:
+          if (evt.isAltDown() || !viewport.cursorMode)
+            viewport.firePropertyChange("alignment", null, viewport
+                    .getAlignment().getSequences());
+          break;
+
+        case KeyEvent.VK_RIGHT:
+          if (evt.isAltDown() || !viewport.cursorMode)
+            viewport.firePropertyChange("alignment", null, viewport
+                    .getAlignment().getSequences());
+          break;
         }
       }
-      });
+    });
   }
 
-
-  public void addAlignmentPanel(final AlignmentPanel ap,
-                                boolean newPanel)
+  public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
   {
     ap.alignFrame = this;
 
@@ -423,9 +419,9 @@ public class AlignFrame
 
     int aSize = alignPanels.size();
 
-    tabbedPane.setVisible(aSize>1 || ap.av.viewName!=null);
+    tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 
-    if (aSize == 1 && ap.av.viewName==null)
+    if (aSize == 1 && ap.av.viewName == null)
     {
       this.getContentPane().add(ap, BorderLayout.CENTER);
     }
@@ -443,7 +439,7 @@ public class AlignFrame
       ap.setVisible(false);
     }
 
-    if(newPanel)
+    if (newPanel)
     {
       if (ap.av.padGaps)
       {
@@ -460,11 +456,10 @@ public class AlignFrame
     gatherViews.setEnabled(true);
     tabbedPane.setVisible(true);
     AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
-    tabbedPane.addTab(first.av.viewName,first);
+    tabbedPane.addTab(first.av.viewName, first);
     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
   }
 
-
   public AlignViewport getViewport()
   {
     return viewport;
@@ -476,60 +471,61 @@ public class AlignFrame
     final java.beans.PropertyChangeListener thisListener;
     // Do this once to get current state
     BuildWebServiceMenu();
-    Desktop.discoverer.addPropertyChangeListener(
-        thisListener = new java.beans.PropertyChangeListener()
-    {
-      public void propertyChange(PropertyChangeEvent evt)
-      {
-        // System.out.println("Discoverer property change.");
-        if (evt.getPropertyName().equals("services"))
-        {
-          // System.out.println("Rebuilding web service menu");
-          BuildWebServiceMenu();
-        }
-      }
-    });
+    Desktop.discoverer
+            .addPropertyChangeListener(thisListener = new java.beans.PropertyChangeListener()
+            {
+              public void propertyChange(PropertyChangeEvent evt)
+              {
+                // System.out.println("Discoverer property change.");
+                if (evt.getPropertyName().equals("services"))
+                {
+                  // System.out.println("Rebuilding web service menu");
+                  BuildWebServiceMenu();
+                }
+              }
+            });
 
-    addInternalFrameListener(new javax.swing.event.
-                             InternalFrameAdapter()
+    addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
     {
       public void internalFrameClosed(
-          javax.swing.event.InternalFrameEvent evt)
+              javax.swing.event.InternalFrameEvent evt)
       {
         // System.out.println("deregistering discoverer listener");
         Desktop.discoverer.removePropertyChangeListener(thisListener);
         closeMenuItem_actionPerformed(true);
-      }
-      ;
+      };
     });
   }
 
   public void setGUINucleotide(boolean nucleotide)
   {
-    showTranslation.setVisible( nucleotide );
-    conservationMenuItem.setEnabled( !nucleotide );
-    modifyConservation.setEnabled(   !nucleotide );
-    
-    //Remember AlignFrame always starts as protein
-    if(!nucleotide)
+    showTranslation.setVisible(nucleotide);
+    conservationMenuItem.setEnabled(!nucleotide);
+    modifyConservation.setEnabled(!nucleotide);
+
+    // Remember AlignFrame always starts as protein
+    if (!nucleotide)
     {
-      calculateMenu.remove(calculateMenu.getItemCount()-2);
+      calculateMenu.remove(calculateMenu.getItemCount() - 2);
     }
   }
 
-
   /**
-   * set up menus for the currently viewport.
-   * This may be called after any operation that affects the data in the current view (selection changed, etc) to update the menus to reflect the new state.
+   * set up menus for the currently viewport. This may be called after any
+   * operation that affects the data in the current view (selection changed,
+   * etc) to update the menus to reflect the new state.
    */
   public void setMenusForViewport()
   {
     setMenusFromViewport(viewport);
   }
+
   /**
-   * Need to call this method when tabs are selected for multiple views,
-   * or when loading from Jalview2XML.java
-   * @param av AlignViewport
+   * Need to call this method when tabs are selected for multiple views, or when
+   * loading from Jalview2XML.java
+   * 
+   * @param av
+   *                AlignViewport
    */
   void setMenusFromViewport(AlignViewport av)
   {
@@ -549,8 +545,8 @@ public class AlignFrame
     viewBoxesMenuItem.setSelected(av.showBoxes);
     viewTextMenuItem.setSelected(av.showText);
 
-    setColourSelected(ColourSchemeProperty.
-                      getColourName(av.getGlobalColourScheme()));
+    setColourSelected(ColourSchemeProperty.getColourName(av
+            .getGlobalColourScheme()));
 
     showSeqFeatures.setSelected(av.showSequenceFeatures);
     hiddenMarkers.setState(av.showHiddenMarkers);
@@ -561,33 +557,35 @@ public class AlignFrame
     updateEditMenuBar();
   }
 
-
   Hashtable progressBars;
-  /* (non-Javadoc)
+
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
    */
   public void setProgressBar(String message, long id)
   {
-    if(progressBars == null)
+    if (progressBars == null)
     {
       progressBars = new Hashtable();
     }
 
     JPanel progressPanel;
     GridLayout layout = (GridLayout) statusPanel.getLayout();
-    if(progressBars.get( new Long(id) )!=null)
-     {
-       progressPanel = (JPanel)progressBars.get( new Long(id) );
-       statusPanel.remove(progressPanel);
-       progressBars.remove( progressPanel );
-       progressPanel = null;
-       if(message!=null)
+    if (progressBars.get(new Long(id)) != null)
+    {
+      progressPanel = (JPanel) progressBars.get(new Long(id));
+      statusPanel.remove(progressPanel);
+      progressBars.remove(progressPanel);
+      progressPanel = null;
+      if (message != null)
       {
-         statusBar.setText(message);
+        statusBar.setText(message);
       }
 
-       layout.setRows(layout.getRows() - 1);
-     }
+      layout.setRows(layout.getRows() - 1);
+    }
     else
     {
       progressPanel = new JPanel(new BorderLayout(10, 5));
@@ -607,24 +605,26 @@ public class AlignFrame
     setMenusForViewport();
     validate();
   }
+
   /**
    * 
    * @return true if any progress bars are still active
    */
   public boolean operationInProgress()
   {
-    if (progressBars!=null && progressBars.size()>0)
+    if (progressBars != null && progressBars.size() > 0)
     {
       return true;
     }
     return false;
   }
+
   /*
-   Added so Castor Mapping file can obtain Jalview Version
-  */
+   * Added so Castor Mapping file can obtain Jalview Version
+   */
   public String getVersion()
   {
-    return  jalview.bin.Cache.getProperty("VERSION");
+    return jalview.bin.Cache.getProperty("VERSION");
   }
 
   public FeatureRenderer getFeatureRenderer()
@@ -632,7 +632,6 @@ public class AlignFrame
     return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
   }
 
-
   public void fetchSequence_actionPerformed(ActionEvent e)
   {
     new SequenceFetcher(this);
@@ -645,31 +644,30 @@ public class AlignFrame
 
   public void reload_actionPerformed(ActionEvent e)
   {
-    if(fileName!=null)
+    if (fileName != null)
     {
-      if(currentFileFormat.equals("Jalview"))
+      if (currentFileFormat.equals("Jalview"))
       {
-        JInternalFrame [] frames = Desktop.desktop.getAllFrames();
-        for(int i=0; i<frames.length; i++)
+        JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+        for (int i = 0; i < frames.length; i++)
         {
-          if (frames[i] instanceof AlignFrame
-              && frames[i] != this
-              && ( (AlignFrame) frames[i]).fileName.equals(fileName))
+          if (frames[i] instanceof AlignFrame && frames[i] != this
+                  && ((AlignFrame) frames[i]).fileName.equals(fileName))
           {
             try
             {
               frames[i].setSelected(true);
               Desktop.instance.closeAssociatedWindows();
-          }
-            catch (java.beans.PropertyVetoException ex)
-            {}
+            } catch (java.beans.PropertyVetoException ex)
+            {
+            }
           }
 
         }
         Desktop.instance.closeAssociatedWindows();
 
         FileLoader loader = new FileLoader();
-        String protocol = fileName.startsWith("http:")? "URL":"File";
+        String protocol = fileName.startsWith("http:") ? "URL" : "File";
         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
       }
       else
@@ -678,8 +676,8 @@ public class AlignFrame
 
         FileLoader loader = new FileLoader();
         String protocol = fileName.startsWith("http:") ? "URL" : "File";
-        AlignFrame newframe =
-            loader.LoadFileWaitTillLoaded(fileName, protocol, currentFileFormat);
+        AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
+                protocol, currentFileFormat);
 
         newframe.setBounds(bounds);
 
@@ -688,7 +686,6 @@ public class AlignFrame
     }
   }
 
-
   public void addFromText_actionPerformed(ActionEvent e)
   {
     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
@@ -699,36 +696,34 @@ public class AlignFrame
     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
   }
 
-
   public void save_actionPerformed(ActionEvent e)
   {
-    if(fileName==null
-       || (currentFileFormat==null || jalview.io.AppletFormatAdapter.isValidFormat(currentFileFormat, true))
-       || fileName.startsWith("http")
-        )
+    if (fileName == null
+            || (currentFileFormat == null || jalview.io.AppletFormatAdapter
+                    .isValidFormat(currentFileFormat, true))
+            || fileName.startsWith("http"))
     {
       saveAs_actionPerformed(null);
     }
     else
     {
       saveAlignment(fileName, currentFileFormat);
-  }
+    }
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void saveAs_actionPerformed(ActionEvent e)
   {
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-        getProperty( "LAST_DIRECTORY"),
-        jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
-        jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
-        currentFileFormat,
-        false);
-
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+            .getProperty("LAST_DIRECTORY"),
+            jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
+            jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
+            currentFileFormat, false);
 
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle("Save Alignment to file");
@@ -738,26 +733,26 @@ public class AlignFrame
 
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
-        currentFileFormat = chooser.getSelectedFormat();
-        if (currentFileFormat == null)
-        {
-          JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                                "You must select a file format before saving!",
-                                                "File format not specified",
-                                                JOptionPane.WARNING_MESSAGE);
-          value = chooser.showSaveDialog(this);
-          return;
-        }
+      currentFileFormat = chooser.getSelectedFormat();
+      if (currentFileFormat == null)
+      {
+        JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                "You must select a file format before saving!",
+                "File format not specified", JOptionPane.WARNING_MESSAGE);
+        value = chooser.showSaveDialog(this);
+        return;
+      }
 
-        fileName = chooser.getSelectedFile().getPath();
+      fileName = chooser.getSelectedFile().getPath();
 
       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
-                                    currentFileFormat);
+              currentFileFormat);
 
       jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
-      if (currentFileFormat.indexOf(" ")>-1)
+      if (currentFileFormat.indexOf(" ") > -1)
       {
-        currentFileFormat = currentFileFormat.substring(0, currentFileFormat.indexOf(" "));
+        currentFileFormat = currentFileFormat.substring(0,
+                currentFileFormat.indexOf(" "));
       }
       saveAlignment(fileName, currentFileFormat);
     }
@@ -773,50 +768,52 @@ public class AlignFrame
 
       if (shortName.indexOf(java.io.File.separatorChar) > -1)
       {
-        shortName = shortName.substring(shortName.lastIndexOf(
-            java.io.File.separatorChar) + 1);
+        shortName = shortName.substring(shortName
+                .lastIndexOf(java.io.File.separatorChar) + 1);
       }
 
       success = new Jalview2XML().SaveAlignment(this, file, shortName);
 
-      statusBar.setText("Successfully saved to file: "
-                          +fileName+" in "
-                          +format +" format.");
+      statusBar.setText("Successfully saved to file: " + fileName + " in "
+              + format + " format.");
 
     }
     else
-    {        
+    {
       if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
       {
         // JBPNote need to have a raise_gui flag here
-        JOptionPane.showInternalMessageDialog(
-                this, "Cannot save file " + fileName + " using format "+format,
+        JOptionPane.showInternalMessageDialog(this, "Cannot save file "
+                + fileName + " using format " + format,
                 "Alignment output format not supported",
                 JOptionPane.WARNING_MESSAGE);
         saveAs_actionPerformed(null);
         return false;
       }
-        
+
       String[] omitHidden = null;
 
       if (viewport.hasHiddenColumns)
       {
-        int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
-            "The Alignment contains hidden columns."
-            + "\nDo you want to save only the visible alignment?",
-            "Save / Omit Hidden Columns",
-            JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
+        int reply = JOptionPane
+                .showInternalConfirmDialog(
+                        Desktop.desktop,
+                        "The Alignment contains hidden columns."
+                                + "\nDo you want to save only the visible alignment?",
+                        "Save / Omit Hidden Columns",
+                        JOptionPane.YES_NO_OPTION,
+                        JOptionPane.QUESTION_MESSAGE);
 
         if (reply == JOptionPane.YES_OPTION)
         {
           omitHidden = viewport.getViewAsString(false);
-      }
+        }
       }
       FormatAdapter f = new FormatAdapter();
-      String output = f.formatSequences(
-          format,
-          (Alignment) viewport.alignment, // class cast exceptions will occur in the distant future
-          omitHidden, f.getCacheSuffixDefault(format), viewport.colSel);
+      String output = f.formatSequences(format,
+              (Alignment) viewport.alignment, // class cast exceptions will
+              // occur in the distant future
+              omitHidden, f.getCacheSuffixDefault(format), viewport.colSel);
 
       if (output == null)
       {
@@ -827,16 +824,14 @@ public class AlignFrame
         try
         {
           java.io.PrintWriter out = new java.io.PrintWriter(
-              new java.io.FileWriter(file));
+                  new java.io.FileWriter(file));
 
           out.print(output);
           out.close();
           this.setTitle(file);
-          statusBar.setText("Successfully saved to file: "
-                            + fileName + " in "
-                            + format + " format.");
-        }
-        catch (Exception ex)
+          statusBar.setText("Successfully saved to file: " + fileName
+                  + " in " + format + " format.");
+        } catch (Exception ex)
         {
           success = false;
           ex.printStackTrace();
@@ -846,10 +841,8 @@ public class AlignFrame
 
     if (!success)
     {
-      JOptionPane.showInternalMessageDialog(
-          this, "Couldn't save file: " + fileName,
-          "Error Saving File",
-          JOptionPane.WARNING_MESSAGE);
+      JOptionPane.showInternalMessageDialog(this, "Couldn't save file: "
+              + fileName, "Error Saving File", JOptionPane.WARNING_MESSAGE);
     }
 
     return success;
@@ -857,22 +850,26 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void outputText_actionPerformed(ActionEvent e)
   {
-    String [] omitHidden = null;
+    String[] omitHidden = null;
 
-    if(viewport.hasHiddenColumns)
+    if (viewport.hasHiddenColumns)
     {
-      int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
-          "The Alignment contains hidden columns."
-      +"\nDo you want to output only the visible alignment?",
-      "Save / Omit Hidden Columns",
-      JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
+      int reply = JOptionPane
+              .showInternalConfirmDialog(
+                      Desktop.desktop,
+                      "The Alignment contains hidden columns."
+                              + "\nDo you want to output only the visible alignment?",
+                      "Save / Omit Hidden Columns",
+                      JOptionPane.YES_NO_OPTION,
+                      JOptionPane.QUESTION_MESSAGE);
 
-      if(reply==JOptionPane.YES_OPTION)
+      if (reply == JOptionPane.YES_OPTION)
       {
         omitHidden = viewport.getViewAsString(false);
       }
@@ -880,27 +877,24 @@ public class AlignFrame
 
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
     cap.setForInput(null);
-    Desktop.addInternalFrame(cap,
-                             "Alignment output - " + e.getActionCommand(), 600,
-                             500);
-
+    Desktop.addInternalFrame(cap, "Alignment output - "
+            + e.getActionCommand(), 600, 500);
 
-    cap.setText(new FormatAdapter().formatSequences(
-        e.getActionCommand(),
-        viewport.alignment,
-        omitHidden, viewport.colSel));
+    cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
+            viewport.alignment, omitHidden, viewport.colSel));
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
-    new HTMLOutput(alignPanel,
-                   alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
-        alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+    new HTMLOutput(alignPanel, alignPanel.seqPanel.seqCanvas
+            .getSequenceRenderer(), alignPanel.seqPanel.seqCanvas
+            .getFeatureRenderer());
   }
 
   public void createImageMap(File file, String image)
@@ -910,8 +904,9 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void createPNG(File f)
   {
@@ -920,15 +915,15 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void createEPS(File f)
   {
     alignPanel.makeEPS(f);
   }
 
-
   public void pageSetup_actionPerformed(ActionEvent e)
   {
     PrinterJob printJob = PrinterJob.getPrinterJob();
@@ -937,12 +932,13 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void printMenuItem_actionPerformed(ActionEvent e)
   {
-    //Putting in a thread avoids Swing painting problems
+    // Putting in a thread avoids Swing painting problems
     PrintThread thread = new PrintThread(alignPanel);
     thread.start();
   }
@@ -952,24 +948,20 @@ public class AlignFrame
     new AnnotationExporter().exportFeatures(alignPanel);
   }
 
-
   public void exportAnnotations_actionPerformed(ActionEvent e)
   {
-    new AnnotationExporter().exportAnnotations(
-      alignPanel,
-        viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null,
-      viewport.alignment.getGroups(),
-      ((Alignment)viewport.alignment).alignmentProperties
-        );
+    new AnnotationExporter().exportAnnotations(alignPanel,
+            viewport.showAnnotation ? viewport.alignment
+                    .getAlignmentAnnotation() : null, viewport.alignment
+                    .getGroups(),
+            ((Alignment) viewport.alignment).alignmentProperties);
   }
 
-
   public void associatedData_actionPerformed(ActionEvent e)
   {
     // Pick the tree file
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-        getProperty(
-            "LAST_DIRECTORY"));
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+            .getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle("Load Jalview Annotations or Features File");
     chooser.setToolTipText("Load Jalview Annotations / Features file");
@@ -985,30 +977,31 @@ public class AlignFrame
 
   }
 
-
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
   {
-    if(alignPanels!=null && alignPanels.size()<2)
+    if (alignPanels != null && alignPanels.size() < 2)
     {
       closeAllTabs = true;
     }
 
     try
     {
-      if(alignPanels!=null)
+      if (alignPanels != null)
       {
         if (closeAllTabs)
         {
           for (int i = 0; i < alignPanels.size(); i++)
           {
             AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
-            jalview.structure.StructureSelectionManager.getStructureSelectionManager()
-                .removeStructureViewerListener(ap.seqPanel, null);
+            jalview.structure.StructureSelectionManager
+                    .getStructureSelectionManager()
+                    .removeStructureViewerListener(ap.seqPanel, null);
             PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas);
             PaintRefresher.RemoveComponent(ap.idPanel.idCanvas);
             PaintRefresher.RemoveComponent(ap);
@@ -1030,9 +1023,9 @@ public class AlignFrame
           tabbedPane.removeTabAt(index);
           tabbedPane.validate();
 
-          if(index==tabbedPane.getTabCount())
+          if (index == tabbedPane.getTabCount())
           {
-            index --;
+            index--;
           }
 
           this.tabSelectionChanged(index);
@@ -1042,15 +1035,13 @@ public class AlignFrame
       if (closeAllTabs)
       {
         this.setClosed(true);
-    }
-    }
-    catch (Exception ex)
+      }
+    } catch (Exception ex)
     {
       ex.printStackTrace();
     }
   }
 
-
   /**
    * DOCUMENT ME!
    */
@@ -1083,10 +1074,9 @@ public class AlignFrame
     }
   }
 
-
   public void addHistoryItem(CommandI command)
   {
-    if(command.getSize()>0)
+    if (command.getSize() > 0)
     {
       viewport.historyList.push(command);
       viewport.redoList.clear();
@@ -1096,60 +1086,63 @@ public class AlignFrame
   }
 
   /**
-   *
+   * 
    * @return alignment objects for all views
    */
   AlignmentI[] getViewAlignments()
   {
-    if (alignPanels!=null)
+    if (alignPanels != null)
     {
       Enumeration e = alignPanels.elements();
       AlignmentI[] als = new AlignmentI[alignPanels.size()];
-      for (int i=0; e.hasMoreElements(); i++)
+      for (int i = 0; e.hasMoreElements(); i++)
       {
         als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
       }
       return als;
     }
-    if (viewport!=null)
+    if (viewport != null)
     {
-      return new AlignmentI[] { viewport.alignment };
+      return new AlignmentI[]
+      { viewport.alignment };
     }
     return null;
   }
+
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void undoMenuItem_actionPerformed(ActionEvent e)
   {
     if (viewport.historyList.empty())
       return;
-    CommandI command = (CommandI)viewport.historyList.pop();
+    CommandI command = (CommandI) viewport.historyList.pop();
     viewport.redoList.push(command);
     command.undoCommand(getViewAlignments());
 
     AlignViewport originalSource = getOriginatingSource(command);
     updateEditMenuBar();
 
-    if(originalSource!=null)
+    if (originalSource != null)
     {
       originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
-      originalSource.firePropertyChange("alignment",
-                                        null,
-                                        originalSource.alignment.getSequences());
+      originalSource.firePropertyChange("alignment", null,
+              originalSource.alignment.getSequences());
     }
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void redoMenuItem_actionPerformed(ActionEvent e)
   {
-    if(viewport.redoList.size()<1)
+    if (viewport.redoList.size() < 1)
     {
       return;
     }
@@ -1161,36 +1154,35 @@ public class AlignFrame
     AlignViewport originalSource = getOriginatingSource(command);
     updateEditMenuBar();
 
-    if(originalSource!=null)
+    if (originalSource != null)
     {
       originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
-      originalSource.firePropertyChange("alignment",
-                                        null,
-                                        originalSource.alignment.getSequences());
+      originalSource.firePropertyChange("alignment", null,
+              originalSource.alignment.getSequences());
     }
   }
 
   AlignViewport getOriginatingSource(CommandI command)
   {
     AlignViewport originalSource = null;
-    //For sequence removal and addition, we need to fire
-   //the property change event FROM the viewport where the
-   //original alignment was altered
-    AlignmentI al=null;
+    // For sequence removal and addition, we need to fire
+    // the property change event FROM the viewport where the
+    // original alignment was altered
+    AlignmentI al = null;
     if (command instanceof EditCommand)
     {
       EditCommand editCommand = (EditCommand) command;
       al = editCommand.getAlignment();
-      Vector comps = (Vector) PaintRefresher.components
-          .get(viewport.getSequenceSetId());
+      Vector comps = (Vector) PaintRefresher.components.get(viewport
+              .getSequenceSetId());
 
       for (int i = 0; i < comps.size(); i++)
       {
         if (comps.elementAt(i) instanceof AlignmentPanel)
         {
-          if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)
+          if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
           {
-            originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;
+            originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
             break;
           }
         }
@@ -1199,8 +1191,8 @@ public class AlignFrame
 
     if (originalSource == null)
     {
-      //The original view is closed, we must validate
-      //the current view against the closed view first
+      // The original view is closed, we must validate
+      // the current view against the closed view first
       if (al != null)
       {
         PaintRefresher.validateSequences(al, viewport.alignment);
@@ -1214,8 +1206,9 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param up DOCUMENT ME!
+   * 
+   * @param up
+   *                DOCUMENT ME!
    */
   public void moveSelectedSequences(boolean up)
   {
@@ -1274,25 +1267,23 @@ public class AlignFrame
     alignPanel.paintAlignment(true);
   }
 
-
-
-
   synchronized void slideSequences(boolean right, int size)
   {
     Vector sg = new Vector();
-    if(viewport.cursorMode)
+    if (viewport.cursorMode)
+    {
+      sg.addElement(viewport.alignment
+              .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
+    }
+    else if (viewport.getSelectionGroup() != null
+            && viewport.getSelectionGroup().getSize() != viewport.alignment
+                    .getHeight())
     {
-      sg.addElement(viewport.alignment.getSequenceAt(
-          alignPanel.seqPanel.seqCanvas.cursorY));
+      sg = viewport.getSelectionGroup().getSequences(
+              viewport.hiddenRepSequences);
     }
-    else if(viewport.getSelectionGroup()!=null
-        && viewport.getSelectionGroup().getSize()!=viewport.alignment.getHeight())
-   {
-     sg = viewport.getSelectionGroup().getSequences(
-         viewport.hiddenRepSequences);
-   }
 
-    if(sg.size()<1)
+    if (sg.size() < 1)
     {
       return;
     }
@@ -1301,8 +1292,8 @@ public class AlignFrame
 
     for (int i = 0; i < viewport.alignment.getHeight(); i++)
     {
-      if(!sg.contains(viewport.alignment.getSequenceAt(i)))
-         invertGroup.add(viewport.alignment.getSequenceAt(i));
+      if (!sg.contains(viewport.alignment.getSequenceAt(i)))
+        invertGroup.add(viewport.alignment.getSequenceAt(i));
     }
 
     SequenceI[] seqs1 = new SequenceI[sg.size()];
@@ -1315,15 +1306,11 @@ public class AlignFrame
 
     SlideSequencesCommand ssc;
     if (right)
-      ssc = new SlideSequencesCommand("Slide Sequences",
-                                      seqs2, seqs1, size,
-                                      viewport.getGapCharacter()
-          );
+      ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
+              size, viewport.getGapCharacter());
     else
-      ssc = new SlideSequencesCommand("Slide Sequences",
-                                      seqs1, seqs2, size,
-                                      viewport.getGapCharacter()
-          );
+      ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
+              size, viewport.getGapCharacter());
 
     int groupAdjustment = 0;
     if (ssc.getGapsInsertedBegin() && right)
@@ -1336,7 +1323,7 @@ public class AlignFrame
     else if (!ssc.getGapsInsertedBegin() && !right)
     {
       if (viewport.cursorMode)
-        alignPanel.seqPanel.moveCursor( -size, 0);
+        alignPanel.seqPanel.moveCursor(-size, 0);
       else
         groupAdjustment = -size;
     }
@@ -1344,33 +1331,31 @@ public class AlignFrame
     if (groupAdjustment != 0)
     {
       viewport.getSelectionGroup().setStartRes(
-          viewport.getSelectionGroup().getStartRes() + groupAdjustment);
+              viewport.getSelectionGroup().getStartRes() + groupAdjustment);
       viewport.getSelectionGroup().setEndRes(
-          viewport.getSelectionGroup().getEndRes() + groupAdjustment);
+              viewport.getSelectionGroup().getEndRes() + groupAdjustment);
     }
 
-
     boolean appendHistoryItem = false;
-    if(viewport.historyList!=null
-       && viewport.historyList.size()>0
-      && viewport.historyList.peek() instanceof SlideSequencesCommand)
+    if (viewport.historyList != null && viewport.historyList.size() > 0
+            && viewport.historyList.peek() instanceof SlideSequencesCommand)
     {
-      appendHistoryItem = ssc.appendSlideCommand(
-          (SlideSequencesCommand)viewport.historyList.peek())
-          ;
+      appendHistoryItem = ssc
+              .appendSlideCommand((SlideSequencesCommand) viewport.historyList
+                      .peek());
     }
 
-    if(!appendHistoryItem)
+    if (!appendHistoryItem)
       addHistoryItem(ssc);
 
     repaint();
   }
 
-
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void copy_actionPerformed(ActionEvent e)
   {
@@ -1379,8 +1364,9 @@ public class AlignFrame
     {
       return;
     }
-    //  TODO: preserve the ordering of displayed alignment annotation in any internal paste (particularly sequence associated annotation)
-    SequenceI [] seqs = viewport.getSelectionAsNewSequence();
+    // TODO: preserve the ordering of displayed alignment annotation in any
+    // internal paste (particularly sequence associated annotation)
+    SequenceI[] seqs = viewport.getSelectionAsNewSequence();
     String[] omitHidden = null;
 
     if (viewport.hasHiddenColumns)
@@ -1388,72 +1374,53 @@ public class AlignFrame
       omitHidden = viewport.getViewAsString(true);
     }
 
-    String output = new FormatAdapter().formatSequences(
-        "Fasta",
-        seqs,
-        omitHidden);
+    String output = new FormatAdapter().formatSequences("Fasta", seqs,
+            omitHidden);
 
     StringSelection ss = new StringSelection(output);
 
     try
     {
       jalview.gui.Desktop.internalCopy = true;
-      //Its really worth setting the clipboard contents
-      //to empty before setting the large StringSelection!!
-      Toolkit.getDefaultToolkit().getSystemClipboard()
-          .setContents(new StringSelection(""), null);
+      // Its really worth setting the clipboard contents
+      // to empty before setting the large StringSelection!!
+      Toolkit.getDefaultToolkit().getSystemClipboard().setContents(
+              new StringSelection(""), null);
 
-      Toolkit.getDefaultToolkit().getSystemClipboard()
-          .setContents(ss, Desktop.instance);
-    }
-    catch (OutOfMemoryError er)
+      Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
+              Desktop.instance);
+    } catch (OutOfMemoryError er)
     {
-      er.printStackTrace();
-      javax.swing.SwingUtilities.invokeLater(new Runnable()
-          {
-            public void run()
-            {
-              javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                  "Out of memory copying region!!"
-                  +
-                  "\nSee help files for increasing Java Virtual Machine memory."
-                  , "Out of memory",
-                  javax.swing.JOptionPane.WARNING_MESSAGE);
-            }
-          });
-
+      new OOMWarning("copying region", er);
       return;
     }
 
     Vector hiddenColumns = null;
-    if(viewport.hasHiddenColumns)
+    if (viewport.hasHiddenColumns)
     {
-      hiddenColumns =new Vector();
+      hiddenColumns = new Vector();
       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
-      for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();
-           i++)
+      for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
+              .size(); i++)
       {
-        int[] region = (int[])
-            viewport.getColumnSelection().getHiddenColumns().elementAt(i);
+        int[] region = (int[]) viewport.getColumnSelection()
+                .getHiddenColumns().elementAt(i);
 
         hiddenColumns.addElement(new int[]
-                                 {region[0] - hiddenOffset,
-                          region[1]-hiddenOffset});
+        { region[0] - hiddenOffset, region[1] - hiddenOffset });
       }
     }
 
     Desktop.jalviewClipboard = new Object[]
-        {
-        seqs,
-        viewport.alignment.getDataset(),
-        hiddenColumns};
-    statusBar.setText("Copied "+seqs.length+" sequences to clipboard.");
+    { seqs, viewport.alignment.getDataset(), hiddenColumns };
+    statusBar.setText("Copied " + seqs.length + " sequences to clipboard.");
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void pasteNew_actionPerformed(ActionEvent e)
   {
@@ -1462,8 +1429,9 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void pasteThis_actionPerformed(ActionEvent e)
   {
@@ -1472,12 +1440,13 @@ public class AlignFrame
 
   /**
    * Paste contents of Jalview clipboard
-   *
-   * @param newAlignment true to paste to a new alignment, otherwise add to this.
+   * 
+   * @param newAlignment
+   *                true to paste to a new alignment, otherwise add to this.
    */
   void paste(boolean newAlignment)
   {
-    boolean externalPaste=true;
+    boolean externalPaste = true;
     try
     {
       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
@@ -1499,23 +1468,9 @@ public class AlignFrame
 
         format = new IdentifyFile().Identify(str, "Paste");
 
-      }
-      catch (OutOfMemoryError er)
+      } catch (OutOfMemoryError er)
       {
-        er.printStackTrace();
-        javax.swing.SwingUtilities.invokeLater(new Runnable()
-        {
-          public void run()
-          {
-            javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                "Out of memory pasting sequences!!"
-                +
-                "\nSee help files for increasing Java Virtual Machine memory."
-                , "Out of memory",
-                javax.swing.JOptionPane.WARNING_MESSAGE);
-          }
-        });
-
+        new OOMWarning("Out of memory pasting sequences!!", er);
         return;
       }
 
@@ -1523,56 +1478,58 @@ public class AlignFrame
       boolean annotationAdded = false;
       AlignmentI alignment = null;
 
-     if(Desktop.jalviewClipboard!=null)
-     {
-       // The clipboard was filled from within Jalview, we must use the sequences
-       // And dataset from the copied alignment
-       SequenceI[] newseq = (SequenceI[])Desktop.jalviewClipboard[0];
-       // be doubly sure that we create *new* sequence objects.
-       sequences = new SequenceI[newseq.length];
-       for (int i=0;i<newseq.length;i++) {
-         sequences[i] = new Sequence(newseq[i]);
-       }
-       alignment = new Alignment(sequences);
-       externalPaste = false;
-     }
-     else
-     {
-       // parse the clipboard as an alignment.
-       alignment = new FormatAdapter().readFile(str, "Paste", format);
-       sequences = alignment.getSequencesArray();
-     }
-
-     int alwidth=0;
-
-     if (newAlignment)
-     {
-
-       if (Desktop.jalviewClipboard != null)
-       {
-         // dataset is inherited
-         alignment.setDataset( (Alignment) Desktop.jalviewClipboard[1]);
-       }
-       else
-       {
-         // new dataset is constructed
-         alignment.setDataset(null);
-       }
-       alwidth = alignment.getWidth()+1;
-     }
-     else
-     {
-       AlignmentI pastedal = alignment; // preserve pasted alignment object
-       // Add pasted sequences and dataset into existing alignment.
-       alignment = viewport.getAlignment();
-       alwidth = alignment.getWidth()+1;
+      if (Desktop.jalviewClipboard != null)
+      {
+        // The clipboard was filled from within Jalview, we must use the
+        // sequences
+        // And dataset from the copied alignment
+        SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
+        // be doubly sure that we create *new* sequence objects.
+        sequences = new SequenceI[newseq.length];
+        for (int i = 0; i < newseq.length; i++)
+        {
+          sequences[i] = new Sequence(newseq[i]);
+        }
+        alignment = new Alignment(sequences);
+        externalPaste = false;
+      }
+      else
+      {
+        // parse the clipboard as an alignment.
+        alignment = new FormatAdapter().readFile(str, "Paste", format);
+        sequences = alignment.getSequencesArray();
+      }
+
+      int alwidth = 0;
+
+      if (newAlignment)
+      {
+
+        if (Desktop.jalviewClipboard != null)
+        {
+          // dataset is inherited
+          alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
+        }
+        else
+        {
+          // new dataset is constructed
+          alignment.setDataset(null);
+        }
+        alwidth = alignment.getWidth() + 1;
+      }
+      else
+      {
+        AlignmentI pastedal = alignment; // preserve pasted alignment object
+        // Add pasted sequences and dataset into existing alignment.
+        alignment = viewport.getAlignment();
+        alwidth = alignment.getWidth() + 1;
         // decide if we need to import sequences from an existing dataset
         boolean importDs = Desktop.jalviewClipboard != null
                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
         // importDs==true instructs us to copy over new dataset sequences from
         // an existing alignment
         Vector newDs = (importDs) ? new Vector() : null; // used to create
-                                                          // minimum dataset set
+        // minimum dataset set
 
         for (int i = 0; i < sequences.length; i++)
         {
@@ -1581,7 +1538,7 @@ public class AlignFrame
             newDs.addElement(null);
           }
           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
-                                                            // paste
+          // paste
           if (importDs && ds != null)
           {
             if (!newDs.contains(ds))
@@ -1600,7 +1557,8 @@ public class AlignFrame
           {
             // copy and derive new dataset sequence
             sequences[i] = sequences[i].deriveSequence();
-            alignment.getDataset().addSequence(sequences[i].getDatasetSequence());
+            alignment.getDataset().addSequence(
+                    sequences[i].getDatasetSequence());
             // TODO: avoid creation of duplicate dataset sequences with a
             // 'contains' method using SequenceI.equals()/SequenceI.contains()
           }
@@ -1610,138 +1568,150 @@ public class AlignFrame
         {
           newDs.clear(); // tidy up
         }
-        if (pastedal.getAlignmentAnnotation()!=null) {
+        if (pastedal.getAlignmentAnnotation() != null)
+        {
           // Add any annotation attached to alignment.
           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
-          for (int i=0; i<alann.length; i++)
+          for (int i = 0; i < alann.length; i++)
           {
-            annotationAdded=true;
-            if (alann[i].sequenceRef==null && !alann[i].autoCalculated) {
+            annotationAdded = true;
+            if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
+            {
               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
               newann.padAnnotation(alwidth);
               alignment.addAnnotation(newann);
             }
           }
         }
-     }
-     if (!newAlignment) {
-       ///////
-       // ADD HISTORY ITEM
-       //
-       addHistoryItem(new EditCommand(
-               "Add sequences",
-               EditCommand.PASTE,
-               sequences,
-               0,
-               alignment.getWidth(),
-               alignment)
-              );
-     }
-     // Add any annotations attached to sequences
-     for (int i = 0; i < sequences.length; i++)
-     {
-       if (sequences[i].getAnnotation() != null)
-       {
-         for (int a = 0; a < sequences[i].getAnnotation().length; a++)
-         {
-           annotationAdded=true;
-           sequences[i].getAnnotation()[a].adjustForAlignment();
-           sequences[i].getAnnotation()[a].padAnnotation(alwidth);
-           alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation was duplicated earlier
-           alignment.setAnnotationIndex(sequences[i].getAnnotation()[a], a);
-         }
-       }
-     }
-     if (!newAlignment) {
-
-       // propagate alignment changed.
-       viewport.setEndSeq(alignment.getHeight());
-       if (annotationAdded)
-       {
-         // Duplicate sequence annotation in all views.
-         AlignmentI[] alview = this.getViewAlignments();
-         for (int i = 0; i < sequences.length; i++)
-         {
-           AlignmentAnnotation sann[] = sequences[i].getAnnotation();
-           if (sann == null)
-             continue;
-           for (int avnum=0;avnum<alview.length; avnum++)
-           {
-             if (alview[avnum]!=alignment)
-             {
-               // duplicate in a view other than the one with input focus
-               int avwidth = alview[avnum].getWidth()+1;
-               // this relies on sann being preserved after we 
-               // modify the sequence's annotation array for each duplication
-               for (int a=0; a<sann.length; a++)
-               {
-                 AlignmentAnnotation newann = new AlignmentAnnotation(sann[a]);
-                 sequences[i].addAlignmentAnnotation(newann);
-                 newann.padAnnotation(avwidth);
-                 alview[avnum].addAnnotation(newann); // annotation was duplicated earlier
-                 alview[avnum].setAnnotationIndex(newann, a);
-               }
-             }
-           }
-         }
-         buildSortByAnnotationScoresMenu();
-       }
-       viewport.firePropertyChange("alignment", null, alignment.getSequences());
-
-     } else {
-       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, DEFAULT_HEIGHT);
-       String newtitle = new String("Copied sequences");
-
-       if(Desktop.jalviewClipboard!=null && Desktop.jalviewClipboard[2]!=null)
-         {
-           Vector hc = (Vector)Desktop.jalviewClipboard[2];
-           for(int i=0; i<hc.size(); i++)
-           {
-             int [] region = (int[]) hc.elementAt(i);
-             af.viewport.hideColumns(region[0], region[1]);
-           }
-         }
-
-
-       //>>>This is a fix for the moment, until a better solution is found!!<<<
-       af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
-           alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
-
-       // TODO: maintain provenance of an alignment, rather than just make the title a concatenation of operations.
-       if (!externalPaste) {
-         if (title.startsWith("Copied sequences"))
-         {
-           newtitle = title;
-         }
-         else
-         {
-           newtitle = newtitle.concat("- from " + title);
-         }
-       } else {
-         newtitle = new String("Pasted sequences");
-       }
-
-       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
-                                DEFAULT_HEIGHT);
-
-     }
-
-
-    }
-    catch (Exception ex)
+      }
+      if (!newAlignment)
+      {
+        // /////
+        // ADD HISTORY ITEM
+        //
+        addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
+                sequences, 0, alignment.getWidth(), alignment));
+      }
+      // Add any annotations attached to sequences
+      for (int i = 0; i < sequences.length; i++)
+      {
+        if (sequences[i].getAnnotation() != null)
+        {
+          for (int a = 0; a < sequences[i].getAnnotation().length; a++)
+          {
+            annotationAdded = true;
+            sequences[i].getAnnotation()[a].adjustForAlignment();
+            sequences[i].getAnnotation()[a].padAnnotation(alwidth);
+            alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
+            // was
+            // duplicated
+            // earlier
+            alignment
+                    .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
+          }
+        }
+      }
+      if (!newAlignment)
+      {
+
+        // propagate alignment changed.
+        viewport.setEndSeq(alignment.getHeight());
+        if (annotationAdded)
+        {
+          // Duplicate sequence annotation in all views.
+          AlignmentI[] alview = this.getViewAlignments();
+          for (int i = 0; i < sequences.length; i++)
+          {
+            AlignmentAnnotation sann[] = sequences[i].getAnnotation();
+            if (sann == null)
+              continue;
+            for (int avnum = 0; avnum < alview.length; avnum++)
+            {
+              if (alview[avnum] != alignment)
+              {
+                // duplicate in a view other than the one with input focus
+                int avwidth = alview[avnum].getWidth() + 1;
+                // this relies on sann being preserved after we
+                // modify the sequence's annotation array for each duplication
+                for (int a = 0; a < sann.length; a++)
+                {
+                  AlignmentAnnotation newann = new AlignmentAnnotation(
+                          sann[a]);
+                  sequences[i].addAlignmentAnnotation(newann);
+                  newann.padAnnotation(avwidth);
+                  alview[avnum].addAnnotation(newann); // annotation was
+                  // duplicated earlier
+                  alview[avnum].setAnnotationIndex(newann, a);
+                }
+              }
+            }
+          }
+          buildSortByAnnotationScoresMenu();
+        }
+        viewport.firePropertyChange("alignment", null, alignment
+                .getSequences());
+
+      }
+      else
+      {
+        AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
+                DEFAULT_HEIGHT);
+        String newtitle = new String("Copied sequences");
+
+        if (Desktop.jalviewClipboard != null
+                && Desktop.jalviewClipboard[2] != null)
+        {
+          Vector hc = (Vector) Desktop.jalviewClipboard[2];
+          for (int i = 0; i < hc.size(); i++)
+          {
+            int[] region = (int[]) hc.elementAt(i);
+            af.viewport.hideColumns(region[0], region[1]);
+          }
+        }
+
+        // >>>This is a fix for the moment, until a better solution is
+        // found!!<<<
+        af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
+                .transferSettings(
+                        alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+
+        // TODO: maintain provenance of an alignment, rather than just make the
+        // title a concatenation of operations.
+        if (!externalPaste)
+        {
+          if (title.startsWith("Copied sequences"))
+          {
+            newtitle = title;
+          }
+          else
+          {
+            newtitle = newtitle.concat("- from " + title);
+          }
+        }
+        else
+        {
+          newtitle = new String("Pasted sequences");
+        }
+
+        Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
+                DEFAULT_HEIGHT);
+
+      }
+
+    } catch (Exception ex)
     {
       ex.printStackTrace();
-        System.out.println("Exception whilst pasting: "+ex);
-        // could be anything being pasted in here
+      System.out.println("Exception whilst pasting: " + ex);
+      // could be anything being pasted in here
     }
 
-
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void cut_actionPerformed(ActionEvent e)
   {
@@ -1751,8 +1721,9 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void delete_actionPerformed(ActionEvent evt)
   {
@@ -1771,46 +1742,38 @@ public class AlignFrame
       seqs.addElement(seq);
     }
 
-
-   // If the cut affects all sequences, remove highlighted columns
-   if (sg.getSize() == viewport.alignment.getHeight())
-   {
-     viewport.getColumnSelection().removeElements(sg.getStartRes(),
-         sg.getEndRes() + 1);
-   }
-
-
-    SequenceI [] cut = new SequenceI[seqs.size()];
-    for(int i=0; i<seqs.size(); i++)
+    // If the cut affects all sequences, remove highlighted columns
+    if (sg.getSize() == viewport.alignment.getHeight())
     {
-      cut[i] = (SequenceI)seqs.elementAt(i);
+      viewport.getColumnSelection().removeElements(sg.getStartRes(),
+              sg.getEndRes() + 1);
     }
 
+    SequenceI[] cut = new SequenceI[seqs.size()];
+    for (int i = 0; i < seqs.size(); i++)
+    {
+      cut[i] = (SequenceI) seqs.elementAt(i);
+    }
 
     /*
-    //ADD HISTORY ITEM
-    */
-    addHistoryItem(new EditCommand("Cut Sequences",
-                                      EditCommand.CUT,
-                                      cut,
-                                      sg.getStartRes(),
-                                      sg.getEndRes()-sg.getStartRes()+1,
-                                      viewport.alignment));
-
+     * //ADD HISTORY ITEM
+     */
+    addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
+            sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
+            viewport.alignment));
 
     viewport.setSelectionGroup(null);
     viewport.alignment.deleteGroup(sg);
 
-    viewport.firePropertyChange("alignment", null,
-                                  viewport.getAlignment().getSequences());
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment()
+            .getSequences());
 
     if (viewport.getAlignment().getHeight() < 1)
     {
       try
       {
         this.setClosed(true);
-      }
-      catch (Exception ex)
+      } catch (Exception ex)
       {
       }
     }
@@ -1818,8 +1781,9 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void deleteGroups_actionPerformed(ActionEvent e)
   {
@@ -1832,15 +1796,15 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
     SequenceGroup sg = new SequenceGroup();
 
-    for (int i = 0; i < viewport.getAlignment().getSequences().size();
-         i++)
+    for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
     {
       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
     }
@@ -1853,12 +1817,13 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
-    if(viewport.cursorMode)
+    if (viewport.cursorMode)
     {
       alignPanel.seqPanel.keyboardNo1 = null;
       alignPanel.seqPanel.keyboardNo2 = null;
@@ -1874,8 +1839,9 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
   {
@@ -1888,8 +1854,7 @@ public class AlignFrame
       return;
     }
 
-    for (int i = 0; i < viewport.getAlignment().getSequences().size();
-         i++)
+    for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
     {
       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
     }
@@ -1905,11 +1870,11 @@ public class AlignFrame
     alignPanel.paintAlignment(true);
   }
 
-
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
   {
@@ -1918,12 +1883,13 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
   {
-      trimAlignment(false);
+    trimAlignment(false);
   }
 
   void trimAlignment(boolean trimLeft)
@@ -1933,7 +1899,7 @@ public class AlignFrame
 
     if (colSel.size() > 0)
     {
-      if(trimLeft)
+      if (trimLeft)
       {
         column = colSel.getMin();
       }
@@ -1942,43 +1908,35 @@ public class AlignFrame
         column = colSel.getMax();
       }
 
-      SequenceI [] seqs;
-      if(viewport.getSelectionGroup()!=null)
+      SequenceI[] seqs;
+      if (viewport.getSelectionGroup() != null)
       {
-        seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
-            hiddenRepSequences);
+        seqs = viewport.getSelectionGroup().getSequencesAsArray(
+                viewport.hiddenRepSequences);
       }
       else
       {
         seqs = viewport.alignment.getSequencesArray();
       }
 
-
       TrimRegionCommand trimRegion;
-      if(trimLeft)
+      if (trimLeft)
+      {
+        trimRegion = new TrimRegionCommand("Remove Left",
+                TrimRegionCommand.TRIM_LEFT, seqs, column,
+                viewport.alignment, viewport.colSel,
+                viewport.selectionGroup);
+        viewport.setStartRes(0);
+      }
+      else
       {
-        trimRegion = new TrimRegionCommand("Remove Left",
-                                    TrimRegionCommand.TRIM_LEFT,
-                                    seqs,
-                                    column,
-                                    viewport.alignment,
-                                    viewport.colSel,
-                                    viewport.selectionGroup);
-        viewport.setStartRes(0);
+        trimRegion = new TrimRegionCommand("Remove Right",
+                TrimRegionCommand.TRIM_RIGHT, seqs, column,
+                viewport.alignment, viewport.colSel,
+                viewport.selectionGroup);
       }
-     else
-     {
-       trimRegion = new TrimRegionCommand("Remove Right",
-                                   TrimRegionCommand.TRIM_RIGHT,
-                                   seqs,
-                                   column,
-                                   viewport.alignment,
-                                   viewport.colSel,
-                                   viewport.selectionGroup);
-     }
-
-     statusBar.setText("Removed "+trimRegion.getSize()+" columns.");
 
+      statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
 
       addHistoryItem(trimRegion);
 
@@ -1988,32 +1946,33 @@ public class AlignFrame
       {
         SequenceGroup sg = (SequenceGroup) groups.get(i);
 
-        if ( (trimLeft && !sg.adjustForRemoveLeft(column))
-            || (!trimLeft && !sg.adjustForRemoveRight(column)))
+        if ((trimLeft && !sg.adjustForRemoveLeft(column))
+                || (!trimLeft && !sg.adjustForRemoveRight(column)))
         {
           viewport.alignment.deleteGroup(sg);
         }
       }
 
-      viewport.firePropertyChange("alignment", null,
-                                  viewport.getAlignment().getSequences());
+      viewport.firePropertyChange("alignment", null, viewport
+              .getAlignment().getSequences());
     }
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
   {
-    int start = 0, end = viewport.alignment.getWidth()-1;
+    int start = 0, end = viewport.alignment.getWidth() - 1;
 
     SequenceI[] seqs;
     if (viewport.getSelectionGroup() != null)
     {
-      seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
-          hiddenRepSequences);
+      seqs = viewport.getSelectionGroup().getSequencesAsArray(
+              viewport.hiddenRepSequences);
       start = viewport.getSelectionGroup().getStartRes();
       end = viewport.getSelectionGroup().getEndRes();
     }
@@ -2022,46 +1981,44 @@ public class AlignFrame
       seqs = viewport.alignment.getSequencesArray();
     }
 
-
-    RemoveGapColCommand removeGapCols =
-        new RemoveGapColCommand("Remove Gapped Columns",
-                                seqs,
-                                start, end,
-                                viewport.alignment);
+    RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
+            "Remove Gapped Columns", seqs, start, end, viewport.alignment);
 
     addHistoryItem(removeGapCols);
 
-    statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns.");
+    statusBar.setText("Removed " + removeGapCols.getSize()
+            + " empty columns.");
 
-    //This is to maintain viewport position on first residue
-    //of first sequence
+    // This is to maintain viewport position on first residue
+    // of first sequence
     SequenceI seq = viewport.alignment.getSequenceAt(0);
     int startRes = seq.findPosition(viewport.startRes);
-   // ShiftList shifts;
-   // viewport.getAlignment().removeGaps(shifts=new ShiftList());
-   // edit.alColumnChanges=shifts.getInverse();
-   // if (viewport.hasHiddenColumns)
-   //   viewport.getColumnSelection().compensateForEdits(shifts);
-   viewport.setStartRes(seq.findIndex(startRes)-1);
-    viewport.firePropertyChange("alignment", null,
-                                viewport.getAlignment().getSequences());
+    // ShiftList shifts;
+    // viewport.getAlignment().removeGaps(shifts=new ShiftList());
+    // edit.alColumnChanges=shifts.getInverse();
+    // if (viewport.hasHiddenColumns)
+    // viewport.getColumnSelection().compensateForEdits(shifts);
+    viewport.setStartRes(seq.findIndex(startRes) - 1);
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment()
+            .getSequences());
 
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
   {
-    int start = 0, end = viewport.alignment.getWidth()-1;
+    int start = 0, end = viewport.alignment.getWidth() - 1;
 
     SequenceI[] seqs;
     if (viewport.getSelectionGroup() != null)
     {
-      seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
-          hiddenRepSequences);
+      seqs = viewport.getSelectionGroup().getSequencesAsArray(
+              viewport.hiddenRepSequences);
       start = viewport.getSelectionGroup().getStartRes();
       end = viewport.getSelectionGroup().getEndRes();
     }
@@ -2070,41 +2027,40 @@ public class AlignFrame
       seqs = viewport.alignment.getSequencesArray();
     }
 
-    //This is to maintain viewport position on first residue
-    //of first sequence
+    // This is to maintain viewport position on first residue
+    // of first sequence
     SequenceI seq = viewport.alignment.getSequenceAt(0);
     int startRes = seq.findPosition(viewport.startRes);
 
-    addHistoryItem(new RemoveGapsCommand("Remove Gaps",
-                                         seqs,
-                                         start, end,
-                                         viewport.alignment));
+    addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
+            viewport.alignment));
 
-    viewport.setStartRes(seq.findIndex(startRes)-1);
+    viewport.setStartRes(seq.findIndex(startRes) - 1);
 
-    viewport.firePropertyChange("alignment", null,
-                                viewport.getAlignment().getSequences());
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment()
+            .getSequences());
 
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void padGapsMenuitem_actionPerformed(ActionEvent e)
   {
     viewport.padGaps = padGapsMenuitem.isSelected();
 
-    viewport.firePropertyChange("alignment",
-                                null,
-                                viewport.getAlignment().getSequences());
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment()
+            .getSequences());
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void findMenuItem_actionPerformed(ActionEvent e)
   {
@@ -2113,8 +2069,8 @@ public class AlignFrame
 
   public void newView_actionPerformed(ActionEvent e)
   {
-    AlignmentPanel newap =
-        new Jalview2XML().copyAlignPanel(alignPanel, true);
+    AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
+            true);
 
     newap.av.gatherViewsHere = false;
 
@@ -2127,33 +2083,33 @@ public class AlignFrame
     newap.av.redoList = viewport.redoList;
 
     int index = Desktop.getViewCount(viewport.getSequenceSetId());
-    String newViewName = "View " +index;
+    String newViewName = "View " + index;
 
-    Vector comps = (Vector) PaintRefresher.components.get(viewport.
-        getSequenceSetId());
+    Vector comps = (Vector) PaintRefresher.components.get(viewport
+            .getSequenceSetId());
     Vector existingNames = new Vector();
-    for(int i=0; i<comps.size(); i++)
+    for (int i = 0; i < comps.size(); i++)
     {
-      if(comps.elementAt(i) instanceof AlignmentPanel)
+      if (comps.elementAt(i) instanceof AlignmentPanel)
       {
-        AlignmentPanel ap = (AlignmentPanel)comps.elementAt(i);
-        if(!existingNames.contains(ap.av.viewName))
+        AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
+        if (!existingNames.contains(ap.av.viewName))
         {
           existingNames.addElement(ap.av.viewName);
+        }
       }
     }
-    }
 
-    while(existingNames.contains(newViewName))
+    while (existingNames.contains(newViewName))
     {
-      newViewName = "View "+ (++index);
+      newViewName = "View " + (++index);
     }
 
     newap.av.viewName = newViewName;
 
     addAlignmentPanel(newap, false);
 
-    if(alignPanels.size()==2)
+    if (alignPanels.size() == 2)
     {
       viewport.gatherViewsHere = true;
     }
@@ -2162,7 +2118,7 @@ public class AlignFrame
 
   public void expandViews_actionPerformed(ActionEvent e)
   {
-        Desktop.instance.explodeViews(this);
+    Desktop.instance.explodeViews(this);
   }
 
   public void gatherViews_actionPerformed(ActionEvent e)
@@ -2170,29 +2126,29 @@ public class AlignFrame
     Desktop.instance.gatherViews(this);
   }
 
-
-
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void font_actionPerformed(ActionEvent e)
   {
     new FontChooser(alignPanel);
   }
 
-
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void seqLimit_actionPerformed(ActionEvent e)
   {
     viewport.setShowJVSuffix(seqLimits.isSelected());
 
-    alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
+    alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
+            .calculateIdWidth());
     alignPanel.paintAlignment(true);
   }
 
@@ -2208,12 +2164,11 @@ public class AlignFrame
     alignPanel.paintAlignment(true);
   }
 
-
-
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
   {
@@ -2223,8 +2178,9 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void wrapMenuItem_actionPerformed(ActionEvent e)
   {
@@ -2266,8 +2222,9 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void scaleAbove_actionPerformed(ActionEvent e)
   {
@@ -2277,8 +2234,9 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void scaleLeft_actionPerformed(ActionEvent e)
   {
@@ -2288,8 +2246,9 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void scaleRight_actionPerformed(ActionEvent e)
   {
@@ -2299,8 +2258,9 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
   {
@@ -2310,8 +2270,9 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void viewTextMenuItem_actionPerformed(ActionEvent e)
   {
@@ -2321,8 +2282,9 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
   {
@@ -2330,11 +2292,11 @@ public class AlignFrame
     alignPanel.paintAlignment(true);
   }
 
-
   public FeatureSettings featureSettings;
+
   public void featureSettings_actionPerformed(ActionEvent e)
   {
-    if(featureSettings !=null )
+    if (featureSettings != null)
     {
       featureSettings.close();
       featureSettings = null;
@@ -2344,8 +2306,9 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
    */
   public void showSeqFeatures_actionPerformed(ActionEvent evt)
   {
@@ -2359,8 +2322,9 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
   {
@@ -2370,67 +2334,72 @@ public class AlignFrame
 
   public void alignmentProperties()
   {
-    JEditorPane editPane = new JEditorPane("text/html","");
+    JEditorPane editPane = new JEditorPane("text/html", "");
     editPane.setEditable(false);
     StringBuffer contents = new StringBuffer("<html>");
 
-    float avg  = 0;
-    int min=Integer.MAX_VALUE, max=0;
-    for(int i=0; i<viewport.alignment.getHeight(); i++)
+    float avg = 0;
+    int min = Integer.MAX_VALUE, max = 0;
+    for (int i = 0; i < viewport.alignment.getHeight(); i++)
     {
       int size = viewport.alignment.getSequenceAt(i).getEnd()
-          -viewport.alignment.getSequenceAt(i).getStart();
+              - viewport.alignment.getSequenceAt(i).getStart();
       avg += size;
-      if(size>max)
+      if (size > max)
         max = size;
-      if(size<min)
+      if (size < min)
         min = size;
     }
-    avg = avg/(float)viewport.alignment.getHeight();
+    avg = avg / (float) viewport.alignment.getHeight();
 
-    contents.append("<br>Sequences: "+ viewport.alignment.getHeight());
-    contents.append("<br>Minimum Sequence Length: "+min);
-    contents.append("<br>Maximum Sequence Length: "+max);
-    contents.append("<br>Average Length: "+(int)avg);
+    contents.append("<br>Sequences: " + viewport.alignment.getHeight());
+    contents.append("<br>Minimum Sequence Length: " + min);
+    contents.append("<br>Maximum Sequence Length: " + max);
+    contents.append("<br>Average Length: " + (int) avg);
 
-    if (((Alignment)viewport.alignment).getProperties() != null)
+    if (((Alignment) viewport.alignment).getProperties() != null)
     {
-      Hashtable props = ((Alignment)viewport.alignment).getProperties();
+      Hashtable props = ((Alignment) viewport.alignment).getProperties();
       Enumeration en = props.keys();
       contents.append("<br><br><table border=\"1\">");
-      while(en.hasMoreElements())
+      while (en.hasMoreElements())
       {
         String key = en.nextElement().toString();
         StringBuffer val = new StringBuffer();
         String vals = props.get(key).toString();
-        int pos=0, npos;
-        do {
-          npos = vals.indexOf("\n",pos);
-          if (npos==-1)
+        int pos = 0, npos;
+        do
+        {
+          npos = vals.indexOf("\n", pos);
+          if (npos == -1)
           {
             val.append(vals.substring(pos));
-          } else {
+          }
+          else
+          {
             val.append(vals.substring(pos, npos));
             val.append("<br>");
           }
-          pos = npos+1;
-        } while (npos!=-1);
-        contents.append("<tr><td>"+key+"</td><td>"+val+"</td></tr>");
+          pos = npos + 1;
+        } while (npos != -1);
+        contents
+                .append("<tr><td>" + key + "</td><td>" + val + "</td></tr>");
       }
       contents.append("</table>");
     }
-    editPane.setText(contents.toString()+"</html>");
+    editPane.setText(contents.toString() + "</html>");
     JInternalFrame frame = new JInternalFrame();
     frame.getContentPane().add(new JScrollPane(editPane));
 
-    Desktop.instance.addInternalFrame(frame,"Alignment Properties: "+getTitle(),500,400);
+    Desktop.instance.addInternalFrame(frame, "Alignment Properties: "
+            + getTitle(), 500, 400);
   }
 
-
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void overviewMenuItem_actionPerformed(ActionEvent e)
   {
@@ -2442,19 +2411,19 @@ public class AlignFrame
     JInternalFrame frame = new JInternalFrame();
     OverviewPanel overview = new OverviewPanel(alignPanel);
     frame.setContentPane(overview);
-    Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
-                             frame.getWidth(), frame.getHeight());
+    Desktop.addInternalFrame(frame, "Overview " + this.getTitle(), frame
+            .getWidth(), frame.getHeight());
     frame.pack();
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
-    frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
-    {
-      public void internalFrameClosed(
-          javax.swing.event.InternalFrameEvent evt)
-      {
-        alignPanel.setOverviewPanel(null);
-      }
-      ;
-    });
+    frame
+            .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+            {
+              public void internalFrameClosed(
+                      javax.swing.event.InternalFrameEvent evt)
+              {
+                alignPanel.setOverviewPanel(null);
+              };
+            });
 
     alignPanel.setOverviewPanel(overview);
   }
@@ -2466,8 +2435,9 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void noColourmenuItem_actionPerformed(ActionEvent e)
   {
@@ -2476,19 +2446,22 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void clustalColour_actionPerformed(ActionEvent e)
   {
     changeColour(new ClustalxColourScheme(
-        viewport.alignment.getSequences(), viewport.alignment.getWidth()));
+            viewport.alignment.getSequences(), viewport.alignment
+                    .getWidth()));
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void zappoColour_actionPerformed(ActionEvent e)
   {
@@ -2497,8 +2470,9 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void taylorColour_actionPerformed(ActionEvent e)
   {
@@ -2507,8 +2481,9 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void hydrophobicityColour_actionPerformed(ActionEvent e)
   {
@@ -2517,8 +2492,9 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void helixColour_actionPerformed(ActionEvent e)
   {
@@ -2527,8 +2503,9 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void strandColour_actionPerformed(ActionEvent e)
   {
@@ -2537,8 +2514,9 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void turnColour_actionPerformed(ActionEvent e)
   {
@@ -2547,8 +2525,9 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void buriedColour_actionPerformed(ActionEvent e)
   {
@@ -2557,8 +2536,9 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void nucleotideColour_actionPerformed(ActionEvent e)
   {
@@ -2570,11 +2550,11 @@ public class AlignFrame
     new AnnotationColourChooser(viewport, alignPanel);
   }
 
-
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void applyToAllGroups_actionPerformed(ActionEvent e)
   {
@@ -2583,22 +2563,22 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param cs DOCUMENT ME!
+   * 
+   * @param cs
+   *                DOCUMENT ME!
    */
   public void changeColour(ColourSchemeI cs)
   {
     int threshold = 0;
 
-    if(cs!=null)
+    if (cs != null)
     {
       if (viewport.getAbovePIDThreshold())
       {
         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
-                                                   "Background");
+                "Background");
 
-        cs.setThreshold(threshold,
-                        viewport.getIgnoreGapsConsensus());
+        cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
 
         viewport.setGlobalColourScheme(cs);
       }
@@ -2612,17 +2592,16 @@ public class AlignFrame
 
         Alignment al = (Alignment) viewport.alignment;
         Conservation c = new Conservation("All",
-                                          ResidueProperties.propHash, 3,
-                                          al.getSequences(), 0,
-                                          al.getWidth() - 1);
+                ResidueProperties.propHash, 3, al.getSequences(), 0, al
+                        .getWidth() - 1);
 
         c.calculate();
         c.verdict(false, viewport.ConsPercGaps);
 
         cs.setConservation(c);
 
-        cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
-            "Background"));
+        cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
+                cs, "Background"));
       }
       else
       {
@@ -2650,49 +2629,44 @@ public class AlignFrame
 
         if (cs instanceof ClustalxColourScheme)
         {
-          sg.cs = new ClustalxColourScheme(
-              sg.getSequences(viewport.hiddenRepSequences), sg.getWidth());
+          sg.cs = new ClustalxColourScheme(sg
+                  .getSequences(viewport.hiddenRepSequences), sg.getWidth());
         }
         else if (cs instanceof UserColourScheme)
         {
-          sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
+          sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
         }
         else
         {
           try
           {
             sg.cs = (ColourSchemeI) cs.getClass().newInstance();
-          }
-          catch (Exception ex)
+          } catch (Exception ex)
           {
           }
         }
 
         if (viewport.getAbovePIDThreshold()
-            || cs instanceof PIDColourScheme
-            || cs instanceof Blosum62ColourScheme)
+                || cs instanceof PIDColourScheme
+                || cs instanceof Blosum62ColourScheme)
         {
-         sg.cs.setThreshold(threshold,
-                viewport.getIgnoreGapsConsensus());
+          sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
 
-         sg.cs.setConsensus(AAFrequency.calculate(
-             sg.getSequences(viewport.hiddenRepSequences), sg.getStartRes(),
-             sg.getEndRes()+1));
-       }
+          sg.cs.setConsensus(AAFrequency.calculate(sg
+                  .getSequences(viewport.hiddenRepSequences), sg
+                  .getStartRes(), sg.getEndRes() + 1));
+        }
         else
         {
           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
         }
 
-
         if (viewport.getConservationSelected())
         {
           Conservation c = new Conservation("Group",
-                                            ResidueProperties.propHash, 3,
-                                            sg.getSequences(viewport.
-              hiddenRepSequences),
-                                            sg.getStartRes(),
-                                            sg.getEndRes()+1);
+                  ResidueProperties.propHash, 3, sg
+                          .getSequences(viewport.hiddenRepSequences), sg
+                          .getStartRes(), sg.getEndRes() + 1);
           c.calculate();
           c.verdict(false, viewport.ConsPercGaps);
           sg.cs.setConservation(c);
@@ -2700,57 +2674,57 @@ public class AlignFrame
         else
         {
           sg.cs.setConservation(null);
+        }
       }
     }
-    }
 
     if (alignPanel.getOverviewPanel() != null)
     {
       alignPanel.getOverviewPanel().updateOverviewImage();
     }
 
-
-
-
     alignPanel.paintAlignment(true);
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void modifyPID_actionPerformed(ActionEvent e)
   {
-    if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
+    if (viewport.getAbovePIDThreshold()
+            && viewport.globalColourScheme != null)
     {
-      SliderPanel.setPIDSliderSource(alignPanel,
-                                     viewport.getGlobalColourScheme(),
-                                     "Background");
+      SliderPanel.setPIDSliderSource(alignPanel, viewport
+              .getGlobalColourScheme(), "Background");
       SliderPanel.showPIDSlider();
     }
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void modifyConservation_actionPerformed(ActionEvent e)
   {
-    if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
+    if (viewport.getConservationSelected()
+            && viewport.globalColourScheme != null)
     {
       SliderPanel.setConservationSlider(alignPanel,
-                                        viewport.globalColourScheme,
-                                        "Background");
+              viewport.globalColourScheme, "Background");
       SliderPanel.showConservationSlider();
     }
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void conservationMenuItem_actionPerformed(ActionEvent e)
   {
@@ -2766,8 +2740,9 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void abovePIDThreshold_actionPerformed(ActionEvent e)
   {
@@ -2783,8 +2758,9 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void userDefinedColour_actionPerformed(ActionEvent e)
   {
@@ -2794,8 +2770,8 @@ public class AlignFrame
     }
     else
     {
-      UserColourScheme udc = (UserColourScheme) UserDefinedColours.
-          getUserColourSchemes().get(e.getActionCommand());
+      UserColourScheme udc = (UserColourScheme) UserDefinedColours
+              .getUserColourSchemes().get(e.getActionCommand());
 
       changeColour(udc);
     }
@@ -2808,8 +2784,8 @@ public class AlignFrame
     int i, iSize = menuItems.length;
     for (i = 0; i < iSize; i++)
     {
-      if (menuItems[i].getName() != null &&
-          menuItems[i].getName().equals("USER_DEFINED"))
+      if (menuItems[i].getName() != null
+              && menuItems[i].getName().equals("USER_DEFINED"))
       {
         colourMenu.remove(menuItems[i]);
         iSize--;
@@ -2817,47 +2793,48 @@ public class AlignFrame
     }
     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
     {
-      java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
-          getUserColourSchemes().keys();
+      java.util.Enumeration userColours = jalview.gui.UserDefinedColours
+              .getUserColourSchemes().keys();
 
       while (userColours.hasMoreElements())
       {
         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
-            userColours.
-            nextElement().toString());
+                userColours.nextElement().toString());
         radioItem.setName("USER_DEFINED");
         radioItem.addMouseListener(new MouseAdapter()
+        {
+          public void mousePressed(MouseEvent evt)
+          {
+            if (evt.isControlDown()
+                    || SwingUtilities.isRightMouseButton(evt))
             {
-              public void mousePressed(MouseEvent evt)
-              {
-                if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
-                {
-                  radioItem.removeActionListener(radioItem.getActionListeners()[0]);
+              radioItem
+                      .removeActionListener(radioItem.getActionListeners()[0]);
 
-              int option = JOptionPane.showInternalConfirmDialog(jalview.gui.
-                  Desktop.desktop,
+              int option = JOptionPane.showInternalConfirmDialog(
+                      jalview.gui.Desktop.desktop,
                       "Remove from default list?",
                       "Remove user defined colour",
                       JOptionPane.YES_NO_OPTION);
-                  if(option == JOptionPane.YES_OPTION)
+              if (option == JOptionPane.YES_OPTION)
+              {
+                jalview.gui.UserDefinedColours
+                        .removeColourFromDefaults(radioItem.getText());
+                colourMenu.remove(radioItem);
+              }
+              else
+              {
+                radioItem.addActionListener(new ActionListener()
+                {
+                  public void actionPerformed(ActionEvent evt)
                   {
-                jalview.gui.UserDefinedColours.removeColourFromDefaults(
-                    radioItem.getText());
-                    colourMenu.remove(radioItem);
+                    userDefinedColour_actionPerformed(evt);
                   }
-                  else
-              {
-                    radioItem.addActionListener(new ActionListener()
-                    {
-                      public void actionPerformed(ActionEvent evt)
-                      {
-                        userDefinedColour_actionPerformed(evt);
-                      }
-                    });
-                }
+                });
               }
+            }
           }
-            });
+        });
         radioItem.addActionListener(new ActionListener()
         {
           public void actionPerformed(ActionEvent evt)
@@ -2874,8 +2851,9 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void PIDColour_actionPerformed(ActionEvent e)
   {
@@ -2884,8 +2862,9 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
   {
@@ -2894,27 +2873,29 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
   {
-    SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
-    AlignmentSorter.sortByPID(viewport.getAlignment(),
-                              viewport.getAlignment().getSequenceAt(0), null);
+    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+    AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
+            .getAlignment().getSequenceAt(0), null);
     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
-                                    viewport.alignment));
+            viewport.alignment));
     alignPanel.paintAlignment(true);
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void sortIDMenuItem_actionPerformed(ActionEvent e)
   {
-    SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
+    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByID(viewport.getAlignment());
     addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
     alignPanel.paintAlignment(true);
@@ -2922,42 +2903,45 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
   {
-    SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
+    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByGroup(viewport.getAlignment());
-    addHistoryItem(new OrderCommand("Group Sort", oldOrder, viewport.alignment));
+    addHistoryItem(new OrderCommand("Group Sort", oldOrder,
+            viewport.alignment));
 
     alignPanel.paintAlignment(true);
   }
+
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
   {
     new RedundancyPanel(alignPanel, this);
   }
 
-
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
   {
-    if ( (viewport.getSelectionGroup() == null) ||
-        (viewport.getSelectionGroup().getSize() < 2))
+    if ((viewport.getSelectionGroup() == null)
+            || (viewport.getSelectionGroup().getSize() < 2))
     {
       JOptionPane.showInternalMessageDialog(this,
-                                            "You must select at least 2 sequences.",
-                                            "Invalid Selection",
-                                            JOptionPane.WARNING_MESSAGE);
+              "You must select at least 2 sequences.", "Invalid Selection",
+              JOptionPane.WARNING_MESSAGE);
     }
     else
     {
@@ -2969,45 +2953,44 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void PCAMenuItem_actionPerformed(ActionEvent e)
   {
-    if ( ( (viewport.getSelectionGroup() != null) &&
-          (viewport.getSelectionGroup().getSize() < 4) &&
-          (viewport.getSelectionGroup().getSize() > 0)) ||
-        (viewport.getAlignment().getHeight() < 4))
+    if (((viewport.getSelectionGroup() != null)
+            && (viewport.getSelectionGroup().getSize() < 4) && (viewport
+            .getSelectionGroup().getSize() > 0))
+            || (viewport.getAlignment().getHeight() < 4))
     {
       JOptionPane.showInternalMessageDialog(this,
-                                            "Principal component analysis must take\n" +
-                                            "at least 4 input sequences.",
-                                            "Sequence selection insufficient",
-                                            JOptionPane.WARNING_MESSAGE);
+              "Principal component analysis must take\n"
+                      + "at least 4 input sequences.",
+              "Sequence selection insufficient",
+              JOptionPane.WARNING_MESSAGE);
 
       return;
     }
 
-     new PCAPanel(alignPanel);
+    new PCAPanel(alignPanel);
   }
 
-
   public void autoCalculate_actionPerformed(ActionEvent e)
   {
     viewport.autoCalculateConsensus = autoCalculate.isSelected();
-    if(viewport.autoCalculateConsensus)
+    if (viewport.autoCalculateConsensus)
     {
-      viewport.firePropertyChange("alignment",
-                                  null,
-                                  viewport.getAlignment().getSequences());
+      viewport.firePropertyChange("alignment", null, viewport
+              .getAlignment().getSequences());
     }
   }
 
-
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
   {
@@ -3016,8 +2999,9 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
   {
@@ -3026,8 +3010,9 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
   {
@@ -3036,8 +3021,9 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
   {
@@ -3046,10 +3032,13 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param type DOCUMENT ME!
-   * @param pwType DOCUMENT ME!
-   * @param title DOCUMENT ME!
+   * 
+   * @param type
+   *                DOCUMENT ME!
+   * @param pwType
+   *                DOCUMENT ME!
+   * @param title
+   *                DOCUMENT ME!
    */
   void NewTreePanel(String type, String pwType, String title)
   {
@@ -3059,10 +3048,11 @@ public class AlignFrame
     {
       if (viewport.getSelectionGroup().getSize() < 3)
       {
-        JOptionPane.showMessageDialog(Desktop.desktop,
-                                      "You need to have more than two sequences selected to build a tree!",
-                                      "Not enough sequences",
-                                      JOptionPane.WARNING_MESSAGE);
+        JOptionPane
+                .showMessageDialog(
+                        Desktop.desktop,
+                        "You need to have more than two sequences selected to build a tree!",
+                        "Not enough sequences", JOptionPane.WARNING_MESSAGE);
         return;
       }
 
@@ -3072,15 +3062,17 @@ public class AlignFrame
       /* Decide if the selection is a column region */
       while (s < sg.getSize())
       {
-        if ( ( (SequenceI) sg.getSequences(null).elementAt(s++)).getLength() <
-            sg.getEndRes())
+        if (((SequenceI) sg.getSequences(null).elementAt(s++)).getLength() < sg
+                .getEndRes())
         {
-          JOptionPane.showMessageDialog(Desktop.desktop,
-                                        "The selected region to create a tree may\nonly contain residues or gaps.\n" +
-                                        "Try using the Pad function in the edit menu,\n" +
-                                        "or one of the multiple sequence alignment web services.",
-                                        "Sequences in selection are not aligned",
-                                        JOptionPane.WARNING_MESSAGE);
+          JOptionPane
+                  .showMessageDialog(
+                          Desktop.desktop,
+                          "The selected region to create a tree may\nonly contain residues or gaps.\n"
+                                  + "Try using the Pad function in the edit menu,\n"
+                                  + "or one of the multiple sequence alignment web services.",
+                          "Sequences in selection are not aligned",
+                          JOptionPane.WARNING_MESSAGE);
 
           return;
         }
@@ -3091,20 +3083,22 @@ public class AlignFrame
     }
     else
     {
-      //are the sequences aligned?
+      // are the sequences aligned?
       if (!viewport.alignment.isAligned())
       {
-        JOptionPane.showMessageDialog(Desktop.desktop,
-                                      "The sequences must be aligned before creating a tree.\n" +
-                                      "Try using the Pad function in the edit menu,\n" +
-                                      "or one of the multiple sequence alignment web services.",
-                                      "Sequences not aligned",
-                                      JOptionPane.WARNING_MESSAGE);
+        JOptionPane
+                .showMessageDialog(
+                        Desktop.desktop,
+                        "The sequences must be aligned before creating a tree.\n"
+                                + "Try using the Pad function in the edit menu,\n"
+                                + "or one of the multiple sequence alignment web services.",
+                        "Sequences not aligned",
+                        JOptionPane.WARNING_MESSAGE);
 
         return;
       }
 
-      if(viewport.alignment.getHeight()<2)
+      if (viewport.alignment.getHeight() < 2)
       {
         return;
       }
@@ -3114,9 +3108,9 @@ public class AlignFrame
 
     title += " from ";
 
-    if(viewport.viewName!=null)
+    if (viewport.viewName != null)
     {
-      title+= viewport.viewName+" of ";
+      title += viewport.viewName + " of ";
     }
 
     title += this.title;
@@ -3126,11 +3120,14 @@ public class AlignFrame
 
   /**
    * DOCUMENT ME!
-   *
-   * @param title DOCUMENT ME!
-   * @param order DOCUMENT ME!
+   * 
+   * @param title
+   *                DOCUMENT ME!
+   * @param order
+   *                DOCUMENT ME!
    */
-  public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
+  public void addSortByOrderMenuItem(String title,
+          final AlignmentOrder order)
   {
     final JMenuItem item = new JMenuItem("by " + title);
     sort.add(item);
@@ -3138,24 +3135,31 @@ public class AlignFrame
     {
       public void actionPerformed(ActionEvent e)
       {
-        SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
+        SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
 
-        // TODO: JBPNote - have to map order entries to curent SequenceI pointers
+        // TODO: JBPNote - have to map order entries to curent SequenceI
+        // pointers
         AlignmentSorter.sortBy(viewport.getAlignment(), order);
 
         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
-                                        viewport.alignment));
+                viewport.alignment));
 
         alignPanel.paintAlignment(true);
       }
     });
   }
+
   /**
    * Add a new sort by annotation score menu item
-   * @param sort the menu to add the option to
-   * @param scoreLabel the label used to retrieve scores for each sequence on the alignment
+   * 
+   * @param sort
+   *                the menu to add the option to
+   * @param scoreLabel
+   *                the label used to retrieve scores for each sequence on the
+   *                alignment
    */
-  public void addSortByAnnotScoreMenuItem(JMenu sort, final String scoreLabel)
+  public void addSortByAnnotScoreMenuItem(JMenu sort,
+          final String scoreLabel)
   {
     final JMenuItem item = new JMenuItem(scoreLabel);
     sort.add(item);
@@ -3163,43 +3167,48 @@ public class AlignFrame
     {
       public void actionPerformed(ActionEvent e)
       {
-        SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
-        AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport.getAlignment());//,viewport.getSelectionGroup());
-        addHistoryItem(new OrderCommand("Sort by "+scoreLabel, oldOrder, viewport.alignment));
+        SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+        AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport
+                .getAlignment());// ,viewport.getSelectionGroup());
+        addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
+                viewport.alignment));
         alignPanel.paintAlignment(true);
       }
     });
   }
+
   /**
-   * last hash for alignment's annotation array - used to minimise cost of rebuild.
+   * last hash for alignment's annotation array - used to minimise cost of
+   * rebuild.
    */
   protected int _annotationScoreVectorHash;
+
   /**
-   * search the alignment and rebuild the sort by annotation score submenu
-   * the last alignment annotation vector hash is stored to minimize
-   * cost of rebuilding in subsequence calls.
-   *
+   * search the alignment and rebuild the sort by annotation score submenu the
+   * last alignment annotation vector hash is stored to minimize cost of
+   * rebuilding in subsequence calls.
+   * 
    */
   public void buildSortByAnnotationScoresMenu()
   {
-    if(viewport.alignment.getAlignmentAnnotation()==null)
+    if (viewport.alignment.getAlignmentAnnotation() == null)
     {
       return;
     }
 
-    if (viewport.alignment.getAlignmentAnnotation().hashCode()!=_annotationScoreVectorHash)
+    if (viewport.alignment.getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
     {
       sortByAnnotScore.removeAll();
       // almost certainly a quicker way to do this - but we keep it simple
-      Hashtable scoreSorts=new Hashtable();
+      Hashtable scoreSorts = new Hashtable();
       AlignmentAnnotation aann[];
       Enumeration sq = viewport.alignment.getSequences().elements();
       while (sq.hasMoreElements())
       {
         aann = ((SequenceI) sq.nextElement()).getAnnotation();
-        for (int i=0;aann!=null && i<aann.length; i++)
+        for (int i = 0; aann != null && i < aann.length; i++)
         {
-          if (aann[i].hasScore() && aann[i].sequenceRef!=null)
+          if (aann[i].hasScore() && aann[i].sequenceRef != null)
           {
             scoreSorts.put(aann[i].label, aann[i].label);
           }
@@ -3208,36 +3217,40 @@ public class AlignFrame
       Enumeration labels = scoreSorts.keys();
       while (labels.hasMoreElements())
       {
-        addSortByAnnotScoreMenuItem(sortByAnnotScore, (String) labels.nextElement());
+        addSortByAnnotScoreMenuItem(sortByAnnotScore, (String) labels
+                .nextElement());
       }
-      sortByAnnotScore.setVisible(scoreSorts.size()>0);
+      sortByAnnotScore.setVisible(scoreSorts.size() > 0);
       scoreSorts.clear();
 
-      _annotationScoreVectorHash =
-          viewport.alignment.getAlignmentAnnotation().hashCode();
+      _annotationScoreVectorHash = viewport.alignment
+              .getAlignmentAnnotation().hashCode();
     }
   }
 
   /**
-   * Maintain the Order by->Displayed Tree menu.
-   * Creates a new menu item for a TreePanel with an appropriate
-   * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
-   * to remove the menu item when the treePanel is closed, and adjust
-   * the tree leaf to sequence mapping when the alignment is modified.
-   * @param treePanel Displayed tree window.
-   * @param title SortBy menu item title.
+   * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
+   * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
+   * call. Listeners are added to remove the menu item when the treePanel is
+   * closed, and adjust the tree leaf to sequence mapping when the alignment is
+   * modified.
+   * 
+   * @param treePanel
+   *                Displayed tree window.
+   * @param title
+   *                SortBy menu item title.
    */
   public void buildTreeMenu()
   {
     sortByTreeMenu.removeAll();
 
-    Vector comps = (Vector) PaintRefresher.components.get(viewport.
-        getSequenceSetId());
+    Vector comps = (Vector) PaintRefresher.components.get(viewport
+            .getSequenceSetId());
     Vector treePanels = new Vector();
     int i, iSize = comps.size();
-    for(i=0; i<iSize; i++)
+    for (i = 0; i < iSize; i++)
     {
-      if(comps.elementAt(i) instanceof TreePanel)
+      if (comps.elementAt(i) instanceof TreePanel)
       {
         treePanels.add(comps.elementAt(i));
       }
@@ -3245,7 +3258,7 @@ public class AlignFrame
 
     iSize = treePanels.size();
 
-    if(iSize<1)
+    if (iSize < 1)
     {
       sortByTreeMenu.setVisible(false);
       return;
@@ -3253,21 +3266,21 @@ public class AlignFrame
 
     sortByTreeMenu.setVisible(true);
 
-    for(i=0; i<treePanels.size(); i++)
+    for (i = 0; i < treePanels.size(); i++)
     {
-      TreePanel tp = (TreePanel)treePanels.elementAt(i);
+      TreePanel tp = (TreePanel) treePanels.elementAt(i);
       final JMenuItem item = new JMenuItem(tp.getTitle());
-      final NJTree tree = ((TreePanel)treePanels.elementAt(i)).getTree();
+      final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
       item.addActionListener(new java.awt.event.ActionListener()
       {
         public void actionPerformed(ActionEvent e)
         {
-          SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+          SequenceI[] oldOrder = viewport.getAlignment()
+                  .getSequencesArray();
           AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
 
-          addHistoryItem(new OrderCommand("Tree Sort",
-                                          oldOrder,
-                                          viewport.alignment));
+          addHistoryItem(new OrderCommand("Tree Sort", oldOrder,
+                  viewport.alignment));
 
           alignPanel.paintAlignment(true);
         }
@@ -3278,61 +3291,57 @@ public class AlignFrame
   }
 
   /**
-   * Work out whether the whole set of sequences
-   * or just the selected set will be submitted for multiple alignment.
-   *
+   * Work out whether the whole set of sequences or just the selected set will
+   * be submitted for multiple alignment.
+   * 
    */
   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
   {
     // Now, check we have enough sequences
     AlignmentView msa = null;
 
-    if ( (viewport.getSelectionGroup() != null) &&
-        (viewport.getSelectionGroup().getSize() > 1))
-    {
-      // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
-      /*SequenceGroup seqs = viewport.getSelectionGroup();
-      int sz;
-      msa = new SequenceI[sz = seqs.getSize(false)];
-
-      for (int i = 0; i < sz; i++)
-      {
-        msa[i] = (SequenceI) seqs.getSequenceAt(i);
-      } */
+    if ((viewport.getSelectionGroup() != null)
+            && (viewport.getSelectionGroup().getSize() > 1))
+    {
+      // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
+      // some common interface!
+      /*
+       * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
+       * SequenceI[sz = seqs.getSize(false)];
+       * 
+       * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
+       * seqs.getSequenceAt(i); }
+       */
       msa = viewport.getAlignmentView(true);
     }
     else
     {
-      /*Vector seqs = viewport.getAlignment().getSequences();
-
-      if (seqs.size() > 1)
-      {
-        msa = new SequenceI[seqs.size()];
-
-        for (int i = 0; i < seqs.size(); i++)
-        {
-          msa[i] = (SequenceI) seqs.elementAt(i);
-        }
-      }*/
+      /*
+       * Vector seqs = viewport.getAlignment().getSequences();
+       * 
+       * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
+       * 
+       * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
+       * seqs.elementAt(i); } }
+       */
       msa = viewport.getAlignmentView(false);
     }
     return msa;
   }
 
   /**
-   * Decides what is submitted to a secondary structure prediction service:
-   * the first sequence in the alignment, or in the current selection,
-   * or, if the alignment is 'aligned' (ie padded with gaps), then the
-   * currently selected region or the whole alignment.
-   * (where the first sequence in the set is the one that the prediction
-   * will be for).
+   * Decides what is submitted to a secondary structure prediction service: the
+   * first sequence in the alignment, or in the current selection, or, if the
+   * alignment is 'aligned' (ie padded with gaps), then the currently selected
+   * region or the whole alignment. (where the first sequence in the set is the
+   * one that the prediction will be for).
    */
   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
   {
-   AlignmentView seqs = null;
+    AlignmentView seqs = null;
 
-    if ( (viewport.getSelectionGroup() != null) &&
-        (viewport.getSelectionGroup().getSize() > 0))
+    if ((viewport.getSelectionGroup() != null)
+            && (viewport.getSelectionGroup().getSize() > 0))
     {
       seqs = viewport.getAlignmentView(true);
     }
@@ -3340,26 +3349,29 @@ public class AlignFrame
     {
       seqs = viewport.getAlignmentView(false);
     }
-    // limit sequences - JBPNote in future - could spawn multiple prediction jobs
-    // TODO: viewport.alignment.isAligned is a global state - the local selection may well be aligned - we preserve 2.0.8 behaviour for moment.
+    // limit sequences - JBPNote in future - could spawn multiple prediction
+    // jobs
+    // TODO: viewport.alignment.isAligned is a global state - the local
+    // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
     if (!viewport.alignment.isAligned())
     {
       seqs.setSequences(new SeqCigar[]
-                        {seqs.getSequences()[0]});
+      { seqs.getSequences()[0] });
     }
     return seqs;
   }
+
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
   {
     // Pick the tree file
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-        getProperty(
-            "LAST_DIRECTORY"));
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+            .getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle("Select a newick-like tree file");
     chooser.setToolTipText("Load a tree file");
@@ -3373,60 +3385,62 @@ public class AlignFrame
       jalview.io.NewickFile fin = null;
       try
       {
-        fin = new jalview.io.NewickFile(choice,
-            "File");
+        fin = new jalview.io.NewickFile(choice, "File");
         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
-      }
-      catch (Exception ex)
+      } catch (Exception ex)
       {
-        JOptionPane.showMessageDialog(Desktop.desktop,
-                                      ex.getMessage(),
-                                      "Problem reading tree file",
-                                      JOptionPane.WARNING_MESSAGE);
+        JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
+                "Problem reading tree file", JOptionPane.WARNING_MESSAGE);
         ex.printStackTrace();
       }
-      if (fin!=null && fin.hasWarningMessage())
+      if (fin != null && fin.hasWarningMessage())
       {
-        JOptionPane.showMessageDialog(Desktop.desktop,
-                fin.getWarningMessage(),
-                "Possible problem with tree file",
+        JOptionPane.showMessageDialog(Desktop.desktop, fin
+                .getWarningMessage(), "Possible problem with tree file",
                 JOptionPane.WARNING_MESSAGE);
       }
     }
   }
 
-
   public TreePanel ShowNewickTree(NewickFile nf, String title)
   {
-    return ShowNewickTree(nf,title,600,500,4,5);
+    return ShowNewickTree(nf, title, 600, 500, 4, 5);
   }
 
   public TreePanel ShowNewickTree(NewickFile nf, String title,
-                                  AlignmentView input)
+          AlignmentView input)
   {
-    return ShowNewickTree(nf,title, input, 600,500,4,5);
+    return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
   }
 
-  public TreePanel ShowNewickTree(NewickFile nf, String title, int w, int h,
-                                  int x, int y)
+  public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
+          int h, int x, int y)
   {
     return ShowNewickTree(nf, title, null, w, h, x, y);
   }
+
   /**
-   * Add a treeviewer for the tree extracted from a newick file object to the current alignment view
-   *
-   * @param nf the tree
-   * @param title tree viewer title
-   * @param input Associated alignment input data (or null)
-   * @param w width
-   * @param h height
-   * @param x position
-   * @param y position
+   * Add a treeviewer for the tree extracted from a newick file object to the
+   * current alignment view
+   * 
+   * @param nf
+   *                the tree
+   * @param title
+   *                tree viewer title
+   * @param input
+   *                Associated alignment input data (or null)
+   * @param w
+   *                width
+   * @param h
+   *                height
+   * @param x
+   *                position
+   * @param y
+   *                position
    * @return TreePanel handle
    */
   public TreePanel ShowNewickTree(NewickFile nf, String title,
-                                  AlignmentView input, int w, int h, int x,
-                                  int y)
+          AlignmentView input, int w, int h, int x, int y)
   {
     TreePanel tp = null;
 
@@ -3436,49 +3450,49 @@ public class AlignFrame
 
       if (nf.getTree() != null)
       {
-        tp = new TreePanel(alignPanel,
-                           "FromFile",
-                           title,
-                           nf, input);
+        tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
 
-        tp.setSize(w,h);
+        tp.setSize(w, h);
 
-        if(x>0 && y>0)
+        if (x > 0 && y > 0)
         {
-          tp.setLocation(x,y);
+          tp.setLocation(x, y);
         }
 
-
         Desktop.addInternalFrame(tp, title, w, h);
       }
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       ex.printStackTrace();
     }
-    
+
     return tp;
   }
 
-
   /**
    * Generates menu items and listener event actions for web service clients
-   *
+   * 
    */
   public void BuildWebServiceMenu()
   {
-    // TODO: add support for context dependent disabling of services based on alignment and current selection
-    // TODO: add additional serviceHandle parameter to specify abstract handler class independently of AbstractName
+    // TODO: add support for context dependent disabling of services based on
+    // alignment and current selection
+    // TODO: add additional serviceHandle parameter to specify abstract handler
+    // class independently of AbstractName
     // TODO: add in rediscovery GUI function to restart discoverer
-    // TODO: group services by location as well as function and/or introduce object broker mechanism.
-    if ( (Discoverer.services != null)
-        && (Discoverer.services.size() > 0))
+    // TODO: group services by location as well as function and/or introduce
+    // object broker mechanism.
+    if ((Discoverer.services != null) && (Discoverer.services.size() > 0))
     {
-      // TODO: refactor to allow list of AbstractName/Handler bindings to be stored or retrieved from elsewhere
+      // TODO: refactor to allow list of AbstractName/Handler bindings to be
+      // stored or retrieved from elsewhere
       Vector msaws = (Vector) Discoverer.services.get("MsaWS");
       Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
       Vector seqsrch = (Vector) Discoverer.services.get("SeqSearch");
-      // TODO: move GUI generation code onto service implementation - so a client instance attaches itself to the GUI with method call like jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance, alignframe)
+      // TODO: move GUI generation code onto service implementation - so a
+      // client instance attaches itself to the GUI with method call like
+      // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
+      // alignframe)
       Vector wsmenu = new Vector();
       final IProgressIndicator af = this;
       if (msaws != null)
@@ -3487,11 +3501,12 @@ public class AlignFrame
         final JMenu msawsmenu = new JMenu("Alignment");
         for (int i = 0, j = msaws.size(); i < j; i++)
         {
-          final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
-              get(i);
-          jalview.ws.WSClient impl = jalview.ws.Discoverer.getServiceClient(sh);
+          final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
+                  .get(i);
+          jalview.ws.WSClient impl = jalview.ws.Discoverer
+                  .getServiceClient(sh);
           impl.attachWSMenuEntry(msawsmenu, this);
-        
+
         }
         wsmenu.add(msawsmenu);
       }
@@ -3501,31 +3516,33 @@ public class AlignFrame
         final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
         for (int i = 0, j = secstrpr.size(); i < j; i++)
         {
-          final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
-              secstrpr.get(i);
-          jalview.ws.WSClient impl = jalview.ws.Discoverer.getServiceClient(sh);
+          final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
+                  .get(i);
+          jalview.ws.WSClient impl = jalview.ws.Discoverer
+                  .getServiceClient(sh);
           impl.attachWSMenuEntry(secstrmenu, this);
         }
         wsmenu.add(secstrmenu);
       }
-      if (seqsrch!=null)
+      if (seqsrch != null)
       {
         // Add any sequence search services
         final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
         for (int i = 0, j = seqsrch.size(); i < j; i++)
         {
-          final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
-              seqsrch.elementAt(i);
-          jalview.ws.WSClient impl = jalview.ws.Discoverer.getServiceClient(sh);
+          final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
+                  .elementAt(i);
+          jalview.ws.WSClient impl = jalview.ws.Discoverer
+                  .getServiceClient(sh);
           impl.attachWSMenuEntry(seqsrchmenu, this);
         }
         // finally, add the whole shebang onto the webservices menu
-        wsmenu.add(seqsrchmenu); 
+        wsmenu.add(seqsrchmenu);
       }
       resetWebServiceMenu();
       for (int i = 0, j = wsmenu.size(); i < j; i++)
       {
-        webService.add( (JMenu) wsmenu.get(i));
+        webService.add((JMenu) wsmenu.get(i));
       }
     }
     else
@@ -3535,103 +3552,114 @@ public class AlignFrame
     }
   }
 
-
   /**
-   * empty the web service menu and add any ad-hoc functions
-   * not dynamically discovered.
-   *
+   * empty the web service menu and add any ad-hoc functions not dynamically
+   * discovered.
+   * 
    */
   private void resetWebServiceMenu()
   {
     webService.removeAll();
     // Temporary hack - DBRef Fetcher always top level ws entry.
     JMenuItem rfetch = new JMenuItem("Fetch DB References");
-    rfetch.setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
+    rfetch
+            .setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
     webService.add(rfetch);
-    rfetch.addActionListener(new ActionListener() {
+    rfetch.addActionListener(new ActionListener()
+    {
 
       public void actionPerformed(ActionEvent e)
       {
-        new Thread(new Runnable() {
+        new Thread(new Runnable()
+        {
 
           public void run()
           {
-            new jalview.ws.DBRefFetcher(
-                    alignPanel.av.getSequenceSelection(),
-                    alignPanel.alignFrame).fetchDBRefs(false);
+            new jalview.ws.DBRefFetcher(alignPanel.av
+                    .getSequenceSelection(), alignPanel.alignFrame)
+                    .fetchDBRefs(false);
           }
         }).start();
-        
+
       }
 
     });
   }
 
- /* public void vamsasStore_actionPerformed(ActionEvent e)
-  {
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-        getProperty("LAST_DIRECTORY"));
-
-    chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle("Export to Vamsas file");
-    chooser.setToolTipText("Export");
-
-    int value = chooser.showSaveDialog(this);
-
-    if (value == JalviewFileChooser.APPROVE_OPTION)
-    {
-      jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
-      //vs.store(chooser.getSelectedFile().getAbsolutePath()   );
-      vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
-    }
-  }*/
+  /*
+   * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
+   * chooser = new JalviewFileChooser(jalview.bin.Cache.
+   * getProperty("LAST_DIRECTORY"));
+   * 
+   * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
+   * to Vamsas file"); chooser.setToolTipText("Export");
+   * 
+   * int value = chooser.showSaveDialog(this);
+   * 
+   * if (value == JalviewFileChooser.APPROVE_OPTION) {
+   * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
+   * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
+   * chooser.getSelectedFile().getAbsolutePath(), this); } }
+   */
   /**
    * prototype of an automatically enabled/disabled analysis function
-   *
+   * 
    */
   protected void setShowProductsEnabled()
   {
-    SequenceI [] selection = viewport.getSequenceSelection();
-    if (canShowProducts(selection, viewport.getSelectionGroup()!=null, viewport.getAlignment().getDataset()))
+    SequenceI[] selection = viewport.getSequenceSelection();
+    if (canShowProducts(selection, viewport.getSelectionGroup() != null,
+            viewport.getAlignment().getDataset()))
     {
       showProducts.setEnabled(true);
-      
-    } else {
+
+    }
+    else
+    {
       showProducts.setEnabled(false);
     }
   }
+
   /**
-   * search selection for sequence xRef products and build the
-   * show products menu.
+   * search selection for sequence xRef products and build the show products
+   * menu.
+   * 
    * @param selection
    * @param dataset
    * @return true if showProducts menu should be enabled.
    */
-  public boolean canShowProducts(SequenceI[] selection, boolean isRegionSelection, Alignment dataset)
+  public boolean canShowProducts(SequenceI[] selection,
+          boolean isRegionSelection, Alignment dataset)
   {
-    boolean showp=false;
-    try {
+    boolean showp = false;
+    try
+    {
       showProducts.removeAll();
       final boolean dna = viewport.getAlignment().isNucleotide();
       final Alignment ds = dataset;
-      String[] ptypes = CrossRef.findSequenceXrefTypes(dna, selection, dataset);
-      //Object[] prods = CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(), selection, dataset, true);
+      String[] ptypes = CrossRef.findSequenceXrefTypes(dna, selection,
+              dataset);
+      // Object[] prods =
+      // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
+      // selection, dataset, true);
       final SequenceI[] sel = selection;
-      for (int t=0; ptypes!=null && t<ptypes.length; t++)
+      for (int t = 0; ptypes != null && t < ptypes.length; t++)
       {
-        showp=true;
+        showp = true;
         final boolean isRegSel = isRegionSelection;
         final AlignFrame af = this;
         final String source = ptypes[t];
         JMenuItem xtype = new JMenuItem(ptypes[t]);
-        xtype.addActionListener(new ActionListener() {
+        xtype.addActionListener(new ActionListener()
+        {
 
           public void actionPerformed(ActionEvent e)
           {
             // TODO: new thread for this call with vis-delay
-            af.showProductsFor(af.viewport.getSequenceSelection(), ds, isRegSel, dna, source);
+            af.showProductsFor(af.viewport.getSequenceSelection(), ds,
+                    isRegSel, dna, source);
           }
-          
+
         });
         showProducts.add(xtype);
       }
@@ -3639,164 +3667,202 @@ public class AlignFrame
       showProducts.setEnabled(showp);
     } catch (Exception e)
     {
-      jalview.bin.Cache.log.warn("canTranslate threw an exception - please report to help@jalview.org",e);
-     return false;
+      jalview.bin.Cache.log
+              .warn(
+                      "canTranslate threw an exception - please report to help@jalview.org",
+                      e);
+      return false;
     }
     return showp;
   }
-protected void showProductsFor(SequenceI[] sel, Alignment ds, boolean isRegSel, boolean dna, String source)
-  {
-  final boolean fisRegSel = isRegSel;
-  final boolean fdna = dna;
-  final String fsrc = source;
-  final AlignFrame ths = this;
-  final SequenceI[] fsel = sel;
-  Runnable foo = new Runnable() {
 
-    public void run()
+  protected void showProductsFor(SequenceI[] sel, Alignment ds,
+          boolean isRegSel, boolean dna, String source)
+  {
+    final boolean fisRegSel = isRegSel;
+    final boolean fdna = dna;
+    final String fsrc = source;
+    final AlignFrame ths = this;
+    final SequenceI[] fsel = sel;
+    Runnable foo = new Runnable()
     {
-      final long sttime = System.currentTimeMillis();
-      ths.setProgressBar("Searching for sequences from "+fsrc, sttime);
-      try {
-        Alignment ds = ths.getViewport().alignment.getDataset(); // update our local dataset reference
-      Alignment prods = CrossRef.findXrefSequences(fsel, fdna, fsrc, ds);
-      if (prods!=null)
+
+      public void run()
       {
-        SequenceI[] sprods = new SequenceI[prods.getHeight()];
-        for (int s=0; s<sprods.length;s++)
+        final long sttime = System.currentTimeMillis();
+        ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
+        try
         {
-          sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
-          if (ds.getSequences()==null || !ds.getSequences().contains(sprods[s].getDatasetSequence()))
-            ds.addSequence(sprods[s].getDatasetSequence());
-          sprods[s].updatePDBIds();
-        }
-        Alignment al = new Alignment(sprods);
-        AlignedCodonFrame[] cf = prods.getCodonFrames();
-        for (int s=0; cf!=null && s<cf.length; s++)
+          Alignment ds = ths.getViewport().alignment.getDataset(); // update
+          // our local
+          // dataset
+          // reference
+          Alignment prods = CrossRef
+                  .findXrefSequences(fsel, fdna, fsrc, ds);
+          if (prods != null)
+          {
+            SequenceI[] sprods = new SequenceI[prods.getHeight()];
+            for (int s = 0; s < sprods.length; s++)
+            {
+              sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
+              if (ds.getSequences() == null
+                      || !ds.getSequences().contains(
+                              sprods[s].getDatasetSequence()))
+                ds.addSequence(sprods[s].getDatasetSequence());
+              sprods[s].updatePDBIds();
+            }
+            Alignment al = new Alignment(sprods);
+            AlignedCodonFrame[] cf = prods.getCodonFrames();
+            for (int s = 0; cf != null && s < cf.length; s++)
+            {
+              al.addCodonFrame(cf[s]);
+              cf[s] = null;
+            }
+            al.setDataset(ds);
+            AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
+                    DEFAULT_HEIGHT);
+            String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
+                    + " for " + ((fisRegSel) ? "selected region of " : "")
+                    + getTitle();
+            Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
+                    DEFAULT_HEIGHT);
+          }
+          else
+          {
+            System.err.println("No Sequences generated for xRef type "
+                    + fsrc);
+          }
+        } catch (Exception e)
+        {
+          jalview.bin.Cache.log.error(
+                  "Exception when finding crossreferences", e);
+        } catch (OutOfMemoryError e)
+        {
+          new OOMWarning("whilst fetching crossreferences", e);
+        } catch (Error e)
         {
-          al.addCodonFrame(cf[s]);
-          cf[s] = null;
+          jalview.bin.Cache.log.error("Error when finding crossreferences",
+                  e);
         }
-        al.setDataset(ds);
-        AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
-        String newtitle =""+((fdna) ? "Proteins " : "Nucleotides ") + " for "+((fisRegSel) ? "selected region of " : "")
-                + getTitle();
-        Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
-                DEFAULT_HEIGHT);
-      } else {
-        System.err.println("No Sequences generated for xRef type "+fsrc);
-      }
-      }
-      catch (Exception e)
-      {
-        jalview.bin.Cache.log.error("Exception when finding crossreferences",e);
+        ths.setProgressBar("Finished searching for sequences from " + fsrc,
+                sttime);
       }
-      catch (Error e)
-      {
-        jalview.bin.Cache.log.error("Error when finding crossreferences",e);
-      }
-      ths.setProgressBar("Finished searching for sequences from "+fsrc, sttime);
-    }
-    
-  };
-  Thread frunner = new Thread(foo);
-  frunner.start();
-  }
 
+    };
+    Thread frunner = new Thread(foo);
+    frunner.start();
+  }
 
-public boolean canShowTranslationProducts(SequenceI[] selection, AlignmentI alignment)
-{
-  // old way
-  try {
-      return (jalview.analysis.Dna.canTranslate(selection, viewport.getViewAsVisibleContigs(true)));
-  } catch (Exception e)
+  public boolean canShowTranslationProducts(SequenceI[] selection,
+          AlignmentI alignment)
   {
-    jalview.bin.Cache.log.warn("canTranslate threw an exception - please report to help@jalview.org",e);
-   return false;
+    // old way
+    try
+    {
+      return (jalview.analysis.Dna.canTranslate(selection, viewport
+              .getViewAsVisibleContigs(true)));
+    } catch (Exception e)
+    {
+      jalview.bin.Cache.log
+              .warn(
+                      "canTranslate threw an exception - please report to help@jalview.org",
+                      e);
+      return false;
+    }
   }
-}
 
-public void showProducts_actionPerformed(ActionEvent e)
-{
-  ///////////////////////////////
-  // Collect Data to be translated/transferred
-  
-  SequenceI [] selection = viewport.getSequenceSelection();
-  AlignmentI al  = null;
-  try {
-      al = jalview.analysis.Dna.CdnaTranslate(selection, viewport.getViewAsVisibleContigs(true),
-          viewport.getGapCharacter(), viewport.getAlignment().getDataset());
-    } catch (Exception ex) {
+  public void showProducts_actionPerformed(ActionEvent e)
+  {
+    // /////////////////////////////
+    // Collect Data to be translated/transferred
+
+    SequenceI[] selection = viewport.getSequenceSelection();
+    AlignmentI al = null;
+    try
+    {
+      al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
+              .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
+              viewport.getAlignment().getDataset());
+    } catch (Exception ex)
+    {
       al = null;
-      jalview.bin.Cache.log.debug("Exception during translation.",ex);
+      jalview.bin.Cache.log.debug("Exception during translation.", ex);
+    }
+    if (al == null)
+    {
+      JOptionPane
+              .showMessageDialog(
+                      Desktop.desktop,
+                      "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
+                      "Translation Failed", JOptionPane.WARNING_MESSAGE);
     }
-    if (al==null)
+    else
     {
-      JOptionPane.showMessageDialog(Desktop.desktop,
-          "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
-          "Translation Failed",
-          JOptionPane.WARNING_MESSAGE);
-    } else {
       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
-      Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
-                               DEFAULT_WIDTH,
-                               DEFAULT_HEIGHT);
+      Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
+              DEFAULT_WIDTH, DEFAULT_HEIGHT);
     }
   }
 
-public void showTranslation_actionPerformed(ActionEvent e)
-{
-  ///////////////////////////////
-  // Collect Data to be translated/transferred
-
-  SequenceI [] selection = viewport.getSequenceSelection();
-  String [] seqstring = viewport.getViewAsString(true);
-  AlignmentI al  = null;
-  try {
-    al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring, viewport.getViewAsVisibleContigs(true),
-        viewport.getGapCharacter(), viewport.alignment.getAlignmentAnnotation(),
-        viewport.alignment.getWidth(), viewport.getAlignment().getDataset());
-  } catch (Exception ex) {
-    al = null;
-    jalview.bin.Cache.log.debug("Exception during translation.",ex);
-  }
-  if (al==null)
-  {
-    JOptionPane.showMessageDialog(Desktop.desktop,
-        "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
-        "Translation Failed",
-        JOptionPane.WARNING_MESSAGE);
-  } else {
-    AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
-    Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
-                             DEFAULT_WIDTH,
-                             DEFAULT_HEIGHT);
+  public void showTranslation_actionPerformed(ActionEvent e)
+  {
+    // /////////////////////////////
+    // Collect Data to be translated/transferred
+
+    SequenceI[] selection = viewport.getSequenceSelection();
+    String[] seqstring = viewport.getViewAsString(true);
+    AlignmentI al = null;
+    try
+    {
+      al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
+              viewport.getViewAsVisibleContigs(true), viewport
+                      .getGapCharacter(), viewport.alignment
+                      .getAlignmentAnnotation(), viewport.alignment
+                      .getWidth(), viewport.getAlignment().getDataset());
+    } catch (Exception ex)
+    {
+      al = null;
+      jalview.bin.Cache.log.debug("Exception during translation.", ex);
+    }
+    if (al == null)
+    {
+      JOptionPane
+              .showMessageDialog(
+                      Desktop.desktop,
+                      "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
+                      "Translation Failed", JOptionPane.WARNING_MESSAGE);
+    }
+    else
+    {
+      AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
+      Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
+              DEFAULT_WIDTH, DEFAULT_HEIGHT);
+    }
   }
-}
 
-/**
- * Try to load a features file onto the alignment.
- * @param file contents or path to retrieve file 
- * @param type access mode of file (see jalview.io.AlignFile)
- * @return true if features file was parsed corectly.
- */
-public boolean parseFeaturesFile(String file, String type)
-{
+  /**
+   * Try to load a features file onto the alignment.
+   * 
+   * @param file
+   *                contents or path to retrieve file
+   * @param type
+   *                access mode of file (see jalview.io.AlignFile)
+   * @return true if features file was parsed corectly.
+   */
+  public boolean parseFeaturesFile(String file, String type)
+  {
     boolean featuresFile = false;
     try
     {
-      featuresFile = new FeaturesFile(file,
-          type).parse(viewport.alignment.getDataset(),
-                                         alignPanel.seqPanel.seqCanvas.
-                                         getFeatureRenderer().featureColours,
-                                         false);
-    }
-    catch(Exception ex)
+      featuresFile = new FeaturesFile(file, type).parse(viewport.alignment
+              .getDataset(), alignPanel.seqPanel.seqCanvas
+              .getFeatureRenderer().featureColours, false);
+    } catch (Exception ex)
     {
       ex.printStackTrace();
     }
 
-    if(featuresFile)
+    if (featuresFile)
     {
       viewport.showSequenceFeatures = true;
       showSeqFeatures.setSelected(true);
@@ -3804,35 +3870,39 @@ public boolean parseFeaturesFile(String file, String type)
     }
 
     return featuresFile;
-}
+  }
 
-public void dragEnter(DropTargetDragEvent evt)
-{}
+  public void dragEnter(DropTargetDragEvent evt)
+  {
+  }
 
-public void dragExit(DropTargetEvent evt)
-{}
+  public void dragExit(DropTargetEvent evt)
+  {
+  }
 
-public void dragOver(DropTargetDragEvent evt)
-{}
+  public void dragOver(DropTargetDragEvent evt)
+  {
+  }
 
-public void dropActionChanged(DropTargetDragEvent evt)
-{}
+  public void dropActionChanged(DropTargetDragEvent evt)
+  {
+  }
 
-public void drop(DropTargetDropEvent evt)
-{
+  public void drop(DropTargetDropEvent evt)
+  {
     Transferable t = evt.getTransferable();
     java.util.List files = null;
 
     try
     {
       DataFlavor uriListFlavor = new DataFlavor(
-          "text/uri-list;class=java.lang.String");
+              "text/uri-list;class=java.lang.String");
       if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
       {
-        //Works on Windows and MacOSX
+        // Works on Windows and MacOSX
         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
-        files = (java.util.List) t.getTransferData(DataFlavor.
-            javaFileListFlavor);
+        files = (java.util.List) t
+                .getTransferData(DataFlavor.javaFileListFlavor);
       }
       else if (t.isDataFlavorSupported(uriListFlavor))
       {
@@ -3841,9 +3911,7 @@ public void drop(DropTargetDropEvent evt)
         String data = (String) t.getTransferData(uriListFlavor);
         files = new java.util.ArrayList(1);
         for (java.util.StringTokenizer st = new java.util.StringTokenizer(
-            data,
-            "\r\n");
-             st.hasMoreTokens(); )
+                data, "\r\n"); st.hasMoreTokens();)
         {
           String s = st.nextToken();
           if (s.startsWith("#"))
@@ -3857,8 +3925,7 @@ public void drop(DropTargetDropEvent evt)
           files.add(file);
         }
       }
-    }
-    catch (Exception e)
+    } catch (Exception e)
     {
       e.printStackTrace();
     }
@@ -3871,23 +3938,24 @@ public void drop(DropTargetDropEvent evt)
         {
           loadJalviewDataFile(files.get(i).toString());
         }
-      }
-      catch (Exception ex)
+      } catch (Exception ex)
       {
         ex.printStackTrace();
       }
     }
-}
+  }
 
-  /**     
-   * Attempt to load a "dropped" file: First by testing
-   * whether it's and Annotation file, then a JNet file, and finally a features file. If all are
+  /**
+   * Attempt to load a "dropped" file: First by testing whether it's and
+   * Annotation file, then a JNet file, and finally a features file. If all are
    * false then the user may have dropped an alignment file onto this
    * AlignFrame.
-   * @param file either a filename or a URL string.
+   * 
+   * @param file
+   *                either a filename or a URL string.
    */
-   public void loadJalviewDataFile(String file)
-   {
+  public void loadJalviewDataFile(String file)
+  {
     try
     {
       String protocol = "File";
@@ -3897,45 +3965,47 @@ public void drop(DropTargetDropEvent evt)
         protocol = "URL";
       }
 
-      boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport.
-          alignment, file, protocol);
+      boolean isAnnotation = new AnnotationFile().readAnnotationFile(
+              viewport.alignment, file, protocol);
 
       if (!isAnnotation)
       {
-        // try to see if its a JNet 'concise' style annotation file *before* we try to parse it as a features file
+        // try to see if its a JNet 'concise' style annotation file *before* we
+        // try to parse it as a features file
         String format = new IdentifyFile().Identify(file, protocol);
-        if(format.equalsIgnoreCase("JnetFile"))
+        if (format.equalsIgnoreCase("JnetFile"))
         {
-          jalview.io.JPredFile predictions = new jalview.io.JPredFile(
-                  file, protocol);
-          new JnetAnnotationMaker().add_annotation(predictions,
-                viewport.getAlignment(),
-                0, false);
-          isAnnotation=true;
+          jalview.io.JPredFile predictions = new jalview.io.JPredFile(file,
+                  protocol);
+          new JnetAnnotationMaker().add_annotation(predictions, viewport
+                  .getAlignment(), 0, false);
+          isAnnotation = true;
         }
         else
         {
           // try to parse it as a features file
-          boolean isGroupsFile = parseFeaturesFile(file,protocol);
-          // if it wasn't a features file then we just treat it as a general alignment file to load into the current view.
+          boolean isGroupsFile = parseFeaturesFile(file, protocol);
+          // if it wasn't a features file then we just treat it as a general
+          // alignment file to load into the current view.
           if (!isGroupsFile)
           {
             new FileLoader().LoadFile(viewport, file, protocol, format);
-          } else {
+          }
+          else
+          {
             alignPanel.paintAlignment(true);
           }
         }
       }
       if (isAnnotation)
       {
-        
+
         alignPanel.adjustAnnotationHeight();
         viewport.updateSequenceIdColours();
         buildSortByAnnotationScoresMenu();
         alignPanel.paintAlignment(true);
       }
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       ex.printStackTrace();
     }
@@ -3953,51 +4023,55 @@ public void drop(DropTargetDropEvent evt)
 
   public void tabbedPane_mousePressed(MouseEvent e)
   {
-    if(SwingUtilities.isRightMouseButton(e))
+    if (SwingUtilities.isRightMouseButton(e))
     {
       String reply = JOptionPane.showInternalInputDialog(this,
-          "Enter View Name",
-          "Edit View Name",
-          JOptionPane.QUESTION_MESSAGE);
+              "Enter View Name", "Edit View Name",
+              JOptionPane.QUESTION_MESSAGE);
 
       if (reply != null)
       {
         viewport.viewName = reply;
-        tabbedPane.setTitleAt( tabbedPane.getSelectedIndex() ,reply);
+        tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
       }
     }
   }
 
-
   public AlignViewport getCurrentView()
   {
     return viewport;
   }
 
-
   /**
    * Open the dialog for regex description parsing.
    */
   protected void extractScores_actionPerformed(ActionEvent e)
   {
-    ParseProperties pp = new jalview.analysis.ParseProperties(viewport.alignment);
+    ParseProperties pp = new jalview.analysis.ParseProperties(
+            viewport.alignment);
     // TODO: verify regex and introduce GUI dialog for version 2.5
-    //if (pp.getScoresFromDescription("col", "score column ", "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)", true)>0)
-    if (pp.getScoresFromDescription("description column", "score in description column ", "\\W*([-+eE0-9.]+)", true)>0)    {
+    // if (pp.getScoresFromDescription("col", "score column ",
+    // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
+    // true)>0)
+    if (pp.getScoresFromDescription("description column",
+            "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
+    {
       buildSortByAnnotationScoresMenu();
     }
   }
 }
 
-class PrintThread
-    extends Thread
+class PrintThread extends Thread
 {
   AlignmentPanel ap;
+
   public PrintThread(AlignmentPanel ap)
   {
-   this.ap = ap;
+    this.ap = ap;
   }
+
   static PageFormat pf;
+
   public void run()
   {
     PrinterJob printJob = PrinterJob.getPrinterJob();
@@ -4016,8 +4090,7 @@ class PrintThread
       try
       {
         printJob.print();
-      }
-      catch (Exception PrintException)
+      } catch (Exception PrintException)
       {
         PrintException.printStackTrace();
       }
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index f798671..d7a52c2 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1,4 +1,22 @@
- /*
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+/*
  * Jalview - A Sequence Alignment Editor and Viewer
  * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
@@ -33,1645 +51,1687 @@ import jalview.structure.StructureSelectionManager;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
 public class AlignViewport
 {
-    int startRes;
-    int endRes;
-    int startSeq;
-    int endSeq;
-    boolean showJVSuffix = true;
-    boolean showText = true;
-    boolean showColourText = false;
-    boolean showBoxes = true;
-    boolean wrapAlignment = false;
-    boolean renderGaps = true;
-    boolean showSequenceFeatures = false;
-    boolean showAnnotation = true;
-    boolean colourAppliesToAllGroups = true;
-    ColourSchemeI globalColourScheme = null;
-    boolean conservationColourSelected = false;
-    boolean abovePIDThreshold = false;
-    SequenceGroup selectionGroup;
-    int charHeight;
-    int charWidth;
-    boolean validCharWidth;
-    int wrappedWidth;
-    Font font;
-    boolean seqNameItalics;
-    AlignmentI alignment;
-    ColumnSelection colSel = new ColumnSelection();
-    int threshold;
-    int increment;
-    NJTree currentTree = null;
-    boolean scaleAboveWrapped = false;
-    boolean scaleLeftWrapped = true;
-    boolean scaleRightWrapped = true;
-    boolean hasHiddenColumns = false;
-    boolean hasHiddenRows = false;
-    boolean showHiddenMarkers = true;
-
-    boolean cursorMode = false;
-
-    // The following vector holds the features which are
-    // currently visible, in the correct order or rendering
-    Hashtable featuresDisplayed = null;
-
-
-    /** DOCUMENT ME!! */
-    public Hashtable [] hconsensus;
-    AlignmentAnnotation consensus;
-    AlignmentAnnotation conservation;
-    AlignmentAnnotation quality;
-    boolean autoCalculateConsensus = true;
-
-    /** DOCUMENT ME!! */
-    public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
-
-    // JBPNote Prolly only need this in the applet version.
-  private java.beans.PropertyChangeSupport changeSupport = new java.beans.
-      PropertyChangeSupport(this);
-
-    boolean ignoreGapsInConsensusCalculation = false;
-
-    boolean isDataset = false;
-
-    boolean antiAlias = false;
-
-    boolean padGaps = false;
-
-    Rectangle explodedPosition;
-
-    String viewName;
-
-    String sequenceSetID;
-
-    boolean gatherViewsHere = false;
-
-    Stack historyList = new Stack();
-    Stack redoList = new Stack();
-
-    Hashtable sequenceColours;
-
-    int thresholdTextColour = 0;
-    Color textColour = Color.black;
-    Color textColour2 = Color.white;
-
-    boolean rightAlignIds = false;
-
-    Hashtable hiddenRepSequences;
-
-
-    /**
-     * Creates a new AlignViewport object.
-     *
-     * @param al DOCUMENT ME!
-     */
-    public AlignViewport(AlignmentI al)
-    {
-        setAlignment(al);
-        init();
-    }
-    /**
-     * Create a new AlignViewport with hidden regions
-     * @param al AlignmentI
-     * @param hiddenColumns ColumnSelection
-     */
+  int startRes;
+
+  int endRes;
+
+  int startSeq;
+
+  int endSeq;
+
+  boolean showJVSuffix = true;
+
+  boolean showText = true;
+
+  boolean showColourText = false;
+
+  boolean showBoxes = true;
+
+  boolean wrapAlignment = false;
+
+  boolean renderGaps = true;
+
+  boolean showSequenceFeatures = false;
+
+  boolean showAnnotation = true;
+
+  boolean colourAppliesToAllGroups = true;
+
+  ColourSchemeI globalColourScheme = null;
+
+  boolean conservationColourSelected = false;
+
+  boolean abovePIDThreshold = false;
+
+  SequenceGroup selectionGroup;
+
+  int charHeight;
+
+  int charWidth;
+
+  boolean validCharWidth;
+
+  int wrappedWidth;
+
+  Font font;
+
+  boolean seqNameItalics;
+
+  AlignmentI alignment;
+
+  ColumnSelection colSel = new ColumnSelection();
+
+  int threshold;
+
+  int increment;
+
+  NJTree currentTree = null;
+
+  boolean scaleAboveWrapped = false;
+
+  boolean scaleLeftWrapped = true;
+
+  boolean scaleRightWrapped = true;
+
+  boolean hasHiddenColumns = false;
+
+  boolean hasHiddenRows = false;
+
+  boolean showHiddenMarkers = true;
+
+  boolean cursorMode = false;
+
+  // The following vector holds the features which are
+  // currently visible, in the correct order or rendering
+  Hashtable featuresDisplayed = null;
+
+  /** DOCUMENT ME!! */
+  public Hashtable[] hconsensus;
+
+  AlignmentAnnotation consensus;
+
+  AlignmentAnnotation conservation;
+
+  AlignmentAnnotation quality;
+
+  boolean autoCalculateConsensus = true;
+
+  /** DOCUMENT ME!! */
+  public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
+
+  // JBPNote Prolly only need this in the applet version.
+  private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
+          this);
+
+  boolean ignoreGapsInConsensusCalculation = false;
+
+  boolean isDataset = false;
+
+  boolean antiAlias = false;
+
+  boolean padGaps = false;
+
+  Rectangle explodedPosition;
+
+  String viewName;
+
+  String sequenceSetID;
+
+  boolean gatherViewsHere = false;
+
+  Stack historyList = new Stack();
+
+  Stack redoList = new Stack();
+
+  Hashtable sequenceColours;
+
+  int thresholdTextColour = 0;
+
+  Color textColour = Color.black;
+
+  Color textColour2 = Color.white;
+
+  boolean rightAlignIds = false;
+
+  Hashtable hiddenRepSequences;
+
+  /**
+   * Creates a new AlignViewport object.
+   * 
+   * @param al
+   *                DOCUMENT ME!
+   */
+  public AlignViewport(AlignmentI al)
+  {
+    setAlignment(al);
+    init();
+  }
+
+  /**
+   * Create a new AlignViewport with hidden regions
+   * 
+   * @param al
+   *                AlignmentI
+   * @param hiddenColumns
+   *                ColumnSelection
+   */
   public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns)
   {
-      setAlignment(al);
+    setAlignment(al);
     if (hiddenColumns != null)
     {
-        this.colSel = hiddenColumns;
-        if (hiddenColumns.getHiddenColumns() != null)
+      this.colSel = hiddenColumns;
+      if (hiddenColumns.getHiddenColumns() != null)
       {
-          hasHiddenColumns = true;
+        hasHiddenColumns = true;
       }
     }
-      init();
-    }
-
-    void init()
-    {
-        this.startRes = 0;
-        this.endRes = alignment.getWidth() - 1;
-        this.startSeq = 0;
-        this.endSeq = alignment.getHeight() - 1;
+    init();
+  }
 
-      antiAlias = Cache.getDefault("ANTI_ALIAS", false);
+  void init()
+  {
+    this.startRes = 0;
+    this.endRes = alignment.getWidth() - 1;
+    this.startSeq = 0;
+    this.endSeq = alignment.getHeight() - 1;
 
-      showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
-      showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
+    antiAlias = Cache.getDefault("ANTI_ALIAS", false);
 
-      rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false);
-      centreColumnLabels = Cache.getDefault("CENTRE_COLUMN_LABELS", false);
-      autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
+    showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
+    showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
 
-      padGaps = Cache.getDefault("PAD_GAPS", true);
+    rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false);
+    centreColumnLabels = Cache.getDefault("CENTRE_COLUMN_LABELS", false);
+    autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
 
-       String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
-       String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;
-       String fontSize = Cache.getDefault("FONT_SIZE", "10");
+    padGaps = Cache.getDefault("PAD_GAPS", true);
 
-       seqNameItalics = Cache.getDefault("ID_ITALICS", true);
+    String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
+    String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "");
+    String fontSize = Cache.getDefault("FONT_SIZE", "10");
 
-       int style = 0;
+    seqNameItalics = Cache.getDefault("ID_ITALICS", true);
 
-       if (fontStyle.equals("bold"))
-       {
-         style = 1;
-       }
-       else if (fontStyle.equals("italic"))
-       {
-         style = 2;
-       }
+    int style = 0;
 
-       setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
+    if (fontStyle.equals("bold"))
+    {
+      style = 1;
+    }
+    else if (fontStyle.equals("italic"))
+    {
+      style = 2;
+    }
 
-       alignment.setGapCharacter( Cache.getDefault("GAP_SYMBOL", "-").charAt(0) );
+    setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
 
+    alignment
+            .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
 
-        // We must set conservation and consensus before setting colour,
-        // as Blosum and Clustal require this to be done
-        if(hconsensus==null && !isDataset)
-        {
-          if(!alignment.isNucleotide())
-          {
-            conservation = new AlignmentAnnotation("Conservation",
-                "Conservation of total alignment less than " +
-                ConsPercGaps + "% gaps",
-                new Annotation[1], 0f,
-                11f,
+    // We must set conservation and consensus before setting colour,
+    // as Blosum and Clustal require this to be done
+    if (hconsensus == null && !isDataset)
+    {
+      if (!alignment.isNucleotide())
+      {
+        conservation = new AlignmentAnnotation("Conservation",
+                "Conservation of total alignment less than " + ConsPercGaps
+                        + "% gaps", new Annotation[1], 0f, 11f,
                 AlignmentAnnotation.BAR_GRAPH);
-            conservation.hasText = true;
-            conservation.autoCalculated=true;
+        conservation.hasText = true;
+        conservation.autoCalculated = true;
 
+        if (Cache.getDefault("SHOW_CONSERVATION", true))
+        {
+          alignment.addAnnotation(conservation);
+        }
 
-            if (Cache.getDefault("SHOW_CONSERVATION", true))
-            {
-              alignment.addAnnotation(conservation);
-            }
+        if (Cache.getDefault("SHOW_QUALITY", true))
+        {
+          quality = new AlignmentAnnotation("Quality",
+                  "Alignment Quality based on Blosum62 scores",
+                  new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
+          quality.hasText = true;
+          quality.autoCalculated = true;
 
-            if (Cache.getDefault("SHOW_QUALITY", true))
-            {
-              quality = new AlignmentAnnotation("Quality",
-                                                "Alignment Quality based on Blosum62 scores",
-                                                new Annotation[1],
-                                                0f,
-                                                11f,
-                                                AlignmentAnnotation.BAR_GRAPH);
-              quality.hasText = true;
-              quality.autoCalculated=true;
-
-              alignment.addAnnotation(quality);
-            }
-          }
+          alignment.addAnnotation(quality);
+        }
+      }
 
-          consensus = new AlignmentAnnotation("Consensus", "PID",
-                                               new Annotation[1], 0f, 100f,
-                                               AlignmentAnnotation.BAR_GRAPH);
-          consensus.hasText = true;
-          consensus.autoCalculated=true;
+      consensus = new AlignmentAnnotation("Consensus", "PID",
+              new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
+      consensus.hasText = true;
+      consensus.autoCalculated = true;
 
-           if (Cache.getDefault("SHOW_IDENTITY", true))
-           {
-             alignment.addAnnotation(consensus);
-           }
-        }
+      if (Cache.getDefault("SHOW_IDENTITY", true))
+      {
+        alignment.addAnnotation(consensus);
+      }
+    }
 
-        if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
-        {
-          globalColourScheme = ColourSchemeProperty.getColour(alignment,
+    if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
+    {
+      globalColourScheme = ColourSchemeProperty.getColour(alignment,
               jalview.bin.Cache.getProperty("DEFAULT_COLOUR"));
 
-            if (globalColourScheme instanceof UserColourScheme)
-            {
-                globalColourScheme = UserDefinedColours.loadDefaultColours();
-        ( (UserColourScheme) globalColourScheme).setThreshold(0,
-            getIgnoreGapsConsensus());
-            }
-
-            if (globalColourScheme != null)
-            {
-                globalColourScheme.setConsensus(hconsensus);
-            }
-        }
+      if (globalColourScheme instanceof UserColourScheme)
+      {
+        globalColourScheme = UserDefinedColours.loadDefaultColours();
+        ((UserColourScheme) globalColourScheme).setThreshold(0,
+                getIgnoreGapsConsensus());
+      }
 
-        wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false);
+      if (globalColourScheme != null)
+      {
+        globalColourScheme.setConsensus(hconsensus);
+      }
     }
 
+    wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param b
+   *                DOCUMENT ME!
+   */
+  public void setShowSequenceFeatures(boolean b)
+  {
+    showSequenceFeatures = b;
+  }
 
+  public boolean getShowSequenceFeatures()
+  {
+    return showSequenceFeatures;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setShowSequenceFeatures(boolean b)
-    {
-        showSequenceFeatures = b;
-    }
+  class ConservationThread extends Thread
+  {
+    AlignmentPanel ap;
 
-    public boolean getShowSequenceFeatures()
+    public ConservationThread(AlignmentPanel ap)
     {
-      return showSequenceFeatures;
+      this.ap = ap;
     }
 
-  class ConservationThread
-      extends Thread
+    public void run()
     {
-      AlignmentPanel ap;
-      public ConservationThread(AlignmentPanel ap)
+      try
       {
-        this.ap = ap;
-      }
+        updatingConservation = true;
 
-      public void run()
-      {
-        try
+        while (UPDATING_CONSERVATION)
         {
-          updatingConservation = true;
-
-          while (UPDATING_CONSERVATION)
+          try
           {
-            try
-            {
-              if (ap != null)
-              {
-                ap.paintAlignment(false);
-              }
-              Thread.sleep(200);
-            }
-            catch (Exception ex)
+            if (ap != null)
             {
-              ex.printStackTrace();
+              ap.paintAlignment(false);
             }
+            Thread.sleep(200);
+          } catch (Exception ex)
+          {
+            ex.printStackTrace();
           }
+        }
 
-          UPDATING_CONSERVATION = true;
-
+        UPDATING_CONSERVATION = true;
 
-          int alWidth = alignment.getWidth();
-          if(alWidth<0)
+        int alWidth = alignment.getWidth();
+        if (alWidth < 0)
         {
-            return;
+          return;
         }
 
-          Conservation cons = new jalview.analysis.Conservation("All",
-              jalview.schemes.ResidueProperties.propHash, 3,
-              alignment.getSequences(), 0, alWidth -1);
+        Conservation cons = new jalview.analysis.Conservation("All",
+                jalview.schemes.ResidueProperties.propHash, 3, alignment
+                        .getSequences(), 0, alWidth - 1);
 
-          cons.calculate();
-          cons.verdict(false, ConsPercGaps);
+        cons.calculate();
+        cons.verdict(false, ConsPercGaps);
 
-          if (quality!=null)
-          {
-            cons.findQuality();
-          }
+        if (quality != null)
+        {
+          cons.findQuality();
+        }
 
-          char [] sequence = cons.getConsSequence().getSequence();
-          float minR;
-          float minG;
-          float minB;
-          float maxR;
-          float maxG;
-          float maxB;
-          minR = 0.3f;
-          minG = 0.0f;
-          minB = 0f;
-          maxR = 1.0f - minR;
-          maxG = 0.9f - minG;
-          maxB = 0f - minB; // scalable range for colouring both Conservation and Quality
-
-          float min = 0f;
-          float max = 11f;
-          float qmin = 0f;
-          float qmax = 0f;
-
-          char c;
-
-          conservation.annotations = new Annotation[alWidth];
-
-          if (quality!=null)
-          {
-            quality.graphMax = cons.qualityRange[1].floatValue();
-            quality.annotations = new Annotation[alWidth];
-            qmin = cons.qualityRange[0].floatValue();
-            qmax = cons.qualityRange[1].floatValue();
-          }
+        char[] sequence = cons.getConsSequence().getSequence();
+        float minR;
+        float minG;
+        float minB;
+        float maxR;
+        float maxG;
+        float maxB;
+        minR = 0.3f;
+        minG = 0.0f;
+        minB = 0f;
+        maxR = 1.0f - minR;
+        maxG = 0.9f - minG;
+        maxB = 0f - minB; // scalable range for colouring both Conservation and
+                          // Quality
+
+        float min = 0f;
+        float max = 11f;
+        float qmin = 0f;
+        float qmax = 0f;
+
+        char c;
+
+        conservation.annotations = new Annotation[alWidth];
+
+        if (quality != null)
+        {
+          quality.graphMax = cons.qualityRange[1].floatValue();
+          quality.annotations = new Annotation[alWidth];
+          qmin = cons.qualityRange[0].floatValue();
+          qmax = cons.qualityRange[1].floatValue();
+        }
 
-          for (int i = 0; i < alWidth; i++)
-          {
-            float value = 0;
+        for (int i = 0; i < alWidth; i++)
+        {
+          float value = 0;
 
-            c = sequence[i];
+          c = sequence[i];
 
-            if (Character.isDigit(c))
+          if (Character.isDigit(c))
           {
-              value = (int) (c - '0');
+            value = (int) (c - '0');
           }
-            else if (c == '*')
+          else if (c == '*')
           {
-              value = 11;
+            value = 11;
           }
-            else if (c == '+')
+          else if (c == '+')
           {
-              value = 10;
+            value = 10;
           }
 
-            float vprop = value - min;
-            vprop /= max;
-            conservation.annotations[i] =
-                new Annotation(String.valueOf(c),
-                               String.valueOf(value), ' ', value,
-                               new Color(minR + (maxR * vprop),
-                                         minG + (maxG * vprop),
-                                         minB + (maxB * vprop)));
-
-            // Quality calc
-            if (quality!=null)
-            {
-              value = ( (Double) cons.quality.get(i)).floatValue();
-              vprop = value - qmin;
-              vprop /= qmax;
-            quality.annotations[i] = new Annotation(" ", String.valueOf(value),
-                ' ',
-                                               value,
-                                               new Color(minR + (maxR * vprop),
-                  minG + (maxG * vprop),
-                  minB + (maxB * vprop)));
-            }
+          float vprop = value - min;
+          vprop /= max;
+          conservation.annotations[i] = new Annotation(String.valueOf(c),
+                  String.valueOf(value), ' ', value, new Color(minR
+                          + (maxR * vprop), minG + (maxG * vprop), minB
+                          + (maxB * vprop)));
+
+          // Quality calc
+          if (quality != null)
+          {
+            value = ((Double) cons.quality.get(i)).floatValue();
+            vprop = value - qmin;
+            vprop /= qmax;
+            quality.annotations[i] = new Annotation(" ", String
+                    .valueOf(value), ' ', value, new Color(minR
+                    + (maxR * vprop), minG + (maxG * vprop), minB
+                    + (maxB * vprop)));
           }
         }
-        catch (OutOfMemoryError error)
-        {
-          javax.swing.SwingUtilities.invokeLater(new Runnable()
-          {
-
-
-            public void run()
-            {
-              javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                  "Out of memory calculating conservation!!"
-                  +
-                  "\nSee help files for increasing Java Virtual Machine memory."
-                  , "Out of memory",
-                  javax.swing.JOptionPane.WARNING_MESSAGE);
-            }
-          });
-
-          conservation = null;
-          quality = null;
+      } catch (OutOfMemoryError error)
+      {
+        new OOMWarning("calculating conservation", error);
 
-          System.out.println("Conservation calculation: " + error);
-          System.gc();
+        conservation = null;
+        quality = null;
 
-        }
+      }
 
-        UPDATING_CONSERVATION = false;
-        updatingConservation = false;
+      UPDATING_CONSERVATION = false;
+      updatingConservation = false;
 
-        if(ap!=null)
-        {
+      if (ap != null)
+      {
         ap.paintAlignment(true);
-        }
-
       }
+
     }
+  }
 
+  ConservationThread conservationThread;
 
-    ConservationThread conservationThread;
+  ConsensusThread consensusThread;
 
-    ConsensusThread consensusThread;
+  boolean consUpdateNeeded = false;
 
-    boolean consUpdateNeeded = false;
+  static boolean UPDATING_CONSENSUS = false;
 
-    static boolean UPDATING_CONSENSUS = false;
+  static boolean UPDATING_CONSERVATION = false;
 
-    static boolean UPDATING_CONSERVATION = false;
+  boolean updatingConsensus = false;
 
-    boolean updatingConsensus = false;
+  boolean updatingConservation = false;
 
-    boolean updatingConservation = false;
-    /**
-     * centre columnar annotation labels in displayed alignment annotation
-     * TODO: add to jalviewXML and annotation display settings
-     */
-    boolean centreColumnLabels=false;
+  /**
+   * centre columnar annotation labels in displayed alignment annotation TODO:
+   * add to jalviewXML and annotation display settings
+   */
+  boolean centreColumnLabels = false;
 
-    /**
-     * trigger update of conservation annotation
-     */
-    public void updateConservation(final AlignmentPanel ap)
-    {
-      if (alignment.isNucleotide() || conservation==null)
+  /**
+   * trigger update of conservation annotation
+   */
+  public void updateConservation(final AlignmentPanel ap)
+  {
+    if (alignment.isNucleotide() || conservation == null)
     {
-        return;
+      return;
     }
 
-      conservationThread = new ConservationThread(ap);
-      conservationThread.start();
-    }
+    conservationThread = new ConservationThread(ap);
+    conservationThread.start();
+  }
+
+  /**
+   * trigger update of consensus annotation
+   */
+  public void updateConsensus(final AlignmentPanel ap)
+  {
+    consensusThread = new ConsensusThread(ap);
+    consensusThread.start();
+  }
 
-    /**
-     * trigger update of consensus annotation
-     */
-    public void updateConsensus(final AlignmentPanel ap)
+  class ConsensusThread extends Thread
+  {
+    AlignmentPanel ap;
+
+    public ConsensusThread(AlignmentPanel ap)
     {
-      consensusThread = new ConsensusThread(ap);
-      consensusThread.start();
+      this.ap = ap;
     }
 
-  class ConsensusThread
-      extends Thread
+    public void run()
     {
-      AlignmentPanel ap;
-      public ConsensusThread(AlignmentPanel ap)
+      updatingConsensus = true;
+      while (UPDATING_CONSENSUS)
       {
-        this.ap = ap;
-      }
-      public void run()
-      {
-        updatingConsensus = true;
-        while (UPDATING_CONSENSUS)
+        try
         {
-          try
+          if (ap != null)
           {
-            if (ap != null)
-            {
             ap.paintAlignment(false);
-            }
-
-            Thread.sleep(200);
-          }
-          catch (Exception ex)
-          {
-            ex.printStackTrace();
           }
-        }
 
+          Thread.sleep(200);
+        } catch (Exception ex)
+        {
+          ex.printStackTrace();
+        }
+      }
 
-        UPDATING_CONSENSUS = true;
+      UPDATING_CONSENSUS = true;
 
-        try
-        {
-          int aWidth = (alignment!=null) ? alignment.getWidth() : 0; // null pointer possibility here.
-          if(aWidth<0)
+      try
+      {
+        int aWidth = (alignment != null) ? alignment.getWidth() : 0; // null
+                                                                      // pointer
+                                                                      // possibility
+                                                                      // here.
+        if (aWidth < 0)
         {
-            return;
+          return;
         }
 
-          consensus.annotations = null;
-          consensus.annotations = new Annotation[aWidth];
-
+        consensus.annotations = null;
+        consensus.annotations = new Annotation[aWidth];
 
-          hconsensus = new Hashtable[aWidth];
-          AAFrequency.calculate(alignment.getSequencesArray(),
-                                0,
-                                alignment.getWidth(),
-                                hconsensus);
+        hconsensus = new Hashtable[aWidth];
+        AAFrequency.calculate(alignment.getSequencesArray(), 0, alignment
+                .getWidth(), hconsensus);
 
-          for (int i = 0; i < aWidth; i++)
-          {
-            float value = 0;
-            if (ignoreGapsInConsensusCalculation)
+        for (int i = 0; i < aWidth; i++)
+        {
+          float value = 0;
+          if (ignoreGapsInConsensusCalculation)
           {
-              value = ( (Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)).
-                  floatValue();
+            value = ((Float) hconsensus[i].get(AAFrequency.PID_NOGAPS))
+                    .floatValue();
           }
-            else
+          else
           {
-              value = ( (Float) hconsensus[i].get(AAFrequency.PID_GAPS)).
-                  floatValue();
+            value = ((Float) hconsensus[i].get(AAFrequency.PID_GAPS))
+                    .floatValue();
           }
 
-            String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString();
-            String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " ";
+          String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE)
+                  .toString();
+          String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE)
+                  + " ";
 
-            if (maxRes.length() > 1)
-            {
-              mouseOver = "[" + maxRes + "] ";
-              maxRes = "+";
-            }
-
-            mouseOver += ( (int) value + "%");
-          consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
-              value);
+          if (maxRes.length() > 1)
+          {
+            mouseOver = "[" + maxRes + "] ";
+            maxRes = "+";
           }
 
-
-          if (globalColourScheme != null)
-        {
-            globalColourScheme.setConsensus(hconsensus);
+          mouseOver += ((int) value + "%");
+          consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
+                  value);
         }
 
-        }
-        catch (OutOfMemoryError error)
+        if (globalColourScheme != null)
         {
-          alignment.deleteAnnotation(consensus);
+          globalColourScheme.setConsensus(hconsensus);
+        }
 
-          consensus = null;
-          hconsensus = null;
-          javax.swing.SwingUtilities.invokeLater(new Runnable()
-          {
-            public void run()
-            {
-              javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                  "Out of memory calculating consensus!!"
-                  +
-                  "\nSee help files for increasing Java Virtual Machine memory."
-                  , "Out of memory",
-                  javax.swing.JOptionPane.WARNING_MESSAGE);
-            }
-          });
+      } catch (OutOfMemoryError error)
+      {
+        alignment.deleteAnnotation(consensus);
 
-          System.out.println("Consensus calculation: " + error);
-          System.gc();
-        }
-        UPDATING_CONSENSUS = false;
-        updatingConsensus = false;
+        consensus = null;
+        hconsensus = null;
+        new OOMWarning("calculating consensus", error);
+      }
+      UPDATING_CONSENSUS = false;
+      updatingConsensus = false;
 
-        if (ap != null)
-        {
+      if (ap != null)
+      {
         ap.paintAlignment(true);
-        }
       }
     }
-    /**
-     * get the consensus sequence as displayed under the PID consensus annotation row.
-     * @return consensus sequence as a new sequence object
-     */
+  }
+
+  /**
+   * get the consensus sequence as displayed under the PID consensus annotation
+   * row.
+   * 
+   * @return consensus sequence as a new sequence object
+   */
   public SequenceI getConsensusSeq()
   {
-      if (consensus==null)
+    if (consensus == null)
     {
-        updateConsensus(null);
+      updateConsensus(null);
     }
-      if (consensus==null)
+    if (consensus == null)
     {
-        return null;
+      return null;
     }
-      StringBuffer seqs=new StringBuffer();
+    StringBuffer seqs = new StringBuffer();
     for (int i = 0; i < consensus.annotations.length; i++)
     {
       if (consensus.annotations[i] != null)
       {
-          if (consensus.annotations[i].description.charAt(0) == '[')
+        if (consensus.annotations[i].description.charAt(0) == '[')
         {
-            seqs.append(consensus.annotations[i].description.charAt(1));
+          seqs.append(consensus.annotations[i].description.charAt(1));
         }
-          else
+        else
         {
-            seqs.append(consensus.annotations[i].displayCharacter);
+          seqs.append(consensus.annotations[i].displayCharacter);
         }
       }
     }
 
-      SequenceI sq = new Sequence("Consensus", seqs.toString());
-    sq.setDescription("Percentage Identity Consensus " +
-                      ( (ignoreGapsInConsensusCalculation) ? " without gaps" :
-                       ""));
-      return sq;
-    }
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public SequenceGroup getSelectionGroup()
-    {
-        return selectionGroup;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param sg DOCUMENT ME!
-     */
-    public void setSelectionGroup(SequenceGroup sg)
-    {
-        selectionGroup = sg;
-    }
+    SequenceI sq = new Sequence("Consensus", seqs.toString());
+    sq.setDescription("Percentage Identity Consensus "
+            + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
+    return sq;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getConservationSelected()
-    {
-        return conservationColourSelected;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public SequenceGroup getSelectionGroup()
+  {
+    return selectionGroup;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setConservationSelected(boolean b)
-    {
-        conservationColourSelected = b;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param sg
+   *                DOCUMENT ME!
+   */
+  public void setSelectionGroup(SequenceGroup sg)
+  {
+    selectionGroup = sg;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getAbovePIDThreshold()
-    {
-        return abovePIDThreshold;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public boolean getConservationSelected()
+  {
+    return conservationColourSelected;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setAbovePIDThreshold(boolean b)
-    {
-        abovePIDThreshold = b;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param b
+   *                DOCUMENT ME!
+   */
+  public void setConservationSelected(boolean b)
+  {
+    conservationColourSelected = b;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getStartRes()
-    {
-        return startRes;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public boolean getAbovePIDThreshold()
+  {
+    return abovePIDThreshold;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getEndRes()
-    {
-        return endRes;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param b
+   *                DOCUMENT ME!
+   */
+  public void setAbovePIDThreshold(boolean b)
+  {
+    abovePIDThreshold = b;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getStartSeq()
-    {
-        return startSeq;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public int getStartRes()
+  {
+    return startRes;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param cs DOCUMENT ME!
-     */
-    public void setGlobalColourScheme(ColourSchemeI cs)
-    {
-        globalColourScheme = cs;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public int getEndRes()
+  {
+    return endRes;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public ColourSchemeI getGlobalColourScheme()
-    {
-        return globalColourScheme;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public int getStartSeq()
+  {
+    return startSeq;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param res DOCUMENT ME!
-     */
-    public void setStartRes(int res)
-    {
-        this.startRes = res;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param cs
+   *                DOCUMENT ME!
+   */
+  public void setGlobalColourScheme(ColourSchemeI cs)
+  {
+    globalColourScheme = cs;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param seq DOCUMENT ME!
-     */
-    public void setStartSeq(int seq)
-    {
-        this.startSeq = seq;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public ColourSchemeI getGlobalColourScheme()
+  {
+    return globalColourScheme;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param res DOCUMENT ME!
-     */
-    public void setEndRes(int res)
-    {
-        if (res > (alignment.getWidth() - 1))
-        {
-            // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
-            res = alignment.getWidth() - 1;
-        }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param res
+   *                DOCUMENT ME!
+   */
+  public void setStartRes(int res)
+  {
+    this.startRes = res;
+  }
 
-        if (res < 0)
-        {
-            res = 0;
-        }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param seq
+   *                DOCUMENT ME!
+   */
+  public void setStartSeq(int seq)
+  {
+    this.startSeq = seq;
+  }
 
-        this.endRes = res;
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param res
+   *                DOCUMENT ME!
+   */
+  public void setEndRes(int res)
+  {
+    if (res > (alignment.getWidth() - 1))
+    {
+      // log.System.out.println(" Corrected res from " + res + " to maximum " +
+      // (alignment.getWidth()-1));
+      res = alignment.getWidth() - 1;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param seq DOCUMENT ME!
-     */
-    public void setEndSeq(int seq)
+    if (res < 0)
     {
-        if (seq > alignment.getHeight())
-        {
-            seq = alignment.getHeight();
-        }
-
-        if (seq < 0)
-        {
-            seq = 0;
-        }
-
-        this.endSeq = seq;
+      res = 0;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getEndSeq()
+    this.endRes = res;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param seq
+   *                DOCUMENT ME!
+   */
+  public void setEndSeq(int seq)
+  {
+    if (seq > alignment.getHeight())
     {
-        return endSeq;
+      seq = alignment.getHeight();
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param f DOCUMENT ME!
-     */
-    public void setFont(Font f)
+    if (seq < 0)
     {
-        font = f;
+      seq = 0;
+    }
 
-        Container c = new Container();
+    this.endSeq = seq;
+  }
 
-        java.awt.FontMetrics fm = c.getFontMetrics(font);
-        setCharHeight(fm.getHeight());
-        setCharWidth(fm.charWidth('M'));
-        validCharWidth = true;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public int getEndSeq()
+  {
+    return endSeq;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Font getFont()
-    {
-        return font;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param f
+   *                DOCUMENT ME!
+   */
+  public void setFont(Font f)
+  {
+    font = f;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param w DOCUMENT ME!
-     */
-    public void setCharWidth(int w)
-    {
-        this.charWidth = w;
-    }
+    Container c = new Container();
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getCharWidth()
-    {
-        return charWidth;
-    }
+    java.awt.FontMetrics fm = c.getFontMetrics(font);
+    setCharHeight(fm.getHeight());
+    setCharWidth(fm.charWidth('M'));
+    validCharWidth = true;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param h DOCUMENT ME!
-     */
-    public void setCharHeight(int h)
-    {
-        this.charHeight = h;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public Font getFont()
+  {
+    return font;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getCharHeight()
-    {
-        return charHeight;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param w
+   *                DOCUMENT ME!
+   */
+  public void setCharWidth(int w)
+  {
+    this.charWidth = w;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param w DOCUMENT ME!
-     */
-    public void setWrappedWidth(int w)
-    {
-        this.wrappedWidth = w;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public int getCharWidth()
+  {
+    return charWidth;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getWrappedWidth()
-    {
-        return wrappedWidth;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param h
+   *                DOCUMENT ME!
+   */
+  public void setCharHeight(int h)
+  {
+    this.charHeight = h;
+  }
 
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public int getCharHeight()
+  {
+    return charHeight;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public AlignmentI getAlignment()
-    {
-        return alignment;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param w
+   *                DOCUMENT ME!
+   */
+  public void setWrappedWidth(int w)
+  {
+    this.wrappedWidth = w;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param align DOCUMENT ME!
-     */
-    public void setAlignment(AlignmentI align)
-    {
-      if (alignment!=null && alignment.getCodonFrames()!=null)
-      {
-        StructureSelectionManager.getStructureSelectionManager().removeMappings(alignment.getCodonFrames());
-      }
-        this.alignment = align;
-        if (alignment.getCodonFrames()!=null)
-        {
-          StructureSelectionManager.getStructureSelectionManager().addMappings(alignment.getCodonFrames());
-        }
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public int getWrappedWidth()
+  {
+    return wrappedWidth;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setWrapAlignment(boolean state)
-    {
-        wrapAlignment = state;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public AlignmentI getAlignment()
+  {
+    return alignment;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setShowText(boolean state)
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param align
+   *                DOCUMENT ME!
+   */
+  public void setAlignment(AlignmentI align)
+  {
+    if (alignment != null && alignment.getCodonFrames() != null)
     {
-        showText = state;
+      StructureSelectionManager.getStructureSelectionManager()
+              .removeMappings(alignment.getCodonFrames());
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setRenderGaps(boolean state)
+    this.alignment = align;
+    if (alignment.getCodonFrames() != null)
     {
-        renderGaps = state;
+      StructureSelectionManager.getStructureSelectionManager().addMappings(
+              alignment.getCodonFrames());
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getColourText()
-    {
-        return showColourText;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param state
+   *                DOCUMENT ME!
+   */
+  public void setWrapAlignment(boolean state)
+  {
+    wrapAlignment = state;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setColourText(boolean state)
-    {
-        showColourText = state;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param state
+   *                DOCUMENT ME!
+   */
+  public void setShowText(boolean state)
+  {
+    showText = state;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setShowBoxes(boolean state)
-    {
-        showBoxes = state;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param state
+   *                DOCUMENT ME!
+   */
+  public void setRenderGaps(boolean state)
+  {
+    renderGaps = state;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getWrapAlignment()
-    {
-        return wrapAlignment;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public boolean getColourText()
+  {
+    return showColourText;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getShowText()
-    {
-        return showText;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param state
+   *                DOCUMENT ME!
+   */
+  public void setColourText(boolean state)
+  {
+    showColourText = state;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getShowBoxes()
-    {
-        return showBoxes;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param state
+   *                DOCUMENT ME!
+   */
+  public void setShowBoxes(boolean state)
+  {
+    showBoxes = state;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public char getGapCharacter()
-    {
-        return getAlignment().getGapCharacter();
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public boolean getWrapAlignment()
+  {
+    return wrapAlignment;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param gap DOCUMENT ME!
-     */
-    public void setGapCharacter(char gap)
-    {
-        if (getAlignment() != null)
-        {
-            getAlignment().setGapCharacter(gap);
-        }
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public boolean getShowText()
+  {
+    return showText;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param thresh DOCUMENT ME!
-     */
-    public void setThreshold(int thresh)
-    {
-        threshold = thresh;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public boolean getShowBoxes()
+  {
+    return showBoxes;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getThreshold()
-    {
-        return threshold;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public char getGapCharacter()
+  {
+    return getAlignment().getGapCharacter();
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param inc DOCUMENT ME!
-     */
-    public void setIncrement(int inc)
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param gap
+   *                DOCUMENT ME!
+   */
+  public void setGapCharacter(char gap)
+  {
+    if (getAlignment() != null)
     {
-        increment = inc;
+      getAlignment().setGapCharacter(gap);
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getIncrement()
-    {
-        return increment;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param thresh
+   *                DOCUMENT ME!
+   */
+  public void setThreshold(int thresh)
+  {
+    threshold = thresh;
+  }
 
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public int getThreshold()
+  {
+    return threshold;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public ColumnSelection getColumnSelection()
-    {
-        return colSel;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param inc
+   *                DOCUMENT ME!
+   */
+  public void setIncrement(int inc)
+  {
+    increment = inc;
+  }
 
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public int getIncrement()
+  {
+    return increment;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param tree DOCUMENT ME!
-     */
-    public void setCurrentTree(NJTree tree)
-    {
-        currentTree = tree;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public ColumnSelection getColumnSelection()
+  {
+    return colSel;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public NJTree getCurrentTree()
-    {
-        return currentTree;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param tree
+   *                DOCUMENT ME!
+   */
+  public void setCurrentTree(NJTree tree)
+  {
+    currentTree = tree;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setColourAppliesToAllGroups(boolean b)
-    {
-        colourAppliesToAllGroups = b;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public NJTree getCurrentTree()
+  {
+    return currentTree;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getColourAppliesToAllGroups()
-    {
-        return colourAppliesToAllGroups;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param b
+   *                DOCUMENT ME!
+   */
+  public void setColourAppliesToAllGroups(boolean b)
+  {
+    colourAppliesToAllGroups = b;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getShowJVSuffix()
-    {
-        return showJVSuffix;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public boolean getColourAppliesToAllGroups()
+  {
+    return colourAppliesToAllGroups;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setShowJVSuffix(boolean b)
-    {
-        showJVSuffix = b;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public boolean getShowJVSuffix()
+  {
+    return showJVSuffix;
+  }
 
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param b
+   *                DOCUMENT ME!
+   */
+  public void setShowJVSuffix(boolean b)
+  {
+    showJVSuffix = b;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getShowAnnotation()
-    {
-        return showAnnotation;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public boolean getShowAnnotation()
+  {
+    return showAnnotation;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setShowAnnotation(boolean b)
-    {
-        showAnnotation = b;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param b
+   *                DOCUMENT ME!
+   */
+  public void setShowAnnotation(boolean b)
+  {
+    showAnnotation = b;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getScaleAboveWrapped()
-    {
-        return scaleAboveWrapped;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public boolean getScaleAboveWrapped()
+  {
+    return scaleAboveWrapped;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getScaleLeftWrapped()
-    {
-        return scaleLeftWrapped;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public boolean getScaleLeftWrapped()
+  {
+    return scaleLeftWrapped;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getScaleRightWrapped()
-    {
-        return scaleRightWrapped;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public boolean getScaleRightWrapped()
+  {
+    return scaleRightWrapped;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setScaleAboveWrapped(boolean b)
-    {
-        scaleAboveWrapped = b;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param b
+   *                DOCUMENT ME!
+   */
+  public void setScaleAboveWrapped(boolean b)
+  {
+    scaleAboveWrapped = b;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setScaleLeftWrapped(boolean b)
-    {
-        scaleLeftWrapped = b;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param b
+   *                DOCUMENT ME!
+   */
+  public void setScaleLeftWrapped(boolean b)
+  {
+    scaleLeftWrapped = b;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setScaleRightWrapped(boolean b)
-    {
-        scaleRightWrapped = b;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param b
+   *                DOCUMENT ME!
+   */
+  public void setScaleRightWrapped(boolean b)
+  {
+    scaleRightWrapped = b;
+  }
 
-    /**
-     * Property change listener for changes in alignment
-     *
-     * @param listener DOCUMENT ME!
-     */
-    public void addPropertyChangeListener(
-        java.beans.PropertyChangeListener listener)
-    {
-        changeSupport.addPropertyChangeListener(listener);
-    }
+  /**
+   * Property change listener for changes in alignment
+   * 
+   * @param listener
+   *                DOCUMENT ME!
+   */
+  public void addPropertyChangeListener(
+          java.beans.PropertyChangeListener listener)
+  {
+    changeSupport.addPropertyChangeListener(listener);
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param listener DOCUMENT ME!
-     */
-    public void removePropertyChangeListener(
-        java.beans.PropertyChangeListener listener)
-    {
-        changeSupport.removePropertyChangeListener(listener);
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param listener
+   *                DOCUMENT ME!
+   */
+  public void removePropertyChangeListener(
+          java.beans.PropertyChangeListener listener)
+  {
+    changeSupport.removePropertyChangeListener(listener);
+  }
 
-    /**
-     * Property change listener for changes in alignment
-     *
-     * @param prop DOCUMENT ME!
-     * @param oldvalue DOCUMENT ME!
-     * @param newvalue DOCUMENT ME!
-     */
-    public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
-    {
-        changeSupport.firePropertyChange(prop, oldvalue, newvalue);
-    }
+  /**
+   * Property change listener for changes in alignment
+   * 
+   * @param prop
+   *                DOCUMENT ME!
+   * @param oldvalue
+   *                DOCUMENT ME!
+   * @param newvalue
+   *                DOCUMENT ME!
+   */
+  public void firePropertyChange(String prop, Object oldvalue,
+          Object newvalue)
+  {
+    changeSupport.firePropertyChange(prop, oldvalue, newvalue);
+  }
 
-    public void setIgnoreGapsConsensus(boolean b, AlignmentPanel ap)
+  public void setIgnoreGapsConsensus(boolean b, AlignmentPanel ap)
+  {
+    ignoreGapsInConsensusCalculation = b;
+    updateConsensus(ap);
+    if (globalColourScheme != null)
     {
-      ignoreGapsInConsensusCalculation = b;
-      updateConsensus(ap);
-      if(globalColourScheme!=null)
-      {
       globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
-                                      ignoreGapsInConsensusCalculation);
-      }
-    }
-
-    public boolean getIgnoreGapsConsensus()
-    {
-     return ignoreGapsInConsensusCalculation;
+              ignoreGapsInConsensusCalculation);
     }
+  }
 
-    public void setDataset(boolean b)
-    {
-      isDataset = b;
-    }
+  public boolean getIgnoreGapsConsensus()
+  {
+    return ignoreGapsInConsensusCalculation;
+  }
 
-    public boolean isDataset()
-    {
-      return isDataset;
-    }
+  public void setDataset(boolean b)
+  {
+    isDataset = b;
+  }
 
+  public boolean isDataset()
+  {
+    return isDataset;
+  }
 
-    public void hideSelectedColumns()
-    {
-      if (colSel.size() < 1)
+  public void hideSelectedColumns()
+  {
+    if (colSel.size() < 1)
     {
-        return;
+      return;
     }
 
-      colSel.hideSelectedColumns();
-      setSelectionGroup(null);
-
-      hasHiddenColumns = true;
-    }
+    colSel.hideSelectedColumns();
+    setSelectionGroup(null);
 
+    hasHiddenColumns = true;
+  }
 
-    public void hideColumns(int start, int end)
-    {
-      if(start==end)
+  public void hideColumns(int start, int end)
+  {
+    if (start == end)
     {
-        colSel.hideColumns(start);
+      colSel.hideColumns(start);
     }
-      else
+    else
     {
-        colSel.hideColumns(start, end);
+      colSel.hideColumns(start, end);
     }
 
-      hasHiddenColumns = true;
-    }
+    hasHiddenColumns = true;
+  }
 
-    public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
-    {
-      int sSize = sg.getSize();
-      if(sSize < 2)
+  public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
+  {
+    int sSize = sg.getSize();
+    if (sSize < 2)
     {
-        return;
+      return;
     }
 
-      if(hiddenRepSequences==null)
+    if (hiddenRepSequences == null)
     {
-        hiddenRepSequences = new Hashtable();
+      hiddenRepSequences = new Hashtable();
     }
 
-       hiddenRepSequences.put(repSequence, sg);
+    hiddenRepSequences.put(repSequence, sg);
 
-      //Hide all sequences except the repSequence
-      SequenceI [] seqs = new SequenceI[sSize-1];
-      int index = 0;
-      for(int i=0; i<sSize; i++)
+    // Hide all sequences except the repSequence
+    SequenceI[] seqs = new SequenceI[sSize - 1];
+    int index = 0;
+    for (int i = 0; i < sSize; i++)
     {
-        if(sg.getSequenceAt(i)!=repSequence)
-        {
-          if(index==sSize-1)
+      if (sg.getSequenceAt(i) != repSequence)
+      {
+        if (index == sSize - 1)
         {
-            return;
+          return;
         }
 
-          seqs[index++] = sg.getSequenceAt(i);
-        }
+        seqs[index++] = sg.getSequenceAt(i);
+      }
     }
 
-      hideSequence(seqs);
+    hideSequence(seqs);
 
-    }
+  }
 
-    public void hideAllSelectedSeqs()
-    {
-    if (selectionGroup == null || selectionGroup.getSize()<1)
+  public void hideAllSelectedSeqs()
+  {
+    if (selectionGroup == null || selectionGroup.getSize() < 1)
     {
-        return;
+      return;
     }
 
-      SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
+    SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
 
-      hideSequence(seqs);
+    hideSequence(seqs);
 
-      setSelectionGroup(null);
-    }
+    setSelectionGroup(null);
+  }
 
-    public void hideSequence(SequenceI [] seq)
+  public void hideSequence(SequenceI[] seq)
+  {
+    if (seq != null)
     {
-      if(seq!=null)
+      for (int i = 0; i < seq.length; i++)
       {
-        for (int i = 0; i < seq.length; i++)
-        {
-          alignment.getHiddenSequences().hideSequence(seq[i]);
-        }
-        hasHiddenRows = true;
-        firePropertyChange("alignment", null, alignment.getSequences());
+        alignment.getHiddenSequences().hideSequence(seq[i]);
       }
+      hasHiddenRows = true;
+      firePropertyChange("alignment", null, alignment.getSequences());
     }
+  }
 
-    public void showSequence(int index)
+  public void showSequence(int index)
+  {
+    Vector tmp = alignment.getHiddenSequences().showSequence(index,
+            hiddenRepSequences);
+    if (tmp.size() > 0)
     {
-      Vector tmp = alignment.getHiddenSequences().showSequence(index
-          , hiddenRepSequences);
-      if(tmp.size()>0)
+      if (selectionGroup == null)
       {
-        if(selectionGroup==null)
-        {
-          selectionGroup = new SequenceGroup();
-          selectionGroup.setEndRes(alignment.getWidth()-1);
-        }
-
-        for (int t = 0; t < tmp.size(); t++)
-        {
-          selectionGroup.addSequence(
-              (SequenceI) tmp.elementAt(t), false
-              );
-        }
-        firePropertyChange("alignment", null, alignment.getSequences());
+        selectionGroup = new SequenceGroup();
+        selectionGroup.setEndRes(alignment.getWidth() - 1);
       }
 
-      if(alignment.getHiddenSequences().getSize()<1)
-    {
-        hasHiddenRows = false;
+      for (int t = 0; t < tmp.size(); t++)
+      {
+        selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false);
+      }
+      firePropertyChange("alignment", null, alignment.getSequences());
     }
-  }
 
-    public void showColumn(int col)
-    {
-      colSel.revealHiddenColumns(col);
-      if(colSel.getHiddenColumns()==null)
+    if (alignment.getHiddenSequences().getSize() < 1)
     {
-        hasHiddenColumns = false;
+      hasHiddenRows = false;
     }
   }
 
-    public void showAllHiddenColumns()
+  public void showColumn(int col)
+  {
+    colSel.revealHiddenColumns(col);
+    if (colSel.getHiddenColumns() == null)
     {
-      colSel.revealAllHiddenColumns();
       hasHiddenColumns = false;
     }
+  }
+
+  public void showAllHiddenColumns()
+  {
+    colSel.revealAllHiddenColumns();
+    hasHiddenColumns = false;
+  }
 
-    public void showAllHiddenSeqs()
+  public void showAllHiddenSeqs()
+  {
+    if (alignment.getHiddenSequences().getSize() > 0)
     {
-      if(alignment.getHiddenSequences().getSize()>0)
+      if (selectionGroup == null)
       {
-        if(selectionGroup==null)
-        {
-          selectionGroup = new SequenceGroup();
-          selectionGroup.setEndRes(alignment.getWidth()-1);
-        }
-        Vector tmp = alignment.getHiddenSequences().showAll(hiddenRepSequences);
-        for(int t=0; t<tmp.size(); t++)
-        {
-          selectionGroup.addSequence(
-              (SequenceI)tmp.elementAt(t), false
-              );
-        }
-        firePropertyChange("alignment", null, alignment.getSequences());
-        hasHiddenRows = false;
-        hiddenRepSequences = null;
+        selectionGroup = new SequenceGroup();
+        selectionGroup.setEndRes(alignment.getWidth() - 1);
+      }
+      Vector tmp = alignment.getHiddenSequences().showAll(
+              hiddenRepSequences);
+      for (int t = 0; t < tmp.size(); t++)
+      {
+        selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false);
       }
+      firePropertyChange("alignment", null, alignment.getSequences());
+      hasHiddenRows = false;
+      hiddenRepSequences = null;
     }
+  }
+
+  public void invertColumnSelection()
+  {
+    colSel.invertColumnSelection(0, alignment.getWidth());
+  }
 
+  public int adjustForHiddenSeqs(int alignmentIndex)
+  {
+    return alignment.getHiddenSequences().adjustForHiddenSeqs(
+            alignmentIndex);
+  }
 
+  /**
+   * This method returns an array of new SequenceI objects derived from the
+   * whole alignment or just the current selection with start and end points
+   * adjusted
+   * 
+   * @note if you need references to the actual SequenceI objects in the
+   *       alignment or currently selected then use getSequenceSelection()
+   * @return selection as new sequenceI objects
+   */
+  public SequenceI[] getSelectionAsNewSequence()
+  {
+    SequenceI[] sequences;
 
-    public void invertColumnSelection()
+    if (selectionGroup == null)
     {
-      colSel.invertColumnSelection(0,alignment.getWidth());
+      sequences = alignment.getSequencesArray();
+      AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
+      for (int i = 0; i < sequences.length; i++)
+      {
+        sequences[i] = new Sequence(sequences[i], annots); // construct new
+                                                            // sequence with
+                                                            // subset of visible
+                                                            // annotation
+      }
     }
-
-    public int adjustForHiddenSeqs(int alignmentIndex)
+    else
     {
-      return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
+      sequences = selectionGroup.getSelectionAsNewSequences(alignment);
     }
 
-    /**
-     * This method returns an array of new SequenceI objects
-     * derived from the whole alignment or just the current
-     * selection with start and end points adjusted
-     * @note if you need references to the actual SequenceI objects in the alignment or currently selected then use getSequenceSelection()
-     * @return selection as new sequenceI objects
-     */
-    public SequenceI[] getSelectionAsNewSequence()
-    {
-      SequenceI[] sequences;
+    return sequences;
+  }
 
-      if (selectionGroup == null)
+  /**
+   * get the currently selected sequence objects or all the sequences in the
+   * alignment.
+   * 
+   * @return array of references to sequence objects
+   */
+  public SequenceI[] getSequenceSelection()
+  {
+    SequenceI[] sequences;
+    if (selectionGroup == null)
     {
-        sequences = alignment.getSequencesArray();
-        AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
-        for (int i=0; i<sequences.length; i++)
-        {
-          sequences[i] = new Sequence(sequences[i], annots); // construct new sequence with subset of visible annotation
-        }
+      sequences = alignment.getSequencesArray();
     }
-      else
+    else
     {
-        sequences = selectionGroup.getSelectionAsNewSequences(alignment);
+      sequences = selectionGroup.getSequencesInOrder(alignment);
     }
+    return sequences;
+  }
 
-      return sequences;
+  /**
+   * This method returns the visible alignment as text, as seen on the GUI, ie
+   * if columns are hidden they will not be returned in the result. Use this for
+   * calculating trees, PCA, redundancy etc on views which contain hidden
+   * columns.
+   * 
+   * @return String[]
+   */
+  public jalview.datamodel.CigarArray getViewAsCigars(
+          boolean selectedRegionOnly)
+  {
+    CigarArray selection = null;
+    SequenceI[] seqs = null;
+    int i, iSize;
+    int start = 0, end = 0;
+    if (selectedRegionOnly && selectionGroup != null)
+    {
+      iSize = selectionGroup.getSize();
+      seqs = selectionGroup.getSequencesInOrder(alignment);
+      start = selectionGroup.getStartRes();
+      end = selectionGroup.getEndRes(); // inclusive for start and end in
+                                        // SeqCigar constructor
     }
-    
-    /**
-     * get the currently selected sequence objects or all the sequences in the alignment.
-     * @return array of references to sequence objects
-     */
-    public SequenceI[] getSequenceSelection()
+    else
     {
-      SequenceI[] sequences;
-      if (selectionGroup==null)
-      {
-        sequences = alignment.getSequencesArray();
-      }
-      else
-      {
-        sequences = selectionGroup.getSequencesInOrder(alignment);
-      }
-      return sequences;
-    }
-    /**
-     * This method returns the visible alignment as text, as
-     * seen on the GUI, ie if columns are hidden they will not
-     * be returned in the result.
-     * Use this for calculating trees, PCA, redundancy etc on views
-     * which contain hidden columns.
-     * @return String[]
-     */
-  public jalview.datamodel.CigarArray getViewAsCigars(boolean
-      selectedRegionOnly)
-    {
-      CigarArray selection=null;
-      SequenceI [] seqs= null;
-      int i, iSize;
-      int start = 0, end = 0;
-      if(selectedRegionOnly && selectionGroup!=null)
-      {
-        iSize = selectionGroup.getSize();
-        seqs = selectionGroup.getSequencesInOrder(alignment);
-        start = selectionGroup.getStartRes();
-        end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor
-      }
-      else
-      {
-        iSize = alignment.getHeight();
-        seqs = alignment.getSequencesArray();
-        end = alignment.getWidth()-1;
-      }
-      SeqCigar[] selseqs = new SeqCigar[iSize];
-      for(i=0; i<iSize; i++)
-      {
-        selseqs[i] = new SeqCigar(seqs[i], start, end);
-      }
-      selection=new CigarArray(selseqs);
-      // now construct the CigarArray operations
+      iSize = alignment.getHeight();
+      seqs = alignment.getSequencesArray();
+      end = alignment.getWidth() - 1;
+    }
+    SeqCigar[] selseqs = new SeqCigar[iSize];
+    for (i = 0; i < iSize; i++)
+    {
+      selseqs[i] = new SeqCigar(seqs[i], start, end);
+    }
+    selection = new CigarArray(selseqs);
+    // now construct the CigarArray operations
     if (hasHiddenColumns)
     {
-        Vector regions = colSel.getHiddenColumns();
-        int [] region;
-        int hideStart, hideEnd;
-        int last=start;
-        for (int j = 0; last<end & j < regions.size(); j++)
-        {
-          region = (int[]) regions.elementAt(j);
-          hideStart = region[0];
-          hideEnd = region[1];
-          // edit hidden regions to selection range
+      Vector regions = colSel.getHiddenColumns();
+      int[] region;
+      int hideStart, hideEnd;
+      int last = start;
+      for (int j = 0; last < end & j < regions.size(); j++)
+      {
+        region = (int[]) regions.elementAt(j);
+        hideStart = region[0];
+        hideEnd = region[1];
+        // edit hidden regions to selection range
         if (hideStart < last)
         {
-            if (hideEnd > last)
-            {
-              hideStart = last;
+          if (hideEnd > last)
+          {
+            hideStart = last;
           }
           else
           {
-              continue;
+            continue;
           }
         }
 
-          if (hideStart>end)
+        if (hideStart > end)
         {
-            break;
+          break;
         }
 
-          if (hideEnd>end)
+        if (hideEnd > end)
         {
-            hideEnd=end;
+          hideEnd = end;
         }
 
-          if (hideStart>hideEnd)
+        if (hideStart > hideEnd)
         {
-            break;
+          break;
         }
-          /**
-           * form operations...
-           */
-          if (last<hideStart)
+        /**
+         * form operations...
+         */
+        if (last < hideStart)
         {
-            selection.addOperation(CigarArray.M, hideStart-last);
-        }
-          selection.addOperation(CigarArray.D, 1+hideEnd-hideStart);
-          last = hideEnd+1;
+          selection.addOperation(CigarArray.M, hideStart - last);
         }
-        // Final match if necessary.
-        if (last<end)
+        selection.addOperation(CigarArray.D, 1 + hideEnd - hideStart);
+        last = hideEnd + 1;
+      }
+      // Final match if necessary.
+      if (last < end)
       {
-          selection.addOperation(CigarArray.M, end-last+1);
+        selection.addOperation(CigarArray.M, end - last + 1);
       }
     }
     else
     {
-        selection.addOperation(CigarArray.M, end-start+1);
-      }
-      return selection;
-    }
-    /**
-     * return a compact representation of the current alignment selection to
-     * pass to an analysis function
-     * @param selectedOnly boolean true to just return the selected view
-     * @return AlignmentView
-     */
+      selection.addOperation(CigarArray.M, end - start + 1);
+    }
+    return selection;
+  }
+
+  /**
+   * return a compact representation of the current alignment selection to pass
+   * to an analysis function
+   * 
+   * @param selectedOnly
+   *                boolean true to just return the selected view
+   * @return AlignmentView
+   */
   jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly)
   {
-      // JBPNote:
-      // this is here because the AlignmentView constructor modifies the CigarArray
-      // object. Refactoring of Cigar and alignment view representation should
-      // be done to remove redundancy.
-      CigarArray aligview = getViewAsCigars(selectedOnly);
+    // JBPNote:
+    // this is here because the AlignmentView constructor modifies the
+    // CigarArray
+    // object. Refactoring of Cigar and alignment view representation should
+    // be done to remove redundancy.
+    CigarArray aligview = getViewAsCigars(selectedOnly);
     if (aligview != null)
     {
-        return new AlignmentView(aligview,
-                               (selectedOnly && selectionGroup != null) ?
-                               selectionGroup.getStartRes() : 0);
-      }
-      return null;
+      return new AlignmentView(aligview,
+              (selectedOnly && selectionGroup != null) ? selectionGroup
+                      .getStartRes() : 0);
     }
-    /**
-     * This method returns the visible alignment as text, as
-     * seen on the GUI, ie if columns are hidden they will not
-     * be returned in the result.
-     * Use this for calculating trees, PCA, redundancy etc on views
-     * which contain hidden columns.
-     * @return String[]
-     */
-    public String [] getViewAsString(boolean selectedRegionOnly)
-    {
-      String [] selection = null;
-      SequenceI [] seqs= null;
-      int i, iSize;
-      int start = 0, end = 0;
-      if(selectedRegionOnly && selectionGroup!=null)
-      {
-        iSize = selectionGroup.getSize();
-        seqs = selectionGroup.getSequencesInOrder(alignment);
-        start = selectionGroup.getStartRes();
-        end = selectionGroup.getEndRes()+1;
-      }
-      else
-      {
-        iSize = alignment.getHeight();
-        seqs = alignment.getSequencesArray();
-        end = alignment.getWidth();
-      }
+    return null;
+  }
 
-      selection = new String[iSize];
-    if (hasHiddenColumns)
+  /**
+   * This method returns the visible alignment as text, as seen on the GUI, ie
+   * if columns are hidden they will not be returned in the result. Use this for
+   * calculating trees, PCA, redundancy etc on views which contain hidden
+   * columns.
+   * 
+   * @return String[]
+   */
+  public String[] getViewAsString(boolean selectedRegionOnly)
+  {
+    String[] selection = null;
+    SequenceI[] seqs = null;
+    int i, iSize;
+    int start = 0, end = 0;
+    if (selectedRegionOnly && selectionGroup != null)
     {
-        selection = colSel.getVisibleSequenceStrings(start, end, seqs);
+      iSize = selectionGroup.getSize();
+      seqs = selectionGroup.getSequencesInOrder(alignment);
+      start = selectionGroup.getStartRes();
+      end = selectionGroup.getEndRes() + 1;
     }
     else
     {
-        for(i=0; i<iSize; i++)
-        {
-          selection[i] = seqs[i].getSequenceAsString(start, end);
-        }
+      iSize = alignment.getHeight();
+      seqs = alignment.getSequencesArray();
+      end = alignment.getWidth();
+    }
 
+    selection = new String[iSize];
+    if (hasHiddenColumns)
+    {
+      selection = colSel.getVisibleSequenceStrings(start, end, seqs);
+    }
+    else
+    {
+      for (i = 0; i < iSize; i++)
+      {
+        selection[i] = seqs[i].getSequenceAsString(start, end);
       }
-      return selection;
+
     }
+    return selection;
+  }
 
-  public int [][] getVisibleRegionBoundaries(int min, int max)
+  public int[][] getVisibleRegionBoundaries(int min, int max)
   {
     Vector regions = new Vector();
     int start = min;
@@ -1698,15 +1758,14 @@ public class AlignViewport
       }
 
       regions.addElement(new int[]
-                         {start, end});
+      { start, end });
 
       if (hasHiddenColumns)
       {
         start = colSel.adjustForHiddenColumns(end);
         start = colSel.getHiddenBoundaryLeft(start) + 1;
       }
-    }
-    while (end < max);
+    } while (end < max);
 
     int[][] startEnd = new int[regions.size()][2];
 
@@ -1716,215 +1775,229 @@ public class AlignViewport
 
   }
 
-    public boolean getShowHiddenMarkers()
-    {
-      return showHiddenMarkers;
-    }
+  public boolean getShowHiddenMarkers()
+  {
+    return showHiddenMarkers;
+  }
 
-    public void setShowHiddenMarkers(boolean show)
-    {
-      showHiddenMarkers = show;
-    }
+  public void setShowHiddenMarkers(boolean show)
+  {
+    showHiddenMarkers = show;
+  }
 
-    public String getSequenceSetId()
-    {
-      if(sequenceSetID==null)
+  public String getSequenceSetId()
+  {
+    if (sequenceSetID == null)
     {
-        sequenceSetID =  alignment.hashCode()+"";
+      sequenceSetID = alignment.hashCode() + "";
     }
 
-      return sequenceSetID;
-    }
+    return sequenceSetID;
+  }
 
-    public void alignmentChanged(AlignmentPanel ap)
-    {
-        if (padGaps)
+  public void alignmentChanged(AlignmentPanel ap)
+  {
+    if (padGaps)
     {
-          alignment.padGaps();
+      alignment.padGaps();
     }
 
-        if (hconsensus != null && autoCalculateConsensus)
-        {
-          updateConsensus(ap);
-          updateConservation(ap);
-        }
+    if (hconsensus != null && autoCalculateConsensus)
+    {
+      updateConsensus(ap);
+      updateConservation(ap);
+    }
 
-        //Reset endRes of groups if beyond alignment width
-        int alWidth = alignment.getWidth();
-        Vector groups = alignment.getGroups();
-        if(groups!=null)
-        {
-          for(int i=0; i<groups.size(); i++)
-          {
-            SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
-            if(sg.getEndRes()>alWidth)
+    // Reset endRes of groups if beyond alignment width
+    int alWidth = alignment.getWidth();
+    Vector groups = alignment.getGroups();
+    if (groups != null)
+    {
+      for (int i = 0; i < groups.size(); i++)
+      {
+        SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+        if (sg.getEndRes() > alWidth)
         {
-              sg.setEndRes(alWidth-1);
-          }
+          sg.setEndRes(alWidth - 1);
         }
+      }
     }
 
-        if(selectionGroup!=null && selectionGroup.getEndRes()>alWidth)
+    if (selectionGroup != null && selectionGroup.getEndRes() > alWidth)
     {
-          selectionGroup.setEndRes(alWidth-1);
+      selectionGroup.setEndRes(alWidth - 1);
     }
 
-        resetAllColourSchemes();
-
-       // alignment.adjustSequenceAnnotations();
-    }
+    resetAllColourSchemes();
 
+    // alignment.adjustSequenceAnnotations();
+  }
 
-    void resetAllColourSchemes()
+  void resetAllColourSchemes()
+  {
+    ColourSchemeI cs = globalColourScheme;
+    if (cs != null)
     {
-      ColourSchemeI cs = globalColourScheme;
-      if(cs!=null)
+      if (cs instanceof ClustalxColourScheme)
       {
-        if (cs instanceof ClustalxColourScheme)
-        {
-          ( (ClustalxColourScheme) cs).
-              resetClustalX(alignment.getSequences(),
-                            alignment.getWidth());
-        }
+        ((ClustalxColourScheme) cs).resetClustalX(alignment.getSequences(),
+                alignment.getWidth());
+      }
 
-        cs.setConsensus(hconsensus);
-        if (cs.conservationApplied())
-        {
-          Alignment al = (Alignment) alignment;
-          Conservation c = new Conservation("All",
-                                            ResidueProperties.propHash, 3,
-                                            al.getSequences(), 0,
-                                            al.getWidth() - 1);
-          c.calculate();
-          c.verdict(false, ConsPercGaps);
-
-          cs.setConservation(c);
-        }
+      cs.setConsensus(hconsensus);
+      if (cs.conservationApplied())
+      {
+        Alignment al = (Alignment) alignment;
+        Conservation c = new Conservation("All",
+                ResidueProperties.propHash, 3, al.getSequences(), 0, al
+                        .getWidth() - 1);
+        c.calculate();
+        c.verdict(false, ConsPercGaps);
+
+        cs.setConservation(c);
       }
+    }
 
-      int s, sSize = alignment.getGroups().size();
-      for(s=0; s<sSize; s++)
+    int s, sSize = alignment.getGroups().size();
+    for (s = 0; s < sSize; s++)
+    {
+      SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s);
+      if (sg.cs != null && sg.cs instanceof ClustalxColourScheme)
       {
-        SequenceGroup sg = (SequenceGroup)alignment.getGroups().elementAt(s);
-        if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
-        {
-          ((ClustalxColourScheme)sg.cs).resetClustalX(
-              sg.getSequences(hiddenRepSequences), sg.getWidth());
-        }
-        sg.recalcConservation();
+        ((ClustalxColourScheme) sg.cs).resetClustalX(sg
+                .getSequences(hiddenRepSequences), sg.getWidth());
       }
+      sg.recalcConservation();
     }
+  }
 
+  public Color getSequenceColour(SequenceI seq)
+  {
+    if (sequenceColours == null || !sequenceColours.containsKey(seq))
+    {
+      return Color.white;
+    }
+    else
+    {
+      return (Color) sequenceColours.get(seq);
+    }
+  }
 
-    public Color getSequenceColour(SequenceI seq)
+  public void setSequenceColour(SequenceI seq, Color col)
+  {
+    if (sequenceColours == null)
     {
-      if(sequenceColours==null || !sequenceColours.containsKey(seq))
+      sequenceColours = new Hashtable();
+    }
+
+    if (col == null)
     {
-        return Color.white;
+      sequenceColours.remove(seq);
     }
-      else
+    else
     {
-        return (Color)sequenceColours.get(seq);
+      sequenceColours.put(seq, col);
     }
   }
 
-    public void setSequenceColour(SequenceI seq, Color col)
+  /**
+   * returns the visible column regions of the alignment
+   * 
+   * @param selectedRegionOnly
+   *                true to just return the contigs intersecting with the
+   *                selected area
+   * @return
+   */
+  public int[] getViewAsVisibleContigs(boolean selectedRegionOnly)
+  {
+    int[] viscontigs = null;
+    int start = 0, end = 0;
+    if (selectedRegionOnly && selectionGroup != null)
     {
-      if(sequenceColours==null)
+      start = selectionGroup.getStartRes();
+      end = selectionGroup.getEndRes() + 1;
+    }
+    else
     {
-        sequenceColours = new Hashtable();
+      end = alignment.getWidth();
     }
+    viscontigs = colSel.getVisibleContigs(start, end);
+    return viscontigs;
+  }
+
+  /**
+   * get hash of undo and redo list for the alignment
+   * 
+   * @return long[] { historyList.hashCode, redoList.hashCode };
+   */
+  public long[] getUndoRedoHash()
+  {
+    if (historyList == null || redoList == null)
+      return new long[]
+      { -1, -1 };
+    return new long[]
+    { historyList.hashCode(), this.redoList.hashCode() };
+  }
 
-      if(col == null)
+  /**
+   * test if a particular set of hashcodes are different to the hashcodes for
+   * the undo and redo list.
+   * 
+   * @param undoredo
+   *                the stored set of hashcodes as returned by getUndoRedoHash
+   * @return true if the hashcodes differ (ie the alignment has been edited) or
+   *         the stored hashcode array differs in size
+   */
+  public boolean isUndoRedoHashModified(long[] undoredo)
+  {
+    if (undoredo == null)
     {
-        sequenceColours.remove(seq);
+      return true;
     }
-      else
+    long[] cstate = getUndoRedoHash();
+    if (cstate.length != undoredo.length)
     {
-        sequenceColours.put(seq, col);
+      return true;
     }
-    }
-    /**
-     * returns the visible column regions of the alignment
-     * @param selectedRegionOnly true to just return the contigs intersecting with the selected area
-     * @return
-     */
-    public int[] getViewAsVisibleContigs(boolean selectedRegionOnly) {
-      int[] viscontigs=null;
-      int start = 0, end = 0;
-      if(selectedRegionOnly && selectionGroup!=null)
-      {
-        start = selectionGroup.getStartRes();
-        end = selectionGroup.getEndRes()+1;
-      }
-      else
-      {
-        end = alignment.getWidth();
-      }
-      viscontigs = colSel.getVisibleContigs(start, end);
-      return viscontigs;
-    }
-    /**
-     * get hash of undo and redo list for the alignment
-     * @return long[] { historyList.hashCode, redoList.hashCode };
-     */
-    public long[] getUndoRedoHash()
-    {
-      if (historyList==null || redoList==null)
-        return new long[] { -1, -1};
-      return new long[] { historyList.hashCode(), this.redoList.hashCode() };
-    }
-    /**
-     * test if a particular set of hashcodes are different to the hashcodes for the undo and redo list.
-     * @param undoredo the stored set of hashcodes as returned by getUndoRedoHash
-     * @return true if the hashcodes differ (ie the alignment has been edited) or the stored hashcode array differs in size
-     */
-    public boolean isUndoRedoHashModified(long[] undoredo)
-    {
-      if (undoredo==null)
+
+    for (int i = 0; i < cstate.length; i++)
+    {
+      if (cstate[i] != undoredo[i])
       {
         return true;
       }
-      long[] cstate = getUndoRedoHash();
-      if (cstate.length!=undoredo.length)
-      {  return true; }
-      
-      for (int i=0; i<cstate.length; i++)
-      {
-        if (cstate[i]!=undoredo[i])
-        {
-          return true;
-        }
-      }
-      return false;
-    }
-    
-    public boolean getCentreColumnLabels()
-    {
-      return centreColumnLabels;
     }
-    public void setCentreColumnLabels(boolean centrecolumnlabels)
+    return false;
+  }
+
+  public boolean getCentreColumnLabels()
+  {
+    return centreColumnLabels;
+  }
+
+  public void setCentreColumnLabels(boolean centrecolumnlabels)
+  {
+    centreColumnLabels = centrecolumnlabels;
+  }
+
+  public void updateSequenceIdColours()
+  {
+    Vector groups = alignment.getGroups();
+    if (sequenceColours == null)
     {
-      centreColumnLabels =  centrecolumnlabels;
+      sequenceColours = new Hashtable();
     }
-    public void updateSequenceIdColours()
+    for (int ig = 0, igSize = groups.size(); ig < igSize; ig++)
     {
-      Vector groups = alignment.getGroups();
-      if (sequenceColours==null)
+      SequenceGroup sg = (SequenceGroup) groups.elementAt(ig);
+      if (sg.idColour != null)
       {
-        sequenceColours = new Hashtable();
-      }
-      for (int ig=0,igSize=groups.size(); ig<igSize; ig++)
-      {
-        SequenceGroup sg = (SequenceGroup) groups.elementAt(ig);
-        if (sg.idColour!=null)
+        Vector sqs = sg.getSequences(hiddenRepSequences);
+        for (int s = 0, sSize = sqs.size(); s < sSize; s++)
         {
-          Vector sqs = sg.getSequences(hiddenRepSequences);
-          for (int s=0,sSize=sqs.size();s<sSize;s++)
-          {
-            sequenceColours.put(sqs.elementAt(s), sg.idColour);
-          } 
+          sequenceColours.put(sqs.elementAt(s), sg.idColour);
         }
       }
     }
+  }
 }
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 95b4220..c8fcd39 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -32,35 +32,46 @@ import jalview.schemes.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class AlignmentPanel
-    extends GAlignmentPanel implements AdjustmentListener, Printable
+public class AlignmentPanel extends GAlignmentPanel implements
+        AdjustmentListener, Printable
 {
   public AlignViewport av;
+
   OverviewPanel overviewPanel;
+
   SeqPanel seqPanel;
+
   IdPanel idPanel;
+
   IdwidthAdjuster idwidthAdjuster;
 
   /** DOCUMENT ME!! */
   public AlignFrame alignFrame;
+
   ScalePanel scalePanel;
+
   AnnotationPanel annotationPanel;
+
   AnnotationLabels alabels;
 
   // this value is set false when selection area being dragged
   boolean fastPaint = true;
+
   int hextent = 0;
+
   int vextent = 0;
 
   /**
    * Creates a new AlignmentPanel object.
-   *
-   * @param af DOCUMENT ME!
-   * @param av DOCUMENT ME!
+   * 
+   * @param af
+   *                DOCUMENT ME!
+   * @param av
+   *                DOCUMENT ME!
    */
   public AlignmentPanel(AlignFrame af, final AlignViewport av)
   {
@@ -98,10 +109,7 @@ public class AlignmentPanel
       {
         if (evt.getPropertyName().equals("alignment"))
         {
-          PaintRefresher.Refresh(ap,
-                                 av.getSequenceSetId(),
-                                 true,
-                                 true);
+          PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true);
           alignmentChanged();
         }
       }
@@ -131,10 +139,10 @@ public class AlignmentPanel
     // to prevent drawing old image
     FontMetrics fm = getFontMetrics(av.getFont());
 
-    scalePanelHolder.setPreferredSize(new Dimension(10,
-        av.charHeight + fm.getDescent()));
-    idSpaceFillerPanel1.setPreferredSize(new Dimension(10,
-        av.charHeight + fm.getDescent()));
+    scalePanelHolder.setPreferredSize(new Dimension(10, av.charHeight
+            + fm.getDescent()));
+    idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av.charHeight
+            + fm.getDescent()));
 
     idPanel.idCanvas.gg = null;
     seqPanel.seqCanvas.img = null;
@@ -154,25 +162,28 @@ public class AlignmentPanel
   }
 
   /**
-   * Calculate the width of the alignment labels based on the displayed names and any bounds on label width set in preferences.
-   *
-   * @return Dimension giving the maximum width of the alignment label panel that should be used.
+   * Calculate the width of the alignment labels based on the displayed names
+   * and any bounds on label width set in preferences.
+   * 
+   * @return Dimension giving the maximum width of the alignment label panel
+   *         that should be used.
    */
   public Dimension calculateIdWidth()
   {
     Container c = new Container();
 
-    FontMetrics fm = c.getFontMetrics(
-        new Font(av.font.getName(), Font.ITALIC, av.font.getSize()));
+    FontMetrics fm = c.getFontMetrics(new Font(av.font.getName(),
+            Font.ITALIC, av.font.getSize()));
 
     AlignmentI al = av.getAlignment();
-    int afwidth = (alignFrame!=null ? alignFrame.getWidth() : 300); 
-    int maxwidth = Math.max(20,Math.min(afwidth-200,(int) 2*afwidth/3));  
+    int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
+    int maxwidth = Math.max(20, Math.min(afwidth - 200, (int) 2 * afwidth
+            / 3));
     int i = 0;
     int idWidth = 0;
     String id;
 
-    while ( (i < al.getHeight()) && (al.getSequenceAt(i) != null))
+    while ((i < al.getHeight()) && (al.getSequenceAt(i) != null))
     {
       SequenceI s = al.getSequenceAt(i);
 
@@ -211,8 +222,9 @@ public class AlignmentPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param results DOCUMENT ME!
+   * 
+   * @param results
+   *                DOCUMENT ME!
    */
   public void highlightSearchResults(SearchResults results)
   {
@@ -228,8 +240,9 @@ public class AlignmentPanel
 
       if (!av.wrapAlignment)
       {
-        if ( (av.getStartRes() > end) || (av.getEndRes() < start) ||
-            ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
+        if ((av.getStartRes() > end)
+                || (av.getEndRes() < start)
+                || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
         {
           setScrollValues(start, seqIndex);
         }
@@ -245,8 +258,8 @@ public class AlignmentPanel
 
   void scrollToWrappedVisible(int res)
   {
-    int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.
-        getWidth());
+    int cwidth = seqPanel.seqCanvas
+            .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
     if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
     {
       vscroll.setValue(res / cwidth);
@@ -256,7 +269,7 @@ public class AlignmentPanel
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public OverviewPanel getOverviewPanel()
@@ -266,8 +279,9 @@ public class AlignmentPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param op DOCUMENT ME!
+   * 
+   * @param op
+   *                DOCUMENT ME!
    */
   public void setOverviewPanel(OverviewPanel op)
   {
@@ -276,8 +290,9 @@ public class AlignmentPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param b DOCUMENT ME!
+   * 
+   * @param b
+   *                DOCUMENT ME!
    */
   public void setAnnotationVisible(boolean b)
   {
@@ -291,7 +306,7 @@ public class AlignmentPanel
 
   public void adjustAnnotationHeight()
   {
-    //TODO: display vertical annotation scrollbar if necessary 
+    // TODO: display vertical annotation scrollbar if necessary
     // this is called after loading new annotation onto alignment
     if (alignFrame.getHeight() == 0)
     {
@@ -311,21 +326,20 @@ public class AlignmentPanel
 
     hscroll.addNotify();
 
-    annotationScroller.setPreferredSize(
-        new Dimension(annotationScroller.getWidth(), height));
-
+    annotationScroller.setPreferredSize(new Dimension(annotationScroller
+            .getWidth(), height));
 
     annotationSpaceFillerHolder.setPreferredSize(new Dimension(
-        annotationSpaceFillerHolder.getWidth(),
-        height));
+            annotationSpaceFillerHolder.getWidth(), height));
     annotationScroller.validate();// repaint();
     repaint();
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param wrap DOCUMENT ME!
+   * 
+   * @param wrap
+   *                DOCUMENT ME!
    */
   public void setWrapAlignment(boolean wrap)
   {
@@ -365,7 +379,7 @@ public class AlignmentPanel
     }
     else
     {
-      if ( (vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
+      if ((vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
       {
         return false;
       }
@@ -381,9 +395,10 @@ public class AlignmentPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param right DOCUMENT ME!
-   *
+   * 
+   * @param right
+   *                DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   public boolean scrollRight(boolean right)
@@ -400,7 +415,7 @@ public class AlignmentPanel
     }
     else
     {
-      if ( (hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
+      if ((hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
       {
         return false;
       }
@@ -416,9 +431,11 @@ public class AlignmentPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param x DOCUMENT ME!
-   * @param y DOCUMENT ME!
+   * 
+   * @param x
+   *                DOCUMENT ME!
+   * @param y
+   *                DOCUMENT ME!
    */
   public void setScrollValues(int x, int y)
   {
@@ -431,7 +448,7 @@ public class AlignmentPanel
       width = av.getColumnSelection().findColumnPosition(width);
     }
 
-    av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) - 1);
+    av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) - 1);
 
     hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
     vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
@@ -446,12 +463,12 @@ public class AlignmentPanel
       vextent = height;
     }
 
-    if ( (hextent + x) > width)
+    if ((hextent + x) > width)
     {
       x = width - hextent;
     }
 
-    if ( (vextent + y) > height)
+    if ((vextent + y) > height)
     {
       y = height - vextent;
     }
@@ -472,8 +489,9 @@ public class AlignmentPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
    */
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
@@ -485,8 +503,9 @@ public class AlignmentPanel
     {
       int x = hscroll.getValue();
       av.setStartRes(x);
-      av.setEndRes( (x +
-                     (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
+      av
+              .setEndRes((x + (seqPanel.seqCanvas.getWidth() / av
+                      .getCharWidth())) - 1);
     }
 
     if (evt.getSource() == vscroll)
@@ -497,16 +516,16 @@ public class AlignmentPanel
       {
         if (offy > -1)
         {
-          int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
-              seqCanvas.getWidth());
+          int rowSize = seqPanel.seqCanvas
+                  .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
           av.setStartRes(offy * rowSize);
-          av.setEndRes( (offy + 1) * rowSize);
+          av.setEndRes((offy + 1) * rowSize);
         }
         else
         {
-          //This is only called if file loaded is a jar file that
-          //was wrapped when saved and user has wrap alignment true
-          //as preference setting
+          // This is only called if file loaded is a jar file that
+          // was wrapped when saved and user has wrap alignment true
+          // as preference setting
           SwingUtilities.invokeLater(new Runnable()
           {
             public void run()
@@ -519,8 +538,8 @@ public class AlignmentPanel
       else
       {
         av.setStartSeq(offy);
-        av.setEndSeq(offy +
-                     (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
+        av.setEndSeq(offy
+                + (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
       }
     }
 
@@ -552,8 +571,7 @@ public class AlignmentPanel
       if (scrollX != 0 || scrollY != 0)
       {
         idPanel.idCanvas.fastPaint(scrollY);
-        seqPanel.seqCanvas.fastPaint(scrollX,
-                                     scrollY);
+        seqPanel.seqCanvas.fastPaint(scrollX, scrollY);
         scalePanel.repaint();
 
         if (av.getShowAnnotation())
@@ -568,10 +586,10 @@ public class AlignmentPanel
   {
     repaint();
 
-    if(updateOverview)
+    if (updateOverview)
     {
-      jalview.structure.StructureSelectionManager.getStructureSelectionManager()
-          .sequenceColoursChanged(this);
+      jalview.structure.StructureSelectionManager
+              .getStructureSelectionManager().sequenceColoursChanged(this);
 
       if (overviewPanel != null)
       {
@@ -582,8 +600,9 @@ public class AlignmentPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param g DOCUMENT ME!
+   * 
+   * @param g
+   *                DOCUMENT ME!
    */
   public void paintComponent(Graphics g)
   {
@@ -603,14 +622,14 @@ public class AlignmentPanel
         maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
       }
 
-      int canvasWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
-          seqCanvas.getWidth());
+      int canvasWidth = seqPanel.seqCanvas
+              .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
       if (canvasWidth > 0)
       {
-        int max = maxwidth /
-            seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.
-            getWidth()) +
-            1;
+        int max = maxwidth
+                / seqPanel.seqCanvas
+                        .getWrappedCanvasWidth(seqPanel.seqCanvas
+                                .getWidth()) + 1;
         vscroll.setMaximum(max);
         vscroll.setUnitIncrement(1);
         vscroll.setVisibleAmount(1);
@@ -624,19 +643,23 @@ public class AlignmentPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param pg DOCUMENT ME!
-   * @param pf DOCUMENT ME!
-   * @param pi DOCUMENT ME!
-   *
+   * 
+   * @param pg
+   *                DOCUMENT ME!
+   * @param pf
+   *                DOCUMENT ME!
+   * @param pi
+   *                DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
-   *
-   * @throws PrinterException DOCUMENT ME!
+   * 
+   * @throws PrinterException
+   *                 DOCUMENT ME!
    */
   public int print(Graphics pg, PageFormat pf, int pi)
-      throws PrinterException
+          throws PrinterException
   {
-    pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
+    pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
 
     int pwidth = (int) pf.getImageableWidth();
     int pheight = (int) pf.getImageableHeight();
@@ -653,18 +676,23 @@ public class AlignmentPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param pg DOCUMENT ME!
-   * @param pwidth DOCUMENT ME!
-   * @param pheight DOCUMENT ME!
-   * @param pi DOCUMENT ME!
-   *
+   * 
+   * @param pg
+   *                DOCUMENT ME!
+   * @param pwidth
+   *                DOCUMENT ME!
+   * @param pheight
+   *                DOCUMENT ME!
+   * @param pi
+   *                DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
-   *
-   * @throws PrinterException DOCUMENT ME!
+   * 
+   * @throws PrinterException
+   *                 DOCUMENT ME!
    */
   public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
-      throws PrinterException
+          throws PrinterException
   {
     int idWidth = getVisibleIdWidth();
     FontMetrics fm = getFontMetrics(av.getFont());
@@ -674,29 +702,28 @@ public class AlignmentPanel
     pg.fillRect(0, 0, pwidth, pheight);
     pg.setFont(av.getFont());
 
-    ////////////////////////////////////
-    /// How many sequences and residues can we fit on a printable page?
+    // //////////////////////////////////
+    // / How many sequences and residues can we fit on a printable page?
     int totalRes = (pwidth - idWidth) / av.getCharWidth();
 
-    int totalSeq = (int) ( (pheight - scaleHeight) / av.getCharHeight()) -
-        1;
+    int totalSeq = (int) ((pheight - scaleHeight) / av.getCharHeight()) - 1;
 
     int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
 
-    /////////////////////////////
-    /// Only print these sequences and residues on this page
+    // ///////////////////////////
+    // / Only print these sequences and residues on this page
     int startRes;
 
-    /////////////////////////////
-    /// Only print these sequences and residues on this page
+    // ///////////////////////////
+    // / Only print these sequences and residues on this page
     int endRes;
 
-    /////////////////////////////
-    /// Only print these sequences and residues on this page
+    // ///////////////////////////
+    // / Only print these sequences and residues on this page
     int startSeq;
 
-    /////////////////////////////
-    /// Only print these sequences and residues on this page
+    // ///////////////////////////
+    // / Only print these sequences and residues on this page
     int endSeq;
     startRes = (pi % pagesWide) * totalRes;
     endRes = (startRes + totalRes) - 1;
@@ -714,7 +741,7 @@ public class AlignmentPanel
       endSeq = av.getAlignment().getHeight();
     }
 
-    int pagesHigh = ( (av.alignment.getHeight() / totalSeq) + 1) * pheight;
+    int pagesHigh = ((av.alignment.getHeight() / totalSeq) + 1) * pheight;
 
     if (av.showAnnotation)
     {
@@ -728,12 +755,13 @@ public class AlignmentPanel
       return Printable.NO_SUCH_PAGE;
     }
 
-    //draw Scale
+    // draw Scale
     pg.translate(idWidth, 0);
-    scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);
-    pg.translate( -idWidth, scaleHeight);
+    scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth,
+            scaleHeight);
+    pg.translate(-idWidth, scaleHeight);
 
-    ////////////////
+    // //////////////
     // Draw the ids
     Color currentColor = null;
     Color currentTextColor = null;
@@ -744,8 +772,8 @@ public class AlignmentPanel
     for (int i = startSeq; i < endSeq; i++)
     {
       seq = av.getAlignment().getSequenceAt(i);
-      if ( (av.getSelectionGroup() != null) &&
-          av.getSelectionGroup().getSequences(null).contains(seq))
+      if ((av.getSelectionGroup() != null)
+              && av.getSelectionGroup().getSequences(null).contains(seq))
       {
         currentColor = Color.gray;
         currentTextColor = Color.black;
@@ -757,8 +785,8 @@ public class AlignmentPanel
       }
 
       pg.setColor(currentColor);
-      pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,
-                  av.getCharHeight());
+      pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth, av
+              .getCharHeight());
 
       pg.setColor(currentTextColor);
 
@@ -766,15 +794,14 @@ public class AlignmentPanel
       if (av.rightAlignIds)
       {
         fm = pg.getFontMetrics();
-        xPos = idWidth - fm.stringWidth(
-            seq.getDisplayId(av.getShowJVSuffix())
-            ) - 4;
+        xPos = idWidth
+                - fm.stringWidth(seq.getDisplayId(av.getShowJVSuffix()))
+                - 4;
       }
 
-      pg.drawString(seq.getDisplayId(av.getShowJVSuffix()),
-                    xPos,
-                    ( ( (i - startSeq) * av.charHeight) + av.getCharHeight()) -
-                    (av.getCharHeight() / 5));
+      pg.drawString(seq.getDisplayId(av.getShowJVSuffix()), xPos,
+              (((i - startSeq) * av.charHeight) + av.getCharHeight())
+                      - (av.getCharHeight() / 5));
     }
 
     pg.setFont(av.getFont());
@@ -785,11 +812,10 @@ public class AlignmentPanel
 
     if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
     {
-      pg.translate( -idWidth - 3, (endSeq - startSeq) * av.charHeight + 3);
-      alabels.drawComponent( (Graphics2D) pg, idWidth);
+      pg.translate(-idWidth - 3, (endSeq - startSeq) * av.charHeight + 3);
+      alabels.drawComponent((Graphics2D) pg, idWidth);
       pg.translate(idWidth + 3, 0);
-      annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes +
-                                    1);
+      annotationPanel.drawComponent((Graphics2D) pg, startRes, endRes + 1);
     }
 
     return Printable.PAGE_EXISTS;
@@ -797,19 +823,23 @@ public class AlignmentPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param pg DOCUMENT ME!
-   * @param pwidth DOCUMENT ME!
-   * @param pheight DOCUMENT ME!
-   * @param pi DOCUMENT ME!
-   *
+   * 
+   * @param pg
+   *                DOCUMENT ME!
+   * @param pwidth
+   *                DOCUMENT ME!
+   * @param pheight
+   *                DOCUMENT ME!
+   * @param pi
+   *                DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
-   *
-   * @throws PrinterException DOCUMENT ME!
+   * 
+   * @throws PrinterException
+   *                 DOCUMENT ME!
    */
   public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
-                                   int pi)
-      throws PrinterException
+          int pi) throws PrinterException
   {
 
     int annotationHeight = 0;
@@ -826,9 +856,8 @@ public class AlignmentPanel
       hgap += av.charHeight;
     }
 
-    int cHeight = av.getAlignment().getHeight() * av.charHeight
-        + hgap
-        + annotationHeight;
+    int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+            + annotationHeight;
 
     int idWidth = getVisibleIdWidth();
 
@@ -838,8 +867,8 @@ public class AlignmentPanel
       maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
     }
 
-    int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -
-        idWidth);
+    int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth
+            - idWidth);
 
     int totalHeight = cHeight * (maxwidth / resWidth + 1);
 
@@ -847,7 +876,7 @@ public class AlignmentPanel
     pg.fillRect(0, 0, pwidth, pheight);
     pg.setFont(av.getFont());
 
-    ////////////////
+    // //////////////
     // Draw the ids
     pg.setColor(Color.black);
 
@@ -871,31 +900,29 @@ public class AlignmentPanel
           xPos = idWidth - fm.stringWidth(string) - 4;
         }
         pg.drawString(string, xPos,
-                      ( (i * av.charHeight) + ypos + av.charHeight) -
-                      (av.charHeight / 5));
+                ((i * av.charHeight) + ypos + av.charHeight)
+                        - (av.charHeight / 5));
       }
       if (labels != null)
       {
-        pg.translate( -3,
-                     ypos +
-                     (av.getAlignment().getHeight() * av.charHeight));
+        pg.translate(-3, ypos
+                + (av.getAlignment().getHeight() * av.charHeight));
 
         pg.setFont(av.getFont());
         labels.drawComponent(pg, idWidth);
-        pg.translate( +3,
-                     -ypos -
-                     (av.getAlignment().getHeight() * av.charHeight));
+        pg.translate(+3, -ypos
+                - (av.getAlignment().getHeight() * av.charHeight));
       }
 
       ypos += cHeight;
-    }
-    while (ypos < totalHeight);
+    } while (ypos < totalHeight);
 
     pg.translate(idWidth, 0);
 
-    seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);
+    seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight,
+            0);
 
-    if ( (pi * pheight) < totalHeight)
+    if ((pi * pheight) < totalHeight)
     {
       return Printable.PAGE_EXISTS;
 
@@ -908,9 +935,8 @@ public class AlignmentPanel
 
   int getVisibleIdWidth()
   {
-    return
-        idPanel.getWidth() > 0 ? idPanel.getWidth() :
-        calculateIdWidth().width + 4;
+    return idPanel.getWidth() > 0 ? idPanel.getWidth()
+            : calculateIdWidth().width + 4;
   }
 
   void makeAlignmentImage(int type, File file)
@@ -921,20 +947,19 @@ public class AlignmentPanel
       maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
     }
 
-    int height = ( (av.alignment.getHeight() + 1) * av.charHeight)
-        + scalePanel.getHeight();
+    int height = ((av.alignment.getHeight() + 1) * av.charHeight)
+            + scalePanel.getHeight();
     int width = getVisibleIdWidth() + (maxwidth * av.charWidth);
 
     if (av.getWrapAlignment())
     {
       height = getWrappedHeight();
       if (System.getProperty("java.awt.headless") != null
-          && System.getProperty("java.awt.headless").equals("true"))
+              && System.getProperty("java.awt.headless").equals("true"))
       {
-        width = alignFrame.getWidth()
-            - vscroll.getPreferredSize().width
-            - alignFrame.getInsets().left
-            - alignFrame.getInsets().right;
+        width = alignFrame.getWidth() - vscroll.getPreferredSize().width
+                - alignFrame.getInsets().left
+                - alignFrame.getInsets().right;
       }
       else
       {
@@ -953,18 +978,15 @@ public class AlignmentPanel
       jalview.util.ImageMaker im;
       if (type == jalview.util.ImageMaker.PNG)
       {
-        im = new jalview.util.ImageMaker(this,
-                                         jalview.util.ImageMaker.PNG,
-                                         "Create PNG image from alignment",
-                                         width, height, file, null);
+        im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
+                "Create PNG image from alignment", width, height, file,
+                null);
       }
       else
       {
-        im = new jalview.util.ImageMaker(this,
-                                         jalview.util.ImageMaker.EPS,
-                                         "Create EPS file from alignment",
-                                         width, height, file,
-                                         alignFrame.getTitle());
+        im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
+                "Create EPS file from alignment", width, height, file,
+                alignFrame.getTitle());
       }
 
       if (av.getWrapAlignment())
@@ -983,24 +1005,14 @@ public class AlignmentPanel
           im.writeImage();
         }
       }
-    }
-    catch (OutOfMemoryError err)
+    } catch (OutOfMemoryError err)
     {
-      System.out.println("########################\n"
-                         + "OUT OF MEMORY " + file + "\n"
-                         + "########################");
-
-      JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                            "Out of Memory Creating Image!!"
-                                            +
-                                            "\nSee help files for increasing Java Virtual Machine memory."
-                                            , "Out of memory",
-                                            JOptionPane.WARNING_MESSAGE);
-      System.out.println("Create IMAGE: " + err);
-      System.gc();
-
-    }
-    catch (Exception ex)
+      // Be noisy here.
+      System.out.println("########################\n" + "OUT OF MEMORY "
+              + file + "\n" + "########################");
+      new OOMWarning("Creating Image for " + file, err);
+      // System.out.println("Create IMAGE: " + err);
+    } catch (Exception ex)
     {
       ex.printStackTrace();
     }
@@ -1024,34 +1036,34 @@ public class AlignmentPanel
 
   public void makePNGImageMap(File imgMapFile, String imageName)
   {
-    ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
-    //////////////////////////////////////////////
+    // /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
+    // ////////////////////////////////////////////
     int idWidth = getVisibleIdWidth();
     FontMetrics fm = getFontMetrics(av.getFont());
     int scaleHeight = av.charHeight + fm.getDescent();
 
     // Gen image map
-    //////////////////////////////////
+    // ////////////////////////////////
     if (imgMapFile != null)
     {
       try
       {
-        int s, sSize = av.alignment.getHeight(),
-            res, alwidth = av.alignment.getWidth(), g, gSize, f, fSize, sy;
+        int s, sSize = av.alignment.getHeight(), res, alwidth = av.alignment
+                .getWidth(), g, gSize, f, fSize, sy;
         StringBuffer text = new StringBuffer();
         PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
         out.println(jalview.io.HTMLOutput.getImageMapHTML());
-        out.println("<img src=\"" + imageName +
-                    "\" border=\"0\" usemap=\"#Map\" >"
-                    + "<map name=\"Map\">");
+        out.println("<img src=\"" + imageName
+                + "\" border=\"0\" usemap=\"#Map\" >"
+                + "<map name=\"Map\">");
 
         for (s = 0; s < sSize; s++)
         {
           sy = s * av.charHeight + scaleHeight;
 
           SequenceI seq = av.alignment.getSequenceAt(s);
-          SequenceFeature[] features = seq.getDatasetSequence().
-              getSequenceFeatures();
+          SequenceFeature[] features = seq.getDatasetSequence()
+                  .getSequenceFeatures();
           SequenceGroup[] groups = av.alignment.findAllGroups(seq);
           for (res = 0; res < alwidth; res++)
           {
@@ -1059,13 +1071,13 @@ public class AlignmentPanel
             Object obj = null;
             if (av.alignment.isNucleotide())
             {
-              obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res) +
-                  "");
+              obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res)
+                      + "");
             }
             else
             {
-              obj = ResidueProperties.aa2Triplet.get(
-                  seq.getCharAt(res) + "");
+              obj = ResidueProperties.aa2Triplet.get(seq.getCharAt(res)
+                      + "");
             }
 
             if (obj == null)
@@ -1081,15 +1093,15 @@ public class AlignmentPanel
               if (text.length() < 1)
               {
                 text.append("<area shape=\"rect\" coords=\""
-                            + (idWidth + res * av.charWidth) + ","
-                            + sy + ","
-                            + (idWidth + (res + 1) * av.charWidth) + ","
-                            + (av.charHeight + sy) + "\""
-                            + " onMouseOver=\"toolTip('"
-                            + alIndex + " " + triplet);
+                        + (idWidth + res * av.charWidth) + "," + sy + ","
+                        + (idWidth + (res + 1) * av.charWidth) + ","
+                        + (av.charHeight + sy) + "\""
+                        + " onMouseOver=\"toolTip('" + alIndex + " "
+                        + triplet);
               }
 
-              if (groups[g].getStartRes() < res && groups[g].getEndRes() > res)
+              if (groups[g].getStartRes() < res
+                      && groups[g].getEndRes() > res)
               {
                 text.append("<br><em>" + groups[g].getName() + "</em>");
               }
@@ -1100,44 +1112,45 @@ public class AlignmentPanel
               if (text.length() < 1)
               {
                 text.append("<area shape=\"rect\" coords=\""
-                            + (idWidth + res * av.charWidth) + ","
-                            + sy + ","
-                            + (idWidth + (res + 1) * av.charWidth) + ","
-                            + (av.charHeight + sy) + "\""
-                            + " onMouseOver=\"toolTip('"
-                            + alIndex + " " + triplet);
+                        + (idWidth + res * av.charWidth) + "," + sy + ","
+                        + (idWidth + (res + 1) * av.charWidth) + ","
+                        + (av.charHeight + sy) + "\""
+                        + " onMouseOver=\"toolTip('" + alIndex + " "
+                        + triplet);
               }
               fSize = features.length;
               for (f = 0; f < fSize; f++)
               {
 
-                if ( (features[f].getBegin() <= seq.findPosition(res)) &&
-                    (features[f].getEnd() >= seq.findPosition(res)))
+                if ((features[f].getBegin() <= seq.findPosition(res))
+                        && (features[f].getEnd() >= seq.findPosition(res)))
                 {
                   if (features[f].getType().equals("disulfide bond"))
                   {
                     if (features[f].getBegin() == seq.findPosition(res)
-                        || features[f].getEnd() == seq.findPosition(res))
+                            || features[f].getEnd() == seq
+                                    .findPosition(res))
                     {
-                      text.append("<br>disulfide bond " + features[f].getBegin() +
-                                  ":" +
-                                  features[f].getEnd());
+                      text.append("<br>disulfide bond "
+                              + features[f].getBegin() + ":"
+                              + features[f].getEnd());
                     }
                   }
                   else
                   {
                     text.append("<br>");
                     text.append(features[f].getType());
-                    if (features[f].getDescription() != null &&
-                        !features[f].
-                        getType().equals(features[f].getDescription()))
+                    if (features[f].getDescription() != null
+                            && !features[f].getType().equals(
+                                    features[f].getDescription()))
                     {
                       text.append(" " + features[f].getDescription());
                     }
 
                     if (features[f].getValue("status") != null)
                     {
-                      text.append(" (" + features[f].getValue("status") + ")");
+                      text.append(" (" + features[f].getValue("status")
+                              + ")");
                     }
                   }
                 }
@@ -1154,12 +1167,11 @@ public class AlignmentPanel
         out.println("</map></body></html>");
         out.close();
 
-      }
-      catch (Exception ex)
+      } catch (Exception ex)
       {
         ex.printStackTrace();
       }
-    } ///////////END OF IMAGE MAP
+    } // /////////END OF IMAGE MAP
 
   }
 
@@ -1168,18 +1180,15 @@ public class AlignmentPanel
     int seqPanelWidth = seqPanel.seqCanvas.getWidth();
 
     if (System.getProperty("java.awt.headless") != null
-        && System.getProperty("java.awt.headless").equals("true"))
+            && System.getProperty("java.awt.headless").equals("true"))
     {
-      seqPanelWidth = alignFrame.getWidth()
-          - getVisibleIdWidth()
-          - vscroll.getPreferredSize().width
-          - alignFrame.getInsets().left
-          - alignFrame.getInsets().right;
+      seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth()
+              - vscroll.getPreferredSize().width
+              - alignFrame.getInsets().left - alignFrame.getInsets().right;
     }
 
-    int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(
-        seqPanelWidth
-        );
+    int chunkWidth = seqPanel.seqCanvas
+            .getWrappedCanvasWidth(seqPanelWidth);
 
     int hgap = av.charHeight;
     if (av.scaleAboveWrapped)
@@ -1193,9 +1202,8 @@ public class AlignmentPanel
       annotationHeight = annotationPanel.adjustPanelHeight();
     }
 
-    int cHeight = av.getAlignment().getHeight() * av.charHeight
-        + hgap
-        + annotationHeight;
+    int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+            + annotationHeight;
 
     int maxwidth = av.alignment.getWidth();
     if (av.hasHiddenColumns)
@@ -1203,7 +1211,7 @@ public class AlignmentPanel
       maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
     }
 
-    int height = ( (maxwidth / chunkWidth) + 1) * cHeight;
+    int height = ((maxwidth / chunkWidth) + 1) * cHeight;
 
     return height;
   }
diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index 83a8a12..4c7bc0c 100755
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -1,517 +1,524 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.gui;
-
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.event.*;
-
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import java.awt.Dimension;
-
-public class AnnotationColourChooser
-    extends JPanel
-{
-  JInternalFrame frame;
-  AlignViewport av;
-  AlignmentPanel ap;
-  ColourSchemeI oldcs;
-  Hashtable oldgroupColours;
-  jalview.datamodel.AlignmentAnnotation currentAnnotation;
-  boolean adjusting = false;
-
-  public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
-  {
-    oldcs = av.getGlobalColourScheme();
-    if (av.alignment.getGroups() != null)
-    {
-      oldgroupColours = new Hashtable();
-      Vector allGroups = ap.av.alignment.getGroups();
-      SequenceGroup sg;
-      for (int g = 0; g < allGroups.size(); g++)
-      {
-        sg = (SequenceGroup) allGroups.get(g);
-        if (sg.cs != null)
-        {
-          oldgroupColours.put(sg, sg.cs);
-        }
-      }
-    }
-    this.av = av;
-    this.ap = ap;
-    frame = new JInternalFrame();
-    frame.setContentPane(this);
-    frame.setLayer(JLayeredPane.PALETTE_LAYER);
-    Desktop.addInternalFrame(frame, "Colour by Annotation", 480, 145);
-
-
-    slider.addChangeListener(new ChangeListener()
-    {
-      public void stateChanged(ChangeEvent evt)
-      {
-        if (!adjusting)
-        {
-          thresholdValue.setText( ( (float) slider.getValue() / 1000f) + "");
-          valueChanged();
-        }
-      }
-    });
-    slider.addMouseListener(new MouseAdapter()
-        {
-          public void mouseReleased(MouseEvent evt)
-          {
-            ap.paintAlignment(true);
-          }
-        });
-
-    if (av.alignment.getAlignmentAnnotation() == null)
-    {
-      return;
-    }
-
-    if (oldcs instanceof AnnotationColourGradient)
-    {
-      AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
-      minColour.setBackground(acg.getMinColour());
-      maxColour.setBackground(acg.getMaxColour());
-    }
-    else
-    {
-      minColour.setBackground(Color.orange);
-      maxColour.setBackground(Color.red);
-    }
-
-    adjusting = true;
-    Vector list = new Vector();
-    int index = 1;
-    for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
-    {
-      String label = av.alignment.getAlignmentAnnotation()[i].label;
-      if (!list.contains(label))
-        list.addElement(label);
-      else
-        list.addElement(label+"_"+(index++));
-    }
-
-    annotations = new JComboBox(list);
-
-    threshold.addItem("No Threshold");
-    threshold.addItem("Above Threshold");
-    threshold.addItem("Below Threshold");
-
-    try
-    {
-      jbInit();
-    }
-    catch (Exception ex)
-    {}
-
-    adjusting = false;
-
-    changeColour();
-
-  }
-
-  public AnnotationColourChooser()
-  {
-    try
-    {
-      jbInit();
-    }
-    catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
-  }
-
-  private void jbInit()
-      throws Exception
-  {
-    minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    minColour.setBorder(BorderFactory.createEtchedBorder());
-    minColour.setPreferredSize(new Dimension(40, 20));
-    minColour.setToolTipText("Minimum Colour");
-    minColour.addMouseListener(new MouseAdapter()
-    {
-      public void mousePressed(MouseEvent e)
-      {
-        if (minColour.isEnabled())
-        {
-          minColour_actionPerformed();
-        }
-      }
-    });
-    maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    maxColour.setBorder(BorderFactory.createEtchedBorder());
-    maxColour.setPreferredSize(new Dimension(40, 20));
-    maxColour.setToolTipText("Maximum Colour");
-    maxColour.addMouseListener(new MouseAdapter()
-    {
-      public void mousePressed(MouseEvent e)
-      {
-        if (maxColour.isEnabled())
-        {
-          maxColour_actionPerformed();
-        }
-      }
-    });
-    ok.setOpaque(false);
-    ok.setText("OK");
-    ok.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        ok_actionPerformed(e);
-      }
-    });
-    cancel.setOpaque(false);
-    cancel.setText("Cancel");
-    cancel.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        cancel_actionPerformed(e);
-      }
-    });
-    this.setLayout(borderLayout1);
-    jPanel2.setLayout(flowLayout1);
-    annotations.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        annotations_actionPerformed(e);
-      }
-    });
-    jPanel1.setBackground(Color.white);
-    jPanel2.setBackground(Color.white);
-    threshold.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        threshold_actionPerformed(e);
-      }
-    });
-    jPanel3.setLayout(flowLayout2);
-    thresholdValue.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        thresholdValue_actionPerformed(e);
-      }
-    });
-    slider.setPaintLabels(false);
-    slider.setPaintTicks(true);
-    slider.setBackground(Color.white);
-    slider.setEnabled(false);
-    slider.setOpaque(false);
-    slider.setPreferredSize(new Dimension(100, 32));
-    thresholdValue.setEnabled(false);
-    thresholdValue.setColumns(7);
-    jPanel3.setBackground(Color.white);
-    currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    currentColours.setOpaque(false);
-    currentColours.setText("Use Original Colours");
-    currentColours.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        currentColours_actionPerformed(e);
-      }
-    });
-    thresholdIsMin.setBackground(Color.white);
-    thresholdIsMin.setText("Threshold is Min/Max");
-    thresholdIsMin.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        thresholdIsMin_actionPerformed(actionEvent);
-      }
-    });
-    jPanel1.add(ok);
-    jPanel1.add(cancel);
-    jPanel2.add(annotations);
-    jPanel2.add(currentColours);
-    jPanel2.add(minColour);
-    jPanel2.add(maxColour);
-    this.add(jPanel3, java.awt.BorderLayout.CENTER);
-    jPanel3.add(threshold);
-    jPanel3.add(slider);
-    jPanel3.add(thresholdValue);
-    jPanel3.add(thresholdIsMin);
-    this.add(jPanel1, java.awt.BorderLayout.SOUTH);
-    this.add(jPanel2, java.awt.BorderLayout.NORTH);
-  }
-
-  JComboBox annotations;
-  JPanel minColour = new JPanel();
-  JPanel maxColour = new JPanel();
-  JButton ok = new JButton();
-  JButton cancel = new JButton();
-  JPanel jPanel1 = new JPanel();
-  JPanel jPanel2 = new JPanel();
-  BorderLayout borderLayout1 = new BorderLayout();
-  JComboBox threshold = new JComboBox();
-  FlowLayout flowLayout1 = new FlowLayout();
-  JPanel jPanel3 = new JPanel();
-  FlowLayout flowLayout2 = new FlowLayout();
-  JSlider slider = new JSlider();
-  JTextField thresholdValue = new JTextField(20);
-  JCheckBox currentColours = new JCheckBox();
-  JCheckBox thresholdIsMin = new JCheckBox();
-
-  public void minColour_actionPerformed()
-  {
-    Color col = JColorChooser.showDialog(this,
-                                         "Select Colour for Minimum Value",
-                                         minColour.getBackground());
-    if (col != null)
-    {
-      minColour.setBackground(col);
-    }
-    minColour.repaint();
-    changeColour();
-  }
-
-  public void maxColour_actionPerformed()
-  {
-    Color col = JColorChooser.showDialog(this,
-                                         "Select Colour for Maximum Value",
-                                         maxColour.getBackground());
-    if (col != null)
-    {
-      maxColour.setBackground(col);
-    }
-    maxColour.repaint();
-    changeColour();
-  }
-
-  void changeColour()
-  {
-    // Check if combobox is still adjusting
-    if (adjusting)
-    {
-      return;
-    }
-
-
-    currentAnnotation = av.alignment.getAlignmentAnnotation()[annotations.getSelectedIndex()];
-
-    int aboveThreshold = -1;
-    if (threshold.getSelectedItem().equals("Above Threshold"))
-    {
-      aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
-    }
-    else if (threshold.getSelectedItem().equals("Below Threshold"))
-    {
-      aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
-    }
-
-    slider.setEnabled(true);
-    thresholdValue.setEnabled(true);
-
-    if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
-    {
-      slider.setEnabled(false);
-      thresholdValue.setEnabled(false);
-      thresholdValue.setText("");
-    }
-    else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD &&
-             currentAnnotation.threshold == null)
-    {
-      currentAnnotation.setThreshold(new jalview.datamodel.GraphLine
-                                     ( (currentAnnotation.graphMax -
-                                        currentAnnotation.graphMin) / 2f,
-                                      "Threshold",
-                                      Color.black));
-    }
-
-    if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
-    {
-      adjusting = true;
-      float range = currentAnnotation.graphMax * 1000 -
-          currentAnnotation.graphMin * 1000;
-
-      slider.setMinimum( (int) (currentAnnotation.graphMin * 1000));
-      slider.setMaximum( (int) (currentAnnotation.graphMax * 1000));
-      slider.setValue( (int) (currentAnnotation.threshold.value * 1000));
-      thresholdValue.setText(currentAnnotation.threshold.value + "");
-      slider.setMajorTickSpacing( (int) (range / 10f));
-      slider.setEnabled(true);
-      thresholdValue.setEnabled(true);
-      adjusting = false;
-    }
-
-    AnnotationColourGradient acg = null;
-    if (currentColours.isSelected())
-    {
-      acg = new AnnotationColourGradient(
-          currentAnnotation,
-          av.getGlobalColourScheme(), aboveThreshold);
-    }
-    else
-    {
-      acg =
-          new AnnotationColourGradient(
-              currentAnnotation,
-              minColour.getBackground(),
-              maxColour.getBackground(),
-              aboveThreshold);
-    }
-
-    if(currentAnnotation.graphMin==0f&& currentAnnotation.graphMax==0f)
-    {
-      acg.predefinedColours = true;
-    }
-
-    acg.thresholdIsMinMax = thresholdIsMin.isSelected();
-
-    av.setGlobalColourScheme(acg);
-
-    if (av.alignment.getGroups() != null)
-    {
-      Vector allGroups = ap.av.alignment.getGroups();
-      SequenceGroup sg;
-      for (int g = 0; g < allGroups.size(); g++)
-      {
-        sg = (SequenceGroup) allGroups.get(g);
-
-        if (sg.cs == null)
-        {
-          continue;
-        }
-
-        if (currentColours.isSelected())
-        {
-          sg.cs = new AnnotationColourGradient(
-              currentAnnotation,
-              sg.cs, aboveThreshold);
-        }
-        else
-        {
-          sg.cs = new AnnotationColourGradient(
-              currentAnnotation,
-              minColour.getBackground(),
-              maxColour.getBackground(),
-              aboveThreshold);
-        }
-
-      }
-    }
-
-    ap.paintAlignment(false);
-  }
-
-  public void ok_actionPerformed(ActionEvent e)
-  {
-    changeColour();
-    try
-    {
-      frame.setClosed(true);
-    }
-    catch (Exception ex)
-    {}
-  }
-
-  public void cancel_actionPerformed(ActionEvent e)
-  {
-    reset();
-    try
-    {
-      frame.setClosed(true);
-    }
-    catch (Exception ex)
-    {}
-  }
-
-  void reset()
-  {
-    av.setGlobalColourScheme(oldcs);
-    if (av.alignment.getGroups() != null)
-    {
-      Vector allGroups = ap.av.alignment.getGroups();
-      SequenceGroup sg;
-      for (int g = 0; g < allGroups.size(); g++)
-      {
-        sg = (SequenceGroup) allGroups.get(g);
-        sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
-      }
-    }
-  }
-
-  public void thresholdCheck_actionPerformed(ActionEvent e)
-  {
-    changeColour();
-  }
-
-  public void annotations_actionPerformed(ActionEvent e)
-  {
-    changeColour();
-  }
-
-  public void threshold_actionPerformed(ActionEvent e)
-  {
-    changeColour();
-  }
-
-  public void thresholdValue_actionPerformed(ActionEvent e)
-  {
-    try
-    {
-      float f = Float.parseFloat(thresholdValue.getText());
-      slider.setValue( (int) (f * 1000));
-    }
-    catch (NumberFormatException ex)
-    {}
-  }
-
-  public void valueChanged()
-  {
-    if (currentColours.isSelected()
-        && ! (av.getGlobalColourScheme() instanceof AnnotationColourGradient))
-    {
-      changeColour();
-    }
-
-    currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
-    ap.paintAlignment(false);
-  }
-
-  public void currentColours_actionPerformed(ActionEvent e)
-  {
-    if (currentColours.isSelected())
-    {
-      reset();
-    }
-
-    maxColour.setEnabled(!currentColours.isSelected());
-    minColour.setEnabled(!currentColours.isSelected());
-
-    changeColour();
-  }
-
-  public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
-  {
-    changeColour();
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.gui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+import javax.swing.event.*;
+
+import jalview.datamodel.*;
+import jalview.schemes.*;
+import java.awt.Dimension;
+
+public class AnnotationColourChooser extends JPanel
+{
+  JInternalFrame frame;
+
+  AlignViewport av;
+
+  AlignmentPanel ap;
+
+  ColourSchemeI oldcs;
+
+  Hashtable oldgroupColours;
+
+  jalview.datamodel.AlignmentAnnotation currentAnnotation;
+
+  boolean adjusting = false;
+
+  public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
+  {
+    oldcs = av.getGlobalColourScheme();
+    if (av.alignment.getGroups() != null)
+    {
+      oldgroupColours = new Hashtable();
+      Vector allGroups = ap.av.alignment.getGroups();
+      SequenceGroup sg;
+      for (int g = 0; g < allGroups.size(); g++)
+      {
+        sg = (SequenceGroup) allGroups.get(g);
+        if (sg.cs != null)
+        {
+          oldgroupColours.put(sg, sg.cs);
+        }
+      }
+    }
+    this.av = av;
+    this.ap = ap;
+    frame = new JInternalFrame();
+    frame.setContentPane(this);
+    frame.setLayer(JLayeredPane.PALETTE_LAYER);
+    Desktop.addInternalFrame(frame, "Colour by Annotation", 480, 145);
+
+    slider.addChangeListener(new ChangeListener()
+    {
+      public void stateChanged(ChangeEvent evt)
+      {
+        if (!adjusting)
+        {
+          thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
+          valueChanged();
+        }
+      }
+    });
+    slider.addMouseListener(new MouseAdapter()
+    {
+      public void mouseReleased(MouseEvent evt)
+      {
+        ap.paintAlignment(true);
+      }
+    });
+
+    if (av.alignment.getAlignmentAnnotation() == null)
+    {
+      return;
+    }
+
+    if (oldcs instanceof AnnotationColourGradient)
+    {
+      AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
+      minColour.setBackground(acg.getMinColour());
+      maxColour.setBackground(acg.getMaxColour());
+    }
+    else
+    {
+      minColour.setBackground(Color.orange);
+      maxColour.setBackground(Color.red);
+    }
+
+    adjusting = true;
+    Vector list = new Vector();
+    int index = 1;
+    for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
+    {
+      String label = av.alignment.getAlignmentAnnotation()[i].label;
+      if (!list.contains(label))
+        list.addElement(label);
+      else
+        list.addElement(label + "_" + (index++));
+    }
+
+    annotations = new JComboBox(list);
+
+    threshold.addItem("No Threshold");
+    threshold.addItem("Above Threshold");
+    threshold.addItem("Below Threshold");
+
+    try
+    {
+      jbInit();
+    } catch (Exception ex)
+    {
+    }
+
+    adjusting = false;
+
+    changeColour();
+
+  }
+
+  public AnnotationColourChooser()
+  {
+    try
+    {
+      jbInit();
+    } catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
+
+  private void jbInit() throws Exception
+  {
+    minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    minColour.setBorder(BorderFactory.createEtchedBorder());
+    minColour.setPreferredSize(new Dimension(40, 20));
+    minColour.setToolTipText("Minimum Colour");
+    minColour.addMouseListener(new MouseAdapter()
+    {
+      public void mousePressed(MouseEvent e)
+      {
+        if (minColour.isEnabled())
+        {
+          minColour_actionPerformed();
+        }
+      }
+    });
+    maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    maxColour.setBorder(BorderFactory.createEtchedBorder());
+    maxColour.setPreferredSize(new Dimension(40, 20));
+    maxColour.setToolTipText("Maximum Colour");
+    maxColour.addMouseListener(new MouseAdapter()
+    {
+      public void mousePressed(MouseEvent e)
+      {
+        if (maxColour.isEnabled())
+        {
+          maxColour_actionPerformed();
+        }
+      }
+    });
+    ok.setOpaque(false);
+    ok.setText("OK");
+    ok.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        ok_actionPerformed(e);
+      }
+    });
+    cancel.setOpaque(false);
+    cancel.setText("Cancel");
+    cancel.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        cancel_actionPerformed(e);
+      }
+    });
+    this.setLayout(borderLayout1);
+    jPanel2.setLayout(flowLayout1);
+    annotations.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        annotations_actionPerformed(e);
+      }
+    });
+    jPanel1.setBackground(Color.white);
+    jPanel2.setBackground(Color.white);
+    threshold.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        threshold_actionPerformed(e);
+      }
+    });
+    jPanel3.setLayout(flowLayout2);
+    thresholdValue.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        thresholdValue_actionPerformed(e);
+      }
+    });
+    slider.setPaintLabels(false);
+    slider.setPaintTicks(true);
+    slider.setBackground(Color.white);
+    slider.setEnabled(false);
+    slider.setOpaque(false);
+    slider.setPreferredSize(new Dimension(100, 32));
+    thresholdValue.setEnabled(false);
+    thresholdValue.setColumns(7);
+    jPanel3.setBackground(Color.white);
+    currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    currentColours.setOpaque(false);
+    currentColours.setText("Use Original Colours");
+    currentColours.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        currentColours_actionPerformed(e);
+      }
+    });
+    thresholdIsMin.setBackground(Color.white);
+    thresholdIsMin.setText("Threshold is Min/Max");
+    thresholdIsMin.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        thresholdIsMin_actionPerformed(actionEvent);
+      }
+    });
+    jPanel1.add(ok);
+    jPanel1.add(cancel);
+    jPanel2.add(annotations);
+    jPanel2.add(currentColours);
+    jPanel2.add(minColour);
+    jPanel2.add(maxColour);
+    this.add(jPanel3, java.awt.BorderLayout.CENTER);
+    jPanel3.add(threshold);
+    jPanel3.add(slider);
+    jPanel3.add(thresholdValue);
+    jPanel3.add(thresholdIsMin);
+    this.add(jPanel1, java.awt.BorderLayout.SOUTH);
+    this.add(jPanel2, java.awt.BorderLayout.NORTH);
+  }
+
+  JComboBox annotations;
+
+  JPanel minColour = new JPanel();
+
+  JPanel maxColour = new JPanel();
+
+  JButton ok = new JButton();
+
+  JButton cancel = new JButton();
+
+  JPanel jPanel1 = new JPanel();
+
+  JPanel jPanel2 = new JPanel();
+
+  BorderLayout borderLayout1 = new BorderLayout();
+
+  JComboBox threshold = new JComboBox();
+
+  FlowLayout flowLayout1 = new FlowLayout();
+
+  JPanel jPanel3 = new JPanel();
+
+  FlowLayout flowLayout2 = new FlowLayout();
+
+  JSlider slider = new JSlider();
+
+  JTextField thresholdValue = new JTextField(20);
+
+  JCheckBox currentColours = new JCheckBox();
+
+  JCheckBox thresholdIsMin = new JCheckBox();
+
+  public void minColour_actionPerformed()
+  {
+    Color col = JColorChooser.showDialog(this,
+            "Select Colour for Minimum Value", minColour.getBackground());
+    if (col != null)
+    {
+      minColour.setBackground(col);
+    }
+    minColour.repaint();
+    changeColour();
+  }
+
+  public void maxColour_actionPerformed()
+  {
+    Color col = JColorChooser.showDialog(this,
+            "Select Colour for Maximum Value", maxColour.getBackground());
+    if (col != null)
+    {
+      maxColour.setBackground(col);
+    }
+    maxColour.repaint();
+    changeColour();
+  }
+
+  void changeColour()
+  {
+    // Check if combobox is still adjusting
+    if (adjusting)
+    {
+      return;
+    }
+
+    currentAnnotation = av.alignment.getAlignmentAnnotation()[annotations
+            .getSelectedIndex()];
+
+    int aboveThreshold = -1;
+    if (threshold.getSelectedItem().equals("Above Threshold"))
+    {
+      aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
+    }
+    else if (threshold.getSelectedItem().equals("Below Threshold"))
+    {
+      aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
+    }
+
+    slider.setEnabled(true);
+    thresholdValue.setEnabled(true);
+
+    if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
+    {
+      slider.setEnabled(false);
+      thresholdValue.setEnabled(false);
+      thresholdValue.setText("");
+    }
+    else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
+            && currentAnnotation.threshold == null)
+    {
+      currentAnnotation
+              .setThreshold(new jalview.datamodel.GraphLine(
+                      (currentAnnotation.graphMax - currentAnnotation.graphMin) / 2f,
+                      "Threshold", Color.black));
+    }
+
+    if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
+    {
+      adjusting = true;
+      float range = currentAnnotation.graphMax * 1000
+              - currentAnnotation.graphMin * 1000;
+
+      slider.setMinimum((int) (currentAnnotation.graphMin * 1000));
+      slider.setMaximum((int) (currentAnnotation.graphMax * 1000));
+      slider.setValue((int) (currentAnnotation.threshold.value * 1000));
+      thresholdValue.setText(currentAnnotation.threshold.value + "");
+      slider.setMajorTickSpacing((int) (range / 10f));
+      slider.setEnabled(true);
+      thresholdValue.setEnabled(true);
+      adjusting = false;
+    }
+
+    AnnotationColourGradient acg = null;
+    if (currentColours.isSelected())
+    {
+      acg = new AnnotationColourGradient(currentAnnotation, av
+              .getGlobalColourScheme(), aboveThreshold);
+    }
+    else
+    {
+      acg = new AnnotationColourGradient(currentAnnotation, minColour
+              .getBackground(), maxColour.getBackground(), aboveThreshold);
+    }
+
+    if (currentAnnotation.graphMin == 0f
+            && currentAnnotation.graphMax == 0f)
+    {
+      acg.predefinedColours = true;
+    }
+
+    acg.thresholdIsMinMax = thresholdIsMin.isSelected();
+
+    av.setGlobalColourScheme(acg);
+
+    if (av.alignment.getGroups() != null)
+    {
+      Vector allGroups = ap.av.alignment.getGroups();
+      SequenceGroup sg;
+      for (int g = 0; g < allGroups.size(); g++)
+      {
+        sg = (SequenceGroup) allGroups.get(g);
+
+        if (sg.cs == null)
+        {
+          continue;
+        }
+
+        if (currentColours.isSelected())
+        {
+          sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
+                  aboveThreshold);
+        }
+        else
+        {
+          sg.cs = new AnnotationColourGradient(currentAnnotation, minColour
+                  .getBackground(), maxColour.getBackground(),
+                  aboveThreshold);
+        }
+
+      }
+    }
+
+    ap.paintAlignment(false);
+  }
+
+  public void ok_actionPerformed(ActionEvent e)
+  {
+    changeColour();
+    try
+    {
+      frame.setClosed(true);
+    } catch (Exception ex)
+    {
+    }
+  }
+
+  public void cancel_actionPerformed(ActionEvent e)
+  {
+    reset();
+    try
+    {
+      frame.setClosed(true);
+    } catch (Exception ex)
+    {
+    }
+  }
+
+  void reset()
+  {
+    av.setGlobalColourScheme(oldcs);
+    if (av.alignment.getGroups() != null)
+    {
+      Vector allGroups = ap.av.alignment.getGroups();
+      SequenceGroup sg;
+      for (int g = 0; g < allGroups.size(); g++)
+      {
+        sg = (SequenceGroup) allGroups.get(g);
+        sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
+      }
+    }
+  }
+
+  public void thresholdCheck_actionPerformed(ActionEvent e)
+  {
+    changeColour();
+  }
+
+  public void annotations_actionPerformed(ActionEvent e)
+  {
+    changeColour();
+  }
+
+  public void threshold_actionPerformed(ActionEvent e)
+  {
+    changeColour();
+  }
+
+  public void thresholdValue_actionPerformed(ActionEvent e)
+  {
+    try
+    {
+      float f = Float.parseFloat(thresholdValue.getText());
+      slider.setValue((int) (f * 1000));
+    } catch (NumberFormatException ex)
+    {
+    }
+  }
+
+  public void valueChanged()
+  {
+    if (currentColours.isSelected()
+            && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
+    {
+      changeColour();
+    }
+
+    currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
+    ap.paintAlignment(false);
+  }
+
+  public void currentColours_actionPerformed(ActionEvent e)
+  {
+    if (currentColours.isSelected())
+    {
+      reset();
+    }
+
+    maxColour.setEnabled(!currentColours.isSelected());
+    minColour.setEnabled(!currentColours.isSelected());
+
+    changeColour();
+  }
+
+  public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
+  {
+    changeColour();
+  }
+
+}
diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index ab3f0d1..be0ef74 100755
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.gui;
 
 import java.util.*;
@@ -30,19 +29,24 @@ import jalview.io.*;
 
 /**
  * 
- * GUI dialog for exporting features or alignment annotations depending upon which method is called.
+ * GUI dialog for exporting features or alignment annotations depending upon
+ * which method is called.
  * 
  * @author AMW
- *
+ * 
  */
-public class AnnotationExporter
-    extends JPanel
+public class AnnotationExporter extends JPanel
 {
   JInternalFrame frame;
+
   AlignmentPanel ap;
+
   boolean features = true;
+
   AlignmentAnnotation[] annotations;
+
   Vector sequenceGroups;
+
   Hashtable alignmentProperties;
 
   public AnnotationExporter()
@@ -50,8 +54,7 @@ public class AnnotationExporter
     try
     {
       jbInit();
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       ex.printStackTrace();
     }
@@ -59,9 +62,7 @@ public class AnnotationExporter
     frame = new JInternalFrame();
     frame.setContentPane(this);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
-    Desktop.addInternalFrame(frame,
-                             "",
-                             260, 125);
+    Desktop.addInternalFrame(frame, "", 260, 125);
   }
 
   public void exportFeatures(AlignmentPanel ap)
@@ -73,9 +74,8 @@ public class AnnotationExporter
   }
 
   public void exportAnnotations(AlignmentPanel ap,
-                                AlignmentAnnotation[] annotations,
-                                Vector sequenceGroups,
-                                Hashtable alProperties)
+          AlignmentAnnotation[] annotations, Vector sequenceGroups,
+          Hashtable alProperties)
   {
     this.ap = ap;
     features = false;
@@ -89,12 +89,12 @@ public class AnnotationExporter
 
   public void toFile_actionPerformed(ActionEvent e)
   {
-    JalviewFileChooser chooser = new JalviewFileChooser(
-        jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+            .getProperty("LAST_DIRECTORY"));
 
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle(
-        features ? "Save Features to File" : "Save Annotation to File");
+    chooser.setDialogTitle(features ? "Save Features to File"
+            : "Save Annotation to File");
     chooser.setToolTipText("Save");
 
     int value = chooser.showSaveDialog(this);
@@ -106,15 +106,15 @@ public class AnnotationExporter
       {
         if (GFFFormat.isSelected())
         {
-          text = new FeaturesFile().printGFFFormat(
-              ap.av.alignment.getDataset().getSequencesArray(),
-              ap.av.featuresDisplayed);
+          text = new FeaturesFile().printGFFFormat(ap.av.alignment
+                  .getDataset().getSequencesArray(),
+                  ap.av.featuresDisplayed);
         }
         else
         {
-          text = new FeaturesFile().printJalviewFormat(
-              ap.av.alignment.getDataset().getSequencesArray(),
-              ap.av.featuresDisplayed);
+          text = new FeaturesFile().printJalviewFormat(ap.av.alignment
+                  .getDataset().getSequencesArray(),
+                  ap.av.featuresDisplayed);
         }
       }
       else
@@ -122,23 +122,22 @@ public class AnnotationExporter
         if (CSVFormat.isSelected())
         {
           text = new AnnotationFile().printCSVAnnotations(annotations);
-        } else {
-          text = new AnnotationFile().printAnnotations(
-            annotations,
-            sequenceGroups,
-            alignmentProperties);
+        }
+        else
+        {
+          text = new AnnotationFile().printAnnotations(annotations,
+                  sequenceGroups, alignmentProperties);
         }
       }
 
       try
       {
         java.io.PrintWriter out = new java.io.PrintWriter(
-            new java.io.FileWriter(chooser.getSelectedFile()));
+                new java.io.FileWriter(chooser.getSelectedFile()));
 
         out.print(text);
         out.close();
-      }
-      catch (Exception ex)
+      } catch (Exception ex)
       {
         ex.printStackTrace();
       }
@@ -154,15 +153,13 @@ public class AnnotationExporter
     {
       if (GFFFormat.isSelected())
       {
-        text = new FeaturesFile().printGFFFormat(
-            ap.av.alignment.getDataset().getSequencesArray(),
-            ap.av.featuresDisplayed);
+        text = new FeaturesFile().printGFFFormat(ap.av.alignment
+                .getDataset().getSequencesArray(), ap.av.featuresDisplayed);
       }
       else
       {
-        text = new FeaturesFile().printJalviewFormat(
-            ap.av.alignment.getDataset().getSequencesArray(),
-            ap.av.featuresDisplayed);
+        text = new FeaturesFile().printJalviewFormat(ap.av.alignment
+                .getDataset().getSequencesArray(), ap.av.featuresDisplayed);
       }
     }
     else if (!features)
@@ -170,22 +167,19 @@ public class AnnotationExporter
       if (CSVFormat.isSelected())
       {
         text = new AnnotationFile().printCSVAnnotations(annotations);
-      } else {
-        text = new AnnotationFile().printAnnotations(
-          annotations,
-          sequenceGroups,
-          alignmentProperties);
+      }
+      else
+      {
+        text = new AnnotationFile().printAnnotations(annotations,
+                sequenceGroups, alignmentProperties);
       }
     }
 
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
     cap.setText(text);
-    Desktop.addInternalFrame(cap,
-                             (features ? "Features for - " :
-                              "Annotations for - ")
-                             + ap.alignFrame.getTitle(),
-                             600,
-                             500);
+    Desktop.addInternalFrame(cap, (features ? "Features for - "
+            : "Annotations for - ")
+            + ap.alignFrame.getTitle(), 600, 500);
 
     close_actionPerformed(null);
   }
@@ -195,13 +189,12 @@ public class AnnotationExporter
     try
     {
       frame.setClosed(true);
+    } catch (java.beans.PropertyVetoException ex)
+    {
     }
-    catch (java.beans.PropertyVetoException ex)
-    {}
   }
 
-  private void jbInit()
-      throws Exception
+  private void jbInit() throws Exception
   {
     this.setLayout(flowLayout1);
     toFile.setText("to File");
@@ -256,15 +249,25 @@ public class AnnotationExporter
   }
 
   JPanel jPanel1 = new JPanel();
+
   JButton toFile = new JButton();
+
   JButton toTextbox = new JButton();
+
   JButton close = new JButton();
+
   ButtonGroup buttonGroup = new ButtonGroup();
+
   JRadioButton jalviewFormat = new JRadioButton();
+
   JRadioButton GFFFormat = new JRadioButton();
+
   JRadioButton CSVFormat = new JRadioButton();
+
   JLabel jLabel1 = new JLabel();
+
   JPanel jPanel3 = new JPanel();
+
   FlowLayout flowLayout1 = new FlowLayout();
 
 }
diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 2eda839..8050490 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -31,36 +31,52 @@ import jalview.io.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class AnnotationLabels
-    extends JPanel implements MouseListener,
-    MouseMotionListener, ActionListener
+public class AnnotationLabels extends JPanel implements MouseListener,
+        MouseMotionListener, ActionListener
 {
   static String ADDNEW = "Add New Row";
+
   static String EDITNAME = "Edit Label/Description";
+
   static String HIDE = "Hide This Row";
+
   static String DELETE = "Delete This Row";
+
   static String SHOWALL = "Show All Hidden Rows";
+
   static String OUTPUT_TEXT = "Export Annotation";
+
   static String COPYCONS_SEQ = "Copy Consensus Sequence";
+
   boolean resizePanel = false;
+
   Image image;
+
   AlignmentPanel ap;
+
   AlignViewport av;
+
   boolean resizing = false;
+
   MouseEvent dragEvent;
+
   int oldY;
+
   int selectedRow;
+
   int scrollOffset = 0;
+
   Font font = new Font("Arial", Font.PLAIN, 11);
 
   /**
    * Creates a new AnnotationLabels object.
-   *
-   * @param ap DOCUMENT ME!
+   * 
+   * @param ap
+   *                DOCUMENT ME!
    */
   public AnnotationLabels(AlignmentPanel ap)
   {
@@ -81,14 +97,12 @@ public class AnnotationLabels
       MediaTracker mt = new MediaTracker(this);
       mt.addImage(temp, 0);
       mt.waitForID(0);
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
     }
 
-    BufferedImage bi = new BufferedImage(temp.getHeight(this),
-                                         temp.getWidth(this),
-                                         BufferedImage.TYPE_INT_RGB);
+    BufferedImage bi = new BufferedImage(temp.getHeight(this), temp
+            .getWidth(this), BufferedImage.TYPE_INT_RGB);
     Graphics2D g = (Graphics2D) bi.getGraphics();
     g.rotate(Math.toRadians(90));
     g.drawImage(temp, 0, -bi.getWidth(this), this);
@@ -105,8 +119,9 @@ public class AnnotationLabels
 
   /**
    * DOCUMENT ME!
-   *
-   * @param y DOCUMENT ME!
+   * 
+   * @param y
+   *                DOCUMENT ME!
    */
   public void setScrollOffset(int y)
   {
@@ -142,8 +157,9 @@ public class AnnotationLabels
 
   /**
    * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
    */
   public void actionPerformed(ActionEvent evt)
   {
@@ -152,8 +168,7 @@ public class AnnotationLabels
     if (evt.getActionCommand().equals(ADDNEW))
     {
       AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null,
-          null,
-          new Annotation[ap.av.alignment.getWidth()]);
+              null, new Annotation[ap.av.alignment.getWidth()]);
 
       if (!editLabelDescription(newAnnotation))
       {
@@ -185,7 +200,7 @@ public class AnnotationLabels
     {
       for (int i = 0; i < aa.length; i++)
       {
-        if (!aa[i].visible && aa[i].annotations!=null)
+        if (!aa[i].visible && aa[i].annotations != null)
         {
           aa[i].visible = true;
         }
@@ -193,12 +208,9 @@ public class AnnotationLabels
     }
     else if (evt.getActionCommand().equals(OUTPUT_TEXT))
     {
-      new AnnotationExporter().exportAnnotations(
-          ap,
-          new AlignmentAnnotation[]
-          {aa[selectedRow]},
-          null, null
-          );
+      new AnnotationExporter().exportAnnotations(ap,
+              new AlignmentAnnotation[]
+              { aa[selectedRow] }, null, null);
     }
     else if (evt.getActionCommand().equals(COPYCONS_SEQ))
     {
@@ -217,16 +229,15 @@ public class AnnotationLabels
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   boolean editLabelDescription(AlignmentAnnotation annotation)
   {
     EditNameDialog dialog = new EditNameDialog(annotation.label,
-                                               annotation.description,
-                                               "       Annotation Name ",
-                                               "Annotation Description ",
-                                               "Edit Annotation Name/Description");
+            annotation.description, "       Annotation Name ",
+            "Annotation Description ", "Edit Annotation Name/Description");
 
     if (!dialog.accept)
     {
@@ -236,7 +247,7 @@ public class AnnotationLabels
     annotation.label = dialog.getName();
 
     String text = dialog.getDescription();
-    if (text!=null && text.length() == 0)
+    if (text != null && text.length() == 0)
     {
       text = null;
     }
@@ -247,8 +258,9 @@ public class AnnotationLabels
 
   /**
    * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
    */
   public void mousePressed(MouseEvent evt)
   {
@@ -258,8 +270,9 @@ public class AnnotationLabels
 
   /**
    * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
    */
   public void mouseReleased(MouseEvent evt)
   {
@@ -269,9 +282,9 @@ public class AnnotationLabels
 
     if (start != end)
     {
-      //Swap these annotations
-      AlignmentAnnotation startAA = ap.av.alignment.getAlignmentAnnotation()[
-          start];
+      // Swap these annotations
+      AlignmentAnnotation startAA = ap.av.alignment
+              .getAlignmentAnnotation()[start];
       AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end];
 
       ap.av.alignment.getAlignmentAnnotation()[end] = startAA;
@@ -286,8 +299,9 @@ public class AnnotationLabels
 
   /**
    * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
    */
   public void mouseEntered(MouseEvent evt)
   {
@@ -300,8 +314,9 @@ public class AnnotationLabels
 
   /**
    * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
    */
   public void mouseExited(MouseEvent evt)
   {
@@ -314,8 +329,9 @@ public class AnnotationLabels
 
   /**
    * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
    */
   public void mouseDragged(MouseEvent evt)
   {
@@ -329,13 +345,13 @@ public class AnnotationLabels
       dif /= ap.av.charHeight;
       dif *= ap.av.charHeight;
 
-      if ( (d.height - dif) > 20)
+      if ((d.height - dif) > 20)
       {
         ap.annotationScroller.setPreferredSize(new Dimension(d.width,
-            d.height - dif));
+                d.height - dif));
         d = ap.annotationSpaceFillerHolder.getPreferredSize();
         ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
-            d.width, d.height - dif));
+                d.width, d.height - dif));
         ap.paintAlignment(true);
       }
 
@@ -349,8 +365,9 @@ public class AnnotationLabels
 
   /**
    * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
    */
   public void mouseMoved(MouseEvent evt)
   {
@@ -358,27 +375,26 @@ public class AnnotationLabels
 
     getSelectedRow(evt.getY() - scrollOffset);
 
-
     if (selectedRow > -1
-        && ap.av.alignment.getAlignmentAnnotation().length > selectedRow)
+            && ap.av.alignment.getAlignmentAnnotation().length > selectedRow)
     {
-      AlignmentAnnotation aa = ap.av.alignment.
-          getAlignmentAnnotation()[selectedRow];
+      AlignmentAnnotation aa = ap.av.alignment.getAlignmentAnnotation()[selectedRow];
 
       StringBuffer desc = new StringBuffer("<html>");
 
-      if (aa.description != null && !aa.description.equals("New description"))
+      if (aa.description != null
+              && !aa.description.equals("New description"))
       {
         desc.append(aa.getDescription(true));
-        if(aa.hasScore)
+        if (aa.hasScore)
           desc.append("<br>");
       }
-      if(aa.hasScore())
+      if (aa.hasScore())
       {
-        desc.append("Score: "+aa.score);
+        desc.append("Score: " + aa.score);
       }
 
-      if(desc.length()!=6)
+      if (desc.length() != 6)
       {
         desc.append("</html>");
         this.setToolTipText(desc.toString());
@@ -391,8 +407,9 @@ public class AnnotationLabels
 
   /**
    * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
    */
   public void mouseClicked(MouseEvent evt)
   {
@@ -407,7 +424,7 @@ public class AnnotationLabels
     JMenuItem item = new JMenuItem(ADDNEW);
     item.addActionListener(this);
 
-    if ( (aa == null) || (aa.length == 0))
+    if ((aa == null) || (aa.length == 0))
     {
       item = new JMenuItem(SHOWALL);
       item.addActionListener(this);
@@ -433,12 +450,11 @@ public class AnnotationLabels
     item.addActionListener(this);
     pop.add(item);
     // annotation object should be typed
-    if (selectedRow<aa.length && aa[selectedRow] == ap.av.consensus)
+    if (selectedRow < aa.length && aa[selectedRow] == ap.av.consensus)
     {
       pop.addSeparator();
       final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
-          "Ignore Gaps In Consensus",
-          ap.av.getIgnoreGapsConsensus());
+              "Ignore Gaps In Consensus", ap.av.getIgnoreGapsConsensus());
       cbmi.addActionListener(new ActionListener()
       {
         public void actionPerformed(ActionEvent e)
@@ -457,25 +473,22 @@ public class AnnotationLabels
 
   /**
    * do a single sequence copy to jalview and the system clipboard
-   *
-   * @param sq sequence to be copied to clipboard
+   * 
+   * @param sq
+   *                sequence to be copied to clipboard
    */
   protected void copy_annotseqtoclipboard(SequenceI sq)
   {
     SequenceI[] seqs = new SequenceI[]
-        {
-        sq};
+    { sq };
     String[] omitHidden = null;
     SequenceI[] dseqs = new SequenceI[]
-        {
-        sq.getDatasetSequence()};
+    { sq.getDatasetSequence() };
     if (dseqs[0] == null)
     {
       dseqs[0] = new Sequence(sq);
-      dseqs[0].setSequence(
-          jalview.analysis.AlignSeq.extractGaps(
-              jalview.util.Comparison.GapChars,
-              sq.getSequenceAsString()));
+      dseqs[0].setSequence(jalview.analysis.AlignSeq.extractGaps(
+              jalview.util.Comparison.GapChars, sq.getSequenceAsString()));
 
       sq.setDatasetSequence(dseqs[0]);
     }
@@ -483,16 +496,14 @@ public class AnnotationLabels
     if (av.hasHiddenColumns)
     {
       omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0,
-          sq.getLength(), seqs);
+              sq.getLength(), seqs);
     }
 
-    String output = new FormatAdapter().formatSequences(
-        "Fasta",
-        seqs,
-        omitHidden);
+    String output = new FormatAdapter().formatSequences("Fasta", seqs,
+            omitHidden);
 
-    Toolkit.getDefaultToolkit().getSystemClipboard()
-        .setContents(new StringSelection(output), Desktop.instance);
+    Toolkit.getDefaultToolkit().getSystemClipboard().setContents(
+            new StringSelection(output), Desktop.instance);
 
     Vector hiddenColumns = null;
     if (av.hasHiddenColumns)
@@ -500,26 +511,25 @@ public class AnnotationLabels
       hiddenColumns = new Vector();
       for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
       {
-        int[] region = (int[])
-            av.getColumnSelection().getHiddenColumns().elementAt(i);
+        int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
+                .elementAt(i);
 
         hiddenColumns.addElement(new int[]
-                                 {region[0],
-                                 region[1]});
+        { region[0], region[1] });
       }
     }
 
     Desktop.jalviewClipboard = new Object[]
-        {
-        seqs,
-        ds, // what is the dataset of a consensus sequence ? need to flag sequence as special.
-        hiddenColumns};
+    { seqs, ds, // what is the dataset of a consensus sequence ? need to flag
+                // sequence as special.
+        hiddenColumns };
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param g1 DOCUMENT ME!
+   * 
+   * @param g1
+   *                DOCUMENT ME!
    */
   public void paintComponent(Graphics g)
   {
@@ -534,7 +544,7 @@ public class AnnotationLabels
     if (av.antiAlias)
     {
       g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-                          RenderingHints.VALUE_ANTIALIAS_ON);
+              RenderingHints.VALUE_ANTIALIAS_ON);
     }
 
     drawComponent(g2, width);
@@ -543,8 +553,9 @@ public class AnnotationLabels
 
   /**
    * DOCUMENT ME!
-   *
-   * @param g DOCUMENT ME!
+   * 
+   * @param g
+   *                DOCUMENT ME!
    */
   public void drawComponent(Graphics g, int width)
   {
@@ -569,7 +580,7 @@ public class AnnotationLabels
     int y = 0;
     int x = 0;
     int graphExtras = 0;
-    int offset =0;
+    int offset = 0;
 
     if (aa != null)
     {
@@ -582,14 +593,13 @@ public class AnnotationLabels
           continue;
         }
 
-
         y += aa[i].height;
 
-        offset = -aa[i].height/2;
+        offset = -aa[i].height / 2;
 
-        if(aa[i].hasText)
+        if (aa[i].hasText)
         {
-          offset += fm.getHeight()/2;
+          offset += fm.getHeight() / 2;
           offset -= fm.getDescent();
         }
         else
@@ -618,15 +628,14 @@ public class AnnotationLabels
             if (aa[gg].graphGroup == aa[i].graphGroup)
             {
               x = width - fm.stringWidth(aa[gg].label) - 3;
-              g.drawString(aa[gg].label, x,y - graphExtras);
+              g.drawString(aa[gg].label, x, y - graphExtras);
               if (aa[gg].annotations[0] != null)
               {
                 g.setColor(aa[gg].annotations[0].colour);
               }
 
-              g.drawLine(x, y - graphExtras - 3,
-                         x + fm.stringWidth(aa[gg].label),
-                         y - graphExtras - 3);
+              g.drawLine(x, y - graphExtras - 3, x
+                      + fm.stringWidth(aa[gg].label), y - graphExtras - 3);
 
               g.setColor(Color.black);
               graphExtras += fontHeight + 8;
@@ -635,7 +644,7 @@ public class AnnotationLabels
         }
         else
         {
-          g.drawString(aa[i].label, x, y +offset);
+          g.drawString(aa[i].label, x, y + offset);
         }
       }
     }
@@ -647,11 +656,12 @@ public class AnnotationLabels
     else if (dragEvent != null && aa != null)
     {
       g.setColor(Color.lightGray);
-      g.drawString(aa[selectedRow].label, dragEvent.getX(),
-                   dragEvent.getY() - scrollOffset);
+      g.drawString(aa[selectedRow].label, dragEvent.getX(), dragEvent
+              .getY()
+              - scrollOffset);
     }
 
-    if ( (aa == null) || (aa.length < 1))
+    if ((aa == null) || (aa.length < 1))
     {
       g.drawString("Right click", 2, 8);
       g.drawString("to add annotation", 2, 18);
diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 6371e86..af1ff7a 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -27,45 +27,64 @@ import jalview.datamodel.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class AnnotationPanel
-    extends JPanel implements MouseListener,
-    MouseMotionListener, ActionListener, AdjustmentListener
+public class AnnotationPanel extends JPanel implements MouseListener,
+        MouseMotionListener, ActionListener, AdjustmentListener
 {
   final String HELIX = "Helix";
+
   final String SHEET = "Sheet";
+
   final String LABEL = "Label";
+
   final String REMOVE = "Remove Annotation";
+
   final String COLOUR = "Colour";
+
   final Color HELIX_COLOUR = Color.red.darker();
+
   final Color SHEET_COLOUR = Color.green.darker().darker();
+
   /** DOCUMENT ME!! */
   AlignViewport av;
+
   AlignmentPanel ap;
+
   int activeRow = -1;
+
   BufferedImage image;
+
   BufferedImage fadedImage;
+
   Graphics2D gg;
+
   FontMetrics fm;
+
   int imgWidth = 0;
+
   boolean fastPaint = false;
 
-  //Used For mouse Dragging and resizing graphs
+  // Used For mouse Dragging and resizing graphs
   int graphStretch = -1;
+
   int graphStretchY = -1;
-  int min; //used by mouseDragged to see if user
-  int max; //used by mouseDragged to see if user
+
+  int min; // used by mouseDragged to see if user
+
+  int max; // used by mouseDragged to see if user
+
   boolean mouseDragging = false;
 
   boolean MAC = false;
 
   /**
    * Creates a new AnnotationPanel object.
-   *
-   * @param ap DOCUMENT ME!
+   * 
+   * @param ap
+   *                DOCUMENT ME!
    */
   public AnnotationPanel(AlignmentPanel ap)
   {
@@ -80,7 +99,8 @@ public class AnnotationPanel
     this.setLayout(null);
     addMouseListener(this);
     addMouseMotionListener(this);
-    ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener(this);
+    ap.annotationScroller.getVerticalScrollBar()
+            .addAdjustmentListener(this);
   }
 
   public AnnotationPanel(AlignViewport av)
@@ -90,12 +110,13 @@ public class AnnotationPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
    */
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
-    ap.alabels.setScrollOffset( -evt.getValue());
+    ap.alabels.setScrollOffset(-evt.getValue());
   }
 
   /**
@@ -153,8 +174,9 @@ public class AnnotationPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
    */
   public void actionPerformed(ActionEvent evt)
   {
@@ -179,14 +201,15 @@ public class AnnotationPanel
     else if (evt.getActionCommand().equals(LABEL))
     {
       String exMesg = collectAnnotVals(anot, av.getColumnSelection(), LABEL);
-      String label = JOptionPane.showInputDialog(this,"Enter label",exMesg);
-      
+      String label = JOptionPane.showInputDialog(this, "Enter label",
+              exMesg);
+
       if (label == null)
       {
         return;
       }
 
-      if ( (label.length() > 0) && !aa[activeRow].hasText)
+      if ((label.length() > 0) && !aa[activeRow].hasText)
       {
         aa[activeRow].hasText = true;
       }
@@ -195,13 +218,18 @@ public class AnnotationPanel
       {
         int index = av.getColumnSelection().columnAt(i);
 
-        if(!av.colSel.isVisible(index))
+        if (!av.colSel.isVisible(index))
           continue;
 
         if (anot[index] == null)
         {
-          anot[index] = new Annotation(label, "", ' ', 0); // TODO: verify that null exceptions aren't raised elsewhere.
-        } else {
+          anot[index] = new Annotation(label, "", ' ', 0); // TODO: verify that
+                                                            // null exceptions
+                                                            // aren't raised
+                                                            // elsewhere.
+        }
+        else
+        {
           anot[index].displayCharacter = label;
         }
       }
@@ -209,14 +237,13 @@ public class AnnotationPanel
     else if (evt.getActionCommand().equals(COLOUR))
     {
       Color col = JColorChooser.showDialog(this,
-                                           "Choose foreground colour",
-                                           Color.black);
+              "Choose foreground colour", Color.black);
 
       for (int i = 0; i < av.getColumnSelection().size(); i++)
       {
         int index = av.getColumnSelection().columnAt(i);
 
-        if(!av.colSel.isVisible(index))
+        if (!av.colSel.isVisible(index))
           continue;
 
         if (anot[index] == null)
@@ -227,7 +254,8 @@ public class AnnotationPanel
         anot[index].colour = col;
       }
     }
-    else // HELIX OR SHEET
+    else
+    // HELIX OR SHEET
     {
       char type = 0;
       String symbol = "\u03B1";
@@ -248,15 +276,14 @@ public class AnnotationPanel
       }
 
       String label = JOptionPane.showInputDialog(
-          "Enter a label for the structure?",
-          symbol);
+              "Enter a label for the structure?", symbol);
 
       if (label == null)
       {
         return;
       }
 
-      if ( (label.length() > 0) && !aa[activeRow].hasText)
+      if ((label.length() > 0) && !aa[activeRow].hasText)
       {
         aa[activeRow].hasText = true;
       }
@@ -265,7 +292,7 @@ public class AnnotationPanel
       {
         int index = av.getColumnSelection().columnAt(i);
 
-        if(!av.colSel.isVisible(index))
+        if (!av.colSel.isVisible(index))
           continue;
 
         if (anot[index] == null)
@@ -284,40 +311,43 @@ public class AnnotationPanel
     return;
   }
 
-  private String collectAnnotVals(Annotation[] anot, ColumnSelection columnSelection,
-          String label2)
+  private String collectAnnotVals(Annotation[] anot,
+          ColumnSelection columnSelection, String label2)
   {
-    String collatedInput="";
-    String last="";
+    String collatedInput = "";
+    String last = "";
     for (int i = 0; i < columnSelection.size(); i++)
     {
       int index = columnSelection.columnAt(i);
       // always check for current display state - just in case
-      if(!av.colSel.isVisible(index))
+      if (!av.colSel.isVisible(index))
         continue;
-      String tlabel=null;
+      String tlabel = null;
       if (anot[index] != null)
       {
-        if (label2.equals(HELIX) || label2.equals(SHEET) || label2.equals(LABEL))
+        if (label2.equals(HELIX) || label2.equals(SHEET)
+                || label2.equals(LABEL))
         {
           tlabel = anot[index].description;
           if (tlabel == null)
           {
             if (label2.equals(HELIX) || label2.equals(SHEET))
             {
-              tlabel = ""+anot[index].secondaryStructure;
-            } else {
-              tlabel = ""+anot[index].displayCharacter;
-            }            
+              tlabel = "" + anot[index].secondaryStructure;
+            }
+            else
+            {
+              tlabel = "" + anot[index].displayCharacter;
+            }
           }
         }
-        if (tlabel!=null && !tlabel.equals(last))
+        if (tlabel != null && !tlabel.equals(last))
         {
-          if (last.length()>0)
+          if (last.length() > 0)
           {
-            collatedInput+=" ";
+            collatedInput += " ";
           }
-          collatedInput+=tlabel;
+          collatedInput += tlabel;
         }
       }
     }
@@ -326,8 +356,9 @@ public class AnnotationPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
    */
   public void mousePressed(MouseEvent evt)
   {
@@ -356,7 +387,7 @@ public class AnnotationPanel
         }
         else if (aa[i].graph > 0)
         {
-          //Stretch Graph
+          // Stretch Graph
           graphStretch = i;
           graphStretchY = evt.getY();
         }
@@ -404,8 +435,9 @@ public class AnnotationPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
    */
   public void mouseReleased(MouseEvent evt)
   {
@@ -417,18 +449,20 @@ public class AnnotationPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
    */
   public void mouseEntered(MouseEvent evt)
   {
-     ap.scalePanel.mouseEntered(evt);
+    ap.scalePanel.mouseEntered(evt);
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
    */
   public void mouseExited(MouseEvent evt)
   {
@@ -437,15 +471,16 @@ public class AnnotationPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
    */
   public void mouseDragged(MouseEvent evt)
   {
     if (graphStretch > -1)
     {
-      av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight +=
-          graphStretchY - evt.getY();
+      av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY
+              - evt.getY();
       if (av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight < 0)
       {
         av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 0;
@@ -462,8 +497,9 @@ public class AnnotationPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
    */
   public void mouseMoved(MouseEvent evt)
   {
@@ -506,19 +542,19 @@ public class AnnotationPanel
       res = av.getColumnSelection().adjustForHiddenColumns(res);
     }
 
-    if (aa[row].annotations != null
-        && row > -1
-        && res < (int) aa[row].annotations.length)
+    if (aa[row].annotations != null && row > -1
+            && res < (int) aa[row].annotations.length)
     {
       if (aa[row].graphGroup > -1)
       {
         StringBuffer tip = new StringBuffer("<html>");
         for (int gg = 0; gg < aa.length; gg++)
         {
-          if (aa[gg].graphGroup == aa[row].graphGroup && aa[gg].annotations[res] != null)
+          if (aa[gg].graphGroup == aa[row].graphGroup
+                  && aa[gg].annotations[res] != null)
           {
-            tip.append(aa[gg].label + " " + aa[gg].annotations[res].description +
-                       "<br>");
+            tip.append(aa[gg].label + " "
+                    + aa[gg].annotations[res].description + "<br>");
           }
         }
         if (tip.length() != 6)
@@ -528,15 +564,15 @@ public class AnnotationPanel
         }
       }
       else if (aa[row].annotations[res] != null
-               && aa[row].annotations[res].description != null)
+              && aa[row].annotations[res].description != null)
       {
         this.setToolTipText(aa[row].annotations[res].description);
       }
 
       if (aa[row].annotations[res] != null)
       {
-        StringBuffer text = new StringBuffer("Sequence position " +
-                                             (res + 1));
+        StringBuffer text = new StringBuffer("Sequence position "
+                + (res + 1));
 
         if (aa[row].annotations[res].description != null)
         {
@@ -554,8 +590,9 @@ public class AnnotationPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
    */
   public void mouseClicked(MouseEvent evt)
   {
@@ -563,8 +600,9 @@ public class AnnotationPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param g DOCUMENT ME!
+   * 
+   * @param g
+   *                DOCUMENT ME!
    */
   public void paintComponent(Graphics g)
   {
@@ -573,9 +611,8 @@ public class AnnotationPanel
 
     if (image != null)
     {
-      if (fastPaint
-          || (getVisibleRect().width != g.getClipBounds().width)
-          || (getVisibleRect().height != g.getClipBounds().height))
+      if (fastPaint || (getVisibleRect().width != g.getClipBounds().width)
+              || (getVisibleRect().height != g.getClipBounds().height))
       {
         g.drawImage(image, 0, 0, this);
         fastPaint = false;
@@ -583,19 +620,19 @@ public class AnnotationPanel
       }
     }
     imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;
-    if (imgWidth<1)
+    if (imgWidth < 1)
       return;
     if (image == null || imgWidth != image.getWidth()
-        || image.getHeight(this) != getHeight())
+            || image.getHeight(this) != getHeight())
     {
       image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),
-                                BufferedImage.TYPE_INT_RGB);
+              BufferedImage.TYPE_INT_RGB);
       gg = (Graphics2D) image.getGraphics();
 
       if (av.antiAlias)
       {
         gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-                            RenderingHints.VALUE_ANTIALIAS_ON);
+                RenderingHints.VALUE_ANTIALIAS_ON);
       }
 
       gg.setFont(av.getFont());
@@ -607,20 +644,20 @@ public class AnnotationPanel
     drawComponent(gg, av.startRes, av.endRes + 1);
     g.drawImage(image, 0, 0, this);
   }
+
   /**
    * non-Thread safe repaint
-   *
-   * @param horizontal repaint with horizontal shift in alignment
+   * 
+   * @param horizontal
+   *                repaint with horizontal shift in alignment
    */
   public void fastPaint(int horizontal)
   {
 
-    if ( (horizontal == 0)
-        || gg == null
-        || av.alignment.getAlignmentAnnotation() == null
-        || av.alignment.getAlignmentAnnotation().length < 1
-        || av.updatingConsensus
-        || av.updatingConservation)
+    if ((horizontal == 0) || gg == null
+            || av.alignment.getAlignmentAnnotation() == null
+            || av.alignment.getAlignmentAnnotation().length < 1
+            || av.updatingConsensus || av.updatingConservation)
     {
       repaint();
       return;
@@ -645,7 +682,7 @@ public class AnnotationPanel
 
     drawComponent(gg, sr, er);
 
-    gg.translate( -transX, 0);
+    gg.translate(-transX, 0);
 
     fastPaint = true;
     repaint();
@@ -654,10 +691,13 @@ public class AnnotationPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param g DOCUMENT ME!
-   * @param startRes DOCUMENT ME!
-   * @param endRes DOCUMENT ME!
+   * 
+   * @param g
+   *                DOCUMENT ME!
+   * @param startRes
+   *                DOCUMENT ME!
+   * @param endRes
+   *                DOCUMENT ME!
    */
   public void drawComponent(Graphics g, int startRes, int endRes)
   {
@@ -667,24 +707,21 @@ public class AnnotationPanel
       {
         return;
       }
-      //We'll keep a record of the old image,
-      //and draw a faded image until the calculation
-      //has completed
-      if (fadedImage == null
-          || fadedImage.getWidth() != imgWidth
-          || fadedImage.getHeight() != image.getHeight())
+      // We'll keep a record of the old image,
+      // and draw a faded image until the calculation
+      // has completed
+      if (fadedImage == null || fadedImage.getWidth() != imgWidth
+              || fadedImage.getHeight() != image.getHeight())
       {
-        fadedImage = new BufferedImage(
-            imgWidth, image.getHeight(),
-            BufferedImage.TYPE_INT_RGB);
+        fadedImage = new BufferedImage(imgWidth, image.getHeight(),
+                BufferedImage.TYPE_INT_RGB);
 
         Graphics2D fadedG = (Graphics2D) fadedImage.getGraphics();
 
         fadedG.setColor(Color.white);
         fadedG.fillRect(0, 0, imgWidth, image.getHeight());
 
-        fadedG.setComposite(
-            AlphaComposite.getInstance(
+        fadedG.setComposite(AlphaComposite.getInstance(
                 AlphaComposite.SRC_OVER, .3f));
         fadedG.drawImage(image, 0, 0, this);
 
@@ -705,8 +742,8 @@ public class AnnotationPanel
       fm = g.getFontMetrics();
     }
 
-    if ( (av.alignment.getAlignmentAnnotation() == null) ||
-        (av.alignment.getAlignmentAnnotation().length < 1))
+    if ((av.alignment.getAlignmentAnnotation() == null)
+            || (av.alignment.getAlignmentAnnotation().length < 1))
     {
       g.setColor(Color.white);
       g.fillRect(0, 0, getWidth(), getHeight());
@@ -721,7 +758,7 @@ public class AnnotationPanel
 
     AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
 
-    int x = 0, y=0;
+    int x = 0, y = 0;
     int column = 0;
     char lastSS;
     int lastSSX;
@@ -730,7 +767,7 @@ public class AnnotationPanel
     boolean validEnd = false;
     boolean[] graphGroupDrawn = new boolean[aa.length];
 
-    //\u03B2 \u03B1
+    // \u03B2 \u03B1
     for (int i = 0; i < aa.length; i++)
     {
       AlignmentAnnotation row = aa[i];
@@ -755,13 +792,13 @@ public class AnnotationPanel
 
         if (row.hasText)
         {
-          iconOffset =av.charHeight -fm.getDescent();
+          iconOffset = av.charHeight - fm.getDescent();
           y -= av.charHeight;
         }
       }
       else if (row.hasText)
       {
-        iconOffset = av.charHeight -fm.getDescent();
+        iconOffset = av.charHeight - fm.getDescent();
 
       }
       else
@@ -769,29 +806,27 @@ public class AnnotationPanel
         iconOffset = 0;
       }
 
-
       if (av.updatingConsensus && aa[i] == av.consensus)
       {
         y += av.charHeight;
 
-        g.drawImage(fadedImage,
-                    0, y - row.height, imgWidth, y,
-                    0, y - row.height, imgWidth, y, this);
+        g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y
+                - row.height, imgWidth, y, this);
         g.setColor(Color.black);
         // g.drawString("Calculating Consensus....",20, y-row.height/2);
 
         continue;
       }
-      else if (av.updatingConservation && aa[i].label.equals("Conservation"))
+      else if (av.updatingConservation
+              && aa[i].label.equals("Conservation"))
       {
 
         y += av.charHeight;
-        g.drawImage(fadedImage,
-                    0, y - row.height, imgWidth, y,
-                    0, y - row.height, imgWidth, y, this);
+        g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y
+                - row.height, imgWidth, y, this);
 
         g.setColor(Color.black);
-        //  g.drawString("Calculating Conservation.....",20, y-row.height/2);
+        // g.drawString("Calculating Conservation.....",20, y-row.height/2);
 
         continue;
       }
@@ -799,23 +834,21 @@ public class AnnotationPanel
       {
 
         y += av.charHeight;
-        g.drawImage(fadedImage,
-                    0, y - row.height, imgWidth, y,
-                    0, y - row.height, imgWidth, y, this);
+        g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y
+                - row.height, imgWidth, y, this);
         g.setColor(Color.black);
-        /// g.drawString("Calculating Quality....",20, y-row.height/2);
+        // / g.drawString("Calculating Quality....",20, y-row.height/2);
 
         continue;
       }
 
-
-
       x = 0;
       while (x < endRes - startRes)
       {
         if (av.hasHiddenColumns)
         {
-          column = av.getColumnSelection().adjustForHiddenColumns(startRes + x);
+          column = av.getColumnSelection().adjustForHiddenColumns(
+                  startRes + x);
           if (column > row.annotations.length - 1)
           {
             break;
@@ -826,8 +859,7 @@ public class AnnotationPanel
           column = startRes + x;
         }
 
-        if ( (row.annotations==null) 
-                || (row.annotations.length <= column) 
+        if ((row.annotations == null) || (row.annotations.length <= column)
                 || (row.annotations[column] == null))
         {
           validRes = false;
@@ -849,25 +881,26 @@ public class AnnotationPanel
 
               if (v == column)
               {
-                g.fillRect(x * av.charWidth, y,
-                           av.charWidth, av.charHeight);
+                g
+                        .fillRect(x * av.charWidth, y, av.charWidth,
+                                av.charHeight);
               }
             }
           }
         }
 
         if (av.validCharWidth && validRes
-            && row.annotations[column].displayCharacter != null
-            && (row.annotations[column].displayCharacter.length() > 0))
+                && row.annotations[column].displayCharacter != null
+                && (row.annotations[column].displayCharacter.length() > 0))
         {
 
-          int charOffset = (av.getCentreColumnLabels()) ? ((av.charWidth -
-                            fm.charsWidth(row.annotations[column].
-                                         displayCharacter.toCharArray(),0,
-                                         row.annotations[column].
-                                         displayCharacter.length())) / 2)
-                                         : (av.charWidth - fm.charWidth(row.annotations[column].
-                                                 displayCharacter.charAt(0))) / 2;
+          int charOffset = (av.getCentreColumnLabels()) ? ((av.charWidth - fm
+                  .charsWidth(row.annotations[column].displayCharacter
+                          .toCharArray(), 0,
+                          row.annotations[column].displayCharacter.length())) / 2)
+                  : (av.charWidth - fm
+                          .charWidth(row.annotations[column].displayCharacter
+                                  .charAt(0))) / 2;
 
           if (row.annotations[column].colour == null)
             g.setColor(Color.black);
@@ -877,87 +910,78 @@ public class AnnotationPanel
           if (column == 0 || row.graph > 0)
           {
             g.drawString(row.annotations[column].displayCharacter,
-                         (x * av.charWidth) + charOffset,
-                         y + iconOffset);
+                    (x * av.charWidth) + charOffset, y + iconOffset);
           }
-          else if (
-              row.annotations[column - 1] == null
-              || (!row.annotations[column].displayCharacter.equals(
-                  row.annotations[column - 1].displayCharacter)
-                  ||
-                  (row.annotations[column].displayCharacter.length() < 2 &&
-                   row.annotations[column].secondaryStructure == ' ')))
+          else if (row.annotations[column - 1] == null
+                  || (!row.annotations[column].displayCharacter
+                          .equals(row.annotations[column - 1].displayCharacter) || (row.annotations[column].displayCharacter
+                          .length() < 2 && row.annotations[column].secondaryStructure == ' ')))
           {
-            g.drawString(row.annotations[column].displayCharacter,
-                         x * av.charWidth + charOffset,
-                         y + iconOffset);
+            g.drawString(row.annotations[column].displayCharacter, x
+                    * av.charWidth + charOffset, y + iconOffset);
           }
         }
 
         if (row.hasIcons)
         {
-          if (!validRes ||
-              (row.annotations[column].secondaryStructure != lastSS))
+          if (!validRes
+                  || (row.annotations[column].secondaryStructure != lastSS))
           {
             switch (lastSS)
             {
-              case 'H':
-                g.setColor(HELIX_COLOUR);
-                if (MAC)
-                {
-                  //Off by 1 offset when drawing rects and ovals
-                  //to offscreen image on the MAC
-                  g.fillRoundRect(lastSSX, y + 4 + iconOffset,
-                                  (x * av.charWidth) - lastSSX, 7, 8, 8);
-                  break;
-                }
-
-                int sCol = (lastSSX / av.charWidth) + startRes;
-                int x1 = lastSSX;
-                int x2 = (x * av.charWidth);
-
-                if (sCol == 0 ||
-                    row.annotations[sCol - 1] == null ||
-                    row.annotations[sCol - 1].secondaryStructure != 'H')
-                {
-                  g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90,
-                            180);
-                  x1 += av.charWidth / 2;
-                }
-
-                if (row.annotations[column] == null ||
-                    row.annotations[column].secondaryStructure != 'H')
-                {
-                  g.fillArc( (x * av.charWidth) - av.charWidth,
-                            y + 4 + iconOffset, av.charWidth, 8, 270, 180);
-                  x2 -= av.charWidth / 2;
-                }
-
-                g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
+            case 'H':
+              g.setColor(HELIX_COLOUR);
+              if (MAC)
+              {
+                // Off by 1 offset when drawing rects and ovals
+                // to offscreen image on the MAC
+                g.fillRoundRect(lastSSX, y + 4 + iconOffset,
+                        (x * av.charWidth) - lastSSX, 7, 8, 8);
                 break;
+              }
 
-              case 'E':
-                g.setColor(SHEET_COLOUR);
-                g.fillRect(lastSSX, y + 4 + iconOffset,
-                           (x * av.charWidth) - lastSSX - 4, 7);
-                g.fillPolygon(new int[]
-                              { (x * av.charWidth) - 4,
-                              (x * av.charWidth) - 4,
-                              (x * av.charWidth)},
-                              new int[]
-                              {
-                              y + iconOffset, y + 14 + iconOffset,
-                              y + 8 + iconOffset
-                }, 3);
+              int sCol = (lastSSX / av.charWidth) + startRes;
+              int x1 = lastSSX;
+              int x2 = (x * av.charWidth);
 
-                break;
+              if (sCol == 0
+                      || row.annotations[sCol - 1] == null
+                      || row.annotations[sCol - 1].secondaryStructure != 'H')
+              {
+                g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90,
+                        180);
+                x1 += av.charWidth / 2;
+              }
+
+              if (row.annotations[column] == null
+                      || row.annotations[column].secondaryStructure != 'H')
+              {
+                g.fillArc((x * av.charWidth) - av.charWidth, y + 4
+                        + iconOffset, av.charWidth, 8, 270, 180);
+                x2 -= av.charWidth / 2;
+              }
 
-              default:
-                g.setColor(Color.gray);
-                g.fillRect(lastSSX, y + 6 + iconOffset,
-                           (x * av.charWidth) - lastSSX, 2);
+              g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
+              break;
 
-                break;
+            case 'E':
+              g.setColor(SHEET_COLOUR);
+              g.fillRect(lastSSX, y + 4 + iconOffset, (x * av.charWidth)
+                      - lastSSX - 4, 7);
+              g.fillPolygon(new int[]
+              { (x * av.charWidth) - 4, (x * av.charWidth) - 4,
+                  (x * av.charWidth) }, new int[]
+              { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
+                      3);
+
+              break;
+
+            default:
+              g.setColor(Color.gray);
+              g.fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth)
+                      - lastSSX, 2);
+
+              break;
             }
 
             if (validRes)
@@ -981,83 +1005,80 @@ public class AnnotationPanel
       {
         column = row.annotations.length - 1;
         validEnd = false;
-      } else {
+      }
+      else
+      {
         validEnd = true;
       }
 
-      //  x ++;
+      // x ++;
 
       if (row.hasIcons)
       {
         switch (lastSS)
         {
-          case 'H':
-            g.setColor(HELIX_COLOUR);
-            if (MAC)
-            {
-              //Off by 1 offset when drawing rects and ovals
-              //to offscreen image on the MAC
-              g.fillRoundRect(lastSSX, y + 4 + iconOffset,
-                              (x * av.charWidth) - lastSSX, 7, 8, 8);
-              break;
-            }
+        case 'H':
+          g.setColor(HELIX_COLOUR);
+          if (MAC)
+          {
+            // Off by 1 offset when drawing rects and ovals
+            // to offscreen image on the MAC
+            g.fillRoundRect(lastSSX, y + 4 + iconOffset, (x * av.charWidth)
+                    - lastSSX, 7, 8, 8);
+            break;
+          }
 
-            int sCol = (lastSSX / av.charWidth) + startRes;
-            int x1 = lastSSX;
-            int x2 = (x * av.charWidth);
+          int sCol = (lastSSX / av.charWidth) + startRes;
+          int x1 = lastSSX;
+          int x2 = (x * av.charWidth);
 
-            if (sCol == 0 ||
-                row.annotations[sCol - 1] == null ||
-                row.annotations[sCol - 1].secondaryStructure != 'H')
-            {
-              g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90, 180);
-              x1 += av.charWidth / 2;
-            }
+          if (sCol == 0 || row.annotations[sCol - 1] == null
+                  || row.annotations[sCol - 1].secondaryStructure != 'H')
+          {
+            g
+                    .fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8,
+                            90, 180);
+            x1 += av.charWidth / 2;
+          }
 
-            if (row.annotations[column] == null ||
-                row.annotations[column].secondaryStructure != 'H')
-            {
-              g.fillArc( (x * av.charWidth) - av.charWidth,
-                        y + 4 + iconOffset, av.charWidth, 8, 270,
-                        180);
-              x2 -= av.charWidth / 2;
-            }
+          if (row.annotations[column] == null
+                  || row.annotations[column].secondaryStructure != 'H')
+          {
+            g.fillArc((x * av.charWidth) - av.charWidth,
+                    y + 4 + iconOffset, av.charWidth, 8, 270, 180);
+            x2 -= av.charWidth / 2;
+          }
 
-            g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
+          g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
 
-            break;
+          break;
 
-          case 'E':
-            g.setColor(SHEET_COLOUR);
+        case 'E':
+          g.setColor(SHEET_COLOUR);
 
-            if (!validEnd || row.annotations[endRes] == null
-                || row.annotations[endRes].secondaryStructure != 'E')
-            {
-              g.fillRect(lastSSX, y + 4 + iconOffset,
-                         (x * av.charWidth) - lastSSX - 4, 7);
-              g.fillPolygon(new int[]
-                            { (x * av.charWidth) - 4,
-                            (x * av.charWidth) - 4,
-                            (x * av.charWidth)},
-                            new int[]
-                            {
-                            y + iconOffset, y + 14 + iconOffset,
-                            y + 7 + iconOffset
-              }, 3);
-            }
-            else
-            {
-              g.fillRect(lastSSX, y + 4 + iconOffset,
-                         (x + 1) * av.charWidth - lastSSX, 7);
-            }
-            break;
+          if (!validEnd || row.annotations[endRes] == null
+                  || row.annotations[endRes].secondaryStructure != 'E')
+          {
+            g.fillRect(lastSSX, y + 4 + iconOffset, (x * av.charWidth)
+                    - lastSSX - 4, 7);
+            g.fillPolygon(new int[]
+            { (x * av.charWidth) - 4, (x * av.charWidth) - 4,
+                (x * av.charWidth) }, new int[]
+            { y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset }, 3);
+          }
+          else
+          {
+            g.fillRect(lastSSX, y + 4 + iconOffset, (x + 1) * av.charWidth
+                    - lastSSX, 7);
+          }
+          break;
 
-          default:
-            g.setColor(Color.gray);
-            g.fillRect(lastSSX, y + 6 + iconOffset,
-                       (x * av.charWidth) - lastSSX, 2);
+        default:
+          g.setColor(Color.gray);
+          g.fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth)
+                  - lastSSX, 2);
 
-            break;
+          break;
         }
       }
 
@@ -1094,9 +1115,8 @@ public class AnnotationPanel
             {
               if (aa[gg].graphGroup == row.graphGroup)
               {
-                drawLineGraph(g, aa[gg], startRes, endRes, y,
-                              groupmin, groupmax,
-                              row.graphHeight);
+                drawLineGraph(g, aa[gg], startRes, endRes, y, groupmin,
+                        groupmax, row.graphHeight);
               }
             }
 
@@ -1104,14 +1124,14 @@ public class AnnotationPanel
           }
           else
           {
-            drawLineGraph(g, row, startRes, endRes,
-                          y, row.graphMin, row.graphMax, row.graphHeight);
+            drawLineGraph(g, row, startRes, endRes, y, row.graphMin,
+                    row.graphMax, row.graphHeight);
           }
         }
         else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
         {
-          drawBarGraph(g, row, startRes, endRes,
-                       row.graphMin, row.graphMax, y);
+          drawBarGraph(g, row, startRes, endRes, row.graphMin,
+                  row.graphMax, y);
         }
       }
 
@@ -1127,11 +1147,8 @@ public class AnnotationPanel
     }
   }
 
-  public void drawLineGraph(Graphics g, AlignmentAnnotation aa,
-                            int sRes, int eRes,
-                            int y,
-                            float min, float max,
-                            int graphHeight)
+  public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes,
+          int eRes, int y, float min, float max, int graphHeight)
   {
     if (sRes > aa.annotations.length)
     {
@@ -1140,7 +1157,7 @@ public class AnnotationPanel
 
     int x = 0;
 
-    //Adjustment for fastpaint to left
+    // Adjustment for fastpaint to left
     if (eRes < av.endRes)
     {
       eRes++;
@@ -1156,10 +1173,10 @@ public class AnnotationPanel
     int y1 = y, y2 = y;
     float range = max - min;
 
-    ////Draw origin
+    // //Draw origin
     if (min < 0)
     {
-      y2 = y - (int) ( (0 - min / range) * graphHeight);
+      y2 = y - (int) ((0 - min / range) * graphHeight);
     }
 
     g.setColor(Color.gray);
@@ -1183,7 +1200,8 @@ public class AnnotationPanel
         break;
       }
 
-      if (aa.annotations[column] == null || aa.annotations[column - 1] == null)
+      if (aa.annotations[column] == null
+              || aa.annotations[column - 1] == null)
       {
         x++;
         continue;
@@ -1194,13 +1212,13 @@ public class AnnotationPanel
       else
         g.setColor(aa.annotations[column].colour);
 
-      y1 = y -
-          (int) ( ( (aa.annotations[column - 1].value - min) / range) * graphHeight);
-      y2 = y -
-          (int) ( ( (aa.annotations[column].value - min) / range) * graphHeight);
+      y1 = y
+              - (int) (((aa.annotations[column - 1].value - min) / range) * graphHeight);
+      y2 = y
+              - (int) (((aa.annotations[column].value - min) / range) * graphHeight);
 
-      g.drawLine(x * av.charWidth - av.charWidth / 2, y1,
-                 x * av.charWidth + av.charWidth / 2, y2);
+      g.drawLine(x * av.charWidth - av.charWidth / 2, y1, x * av.charWidth
+              + av.charWidth / 2, y2);
       x++;
     }
 
@@ -1208,22 +1226,18 @@ public class AnnotationPanel
     {
       g.setColor(aa.threshold.colour);
       Graphics2D g2 = (Graphics2D) g;
-      g2.setStroke(new BasicStroke(1,
-                                   BasicStroke.CAP_SQUARE,
-                                   BasicStroke.JOIN_ROUND, 3f,
-                                   new float[]
-                                   {5f, 3f}, 0f));
+      g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
+              BasicStroke.JOIN_ROUND, 3f, new float[]
+              { 5f, 3f }, 0f));
 
-      y2 = (int) (y - ( (aa.threshold.value - min) / range) * graphHeight);
+      y2 = (int) (y - ((aa.threshold.value - min) / range) * graphHeight);
       g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2);
       g2.setStroke(new BasicStroke());
     }
   }
 
-  public void drawBarGraph(Graphics g, AlignmentAnnotation aa,
-                           int sRes, int eRes,
-                           float min, float max,
-                           int y)
+  public void drawBarGraph(Graphics g, AlignmentAnnotation aa, int sRes,
+          int eRes, float min, float max, int y)
   {
     if (sRes > aa.annotations.length)
     {
@@ -1238,7 +1252,7 @@ public class AnnotationPanel
 
     if (min < 0)
     {
-      y2 = y - (int) ( (0 - min / (range)) * aa.graphHeight);
+      y2 = y - (int) ((0 - min / (range)) * aa.graphHeight);
     }
 
     g.setColor(Color.gray);
@@ -1272,8 +1286,8 @@ public class AnnotationPanel
       else
         g.setColor(aa.annotations[column].colour);
 
-      y1 = y -
-          (int) ( ( (aa.annotations[column].value - min) / (range)) * aa.graphHeight);
+      y1 = y
+              - (int) (((aa.annotations[column].value - min) / (range)) * aa.graphHeight);
 
       if (y1 - y2 > 0)
       {
@@ -1291,21 +1305,19 @@ public class AnnotationPanel
     {
       g.setColor(aa.threshold.colour);
       Graphics2D g2 = (Graphics2D) g;
-      g2.setStroke(new BasicStroke(1,
-                                   BasicStroke.CAP_SQUARE,
-                                   BasicStroke.JOIN_ROUND, 3f,
-                                   new float[]
-                                   {5f, 3f}, 0f));
+      g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
+              BasicStroke.JOIN_ROUND, 3f, new float[]
+              { 5f, 3f }, 0f));
 
-      y2 = (int) (y - ( (aa.threshold.value - min) / range) * aa.graphHeight);
+      y2 = (int) (y - ((aa.threshold.value - min) / range) * aa.graphHeight);
       g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2);
       g2.setStroke(new BasicStroke());
     }
   }
 
   // used by overview window
-  public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y,
-                        int sRes, int eRes)
+  public void drawGraph(Graphics g, AlignmentAnnotation aa, int width,
+          int y, int sRes, int eRes)
   {
     eRes = Math.min(eRes, aa.annotations.length);
     g.setColor(Color.white);
@@ -1323,7 +1335,7 @@ public class AnnotationPanel
         else
           g.setColor(aa.annotations[j].colour);
 
-        height = (int) ( (aa.annotations[j].value / aa.graphMax) * y);
+        height = (int) ((aa.annotations[j].value / aa.graphMax) * y);
         if (height > y)
         {
           height = y;
diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 50e5644..3a87f8c 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -39,32 +39,40 @@ import org.jmol.api.*;
 import org.jmol.adapter.smarter.SmarterJmolAdapter;
 import org.jmol.popup.*;
 
-
-public class AppJmol
-    extends GStructureViewer
-    implements StructureListener, JmolStatusListener, Runnable
+public class AppJmol extends GStructureViewer implements StructureListener,
+        JmolStatusListener, Runnable
 
 {
   JmolViewer viewer;
+
   JmolPopup jmolpopup;
+
   ScriptWindow scriptWindow;
+
   PDBEntry pdbentry;
+
   SequenceI[] sequence;
-  String [] chains;
+
+  String[] chains;
+
   StructureSelectionManager ssm;
+
   JSplitPane splitPane;
+
   RenderPanel renderPanel;
+
   AlignmentPanel ap;
+
   String fileLoadingError;
+
   boolean colourBySequence = true;
+
   boolean loadingFromArchive = false;
+
   Vector atomsPicked = new Vector();
 
-  public AppJmol(String file, String id,
-                 SequenceI[] seq,
-                 AlignmentPanel ap,
-                 String loadStatus,
-                 Rectangle bounds)
+  public AppJmol(String file, String id, SequenceI[] seq,
+          AlignmentPanel ap, String loadStatus, Rectangle bounds)
   {
     loadingFromArchive = true;
     pdbentry = new PDBEntry();
@@ -77,8 +85,8 @@ public class AppJmol
     colourBySequence = false;
     seqColour.setSelected(false);
 
-    //jalview.gui.Desktop.addInternalFrame(this, "Loading File",
-    //                                     bounds.width,bounds.height);
+    // jalview.gui.Desktop.addInternalFrame(this, "Loading File",
+    // bounds.width,bounds.height);
 
     initJmol(loadStatus);
 
@@ -91,78 +99,85 @@ public class AppJmol
     });
   }
 
-public synchronized void addSequence(SequenceI [] seq)
-   {
+  public synchronized void addSequence(SequenceI[] seq)
+  {
     Vector v = new Vector();
-     for(int i=0; i<sequence.length; i++)
-       v.addElement(sequence[i]);
+    for (int i = 0; i < sequence.length; i++)
+      v.addElement(sequence[i]);
 
-     for(int i=0; i<seq.length; i++)
-      if(!v.contains(seq[i]))
-          v.addElement(seq[i]);
+    for (int i = 0; i < seq.length; i++)
+      if (!v.contains(seq[i]))
+        v.addElement(seq[i]);
 
-     SequenceI [] tmp = new SequenceI[v.size()];
-     v.copyInto(tmp);
-     sequence = tmp;
-   }
+    SequenceI[] tmp = new SequenceI[v.size()];
+    v.copyInto(tmp);
+    sequence = tmp;
+  }
 
-  public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String [] chains, AlignmentPanel ap)
+  public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
+          AlignmentPanel ap)
   {
-    //////////////////////////////////
-    //Is the pdb file already loaded?
+    // ////////////////////////////////
+    // Is the pdb file already loaded?
     String alreadyMapped = StructureSelectionManager
-        .getStructureSelectionManager()
-        .alreadyMappedToFile(pdbentry.getId());
+            .getStructureSelectionManager().alreadyMappedToFile(
+                    pdbentry.getId());
 
     if (alreadyMapped != null)
     {
-      int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
-          pdbentry.getId() + " is already displayed."
-          + "\nDo you want to map sequences to the visible structure?",
-          "Map Sequences to Visible Window: " + pdbentry.getId(),
-          JOptionPane.YES_NO_OPTION);
+      int option = JOptionPane
+              .showInternalConfirmDialog(
+                      Desktop.desktop,
+                      pdbentry.getId()
+                              + " is already displayed."
+                              + "\nDo you want to map sequences to the visible structure?",
+                      "Map Sequences to Visible Window: "
+                              + pdbentry.getId(), JOptionPane.YES_NO_OPTION);
 
       if (option == JOptionPane.YES_OPTION)
       {
         StructureSelectionManager.getStructureSelectionManager()
-            .setMapping(seq, chains, alreadyMapped, AppletFormatAdapter.FILE);
-        if (ap.seqPanel.seqCanvas.fr!=null) {
+                .setMapping(seq, chains, alreadyMapped,
+                        AppletFormatAdapter.FILE);
+        if (ap.seqPanel.seqCanvas.fr != null)
+        {
           ap.seqPanel.seqCanvas.fr.featuresAdded();
           ap.paintAlignment(true);
         }
 
-        //Now this AppJmol is mapped to new sequences. We must add them to
+        // Now this AppJmol is mapped to new sequences. We must add them to
         // the exisiting array
-        JInternalFrame [] frames = Desktop.instance.getAllFrames();
+        JInternalFrame[] frames = Desktop.instance.getAllFrames();
 
-        for(int i=0; i<frames.length; i++)
+        for (int i = 0; i < frames.length; i++)
         {
-          if(frames[i] instanceof AppJmol)
+          if (frames[i] instanceof AppJmol)
           {
-           AppJmol topJmol = ((AppJmol)frames[i]);
-           if(topJmol.pdbentry.getFile().equals(alreadyMapped))
-           {
-             topJmol.addSequence(seq);
-             break;
-           }
+            AppJmol topJmol = ((AppJmol) frames[i]);
+            if (topJmol.pdbentry.getFile().equals(alreadyMapped))
+            {
+              topJmol.addSequence(seq);
+              break;
+            }
           }
         }
 
         return;
       }
     }
-    ///////////////////////////////////
+    // /////////////////////////////////
 
     this.ap = ap;
     this.pdbentry = pdbentry;
     this.sequence = seq;
-    this.setSize(400,400);
-    //jalview.gui.Desktop.addInternalFrame(this, "Jmol View"+(pdbentry.getId()!=null ? "for "+pdbentry.getId() 
-    //          : ""), 400, 400);
+    this.setSize(400, 400);
+    // jalview.gui.Desktop.addInternalFrame(this, "Jmol
+    // View"+(pdbentry.getId()!=null ? "for "+pdbentry.getId()
+    // : ""), 400, 400);
 
     if (pdbentry.getFile() != null)
     {
-      initJmol("load \""+pdbentry.getFile()+"\"");
+      initJmol("load \"" + pdbentry.getFile() + "\"");
     }
     else
     {
@@ -179,15 +194,14 @@ public synchronized void addSequence(SequenceI [] seq)
     });
   }
 
-
   void initJmol(String command)
   {
     renderPanel = new RenderPanel();
 
     this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
 
-    StringBuffer title = new StringBuffer(sequence[0].getName() + ":" +
-                                          pdbentry.getId());
+    StringBuffer title = new StringBuffer(sequence[0].getName() + ":"
+            + pdbentry.getId());
 
     if (pdbentry.getProperty() != null)
     {
@@ -204,12 +218,11 @@ public synchronized void addSequence(SequenceI [] seq)
     }
 
     this.setTitle(title.toString());
-    jalview.gui.Desktop.addInternalFrame(this, title.toString(), 
-                                         getBounds().width,getBounds().height);
+    jalview.gui.Desktop.addInternalFrame(this, title.toString(),
+            getBounds().width, getBounds().height);
 
     viewer = org.jmol.api.JmolViewer.allocateViewer(renderPanel,
-        new SmarterJmolAdapter());
-
+            new SmarterJmolAdapter());
 
     viewer.setAppletContext("", null, null, "");
 
@@ -220,26 +233,25 @@ public synchronized void addSequence(SequenceI [] seq)
     viewer.evalStringQuiet(command);
   }
 
-
   void setChainMenuItems(Vector chains)
   {
     chainMenu.removeAll();
 
     JMenuItem menuItem = new JMenuItem("All");
     menuItem.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent evt)
+      {
+        allChainsSelected = true;
+        for (int i = 0; i < chainMenu.getItemCount(); i++)
         {
-          public void actionPerformed(ActionEvent evt)
-          {
-            allChainsSelected = true;
-            for(int i=0; i<chainMenu.getItemCount(); i++)
-            {
-              if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
-                ( (JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
-            }
-            centerViewer();
-            allChainsSelected = false;
-          }
-        });
+          if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
+            ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
+        }
+        centerViewer();
+        allChainsSelected = false;
+      }
+    });
 
     chainMenu.add(menuItem);
 
@@ -260,24 +272,25 @@ public synchronized void addSequence(SequenceI [] seq)
   }
 
   boolean allChainsSelected = false;
+
   void centerViewer()
   {
     StringBuffer cmd = new StringBuffer();
-    for(int i=0; i<chainMenu.getItemCount(); i++)
+    for (int i = 0; i < chainMenu.getItemCount(); i++)
     {
       if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
       {
-       JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
-       if(item.isSelected())
-         cmd.append(":"+item.getText()+" or ");
+        JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
+        if (item.isSelected())
+          cmd.append(":" + item.getText() + " or ");
       }
     }
 
     if (cmd.length() > 0)
       cmd.setLength(cmd.length() - 4);
 
-    viewer.evalStringQuiet("select *;restrict "
-                      +cmd+";cartoon;center "+cmd);
+    viewer.evalStringQuiet("select *;restrict " + cmd + ";cartoon;center "
+            + cmd);
   }
 
   void closeViewer()
@@ -287,11 +300,10 @@ public synchronized void addSequence(SequenceI [] seq)
     viewer.setJmolStatusListener(null);
     viewer = null;
 
-    //We'll need to find out what other
+    // We'll need to find out what other
     // listeners need to be shut down in Jmol
-    StructureSelectionManager
-        .getStructureSelectionManager()
-        .removeStructureViewerListener(this, pdbentry.getFile());
+    StructureSelectionManager.getStructureSelectionManager()
+            .removeStructureViewerListener(this, pdbentry.getFile());
   }
 
   public void run()
@@ -301,10 +313,13 @@ public synchronized void addSequence(SequenceI [] seq)
       EBIFetchClient ebi = new EBIFetchClient();
       String query = "pdb:" + pdbentry.getId();
       pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw")
-                       .getAbsolutePath());
-      initJmol("load "+pdbentry.getFile());
-    }
-    catch (Exception ex)
+              .getAbsolutePath());
+      initJmol("load " + pdbentry.getFile());
+    } catch (OutOfMemoryError oomerror)
+    {
+      new OOMWarning("Retrieving PDB id " + pdbentry.getId() + " from MSD",
+              oomerror);
+    } catch (Exception ex)
     {
       ex.printStackTrace();
     }
@@ -312,9 +327,8 @@ public synchronized void addSequence(SequenceI [] seq)
 
   public void pdbFile_actionPerformed(ActionEvent actionEvent)
   {
-    JalviewFileChooser chooser = new JalviewFileChooser(
-        jalview.bin.Cache.getProperty(
-            "LAST_DIRECTORY"));
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+            .getProperty("LAST_DIRECTORY"));
 
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle("Save PDB File");
@@ -326,23 +340,21 @@ public synchronized void addSequence(SequenceI [] seq)
     {
       try
       {
-        BufferedReader in = new BufferedReader(new FileReader(pdbentry.getFile()));
+        BufferedReader in = new BufferedReader(new FileReader(pdbentry
+                .getFile()));
         File outFile = chooser.getSelectedFile();
 
         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
         String data;
-        while ( (data = in.readLine()) != null)
+        while ((data = in.readLine()) != null)
         {
-          if (
-              ! (data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1)
-              )
+          if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
           {
             out.println(data);
           }
         }
         out.close();
-      }
-      catch (Exception ex)
+      } catch (Exception ex)
       {
         ex.printStackTrace();
       }
@@ -352,18 +364,17 @@ public synchronized void addSequence(SequenceI [] seq)
   public void viewMapping_actionPerformed(ActionEvent actionEvent)
   {
     jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
-    jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550,
-                                         600);
-    cap.setText(
-        StructureSelectionManager.getStructureSelectionManager().printMapping(
-            pdbentry.getFile())
-        );
+    jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping",
+            550, 600);
+    cap.setText(StructureSelectionManager.getStructureSelectionManager()
+            .printMapping(pdbentry.getFile()));
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void eps_actionPerformed(ActionEvent e)
   {
@@ -372,8 +383,9 @@ public synchronized void addSequence(SequenceI [] seq)
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void png_actionPerformed(ActionEvent e)
   {
@@ -389,31 +401,24 @@ public synchronized void addSequence(SequenceI [] seq)
 
     if (type == jalview.util.ImageMaker.PNG)
     {
-      im = new jalview.util.ImageMaker(this,
-                                       jalview.util.ImageMaker.PNG,
-                                       "Make PNG image from view",
-                                       width, height,
-                                       null, null);
+      im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
+              "Make PNG image from view", width, height, null, null);
     }
     else
     {
-      im = new jalview.util.ImageMaker(this,
-                                       jalview.util.ImageMaker.EPS,
-                                       "Make EPS file from view",
-                                       width, height,
-                                       null, this.getTitle());
+      im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
+              "Make EPS file from view", width, height, null, this
+                      .getTitle());
     }
 
     if (im.getGraphics() != null)
     {
       Rectangle rect = new Rectangle(width, height);
-      viewer.renderScreenImage(im.getGraphics(),
-                               rect.getSize(), rect);
+      viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect);
       im.writeImage();
     }
   }
 
-
   public void seqColour_actionPerformed(ActionEvent actionEvent)
   {
     lastCommand = null;
@@ -433,7 +438,7 @@ public synchronized void addSequence(SequenceI [] seq)
     colourBySequence = false;
     seqColour.setSelected(false);
     viewer.evalStringQuiet("select *;color white;select ASP,GLU;color red;"
-                      +"select LYS,ARG;color blue;select CYS;color yellow");
+            + "select LYS,ARG;color blue;select CYS;color yellow");
   }
 
   public void zappoColour_actionPerformed(ActionEvent actionEvent)
@@ -476,7 +481,7 @@ public synchronized void addSequence(SequenceI [] seq)
     colourBySequence = false;
     seqColour.setSelected(false);
 
-    if(cs==null)
+    if (cs == null)
       return;
 
     String res;
@@ -485,19 +490,17 @@ public synchronized void addSequence(SequenceI [] seq)
 
     Enumeration en = ResidueProperties.aa3Hash.keys();
     StringBuffer command = new StringBuffer("select *;color white;");
-    while(en.hasMoreElements())
+    while (en.hasMoreElements())
     {
       res = en.nextElement().toString();
       index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();
-      if(index>20)
+      if (index > 20)
         continue;
 
       col = cs.findColour(ResidueProperties.aa[index].charAt(0));
 
-      command.append("select "+res+";color["
-                        + col.getRed() + ","
-                        + col.getGreen() + ","
-                        + col.getBlue() + "];");
+      command.append("select " + res + ";color[" + col.getRed() + ","
+              + col.getGreen() + "," + col.getBlue() + "];");
     }
 
     viewer.evalStringQuiet(command.toString());
@@ -511,40 +514,38 @@ public synchronized void addSequence(SequenceI [] seq)
   public void backGround_actionPerformed(ActionEvent actionEvent)
   {
     java.awt.Color col = JColorChooser.showDialog(this,
-                                                  "Select Background Colour",
-                                                  null);
+            "Select Background Colour", null);
 
     if (col != null)
     {
-      viewer.evalStringQuiet("background ["
-                        + col.getRed() + ","
-                        + col.getGreen() + ","
-                        + col.getBlue() + "];");
+      viewer.evalStringQuiet("background [" + col.getRed() + ","
+              + col.getGreen() + "," + col.getBlue() + "];");
     }
   }
 
-
   public void jmolHelp_actionPerformed(ActionEvent actionEvent)
   {
-       try{
-         jalview.util.BrowserLauncher.openURL(
-             "http://jmol.sourceforge.net/docs/JmolUserGuide/");
-       }catch(Exception ex){}
-   }
-
+    try
+    {
+      jalview.util.BrowserLauncher
+              .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/");
+    } catch (Exception ex)
+    {
+    }
+  }
 
-  //////////////////////////////////
-  ///StructureListener
+  // ////////////////////////////////
+  // /StructureListener
   public String getPdbFile()
   {
     return pdbentry.getFile();
   }
 
-  Pattern pattern = Pattern.compile(
-      "\\[(.*)\\]([0-9]+)(:[a-zA-Z]*)?\\.([a-zA-Z]+)(/[0-9]*)?"
-      );
+  Pattern pattern = Pattern
+          .compile("\\[(.*)\\]([0-9]+)(:[a-zA-Z]*)?\\.([a-zA-Z]+)(/[0-9]*)?");
 
   String lastMessage;
+
   public void mouseOverStructure(int atomIndex, String strInfo)
   {
     Matcher matcher = pattern.matcher(strInfo);
@@ -568,9 +569,11 @@ public synchronized void addSequence(SequenceI [] seq)
   }
 
   StringBuffer resetLastRes = new StringBuffer();
+
   StringBuffer eval = new StringBuffer();
 
-  public void highlightAtom(int atomIndex, int pdbResNum, String chain, String pdbfile)
+  public void highlightAtom(int atomIndex, int pdbResNum, String chain,
+          String pdbfile)
   {
     if (!pdbfile.equals(pdbentry.getFile()))
       return;
@@ -592,16 +595,18 @@ public synchronized void addSequence(SequenceI [] seq)
       resetLastRes.append(":" + chain);
     }
 
-    eval.append(";wireframe 100;"+eval.toString()+".CA;");
+    eval.append(";wireframe 100;" + eval.toString() + ".CA;");
 
-    resetLastRes.append(";wireframe 0;"+resetLastRes.toString()+".CA;spacefill 0;");
+    resetLastRes.append(";wireframe 0;" + resetLastRes.toString()
+            + ".CA;spacefill 0;");
 
     eval.append("spacefill 200;select none");
 
     viewer.evalStringQuiet(eval.toString());
   }
 
-  public Color getColour(int atomIndex, int pdbResNum, String chain, String pdbfile)
+  public Color getColour(int atomIndex, int pdbResNum, String chain,
+          String pdbfile)
   {
     if (!pdbfile.equals(pdbentry.getFile()))
       return null;
@@ -611,27 +616,27 @@ public synchronized void addSequence(SequenceI [] seq)
 
   public void updateColours(Object source)
   {
-    colourBySequence( (AlignmentPanel) source);
+    colourBySequence((AlignmentPanel) source);
   }
 
-
-//End StructureListener
-////////////////////////////
+  // End StructureListener
+  // //////////////////////////
 
   String lastCommand;
-  FeatureRenderer fr=null;
+
+  FeatureRenderer fr = null;
+
   public void colourBySequence(AlignmentPanel sourceap)
   {
     this.ap = sourceap;
 
-    if(!colourBySequence || ap.alignFrame.getCurrentView()!=ap.av)
+    if (!colourBySequence || ap.alignFrame.getCurrentView() != ap.av)
       return;
 
     StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
 
     if (mapping.length < 1)
-     return;
-
+      return;
 
     SequenceRenderer sr = new SequenceRenderer(ap.av);
 
@@ -651,12 +656,12 @@ public synchronized void addSequence(SequenceI [] seq)
     StringBuffer command = new StringBuffer();
 
     int lastPos = -1;
-    for (int sp,s = 0; s < sequence.length; s++)
+    for (int sp, s = 0; s < sequence.length; s++)
     {
       for (int m = 0; m < mapping.length; m++)
       {
         if (mapping[m].getSequence() == sequence[s]
-            && (sp=ap.av.alignment.findIndex(sequence[s]))>-1)
+                && (sp = ap.av.alignment.findIndex(sequence[s])) > -1)
         {
           SequenceI asp = ap.av.alignment.getSequenceAt(sp);
           for (int r = 0; r < asp.getLength(); r++)
@@ -666,10 +671,9 @@ public synchronized void addSequence(SequenceI [] seq)
             {
               continue;
             }
-            int pos = mapping[m].getPDBResNum(
-                    asp.findPosition(r));
+            int pos = mapping[m].getPDBResNum(asp.findPosition(r));
 
-            if (pos < 1 || pos==lastPos)
+            if (pos < 1 || pos == lastPos)
               continue;
 
             lastPos = pos;
@@ -679,11 +683,10 @@ public synchronized void addSequence(SequenceI [] seq)
             if (showFeatures)
               col = fr.findFeatureColour(col, asp, r);
 
-            if (command.toString().endsWith(":" + mapping[m].getChain()+
-                                            ";color["
-                                            + col.getRed() + ","
-                                            + col.getGreen() + ","
-                                            + col.getBlue() + "]"))
+            if (command.toString().endsWith(
+                    ":" + mapping[m].getChain() + ";color[" + col.getRed()
+                            + "," + col.getGreen() + "," + col.getBlue()
+                            + "]"))
             {
               command = condenseCommand(command, pos);
               continue;
@@ -696,10 +699,8 @@ public synchronized void addSequence(SequenceI [] seq)
               command.append(":" + mapping[m].getChain());
             }
 
-            command.append(";color["
-                             + col.getRed() + ","
-                             + col.getGreen() + ","
-                             + col.getBlue() + "]");
+            command.append(";color[" + col.getRed() + "," + col.getGreen()
+                    + "," + col.getBlue() + "]");
 
           }
           break;
@@ -716,7 +717,8 @@ public synchronized void addSequence(SequenceI [] seq)
 
   StringBuffer condenseCommand(StringBuffer command, int pos)
   {
-    StringBuffer sb = new StringBuffer(command.substring(0, command.lastIndexOf("select")+7));
+    StringBuffer sb = new StringBuffer(command.substring(0, command
+            .lastIndexOf("select") + 7));
 
     command.delete(0, sb.length());
 
@@ -724,25 +726,25 @@ public synchronized void addSequence(SequenceI [] seq)
 
     if (command.indexOf("-") > -1)
     {
-      start = command.substring(0,command.indexOf("-"));
+      start = command.substring(0, command.indexOf("-"));
     }
     else
     {
       start = command.substring(0, command.indexOf(":"));
     }
 
-    sb.append(start+"-"+pos+command.substring(command.indexOf(":")));
+    sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
 
     return sb;
   }
 
-  /////////////////////////////////
-  //JmolStatusListener
+  // ///////////////////////////////
+  // JmolStatusListener
 
   public String eval(String strEval)
   {
-   // System.out.println(strEval);
-   //"# 'eval' is implemented only for the applet.";
+    // System.out.println(strEval);
+    // "# 'eval' is implemented only for the applet.";
     return null;
   }
 
@@ -752,14 +754,14 @@ public synchronized void addSequence(SequenceI [] seq)
   }
 
   public void setCallbackFunction(String callbackType,
-                                  String callbackFunction)
-  {}
+          String callbackFunction)
+  {
+  }
 
   public void notifyFileLoaded(String fullPathName, String fileName,
-                               String modelName, Object clientFile,
-                               String errorMsg)
+          String modelName, Object clientFile, String errorMsg)
   {
-    if(errorMsg!=null)
+    if (errorMsg != null)
     {
       fileLoadingError = errorMsg;
       repaint();
@@ -771,27 +773,29 @@ public synchronized void addSequence(SequenceI [] seq)
     if (fileName != null)
     {
 
-      //FILE LOADED OK
+      // FILE LOADED OK
       ssm = StructureSelectionManager.getStructureSelectionManager();
-      MCview.PDBfile pdbFile = ssm.setMapping(sequence,chains,pdbentry.getFile(), AppletFormatAdapter.FILE);
+      MCview.PDBfile pdbFile = ssm.setMapping(sequence, chains, pdbentry
+              .getFile(), AppletFormatAdapter.FILE);
       ssm.addStructureViewerListener(this);
       Vector chains = new Vector();
-      for(int i=0; i<pdbFile.chains.size(); i++)
+      for (int i = 0; i < pdbFile.chains.size(); i++)
       {
-        chains.addElement(((MCview.PDBChain)pdbFile.chains.elementAt(i)).id);
+        chains
+                .addElement(((MCview.PDBChain) pdbFile.chains.elementAt(i)).id);
       }
       setChainMenuItems(chains);
 
       jmolpopup.updateComputedMenus();
 
-      if(!loadingFromArchive)
+      if (!loadingFromArchive)
       {
-        viewer.evalStringQuiet(
-             "select backbone;restrict;cartoon;wireframe off;spacefill off");
+        viewer
+                .evalStringQuiet("select backbone;restrict;cartoon;wireframe off;spacefill off");
 
         colourBySequence(ap);
       }
-      if (fr!=null)
+      if (fr != null)
         fr.featuresAdded();
 
       loadingFromArchive = false;
@@ -806,7 +810,8 @@ public synchronized void addSequence(SequenceI [] seq)
   }
 
   public void notifyScriptStart(String statusMessage, String additionalInfo)
-  {}
+  {
+  }
 
   public void sendConsoleEcho(String strEcho)
   {
@@ -837,7 +842,8 @@ public synchronized void addSequence(SequenceI [] seq)
   }
 
   public void notifyNewDefaultModeMeasurement(int count, String strInfo)
-  {}
+  {
+  }
 
   public void notifyAtomPicked(int atomIndex, String strInfo)
   {
@@ -851,22 +857,21 @@ public synchronized void addSequence(SequenceI [] seq)
     String picked = resnum;
 
     if (chainId != null)
-      picked+=(":"+chainId.substring(1, chainId.length()));
-
-    picked+=".CA";
+      picked += (":" + chainId.substring(1, chainId.length()));
 
+    picked += ".CA";
 
     if (!atomsPicked.contains(picked))
     {
-      if(chainId!=null)
-      viewer.evalString("select "+picked+";label %n %r:%c");
-    else
-      viewer.evalString("select "+picked+";label %n %r");
+      if (chainId != null)
+        viewer.evalString("select " + picked + ";label %n %r:%c");
+      else
+        viewer.evalString("select " + picked + ";label %n %r");
       atomsPicked.addElement(picked);
     }
     else
     {
-      viewer.evalString("select "+picked+";label off");
+      viewer.evalString("select " + picked + ";label off");
       atomsPicked.removeElement(picked);
     }
 
@@ -883,19 +888,21 @@ public synchronized void addSequence(SequenceI [] seq)
   }
 
   public void sendSyncScript(String script, String appletName)
-  {}
+  {
+  }
 
   public void showUrl(String url)
-  {}
+  {
+  }
 
   public void showConsole(boolean showConsole)
   {
     if (scriptWindow == null)
       scriptWindow = new ScriptWindow(this);
 
-    if(showConsole)
+    if (showConsole)
     {
-      if(splitPane==null)
+      if (splitPane == null)
       {
         splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
         splitPane.setTopComponent(renderPanel);
@@ -903,7 +910,7 @@ public synchronized void addSequence(SequenceI [] seq)
         this.getContentPane().add(splitPane, BorderLayout.CENTER);
       }
 
-      splitPane.setDividerLocation(getHeight()-200);
+      splitPane.setDividerLocation(getHeight() - 200);
       splitPane.validate();
     }
     else
@@ -924,14 +931,13 @@ public synchronized void addSequence(SequenceI [] seq)
     return 0;
   }
 
-  ///End JmolStatusListener
-  ///////////////////////////////
+  // /End JmolStatusListener
+  // /////////////////////////////
 
-
-  class RenderPanel
-      extends JPanel
+  class RenderPanel extends JPanel
   {
     final Dimension currentSize = new Dimension();
+
     final Rectangle rectClip = new Rectangle();
 
     public void paintComponent(Graphics g)
@@ -947,14 +953,14 @@ public synchronized void addSequence(SequenceI [] seq)
         g.setFont(new Font("Verdana", Font.BOLD, 14));
         g.drawString("Retrieving PDB data....", 20, currentSize.height / 2);
       }
-      else if(fileLoadingError!=null)
+      else if (fileLoadingError != null)
       {
         g.setColor(Color.black);
         g.fillRect(0, 0, currentSize.width, currentSize.height);
         g.setColor(Color.white);
         g.setFont(new Font("Verdana", Font.BOLD, 14));
         g.drawString("Error loading file..." + pdbentry.getId(), 20,
-                     currentSize.height / 2);
+                currentSize.height / 2);
       }
       else
       {
diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index a3fa7c7..6459de4 100755
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -1,265 +1,260 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.gui;
-
-import java.awt.*;
-import java.awt.datatransfer.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.jbgui.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class CutAndPasteTransfer
-    extends GCutAndPasteTransfer
-{
-
-  AlignViewport viewport;
-
-  public CutAndPasteTransfer()
-  {
-    SwingUtilities.invokeLater(new Runnable()
-    {
-      public void run()
-      {
-        textarea.requestFocus();
-      }
-    });
-
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  public void setForInput(AlignViewport viewport)
-  {
-    this.viewport = viewport;
-    if (viewport != null)
-    {
-      ok.setText("Add");
-    }
-
-    getContentPane().add(inputButtonPanel, java.awt.BorderLayout.SOUTH);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public String getText()
-  {
-    return textarea.getText();
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param text DOCUMENT ME!
-   */
-  public void setText(String text)
-  {
-    textarea.setText(text);
-  }
-
-  public void appendText(String text)
-  {
-    textarea.append(text);
-  }
-
-  public void save_actionPerformed(ActionEvent e)
-  {
-    JalviewFileChooser chooser = new JalviewFileChooser(
-        jalview.bin.Cache.getProperty(
-            "LAST_DIRECTORY"));
-
-    chooser.setAcceptAllFileFilterUsed(false);
-    chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle("Save Text to File");
-    chooser.setToolTipText("Save");
-
-    int value = chooser.showSaveDialog(this);
-
-    if (value == JalviewFileChooser.APPROVE_OPTION)
-    {
-      try
-      {
-        java.io.PrintWriter out = new java.io.PrintWriter(
-            new java.io.FileWriter(chooser.getSelectedFile()));
-
-        out.print(getText());
-        out.close();
-      }
-      catch (Exception ex)
-      {
-        ex.printStackTrace();
-      }
-
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  public void copyItem_actionPerformed(ActionEvent e)
-  {
-    textarea.getSelectedText();
-    Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
-    c.setContents(new StringSelection(textarea.getSelectedText()), null);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  public void pasteMenu_actionPerformed(ActionEvent e)
-  {
-    Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
-    Transferable contents = c.getContents(this);
-
-    if (contents == null)
-    {
-      return;
-    }
-
-    try
-    {
-      textarea.append( (String) contents.getTransferData(
-          DataFlavor.stringFlavor));
-    }
-    catch (Exception ex)
-    {
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  public void ok_actionPerformed(ActionEvent e)
-  {
-    String format = new IdentifyFile().Identify(getText(), "Paste");
-    Alignment al = null;
-
-    if (FormatAdapter.isValidFormat(format))
-    {
-      try
-      {
-        al = new FormatAdapter().readFile(getText(), "Paste", format);
-      }
-      catch (java.io.IOException ex)
-      {
-        JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                              "Couldn't read the pasted text.\n" +
-                                              ex.toString(),
-                                              "Error parsing text",
-                                              JOptionPane.WARNING_MESSAGE);
-      }
-    }
-
-    if (al != null)
-    {
-      if (viewport != null)
-      {
-        for (int i = 0; i < al.getHeight(); i++)
-        {
-          viewport.getAlignment().addSequence(al.getSequenceAt(i));
-        }
-
-        viewport.firePropertyChange("alignment", null,
-                                    viewport.getAlignment().getSequences());
-      }
-      else
-      {
-        AlignFrame af = new AlignFrame(al,
-                                       AlignFrame.DEFAULT_WIDTH,
-                                       AlignFrame.DEFAULT_HEIGHT);
-        af.currentFileFormat = format;
-        Desktop.addInternalFrame(af, "Cut & Paste input - " + format,
-                                 AlignFrame.DEFAULT_WIDTH,
-                                 AlignFrame.DEFAULT_HEIGHT);
-        af.statusBar.setText("Successfully pasted alignment file");
-
-        try
-        {
-          af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
-        }
-        catch (Exception ex)
-        {
-        }
-      }
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  public void cancel_actionPerformed(ActionEvent e)
-  {
-    try
-    {
-      this.setClosed(true);
-    }
-    catch (Exception ex)
-    {
-    }
-  }
-
-  public void textarea_mousePressed(MouseEvent e)
-  {
-    if (SwingUtilities.isRightMouseButton(e))
-    {
-      JPopupMenu popup = new JPopupMenu("Edit");
-      JMenuItem item = new JMenuItem("Copy");
-      item.addActionListener(new ActionListener()
-      {
-        public void actionPerformed(ActionEvent e)
-        {
-          copyItem_actionPerformed(e);
-        }
-      });
-      popup.add(item);
-      item = new JMenuItem("Paste");
-      item.addActionListener(new ActionListener()
-      {
-        public void actionPerformed(ActionEvent e)
-        {
-          pasteMenu_actionPerformed(e);
-        }
-      });
-      popup.add(item);
-      popup.show(this, e.getX() + 10, e.getY() + textarea.getY() + 40);
-
-    }
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.gui;
+
+import java.awt.*;
+import java.awt.datatransfer.*;
+import java.awt.event.*;
+import javax.swing.*;
+
+import jalview.datamodel.*;
+import jalview.io.*;
+import jalview.jbgui.*;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class CutAndPasteTransfer extends GCutAndPasteTransfer
+{
+
+  AlignViewport viewport;
+
+  public CutAndPasteTransfer()
+  {
+    SwingUtilities.invokeLater(new Runnable()
+    {
+      public void run()
+      {
+        textarea.requestFocus();
+      }
+    });
+
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void setForInput(AlignViewport viewport)
+  {
+    this.viewport = viewport;
+    if (viewport != null)
+    {
+      ok.setText("Add");
+    }
+
+    getContentPane().add(inputButtonPanel, java.awt.BorderLayout.SOUTH);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public String getText()
+  {
+    return textarea.getText();
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param text
+   *                DOCUMENT ME!
+   */
+  public void setText(String text)
+  {
+    textarea.setText(text);
+  }
+
+  public void appendText(String text)
+  {
+    textarea.append(text);
+  }
+
+  public void save_actionPerformed(ActionEvent e)
+  {
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+            .getProperty("LAST_DIRECTORY"));
+
+    chooser.setAcceptAllFileFilterUsed(false);
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle("Save Text to File");
+    chooser.setToolTipText("Save");
+
+    int value = chooser.showSaveDialog(this);
+
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      try
+      {
+        java.io.PrintWriter out = new java.io.PrintWriter(
+                new java.io.FileWriter(chooser.getSelectedFile()));
+
+        out.print(getText());
+        out.close();
+      } catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
+
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
+   */
+  public void copyItem_actionPerformed(ActionEvent e)
+  {
+    textarea.getSelectedText();
+    Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+    c.setContents(new StringSelection(textarea.getSelectedText()), null);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
+   */
+  public void pasteMenu_actionPerformed(ActionEvent e)
+  {
+    Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+    Transferable contents = c.getContents(this);
+
+    if (contents == null)
+    {
+      return;
+    }
+
+    try
+    {
+      textarea.append((String) contents
+              .getTransferData(DataFlavor.stringFlavor));
+    } catch (Exception ex)
+    {
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
+   */
+  public void ok_actionPerformed(ActionEvent e)
+  {
+    String format = new IdentifyFile().Identify(getText(), "Paste");
+    Alignment al = null;
+
+    if (FormatAdapter.isValidFormat(format))
+    {
+      try
+      {
+        al = new FormatAdapter().readFile(getText(), "Paste", format);
+      } catch (java.io.IOException ex)
+      {
+        JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                "Couldn't read the pasted text.\n" + ex.toString(),
+                "Error parsing text", JOptionPane.WARNING_MESSAGE);
+      }
+    }
+
+    if (al != null)
+    {
+      if (viewport != null)
+      {
+        for (int i = 0; i < al.getHeight(); i++)
+        {
+          viewport.getAlignment().addSequence(al.getSequenceAt(i));
+        }
+
+        viewport.firePropertyChange("alignment", null, viewport
+                .getAlignment().getSequences());
+      }
+      else
+      {
+        AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+                AlignFrame.DEFAULT_HEIGHT);
+        af.currentFileFormat = format;
+        Desktop.addInternalFrame(af, "Cut & Paste input - " + format,
+                AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+        af.statusBar.setText("Successfully pasted alignment file");
+
+        try
+        {
+          af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
+                  false));
+        } catch (Exception ex)
+        {
+        }
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
+   */
+  public void cancel_actionPerformed(ActionEvent e)
+  {
+    try
+    {
+      this.setClosed(true);
+    } catch (Exception ex)
+    {
+    }
+  }
+
+  public void textarea_mousePressed(MouseEvent e)
+  {
+    if (SwingUtilities.isRightMouseButton(e))
+    {
+      JPopupMenu popup = new JPopupMenu("Edit");
+      JMenuItem item = new JMenuItem("Copy");
+      item.addActionListener(new ActionListener()
+      {
+        public void actionPerformed(ActionEvent e)
+        {
+          copyItem_actionPerformed(e);
+        }
+      });
+      popup.add(item);
+      item = new JMenuItem("Paste");
+      item.addActionListener(new ActionListener()
+      {
+        public void actionPerformed(ActionEvent e)
+        {
+          pasteMenu_actionPerformed(e);
+        }
+      });
+      popup.add(item);
+      popup.show(this, e.getX() + 10, e.getY() + textarea.getY() + 40);
+
+    }
+  }
+
+}
diff --git a/src/jalview/gui/DasSourceBrowser.java b/src/jalview/gui/DasSourceBrowser.java
index 807aa4b..e336d9a 100755
--- a/src/jalview/gui/DasSourceBrowser.java
+++ b/src/jalview/gui/DasSourceBrowser.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -30,8 +30,8 @@ import org.biojava.dasobert.dasregistry.*;
 import jalview.jbgui.*;
 import jalview.util.*;
 
-public class DasSourceBrowser
-    extends GDasSourceBrowser implements Runnable, ListSelectionListener
+public class DasSourceBrowser extends GDasSourceBrowser implements
+        Runnable, ListSelectionListener
 {
   static DasSource[] dasSources = null;
 
@@ -39,17 +39,17 @@ public class DasSourceBrowser
 
   Vector selectedSources;
 
-  public static String DEFAULT_REGISTRY =
-      "http://www.dasregistry.org/das1/sources/";
+  public static String DEFAULT_REGISTRY = "http://www.dasregistry.org/das1/sources/";
 
   /**
    * true if thread is running and we are talking to DAS registry service
    */
   public boolean loadingDasSources = false;
+
   protected static String getDasRegistryURL()
   {
     String registry = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
-        DEFAULT_REGISTRY);
+            DEFAULT_REGISTRY);
 
     if (registry.indexOf("/registry/das1/sources/") > -1)
     {
@@ -58,10 +58,11 @@ public class DasSourceBrowser
     }
     return registry;
   }
+
   public DasSourceBrowser()
   {
     String registry = getDasRegistryURL();
-    
+
     registryURL.setText(registry);
 
     setSelectedFromProperties();
@@ -73,7 +74,7 @@ public class DasSourceBrowser
     filter2.addListSelectionListener(this);
     filter3.addListSelectionListener(this);
 
-    //Ask to be notified of selection changes.
+    // Ask to be notified of selection changes.
     ListSelectionModel rowSM = table.getSelectionModel();
     rowSM.addListSelectionListener(new ListSelectionListener()
     {
@@ -93,7 +94,7 @@ public class DasSourceBrowser
       public void mouseClicked(MouseEvent evt)
       {
         if (evt.getClickCount() == 2
-            || SwingUtilities.isRightMouseButton(evt))
+                || SwingUtilities.isRightMouseButton(evt))
         {
           editRemoveLocalSource(evt);
         }
@@ -122,8 +123,8 @@ public class DasSourceBrowser
     for (int i = 0; i < dSize; i++)
     {
       data[i][0] = dasSources[i].getNickname();
-      data[i][1] = new Boolean(selectedSources.contains(dasSources[i].
-          getNickname()));
+      data[i][1] = new Boolean(selectedSources.contains(dasSources[i]
+              .getNickname()));
     }
 
     refreshTableData(data);
@@ -156,13 +157,12 @@ public class DasSourceBrowser
   {
 
     StringBuffer text = new StringBuffer(
-        "<HTML><font size=\"2\" face=\"Verdana, Arial, Helvetica, sans-serif\">");
+            "<HTML><font size=\"2\" face=\"Verdana, Arial, Helvetica, sans-serif\">");
 
     if (nickName == null)
     {
-      fullDetails.setText(text +
-                          "Select a DAS service from the table"
-                          + " to read a full description here.</font></html>");
+      fullDetails.setText(text + "Select a DAS service from the table"
+              + " to read a full description here.</font></html>");
       return;
     }
 
@@ -176,26 +176,24 @@ public class DasSourceBrowser
 
       DasSource ds = dasSources[i];
 
-      text.append("<font color=\"#0000FF\">Id:</font> " + dasSources[i].getId() +
-                  "<br>");
-      text.append("<font color=\"#0000FF\">Nickname:</font> " +
-                  dasSources[i].getNickname() + "<br>");
-      text.append("<font color=\"#0000FF\">URL:</font> " + dasSources[i].getUrl() +
-                  "<br>");
+      text.append("<font color=\"#0000FF\">Id:</font> "
+              + dasSources[i].getId() + "<br>");
+      text.append("<font color=\"#0000FF\">Nickname:</font> "
+              + dasSources[i].getNickname() + "<br>");
+      text.append("<font color=\"#0000FF\">URL:</font> "
+              + dasSources[i].getUrl() + "<br>");
 
-      text.append(
-          "<font color=\"#0000FF\">Admin Email:</font> <a href=\"mailto:"
-          + dasSources[i].getAdminemail()
-          + "\">" + dasSources[i].getAdminemail() + "</a>" +
-          "<br>");
+      text
+              .append("<font color=\"#0000FF\">Admin Email:</font> <a href=\"mailto:"
+                      + dasSources[i].getAdminemail()
+                      + "\">"
+                      + dasSources[i].getAdminemail() + "</a>" + "<br>");
 
-      text.append("<font color=\"#0000FF\">Registered at:</font> " +
-                  dasSources[i].getRegisterDate() +
-                  "<br>");
+      text.append("<font color=\"#0000FF\">Registered at:</font> "
+              + dasSources[i].getRegisterDate() + "<br>");
 
-      text.append("<font color=\"#0000FF\">Last successful test:</font> " +
-                  dasSources[i].getLeaseDate() +
-                  "<br>");
+      text.append("<font color=\"#0000FF\">Last successful test:</font> "
+              + dasSources[i].getLeaseDate() + "<br>");
 
       text.append("<font color=\"#0000FF\">Labels:</font> ");
       for (int s = 0; s < dasSources[i].getLabels().length; s++)
@@ -226,7 +224,7 @@ public class DasSourceBrowser
       for (int j = 0; j < dcs.length; j++)
       {
         text.append("(" + dcs[j].getUniqueId() + ") "
-                    + dcs[j].getCategory() + ", " + dcs[j].getName());
+                + dcs[j].getCategory() + ", " + dcs[j].getName());
         if (dcs[j].getNCBITaxId() != 0)
         {
           text.append(", " + dcs[j].getNCBITaxId());
@@ -239,15 +237,15 @@ public class DasSourceBrowser
         text.append("<br>");
       }
 
-      text.append("<font color=\"#0000FF\">Description:</font> " +
-                  dasSources[i].getDescription() + "<br>");
+      text.append("<font color=\"#0000FF\">Description:</font> "
+              + dasSources[i].getDescription() + "<br>");
 
       if (dasSources[i].getHelperurl() != null
-          && dasSources[i].getHelperurl().length() > 0)
+              && dasSources[i].getHelperurl().length() > 0)
       {
-        text.append("<font color=\"#0000FF\"><a href=\"" +
-                    dasSources[i].getHelperurl()
-                    + "\">Go to site</a></font<br>");
+        text.append("<font color=\"#0000FF\"><a href=\""
+                + dasSources[i].getHelperurl()
+                + "\">Go to site</a></font<br>");
       }
 
       text.append("</font></html>");
@@ -274,9 +272,9 @@ public class DasSourceBrowser
     progressBar.setVisible(true);
     progressBar.setIndeterminate(true);
     // Refresh the source list.
-    dasSources=null;
+    dasSources = null;
     getDASSource();
-    
+
     init();
 
     loadingDasSources = false;
@@ -290,8 +288,8 @@ public class DasSourceBrowser
     {
       for (int i = 0; i < dasSources.length; i++)
       {
-        if (dasSources[i].getNickname().equals(
-            selectedSources.elementAt(r)))
+        if (dasSources[i].getNickname()
+                .equals(selectedSources.elementAt(r)))
         {
           selected.addElement(dasSources[i]);
           break;
@@ -301,8 +299,10 @@ public class DasSourceBrowser
 
     return selected;
   }
+
   /**
    * retrieve das sources from registry and add local source list
+   * 
    * @return
    */
   public DasSource[] getDASSource()
@@ -387,7 +387,7 @@ public class DasSourceBrowser
     {
       int selectedRow = table.getSelectionModel().getMinSelectionIndex();
       nickname = table.getValueAt(selectedRow, 0).toString();
-      url = ( (DasSource) localSources.get(nickname)).getUrl();
+      url = ((DasSource) localSources.get(nickname)).getUrl();
     }
 
     JTextField nametf = new JTextField(nickname, 40);
@@ -404,8 +404,8 @@ public class DasSourceBrowser
     panel.add(pane12, BorderLayout.SOUTH);
 
     int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
-        panel, "Enter Nickname & URL of Local DAS Source",
-        JOptionPane.OK_CANCEL_OPTION);
+            panel, "Enter Nickname & URL of Local DAS Source",
+            JOptionPane.OK_CANCEL_OPTION);
 
     if (reply != JOptionPane.OK_OPTION)
     {
@@ -442,16 +442,16 @@ public class DasSourceBrowser
     {
       if (!newSource && dasSources[i].getNickname().equals(nickname))
       {
-        ( (DasSource) dasSources[i]).setNickname(local.getNickname());
-        ( (DasSource) dasSources[i]).setUrl(local.getUrl());
+        ((DasSource) dasSources[i]).setNickname(local.getNickname());
+        ((DasSource) dasSources[i]).setUrl(local.getUrl());
         data[i][0] = local.getNickname();
         data[i][1] = new Boolean(true);
       }
       else
       {
         data[i][0] = dasSources[i].getNickname();
-        data[i][1] = new Boolean(selectedSources.contains(dasSources[i].
-            getNickname()));
+        data[i][1] = new Boolean(selectedSources.contains(dasSources[i]
+                .getNickname()));
       }
     }
 
@@ -480,8 +480,7 @@ public class DasSourceBrowser
       public void run()
       {
         scrollPane.getVerticalScrollBar().setValue(
-            scrollPane.getVerticalScrollBar().getMaximum()
-            );
+                scrollPane.getVerticalScrollBar().getMaximum());
       }
     });
 
@@ -501,63 +500,58 @@ public class DasSourceBrowser
     if (!localSources.containsKey(nickname))
     {
       JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                            "You can only edit or remove local DAS Sources!",
-                                            "Public DAS source - not editable",
-                                            JOptionPane.WARNING_MESSAGE);
+              "You can only edit or remove local DAS Sources!",
+              "Public DAS source - not editable",
+              JOptionPane.WARNING_MESSAGE);
       return;
     }
 
     Object[] options =
-        {
-        "Edit", "Remove", "Cancel"};
+    { "Edit", "Remove", "Cancel" };
     int choice = JOptionPane.showInternalOptionDialog(Desktop.desktop,
-        "Do you want to edit or remove " + nickname + "?",
-        "Edit / Remove Local DAS Source",
-        JOptionPane.YES_NO_CANCEL_OPTION,
-        JOptionPane.QUESTION_MESSAGE,
-        null,
-        options,
-        options[2]);
+            "Do you want to edit or remove " + nickname + "?",
+            "Edit / Remove Local DAS Source",
+            JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE,
+            null, options, options[2]);
 
     switch (choice)
     {
-      case 0:
-        amendLocal(false);
-        break;
-      case 1:
-        localSources.remove(nickname);
-        selectedSources.remove(nickname);
-        Object[][] data = new Object[dasSources.length - 1][2];
-        DasSource[] tmp = new DasSource[dasSources.length - 1];
-        int index = 0;
-        for (int i = 0; i < dasSources.length; i++)
+    case 0:
+      amendLocal(false);
+      break;
+    case 1:
+      localSources.remove(nickname);
+      selectedSources.remove(nickname);
+      Object[][] data = new Object[dasSources.length - 1][2];
+      DasSource[] tmp = new DasSource[dasSources.length - 1];
+      int index = 0;
+      for (int i = 0; i < dasSources.length; i++)
+      {
+        if (dasSources[i].getNickname().equals(nickname))
+        {
+          continue;
+        }
+        else
         {
-          if (dasSources[i].getNickname().equals(nickname))
-          {
-            continue;
-          }
-          else
-          {
-            tmp[index] = dasSources[i];
-            data[index][0] = dasSources[i].getNickname();
-            data[index][1] = new Boolean(selectedSources.contains(dasSources[i].
-                getNickname()));
-            index++;
-          }
+          tmp[index] = dasSources[i];
+          data[index][0] = dasSources[i].getNickname();
+          data[index][1] = new Boolean(selectedSources
+                  .contains(dasSources[i].getNickname()));
+          index++;
         }
-        dasSources = tmp;
-        refreshTableData(data);
-        SwingUtilities.invokeLater(new Runnable()
+      }
+      dasSources = tmp;
+      refreshTableData(data);
+      SwingUtilities.invokeLater(new Runnable()
+      {
+        public void run()
         {
-          public void run()
-          {
-            scrollPane.getVerticalScrollBar().setValue(
-                scrollPane.getVerticalScrollBar().getMaximum()
-                );
-          }
-        });
+          scrollPane.getVerticalScrollBar().setValue(
+                  scrollPane.getVerticalScrollBar().getMaximum());
+        }
+      });
 
-        break;
+      break;
     }
   }
 
@@ -575,8 +569,8 @@ public class DasSourceBrowser
     for (int i = 0; i < size; i++)
     {
       data[i][0] = dasSources[i].getNickname();
-      data[i][1] = new Boolean(selectedSources.contains(dasSources[i].
-          getNickname()));
+      data[i][1] = new Boolean(selectedSources.contains(dasSources[i]
+              .getNickname()));
     }
 
     DasSource[] tmp = new DasSource[size + lsize];
@@ -594,7 +588,7 @@ public class DasSourceBrowser
       data[index][1] = new Boolean(false);
       tmp[index] = new Das1Source();
       tmp[index].setNickname(key);
-      tmp[index].setUrl( ( (DasSource) localSources.get(key)).getUrl());
+      tmp[index].setUrl(((DasSource) localSources.get(key)).getUrl());
 
       index++;
     }
@@ -606,7 +600,7 @@ public class DasSourceBrowser
 
   public void valueChanged(ListSelectionEvent evt)
   {
-    //Called when the MainTable selection changes
+    // Called when the MainTable selection changes
     if (evt.getValueIsAdjusting())
     {
       return;
@@ -621,12 +615,11 @@ public class DasSourceBrowser
     ArrayList selected = new ArrayList();
     DasSource ds;
 
-    //The features filter is not visible, but we must still
-    //filter the das source list here.
-    //July 2006 - only 6 sources fo not serve features
+    // The features filter is not visible, but we must still
+    // filter the das source list here.
+    // July 2006 - only 6 sources fo not serve features
     Object[] dummyFeatureList = new Object[]
-        {
-        "features"};
+    { "features" };
 
     for (int i = 0; i < dSize; i++)
     {
@@ -634,38 +627,36 @@ public class DasSourceBrowser
       DasCoordinateSystem[] dcs = ds.getCoordinateSystem();
 
       if (dcs.length == 0 && ds.getCapabilities().length == 0
-          && filter1.getSelectedIndex() == 0
-          && filter2.getSelectedIndex() == 0
-          && filter3.getSelectedIndex() == 0)
+              && filter1.getSelectedIndex() == 0
+              && filter2.getSelectedIndex() == 0
+              && filter3.getSelectedIndex() == 0)
       {
-        //THIS IS A FIX FOR LOCAL SOURCES WHICH DO NOT
-        //HAVE COORDINATE SYSTEMS, INFO WHICH AT PRESENT
-        //IS ADDED FROM THE REGISTRY
+        // THIS IS A FIX FOR LOCAL SOURCES WHICH DO NOT
+        // HAVE COORDINATE SYSTEMS, INFO WHICH AT PRESENT
+        // IS ADDED FROM THE REGISTRY
         names.add(ds.getNickname());
-        selected.add(new Boolean(
-            selectedSources.contains(ds.getNickname())));
+        selected
+                .add(new Boolean(selectedSources.contains(ds.getNickname())));
         continue;
       }
 
       if (!selectedInList(dummyFeatureList, ds.getCapabilities())
-          || !selectedInList(filter3.getSelectedValues(),
-                             ds.getLabels()))
+              || !selectedInList(filter3.getSelectedValues(), ds
+                      .getLabels()))
       {
         continue;
       }
 
       for (int j = 0; j < dcs.length; j++)
       {
-        if (selectedInList(filter1.getSelectedValues(),
-                           new String[]
-                           {dcs[j].getName()})
-            && selectedInList(filter2.getSelectedValues(),
-                              new String[]
-                              {dcs[j].getCategory()}))
+        if (selectedInList(filter1.getSelectedValues(), new String[]
+        { dcs[j].getName() })
+                && selectedInList(filter2.getSelectedValues(), new String[]
+                { dcs[j].getCategory() }))
         {
           names.add(ds.getNickname());
-          selected.add(new Boolean(
-              selectedSources.contains(ds.getNickname())));
+          selected.add(new Boolean(selectedSources.contains(ds
+                  .getNickname())));
           break;
         }
       }
@@ -705,7 +696,8 @@ public class DasSourceBrowser
 
   void setSelectedFromProperties()
   {
-    String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE", "uniprot");
+    String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE",
+            "uniprot");
     StringTokenizer st = new StringTokenizer(active, "\t");
     selectedSources = new Vector();
     while (st.hasMoreTokens())
@@ -755,7 +747,7 @@ public class DasSourceBrowser
     StringBuffer sb = new StringBuffer();
     for (int r = 0; r < table.getModel().getRowCount(); r++)
     {
-      if ( ( (Boolean) table.getValueAt(r, 1)).booleanValue())
+      if (((Boolean) table.getValueAt(r, 1)).booleanValue())
       {
         sb.append(table.getValueAt(r, 0) + "\t");
       }
@@ -771,8 +763,7 @@ public class DasSourceBrowser
       {
         String token = en.nextElement().toString();
         sb.append(token + "|"
-                  + ( (DasSource) localSources.get(token)).getUrl()
-                  + "\t");
+                + ((DasSource) localSources.get(token)).getUrl() + "\t");
       }
 
       properties.setProperty("DAS_LOCAL_SOURCE", sb.toString());
@@ -780,8 +771,7 @@ public class DasSourceBrowser
 
   }
 
-  class DASTableModel
-      extends AbstractTableModel
+  class DASTableModel extends AbstractTableModel
   {
 
     public DASTableModel(Object[][] data)
@@ -790,8 +780,7 @@ public class DasSourceBrowser
     }
 
     private String[] columnNames = new String[]
-        {
-        "Nickname", "Use Source"};
+    { "Nickname", "Use Source" };
 
     private Object[][] data;
 
@@ -816,10 +805,9 @@ public class DasSourceBrowser
     }
 
     /*
-     * JTable uses this method to determine the default renderer/
-     * editor for each cell.  If we didn't implement this method,
-     * then the last column would contain text ("true"/"false"),
-     * rather than a check box.
+     * JTable uses this method to determine the default renderer/ editor for
+     * each cell. If we didn't implement this method, then the last column would
+     * contain text ("true"/"false"), rather than a check box.
      */
     public Class getColumnClass(int c)
     {
@@ -827,20 +815,18 @@ public class DasSourceBrowser
     }
 
     /*
-     * Don't need to implement this method unless your table's
-     * editable.
+     * Don't need to implement this method unless your table's editable.
      */
     public boolean isCellEditable(int row, int col)
     {
-      //Note that the data/cell address is constant,
-      //no matter where the cell appears onscreen.
+      // Note that the data/cell address is constant,
+      // no matter where the cell appears onscreen.
       return col == 1;
 
     }
 
     /*
-     * Don't need to implement this method unless your table's
-     * data can change.
+     * Don't need to implement this method unless your table's data can change.
      */
     public void setValueAt(Object value, int row, int col)
     {
@@ -848,7 +834,7 @@ public class DasSourceBrowser
       fireTableCellUpdated(row, col);
 
       String name = getValueAt(row, 0).toString();
-      boolean selected = ( (Boolean) value).booleanValue();
+      boolean selected = ((Boolean) value).booleanValue();
 
       if (selectedSources.contains(name) && !selected)
       {
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 10687cd..9a89b0a 100755
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -33,29 +33,32 @@ import javax.swing.event.MenuListener;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class Desktop
-    extends jalview.jbgui.GDesktop implements DropTargetListener,
-    ClipboardOwner, IProgressIndicator
+public class Desktop extends jalview.jbgui.GDesktop implements
+        DropTargetListener, ClipboardOwner, IProgressIndicator
 {
   /** DOCUMENT ME!! */
   public static Desktop instance;
 
-  //Need to decide if the Memory Usage is to be included in
-  //Next release or not.
+  // Need to decide if the Memory Usage is to be included in
+  // Next release or not.
   public static MyDesktopPane desktop;
-  // public static JDesktopPane desktop;
 
+  // public static JDesktopPane desktop;
 
   static int openFrameCount = 0;
+
   static final int xOffset = 30;
+
   static final int yOffset = 30;
+
   public static jalview.ws.Discoverer discoverer;
 
   public static Object[] jalviewClipboard;
+
   public static boolean internalCopy = false;
 
   static int fileLoadingCount = 0;
@@ -66,18 +69,18 @@ public class Desktop
   public Desktop()
   {
     /**
-     * A note to implementors. It is ESSENTIAL that any 
-     * activities that might block are spawned off as threads rather 
-     * than waited for during this constructor.
+     * A note to implementors. It is ESSENTIAL that any activities that might
+     * block are spawned off as threads rather than waited for during this
+     * constructor.
      */
     instance = this;
     doVamsasClientCheck();
     doGroovyCheck();
 
-
     setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION"));
     setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
-    boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE",false);
+    boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE",
+            false);
     desktop = new MyDesktopPane(selmemusage);
     showMemusage.setSelected(selmemusage);
     desktop.setBackground(Color.white);
@@ -95,15 +98,15 @@ public class Desktop
     String width = jalview.bin.Cache.getProperty("SCREEN_WIDTH");
     String height = jalview.bin.Cache.getProperty("SCREEN_HEIGHT");
 
-    if ( (x != null) && (y != null) && (width != null) && (height != null))
+    if ((x != null) && (y != null) && (width != null) && (height != null))
     {
-      setBounds(Integer.parseInt(x), Integer.parseInt(y),
-                Integer.parseInt(width), Integer.parseInt(height));
+      setBounds(Integer.parseInt(x), Integer.parseInt(y), Integer
+              .parseInt(width), Integer.parseInt(height));
     }
     else
     {
-      setBounds( (int) (screenSize.width - 900) / 2,
-                (int) (screenSize.height - 650) / 2, 900, 650);
+      setBounds((int) (screenSize.width - 900) / 2,
+              (int) (screenSize.height - 650) / 2, 900, 650);
     }
 
     this.addWindowListener(new WindowAdapter()
@@ -115,24 +118,22 @@ public class Desktop
     });
 
     this.addMouseListener(new MouseAdapter()
+    {
+      public void mousePressed(MouseEvent evt)
+      {
+        if (SwingUtilities.isRightMouseButton(evt))
         {
-          public void mousePressed(MouseEvent evt)
-          {
-            if(SwingUtilities.isRightMouseButton(evt))
-            {
-              showPasteMenu(evt.getX(), evt.getY());
-            }
-          }
-        });
-
+          showPasteMenu(evt.getX(), evt.getY());
+        }
+      }
+    });
 
     this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
     // Spawn a thread that shows the splashscreen
-    new SplashScreen();     
-
+    new SplashScreen();
 
-
-    discoverer = new jalview.ws.Discoverer(); // Only gets started if gui is displayed.
+    discoverer = new jalview.ws.Discoverer(); // Only gets started if gui is
+                                              // displayed.
   }
 
   private void doVamsasClientCheck()
@@ -142,14 +143,16 @@ public class Desktop
       setupVamsasDisconnectedGui();
       VamsasMenu.setVisible(true);
       final Desktop us = this;
-      VamsasMenu.addMenuListener(new MenuListener() {
+      VamsasMenu.addMenuListener(new MenuListener()
+      {
         // this listener remembers when the menu was first selected, and
         // doesn't rebuild the session list until it has been cleared and
         // reselected again.
-        boolean refresh=true;
+        boolean refresh = true;
+
         public void menuCanceled(MenuEvent e)
         {
-          refresh=true;
+          refresh = true;
         }
 
         public void menuDeselected(MenuEvent e)
@@ -162,7 +165,7 @@ public class Desktop
           if (refresh)
           {
             us.buildVamsasStMenu();
-            refresh=false;
+            refresh = false;
           }
         }
       });
@@ -196,50 +199,61 @@ public class Desktop
       if (contents != null)
       {
         String file = (String) contents
-            .getTransferData(DataFlavor.stringFlavor);
+                .getTransferData(DataFlavor.stringFlavor);
 
         String format = new IdentifyFile().Identify(file,
-                                                    FormatAdapter.PASTE);
+                FormatAdapter.PASTE);
 
         new FileLoader().LoadFile(file, FormatAdapter.PASTE, format);
 
       }
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
-      System.out.println("Unable to paste alignment from system clipboard:\n"
-                         + ex);
+      System.out
+              .println("Unable to paste alignment from system clipboard:\n"
+                      + ex);
     }
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param frame DOCUMENT ME!
-   * @param title DOCUMENT ME!
-   * @param w DOCUMENT ME!
-   * @param h DOCUMENT ME!
+   * 
+   * @param frame
+   *                DOCUMENT ME!
+   * @param title
+   *                DOCUMENT ME!
+   * @param w
+   *                DOCUMENT ME!
+   * @param h
+   *                DOCUMENT ME!
    */
-  public static synchronized void addInternalFrame(final JInternalFrame frame,
-      String title, int w, int h)
+  public static synchronized void addInternalFrame(
+          final JInternalFrame frame, String title, int w, int h)
   {
     addInternalFrame(frame, title, w, h, true);
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param frame DOCUMENT ME!
-   * @param title DOCUMENT ME!
-   * @param w DOCUMENT ME!
-   * @param h DOCUMENT ME!
-   * @param resizable DOCUMENT ME!
+   * 
+   * @param frame
+   *                DOCUMENT ME!
+   * @param title
+   *                DOCUMENT ME!
+   * @param w
+   *                DOCUMENT ME!
+   * @param h
+   *                DOCUMENT ME!
+   * @param resizable
+   *                DOCUMENT ME!
    */
-  public static synchronized void addInternalFrame(final JInternalFrame frame,
-      String title, int w, int h, boolean resizable)
+  public static synchronized void addInternalFrame(
+          final JInternalFrame frame, String title, int w, int h,
+          boolean resizable)
   {
 
-    // TODO: consider fixing method to update entries in the window submenu with the current window title 
+    // TODO: consider fixing method to update entries in the window submenu with
+    // the current window title
 
     frame.setTitle(title);
     if (frame.getWidth() < 1 || frame.getHeight() < 1)
@@ -249,9 +263,9 @@ public class Desktop
     // THIS IS A PUBLIC STATIC METHOD, SO IT MAY BE CALLED EVEN IN
     // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN
     // IF JALVIEW IS RUNNING HEADLESS
-    /////////////////////////////////////////////////
+    // ///////////////////////////////////////////////
     if (System.getProperty("java.awt.headless") != null
-        && System.getProperty("java.awt.headless").equals("true"))
+            && System.getProperty("java.awt.headless").equals("true"))
     {
       return;
     }
@@ -267,39 +281,39 @@ public class Desktop
 
     if (frame.getX() < 1 && frame.getY() < 1)
     {
-      frame.setLocation(xOffset * openFrameCount,
-                        yOffset * ( (openFrameCount - 1) % 10) + yOffset);
+      frame.setLocation(xOffset * openFrameCount, yOffset
+              * ((openFrameCount - 1) % 10) + yOffset);
     }
 
     final JMenuItem menuItem = new JMenuItem(title);
-    frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
-    {
-      public void internalFrameActivated(javax.swing.event.
-                                         InternalFrameEvent evt)
-      {
-        JInternalFrame itf = desktop.getSelectedFrame();
-        if (itf != null)
-        {
-          itf.requestFocus();
-        }
+    frame
+            .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+            {
+              public void internalFrameActivated(
+                      javax.swing.event.InternalFrameEvent evt)
+              {
+                JInternalFrame itf = desktop.getSelectedFrame();
+                if (itf != null)
+                {
+                  itf.requestFocus();
+                }
 
-      }
+              }
 
-      public void internalFrameClosed(
-          javax.swing.event.InternalFrameEvent evt)
-      {
-        PaintRefresher.RemoveComponent(frame);
-        openFrameCount--;
-        windowMenu.remove(menuItem);
-        JInternalFrame itf = desktop.getSelectedFrame();
-        if (itf != null)
-        {
-          itf.requestFocus();
-        }
-        System.gc();
-      }
-      ;
-    });
+              public void internalFrameClosed(
+                      javax.swing.event.InternalFrameEvent evt)
+              {
+                PaintRefresher.RemoveComponent(frame);
+                openFrameCount--;
+                windowMenu.remove(menuItem);
+                JInternalFrame itf = desktop.getSelectedFrame();
+                if (itf != null)
+                {
+                  itf.requestFocus();
+                }
+                System.gc();
+              };
+            });
 
     menuItem.addActionListener(new ActionListener()
     {
@@ -309,8 +323,7 @@ public class Desktop
         {
           frame.setSelected(true);
           frame.setIcon(false);
-        }
-        catch (java.beans.PropertyVetoException ex)
+        } catch (java.beans.PropertyVetoException ex)
         {
 
         }
@@ -325,9 +338,9 @@ public class Desktop
     {
       frame.setSelected(true);
       frame.requestFocus();
+    } catch (java.beans.PropertyVetoException ve)
+    {
     }
-    catch (java.beans.PropertyVetoException ve)
-    {}
   }
 
   public void lostOwnership(Clipboard clipboard, Transferable contents)
@@ -341,21 +354,26 @@ public class Desktop
   }
 
   public void dragEnter(DropTargetDragEvent evt)
-  {}
+  {
+  }
 
   public void dragExit(DropTargetEvent evt)
-  {}
+  {
+  }
 
   public void dragOver(DropTargetDragEvent evt)
-  {}
+  {
+  }
 
   public void dropActionChanged(DropTargetDragEvent evt)
-  {}
+  {
+  }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
    */
   public void drop(DropTargetDropEvent evt)
   {
@@ -365,13 +383,13 @@ public class Desktop
     try
     {
       DataFlavor uriListFlavor = new DataFlavor(
-          "text/uri-list;class=java.lang.String");
+              "text/uri-list;class=java.lang.String");
       if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
       {
-        //Works on Windows and MacOSX
+        // Works on Windows and MacOSX
         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
-        files = (java.util.List) t.getTransferData(DataFlavor.
-            javaFileListFlavor);
+        files = (java.util.List) t
+                .getTransferData(DataFlavor.javaFileListFlavor);
       }
       else if (t.isDataFlavorSupported(uriListFlavor))
       {
@@ -380,9 +398,7 @@ public class Desktop
         String data = (String) t.getTransferData(uriListFlavor);
         files = new java.util.ArrayList(1);
         for (java.util.StringTokenizer st = new java.util.StringTokenizer(
-            data,
-            "\r\n");
-             st.hasMoreTokens(); )
+                data, "\r\n"); st.hasMoreTokens();)
         {
           String s = st.nextToken();
           if (s.startsWith("#"))
@@ -396,9 +412,9 @@ public class Desktop
           files.add(file);
         }
       }
+    } catch (Exception e)
+    {
     }
-    catch (Exception e)
-    {}
 
     if (files != null)
     {
@@ -417,31 +433,30 @@ public class Desktop
           }
           else
           {
-            format = new IdentifyFile().Identify(file,
-                                                 protocol);
+            format = new IdentifyFile().Identify(file, protocol);
           }
 
           new FileLoader().LoadFile(file, protocol, format);
 
         }
+      } catch (Exception ex)
+      {
       }
-      catch (Exception ex)
-      {}
     }
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
   {
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-        getProperty(
-            "LAST_DIRECTORY"),
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+            .getProperty("LAST_DIRECTORY"),
             jalview.io.AppletFormatAdapter.READABLE_EXTENSIONS,
-            jalview.io.AppletFormatAdapter.READABLE_FNAMES, 
+            jalview.io.AppletFormatAdapter.READABLE_FNAMES,
             jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
 
     chooser.setFileView(new JalviewFileView());
@@ -453,8 +468,8 @@ public class Desktop
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       String choice = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-                                    chooser.getSelectedFile().getParent());
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+              .getSelectedFile().getParent());
 
       String format = null;
       if (chooser.getSelectedFormat().equals("Jalview"))
@@ -468,7 +483,8 @@ public class Desktop
 
       if (viewport != null)
       {
-        new FileLoader().LoadFile(viewport, choice, FormatAdapter.FILE, format);
+        new FileLoader().LoadFile(viewport, choice, FormatAdapter.FILE,
+                format);
       }
       else
       {
@@ -479,8 +495,9 @@ public class Desktop
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void inputURLMenuItem_actionPerformed(AlignViewport viewport)
   {
@@ -510,9 +527,8 @@ public class Desktop
       }
     }
 
-    int reply = JOptionPane.showInternalConfirmDialog(desktop,
-        panel, "Input Alignment From URL",
-        JOptionPane.OK_CANCEL_OPTION);
+    int reply = JOptionPane.showInternalConfirmDialog(desktop, panel,
+            "Input Alignment From URL", JOptionPane.OK_CANCEL_OPTION);
 
     if (reply != JOptionPane.OK_OPTION)
     {
@@ -525,7 +541,8 @@ public class Desktop
     {
       if (viewport != null)
       {
-        new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, "Jalview");
+        new FileLoader().LoadFile(viewport, url, FormatAdapter.URL,
+                "Jalview");
       }
       else
       {
@@ -539,9 +556,8 @@ public class Desktop
       if (format.equals("URL NOT FOUND"))
       {
         JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                              "Couldn't locate " + url,
-                                              "URL not found",
-                                              JOptionPane.WARNING_MESSAGE);
+                "Couldn't locate " + url, "URL not found",
+                JOptionPane.WARNING_MESSAGE);
 
         return;
       }
@@ -559,8 +575,9 @@ public class Desktop
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void inputTextboxMenuItem_actionPerformed(AlignViewport viewport)
   {
@@ -583,47 +600,45 @@ public class Desktop
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void aboutMenuItem_actionPerformed(ActionEvent e)
   {
-    StringBuffer message = new StringBuffer("Jalview version " +
-                                            jalview.bin.Cache.getProperty(
-                                                "VERSION") +
-                                            "; last updated: " +
-                                            jalview.bin.
-                                            Cache.getDefault("BUILD_DATE",
-        "unknown"));
+    StringBuffer message = new StringBuffer("Jalview version "
+            + jalview.bin.Cache.getProperty("VERSION") + "; last updated: "
+            + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
 
     if (!jalview.bin.Cache.getProperty("LATEST_VERSION").equals(
-        jalview.bin.Cache.getProperty("VERSION")))
+            jalview.bin.Cache.getProperty("VERSION")))
     {
-      message.append("\n\n!! Jalview version "
-                     + jalview.bin.Cache.getProperty("LATEST_VERSION")
-                     +
-          " is available for download from http://www.jalview.org !!\n");
+      message
+              .append("\n\n!! Jalview version "
+                      + jalview.bin.Cache.getProperty("LATEST_VERSION")
+                      + " is available for download from http://www.jalview.org !!\n");
 
     }
-
-    message.append("\nAuthors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton." +
-                   "\nDevelopment managed by The Barton Group, University of Dundee.\n"+
-                   "\nFor specific issues relating to Jalview, email help@jalview.org\n"+
-                   " or join the jalview-discuss@jalview.org mailing list" +
-                   "\n\nIf  you use Jalview, please cite:" +
-                   "\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"" +
-                   "\nBioinformatics,  2004 20;426-7.");
+    // TODO: update this text for each release or centrally store it for lite
+    // and application
+    message
+            .append("\nAuthors:  Andrew Waterhouse, Jim Procter, Michele Clamp, James Cuff, Steve Searle,\n    David Martin & Geoff Barton."
+                    + "\nDevelopment managed by The Barton Group, University of Dundee, Scotland, UK.\n"
+                    + "\nFor help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list\n"
+                    + "\nIf  you use Jalview, please cite:"
+                    + "\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\""
+                    + "\nBioinformatics,  2004 20;426-7.");
 
     JOptionPane.showInternalMessageDialog(Desktop.desktop,
 
-                                          message.toString(), "About Jalview",
-                                          JOptionPane.INFORMATION_MESSAGE);
+    message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE);
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void documentationMenuItem_actionPerformed(ActionEvent e)
   {
@@ -636,9 +651,9 @@ public class Desktop
       javax.help.HelpBroker hb = hs.createHelpBroker();
       hb.setCurrentID("home");
       hb.setDisplayed(true);
+    } catch (Exception ex)
+    {
     }
-    catch (Exception ex)
-    {}
   }
 
   public void closeAll_actionPerformed(ActionEvent e)
@@ -649,9 +664,9 @@ public class Desktop
       try
       {
         frames[i].setClosed(true);
+      } catch (java.beans.PropertyVetoException ex)
+      {
       }
-      catch (java.beans.PropertyVetoException ex)
-      {}
     }
     System.out.println("ALL CLOSED");
 
@@ -672,7 +687,9 @@ public class Desktop
     reorderAssociatedWindows(false, true);
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.jbgui.GDesktop#garbageCollect_actionPerformed(java.awt.event.ActionEvent)
    */
   protected void garbageCollect_actionPerformed(ActionEvent e)
@@ -683,7 +700,9 @@ public class Desktop
     jalview.bin.Cache.log.debug("Finished garbage collection.");
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event.ActionEvent)
    */
   protected void showMemusage_actionPerformed(ActionEvent e)
@@ -702,19 +721,19 @@ public class Desktop
     AlignViewport source = null, target = null;
     if (frames[0] instanceof AlignFrame)
     {
-      source = ( (AlignFrame) frames[0]).getCurrentView();
+      source = ((AlignFrame) frames[0]).getCurrentView();
     }
     else if (frames[0] instanceof TreePanel)
     {
-      source = ( (TreePanel) frames[0]).getViewPort();
+      source = ((TreePanel) frames[0]).getViewPort();
     }
     else if (frames[0] instanceof PCAPanel)
     {
-      source = ( (PCAPanel) frames[0]).av;
+      source = ((PCAPanel) frames[0]).av;
     }
     else if (frames[0].getContentPane() instanceof PairwiseAlignPanel)
     {
-      source = ( (PairwiseAlignPanel) frames[0].getContentPane()).av;
+      source = ((PairwiseAlignPanel) frames[0].getContentPane()).av;
     }
 
     if (source != null)
@@ -728,19 +747,19 @@ public class Desktop
         }
         if (frames[i] instanceof AlignFrame)
         {
-          target = ( (AlignFrame) frames[i]).getCurrentView();
+          target = ((AlignFrame) frames[i]).getCurrentView();
         }
         else if (frames[i] instanceof TreePanel)
         {
-          target = ( (TreePanel) frames[i]).getViewPort();
+          target = ((TreePanel) frames[i]).getViewPort();
         }
         else if (frames[i] instanceof PCAPanel)
         {
-          target = ( (PCAPanel) frames[i]).av;
+          target = ((PCAPanel) frames[i]).av;
         }
         else if (frames[i].getContentPane() instanceof PairwiseAlignPanel)
         {
-          target = ( (PairwiseAlignPanel) frames[i].getContentPane()).av;
+          target = ((PairwiseAlignPanel) frames[i].getContentPane()).av;
         }
 
         if (source == target)
@@ -760,17 +779,19 @@ public class Desktop
               }
             }
 
+          } catch (java.beans.PropertyVetoException ex)
+          {
           }
-          catch (java.beans.PropertyVetoException ex)
-          {}
         }
       }
     }
   }
+
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void preferences_actionPerformed(ActionEvent e)
   {
@@ -779,17 +800,16 @@ public class Desktop
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void saveState_actionPerformed(ActionEvent e)
   {
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-        getProperty(
-            "LAST_DIRECTORY"), new String[]
-        {"jar"},
-        new String[]
-        {"Jalview Project"}, "Jalview Project");
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+            .getProperty("LAST_DIRECTORY"), new String[]
+    { "jar" }, new String[]
+    { "Jalview Project" }, "Jalview Project");
 
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle("Save State");
@@ -806,17 +826,16 @@ public class Desktop
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void loadState_actionPerformed(ActionEvent e)
   {
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-        getProperty(
-            "LAST_DIRECTORY"), new String[]
-        {"jar"},
-        new String[]
-        {"Jalview Project"}, "Jalview Project");
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+            .getProperty("LAST_DIRECTORY"), new String[]
+    { "jar" }, new String[]
+    { "Jalview Project" }, "Jalview Project");
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle("Restore state");
 
@@ -825,8 +844,8 @@ public class Desktop
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       String choice = chooser.getSelectedFile().getAbsolutePath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-                                    chooser.getSelectedFile().getParent());
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+              .getSelectedFile().getParent());
       new Jalview2XML().LoadJalviewAlign(choice);
     }
   }
@@ -843,22 +862,22 @@ public class Desktop
     if (fileLoadingCount == 0)
     {
       addProgressPanel("Loading File: " + fileName + "   ");
-      
+
     }
     fileLoadingCount++;
   }
+
   private JProgressBar addProgressPanel(String string)
   {
-    if (progressPanel==null)
+    if (progressPanel == null)
     {
       progressPanel = new JPanel(new BorderLayout());
-      totalProgressCount=0;
+      totalProgressCount = 0;
     }
     JProgressBar progressBar = new JProgressBar();
     progressBar.setIndeterminate(true);
 
-    progressPanel.add(new JLabel(string),
-                      BorderLayout.WEST);
+    progressPanel.add(new JLabel(string), BorderLayout.WEST);
 
     progressPanel.add(progressBar, BorderLayout.CENTER);
 
@@ -867,13 +886,15 @@ public class Desktop
     validate();
     return progressBar;
   }
-  int totalProgressCount=0;
+
+  int totalProgressCount = 0;
+
   private void removeProgressPanel(JProgressBar progbar)
   {
-    if (progressPanel!=null)
+    if (progressPanel != null)
     {
       progressPanel.remove(progbar);
-      if (--totalProgressCount<1)
+      if (--totalProgressCount < 1)
       {
         this.getContentPane().remove(progressPanel);
         progressPanel = null;
@@ -881,6 +902,7 @@ public class Desktop
     }
     validate();
   }
+
   public void stopLoading()
   {
     fileLoadingCount--;
@@ -895,6 +917,7 @@ public class Desktop
     }
     validate();
   }
+
   public static int getViewCount(String viewId)
   {
     int count = 0;
@@ -906,10 +929,9 @@ public class Desktop
         AlignFrame af = (AlignFrame) frames[t];
         for (int a = 0; a < af.alignPanels.size(); a++)
         {
-          if (viewId.equals(
-              ( (AlignmentPanel) af.alignPanels.elementAt(a)).av.
-              getSequenceSetId())
-              )
+          if (viewId
+                  .equals(((AlignmentPanel) af.alignPanels.elementAt(a)).av
+                          .getSequenceSetId()))
           {
             count++;
           }
@@ -932,17 +954,16 @@ public class Desktop
     {
       AlignmentPanel ap = (AlignmentPanel) af.alignPanels.elementAt(i);
       AlignFrame newaf = new AlignFrame(ap);
-      if (ap.av.explodedPosition != null &&
-          !ap.av.explodedPosition.equals(af.getBounds()))
+      if (ap.av.explodedPosition != null
+              && !ap.av.explodedPosition.equals(af.getBounds()))
       {
         newaf.setBounds(ap.av.explodedPosition);
       }
 
       ap.av.gatherViewsHere = false;
 
-      addInternalFrame(newaf, af.getTitle(),
-                       AlignFrame.DEFAULT_WIDTH,
-                       AlignFrame.DEFAULT_HEIGHT);
+      addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH,
+              AlignFrame.DEFAULT_HEIGHT);
     }
 
     af.alignPanels.clear();
@@ -986,35 +1007,43 @@ public class Desktop
   }
 
   jalview.gui.VamsasApplication v_client = null;
+
   public void vamsasImport_actionPerformed(ActionEvent e)
   {
-    if (v_client==null)
+    if (v_client == null)
     {
       // Load and try to start a session.
-      JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-          getProperty("LAST_DIRECTORY"));
+      JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+              .getProperty("LAST_DIRECTORY"));
 
       chooser.setFileView(new JalviewFileView());
       chooser.setDialogTitle("Open a saved VAMSAS session");
-      chooser.setToolTipText("select a vamsas session to be opened as a new vamsas session.");
+      chooser
+              .setToolTipText("select a vamsas session to be opened as a new vamsas session.");
 
       int value = chooser.showOpenDialog(this);
 
       if (value == JalviewFileChooser.APPROVE_OPTION)
       {
-        try {
-          v_client = new jalview.gui.VamsasApplication(this,
-                                                chooser.getSelectedFile());
+        try
+        {
+          v_client = new jalview.gui.VamsasApplication(this, chooser
+                  .getSelectedFile());
         } catch (Exception ex)
         {
-          jalview.bin.Cache.log.error("New vamsas session from existing session file failed:",ex);
+          jalview.bin.Cache.log.error(
+                  "New vamsas session from existing session file failed:",
+                  ex);
           return;
         }
         setupVamsasConnectedGui();
         v_client.initial_update(); // TODO: thread ?
       }
-    }else {
-      jalview.bin.Cache.log.error("Implementation error - load session from a running session is not supported.");
+    }
+    else
+    {
+      jalview.bin.Cache.log
+              .error("Implementation error - load session from a running session is not supported.");
     }
   }
 
@@ -1025,21 +1054,19 @@ public class Desktop
       // Start a session.
       // we just start a default session for moment.
       /*
-      JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-          getProperty("LAST_DIRECTORY"));
-
-      chooser.setFileView(new JalviewFileView());
-      chooser.setDialogTitle("Load Vamsas file");
-      chooser.setToolTipText("Import");
-
-      int value = chooser.showOpenDialog(this);
-
-      if (value == JalviewFileChooser.APPROVE_OPTION)
-      {
-        v_client = new jalview.gui.VamsasApplication(this,
-                                                chooser.getSelectedFile());
-                                                *
-                                                */
+       * JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+       * getProperty("LAST_DIRECTORY"));
+       * 
+       * chooser.setFileView(new JalviewFileView());
+       * chooser.setDialogTitle("Load Vamsas file");
+       * chooser.setToolTipText("Import");
+       * 
+       * int value = chooser.showOpenDialog(this);
+       * 
+       * if (value == JalviewFileChooser.APPROVE_OPTION) { v_client = new
+       * jalview.gui.VamsasApplication(this, chooser.getSelectedFile());
+       * 
+       */
       v_client = new VamsasApplication(this);
       setupVamsasConnectedGui();
       v_client.initial_update(); // TODO: thread ?
@@ -1056,8 +1083,10 @@ public class Desktop
     vamsasStart.setText("Session Update");
     vamsasSave.setVisible(true);
     vamsasStop.setVisible(true);
-    vamsasImport.setVisible(false); // Document import to existing session is not possible for vamsas-client-1.0.
+    vamsasImport.setVisible(false); // Document import to existing session is
+                                    // not possible for vamsas-client-1.0.
   }
+
   protected void setupVamsasDisconnectedGui()
   {
     vamsasSave.setVisible(false);
@@ -1075,6 +1104,7 @@ public class Desktop
       setupVamsasDisconnectedGui();
     }
   }
+
   protected void buildVamsasStMenu()
   {
     if (v_client == null)
@@ -1108,7 +1138,8 @@ public class Desktop
             {
               if (dsktp.v_client == null)
               {
-                Thread rthr = new Thread(new Runnable() {
+                Thread rthr = new Thread(new Runnable()
+                {
 
                   public void run()
                   {
@@ -1116,7 +1147,7 @@ public class Desktop
                     dsktp.setupVamsasConnectedGui();
                     dsktp.v_client.initial_update();
                   }
-                  
+
                 });
                 rthr.start();
               }
@@ -1125,8 +1156,8 @@ public class Desktop
           VamsasStMenu.add(sessit);
         }
         // don't show an empty menu.
-        VamsasStMenu.setVisible(sess.length>0);
-        
+        VamsasStMenu.setVisible(sess.length > 0);
+
       }
       else
       {
@@ -1134,71 +1165,77 @@ public class Desktop
         VamsasStMenu.removeAll();
         VamsasStMenu.setVisible(false);
       }
-    } else {
+    }
+    else
+    {
       // Not interested in the content. Just hide ourselves.
       VamsasStMenu.setVisible(false);
     }
   }
+
   public void vamsasSave_actionPerformed(ActionEvent e)
   {
     if (v_client != null)
     {
-      JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-            getProperty(
-                "LAST_DIRECTORY"), new String[]
-            {"vdj"}, // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
-            new String[]
-            {"Vamsas Document"}, "Vamsas Document");
+      JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+              .getProperty("LAST_DIRECTORY"), new String[]
+      { "vdj" }, // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
+              new String[]
+              { "Vamsas Document" }, "Vamsas Document");
 
-        chooser.setFileView(new JalviewFileView());
-        chooser.setDialogTitle("Save Vamsas Document Archive");
+      chooser.setFileView(new JalviewFileView());
+      chooser.setDialogTitle("Save Vamsas Document Archive");
 
-        int value = chooser.showSaveDialog(this);
+      int value = chooser.showSaveDialog(this);
 
-        if (value == JalviewFileChooser.APPROVE_OPTION)
+      if (value == JalviewFileChooser.APPROVE_OPTION)
+      {
+        java.io.File choice = chooser.getSelectedFile();
+        jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
+        String warnmsg = null;
+        String warnttl = null;
+        try
         {
-          java.io.File choice = chooser.getSelectedFile();
-          jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
-          String warnmsg=null;
-          String warnttl=null;
-          try {
-            v_client.vclient.storeDocument(choice);
-          }
-          catch (Error ex)
-          {
-            warnttl = "Serious Problem saving Vamsas Document";
-            warnmsg = ex.toString();
-            jalview.bin.Cache.log.error("Error Whilst saving document to "+choice,ex);
-            
-          }
-          catch (Exception ex)
-          {
-            warnttl = "Problem saving Vamsas Document.";
-            warnmsg = ex.toString();
-            jalview.bin.Cache.log.warn("Exception Whilst saving document to "+choice,ex);
-            
-          }
-          if (warnmsg!=null)
-          {
-            JOptionPane.showInternalMessageDialog(Desktop.desktop,
+          v_client.vclient.storeDocument(choice);
+        } catch (Error ex)
+        {
+          warnttl = "Serious Problem saving Vamsas Document";
+          warnmsg = ex.toString();
+          jalview.bin.Cache.log.error("Error Whilst saving document to "
+                  + choice, ex);
 
-                  warnmsg, warnttl,
-                  JOptionPane.ERROR_MESSAGE);
-          }
+        } catch (Exception ex)
+        {
+          warnttl = "Problem saving Vamsas Document.";
+          warnmsg = ex.toString();
+          jalview.bin.Cache.log.warn("Exception Whilst saving document to "
+                  + choice, ex);
+
+        }
+        if (warnmsg != null)
+        {
+          JOptionPane.showInternalMessageDialog(Desktop.desktop,
+
+          warnmsg, warnttl, JOptionPane.ERROR_MESSAGE);
         }
+      }
     }
   }
+
   JProgressBar vamUpdate = null;
+
   /**
    * hide vamsas user gui bits when a vamsas document event is being handled.
-   * @param b true to hide gui, false to reveal gui
+   * 
+   * @param b
+   *                true to hide gui, false to reveal gui
    */
   public void setVamsasUpdate(boolean b)
   {
-    jalview.bin.Cache.log.debug("Setting gui for Vamsas update " +
-                                (b ? "in progress" : "finished"));
-    
-    if (vamUpdate!=null)
+    jalview.bin.Cache.log.debug("Setting gui for Vamsas update "
+            + (b ? "in progress" : "finished"));
+
+    if (vamUpdate != null)
     {
       this.removeProgressPanel(vamUpdate);
     }
@@ -1216,32 +1253,37 @@ public class Desktop
     return desktop.getAllFrames();
   }
 
-
   /**
-   * Checks the given url to see if it gives a response indicating that
-   * the user should be informed of a new questionnaire.
+   * Checks the given url to see if it gives a response indicating that the user
+   * should be informed of a new questionnaire.
+   * 
    * @param url
    */
   public void checkForQuestionnaire(String url)
   {
     UserQuestionnaireCheck jvq = new UserQuestionnaireCheck(url);
-    //javax.swing.SwingUtilities.invokeLater(jvq);
+    // javax.swing.SwingUtilities.invokeLater(jvq);
     new Thread(jvq).start();
   }
+
   /**
-   * Proxy class for JDesktopPane which optionally 
-   * displays the current memory usage and highlights 
-   * the desktop area with a red bar if free memory runs low.
+   * Proxy class for JDesktopPane which optionally displays the current memory
+   * usage and highlights the desktop area with a red bar if free memory runs
+   * low.
+   * 
    * @author AMW
    */
-  public class  MyDesktopPane extends JDesktopPane implements Runnable
+  public class MyDesktopPane extends JDesktopPane implements Runnable
   {
-    
+
     boolean showMemoryUsage = false;
+
     Runtime runtime;
+
     java.text.NumberFormat df;
 
-    float maxMemory, allocatedMemory, freeMemory, totalFreeMemory, percentUsage;
+    float maxMemory, allocatedMemory, freeMemory, totalFreeMemory,
+            percentUsage;
 
     public MyDesktopPane(boolean showMemoryUsage)
     {
@@ -1257,10 +1299,12 @@ public class Desktop
         worker.start();
       }
     }
+
     public boolean isShowMemoryUsage()
     {
       return showMemoryUsage;
     }
+
     public void run()
     {
       df = java.text.NumberFormat.getNumberInstance();
@@ -1279,15 +1323,15 @@ public class Desktop
 
           percentUsage = (totalFreeMemory / maxMemory) * 100;
 
-        //  if (percentUsage < 20)
+          // if (percentUsage < 20)
           {
-            //   border1 = BorderFactory.createMatteBorder(12, 12, 12, 12, Color.red);
-            //    instance.set.setBorder(border1);
+            // border1 = BorderFactory.createMatteBorder(12, 12, 12, 12,
+            // Color.red);
+            // instance.set.setBorder(border1);
           }
           repaint();
 
-        }
-        catch (Exception ex)
+        } catch (Exception ex)
         {
           ex.printStackTrace();
         }
@@ -1296,124 +1340,142 @@ public class Desktop
 
     public void paintComponent(Graphics g)
     {
-      if(showMemoryUsage)
+      if (showMemoryUsage)
       {
         if (percentUsage < 20)
           g.setColor(Color.red);
 
         g.drawString("Total Free Memory: " + df.format(totalFreeMemory)
-                     + "MB; Max Memory: " + df.format(maxMemory)
-                     + "MB; " + df.format(percentUsage) + "%", 10,
-                     getHeight() - g.getFontMetrics().getHeight());
+                + "MB; Max Memory: " + df.format(maxMemory) + "MB; "
+                + df.format(percentUsage) + "%", 10, getHeight()
+                - g.getFontMetrics().getHeight());
       }
     }
 
-    
-    
   }
+
   protected JMenuItem groovyShell;
-  public void doGroovyCheck() {
+
+  public void doGroovyCheck()
+  {
     if (jalview.bin.Cache.groovyJarsPresent())
     {
       groovyShell = new JMenuItem();
       groovyShell.setText("Groovy Console...");
       groovyShell.addActionListener(new ActionListener()
       {
-          public void actionPerformed(ActionEvent e) {
-              groovyShell_actionPerformed(e);
-          }
+        public void actionPerformed(ActionEvent e)
+        {
+          groovyShell_actionPerformed(e);
+        }
       });
       toolsMenu.add(groovyShell);
       groovyShell.setVisible(true);
     }
   }
+
   /**
-   * Accessor method to quickly get all the AlignmentFrames
-   * loaded.
+   * Accessor method to quickly get all the AlignmentFrames loaded.
    */
-  public static AlignFrame[] getAlignframes() {
+  public static AlignFrame[] getAlignframes()
+  {
     JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 
     if (frames == null)
     {
       return null;
-      }
-      Vector avp=new Vector();
-      try
-      {
-          //REVERSE ORDER
-          for (int i = frames.length - 1; i > -1; i--)
-          {
-              if (frames[i] instanceof AlignFrame)
-              {
-                  AlignFrame af = (AlignFrame) frames[i];
-                  avp.addElement(af);
-              }
-          }
-      }
-      catch (Exception ex)
-      {
-          ex.printStackTrace();
-      }
-      if (avp.size()==0)
+    }
+    Vector avp = new Vector();
+    try
+    {
+      // REVERSE ORDER
+      for (int i = frames.length - 1; i > -1; i--)
       {
-          return null;
-      }
-      AlignFrame afs[] = new AlignFrame[avp.size()];
-      for (int i=0,j=avp.size(); i<j; i++) {
-          afs[i] = (AlignFrame) avp.elementAt(i);
+        if (frames[i] instanceof AlignFrame)
+        {
+          AlignFrame af = (AlignFrame) frames[i];
+          avp.addElement(af);
+        }
       }
-      avp.clear();
-      return afs;
+    } catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+    if (avp.size() == 0)
+    {
+      return null;
+    }
+    AlignFrame afs[] = new AlignFrame[avp.size()];
+    for (int i = 0, j = avp.size(); i < j; i++)
+    {
+      afs[i] = (AlignFrame) avp.elementAt(i);
+    }
+    avp.clear();
+    return afs;
   }
 
   /**
-    * Add Groovy Support to Jalview
-    */
-  public void groovyShell_actionPerformed(ActionEvent e) {
+   * Add Groovy Support to Jalview
+   */
+  public void groovyShell_actionPerformed(ActionEvent e)
+  {
     // use reflection to avoid creating compilation dependency.
     if (!jalview.bin.Cache.groovyJarsPresent())
     {
-      throw new Error("Implementation Error. Cannot create groovyShell without Groovy on the classpath!");
-    }
-    try {
-    Class gcClass = Desktop.class.getClassLoader().loadClass("groovy.ui.Console");
-    Constructor gccons = gcClass.getConstructor(null);
-    java.lang.reflect.Method setvar = gcClass.getMethod("setVariable", new Class[] { String.class, Object.class} );
-    java.lang.reflect.Method run = gcClass.getMethod("run", null);
-    Object gc = gccons.newInstance(null);
-    setvar.invoke(gc, new Object[] { "Jalview", this});
-    run.invoke(gc, null);
+      throw new Error(
+              "Implementation Error. Cannot create groovyShell without Groovy on the classpath!");
     }
-    catch (Exception ex)
+    try
     {
-      jalview.bin.Cache.log.error("Groovy Shell Creation failed.",ex);
-      JOptionPane.showInternalMessageDialog(Desktop.desktop,
-
-              "Couldn't create the groovy Shell. Check the error log for the details of what went wrong.", "Jalview Groovy Support Failed",
-              JOptionPane.ERROR_MESSAGE);
+      Class gcClass = Desktop.class.getClassLoader().loadClass(
+              "groovy.ui.Console");
+      Constructor gccons = gcClass.getConstructor(null);
+      java.lang.reflect.Method setvar = gcClass.getMethod("setVariable",
+              new Class[]
+              { String.class, Object.class });
+      java.lang.reflect.Method run = gcClass.getMethod("run", null);
+      Object gc = gccons.newInstance(null);
+      setvar.invoke(gc, new Object[]
+      { "Jalview", this });
+      run.invoke(gc, null);
+    } catch (Exception ex)
+    {
+      jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex);
+      JOptionPane
+              .showInternalMessageDialog(
+                      Desktop.desktop,
+
+                      "Couldn't create the groovy Shell. Check the error log for the details of what went wrong.",
+                      "Jalview Groovy Support Failed",
+                      JOptionPane.ERROR_MESSAGE);
     }
   }
 
   /**
-   *  Progress bars managed by the IProgressIndicator method.
+   * Progress bars managed by the IProgressIndicator method.
    */
   private Hashtable progressBars;
-  /* (non-Javadoc)
+
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
    */
   public void setProgressBar(String message, long id)
   {
-    if(progressBars == null)
+    if (progressBars == null)
     {
       progressBars = new Hashtable();
     }
 
-    if(progressBars.get( new Long(id) )!=null)
+    if (progressBars.get(new Long(id)) != null)
+    {
+      JProgressBar progressPanel = (JProgressBar) progressBars
+              .remove(new Long(id));
+      removeProgressPanel(progressPanel);
+    }
+    else
     {
-      JProgressBar progressPanel = (JProgressBar)progressBars.remove( new Long(id) );
-       removeProgressPanel(progressPanel);
-    } else {
       progressBars.put(new Long(id), addProgressPanel(message));
     }
   }
diff --git a/src/jalview/gui/EPSOptions.java b/src/jalview/gui/EPSOptions.java
index dc7b650..193cfcc 100755
--- a/src/jalview/gui/EPSOptions.java
+++ b/src/jalview/gui/EPSOptions.java
@@ -1,143 +1,149 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.gui;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-public class EPSOptions
-    extends JPanel
-{
-  JDialog dialog;
-  public boolean cancelled = false;
-  String value;
-
-  public EPSOptions()
-  {
-    try
-    {
-      jbInit();
-    }
-    catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
-
-    ButtonGroup bg = new ButtonGroup();
-    bg.add(lineart);
-    bg.add(text);
-
-    JOptionPane pane = new JOptionPane(null,
-                                       JOptionPane.DEFAULT_OPTION,
-                                       JOptionPane.DEFAULT_OPTION,
-                                       null, new Object[]
-                                       {this});
-
-    dialog = pane.createDialog(Desktop.desktop, "EPS Rendering options");
-    dialog.setVisible(true);
-
-  }
-
-  private void jbInit()
-      throws Exception
-  {
-    lineart.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    lineart.setText("Lineart");
-    text.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    text.setText("Text");
-    text.setSelected(true);
-    askAgain.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    askAgain.setText("Don\'t ask me again");
-    ok.setText("OK");
-    ok.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        ok_actionPerformed(e);
-      }
-    });
-    cancel.setText("Cancel");
-    cancel.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        cancel_actionPerformed(e);
-      }
-    });
-    jLabel1.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    jLabel1.setText("Select EPS character rendering style");
-    this.setLayout(borderLayout1);
-    jPanel3.setBorder(BorderFactory.createEtchedBorder());
-    jPanel2.add(text);
-    jPanel2.add(lineart);
-    jPanel2.add(askAgain);
-    jPanel1.add(ok);
-    jPanel1.add(cancel);
-    jPanel3.add(jLabel1);
-    jPanel3.add(jPanel2);
-    this.add(jPanel3, java.awt.BorderLayout.CENTER);
-    this.add(jPanel1, java.awt.BorderLayout.SOUTH);
-  }
-
-  JRadioButton lineart = new JRadioButton();
-  JRadioButton text = new JRadioButton();
-  JCheckBox askAgain = new JCheckBox();
-  JButton ok = new JButton();
-  JButton cancel = new JButton();
-  JPanel jPanel1 = new JPanel();
-  JLabel jLabel1 = new JLabel();
-  JPanel jPanel2 = new JPanel();
-  JPanel jPanel3 = new JPanel();
-  BorderLayout borderLayout1 = new BorderLayout();
-
-  public void ok_actionPerformed(ActionEvent e)
-  {
-    if (lineart.isSelected())
-    {
-      value = "Lineart";
-    }
-    else
-    {
-      value = "Text";
-    }
-
-    if (!askAgain.isSelected())
-    {
-      jalview.bin.Cache.applicationProperties.remove("EPS_RENDERING");
-    }
-    else
-    {
-      jalview.bin.Cache.setProperty("EPS_RENDERING", value);
-    }
-
-    dialog.setVisible(false);
-  }
-
-  public void cancel_actionPerformed(ActionEvent e)
-  {
-    cancelled = true;
-    dialog.setVisible(false);
-  }
-
-  public String getValue()
-  {
-    return value;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.gui;
+
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+
+public class EPSOptions extends JPanel
+{
+  JDialog dialog;
+
+  public boolean cancelled = false;
+
+  String value;
+
+  public EPSOptions()
+  {
+    try
+    {
+      jbInit();
+    } catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+
+    ButtonGroup bg = new ButtonGroup();
+    bg.add(lineart);
+    bg.add(text);
+
+    JOptionPane pane = new JOptionPane(null, JOptionPane.DEFAULT_OPTION,
+            JOptionPane.DEFAULT_OPTION, null, new Object[]
+            { this });
+
+    dialog = pane.createDialog(Desktop.desktop, "EPS Rendering options");
+    dialog.setVisible(true);
+
+  }
+
+  private void jbInit() throws Exception
+  {
+    lineart.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    lineart.setText("Lineart");
+    text.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    text.setText("Text");
+    text.setSelected(true);
+    askAgain.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    askAgain.setText("Don\'t ask me again");
+    ok.setText("OK");
+    ok.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        ok_actionPerformed(e);
+      }
+    });
+    cancel.setText("Cancel");
+    cancel.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        cancel_actionPerformed(e);
+      }
+    });
+    jLabel1.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    jLabel1.setText("Select EPS character rendering style");
+    this.setLayout(borderLayout1);
+    jPanel3.setBorder(BorderFactory.createEtchedBorder());
+    jPanel2.add(text);
+    jPanel2.add(lineart);
+    jPanel2.add(askAgain);
+    jPanel1.add(ok);
+    jPanel1.add(cancel);
+    jPanel3.add(jLabel1);
+    jPanel3.add(jPanel2);
+    this.add(jPanel3, java.awt.BorderLayout.CENTER);
+    this.add(jPanel1, java.awt.BorderLayout.SOUTH);
+  }
+
+  JRadioButton lineart = new JRadioButton();
+
+  JRadioButton text = new JRadioButton();
+
+  JCheckBox askAgain = new JCheckBox();
+
+  JButton ok = new JButton();
+
+  JButton cancel = new JButton();
+
+  JPanel jPanel1 = new JPanel();
+
+  JLabel jLabel1 = new JLabel();
+
+  JPanel jPanel2 = new JPanel();
+
+  JPanel jPanel3 = new JPanel();
+
+  BorderLayout borderLayout1 = new BorderLayout();
+
+  public void ok_actionPerformed(ActionEvent e)
+  {
+    if (lineart.isSelected())
+    {
+      value = "Lineart";
+    }
+    else
+    {
+      value = "Text";
+    }
+
+    if (!askAgain.isSelected())
+    {
+      jalview.bin.Cache.applicationProperties.remove("EPS_RENDERING");
+    }
+    else
+    {
+      jalview.bin.Cache.setProperty("EPS_RENDERING", value);
+    }
+
+    dialog.setVisible(false);
+  }
+
+  public void cancel_actionPerformed(ActionEvent e)
+  {
+    cancelled = true;
+    dialog.setVisible(false);
+  }
+
+  public String getValue()
+  {
+    return value;
+  }
+}
diff --git a/src/jalview/gui/EditNameDialog.java b/src/jalview/gui/EditNameDialog.java
index a3d2d47..cf11803 100644
--- a/src/jalview/gui/EditNameDialog.java
+++ b/src/jalview/gui/EditNameDialog.java
@@ -1,83 +1,81 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.gui;
-
-import java.awt.*;
-import javax.swing.*;
-
-public class EditNameDialog
-{
-  JTextField id, description;
-  JButton ok = new JButton("Accept");
-  JButton cancel = new JButton("Cancel");
-  boolean accept = false;
-
-  public String getName()
-  {
-    return id.getText();
-  }
-
-  public String getDescription()
-  {
-    if (description.getText().length() < 1)
-    {
-      return null;
-    }
-    else
-    {
-      return description.getText();
-    }
-  }
-
-  public EditNameDialog(String name,
-                        String desc,
-                        String label1,
-                        String label2,
-                        String title)
-  {
-    JLabel idlabel = new JLabel(label1);
-    JLabel desclabel = new JLabel(label2);
-    idlabel.setFont(new Font("Courier", Font.PLAIN, 12));
-    desclabel.setFont(new Font("Courier", Font.PLAIN, 12));
-    id = new JTextField(name, 40);
-    description = new JTextField(desc, 40);
-    JPanel panel = new JPanel(new BorderLayout());
-    JPanel panel2 = new JPanel(new BorderLayout());
-    panel2.add(idlabel, BorderLayout.WEST);
-    panel2.add(id, BorderLayout.CENTER);
-    panel.add(panel2, BorderLayout.NORTH);
-    if(desc!=null || label2!=null)
-    {
-      panel2 = new JPanel(new BorderLayout());
-      panel2.add(desclabel, BorderLayout.WEST);
-      panel2.add(description, BorderLayout.CENTER);
-      panel.add(panel2, BorderLayout.SOUTH);
-    }
-
-    int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
-        panel, title,
-        JOptionPane.OK_CANCEL_OPTION);
-
-    if (reply == JOptionPane.OK_OPTION)
-    {
-      accept = true;
-    }
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.gui;
+
+import java.awt.*;
+import javax.swing.*;
+
+public class EditNameDialog
+{
+  JTextField id, description;
+
+  JButton ok = new JButton("Accept");
+
+  JButton cancel = new JButton("Cancel");
+
+  boolean accept = false;
+
+  public String getName()
+  {
+    return id.getText();
+  }
+
+  public String getDescription()
+  {
+    if (description.getText().length() < 1)
+    {
+      return null;
+    }
+    else
+    {
+      return description.getText();
+    }
+  }
+
+  public EditNameDialog(String name, String desc, String label1,
+          String label2, String title)
+  {
+    JLabel idlabel = new JLabel(label1);
+    JLabel desclabel = new JLabel(label2);
+    idlabel.setFont(new Font("Courier", Font.PLAIN, 12));
+    desclabel.setFont(new Font("Courier", Font.PLAIN, 12));
+    id = new JTextField(name, 40);
+    description = new JTextField(desc, 40);
+    JPanel panel = new JPanel(new BorderLayout());
+    JPanel panel2 = new JPanel(new BorderLayout());
+    panel2.add(idlabel, BorderLayout.WEST);
+    panel2.add(id, BorderLayout.CENTER);
+    panel.add(panel2, BorderLayout.NORTH);
+    if (desc != null || label2 != null)
+    {
+      panel2 = new JPanel(new BorderLayout());
+      panel2.add(desclabel, BorderLayout.WEST);
+      panel2.add(description, BorderLayout.CENTER);
+      panel.add(panel2, BorderLayout.SOUTH);
+    }
+
+    int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+            panel, title, JOptionPane.OK_CANCEL_OPTION);
+
+    if (reply == JOptionPane.OK_OPTION)
+    {
+      accept = true;
+    }
+  }
+}
diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index b643efb..9eacb6c 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -32,17 +32,22 @@ import jalview.datamodel.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
 public class FeatureRenderer
 {
   AlignmentPanel ap;
+
   AlignViewport av;
+
   Color resBoxColour;
+
   float transparency = 1.0f;
+
   FontMetrics fm;
+
   int charOffset;
 
   Hashtable featureColours = new Hashtable();
@@ -56,15 +61,16 @@ public class FeatureRenderer
   Object currentColour;
 
   String[] renderOrder;
-  PropertyChangeSupport changeSupport=new PropertyChangeSupport(this);
+
+  PropertyChangeSupport changeSupport = new PropertyChangeSupport(this);
 
   Vector allfeatures;
 
   /**
    * Creates a new FeatureRenderer object.
-   *
+   * 
    * @param av
-   *          DOCUMENT ME!
+   *                DOCUMENT ME!
    */
   public FeatureRenderer(AlignmentPanel ap)
   {
@@ -72,12 +78,18 @@ public class FeatureRenderer
     this.av = ap.av;
   }
 
-  public class FeatureRendererSettings implements Cloneable {
+  public class FeatureRendererSettings implements Cloneable
+  {
     String[] renderOrder;
+
     Hashtable featureGroups;
+
     Hashtable featureColours;
+
     float transparency;
+
     Hashtable featureOrder;
+
     public FeatureRendererSettings(String[] renderOrder,
             Hashtable featureGroups, Hashtable featureColours,
             float transparency, Hashtable featureOrder)
@@ -89,6 +101,7 @@ public class FeatureRenderer
       this.transparency = transparency;
       this.featureOrder = featureOrder;
     }
+
     public FeatureRendererSettings(FeatureRenderer fr)
     {
       this.renderOrder = fr.renderOrder;
@@ -98,10 +111,12 @@ public class FeatureRenderer
       this.featureOrder = fr.featureOrder;
     }
   }
+
   public FeatureRendererSettings getSettings()
   {
     return new FeatureRendererSettings(this);
   }
+
   public void transferSettings(FeatureRendererSettings fr)
   {
     this.renderOrder = fr.renderOrder;
@@ -110,6 +125,7 @@ public class FeatureRenderer
     this.transparency = fr.transparency;
     this.featureOrder = fr.featureOrder;
   }
+
   public void transferSettings(FeatureRenderer fr)
   {
     this.renderOrder = fr.renderOrder;
@@ -120,11 +136,12 @@ public class FeatureRenderer
   }
 
   BufferedImage offscreenImage;
+
   boolean offscreenRender = false;
+
   public Color findFeatureColour(Color initialCol, SequenceI seq, int res)
   {
-    return new Color(findFeatureColour(initialCol.getRGB(),
-                                       seq, res));
+    return new Color(findFeatureColour(initialCol.getRGB(), seq, res));
   }
 
   /**
@@ -142,13 +159,15 @@ public class FeatureRenderer
     {
       lastSeq = seq;
       sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
-      if (sequenceFeatures!=null)
+      if (sequenceFeatures != null)
       {
         sfSize = sequenceFeatures.length;
       }
     }
 
-    if (sequenceFeatures!=lastSeq.getDatasetSequence().getSequenceFeatures()) {
+    if (sequenceFeatures != lastSeq.getDatasetSequence()
+            .getSequenceFeatures())
+    {
       sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
       if (sequenceFeatures != null)
       {
@@ -156,12 +175,11 @@ public class FeatureRenderer
       }
     }
 
-    if (sequenceFeatures == null || sfSize==0)
+    if (sequenceFeatures == null || sfSize == 0)
     {
       return initialCol;
     }
 
-
     if (jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))
     {
       return Color.white.getRGB();
@@ -180,18 +198,13 @@ public class FeatureRenderer
     if (offscreenImage != null)
     {
       offscreenImage.setRGB(0, 0, initialCol);
-      drawSequence(offscreenImage.getGraphics(),
-                   lastSeq,
-                   column, column, 0);
+      drawSequence(offscreenImage.getGraphics(), lastSeq, column, column, 0);
 
       return offscreenImage.getRGB(0, 0);
     }
     else
     {
-      drawSequence(null,
-                   lastSeq,
-                   lastSeq.findPosition(column),
-                   -1, -1);
+      drawSequence(null, lastSeq, lastSeq.findPosition(column), -1, -1);
 
       if (currentColour == null)
       {
@@ -199,7 +212,7 @@ public class FeatureRenderer
       }
       else
       {
-        return ( (Integer) currentColour).intValue();
+        return ((Integer) currentColour).intValue();
       }
     }
 
@@ -207,38 +220,40 @@ public class FeatureRenderer
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param g
-   *          DOCUMENT ME!
+   *                DOCUMENT ME!
    * @param seq
-   *          DOCUMENT ME!
+   *                DOCUMENT ME!
    * @param sg
-   *          DOCUMENT ME!
+   *                DOCUMENT ME!
    * @param start
-   *          DOCUMENT ME!
+   *                DOCUMENT ME!
    * @param end
-   *          DOCUMENT ME!
+   *                DOCUMENT ME!
    * @param x1
-   *          DOCUMENT ME!
+   *                DOCUMENT ME!
    * @param y1
-   *          DOCUMENT ME!
+   *                DOCUMENT ME!
    * @param width
-   *          DOCUMENT ME!
+   *                DOCUMENT ME!
    * @param height
-   *          DOCUMENT ME!
+   *                DOCUMENT ME!
    */
   // String type;
   // SequenceFeature sf;
   SequenceI lastSeq;
+
   SequenceFeature[] sequenceFeatures;
+
   int sfSize, sfindex, spos, epos;
 
   synchronized public void drawSequence(Graphics g, SequenceI seq,
-                           int start, int end, int y1)
+          int start, int end, int y1)
   {
 
     if (seq.getDatasetSequence().getSequenceFeatures() == null
-        || seq.getDatasetSequence().getSequenceFeatures().length == 0)
+            || seq.getDatasetSequence().getSequenceFeatures().length == 0)
     {
       return;
     }
@@ -248,9 +263,8 @@ public class FeatureRenderer
       fm = g.getFontMetrics();
     }
 
-    if (av.featuresDisplayed == null
-        || renderOrder == null
-        || newFeatureAdded)
+    if (av.featuresDisplayed == null || renderOrder == null
+            || newFeatureAdded)
     {
       findAllFeatures();
       if (av.featuresDisplayed.size() < 1)
@@ -261,8 +275,9 @@ public class FeatureRenderer
       sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
     }
 
-    if (lastSeq == null || seq != lastSeq
-        || seq.getDatasetSequence().getSequenceFeatures()!=sequenceFeatures)
+    if (lastSeq == null
+            || seq != lastSeq
+            || seq.getDatasetSequence().getSequenceFeatures() != sequenceFeatures)
     {
       lastSeq = seq;
       sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
@@ -271,9 +286,8 @@ public class FeatureRenderer
     if (transparency != 1 && g != null)
     {
       Graphics2D g2 = (Graphics2D) g;
-      g2.setComposite(
-          AlphaComposite.getInstance(
-              AlphaComposite.SRC_OVER, transparency));
+      g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
+              transparency));
     }
 
     if (!offscreenRender)
@@ -303,57 +317,60 @@ public class FeatureRenderer
         }
 
         if (featureGroups != null
-            && sequenceFeatures[sfindex].featureGroup != null
-            &&
-            sequenceFeatures[sfindex].featureGroup.length()!=0
-            && featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
-            &&
-            ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].
-                                            featureGroup)).
-            booleanValue())
+                && sequenceFeatures[sfindex].featureGroup != null
+                && sequenceFeatures[sfindex].featureGroup.length() != 0
+                && featureGroups
+                        .containsKey(sequenceFeatures[sfindex].featureGroup)
+                && !((Boolean) featureGroups
+                        .get(sequenceFeatures[sfindex].featureGroup))
+                        .booleanValue())
         {
           continue;
         }
 
-        if (!offscreenRender && (sequenceFeatures[sfindex].getBegin() > epos
-                                 || sequenceFeatures[sfindex].getEnd() < spos))
+        if (!offscreenRender
+                && (sequenceFeatures[sfindex].getBegin() > epos || sequenceFeatures[sfindex]
+                        .getEnd() < spos))
         {
           continue;
         }
 
         if (offscreenRender && offscreenImage == null)
         {
-          if (sequenceFeatures[sfindex].begin <= start &&
-              sequenceFeatures[sfindex].end >= start)
+          if (sequenceFeatures[sfindex].begin <= start
+                  && sequenceFeatures[sfindex].end >= start)
           {
-            currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].
-                type);
+            currentColour = av.featuresDisplayed
+                    .get(sequenceFeatures[sfindex].type);
           }
         }
         else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
         {
 
-          renderFeature(g, seq,
-                        seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
-                        seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
-                        new Color( ( (Integer) av.featuresDisplayed.get(
-                            sequenceFeatures[sfindex].type)).intValue()),
-                        start, end, y1);
-          renderFeature(g, seq,
-                        seq.findIndex(sequenceFeatures[sfindex].end) - 1,
-                        seq.findIndex(sequenceFeatures[sfindex].end) - 1,
-                        new Color( ( (Integer) av.featuresDisplayed.get(
-                            sequenceFeatures[sfindex].type)).intValue()),
-                        start, end, y1);
+          renderFeature(
+                  g,
+                  seq,
+                  seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+                  seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+                  new Color(((Integer) av.featuresDisplayed
+                          .get(sequenceFeatures[sfindex].type)).intValue()),
+                  start, end, y1);
+          renderFeature(
+                  g,
+                  seq,
+                  seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+                  seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+                  new Color(((Integer) av.featuresDisplayed
+                          .get(sequenceFeatures[sfindex].type)).intValue()),
+                  start, end, y1);
 
         }
         else
         {
-          renderFeature(g, seq,
-                        seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
-                        seq.findIndex(sequenceFeatures[sfindex].end) - 1,
-                        getColour(sequenceFeatures[sfindex].type),
-                        start, end, y1);
+          renderFeature(g, seq, seq
+                  .findIndex(sequenceFeatures[sfindex].begin) - 1, seq
+                  .findIndex(sequenceFeatures[sfindex].end) - 1,
+                  getColour(sequenceFeatures[sfindex].type), start, end, y1);
         }
 
       }
@@ -363,20 +380,20 @@ public class FeatureRenderer
     if (transparency != 1.0f && g != null)
     {
       Graphics2D g2 = (Graphics2D) g;
-      g2.setComposite(
-          AlphaComposite.getInstance(
-              AlphaComposite.SRC_OVER, 1.0f));
+      g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
+              1.0f));
     }
   }
 
   char s;
+
   int i;
-  void renderFeature(Graphics g, SequenceI seq,
-                     int fstart, int fend, Color featureColour, int start,
-                     int end, int y1)
+
+  void renderFeature(Graphics g, SequenceI seq, int fstart, int fend,
+          Color featureColour, int start, int end, int y1)
   {
 
-    if ( ( (fstart <= end) && (fend >= start)))
+    if (((fstart <= end) && (fend >= start)))
     {
       if (fstart < start)
       { // fix for if the feature we have starts before the sequence start,
@@ -399,7 +416,8 @@ public class FeatureRenderer
 
         g.setColor(featureColour);
 
-        g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight);
+        g.fillRect((i - start) * av.charWidth, y1, av.charWidth,
+                av.charHeight);
 
         if (offscreenRender || !av.validCharWidth)
         {
@@ -408,51 +426,56 @@ public class FeatureRenderer
 
         g.setColor(Color.white);
         charOffset = (av.charWidth - fm.charWidth(s)) / 2;
-        g.drawString(String.valueOf(s),
-                     charOffset + (av.charWidth * (i - start)),
-                     pady);
+        g.drawString(String.valueOf(s), charOffset
+                + (av.charWidth * (i - start)), pady);
 
       }
     }
   }
 
   boolean newFeatureAdded = false;
+
   /**
-   * Called when alignment in associated view has new/modified features
-   * to discover and display.
-   *
+   * Called when alignment in associated view has new/modified features to
+   * discover and display.
+   * 
    */
   public void featuresAdded()
   {
-    lastSeq=null;
+    lastSeq = null;
     findAllFeatures();
   }
 
   boolean findingFeatures = false;
+
   /**
    * search the alignment for all new features, give them a colour and display
    * them. Then fires a PropertyChangeEvent on the changeSupport object.
-   *
+   * 
    */
   void findAllFeatures()
   {
     synchronized (firing)
     {
-        if (firing.equals(Boolean.FALSE)) {
-          firing=Boolean.TRUE;
-          findAllFeatures(true); // add all new features as visible
-          changeSupport.firePropertyChange("changeSupport",null,null);
-          firing=Boolean.FALSE;
+      if (firing.equals(Boolean.FALSE))
+      {
+        firing = Boolean.TRUE;
+        findAllFeatures(true); // add all new features as visible
+        changeSupport.firePropertyChange("changeSupport", null, null);
+        firing = Boolean.FALSE;
       }
     }
   }
+
   /**
    * Searches alignment for all features and updates colours
-   *
+   * 
    * @param newMadeVisible
-   *          if true newly added feature types will be rendered immediatly
+   *                if true newly added feature types will be rendered
+   *                immediatly
    */
-  synchronized void findAllFeatures(boolean newMadeVisible) {
+  synchronized void findAllFeatures(boolean newMadeVisible)
+  {
     newFeatureAdded = false;
 
     if (findingFeatures)
@@ -470,10 +493,11 @@ public class FeatureRenderer
 
     allfeatures = new Vector();
     Vector oldfeatures = new Vector();
-    if (renderOrder!=null)
+    if (renderOrder != null)
     {
-      for (int i=0; i<renderOrder.length; i++) {
-        if (renderOrder[i]!=null)
+      for (int i = 0; i < renderOrder.length; i++)
+      {
+        if (renderOrder[i] != null)
         {
           oldfeatures.addElement(renderOrder[i]);
         }
@@ -481,9 +505,8 @@ public class FeatureRenderer
     }
     for (int i = 0; i < av.alignment.getHeight(); i++)
     {
-      SequenceFeature[] features
-          = av.alignment.getSequenceAt(i).getDatasetSequence().
-          getSequenceFeatures();
+      SequenceFeature[] features = av.alignment.getSequenceAt(i)
+              .getDatasetSequence().getSequenceFeatures();
 
       if (features == null)
       {
@@ -496,33 +519,34 @@ public class FeatureRenderer
         if (!av.featuresDisplayed.containsKey(features[index].getType()))
         {
 
-          if(featureGroups.containsKey(features[index].getType()))
+          if (featureGroups.containsKey(features[index].getType()))
           {
-            boolean visible = ( (Boolean) featureGroups.get(
-                features[index].featureGroup)).booleanValue();
+            boolean visible = ((Boolean) featureGroups
+                    .get(features[index].featureGroup)).booleanValue();
 
-            if(!visible)
+            if (!visible)
             {
               index++;
               continue;
             }
           }
 
-
-          if (! (features[index].begin == 0 && features[index].end == 0))
+          if (!(features[index].begin == 0 && features[index].end == 0))
           {
             // If beginning and end are 0, the feature is for the whole sequence
             // and we don't want to render the feature in the normal way
 
-            if (newMadeVisible && !oldfeatures.contains(features[index].getType())) {
+            if (newMadeVisible
+                    && !oldfeatures.contains(features[index].getType()))
+            {
               // this is a new feature type on the alignment. Mark it for
               // display.
               av.featuresDisplayed.put(features[index].getType(),
-                                     new Integer(getColour(features[index].
-                getType()).getRGB()));
-              setOrder(features[index].getType(),0);
+                      new Integer(getColour(features[index].getType())
+                              .getRGB()));
+              setOrder(features[index].getType(), 0);
             }
-           }
+          }
         }
         if (!allfeatures.contains(features[index].getType()))
         {
@@ -534,48 +558,54 @@ public class FeatureRenderer
     updateRenderOrder(allfeatures);
     findingFeatures = false;
   }
-  protected Boolean firing=Boolean.FALSE;
+
+  protected Boolean firing = Boolean.FALSE;
+
   /**
-   * replaces the current renderOrder with the unordered features in allfeatures.
-   * The ordering of any types in both renderOrder and allfeatures is preserved,
-   * and all new feature types are rendered on top of the existing types, in
-   * the order given by getOrder or the order given in allFeatures.
+   * replaces the current renderOrder with the unordered features in
+   * allfeatures. The ordering of any types in both renderOrder and allfeatures
+   * is preserved, and all new feature types are rendered on top of the existing
+   * types, in the order given by getOrder or the order given in allFeatures.
    * Note. this operates directly on the featureOrder hash for efficiency. TODO:
    * eliminate the float storage for computing/recalling the persistent ordering
-   *
+   * 
    * @param allFeatures
    */
-  private void updateRenderOrder(Vector allFeatures) {
+  private void updateRenderOrder(Vector allFeatures)
+  {
     Vector allfeatures = new Vector(allFeatures);
     String[] oldRender = renderOrder;
     renderOrder = new String[allfeatures.size()];
-    boolean initOrders=(featureOrder==null);
-    int opos=0;
-    if (oldRender!=null && oldRender.length>0)
+    boolean initOrders = (featureOrder == null);
+    int opos = 0;
+    if (oldRender != null && oldRender.length > 0)
     {
-      for (int j=0; j<oldRender.length; j++)
+      for (int j = 0; j < oldRender.length; j++)
       {
-        if (oldRender[j]!=null)
+        if (oldRender[j] != null)
+        {
+          if (initOrders)
           {
-            if (initOrders)
-            {
-              setOrder(oldRender[j], (1-(1+(float)j)/(float) oldRender.length));
-            }
-            if (allfeatures.contains(oldRender[j])) {
-              renderOrder[opos++]  = oldRender[j]; // existing features always
-                                                    // appear below new features
-              allfeatures.removeElement(oldRender[j]);
-            }
+            setOrder(oldRender[j], (1 - (1 + (float) j)
+                    / (float) oldRender.length));
+          }
+          if (allfeatures.contains(oldRender[j]))
+          {
+            renderOrder[opos++] = oldRender[j]; // existing features always
+            // appear below new features
+            allfeatures.removeElement(oldRender[j]);
           }
         }
+      }
     }
-    if (allfeatures.size()==0) {
+    if (allfeatures.size() == 0)
+    {
       // no new features - leave order unchanged.
       return;
     }
-    int i=allfeatures.size()-1;
-    int iSize=i;
-    boolean sort=false;
+    int i = allfeatures.size() - 1;
+    int iSize = i;
+    boolean sort = false;
     String[] newf = new String[allfeatures.size()];
     float[] sortOrder = new float[allfeatures.size()];
     Enumeration en = allfeatures.elements();
@@ -586,30 +616,30 @@ public class FeatureRenderer
       if (initOrders || !featureOrder.containsKey(newf[i]))
       {
         int denom = initOrders ? allfeatures.size() : featureOrder.size();
-          // new unordered feature - compute persistent ordering at head of
-          // existing features.
-        setOrder(newf[i], i/(float) denom);
+        // new unordered feature - compute persistent ordering at head of
+        // existing features.
+        setOrder(newf[i], i / (float) denom);
       }
       // set order from newly found feature from persisted ordering.
-      sortOrder[i] = 2-((Float) featureOrder.get(newf[i])).floatValue();
-      if (i<iSize)
+      sortOrder[i] = 2 - ((Float) featureOrder.get(newf[i])).floatValue();
+      if (i < iSize)
       {
         // only sort if we need to
-        sort = sort || sortOrder[i]>sortOrder[i+1];
+        sort = sort || sortOrder[i] > sortOrder[i + 1];
       }
       i--;
     }
-    if (iSize>1 && sort)
+    if (iSize > 1 && sort)
       jalview.util.QuickSort.sort(sortOrder, newf);
-    sortOrder=null;
+    sortOrder = null;
     System.arraycopy(newf, 0, renderOrder, opos, newf.length);
   }
+
   public Color getColour(String featureType)
   {
     if (!featureColours.containsKey(featureType))
     {
-      jalview.schemes.UserColourScheme ucs = new
-          jalview.schemes.UserColourScheme();
+      jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
       Color col = ucs.createColourFromName(featureType);
       featureColours.put(featureType, col);
       return col;
@@ -619,14 +649,16 @@ public class FeatureRenderer
   }
 
   static String lastFeatureAdded;
+
   static String lastFeatureGroupAdded;
+
   static String lastDescriptionAdded;
 
   int featureIndex = 0;
+
   boolean amendFeatures(final SequenceI[] sequences,
-                        final SequenceFeature[] features,
-                        boolean newFeatures,
-                        final AlignmentPanel ap)
+          final SequenceFeature[] features, boolean newFeatures,
+          final AlignmentPanel ap)
   {
 
     featureIndex = 0;
@@ -649,8 +681,7 @@ public class FeatureRenderer
       public void mousePressed(MouseEvent evt)
       {
         Color col = JColorChooser.showDialog(Desktop.desktop,
-                                             "Select Feature Colour",
-                                             colour.getBackground());
+                "Select Feature Colour", colour.getBackground());
         if (col != null)
           colour.setBackground(col);
 
@@ -660,62 +691,59 @@ public class FeatureRenderer
     JPanel tmp = new JPanel();
     JPanel panel = new JPanel(new GridLayout(3, 1));
 
-    ///////////////////////////////////////
-    ///MULTIPLE FEATURES AT SELECTED RESIDUE
-    if(!newFeatures && features.length>1)
+    // /////////////////////////////////////
+    // /MULTIPLE FEATURES AT SELECTED RESIDUE
+    if (!newFeatures && features.length > 1)
     {
-     panel = new JPanel(new GridLayout(4, 1));
-     tmp = new JPanel();
-     tmp.add(new JLabel("Select Feature: "));
-     overlaps = new JComboBox();
-     for(int i=0; i<features.length; i++)
-     {
-       overlaps.addItem(features[i].getType()
-        +"/"+features[i].getBegin()+"-"+features[i].getEnd()
-        +" ("+features[i].getFeatureGroup()+")");
-     }
-
-     tmp.add(overlaps);
-
-     overlaps.addItemListener(new ItemListener()
-     {
-       public void itemStateChanged(ItemEvent e)
-       {
-         int index = overlaps.getSelectedIndex();
-         if (index != -1)
-         {
-           featureIndex = index;
-           name.setText(features[index].getType());
-           description.setText(features[index].getDescription());
-           source.setText(features[index].getFeatureGroup());
-           start.setValue(new Integer(features[index].getBegin()));
-           end.setValue(new Integer(features[index].getEnd()));
-
-           SearchResults highlight = new SearchResults();
-           highlight.addResult(sequences[0],
-                               features[index].getBegin(),
-                               features[index].getEnd());
-
-           ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
-
-         }
-         Color col = getColour(name.getText());
-         if (col == null)
-         {
-           col = new
-               jalview.schemes.UserColourScheme()
-               .createColourFromName(name.getText());
-         }
-
-         colour.setBackground(col);
-       }
-     });
-
-
-     panel.add(tmp);
+      panel = new JPanel(new GridLayout(4, 1));
+      tmp = new JPanel();
+      tmp.add(new JLabel("Select Feature: "));
+      overlaps = new JComboBox();
+      for (int i = 0; i < features.length; i++)
+      {
+        overlaps.addItem(features[i].getType() + "/"
+                + features[i].getBegin() + "-" + features[i].getEnd()
+                + " (" + features[i].getFeatureGroup() + ")");
+      }
+
+      tmp.add(overlaps);
+
+      overlaps.addItemListener(new ItemListener()
+      {
+        public void itemStateChanged(ItemEvent e)
+        {
+          int index = overlaps.getSelectedIndex();
+          if (index != -1)
+          {
+            featureIndex = index;
+            name.setText(features[index].getType());
+            description.setText(features[index].getDescription());
+            source.setText(features[index].getFeatureGroup());
+            start.setValue(new Integer(features[index].getBegin()));
+            end.setValue(new Integer(features[index].getEnd()));
+
+            SearchResults highlight = new SearchResults();
+            highlight.addResult(sequences[0], features[index].getBegin(),
+                    features[index].getEnd());
+
+            ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
+
+          }
+          Color col = getColour(name.getText());
+          if (col == null)
+          {
+            col = new jalview.schemes.UserColourScheme()
+                    .createColourFromName(name.getText());
+          }
+
+          colour.setBackground(col);
+        }
+      });
+
+      panel.add(tmp);
     }
-    //////////
-    //////////////////////////////////////
+    // ////////
+    // ////////////////////////////////////
 
     tmp = new JPanel();
     panel.add(tmp);
@@ -781,7 +809,7 @@ public class FeatureRenderer
       }
     }
 
-    if(newFeatures)
+    if (newFeatures)
     {
       name.setText(lastFeatureAdded);
       source.setText(lastFeatureGroupAdded);
@@ -797,36 +825,28 @@ public class FeatureRenderer
     description.setText(features[0].getDescription());
     colour.setBackground(getColour(name.getText()));
 
-
     Object[] options;
     if (!newFeatures)
     {
       options = new Object[]
-          {
-          "Amend", "Delete", "Cancel"};
+      { "Amend", "Delete", "Cancel" };
     }
     else
     {
       options = new Object[]
-          {
-          "OK", "Cancel"};
+      { "OK", "Cancel" };
     }
 
-    String title = newFeatures ? "Create New Sequence Feature(s)" :
-        "Amend/Delete Features for "
-        + sequences[0].getName();
+    String title = newFeatures ? "Create New Sequence Feature(s)"
+            : "Amend/Delete Features for " + sequences[0].getName();
 
     int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
-        bigPanel,
-        title,
-        JOptionPane.YES_NO_CANCEL_OPTION,
-        JOptionPane.QUESTION_MESSAGE,
-        null,
-        options, "OK");
+            bigPanel, title, JOptionPane.YES_NO_CANCEL_OPTION,
+            JOptionPane.QUESTION_MESSAGE, null, options, "OK");
 
     jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
 
-    if (reply == JOptionPane.OK_OPTION && name.getText().length()>0)
+    if (reply == JOptionPane.OK_OPTION && name.getText().length() > 0)
     {
       // This ensures that the last sequence
       // is refreshed and new features are rendered
@@ -835,7 +855,7 @@ public class FeatureRenderer
       lastFeatureGroupAdded = source.getText().trim();
       lastDescriptionAdded = description.getText().replaceAll("\n", " ");
 
-      if(lastFeatureGroupAdded.length()<1)
+      if (lastFeatureGroupAdded.length() < 1)
         lastFeatureGroupAdded = null;
     }
 
@@ -854,29 +874,29 @@ public class FeatureRenderer
         sf.description = lastDescriptionAdded;
 
         setColour(sf.type, colour.getBackground());
-        av.featuresDisplayed.put(sf.type,
-                                 new Integer(colour.getBackground().getRGB()));
+        av.featuresDisplayed.put(sf.type, new Integer(colour
+                .getBackground().getRGB()));
 
         try
         {
-          sf.begin = ( (Integer) start.getValue()).intValue();
-          sf.end = ( (Integer) end.getValue()).intValue();
+          sf.begin = ((Integer) start.getValue()).intValue();
+          sf.end = ((Integer) end.getValue()).intValue();
+        } catch (NumberFormatException ex)
+        {
         }
-        catch (NumberFormatException ex)
-        {}
 
         ffile.parseDescriptionHTML(sf, false);
       }
     }
-    else //NEW FEATURES ADDED
+    else
+    // NEW FEATURES ADDED
     {
-      if (reply == JOptionPane.OK_OPTION
-          && lastFeatureAdded.length()>0)
+      if (reply == JOptionPane.OK_OPTION && lastFeatureAdded.length() > 0)
       {
         for (int i = 0; i < sequences.length; i++)
         {
           features[i].type = lastFeatureAdded;
-          if (lastFeatureGroupAdded!=null)
+          if (lastFeatureGroupAdded != null)
             features[i].featureGroup = lastFeatureGroupAdded;
           features[i].description = lastDescriptionAdded;
           sequences[i].addSequenceFeature(features[i]);
@@ -898,13 +918,12 @@ public class FeatureRenderer
         Color col = colour.getBackground();
         setColour(lastFeatureAdded, colour.getBackground());
         av.featuresDisplayed.put(lastFeatureAdded,
-                                   new Integer(col.getRGB()));
+                new Integer(col.getRGB()));
 
         findAllFeatures(false);
 
         ap.paintAlignment(true);
 
-
         return true;
       }
       else
@@ -932,23 +951,29 @@ public class FeatureRenderer
   {
     return transparency;
   }
+
   /**
    * Replace current ordering with new ordering
-   * @param data { String(Type), Colour(Type), Boolean(Displayed) }
+   * 
+   * @param data {
+   *                String(Type), Colour(Type), Boolean(Displayed) }
    */
   public void setFeaturePriority(Object[][] data)
   {
     setFeaturePriority(data, true);
   }
+
   /**
-   *
-   * @param data { String(Type), Colour(Type), Boolean(Displayed) }
-   * @param visibleNew when true current featureDisplay list will be cleared
+   * 
+   * @param data {
+   *                String(Type), Colour(Type), Boolean(Displayed) }
+   * @param visibleNew
+   *                when true current featureDisplay list will be cleared
    */
   public void setFeaturePriority(Object[][] data, boolean visibleNew)
   {
     if (visibleNew)
-      {
+    {
       if (av.featuresDisplayed != null)
       {
         av.featuresDisplayed.clear();
@@ -958,7 +983,7 @@ public class FeatureRenderer
         av.featuresDisplayed = new Hashtable();
       }
     }
-    if (data==null)
+    if (data == null)
     {
       return;
     }
@@ -974,9 +999,10 @@ public class FeatureRenderer
       {
         String type = data[i][0].toString();
         setColour(type, (Color) data[i][1]);
-        if ( ( (Boolean) data[i][2]).booleanValue())
+        if (((Boolean) data[i][2]).booleanValue())
         {
-          av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));
+          av.featuresDisplayed.put(type, new Integer(getColour(type)
+                  .getRGB()));
         }
 
         renderOrder[data.length - i - 1] = type;
@@ -984,38 +1010,42 @@ public class FeatureRenderer
     }
 
   }
-  Hashtable featureOrder=null;
+
+  Hashtable featureOrder = null;
+
   /**
    * analogous to colour - store a normalized ordering for all feature types in
    * this rendering context.
-   *
+   * 
    * @param type
-   *          Feature type string
+   *                Feature type string
    * @param position
-   *          normalized priority - 0 means always appears on top, 1 means
-   *          always last.
+   *                normalized priority - 0 means always appears on top, 1 means
+   *                always last.
    */
   public float setOrder(String type, float position)
   {
-    if (featureOrder==null)
+    if (featureOrder == null)
     {
       featureOrder = new Hashtable();
     }
     featureOrder.put(type, new Float(position));
     return position;
   }
+
   /**
    * get the global priority (0 (top) to 1 (bottom))
-   *
+   * 
    * @param type
    * @return [0,1] or -1 for a type without a priority
    */
-  public float getOrder(String type) {
-    if (featureOrder!=null)
+  public float getOrder(String type)
+  {
+    if (featureOrder != null)
     {
       if (featureOrder.containsKey(type))
       {
-        return ((Float)featureOrder.get(type)).floatValue();
+        return ((Float) featureOrder.get(type)).floatValue();
       }
     }
     return -1;
diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index ea492e2..632ad00 100755
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -33,21 +33,30 @@ import javax.swing.table.*;
 import jalview.datamodel.*;
 import jalview.io.*;
 
-public class FeatureSettings
-    extends JPanel
+public class FeatureSettings extends JPanel
 {
   DasSourceBrowser dassourceBrowser;
+
   jalview.ws.DasSequenceFeatureFetcher dasFeatureFetcher;
+
   JPanel settingsPane = new JPanel();
+
   JPanel dasSettingsPane = new JPanel();
 
   final FeatureRenderer fr;
+
   public final AlignFrame af;
+
   Object[][] originalData;
+
   final JInternalFrame frame;
+
   JScrollPane scrollPane = new JScrollPane();
+
   JTable table;
+
   JPanel groupPanel;
+
   JSlider transparency = new JSlider();
 
   JPanel transPanel = new JPanel(new FlowLayout());
@@ -62,8 +71,7 @@ public class FeatureSettings
     try
     {
       jbInit();
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       ex.printStackTrace();
     }
@@ -71,11 +79,9 @@ public class FeatureSettings
     table = new JTable();
     table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));
     table.setFont(new Font("Verdana", Font.PLAIN, 12));
-    table.setDefaultRenderer(Color.class,
-                             new ColorRenderer());
+    table.setDefaultRenderer(Color.class, new ColorRenderer());
 
-    table.setDefaultEditor(Color.class,
-                           new ColorEditor());
+    table.setDefaultEditor(Color.class, new ColorEditor());
 
     table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 
@@ -92,9 +98,7 @@ public class FeatureSettings
       public void mouseDragged(MouseEvent evt)
       {
         int newRow = table.rowAtPoint(evt.getPoint());
-        if (newRow != selectedRow
-            && selectedRow != -1
-            && newRow != -1)
+        if (newRow != selectedRow && selectedRow != -1 && newRow != -1)
         {
           Object[] temp = new Object[3];
           temp[0] = table.getValueAt(selectedRow, 0);
@@ -119,21 +123,25 @@ public class FeatureSettings
     dassourceBrowser = new DasSourceBrowser();
     dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER);
 
-    if (af.getViewport().featuresDisplayed == null || fr.renderOrder == null)
+    if (af.getViewport().featuresDisplayed == null
+            || fr.renderOrder == null)
     {
       fr.findAllFeatures(true); // display everything!
     }
 
     setTableData();
     final PropertyChangeListener change;
-    final FeatureSettings fs=this;
-    fr.addPropertyChangeListener(change=new PropertyChangeListener() {
+    final FeatureSettings fs = this;
+    fr.addPropertyChangeListener(change = new PropertyChangeListener()
+    {
       public void propertyChange(PropertyChangeEvent evt)
       {
-        if (!fs.resettingTable && !fs.handlingUpdate) {
-          fs.handlingUpdate=true;
-          fs.resetTable(null); // new groups may be added with new seuqence feature types only
-          fs.handlingUpdate=false;
+        if (!fs.resettingTable && !fs.handlingUpdate)
+        {
+          fs.handlingUpdate = true;
+          fs.resetTable(null); // new groups may be added with new seuqence
+                                // feature types only
+          fs.handlingUpdate = false;
         }
       }
 
@@ -142,26 +150,28 @@ public class FeatureSettings
     frame = new JInternalFrame();
     frame.setContentPane(this);
     Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 450);
-    frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
-    {
-      public void internalFrameClosed(
-          javax.swing.event.InternalFrameEvent evt)
-      {
-        fr.removePropertyChangeListener(change);
-      }
-      ;
-    });
+    frame
+            .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+            {
+              public void internalFrameClosed(
+                      javax.swing.event.InternalFrameEvent evt)
+              {
+                fr.removePropertyChangeListener(change);
+              };
+            });
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
   }
+
   /**
    * true when Feature Settings are updating from feature renderer
    */
-  private boolean handlingUpdate=false;
+  private boolean handlingUpdate = false;
 
   /**
    * contains a float[3] for each feature type string. created by setTableData
    */
-  Hashtable typeWidth=null;
+  Hashtable typeWidth = null;
+
   synchronized public void setTableData()
   {
     if (fr.featureGroups == null)
@@ -174,14 +184,14 @@ public class FeatureSettings
     String group;
     for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)
     {
-      if (af.getViewport().alignment.getSequenceAt(i).getDatasetSequence().
-          getSequenceFeatures() == null)
+      if (af.getViewport().alignment.getSequenceAt(i).getDatasetSequence()
+              .getSequenceFeatures() == null)
       {
         continue;
       }
 
-      tmpfeatures = af.getViewport().alignment.getSequenceAt(i).
-          getDatasetSequence().getSequenceFeatures();
+      tmpfeatures = af.getViewport().alignment.getSequenceAt(i)
+              .getDatasetSequence().getSequenceFeatures();
 
       int index = 0;
       while (index < tmpfeatures.length)
@@ -198,7 +208,7 @@ public class FeatureSettings
           if (!allGroups.contains(group))
           {
             allGroups.addElement(group);
-            if (group!=null)
+            if (group != null)
             {
               checkGroupState(group);
             }
@@ -217,88 +227,95 @@ public class FeatureSettings
 
     validate();
   }
+
   /**
-   *
+   * 
    * @param group
    * @return true if group has been seen before and is already added to set.
    */
-  private boolean checkGroupState(String group) {
+  private boolean checkGroupState(String group)
+  {
     boolean visible;
     if (fr.featureGroups.containsKey(group))
     {
-      visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();
-        } else {
-        visible=true; // new group is always made visible
-      }
+      visible = ((Boolean) fr.featureGroups.get(group)).booleanValue();
+    }
+    else
+    {
+      visible = true; // new group is always made visible
+    }
 
-      if (groupPanel == null)
-      {
-        groupPanel = new JPanel();
-      }
+    if (groupPanel == null)
+    {
+      groupPanel = new JPanel();
+    }
 
-      boolean alreadyAdded = false;
-      for (int g = 0; g < groupPanel.getComponentCount(); g++)
+    boolean alreadyAdded = false;
+    for (int g = 0; g < groupPanel.getComponentCount(); g++)
+    {
+      if (((JCheckBox) groupPanel.getComponent(g)).getText().equals(group))
       {
-        if ( ( (JCheckBox) groupPanel.getComponent(g))
-            .getText().equals(group))
-        {
-          alreadyAdded = true;
-          ((JCheckBox)groupPanel.getComponent(g)).setSelected(visible);
-          break;
-        }
+        alreadyAdded = true;
+        ((JCheckBox) groupPanel.getComponent(g)).setSelected(visible);
+        break;
       }
+    }
 
-      if (alreadyAdded)
-      {
+    if (alreadyAdded)
+    {
 
-        return true;
-      }
+      return true;
+    }
 
-      fr.featureGroups.put(group, new Boolean(visible));
-      final String grp = group;
-      final JCheckBox check = new JCheckBox(group, visible);
-      check.setFont(new Font("Serif", Font.BOLD, 12));
-      check.addItemListener(new ItemListener()
+    fr.featureGroups.put(group, new Boolean(visible));
+    final String grp = group;
+    final JCheckBox check = new JCheckBox(group, visible);
+    check.setFont(new Font("Serif", Font.BOLD, 12));
+    check.addItemListener(new ItemListener()
+    {
+      public void itemStateChanged(ItemEvent evt)
       {
-        public void itemStateChanged(ItemEvent evt)
+        fr.featureGroups.put(check.getText(), new Boolean(check
+                .isSelected()));
+        af.alignPanel.seqPanel.seqCanvas.repaint();
+        if (af.alignPanel.overviewPanel != null)
         {
-          fr.featureGroups.put(check.getText(),
-                               new Boolean(check.isSelected()));
-          af.alignPanel.seqPanel.seqCanvas.repaint();
-          if (af.alignPanel.overviewPanel != null)
-          {
-            af.alignPanel.overviewPanel.updateOverviewImage();
-          }
-
-          resetTable(new String[] { grp } );
+          af.alignPanel.overviewPanel.updateOverviewImage();
         }
-      });
-      groupPanel.add(check);
-      return false;
+
+        resetTable(new String[]
+        { grp });
+      }
+    });
+    groupPanel.add(check);
+    return false;
   }
-  boolean resettingTable=false;
+
+  boolean resettingTable = false;
+
   synchronized void resetTable(String[] groupChanged)
   {
-    if (resettingTable==true)
+    if (resettingTable == true)
     {
       return;
     }
-    resettingTable=true;
-    typeWidth=new Hashtable();
-    // TODO: change avWidth calculation to 'per-sequence' average and use long rather than float
-    float[] avWidth=null;
+    resettingTable = true;
+    typeWidth = new Hashtable();
+    // TODO: change avWidth calculation to 'per-sequence' average and use long
+    // rather than float
+    float[] avWidth = null;
     SequenceFeature[] tmpfeatures;
     String group = null, type;
     Vector visibleChecks = new Vector();
 
-    //Find out which features should be visible depending on which groups
-    //are selected / deselected
-    //and recompute average width ordering
+    // Find out which features should be visible depending on which groups
+    // are selected / deselected
+    // and recompute average width ordering
     for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)
     {
 
-      tmpfeatures = af.getViewport().alignment.getSequenceAt(i).
-          getDatasetSequence().getSequenceFeatures();
+      tmpfeatures = af.getViewport().alignment.getSequenceAt(i)
+              .getDatasetSequence().getSequenceFeatures();
       if (tmpfeatures == null)
       {
         continue;
@@ -315,10 +332,10 @@ public class FeatureSettings
           continue;
         }
 
-        if (group == null || fr.featureGroups.get(group) == null ||
-            ( (Boolean) fr.featureGroups.get(group)).booleanValue())
+        if (group == null || fr.featureGroups.get(group) == null
+                || ((Boolean) fr.featureGroups.get(group)).booleanValue())
         {
-          if (group!=null)
+          if (group != null)
             checkGroupState(group);
           type = tmpfeatures[index].getType();
           if (!visibleChecks.contains(type))
@@ -326,17 +343,25 @@ public class FeatureSettings
             visibleChecks.addElement(type);
           }
         }
-        if (!typeWidth.containsKey(tmpfeatures[index].getType())) {
-          typeWidth.put(tmpfeatures[index].getType(), avWidth=new float[3]);
-        } else {
+        if (!typeWidth.containsKey(tmpfeatures[index].getType()))
+        {
+          typeWidth.put(tmpfeatures[index].getType(),
+                  avWidth = new float[3]);
+        }
+        else
+        {
           avWidth = (float[]) typeWidth.get(tmpfeatures[index].getType());
         }
         avWidth[0]++;
-        if (tmpfeatures[index].getBegin()>tmpfeatures[index].getEnd())
+        if (tmpfeatures[index].getBegin() > tmpfeatures[index].getEnd())
+        {
+          avWidth[1] += 1 + tmpfeatures[index].getBegin()
+                  - tmpfeatures[index].getEnd();
+        }
+        else
         {
-          avWidth[1]+=1+tmpfeatures[index].getBegin()-tmpfeatures[index].getEnd();
-        } else {
-          avWidth[1]+=1+tmpfeatures[index].getEnd()-tmpfeatures[index].getBegin();
+          avWidth[1] += 1 + tmpfeatures[index].getEnd()
+                  - tmpfeatures[index].getBegin();
         }
         index++;
       }
@@ -349,9 +374,11 @@ public class FeatureSettings
     if (fr.renderOrder != null)
     {
       if (!handlingUpdate)
-        fr.findAllFeatures(groupChanged!=null); // prod to update colourschemes. but don't affect display
-      //First add the checks in the previous render order,
-      //in case the window has been closed and reopened
+        fr.findAllFeatures(groupChanged != null); // prod to update
+                                                  // colourschemes. but don't
+                                                  // affect display
+      // First add the checks in the previous render order,
+      // in case the window has been closed and reopened
       for (int ro = fr.renderOrder.length - 1; ro > -1; ro--)
       {
         type = fr.renderOrder[ro];
@@ -363,7 +390,8 @@ public class FeatureSettings
 
         data[dataIndex][0] = type;
         data[dataIndex][1] = fr.getColour(type);
-        data[dataIndex][2] = new Boolean(af.getViewport().featuresDisplayed.containsKey(type));
+        data[dataIndex][2] = new Boolean(af.getViewport().featuresDisplayed
+                .containsKey(type));
         dataIndex++;
         visibleChecks.removeElement(type);
       }
@@ -372,15 +400,15 @@ public class FeatureSettings
     fSize = visibleChecks.size();
     for (int i = 0; i < fSize; i++)
     {
-      //These must be extra features belonging to the group
-      //which was just selected
+      // These must be extra features belonging to the group
+      // which was just selected
       type = visibleChecks.elementAt(i).toString();
       data[dataIndex][0] = type;
 
       data[dataIndex][1] = fr.getColour(type);
       if (data[dataIndex][1] == null)
       {
-        //"Colour has been updated in another view!!"
+        // "Colour has been updated in another view!!"
         fr.renderOrder = null;
         return;
       }
@@ -400,31 +428,33 @@ public class FeatureSettings
 
     if (groupPanel != null)
     {
-      groupPanel.setLayout(
-          new GridLayout(fr.featureGroups.size() / 4 + 1, 4));
+      groupPanel.setLayout(new GridLayout(fr.featureGroups.size() / 4 + 1,
+              4));
 
       groupPanel.validate();
       bigPanel.add(groupPanel, BorderLayout.NORTH);
     }
 
-    updateFeatureRenderer(data, groupChanged!=null);
-    resettingTable=false;
+    updateFeatureRenderer(data, groupChanged != null);
+    resettingTable = false;
   }
+
   /**
    * reorder data based on the featureRenderers global priority list.
+   * 
    * @param data
    */
   private void ensureOrder(Object[][] data)
   {
-    boolean sort=false;
+    boolean sort = false;
     float[] order = new float[data.length];
-    for (int i=0;i<order.length; i++)
+    for (int i = 0; i < order.length; i++)
     {
       order[i] = fr.getOrder(data[i][0].toString());
-      if (order[i]<0)
-        order[i] = fr.setOrder(data[i][0].toString(), i/order.length);
-      if (i>1)
-        sort = sort || order[i-1]>order[i];
+      if (order[i] < 0)
+        order[i] = fr.setOrder(data[i][0].toString(), i / order.length);
+      if (i > 1)
+        sort = sort || order[i - 1] > order[i];
     }
     if (sort)
       jalview.util.QuickSort.sort(order, data);
@@ -432,12 +462,10 @@ public class FeatureSettings
 
   void load()
   {
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-        getProperty(
-            "LAST_DIRECTORY"), new String[]
-        {"fc"},
-        new String[]
-        {"Sequence Feature Colours"}, "Sequence Feature Colours");
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+            .getProperty("LAST_DIRECTORY"), new String[]
+    { "fc" }, new String[]
+    { "Sequence Feature Colours" }, "Sequence Feature Colours");
     chooser.setFileView(new jalview.io.JalviewFileView());
     chooser.setDialogTitle("Load Feature Colours");
     chooser.setToolTipText("Load");
@@ -451,29 +479,28 @@ public class FeatureSettings
       try
       {
         InputStreamReader in = new InputStreamReader(new FileInputStream(
-            file), "UTF-8");
+                file), "UTF-8");
 
-        jalview.binding.JalviewUserColours jucs = new jalview.binding.
-            JalviewUserColours();
+        jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours();
         jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);
 
-        for (int i = jucs.getColourCount()-1; i >=0; i--)
+        for (int i = jucs.getColourCount() - 1; i >= 0; i--)
         {
           String name;
-          fr.setColour(name=jucs.getColour(i).getName(),
-                       new Color(Integer.parseInt(jucs.getColour(i).getRGB(),
-                                                  16)));
-          fr.setOrder(name,(i==0) ? 0 : i/jucs.getColourCount());
+          fr.setColour(name = jucs.getColour(i).getName(), new Color(
+                  Integer.parseInt(jucs.getColour(i).getRGB(), 16)));
+          fr.setOrder(name, (i == 0) ? 0 : i / jucs.getColourCount());
         }
-        if (table!=null) {
+        if (table != null)
+        {
           resetTable(null);
-          Object[][] data=((FeatureTableModel) table.getModel()).getData();
+          Object[][] data = ((FeatureTableModel) table.getModel())
+                  .getData();
           ensureOrder(data);
-          updateFeatureRenderer(data,false);
+          updateFeatureRenderer(data, false);
           table.repaint();
         }
-      }
-      catch (Exception ex)
+      } catch (Exception ex)
       {
         System.out.println("Error loading User Colour File\n" + ex);
       }
@@ -482,12 +509,10 @@ public class FeatureSettings
 
   void save()
   {
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-        getProperty(
-            "LAST_DIRECTORY"), new String[]
-        {"fc"},
-        new String[]
-        {"Sequence Feature Colours"}, "Sequence Feature Colours");
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+            .getProperty("LAST_DIRECTORY"), new String[]
+    { "fc" }, new String[]
+    { "Sequence Feature Colours" }, "Sequence Feature Colours");
     chooser.setFileView(new jalview.io.JalviewFileView());
     chooser.setDialogTitle("Save Feature Colour Scheme");
     chooser.setToolTipText("Save");
@@ -497,37 +522,36 @@ public class FeatureSettings
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       String choice = chooser.getSelectedFile().getPath();
-      jalview.binding.JalviewUserColours ucs = new jalview.binding.
-          JalviewUserColours();
+      jalview.binding.JalviewUserColours ucs = new jalview.binding.JalviewUserColours();
       ucs.setSchemeName("Sequence Features");
       try
       {
         PrintWriter out = new PrintWriter(new OutputStreamWriter(
-            new FileOutputStream(choice), "UTF-8"));
+                new FileOutputStream(choice), "UTF-8"));
 
         Enumeration e = fr.featureColours.keys();
         float[] sortOrder = new float[fr.featureColours.size()];
         String[] sortTypes = new String[fr.featureColours.size()];
-        int i=0;
+        int i = 0;
         while (e.hasMoreElements())
         {
           sortTypes[i] = e.nextElement().toString();
-          sortOrder[i]  = fr.getOrder(sortTypes[i]);
+          sortOrder[i] = fr.getOrder(sortTypes[i]);
           i++;
         }
         jalview.util.QuickSort.sort(sortOrder, sortTypes);
-        sortOrder=null;
-        for (i=0; i<sortTypes.length; i++) {
+        sortOrder = null;
+        for (i = 0; i < sortTypes.length; i++)
+        {
           jalview.binding.Colour col = new jalview.binding.Colour();
           col.setName(sortTypes[i]);
-          col.setRGB(jalview.util.Format.getHexString(
-              fr.getColour(col.getName())));
+          col.setRGB(jalview.util.Format.getHexString(fr.getColour(col
+                  .getName())));
           ucs.addColour(col);
         }
         ucs.marshal(out);
         out.close();
-      }
-      catch (Exception ex)
+      } catch (Exception ex)
       {
         ex.printStackTrace();
       }
@@ -540,63 +564,73 @@ public class FeatureSettings
     {
       Boolean value = (Boolean) table.getValueAt(i, 2);
 
-      table.setValueAt(
-          new Boolean(!value.booleanValue()),
-          i, 2);
+      table.setValueAt(new Boolean(!value.booleanValue()), i, 2);
     }
   }
-  public void orderByAvWidth() {
-    if (table==null || table.getModel()==null)
+
+  public void orderByAvWidth()
+  {
+    if (table == null || table.getModel() == null)
       return;
     Object[][] data = ((FeatureTableModel) table.getModel()).getData();
     float[] width = new float[data.length];
     float[] awidth;
-    float max=0;
-    int num=0;
-    for (int i=0;i<data.length;i++) {
-       awidth = (float[]) typeWidth.get(data[i][0]);
-       if (awidth[0]>0) {
-         width[i] = awidth[1]/awidth[0];// *awidth[0]*awidth[2]; - better weight - but have to make per sequence, too (awidth[2])
-         //if (width[i]==1) // hack to distinguish single width sequences.
-         num++;
-       } else {
-         width[i]=0;
-       }
-       if (max<width[i])
-         max=width[i];
+    float max = 0;
+    int num = 0;
+    for (int i = 0; i < data.length; i++)
+    {
+      awidth = (float[]) typeWidth.get(data[i][0]);
+      if (awidth[0] > 0)
+      {
+        width[i] = awidth[1] / awidth[0];// *awidth[0]*awidth[2]; - better
+                                          // weight - but have to make per
+                                          // sequence, too (awidth[2])
+        // if (width[i]==1) // hack to distinguish single width sequences.
+        num++;
+      }
+      else
+      {
+        width[i] = 0;
+      }
+      if (max < width[i])
+        max = width[i];
     }
-    boolean sort=false;
-    for (int i=0;i<width.length; i++) {
-      //awidth = (float[]) typeWidth.get(data[i][0]);
-      if (width[i]==0)
+    boolean sort = false;
+    for (int i = 0; i < width.length; i++)
+    {
+      // awidth = (float[]) typeWidth.get(data[i][0]);
+      if (width[i] == 0)
       {
         width[i] = fr.getOrder(data[i][0].toString());
-        if (width[i]<0)
+        if (width[i] < 0)
         {
-          width[i] = fr.setOrder(data[i][0].toString(), i/data.length);
+          width[i] = fr.setOrder(data[i][0].toString(), i / data.length);
         }
-      } else {
-        width[i] /=max; // normalize
+      }
+      else
+      {
+        width[i] /= max; // normalize
         fr.setOrder(data[i][0].toString(), width[i]); // store for later
       }
-      if (i>0)
-        sort = sort || width[i-1]>width[i];
+      if (i > 0)
+        sort = sort || width[i - 1] > width[i];
     }
     if (sort)
       jalview.util.QuickSort.sort(width, data);
     // update global priority order
 
-    updateFeatureRenderer(data,false);
+    updateFeatureRenderer(data, false);
     table.repaint();
   }
+
   public void close()
   {
     try
     {
       frame.setClosed(true);
+    } catch (Exception exe)
+    {
     }
-    catch (Exception exe)
-    {}
 
   }
 
@@ -604,6 +638,7 @@ public class FeatureSettings
   {
     updateFeatureRenderer(data, true);
   }
+
   private void updateFeatureRenderer(Object[][] data, boolean visibleNew)
   {
     fr.setFeaturePriority(data, visibleNew);
@@ -611,26 +646,44 @@ public class FeatureSettings
   }
 
   int selectedRow = -1;
+
   JTabbedPane tabbedPane = new JTabbedPane();
+
   BorderLayout borderLayout1 = new BorderLayout();
+
   BorderLayout borderLayout2 = new BorderLayout();
+
   BorderLayout borderLayout3 = new BorderLayout();
+
   JPanel bigPanel = new JPanel();
+
   BorderLayout borderLayout4 = new BorderLayout();
+
   JButton invert = new JButton();
+
   JPanel buttonPanel = new JPanel();
+
   JButton cancel = new JButton();
+
   JButton ok = new JButton();
+
   JButton loadColours = new JButton();
+
   JButton saveColours = new JButton();
+
   JPanel dasButtonPanel = new JPanel();
+
   JButton fetchDAS = new JButton();
+
   JButton saveDAS = new JButton();
+
   JButton cancelDAS = new JButton();
+
   JButton optimizeOrder = new JButton();
+
   JPanel transbuttons = new JPanel(new BorderLayout());
-  private void jbInit()
-      throws Exception
+
+  private void jbInit() throws Exception
   {
     this.setLayout(borderLayout1);
     settingsPane.setLayout(borderLayout2);
@@ -647,8 +700,10 @@ public class FeatureSettings
     });
     optimizeOrder.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
     optimizeOrder.setText("Optimise Order");
-    optimizeOrder.addActionListener(new ActionListener() {
-      public void actionPerformed(ActionEvent e) {
+    optimizeOrder.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
         orderByAvWidth();
       }
     });
@@ -693,7 +748,7 @@ public class FeatureSettings
     {
       public void stateChanged(ChangeEvent evt)
       {
-        fr.setTransparency( (float) (100 - transparency.getValue()) / 100f);
+        fr.setTransparency((float) (100 - transparency.getValue()) / 100f);
         af.alignPanel.paintAlignment(true);
       }
     });
@@ -732,7 +787,7 @@ public class FeatureSettings
     bigPanel.add(transPanel, java.awt.BorderLayout.SOUTH);
     transPanel.add(transparency);
     transbuttons.add(invert, java.awt.BorderLayout.NORTH);
-    transbuttons.add(optimizeOrder,java.awt.BorderLayout.SOUTH);
+    transbuttons.add(optimizeOrder, java.awt.BorderLayout.SOUTH);
     transPanel.add(transbuttons);
     buttonPanel.add(ok);
     buttonPanel.add(cancel);
@@ -754,25 +809,26 @@ public class FeatureSettings
     Vector selectedSources = dassourceBrowser.getSelectedSources();
     doDasFeatureFetch(selectedSources, true, true);
   }
+
   /**
    * get the features from selectedSources for all or the current selection
+   * 
    * @param selectedSources
    * @param checkDbRefs
    * @param promptFetchDbRefs
    */
-  private void doDasFeatureFetch(Vector selectedSources, boolean checkDbRefs, boolean promptFetchDbRefs)
+  private void doDasFeatureFetch(Vector selectedSources,
+          boolean checkDbRefs, boolean promptFetchDbRefs)
   {
     SequenceI[] dataset, seqs;
     int iSize;
     AlignViewport vp = af.getViewport();
     if (vp.getSelectionGroup() != null
-        && vp.getSelectionGroup().getSize() > 0)
+            && vp.getSelectionGroup().getSize() > 0)
     {
       iSize = vp.getSelectionGroup().getSize();
       dataset = new SequenceI[iSize];
-      seqs = vp.getSelectionGroup().
-          getSequencesInOrder(
-              vp.getAlignment());
+      seqs = vp.getSelectionGroup().getSequencesInOrder(vp.getAlignment());
     }
     else
     {
@@ -787,35 +843,44 @@ public class FeatureSettings
     }
 
     cancelDAS.setEnabled(true);
-    dasFeatureFetcher =
-        new jalview.ws.DasSequenceFeatureFetcher(
-            dataset,
-            this,
-            selectedSources, checkDbRefs, promptFetchDbRefs);
+    dasFeatureFetcher = new jalview.ws.DasSequenceFeatureFetcher(dataset,
+            this, selectedSources, checkDbRefs, promptFetchDbRefs);
     af.getViewport().setShowSequenceFeatures(true);
     af.showSeqFeatures.setSelected(true);
   }
+
   /**
-   * properly initialise DAS fetcher and then initiate a new thread to fetch features from the named sources (rather than any turned on by default) 
+   * properly initialise DAS fetcher and then initiate a new thread to fetch
+   * features from the named sources (rather than any turned on by default)
+   * 
    * @param sources
    */
   public void fetchDasFeatures(Vector sources)
   {
-    Thread thr = new Thread(new Runnable() {
-      public void run() {
+    Thread thr = new Thread(new Runnable()
+    {
+      public void run()
+      {
         // this actually initialises the das source list
         dassourceBrowser.paintComponent(null); // yuk
       }
     });
     thr.start();
-    while (dassourceBrowser.loadingDasSources || dassourceBrowser.dasSources==null)
+    while (dassourceBrowser.loadingDasSources
+            || dassourceBrowser.dasSources == null)
     {
-      try { Thread.sleep(10); } catch (Exception e) {};
+      try
+      {
+        Thread.sleep(10);
+      } catch (Exception e)
+      {
+      }
+      ;
     }
     Vector resolved = new Vector();
-    if (sources!=null)
+    if (sources != null)
     {
-      for (int i=0;i<dassourceBrowser.dasSources.length; i++)
+      for (int i = 0; i < dassourceBrowser.dasSources.length; i++)
       {
         if (sources.contains(dassourceBrowser.dasSources[i].getNickname()))
         {
@@ -826,28 +891,31 @@ public class FeatureSettings
         }
       }
     }
-    if (resolved.size()==0)
+    if (resolved.size() == 0)
     {
       resolved = dassourceBrowser.getSelectedSources();
     }
-    if (resolved.size()>0)
+    if (resolved.size() > 0)
     {
       final Vector dassources = resolved;
-      SwingUtilities.invokeLater(new Runnable() {
+      SwingUtilities.invokeLater(new Runnable()
+      {
 
         public void run()
         {
           fetchDAS.setEnabled(false);
           cancelDAS.setEnabled(true);
           doDasFeatureFetch(dassources, true, false);
-          
-        }});
+
+        }
+      });
     }
   }
 
   public void saveDAS_actionPerformed(ActionEvent e)
   {
-    dassourceBrowser.saveProperties(jalview.bin.Cache.applicationProperties);
+    dassourceBrowser
+            .saveProperties(jalview.bin.Cache.applicationProperties);
   }
 
   public void complete()
@@ -858,30 +926,28 @@ public class FeatureSettings
 
   public void cancelDAS_actionPerformed(ActionEvent e)
   {
-    if (dasFeatureFetcher!=null)
+    if (dasFeatureFetcher != null)
     {
       dasFeatureFetcher.cancel();
     }
     fetchDAS.setEnabled(true);
     cancelDAS.setEnabled(false);
   }
+
   public void noDasSourceActive()
   {
     complete();
     JOptionPane.showInternalConfirmDialog(Desktop.desktop,
             "No das sources were selected.\n"
-            + "Please select some sources and\n"
-            +" try again.",
-            "No Sources Selected",
-            JOptionPane.DEFAULT_OPTION,
+                    + "Please select some sources and\n" + " try again.",
+            "No Sources Selected", JOptionPane.DEFAULT_OPTION,
             JOptionPane.INFORMATION_MESSAGE);
   }
 
-  /////////////////////////////////////////////////////////////////////////
+  // ///////////////////////////////////////////////////////////////////////
   // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html
-  /////////////////////////////////////////////////////////////////////////
-  class FeatureTableModel
-      extends AbstractTableModel
+  // ///////////////////////////////////////////////////////////////////////
+  class FeatureTableModel extends AbstractTableModel
   {
     FeatureTableModel(Object[][] data)
     {
@@ -889,8 +955,8 @@ public class FeatureSettings
     }
 
     private String[] columnNames =
-        {
-        "Feature Type", "Colour", "Display"};
+    { "Feature Type", "Colour", "Display" };
+
     private Object[][] data;
 
     public Object[][] getData()
@@ -947,21 +1013,20 @@ public class FeatureSettings
 
   }
 
-  class ColorRenderer
-      extends JLabel implements TableCellRenderer
+  class ColorRenderer extends JLabel implements TableCellRenderer
   {
     javax.swing.border.Border unselectedBorder = null;
+
     javax.swing.border.Border selectedBorder = null;
 
     public ColorRenderer()
     {
-      setOpaque(true); //MUST do this for background to show up.
+      setOpaque(true); // MUST do this for background to show up.
     }
 
-    public Component getTableCellRendererComponent(
-        JTable table, Object color,
-        boolean isSelected, boolean hasFocus,
-        int row, int column)
+    public Component getTableCellRendererComponent(JTable table,
+            Object color, boolean isSelected, boolean hasFocus, int row,
+            int column)
     {
       Color newColor = (Color) color;
       setBackground(newColor);
@@ -970,7 +1035,7 @@ public class FeatureSettings
         if (selectedBorder == null)
         {
           selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
-              table.getSelectionBackground());
+                  table.getSelectionBackground());
         }
         setBorder(selectedBorder);
       }
@@ -979,86 +1044,81 @@ public class FeatureSettings
         if (unselectedBorder == null)
         {
           unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
-              table.getBackground());
+                  table.getBackground());
         }
         setBorder(unselectedBorder);
       }
 
       setToolTipText("RGB value: " + newColor.getRed() + ", "
-                     + newColor.getGreen() + ", "
-                     + newColor.getBlue());
+              + newColor.getGreen() + ", " + newColor.getBlue());
       return this;
     }
   }
 }
 
-class ColorEditor
-    extends AbstractCellEditor implements TableCellEditor,
-    ActionListener
+class ColorEditor extends AbstractCellEditor implements TableCellEditor,
+        ActionListener
 {
   Color currentColor;
+
   JButton button;
+
   JColorChooser colorChooser;
+
   JDialog dialog;
+
   protected static final String EDIT = "edit";
 
   public ColorEditor()
   {
-    //Set up the editor (from the table's point of view),
-    //which is a button.
-    //This button brings up the color chooser dialog,
-    //which is the editor from the user's point of view.
+    // Set up the editor (from the table's point of view),
+    // which is a button.
+    // This button brings up the color chooser dialog,
+    // which is the editor from the user's point of view.
     button = new JButton();
     button.setActionCommand(EDIT);
     button.addActionListener(this);
     button.setBorderPainted(false);
-    //Set up the dialog that the button brings up.
+    // Set up the dialog that the button brings up.
     colorChooser = new JColorChooser();
-    dialog = JColorChooser.createDialog(button,
-                                        "Select new Colour",
-                                        true, //modal
-                                        colorChooser,
-                                        this, //OK button handler
-                                        null); //no CANCEL button handler
+    dialog = JColorChooser.createDialog(button, "Select new Colour", true, // modal
+            colorChooser, this, // OK button handler
+            null); // no CANCEL button handler
   }
 
   /**
-   * Handles events from the editor button and from
-   * the dialog's OK button.
+   * Handles events from the editor button and from the dialog's OK button.
    */
   public void actionPerformed(ActionEvent e)
   {
 
     if (EDIT.equals(e.getActionCommand()))
     {
-      //The user has clicked the cell, so
-      //bring up the dialog.
+      // The user has clicked the cell, so
+      // bring up the dialog.
       button.setBackground(currentColor);
       colorChooser.setColor(currentColor);
       dialog.setVisible(true);
 
-      //Make the renderer reappear.
+      // Make the renderer reappear.
       fireEditingStopped();
 
     }
     else
-    { //User pressed dialog's "OK" button.
+    { // User pressed dialog's "OK" button.
       currentColor = colorChooser.getColor();
     }
   }
 
-  //Implement the one CellEditor method that AbstractCellEditor doesn't.
+  // Implement the one CellEditor method that AbstractCellEditor doesn't.
   public Object getCellEditorValue()
   {
     return currentColor;
   }
 
-  //Implement the one method defined by TableCellEditor.
-  public Component getTableCellEditorComponent(JTable table,
-                                               Object value,
-                                               boolean isSelected,
-                                               int row,
-                                               int column)
+  // Implement the one method defined by TableCellEditor.
+  public Component getTableCellEditorComponent(JTable table, Object value,
+          boolean isSelected, int row, int column)
   {
     currentColor = (Color) value;
     return button;
diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 5668b42..cad734b 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -29,27 +29,33 @@ import jalview.jbgui.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class Finder
-    extends GFinder
+public class Finder extends GFinder
 {
   AlignViewport av;
+
   AlignmentPanel ap;
+
   JInternalFrame frame;
+
   int seqIndex = 0;
+
   int resIndex = 0;
 
   SearchResults searchResults;
 
   /**
    * Creates a new Finder object.
-   *
-   * @param av DOCUMENT ME!
-   * @param ap DOCUMENT ME!
-   * @param f DOCUMENT ME!
+   * 
+   * @param av
+   *                DOCUMENT ME!
+   * @param ap
+   *                DOCUMENT ME!
+   * @param f
+   *                DOCUMENT ME!
    */
   public Finder()
   {
@@ -63,8 +69,9 @@ public class Finder
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void findNext_actionPerformed(ActionEvent e)
   {
@@ -76,8 +83,9 @@ public class Finder
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void findAll_actionPerformed(ActionEvent e)
   {
@@ -95,8 +103,8 @@ public class Finder
 
     if (frame != null && frame instanceof AlignFrame)
     {
-      av = ( (AlignFrame) frame).viewport;
-      ap = ( (AlignFrame) frame).alignPanel;
+      av = ((AlignFrame) frame).viewport;
+      ap = ((AlignFrame) frame).alignPanel;
       return true;
     }
     return false;
@@ -104,27 +112,27 @@ public class Finder
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void createNewGroup_actionPerformed(ActionEvent e)
   {
     SequenceI[] seqs = new SequenceI[searchResults.getSize()];
-    SequenceFeature[] features = new SequenceFeature[searchResults.getSize()];
+    SequenceFeature[] features = new SequenceFeature[searchResults
+            .getSize()];
 
     for (int i = 0; i < searchResults.getSize(); i++)
     {
       seqs[i] = searchResults.getResultSequence(i).getDatasetSequence();
 
       features[i] = new SequenceFeature(textfield.getText().trim(),
-                                        "Search Results", null,
-                                        searchResults.getResultStart(i),
-                                        searchResults.getResultEnd(i),
-                                        "Search Results");
+              "Search Results", null, searchResults.getResultStart(i),
+              searchResults.getResultEnd(i), "Search Results");
     }
 
-    if (ap.seqPanel.seqCanvas.getFeatureRenderer()
-        .amendFeatures(seqs, features, true, ap))
+    if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
+            features, true, ap))
     {
       ap.alignFrame.showSeqFeatures.setSelected(true);
       av.setShowSequenceFeatures(true);
@@ -134,8 +142,9 @@ public class Finder
 
   /**
    * DOCUMENT ME!
-   *
-   * @param findAll DOCUMENT ME!
+   * 
+   * @param findAll
+   *                DOCUMENT ME!
    */
   void doSearch(boolean findAll)
   {
@@ -147,10 +156,12 @@ public class Finder
     {
       return;
     }
-    // TODO: extend finder to match descriptions, features and annotation, and other stuff
-    // TODO: add switches to control what is searched - sequences, IDS, descriptions, features
-    jalview.analysis.Finder finder = new jalview.analysis.Finder(av.alignment,
-        av.getSelectionGroup(), seqIndex, resIndex);
+    // TODO: extend finder to match descriptions, features and annotation, and
+    // other stuff
+    // TODO: add switches to control what is searched - sequences, IDS,
+    // descriptions, features
+    jalview.analysis.Finder finder = new jalview.analysis.Finder(
+            av.alignment, av.getSelectionGroup(), seqIndex, resIndex);
     finder.setCaseSensitive(caseSensitive.isSelected());
     finder.setFindAll(findAll);
 
@@ -159,10 +170,11 @@ public class Finder
     seqIndex = finder.getSeqIndex();
     resIndex = finder.getResIndex();
 
-    searchResults = finder.getSearchResults(); // find(regex, caseSensitive.isSelected(), )
+    searchResults = finder.getSearchResults(); // find(regex,
+                                                // caseSensitive.isSelected(), )
     Vector idMatch = finder.getIdMatch();
     // set or reset the GUI
-    if ( (searchResults.getSize() == 0) && (idMatch.size() > 0))
+    if ((searchResults.getSize() == 0) && (idMatch.size() > 0))
     {
       ap.idPanel.highlightSearchResults(idMatch);
     }
@@ -178,14 +190,15 @@ public class Finder
       searchResults = null;
     }
 
-    // if allResults is null, this effectively switches displaySearch flag in seqCanvas
+    // if allResults is null, this effectively switches displaySearch flag in
+    // seqCanvas
     ap.highlightSearchResults(searchResults);
-    // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or 'SelectRegion' selection
+    // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or
+    // 'SelectRegion' selection
     if (!findAll && resultSize == 0)
     {
       JOptionPane.showInternalMessageDialog(this, "Finished searching",
-                                            null,
-                                            JOptionPane.INFORMATION_MESSAGE);
+              null, JOptionPane.INFORMATION_MESSAGE);
       resIndex = 0;
       seqIndex = 0;
     }
@@ -194,7 +207,7 @@ public class Finder
     {
       String message = resultSize + " matches found.";
       JOptionPane.showInternalMessageDialog(this, message, null,
-                                            JOptionPane.INFORMATION_MESSAGE);
+              JOptionPane.INFORMATION_MESSAGE);
     }
 
   }
diff --git a/src/jalview/gui/FontChooser.java b/src/jalview/gui/FontChooser.java
index aaf0abc..6e99d91 100755
--- a/src/jalview/gui/FontChooser.java
+++ b/src/jalview/gui/FontChooser.java
@@ -1,259 +1,271 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.gui;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-import jalview.bin.*;
-import jalview.jbgui.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class FontChooser
-    extends GFontChooser
-{
-  AlignmentPanel ap;
-  TreePanel tp;
-  Font oldFont;
-  boolean init = true;
-  JInternalFrame frame;
-
-  /**
-   * Creates a new FontChooser object.
-   *
-   * @param ap DOCUMENT ME!
-   */
-  public FontChooser(TreePanel tp)
-  {
-    this.tp = tp;
-    ap = tp.treeCanvas.ap;
-    oldFont = tp.getTreeFont();
-    defaultButton.setVisible(false);
-    smoothFont.setEnabled(false);
-    init();
-  }
-
-  /**
-   * Creates a new FontChooser object.
-   *
-   * @param ap DOCUMENT ME!
-   */
-  public FontChooser(AlignmentPanel ap)
-  {
-    oldFont = ap.av.getFont();
-    this.ap = ap;
-    init();
-  }
-
-  void init()
-  {
-    frame = new JInternalFrame();
-    frame.setContentPane(this);
-
-    smoothFont.setSelected(ap.av.antiAlias);
-
-    if (tp != null)
-    {
-      Desktop.addInternalFrame(frame, "Change Font (Tree Panel)", 340, 170, false);
-    }
-    else
-    {
-      Desktop.addInternalFrame(frame, "Change Font", 340, 170, false);
-    }
-
-    frame.setLayer(JLayeredPane.PALETTE_LAYER);
-
-    String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()
-        .getAvailableFontFamilyNames();
-
-    for (int i = 0; i < fonts.length; i++)
-    {
-      fontName.addItem(fonts[i]);
-    }
-
-    for (int i = 1; i < 51; i++)
-    {
-      fontSize.addItem(i + "");
-    }
-
-    fontStyle.addItem("plain");
-    fontStyle.addItem("bold");
-    fontStyle.addItem("italic");
-
-    fontName.setSelectedItem(oldFont.getName());
-    fontSize.setSelectedItem(oldFont.getSize() + "");
-    fontStyle.setSelectedIndex(oldFont.getStyle());
-
-    FontMetrics fm = getGraphics().getFontMetrics(oldFont);
-    monospaced.setSelected(fm.getStringBounds("M", getGraphics()).getWidth()
-                           == fm.getStringBounds("|", getGraphics()).getWidth());
-
-    init = false;
-  }
-
-  public void smoothFont_actionPerformed(ActionEvent e)
-  {
-    ap.av.antiAlias = smoothFont.isSelected();
-    ap.annotationPanel.image = null;
-    ap.paintAlignment(true);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void ok_actionPerformed(ActionEvent e)
-  {
-    try
-    {
-      frame.setClosed(true);
-    }
-    catch (Exception ex)
-    {
-    }
-
-    if (ap != null)
-    {
-      if (ap.getOverviewPanel() != null)
-      {
-        ap.getOverviewPanel().updateOverviewImage();
-      }
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void cancel_actionPerformed(ActionEvent e)
-  {
-    if (ap != null)
-    {
-      ap.av.setFont(oldFont);
-      ap.paintAlignment(true);
-    }
-    else if (tp != null)
-    {
-      tp.setTreeFont(oldFont);
-    }
-    fontName.setSelectedItem(oldFont.getName());
-    fontSize.setSelectedItem(oldFont.getSize() + "");
-    fontStyle.setSelectedIndex(oldFont.getStyle());
-
-    try
-    {
-      frame.setClosed(true);
-    }
-    catch (Exception ex)
-    {
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  void changeFont()
-  {
-    Font newFont = new Font(fontName.getSelectedItem().toString(),
-                            fontStyle.getSelectedIndex(),
-                            Integer.parseInt(fontSize.getSelectedItem().
-                                             toString()));
-    if (tp != null)
-    {
-      tp.setTreeFont(newFont);
-    }
-    else if (ap != null)
-    {
-      ap.av.setFont(newFont);
-      ap.fontChanged();
-    }
-
-    FontMetrics fm = getGraphics().getFontMetrics(newFont);
-
-    monospaced.setSelected(fm.getStringBounds("M", getGraphics()).getWidth()
-                           == fm.getStringBounds("|", getGraphics()).getWidth());
-
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void fontName_actionPerformed(ActionEvent e)
-  {
-    if (init)
-    {
-      return;
-    }
-
-    changeFont();
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void fontSize_actionPerformed(ActionEvent e)
-  {
-    if (init)
-    {
-      return;
-    }
-
-    changeFont();
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void fontStyle_actionPerformed(ActionEvent e)
-  {
-    if (init)
-    {
-      return;
-    }
-
-    changeFont();
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  public void defaultButton_actionPerformed(ActionEvent e)
-  {
-    Cache.setProperty("FONT_NAME", fontName.getSelectedItem().toString());
-    Cache.setProperty("FONT_STYLE", fontStyle.getSelectedIndex() + "");
-    Cache.setProperty("FONT_SIZE", fontSize.getSelectedItem().toString());
-    Cache.setProperty("ANTI_ALIAS", Boolean.toString(smoothFont.isSelected()));
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.gui;
+
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+
+import jalview.bin.*;
+import jalview.jbgui.*;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class FontChooser extends GFontChooser
+{
+  AlignmentPanel ap;
+
+  TreePanel tp;
+
+  Font oldFont;
+
+  boolean init = true;
+
+  JInternalFrame frame;
+
+  /**
+   * Creates a new FontChooser object.
+   * 
+   * @param ap
+   *                DOCUMENT ME!
+   */
+  public FontChooser(TreePanel tp)
+  {
+    this.tp = tp;
+    ap = tp.treeCanvas.ap;
+    oldFont = tp.getTreeFont();
+    defaultButton.setVisible(false);
+    smoothFont.setEnabled(false);
+    init();
+  }
+
+  /**
+   * Creates a new FontChooser object.
+   * 
+   * @param ap
+   *                DOCUMENT ME!
+   */
+  public FontChooser(AlignmentPanel ap)
+  {
+    oldFont = ap.av.getFont();
+    this.ap = ap;
+    init();
+  }
+
+  void init()
+  {
+    frame = new JInternalFrame();
+    frame.setContentPane(this);
+
+    smoothFont.setSelected(ap.av.antiAlias);
+
+    if (tp != null)
+    {
+      Desktop.addInternalFrame(frame, "Change Font (Tree Panel)", 340, 170,
+              false);
+    }
+    else
+    {
+      Desktop.addInternalFrame(frame, "Change Font", 340, 170, false);
+    }
+
+    frame.setLayer(JLayeredPane.PALETTE_LAYER);
+
+    String[] fonts = java.awt.GraphicsEnvironment
+            .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
+
+    for (int i = 0; i < fonts.length; i++)
+    {
+      fontName.addItem(fonts[i]);
+    }
+
+    for (int i = 1; i < 51; i++)
+    {
+      fontSize.addItem(i + "");
+    }
+
+    fontStyle.addItem("plain");
+    fontStyle.addItem("bold");
+    fontStyle.addItem("italic");
+
+    fontName.setSelectedItem(oldFont.getName());
+    fontSize.setSelectedItem(oldFont.getSize() + "");
+    fontStyle.setSelectedIndex(oldFont.getStyle());
+
+    FontMetrics fm = getGraphics().getFontMetrics(oldFont);
+    monospaced.setSelected(fm.getStringBounds("M", getGraphics())
+            .getWidth() == fm.getStringBounds("|", getGraphics())
+            .getWidth());
+
+    init = false;
+  }
+
+  public void smoothFont_actionPerformed(ActionEvent e)
+  {
+    ap.av.antiAlias = smoothFont.isSelected();
+    ap.annotationPanel.image = null;
+    ap.paintAlignment(true);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
+   */
+  protected void ok_actionPerformed(ActionEvent e)
+  {
+    try
+    {
+      frame.setClosed(true);
+    } catch (Exception ex)
+    {
+    }
+
+    if (ap != null)
+    {
+      if (ap.getOverviewPanel() != null)
+      {
+        ap.getOverviewPanel().updateOverviewImage();
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
+   */
+  protected void cancel_actionPerformed(ActionEvent e)
+  {
+    if (ap != null)
+    {
+      ap.av.setFont(oldFont);
+      ap.paintAlignment(true);
+    }
+    else if (tp != null)
+    {
+      tp.setTreeFont(oldFont);
+    }
+    fontName.setSelectedItem(oldFont.getName());
+    fontSize.setSelectedItem(oldFont.getSize() + "");
+    fontStyle.setSelectedIndex(oldFont.getStyle());
+
+    try
+    {
+      frame.setClosed(true);
+    } catch (Exception ex)
+    {
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  void changeFont()
+  {
+    Font newFont = new Font(fontName.getSelectedItem().toString(),
+            fontStyle.getSelectedIndex(), Integer.parseInt(fontSize
+                    .getSelectedItem().toString()));
+    if (tp != null)
+    {
+      tp.setTreeFont(newFont);
+    }
+    else if (ap != null)
+    {
+      ap.av.setFont(newFont);
+      ap.fontChanged();
+    }
+
+    FontMetrics fm = getGraphics().getFontMetrics(newFont);
+
+    monospaced.setSelected(fm.getStringBounds("M", getGraphics())
+            .getWidth() == fm.getStringBounds("|", getGraphics())
+            .getWidth());
+
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
+   */
+  protected void fontName_actionPerformed(ActionEvent e)
+  {
+    if (init)
+    {
+      return;
+    }
+
+    changeFont();
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
+   */
+  protected void fontSize_actionPerformed(ActionEvent e)
+  {
+    if (init)
+    {
+      return;
+    }
+
+    changeFont();
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
+   */
+  protected void fontStyle_actionPerformed(ActionEvent e)
+  {
+    if (init)
+    {
+      return;
+    }
+
+    changeFont();
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
+   */
+  public void defaultButton_actionPerformed(ActionEvent e)
+  {
+    Cache.setProperty("FONT_NAME", fontName.getSelectedItem().toString());
+    Cache.setProperty("FONT_STYLE", fontStyle.getSelectedIndex() + "");
+    Cache.setProperty("FONT_SIZE", fontSize.getSelectedItem().toString());
+    Cache.setProperty("ANTI_ALIAS", Boolean.toString(smoothFont
+            .isSelected()));
+  }
+}
diff --git a/src/jalview/gui/IProgressIndicator.java b/src/jalview/gui/IProgressIndicator.java
index 4acaba9..43f3cec 100644
--- a/src/jalview/gui/IProgressIndicator.java
+++ b/src/jalview/gui/IProgressIndicator.java
@@ -1,18 +1,41 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.gui;
 
 /**
  * Visual progress indicator interface.
+ * 
  * @author JimP
- *
+ * 
  */
 public interface IProgressIndicator
 {
   /**
-   * Visual indication of some operation taking place. 
-   * On first call with a particular ID an indicator with the given message is added. The indicator is removed with a second call with same ID. 
-   * @param message - displayed message for operation
-   * @param id - unique handle for this indicator
+   * Visual indication of some operation taking place. On first call with a
+   * particular ID an indicator with the given message is added. The indicator
+   * is removed with a second call with same ID.
+   * 
+   * @param message -
+   *                displayed message for operation
+   * @param id -
+   *                unique handle for this indicator
    */
   public abstract void setProgressBar(String message, long id);
 
-}
\ No newline at end of file
+}
diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 97b8669..b1fbe08 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -1,477 +1,489 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.gui;
-
-import java.awt.*;
-import java.awt.image.*;
-import javax.swing.*;
-
-import jalview.datamodel.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class IdCanvas
-    extends JPanel
-{
-  protected AlignViewport av;
-  protected boolean showScores = true;
-  protected int maxIdLength = -1;
-  protected String maxIdStr = null;
-  BufferedImage image;
-  Graphics2D gg;
-  int imgHeight = 0;
-  boolean fastPaint = false;
-  java.util.Vector searchResults;
-  FontMetrics fm;
-  AnnotationLabels labels = null;
-  AnnotationPanel ap;
-  Font idfont;
-
-  /**
-   * Creates a new IdCanvas object.
-   *
-   * @param av DOCUMENT ME!
-   */
-  public IdCanvas(AlignViewport av)
-  {
-    setLayout(new BorderLayout());
-    this.av = av;
-    PaintRefresher.Register(this, av.getSequenceSetId());
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param gg DOCUMENT ME!
-   * @param s DOCUMENT ME!
-   * @param i DOCUMENT ME!
-   * @param starty DOCUMENT ME!
-   * @param ypos DOCUMENT ME!
-   */
-  public void drawIdString(Graphics2D gg, SequenceI s, int i, int starty,
-                           int ypos)
-  {
-    int xPos = 0;
-    int panelWidth = getWidth();
-    int charHeight = av.charHeight;
-
-    if ( (searchResults != null) && searchResults.contains(s))
-    {
-      gg.setColor(Color.black);
-      gg.fillRect(0, ( (i - starty) * charHeight) + ypos, getWidth(),
-                  charHeight);
-      gg.setColor(Color.white);
-    }
-    else if ( (av.getSelectionGroup() != null) &&
-             av.getSelectionGroup().getSequences(null).contains(s))
-    {
-      gg.setColor(Color.lightGray);
-      gg.fillRect(0, ( (i - starty) * charHeight) + ypos, getWidth(),
-                  charHeight);
-      gg.setColor(Color.white);
-    }
-    else
-    {
-      gg.setColor(av.getSequenceColour(s));
-      gg.fillRect(0, ( (i - starty) * charHeight) + ypos, getWidth(),
-                  charHeight);
-      gg.setColor(Color.black);
-    }
-
-    if (av.rightAlignIds)
-    {
-      xPos = panelWidth - fm.stringWidth(
-          s.getDisplayId(av.getShowJVSuffix())
-          ) - 4;
-    }
-
-    gg.drawString(s.getDisplayId(av.getShowJVSuffix()),
-                  xPos,
-                  ( ( (i - starty + 1) * charHeight) + ypos) - (charHeight / 5));
-
-    if (av.hasHiddenRows && av.showHiddenMarkers)
-    {
-      drawMarker(i, starty, ypos);
-    }
-
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param vertical DOCUMENT ME!
-   */
-  public void fastPaint(int vertical)
-  {
-    if (gg == null)
-    {
-      repaint();
-
-      return;
-    }
-
-    gg.copyArea(0, 0, getWidth(), imgHeight, 0, -vertical * av.charHeight);
-
-    int ss = av.startSeq;
-    int es = av.endSeq;
-    int transY = 0;
-
-    if (vertical > 0) // scroll down
-    {
-      ss = es - vertical;
-
-      if (ss < av.startSeq)
-      { // ie scrolling too fast, more than a page at a time
-        ss = av.startSeq;
-      }
-      else
-      {
-        transY = imgHeight - (vertical * av.charHeight);
-      }
-    }
-    else if (vertical < 0)
-    {
-      es = ss - vertical;
-
-      if (es > av.endSeq)
-      {
-        es = av.endSeq;
-      }
-    }
-
-    gg.translate(0, transY);
-
-    drawIds(ss, es);
-
-    gg.translate(0, -transY);
-
-    fastPaint = true;
-    repaint();
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param g DOCUMENT ME!
-   */
-  public void paintComponent(Graphics g)
-  {
-    g.setColor(Color.white);
-    g.fillRect(0, 0, getWidth(), getHeight());
-
-    if (fastPaint)
-    {
-      fastPaint = false;
-      g.drawImage(image, 0, 0, this);
-
-      return;
-    }
-
-    int oldHeight = imgHeight;
-
-    imgHeight = getHeight();
-    imgHeight -= (imgHeight % av.charHeight);
-
-    if (imgHeight < 1)
-    {
-      return;
-    }
-
-    if (oldHeight != imgHeight || image.getWidth(this) != getWidth())
-    {
-      image = new BufferedImage(getWidth(), imgHeight,
-                                BufferedImage.TYPE_INT_RGB);
-    }
-
-    gg = (Graphics2D) image.getGraphics();
-
-    //Fill in the background
-    gg.setColor(Color.white);
-    gg.fillRect(0, 0, getWidth(), imgHeight);
-
-    drawIds(av.getStartSeq(), av.endSeq);
-
-    g.drawImage(image, 0, 0, this);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param starty DOCUMENT ME!
-   * @param endy DOCUMENT ME!
-   */
-  void drawIds(int starty, int endy)
-  {
-    if (av.seqNameItalics)
-    {
-      idfont = new Font(av.getFont().getName(), Font.ITALIC,
-                        av.getFont().getSize());
-    }
-    else
-    {
-      idfont = av.getFont();
-    }
-
-    gg.setFont(idfont);
-    fm = gg.getFontMetrics();
-
-    if (av.antiAlias)
-    {
-      gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-                          RenderingHints.VALUE_ANTIALIAS_ON);
-    }
-
-    Color currentColor = Color.white;
-    Color currentTextColor = Color.black;
-
-    if (av.getWrapAlignment())
-    {
-      int maxwidth = av.alignment.getWidth();
-      int alheight = av.alignment.getHeight();
-
-      if (av.hasHiddenColumns)
-      {
-        maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
-      }
-
-      int annotationHeight = 0;
-
-      if (av.showAnnotation)
-      {
-        if (ap == null)
-        {
-          ap = new AnnotationPanel(av);
-        }
-
-        annotationHeight = ap.adjustPanelHeight();
-        if (labels == null)
-        {
-          labels = new AnnotationLabels(av);
-        }
-      }
-
-      int hgap = av.charHeight;
-      if (av.scaleAboveWrapped)
-      {
-        hgap += av.charHeight;
-      }
-
-      int cHeight = alheight * av.charHeight
-          + hgap
-          + annotationHeight;
-
-      int rowSize = av.getEndRes() - av.getStartRes();
-
-      // Draw the rest of the panels
-      for (int ypos = hgap, row = av.startRes;
-           (ypos <= getHeight()) && (row < maxwidth);
-           ypos += cHeight, row += rowSize)
-      {
-        for (int i = starty; i < alheight; i++)
-        {
-          SequenceI s = av.alignment.getSequenceAt(i);
-          if (av.hasHiddenRows)
-          {
-            setHiddenFont(s);
-          }
-          else
-          {
-            gg.setFont(idfont);
-          }
-
-          drawIdString(gg, s, i, 0, ypos);
-        }
-
-        if (labels != null && av.showAnnotation)
-        {
-          gg.translate(0, ypos + (alheight * av.charHeight));
-          labels.drawComponent(gg, getWidth());
-          gg.translate(0, -ypos - (alheight * av.charHeight));
-        }
-      }
-    }
-    else
-    {
-      //No need to hang on to labels if we're not wrapped
-      labels = null;
-
-      //Now draw the id strings
-      int panelWidth = getWidth();
-      int xPos = 0;
-
-      SequenceI sequence;
-      //Now draw the id strings
-      for (int i = starty; i < endy; i++)
-      {
-        sequence = av.alignment.getSequenceAt(i);
-
-        if (sequence == null)
-        {
-          continue;
-        }
-
-        if (av.hasHiddenRows)
-        {
-          setHiddenFont(sequence);
-        }
-
-        // Selected sequence colours
-        if ( (searchResults != null) &&
-            searchResults.contains(sequence))
-        {
-          currentColor = Color.black;
-          currentTextColor = Color.white;
-        }
-        else if ( (av.getSelectionGroup() != null) &&
-                 av.getSelectionGroup().getSequences(null).contains(
-                     sequence))
-        {
-          currentColor = Color.lightGray;
-          currentTextColor = Color.black;
-        }
-        else
-        {
-          currentColor = av.getSequenceColour(sequence);
-          currentTextColor = Color.black;
-        }
-
-        gg.setColor(currentColor);
-
-        gg.fillRect(0, (i - starty) * av.charHeight, getWidth(),
-                    av.charHeight);
-
-        gg.setColor(currentTextColor);
-
-        String string = sequence.getDisplayId(av.getShowJVSuffix());
-
-        if (av.rightAlignIds)
-        {
-          xPos = panelWidth - fm.stringWidth(string) - 4;
-        }
-
-        gg.drawString(string, xPos,
-                      ( ( (i - starty) * av.charHeight) + av.charHeight) -
-                      (av.charHeight / 5));
-
-        if (av.hasHiddenRows && av.showHiddenMarkers)
-        {
-          drawMarker(i, starty, 0);
-        }
-
-      }
-
-    }
-  }
-
-  void drawMarker(int i, int starty, int yoffset)
-  {
-
-    SequenceI[] hseqs = av.alignment.getHiddenSequences().hiddenSequences;
-    //Use this method here instead of calling hiddenSeq adjust
-    //3 times.
-    int hSize = hseqs.length;
-
-    int hiddenIndex = i;
-    int lastIndex = i - 1;
-    int nextIndex = i + 1;
-
-    for (int j = 0; j < hSize; j++)
-    {
-      if (hseqs[j] != null)
-      {
-        if (j - 1 < hiddenIndex)
-        {
-          hiddenIndex++;
-        }
-        if (j - 1 < lastIndex)
-        {
-          lastIndex++;
-        }
-        if (j - 1 < nextIndex)
-        {
-          nextIndex++;
-        }
-      }
-    }
-
-    boolean below = (hiddenIndex > lastIndex + 1);
-    boolean above = (nextIndex > hiddenIndex + 1);
-
-    gg.setColor(Color.blue);
-    if (below)
-    {
-      gg.fillPolygon(new int[]
-                     {getWidth() - av.charHeight,
-                     getWidth() - av.charHeight,
-                     getWidth()},
-                     new int[]
-                     {
-                     (i - starty) * av.charHeight + yoffset,
-                     (i - starty) * av.charHeight + yoffset + av.charHeight / 4,
-                     (i - starty) * av.charHeight + yoffset
-      }, 3);
-    }
-    if (above)
-    {
-      gg.fillPolygon(new int[]
-                     {getWidth() - av.charHeight,
-                     getWidth() - av.charHeight,
-                     getWidth()},
-                     new int[]
-                     {
-                     (i - starty + 1) * av.charHeight + yoffset,
-                     (i - starty + 1) * av.charHeight + yoffset -
-                     av.charHeight / 4,
-                     (i - starty + 1) * av.charHeight + yoffset
-      }, 3);
-
-    }
-  }
-
-  void setHiddenFont(SequenceI seq)
-  {
-    Font bold = new Font(av.getFont().getName(), Font.BOLD,
-                         av.getFont().getSize());
-
-    if (av.hiddenRepSequences != null &&
-        av.hiddenRepSequences.containsKey(seq))
-    {
-      gg.setFont(bold);
-    }
-    else
-    {
-      gg.setFont(idfont);
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param found DOCUMENT ME!
-   */
-  public void setHighlighted(java.util.Vector found)
-  {
-    searchResults = found;
-    repaint();
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.gui;
+
+import java.awt.*;
+import java.awt.image.*;
+import javax.swing.*;
+
+import jalview.datamodel.*;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class IdCanvas extends JPanel
+{
+  protected AlignViewport av;
+
+  protected boolean showScores = true;
+
+  protected int maxIdLength = -1;
+
+  protected String maxIdStr = null;
+
+  BufferedImage image;
+
+  Graphics2D gg;
+
+  int imgHeight = 0;
+
+  boolean fastPaint = false;
+
+  java.util.Vector searchResults;
+
+  FontMetrics fm;
+
+  AnnotationLabels labels = null;
+
+  AnnotationPanel ap;
+
+  Font idfont;
+
+  /**
+   * Creates a new IdCanvas object.
+   * 
+   * @param av
+   *                DOCUMENT ME!
+   */
+  public IdCanvas(AlignViewport av)
+  {
+    setLayout(new BorderLayout());
+    this.av = av;
+    PaintRefresher.Register(this, av.getSequenceSetId());
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param gg
+   *                DOCUMENT ME!
+   * @param s
+   *                DOCUMENT ME!
+   * @param i
+   *                DOCUMENT ME!
+   * @param starty
+   *                DOCUMENT ME!
+   * @param ypos
+   *                DOCUMENT ME!
+   */
+  public void drawIdString(Graphics2D gg, SequenceI s, int i, int starty,
+          int ypos)
+  {
+    int xPos = 0;
+    int panelWidth = getWidth();
+    int charHeight = av.charHeight;
+
+    if ((searchResults != null) && searchResults.contains(s))
+    {
+      gg.setColor(Color.black);
+      gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
+              charHeight);
+      gg.setColor(Color.white);
+    }
+    else if ((av.getSelectionGroup() != null)
+            && av.getSelectionGroup().getSequences(null).contains(s))
+    {
+      gg.setColor(Color.lightGray);
+      gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
+              charHeight);
+      gg.setColor(Color.white);
+    }
+    else
+    {
+      gg.setColor(av.getSequenceColour(s));
+      gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
+              charHeight);
+      gg.setColor(Color.black);
+    }
+
+    if (av.rightAlignIds)
+    {
+      xPos = panelWidth
+              - fm.stringWidth(s.getDisplayId(av.getShowJVSuffix())) - 4;
+    }
+
+    gg.drawString(s.getDisplayId(av.getShowJVSuffix()), xPos,
+            (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));
+
+    if (av.hasHiddenRows && av.showHiddenMarkers)
+    {
+      drawMarker(i, starty, ypos);
+    }
+
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param vertical
+   *                DOCUMENT ME!
+   */
+  public void fastPaint(int vertical)
+  {
+    if (gg == null)
+    {
+      repaint();
+
+      return;
+    }
+
+    gg.copyArea(0, 0, getWidth(), imgHeight, 0, -vertical * av.charHeight);
+
+    int ss = av.startSeq;
+    int es = av.endSeq;
+    int transY = 0;
+
+    if (vertical > 0) // scroll down
+    {
+      ss = es - vertical;
+
+      if (ss < av.startSeq)
+      { // ie scrolling too fast, more than a page at a time
+        ss = av.startSeq;
+      }
+      else
+      {
+        transY = imgHeight - (vertical * av.charHeight);
+      }
+    }
+    else if (vertical < 0)
+    {
+      es = ss - vertical;
+
+      if (es > av.endSeq)
+      {
+        es = av.endSeq;
+      }
+    }
+
+    gg.translate(0, transY);
+
+    drawIds(ss, es);
+
+    gg.translate(0, -transY);
+
+    fastPaint = true;
+    repaint();
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param g
+   *                DOCUMENT ME!
+   */
+  public void paintComponent(Graphics g)
+  {
+    g.setColor(Color.white);
+    g.fillRect(0, 0, getWidth(), getHeight());
+
+    if (fastPaint)
+    {
+      fastPaint = false;
+      g.drawImage(image, 0, 0, this);
+
+      return;
+    }
+
+    int oldHeight = imgHeight;
+
+    imgHeight = getHeight();
+    imgHeight -= (imgHeight % av.charHeight);
+
+    if (imgHeight < 1)
+    {
+      return;
+    }
+
+    if (oldHeight != imgHeight || image.getWidth(this) != getWidth())
+    {
+      image = new BufferedImage(getWidth(), imgHeight,
+              BufferedImage.TYPE_INT_RGB);
+    }
+
+    gg = (Graphics2D) image.getGraphics();
+
+    // Fill in the background
+    gg.setColor(Color.white);
+    gg.fillRect(0, 0, getWidth(), imgHeight);
+
+    drawIds(av.getStartSeq(), av.endSeq);
+
+    g.drawImage(image, 0, 0, this);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param starty
+   *                DOCUMENT ME!
+   * @param endy
+   *                DOCUMENT ME!
+   */
+  void drawIds(int starty, int endy)
+  {
+    if (av.seqNameItalics)
+    {
+      idfont = new Font(av.getFont().getName(), Font.ITALIC, av.getFont()
+              .getSize());
+    }
+    else
+    {
+      idfont = av.getFont();
+    }
+
+    gg.setFont(idfont);
+    fm = gg.getFontMetrics();
+
+    if (av.antiAlias)
+    {
+      gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+              RenderingHints.VALUE_ANTIALIAS_ON);
+    }
+
+    Color currentColor = Color.white;
+    Color currentTextColor = Color.black;
+
+    if (av.getWrapAlignment())
+    {
+      int maxwidth = av.alignment.getWidth();
+      int alheight = av.alignment.getHeight();
+
+      if (av.hasHiddenColumns)
+      {
+        maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+      }
+
+      int annotationHeight = 0;
+
+      if (av.showAnnotation)
+      {
+        if (ap == null)
+        {
+          ap = new AnnotationPanel(av);
+        }
+
+        annotationHeight = ap.adjustPanelHeight();
+        if (labels == null)
+        {
+          labels = new AnnotationLabels(av);
+        }
+      }
+
+      int hgap = av.charHeight;
+      if (av.scaleAboveWrapped)
+      {
+        hgap += av.charHeight;
+      }
+
+      int cHeight = alheight * av.charHeight + hgap + annotationHeight;
+
+      int rowSize = av.getEndRes() - av.getStartRes();
+
+      // Draw the rest of the panels
+      for (int ypos = hgap, row = av.startRes; (ypos <= getHeight())
+              && (row < maxwidth); ypos += cHeight, row += rowSize)
+      {
+        for (int i = starty; i < alheight; i++)
+        {
+          SequenceI s = av.alignment.getSequenceAt(i);
+          if (av.hasHiddenRows)
+          {
+            setHiddenFont(s);
+          }
+          else
+          {
+            gg.setFont(idfont);
+          }
+
+          drawIdString(gg, s, i, 0, ypos);
+        }
+
+        if (labels != null && av.showAnnotation)
+        {
+          gg.translate(0, ypos + (alheight * av.charHeight));
+          labels.drawComponent(gg, getWidth());
+          gg.translate(0, -ypos - (alheight * av.charHeight));
+        }
+      }
+    }
+    else
+    {
+      // No need to hang on to labels if we're not wrapped
+      labels = null;
+
+      // Now draw the id strings
+      int panelWidth = getWidth();
+      int xPos = 0;
+
+      SequenceI sequence;
+      // Now draw the id strings
+      for (int i = starty; i < endy; i++)
+      {
+        sequence = av.alignment.getSequenceAt(i);
+
+        if (sequence == null)
+        {
+          continue;
+        }
+
+        if (av.hasHiddenRows)
+        {
+          setHiddenFont(sequence);
+        }
+
+        // Selected sequence colours
+        if ((searchResults != null) && searchResults.contains(sequence))
+        {
+          currentColor = Color.black;
+          currentTextColor = Color.white;
+        }
+        else if ((av.getSelectionGroup() != null)
+                && av.getSelectionGroup().getSequences(null).contains(
+                        sequence))
+        {
+          currentColor = Color.lightGray;
+          currentTextColor = Color.black;
+        }
+        else
+        {
+          currentColor = av.getSequenceColour(sequence);
+          currentTextColor = Color.black;
+        }
+
+        gg.setColor(currentColor);
+
+        gg.fillRect(0, (i - starty) * av.charHeight, getWidth(),
+                av.charHeight);
+
+        gg.setColor(currentTextColor);
+
+        String string = sequence.getDisplayId(av.getShowJVSuffix());
+
+        if (av.rightAlignIds)
+        {
+          xPos = panelWidth - fm.stringWidth(string) - 4;
+        }
+
+        gg.drawString(string, xPos,
+                (((i - starty) * av.charHeight) + av.charHeight)
+                        - (av.charHeight / 5));
+
+        if (av.hasHiddenRows && av.showHiddenMarkers)
+        {
+          drawMarker(i, starty, 0);
+        }
+
+      }
+
+    }
+  }
+
+  void drawMarker(int i, int starty, int yoffset)
+  {
+
+    SequenceI[] hseqs = av.alignment.getHiddenSequences().hiddenSequences;
+    // Use this method here instead of calling hiddenSeq adjust
+    // 3 times.
+    int hSize = hseqs.length;
+
+    int hiddenIndex = i;
+    int lastIndex = i - 1;
+    int nextIndex = i + 1;
+
+    for (int j = 0; j < hSize; j++)
+    {
+      if (hseqs[j] != null)
+      {
+        if (j - 1 < hiddenIndex)
+        {
+          hiddenIndex++;
+        }
+        if (j - 1 < lastIndex)
+        {
+          lastIndex++;
+        }
+        if (j - 1 < nextIndex)
+        {
+          nextIndex++;
+        }
+      }
+    }
+
+    boolean below = (hiddenIndex > lastIndex + 1);
+    boolean above = (nextIndex > hiddenIndex + 1);
+
+    gg.setColor(Color.blue);
+    if (below)
+    {
+      gg.fillPolygon(
+              new int[]
+              { getWidth() - av.charHeight, getWidth() - av.charHeight,
+                  getWidth() }, new int[]
+              {
+                  (i - starty) * av.charHeight + yoffset,
+                  (i - starty) * av.charHeight + yoffset + av.charHeight
+                          / 4, (i - starty) * av.charHeight + yoffset }, 3);
+    }
+    if (above)
+    {
+      gg.fillPolygon(
+              new int[]
+              { getWidth() - av.charHeight, getWidth() - av.charHeight,
+                  getWidth() }, new int[]
+              {
+                  (i - starty + 1) * av.charHeight + yoffset,
+                  (i - starty + 1) * av.charHeight + yoffset
+                          - av.charHeight / 4,
+                  (i - starty + 1) * av.charHeight + yoffset }, 3);
+
+    }
+  }
+
+  void setHiddenFont(SequenceI seq)
+  {
+    Font bold = new Font(av.getFont().getName(), Font.BOLD, av.getFont()
+            .getSize());
+
+    if (av.hiddenRepSequences != null
+            && av.hiddenRepSequences.containsKey(seq))
+    {
+      gg.setFont(bold);
+    }
+    else
+    {
+      gg.setFont(idfont);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param found
+   *                DOCUMENT ME!
+   */
+  public void setHighlighted(java.util.Vector found)
+  {
+    searchResults = found;
+    repaint();
+  }
+}
diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 4741974..a781830 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -27,28 +27,35 @@ import jalview.util.UrlLink;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class IdPanel
-    extends JPanel implements MouseListener,
-    MouseMotionListener, MouseWheelListener
+public class IdPanel extends JPanel implements MouseListener,
+        MouseMotionListener, MouseWheelListener
 {
   protected IdCanvas idCanvas;
+
   protected AlignViewport av;
+
   protected AlignmentPanel alignPanel;
+
   ScrollThread scrollThread = null;
+
   int offy;
+
   // int width;
   int lastid = -1;
+
   boolean mouseDragging = false;
 
   /**
    * Creates a new IdPanel object.
-   *
-   * @param av DOCUMENT ME!
-   * @param parent DOCUMENT ME!
+   * 
+   * @param av
+   *                DOCUMENT ME!
+   * @param parent
+   *                DOCUMENT ME!
    */
   public IdPanel(AlignViewport av, AlignmentPanel parent)
   {
@@ -65,8 +72,9 @@ public class IdPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void mouseMoved(MouseEvent e)
   {
@@ -82,7 +90,7 @@ public class IdPanel
       if (sequence.getDescription() != null)
       {
         tmp = sequence.getDescription();
-        tip.append("<br>"+tmp);
+        tip.append("<br>" + tmp);
         maxWidth = Math.max(maxWidth, tmp.length());
       }
 
@@ -98,41 +106,41 @@ public class IdPanel
         }
       }
 
-
-      //ADD NON POSITIONAL SEQUENCE INFO
-      SequenceFeature[] features = sequence.getDatasetSequence().
-          getSequenceFeatures();
+      // ADD NON POSITIONAL SEQUENCE INFO
+      SequenceFeature[] features = sequence.getDatasetSequence()
+              .getSequenceFeatures();
       if (features != null)
       {
         for (int i = 0; i < features.length; i++)
         {
           if (features[i].begin == 0 && features[i].end == 0)
           {
-            tmp = features[i].featureGroup
-                       + " " + features[i].getType() + " " +
-                       features[i].description;
+            tmp = features[i].featureGroup + " " + features[i].getType()
+                    + " " + features[i].description;
             tip.append("<br>" + tmp);
             maxWidth = Math.max(maxWidth, tmp.length());
           }
         }
       }
 
-      if(maxWidth > 60)
+      if (maxWidth > 60)
       {
-         tip.insert(0, "<table width=350 border=0><tr><td><i>");
-         tip.append("</i></td></tr></table>");
+        tip.insert(0, "<table width=350 border=0><tr><td><i>");
+        tip.append("</i></td></tr></table>");
       }
 
       tip.append("</html>");
 
-      setToolTipText("<html>"+sequence.getDisplayId(true)+tip.toString());
+      setToolTipText("<html>" + sequence.getDisplayId(true)
+              + tip.toString());
     }
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void mouseDragged(MouseEvent e)
   {
@@ -156,20 +164,21 @@ public class IdPanel
   public void mouseWheelMoved(MouseWheelEvent e)
   {
     e.consume();
-      if (e.getWheelRotation() > 0)
-      {
-        alignPanel.scrollUp(false);
-      }
-      else
-      {
-        alignPanel.scrollUp(true);
-      }
+    if (e.getWheelRotation() > 0)
+    {
+      alignPanel.scrollUp(false);
+    }
+    else
+    {
+      alignPanel.scrollUp(true);
+    }
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void mouseClicked(MouseEvent e)
   {
@@ -213,7 +222,7 @@ public class IdPanel
       }
 
       String urls[] = urlLink.makeUrls(id, true);
-      if (urls == null || urls[0]==null || urls[0].length()<4)
+      if (urls == null || urls[0] == null || urls[0].length() < 4)
       {
         url = null;
         continue;
@@ -224,24 +233,24 @@ public class IdPanel
     try
     {
       jalview.util.BrowserLauncher.openURL(url);
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
-      JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                            "Unixers: Couldn't find default web browser."
-                                            +
-          "\nAdd the full path to your browser in Preferences.",
-                                            "Web browser not found",
-                                            JOptionPane.WARNING_MESSAGE);
+      JOptionPane
+              .showInternalMessageDialog(
+                      Desktop.desktop,
+                      "Unixers: Couldn't find default web browser."
+                              + "\nAdd the full path to your browser in Preferences.",
+                      "Web browser not found", JOptionPane.WARNING_MESSAGE);
       ex.printStackTrace();
     }
-    
+
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void mouseEntered(MouseEvent e)
   {
@@ -253,8 +262,9 @@ public class IdPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void mouseExited(MouseEvent e)
   {
@@ -268,8 +278,8 @@ public class IdPanel
       scrollThread = new ScrollThread(true);
     }
 
-    if (mouseDragging && (e.getY() >= getHeight()) &&
-        (av.alignment.getHeight() > av.getEndSeq()))
+    if (mouseDragging && (e.getY() >= getHeight())
+            && (av.alignment.getHeight() > av.getEndSeq()))
     {
       scrollThread = new ScrollThread(false);
     }
@@ -277,8 +287,9 @@ public class IdPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void mousePressed(MouseEvent e)
   {
@@ -292,15 +303,16 @@ public class IdPanel
     if (javax.swing.SwingUtilities.isRightMouseButton(e))
     {
       jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel,
-          (Sequence) av.getAlignment().getSequenceAt(seq),
-          Preferences.sequenceURLLinks);
+              (Sequence) av.getAlignment().getSequenceAt(seq),
+              Preferences.sequenceURLLinks);
       pop.show(this, e.getX(), e.getY());
 
       return;
     }
 
-    if ( (av.getSelectionGroup() == null) ||
-        ( (!e.isControlDown() && !e.isShiftDown()) && av.getSelectionGroup() != null))
+    if ((av.getSelectionGroup() == null)
+            || ((!e.isControlDown() && !e.isShiftDown()) && av
+                    .getSelectionGroup() != null))
     {
       av.setSelectionGroup(new SequenceGroup());
       av.getSelectionGroup().setStartRes(0);
@@ -321,8 +333,9 @@ public class IdPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param seq DOCUMENT ME!
+   * 
+   * @param seq
+   *                DOCUMENT ME!
    */
   void selectSeq(int seq)
   {
@@ -334,9 +347,11 @@ public class IdPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param start DOCUMENT ME!
-   * @param end DOCUMENT ME!
+   * 
+   * @param start
+   *                DOCUMENT ME!
+   * @param end
+   *                DOCUMENT ME!
    */
   void selectSeqs(int start, int end)
   {
@@ -362,15 +377,16 @@ public class IdPanel
 
     for (int i = start; i <= end; i++)
     {
-      av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
-                                         true);
+      av.getSelectionGroup().addSequence(
+              av.getAlignment().getSequenceAt(i), true);
     }
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void mouseReleased(MouseEvent e)
   {
@@ -385,8 +401,9 @@ public class IdPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param found DOCUMENT ME!
+   * 
+   * @param found
+   *                DOCUMENT ME!
    */
   public void highlightSearchResults(java.util.Vector found)
   {
@@ -397,20 +414,20 @@ public class IdPanel
       return;
     }
 
-    int index = av.alignment.findIndex( (SequenceI) found.get(0));
+    int index = av.alignment.findIndex((SequenceI) found.get(0));
 
     // do we need to scroll the panel?
-    if ( (av.getStartSeq() > index) || (av.getEndSeq() < index))
+    if ((av.getStartSeq() > index) || (av.getEndSeq() < index))
     {
       alignPanel.setScrollValues(av.getStartRes(), index);
     }
   }
 
   // this class allows scrolling off the bottom of the visible alignment
-  class ScrollThread
-      extends Thread
+  class ScrollThread extends Thread
   {
     boolean running = false;
+
     boolean up = true;
 
     public ScrollThread(boolean up)
@@ -461,8 +478,7 @@ public class IdPanel
         try
         {
           Thread.sleep(100);
-        }
-        catch (Exception ex)
+        } catch (Exception ex)
         {
         }
       }
diff --git a/src/jalview/gui/IdwidthAdjuster.java b/src/jalview/gui/IdwidthAdjuster.java
index 1c7d215..c257900 100755
--- a/src/jalview/gui/IdwidthAdjuster.java
+++ b/src/jalview/gui/IdwidthAdjuster.java
@@ -1,161 +1,172 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.gui;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class IdwidthAdjuster
-    extends JPanel implements MouseListener,
-    MouseMotionListener
-{
-  boolean active = false;
-  int oldX = 0;
-  Image image;
-  AlignmentPanel ap;
-
-  /**
-   * Creates a new IdwidthAdjuster object.
-   *
-   * @param ap DOCUMENT ME!
-   */
-  public IdwidthAdjuster(AlignmentPanel ap)
-  {
-    this.ap = ap;
-
-    java.net.URL url = getClass().getResource("/images/idwidth.gif");
-
-    if (url != null)
-    {
-      image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
-    }
-
-    addMouseListener(this);
-    addMouseMotionListener(this);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
-   */
-  public void mousePressed(MouseEvent evt)
-  {
-    oldX = evt.getX();
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
-   */
-  public void mouseReleased(MouseEvent evt)
-  {
-    active = false;
-    repaint();
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
-   */
-  public void mouseEntered(MouseEvent evt)
-  {
-    active = true;
-    repaint();
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
-   */
-  public void mouseExited(MouseEvent evt)
-  {
-    active = false;
-    repaint();
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
-   */
-  public void mouseDragged(MouseEvent evt)
-  {
-    active = true;
-
-    Dimension d = ap.idPanel.idCanvas.getPreferredSize();
-    int dif = evt.getX() - oldX;
-
-    if ( ( (d.width + dif) > 20) || (dif > 0))
-    {
-      ap.idPanel.idCanvas.setPreferredSize(new Dimension(d.width + dif,
-          d.height));
-      ap.paintAlignment(true);
-    }
-
-    oldX = evt.getX();
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
-   */
-  public void mouseMoved(MouseEvent evt)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
-   */
-  public void mouseClicked(MouseEvent evt)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param g DOCUMENT ME!
-   */
-  public void paintComponent(Graphics g)
-  {
-    g.setColor(Color.white);
-    g.fillRect(0, 0, getWidth(), getHeight());
-
-    if (active)
-    {
-      if (image != null)
-      {
-        g.drawImage(image, getWidth() - 20, 2, this);
-      }
-    }
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.gui;
+
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class IdwidthAdjuster extends JPanel implements MouseListener,
+        MouseMotionListener
+{
+  boolean active = false;
+
+  int oldX = 0;
+
+  Image image;
+
+  AlignmentPanel ap;
+
+  /**
+   * Creates a new IdwidthAdjuster object.
+   * 
+   * @param ap
+   *                DOCUMENT ME!
+   */
+  public IdwidthAdjuster(AlignmentPanel ap)
+  {
+    this.ap = ap;
+
+    java.net.URL url = getClass().getResource("/images/idwidth.gif");
+
+    if (url != null)
+    {
+      image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
+    }
+
+    addMouseListener(this);
+    addMouseMotionListener(this);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
+   */
+  public void mousePressed(MouseEvent evt)
+  {
+    oldX = evt.getX();
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
+   */
+  public void mouseReleased(MouseEvent evt)
+  {
+    active = false;
+    repaint();
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
+   */
+  public void mouseEntered(MouseEvent evt)
+  {
+    active = true;
+    repaint();
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
+   */
+  public void mouseExited(MouseEvent evt)
+  {
+    active = false;
+    repaint();
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
+   */
+  public void mouseDragged(MouseEvent evt)
+  {
+    active = true;
+
+    Dimension d = ap.idPanel.idCanvas.getPreferredSize();
+    int dif = evt.getX() - oldX;
+
+    if (((d.width + dif) > 20) || (dif > 0))
+    {
+      ap.idPanel.idCanvas.setPreferredSize(new Dimension(d.width + dif,
+              d.height));
+      ap.paintAlignment(true);
+    }
+
+    oldX = evt.getX();
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
+   */
+  public void mouseMoved(MouseEvent evt)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
+   */
+  public void mouseClicked(MouseEvent evt)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param g
+   *                DOCUMENT ME!
+   */
+  public void paintComponent(Graphics g)
+  {
+    g.setColor(Color.white);
+    g.fillRect(0, 0, getWidth(), getHeight());
+
+    if (active)
+    {
+      if (image != null)
+      {
+        g.drawImage(image, getWidth() - 20, 2, this);
+      }
+    }
+  }
+}
diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index ebf7aba..f54383e 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -36,13 +36,12 @@ import jalview.schemes.*;
 import jalview.structure.StructureSelectionManager;
 
 /**
- * Write out the current jalview desktop state
- * as a Jalview XML stream.
+ * Write out the current jalview desktop state as a Jalview XML stream.
+ * 
+ * Note: the vamsas objects referred to here are primitive versions of the
+ * VAMSAS project schema elements - they are not the same and most likely never
+ * will be :)
  * 
- * Note: the vamsas objects referred to here are primitive
- * versions of the VAMSAS project schema elements - they are
- * not the same and most likely never will be :)
- *
  * @author $author$
  * @version $Revision$
  */
@@ -50,49 +49,59 @@ public class Jalview2XML
 {
   /**
    * create/return unique hash string for sq
+   * 
    * @param sq
    * @return new or existing unique string for sq
    */
   String seqHash(SequenceI sq)
   {
-    if (seqsToIds==null)
+    if (seqsToIds == null)
     {
       initSeqRefs();
     }
     if (seqsToIds.containsKey(sq))
     {
       return (String) seqsToIds.get(sq);
-    } else {
-      //         create sequential key
-      String key = "sq"+(seqsToIds.size()+1);
+    }
+    else
+    {
+      // create sequential key
+      String key = "sq" + (seqsToIds.size() + 1);
       seqsToIds.put(sq, key);
       return key;
     }
   }
+
   void clearSeqRefs()
   {
     seqRefIds.clear();
     seqsToIds.clear();
   }
+
   void initSeqRefs()
   {
-    if (seqsToIds==null)
+    if (seqsToIds == null)
     {
       seqsToIds = new IdentityHashMap();
     }
-    if (seqRefIds==null)
+    if (seqRefIds == null)
     {
       seqRefIds = new Hashtable();
     }
   }
+
   java.util.IdentityHashMap seqsToIds = null; // SequenceI->key resolution
+
   java.util.Hashtable seqRefIds = null; // key->SequenceI resolution
 
   Vector frefedSequence = null;
+
   boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
+
   public Jalview2XML()
   {
   }
+
   public Jalview2XML(boolean raiseGUI)
   {
     this.raiseGUI = raiseGUI;
@@ -155,7 +164,11 @@ public class Jalview2XML
           }
           else
           {
-            System.err.println("IMPLEMENTATION WARNING: Unresolved forward reference for hash string "+ref[0]+" with objecttype "+ref[1].getClass());
+            System.err
+                    .println("IMPLEMENTATION WARNING: Unresolved forward reference for hash string "
+                            + ref[0]
+                            + " with objecttype "
+                            + ref[1].getClass());
             r++;
           }
         }
@@ -169,9 +182,8 @@ public class Jalview2XML
   }
 
   /**
-   * This maintains a list of viewports, the key being the
-   * seqSetId. Important to set historyItem and redoList
-   * for multiple views
+   * This maintains a list of viewports, the key being the seqSetId. Important
+   * to set historyItem and redoList for multiple views
    */
   Hashtable viewportsAdded;
 
@@ -199,14 +211,14 @@ public class Jalview2XML
       FileOutputStream fos = new FileOutputStream(statefile);
       JarOutputStream jout = new JarOutputStream(fos);
 
-      //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
-      ////////////////////////////////////////////////////
-      //NOTE ALSO new PrintWriter must be used for each new JarEntry
+      // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
+      // //////////////////////////////////////////////////
+      // NOTE ALSO new PrintWriter must be used for each new JarEntry
       PrintWriter out = null;
 
       Vector shortNames = new Vector();
 
-      //REVERSE ORDER
+      // REVERSE ORDER
       for (int i = frames.length - 1; i > -1; i--)
       {
         if (frames[i] instanceof AlignFrame)
@@ -257,11 +269,18 @@ public class Jalview2XML
           }
         }
       }
-      try { jout.flush(); } catch (Exception foo) {};
+      try
+      {
+        jout.flush();
+      } catch (Exception foo)
+      {
+      }
+      ;
       jout.close();
     } catch (Exception ex)
     {
-      //TODO: inform user of the problem - they need to know if their data was not saved !
+      // TODO: inform user of the problem - they need to know if their data was
+      // not saved !
       ex.printStackTrace();
     }
   }
@@ -287,7 +306,13 @@ public class Jalview2XML
         SaveState(apanel, jfileName, jout);
       }
 
-      try { jout.flush(); } catch (Exception foo) {};
+      try
+      {
+        jout.flush();
+      } catch (Exception foo)
+      {
+      }
+      ;
       jout.close();
       return true;
     } catch (Exception ex)
@@ -298,19 +323,23 @@ public class Jalview2XML
   }
 
   /**
-   * create a JalviewModel from an algnment view and marshall it
-   * to a JarOutputStream
-   *
-   * @param ap panel to create jalview model for
-   * @param fileName name of alignment panel written to output stream
-   * @param jout jar output stream
-   * @param out jar entry name
+   * create a JalviewModel from an algnment view and marshall it to a
+   * JarOutputStream
+   * 
+   * @param ap
+   *                panel to create jalview model for
+   * @param fileName
+   *                name of alignment panel written to output stream
+   * @param jout
+   *                jar output stream
+   * @param out
+   *                jar entry name
    */
   public JalviewModel SaveState(AlignmentPanel ap, String fileName,
           JarOutputStream jout)
   {
     initSeqRefs();
-    
+
     Vector userColours = new Vector();
 
     AlignViewport av = ap.av;
@@ -354,7 +383,7 @@ public class Jalview2XML
 
     JSeq jseq;
 
-    //SAVE SEQUENCES
+    // SAVE SEQUENCES
     String id = "";
     jalview.datamodel.SequenceI jds;
     for (int i = 0; i < jal.getHeight(); i++)
@@ -364,14 +393,19 @@ public class Jalview2XML
 
       if (seqRefIds.get(id) != null)
       {
-        // This happens for two reasons: 1. multiple views are being serialised. 2. the hashCode has collided with another sequence's code. This DOES HAPPEN! (PF00072.15.stk does this)
-        // JBPNote: Uncomment to debug writing out of files that do not read back in due to ArrayOutOfBoundExceptions.
-        //System.err.println("vamsasSeq backref: "+id+"");
-        //System.err.println(jds.getName()+" "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
-        //System.err.println("Hashcode: "+seqHash(jds));
-        //SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
-        //System.err.println(rsq.getName()+" "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
-        //System.err.println("Hashcode: "+seqHash(rsq));
+        // This happens for two reasons: 1. multiple views are being serialised.
+        // 2. the hashCode has collided with another sequence's code. This DOES
+        // HAPPEN! (PF00072.15.stk does this)
+        // JBPNote: Uncomment to debug writing out of files that do not read
+        // back in due to ArrayOutOfBoundExceptions.
+        // System.err.println("vamsasSeq backref: "+id+"");
+        // System.err.println(jds.getName()+"
+        // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
+        // System.err.println("Hashcode: "+seqHash(jds));
+        // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
+        // System.err.println(rsq.getName()+"
+        // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
+        // System.err.println("Hashcode: "+seqHash(rsq));
       }
       else
       {
@@ -464,7 +498,7 @@ public class Jalview2XML
           pdb.setType(entry.getType());
 
           AppJmol jmol;
-          //This must have been loaded, is it still visible?
+          // This must have been loaded, is it still visible?
           JInternalFrame[] frames = Desktop.desktop.getAllFrames();
           for (int f = frames.length - 1; f > -1; f--)
           {
@@ -591,8 +625,8 @@ public class Jalview2XML
       }
     }
 
-    //SAVE TREES
-    ///////////////////////////////////
+    // SAVE TREES
+    // /////////////////////////////////
     if (av.currentTree != null)
     {
       // FIND ANY ASSOCIATED TREES
@@ -636,7 +670,7 @@ public class Jalview2XML
       }
     }
 
-    //SAVE ANNOTATIONS
+    // SAVE ANNOTATIONS
     if (jal.getAlignmentAnnotation() != null)
     {
       jalview.datamodel.AlignmentAnnotation[] aa = jal
@@ -739,7 +773,7 @@ public class Jalview2XML
       }
     }
 
-    //SAVE GROUPS
+    // SAVE GROUPS
     if (jal.getGroups() != null)
     {
       JGroup[] groups = new JGroup[jal.getGroups().size()];
@@ -809,7 +843,7 @@ public class Jalview2XML
       jms.setJGroup(groups);
     }
 
-    ///////////SAVE VIEWPORT
+    // /////////SAVE VIEWPORT
     Viewport view = new Viewport();
     view.setTitle(ap.alignFrame.getTitle());
     view.setSequenceSetId(av.getSequenceSetId());
@@ -933,7 +967,7 @@ public class Jalview2XML
         settingsAdded.addElement(renderOrder[ro]);
       }
 
-      //Make sure we save none displayed feature settings
+      // Make sure we save none displayed feature settings
       Enumeration en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours
               .keys();
       while (en.hasMoreElements())
@@ -999,18 +1033,19 @@ public class Jalview2XML
     object.setJalviewModelSequence(jms);
     object.getVamsasModel().addSequenceSet(vamsasSet);
 
-    if (jout!=null && fileName!=null)
+    if (jout != null && fileName != null)
     {
-      //We may not want to write the object to disk,
-      //eg we can copy the alignViewport to a new view object
-      //using save and then load
+      // We may not want to write the object to disk,
+      // eg we can copy the alignViewport to a new view object
+      // using save and then load
       try
       {
         JarEntry entry = new JarEntry(fileName);
         jout.putNextEntry(entry);
         PrintWriter pout = new PrintWriter(new OutputStreamWriter(jout,
-        "UTF-8"));
-        org.exolab.castor.xml.Marshaller marshaller = new org.exolab.castor.xml.Marshaller(pout);
+                "UTF-8"));
+        org.exolab.castor.xml.Marshaller marshaller = new org.exolab.castor.xml.Marshaller(
+                pout);
         marshaller.marshal(object);
         pout.flush();
         jout.closeEntry();
@@ -1047,7 +1082,8 @@ public class Jalview2XML
     }
     else
     {
-      vamsasSeq.setDsseqid(id); // so we can tell which sequences really are dataset sequences only
+      vamsasSeq.setDsseqid(id); // so we can tell which sequences really are
+                                // dataset sequences only
       dbrefs = jds.getDBRef();
     }
     if (dbrefs != null)
@@ -1104,8 +1140,8 @@ public class Jalview2XML
                 && (parentseq != jmp.getTo() || parentseq
                         .getDatasetSequence() != jmp.getTo()))
         {
-          mpc.setSequence(createVamsasSequence(false, seqHash(jmp.getTo())
-                  , jmp.getTo(), jds));
+          mpc.setSequence(createVamsasSequence(false, seqHash(jmp.getTo()),
+                  jmp.getTo(), jds));
         }
         else
         {
@@ -1223,8 +1259,9 @@ public class Jalview2XML
 
   /**
    * DOCUMENT ME!
-   *
-   * @param file DOCUMENT ME!
+   * 
+   * @param file
+   *                DOCUMENT ME!
    */
   public AlignFrame LoadJalviewAlign(final String file)
   {
@@ -1241,7 +1278,7 @@ public class Jalview2XML
 
     try
     {
-      //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
+      // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
       URL url = null;
 
       if (file.startsWith("http://"))
@@ -1287,7 +1324,7 @@ public class Jalview2XML
         }
         else if (jarentry != null)
         {
-          //Some other file here.
+          // Some other file here.
           entryCount++;
         }
       } while (jarentry != null);
@@ -1308,11 +1345,13 @@ public class Jalview2XML
     {
       System.err.println("Parsing as Jalview Version 2 file failed.");
       ex.printStackTrace(System.err);
-      
-      //Is Version 1 Jar file?
-      try {
+
+      // Is Version 1 Jar file?
+      try
+      {
         af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(file);
-      } catch (Exception ex2) {
+      } catch (Exception ex2)
+      {
         System.err.println("Exception whilst loading as jalviewXMLV1:");
         ex2.printStackTrace();
         af = null;
@@ -1348,19 +1387,21 @@ public class Jalview2XML
     {
       final String finalErrorMessage = errorMessage;
       if (raiseGUI)
-        {
+      {
         javax.swing.SwingUtilities.invokeLater(new Runnable()
         {
           public void run()
-        {
-          JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                  finalErrorMessage, "Error loading Jalview file",
-                  JOptionPane.WARNING_MESSAGE);
-        }
-      });
-        } else {
-          System.err.println("Problem loading Jalview file: "+errorMessage);
-        }
+          {
+            JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                    finalErrorMessage, "Error loading Jalview file",
+                    JOptionPane.WARNING_MESSAGE);
+          }
+        });
+      }
+      else
+      {
+        System.err.println("Problem loading Jalview file: " + errorMessage);
+      }
     }
 
     return af;
@@ -1405,7 +1446,13 @@ public class Jalview2XML
       {
         out.println(data);
       }
-      try { out.flush(); } catch (Exception foo) {};
+      try
+      {
+        out.flush();
+      } catch (Exception foo)
+      {
+      }
+      ;
       out.close();
 
       alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath());
@@ -1429,8 +1476,8 @@ public class Jalview2XML
 
     Viewport view = jms.getViewport(0);
 
-    //////////////////////////////////
-    //LOAD SEQUENCES
+    // ////////////////////////////////
+    // LOAD SEQUENCES
 
     Vector hiddenSeqs = null;
     jalview.datamodel.Sequence jseq;
@@ -1440,7 +1487,7 @@ public class Jalview2XML
     boolean multipleView = false;
 
     JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
-    int vi=0; // counter in vamsasSeq array
+    int vi = 0; // counter in vamsasSeq array
     for (int i = 0; i < JSEQ.length; i++)
     {
       String seqId = JSEQ[i].getId() + "";
@@ -1458,7 +1505,7 @@ public class Jalview2XML
         jseq.setStart(JSEQ[i].getStart());
         jseq.setEnd(JSEQ[i].getEnd());
         jseq.setVamsasId(uniqueSetSuffix + seqId);
-        seqRefIds.put(vamsasSeq[vi].getId()+"", jseq);
+        seqRefIds.put(vamsasSeq[vi].getId() + "", jseq);
         tmpseqs.add(jseq);
         vi++;
       }
@@ -1476,9 +1523,9 @@ public class Jalview2XML
 
     }
 
-    ///
+    // /
     // Create the alignment object from the sequence set
-    /////////////////////////////////
+    // ///////////////////////////////
     jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[tmpseqs
             .size()];
 
@@ -1487,17 +1534,17 @@ public class Jalview2XML
     jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(
             orderedSeqs);
 
-    /// Add the alignment properties
+    // / Add the alignment properties
     for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
     {
       SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
       al.setProperty(ssp.getKey(), ssp.getValue());
     }
 
-    ///
+    // /
     // SequenceFeatures are added to the DatasetSequence,
     // so we must create or recover the dataset before loading features
-    /////////////////////////////////
+    // ///////////////////////////////
     if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
     {
       // older jalview projects do not have a dataset id.
@@ -1507,7 +1554,7 @@ public class Jalview2XML
     {
       recoverDatasetFor(vamsasSet, al);
     }
-    /////////////////////////////////
+    // ///////////////////////////////
 
     Hashtable pdbloaded = new Hashtable();
     if (!multipleView)
@@ -1572,7 +1619,7 @@ public class Jalview2XML
       }
     }
 
-    /////////////////////////////////
+    // ///////////////////////////////
     // LOAD SEQUENCE MAPPINGS
     if (vamsasSet.getAlcodonFrameCount() > 0)
     {
@@ -1604,15 +1651,17 @@ public class Jalview2XML
             // attach to dna sequence reference.
             if (maps[m].getMapping() != null)
             {
-              mapping = addMapping(maps[m]
-                      .getMapping());
+              mapping = addMapping(maps[m].getMapping());
             }
             if (dnaseq != null)
             {
-                cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
-            } else {
+              cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
+            }
+            else
+            {
               // defer to later
-              frefedSequence.add(new Object[] { maps[m].getDnasq(), cf, mapping});
+              frefedSequence.add(new Object[]
+              { maps[m].getDnasq(), cf, mapping });
             }
           }
         }
@@ -1621,8 +1670,8 @@ public class Jalview2XML
 
     }
 
-    //////////////////////////////////
-    //LOAD ANNOTATIONS
+    // ////////////////////////////////
+    // LOAD ANNOTATIONS
     boolean hideQuality = true, hideConservation = true, hideConsensus = true;
 
     if (vamsasSet.getAnnotationCount() > 0)
@@ -1678,14 +1727,15 @@ public class Jalview2XML
                     .getSecondaryStructure() == null || ae[aa]
                     .getSecondaryStructure().length() == 0) ? ' ' : ae[aa]
                     .getSecondaryStructure().charAt(0), ae[aa].getValue()
-                    
+
             );
-            // JBPNote: Consider verifying dataflow for IO of secondary structure annotation read from Stockholm files
-            // this was added to try to ensure that 
-            //if (anot[ae[aa].getPosition()].secondaryStructure>' ')
-            //{
-            //  anot[ae[aa].getPosition()].displayCharacter = "";
-            //}
+            // JBPNote: Consider verifying dataflow for IO of secondary
+            // structure annotation read from Stockholm files
+            // this was added to try to ensure that
+            // if (anot[ae[aa].getPosition()].secondaryStructure>' ')
+            // {
+            // anot[ae[aa].getPosition()].displayCharacter = "";
+            // }
             anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa]
                     .getColour());
           }
@@ -1742,8 +1792,8 @@ public class Jalview2XML
       }
     }
 
-    /////////////////////////
-    //LOAD GROUPS
+    // ///////////////////////
+    // LOAD GROUPS
     if (jms.getJGroupCount() > 0)
     {
       JGroup[] groups = jms.getJGroup();
@@ -1815,7 +1865,7 @@ public class Jalview2XML
       }
     }
 
-    /////////////////////////////////
+    // ///////////////////////////////
     // LOAD VIEWPORT
 
     AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
@@ -1828,10 +1878,10 @@ public class Jalview2XML
               new java.awt.Color(JSEQ[i].getColour()));
     }
 
-    //If we just load in the same jar file again, the sequenceSetId
-    //will be the same, and we end up with multiple references
-    //to the same sequenceSet. We must modify this id on load
-    //so that each load of the file gives a unique id
+    // If we just load in the same jar file again, the sequenceSetId
+    // will be the same, and we end up with multiple references
+    // to the same sequenceSet. We must modify this id on load
+    // so that each load of the file gives a unique id
     String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
 
     af.viewport.gatherViewsHere = view.getGatheredViews();
@@ -1948,7 +1998,7 @@ public class Jalview2XML
       }
       else if (view.getBgColour().startsWith("Annotation"))
       {
-        //int find annotation
+        // int find annotation
         for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
         {
           if (af.viewport.alignment.getAlignmentAnnotation()[i].label
@@ -2005,17 +2055,16 @@ public class Jalview2XML
                   continue;
                 }
 
-                /*    if (view.getAnnotationColours().getColourScheme().equals("None"))
-                    {
-                      sg.cs = new AnnotationColourGradient(
-                          af.viewport.alignment.getAlignmentAnnotation()[i],
-                          new java.awt.Color(view.getAnnotationColours().
-                                             getMinColour()),
-                          new java.awt.Color(view.getAnnotationColours().
-                                             getMaxColour()),
-                          view.getAnnotationColours().getAboveThreshold());
-                    }
-                    else*/
+                /*
+                 * if
+                 * (view.getAnnotationColours().getColourScheme().equals("None")) {
+                 * sg.cs = new AnnotationColourGradient(
+                 * af.viewport.alignment.getAlignmentAnnotation()[i], new
+                 * java.awt.Color(view.getAnnotationColours(). getMinColour()),
+                 * new java.awt.Color(view.getAnnotationColours().
+                 * getMaxColour()),
+                 * view.getAnnotationColours().getAboveThreshold()); } else
+                 */
                 {
                   sg.cs = new AnnotationColourGradient(
                           af.viewport.alignment.getAlignmentAnnotation()[i],
@@ -2100,7 +2149,7 @@ public class Jalview2XML
       for (int c = 0; c < view.getHiddenColumnsCount(); c++)
       {
         af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), view
-                .getHiddenColumns(c).getEnd() //+1
+                .getHiddenColumns(c).getEnd() // +1
                 );
       }
     }
@@ -2110,8 +2159,8 @@ public class Jalview2XML
     Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view
             .getHeight());
 
-    //LOAD TREES
-    ///////////////////////////////////////
+    // LOAD TREES
+    // /////////////////////////////////////
     if (loadTreesAndStructures && jms.getTreeCount() > 0)
     {
       try
@@ -2157,7 +2206,7 @@ public class Jalview2XML
       }
     }
 
-    ////LOAD STRUCTURES
+    // //LOAD STRUCTURES
     if (loadTreesAndStructures)
     {
       for (int i = 0; i < JSEQ.length; i++)
@@ -2180,21 +2229,26 @@ public class Jalview2XML
               int height = ids[p].getStructureState(s).getHeight();
 
               java.awt.Component comp = null;
-              
+
               JInternalFrame[] frames = null;
-              do {
-                try {
+              do
+              {
+                try
+                {
                   frames = Desktop.desktop.getAllFrames();
-                }
-                catch (ArrayIndexOutOfBoundsException e)
+                } catch (ArrayIndexOutOfBoundsException e)
                 {
                   // occasional No such child exceptions are thrown here...
                   frames = null;
-                  try {
+                  try
+                  {
                     Thread.sleep(10);
-                  } catch (Exception f) {};
+                  } catch (Exception f)
+                  {
+                  }
+                  ;
                 }
-              } while (frames==null);
+              } while (frames == null);
               for (int f = 0; f < frames.length; f++)
               {
                 if (frames[f] instanceof AppJmol)
@@ -2278,26 +2332,31 @@ public class Jalview2XML
       al.setDataset(ds);
     }
   }
-  
 
   /**
    * 
-   * @param vamsasSeq sequence definition to create/merge dataset sequence for
-   * @param ds dataset alignment 
-   * @param dseqs vector to add new dataset sequence to
+   * @param vamsasSeq
+   *                sequence definition to create/merge dataset sequence for
+   * @param ds
+   *                dataset alignment
+   * @param dseqs
+   *                vector to add new dataset sequence to
    */
-  private void ensureJalviewDatasetSequence(Sequence vamsasSeq, AlignmentI ds, Vector dseqs)
+  private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
+          AlignmentI ds, Vector dseqs)
   {
-    // JBP TODO: Check this is called for AlCodonFrames to support recovery of xRef Codon Maps
-    jalview.datamodel.Sequence sq = (jalview.datamodel.Sequence) seqRefIds.get(vamsasSeq.getId());
+    // JBP TODO: Check this is called for AlCodonFrames to support recovery of
+    // xRef Codon Maps
+    jalview.datamodel.Sequence sq = (jalview.datamodel.Sequence) seqRefIds
+            .get(vamsasSeq.getId());
     jalview.datamodel.SequenceI dsq = null;
-    if (sq!=null && sq.getDatasetSequence()!=null)
+    if (sq != null && sq.getDatasetSequence() != null)
     {
       dsq = (jalview.datamodel.SequenceI) sq.getDatasetSequence();
     }
-    
+
     String sqid = vamsasSeq.getDsseqid();
-    if (dsq==null)
+    if (dsq == null)
     {
       // need to create or add a new dataset sequence reference to this sequence
       if (sqid != null)
@@ -2318,7 +2377,7 @@ public class Jalview2XML
         seqRefIds.put(sqid, dsq);
         if (ds == null)
         {
-          if (dseqs!=null)
+          if (dseqs != null)
           {
             dseqs.addElement(dsq);
           }
@@ -2327,48 +2386,45 @@ public class Jalview2XML
         {
           ds.addSequence(dsq);
         }
-      } else {
-        if (sq!=dsq)
-        {  // make this dataset sequence sq's dataset sequence
+      }
+      else
+      {
+        if (sq != dsq)
+        { // make this dataset sequence sq's dataset sequence
           sq.setDatasetSequence(dsq);
         }
       }
     }
     // TODO: refactor this as a merge dataset sequence function
-    // now check that sq (the dataset sequence) sequence really is the union of all references to it
-    //boolean pre = sq.getStart() < dsq.getStart();
-    //boolean post = sq.getEnd() > dsq.getEnd();
-    //if (pre || post)
-    if (sq!=dsq)
+    // now check that sq (the dataset sequence) sequence really is the union of
+    // all references to it
+    // boolean pre = sq.getStart() < dsq.getStart();
+    // boolean post = sq.getEnd() > dsq.getEnd();
+    // if (pre || post)
+    if (sq != dsq)
     {
       StringBuffer sb = new StringBuffer();
       String newres = jalview.analysis.AlignSeq.extractGaps(
               jalview.util.Comparison.GapChars, sq.getSequenceAsString());
-      if (!newres.equalsIgnoreCase(dsq.getSequenceAsString()) && newres.length()>dsq.getLength())
+      if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
+              && newres.length() > dsq.getLength())
       {
         // Update with the longer sequence.
         synchronized (dsq)
         {
-        /*if (pre)
-        {
-          sb.insert(0, newres
-                  .substring(0, dsq.getStart() - sq.getStart()));
-          dsq.setStart(sq.getStart());
-        }
-        if (post)
-        {
-          sb.append(newres.substring(newres.length() - sq.getEnd()
-                  - dsq.getEnd()));
-          dsq.setEnd(sq.getEnd());
-        }
-        */
-        dsq.setSequence(sb.toString());
+          /*
+           * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
+           * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
+           * sb.append(newres.substring(newres.length() - sq.getEnd() -
+           * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
+           */
+          dsq.setSequence(sb.toString());
         }
-        //TODO: merges will never happen if we 'know' we have the real dataset sequence - this should be detected when id==dssid
-        System.err
-              .println("DEBUG Notice:  Merged dataset sequence"); // ("
-                      // + (pre ? "prepended" : "") + " "
-                      //+ (post ? "appended" : ""));
+        // TODO: merges will never happen if we 'know' we have the real dataset
+        // sequence - this should be detected when id==dssid
+        System.err.println("DEBUG Notice:  Merged dataset sequence"); // ("
+        // + (pre ? "prepended" : "") + " "
+        // + (post ? "appended" : ""));
       }
     }
   }
@@ -2460,35 +2516,41 @@ public class Jalview2XML
          * local sequence definition
          */
         Sequence ms = mc.getSequence();
-        jalview.datamodel.Sequence djs=null;
+        jalview.datamodel.Sequence djs = null;
         String sqid = ms.getDsseqid();
-        if (sqid!=null && sqid.length()>0)
+        if (sqid != null && sqid.length() > 0)
         {
           /*
            * recover dataset sequence
            */
           djs = (jalview.datamodel.Sequence) seqRefIds.get(sqid);
-        } else {
-          System.err.println("Warning - making up dataset sequence id for DbRef sequence map reference");
-          sqid = ((Object)ms).toString(); // make up a new hascode for undefined dataset sequence hash (unlikely to happen)
         }
-        
-        if (djs==null) {
+        else
+        {
+          System.err
+                  .println("Warning - making up dataset sequence id for DbRef sequence map reference");
+          sqid = ((Object) ms).toString(); // make up a new hascode for
+                                            // undefined dataset sequence hash
+                                            // (unlikely to happen)
+        }
+
+        if (djs == null)
+        {
           /**
            * make a new dataset sequence and add it to refIds hash
            */
-          djs = new jalview.datamodel.Sequence(ms
-                .getName(), ms.getSequence());
+          djs = new jalview.datamodel.Sequence(ms.getName(), ms
+                  .getSequence());
           djs.setStart(jmap.getMap().getToLowest());
           djs.setEnd(jmap.getMap().getToHighest());
           djs.setVamsasId(uniqueSetSuffix + sqid);
           jmap.setTo(djs);
           seqRefIds.put(sqid, djs);
-          
+
         }
         jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
         addDBRefs(djs, ms);
-        
+
       }
     }
     return (jmap);
@@ -2498,8 +2560,8 @@ public class Jalview2XML
   public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
           boolean keepSeqRefs)
   {
-    jalview.schemabinding.version2.JalviewModel jm = 
-       SaveState(ap, null, null);
+    jalview.schemabinding.version2.JalviewModel jm = SaveState(ap, null,
+            null);
 
     if (!keepSeqRefs)
     {
@@ -2517,21 +2579,19 @@ public class Jalview2XML
     af.alignPanels.clear();
     af.closeMenuItem_actionPerformed(true);
 
-    /*  if(ap.av.alignment.getAlignmentAnnotation()!=null)
-      {
-        for(int i=0; i<ap.av.alignment.getAlignmentAnnotation().length; i++)
-        {
-          if(!ap.av.alignment.getAlignmentAnnotation()[i].autoCalculated)
-          {
-            af.alignPanel.av.alignment.getAlignmentAnnotation()[i] =
-                ap.av.alignment.getAlignmentAnnotation()[i];
-          }
-        }
-      }   */
+    /*
+     * if(ap.av.alignment.getAlignmentAnnotation()!=null) { for(int i=0; i<ap.av.alignment.getAlignmentAnnotation().length;
+     * i++) { if(!ap.av.alignment.getAlignmentAnnotation()[i].autoCalculated) {
+     * af.alignPanel.av.alignment.getAlignmentAnnotation()[i] =
+     * ap.av.alignment.getAlignmentAnnotation()[i]; } } }
+     */
 
     return af.alignPanel;
   }
-  /* (non-Javadoc)
+
+  /*
+   * (non-Javadoc)
+   * 
    * @see java.lang.Object#finalize()
    */
   protected void finalize() throws Throwable
@@ -2542,5 +2602,5 @@ public class Jalview2XML
     this.seqsToIds = null;
     super.finalize();
   }
-  
+
 }
diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index fe17dff..ca2db7b 100755
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -31,22 +31,26 @@ import jalview.schemes.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
 public class Jalview2XML_V1
 {
-  boolean raiseGUI=true;
-  public Jalview2XML_V1() {
-    
+  boolean raiseGUI = true;
+
+  public Jalview2XML_V1()
+  {
+
   };
-  public Jalview2XML_V1(boolean raiseGUI) {
+
+  public Jalview2XML_V1(boolean raiseGUI)
+  {
     this.raiseGUI = raiseGUI;
   };
-  
+
   jalview.schemes.UserColourScheme GetUserColourScheme(
-      JalviewModelSequence jms, String id)
+          JalviewModelSequence jms, String id)
   {
     UserColours[] uc = jms.getUserColours();
     UserColours colours = null;
@@ -66,8 +70,8 @@ public class Jalview2XML_V1
 
     for (int i = 0; i < csize; i++)
     {
-      newColours[i] = new java.awt.Color(Integer.parseInt(
-          colours.getUserColourScheme().getColour(i).getRGB(), 16));
+      newColours[i] = new java.awt.Color(Integer.parseInt(colours
+              .getUserColourScheme().getColour(i).getRGB(), 16));
     }
 
     return new jalview.schemes.UserColourScheme(newColours);
@@ -75,8 +79,9 @@ public class Jalview2XML_V1
 
   /**
    * DOCUMENT ME!
-   *
-   * @param file DOCUMENT ME!
+   * 
+   * @param file
+   *                DOCUMENT ME!
    */
   public AlignFrame LoadJalviewAlign(final String file)
   {
@@ -85,7 +90,7 @@ public class Jalview2XML_V1
 
     try
     {
-      //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
+      // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
       URL url = null;
 
       if (file.startsWith("http://"))
@@ -113,8 +118,7 @@ public class Jalview2XML_V1
           jarentry = jin.getNextJarEntry();
         }
 
-        class NoDescIDResolver
-            implements IDResolver
+        class NoDescIDResolver implements IDResolver
         {
           public Object resolve(String idref)
           {
@@ -133,43 +137,42 @@ public class Jalview2XML_V1
           af = LoadFromObject(object, file);
           entryCount++;
         }
-      }
-      while (jarentry != null);
-    }
-    catch (final java.net.UnknownHostException ex)
+      } while (jarentry != null);
+    } catch (final java.net.UnknownHostException ex)
     {
       ex.printStackTrace();
       if (raiseGUI)
-        {javax.swing.SwingUtilities.invokeLater(new Runnable()
       {
-        public void run()
+        javax.swing.SwingUtilities.invokeLater(new Runnable()
         {
+          public void run()
+          {
 
-          System.err.println("Couldn't locate Jalview XML file : " +
-                             ex + "\n");
-          JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                                "Couldn't locate " + file,
-                                                "URL not found",
-                                                JOptionPane.WARNING_MESSAGE);
-        }
-      });};
-    }
-    catch (Exception ex)
+            System.err.println("Couldn't locate Jalview XML file : " + ex
+                    + "\n");
+            JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                    "Couldn't locate " + file, "URL not found",
+                    JOptionPane.WARNING_MESSAGE);
+          }
+        });
+      }
+      ;
+    } catch (Exception ex)
     {
       System.err.println("Exception whilst loading jalview XML file : ");
       ex.printStackTrace();
       if (raiseGUI)
-      {  javax.swing.SwingUtilities.invokeLater(new Runnable()
       {
-        public void run()
+        javax.swing.SwingUtilities.invokeLater(new Runnable()
         {
+          public void run()
+          {
 
-          JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                                "Error loading  " + file,
-                                                "Error loading Jalview file",
-                                                JOptionPane.WARNING_MESSAGE);
-        }
-      });
+            JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                    "Error loading  " + file, "Error loading Jalview file",
+                    JOptionPane.WARNING_MESSAGE);
+          }
+        });
       }
     }
 
@@ -184,26 +187,25 @@ public class Jalview2XML_V1
 
     JalviewModelSequence jms = object.getJalviewModelSequence();
 
-    //////////////////////////////////
-    //LOAD SEQUENCES
-    jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[
-        vamsasSeq.length];
+    // ////////////////////////////////
+    // LOAD SEQUENCES
+    jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
     JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
     for (int i = 0; i < vamsasSeq.length; i++)
     {
       jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
-                                                vamsasSeq[i].getSequence());
+              vamsasSeq[i].getSequence());
       jseqs[i].setStart(JSEQ[i].getStart());
       jseqs[i].setEnd(JSEQ[i].getEnd());
       seqids.add(jseqs[i]);
     }
 
-    ///SequenceFeatures are added to the DatasetSequence,
+    // /SequenceFeatures are added to the DatasetSequence,
     // so we must create the dataset before loading features
-    /////////////////////////////////
+    // ///////////////////////////////
     jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
     al.setDataset(null);
-    /////////////////////////////////
+    // ///////////////////////////////
 
     for (int i = 0; i < vamsasSeq.length; i++)
     {
@@ -212,11 +214,10 @@ public class Jalview2XML_V1
         Features[] features = JSEQ[i].getFeatures();
         for (int f = 0; f < features.length; f++)
         {
-          jalview.datamodel.SequenceFeature sf
-              = new jalview.datamodel.SequenceFeature(features[f].getType(),
-              features[f].getDescription(), features[f].getStatus(),
-              features[f].getBegin(), features[f].getEnd(),
-              null);
+          jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
+                  features[f].getType(), features[f].getDescription(),
+                  features[f].getStatus(), features[f].getBegin(),
+                  features[f].getEnd(), null);
 
           al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
         }
@@ -235,9 +236,9 @@ public class Jalview2XML_V1
       }
     }
 
-    /////////////////////////////////
-    //////////////////////////////////
-    //LOAD ANNOTATIONS
+    // ///////////////////////////////
+    // ////////////////////////////////
+    // LOAD ANNOTATIONS
     if (vamsasSet.getAnnotation() != null)
     {
       Annotation[] an = vamsasSet.getAnnotation();
@@ -245,16 +246,15 @@ public class Jalview2XML_V1
       for (int i = 0; i < an.length; i++)
       {
         AnnotationElement[] ae = an[i].getAnnotationElement();
-        jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[
-            al.getWidth()];
+        jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al
+                .getWidth()];
 
         for (int aa = 0; aa < ae.length; aa++)
         {
-          anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].
-              getDisplayCharacter(),
-              ae[aa].getDescription(),
-              ae[aa].getSecondaryStructure().charAt(0),
-              ae[aa].getValue());
+          anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
+                  ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
+                  ae[aa].getSecondaryStructure().charAt(0), ae[aa]
+                          .getValue());
         }
 
         jalview.datamodel.AlignmentAnnotation jaa = null;
@@ -262,20 +262,20 @@ public class Jalview2XML_V1
         if (an[i].getGraph())
         {
           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
-              an[i].getDescription(), anot, 0, 0,
-              jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);
+                  an[i].getDescription(), anot, 0, 0,
+                  jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);
         }
         else
         {
           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
-              an[i].getDescription(), anot);
+                  an[i].getDescription(), anot);
         }
 
         al.addAnnotation(jaa);
       }
     }
 
-    /////////////////////////////////
+    // ///////////////////////////////
     // LOAD VIEWPORT
     Viewport[] views = jms.getViewport();
     Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
@@ -286,15 +286,13 @@ public class Jalview2XML_V1
 
     for (int i = 0; i < JSEQ.length; i++)
     {
-      af.viewport.setSequenceColour(
-          af.viewport.alignment.getSequenceAt(i),
-          new java.awt.Color(
-              JSEQ[i].getColour()));
+      af.viewport.setSequenceColour(af.viewport.alignment.getSequenceAt(i),
+              new java.awt.Color(JSEQ[i].getColour()));
     }
 
-    //  af.changeColour() );
-    /////////////////////////
-    //LOAD GROUPS
+    // af.changeColour() );
+    // ///////////////////////
+    // LOAD GROUPS
     if (jms.getJGroupCount() > 0)
     {
       JGroup[] groups = jms.getJGroup();
@@ -311,8 +309,7 @@ public class Jalview2XML_V1
           }
           else
           {
-            cs = ColourSchemeProperty.getColour(al,
-                                                groups[i].getColour());
+            cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
           }
 
           if (cs != null)
@@ -327,25 +324,24 @@ public class Jalview2XML_V1
 
         for (int s = 0; s < ids.length; s++)
         {
-          seqs.addElement( (jalview.datamodel.SequenceI) seqids.elementAt(
-              ids[s]));
+          seqs.addElement((jalview.datamodel.SequenceI) seqids
+                  .elementAt(ids[s]));
         }
 
-        jalview.datamodel.SequenceGroup sg = new jalview.datamodel.
-            SequenceGroup(seqs,
-                          groups[i].getName(), cs, groups[i].getDisplayBoxes(),
-                          groups[i].getDisplayText(), groups[i].getColourText(),
-                          groups[i].getStart(), groups[i].getEnd());
+        jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
+                seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
+                groups[i].getDisplayText(), groups[i].getColourText(),
+                groups[i].getStart(), groups[i].getEnd());
 
-        sg.setOutlineColour(new java.awt.Color(
-            groups[i].getOutlineColour()));
+        sg
+                .setOutlineColour(new java.awt.Color(groups[i]
+                        .getOutlineColour()));
 
         if (groups[i].getConsThreshold() != 0)
         {
           jalview.analysis.Conservation c = new jalview.analysis.Conservation(
-              "All",
-              ResidueProperties.propHash, 3, sg.getSequences(null), 0,
-              sg.getWidth() - 1);
+                  "All", ResidueProperties.propHash, 3, sg
+                          .getSequences(null), 0, sg.getWidth() - 1);
           c.calculate();
           c.verdict(false, 25);
           sg.cs.setConservation(c);
@@ -355,8 +351,8 @@ public class Jalview2XML_V1
       }
     }
 
-    af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
-                 view.getHeight());
+    af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view
+            .getHeight());
     af.viewport.setStartRes(view.getStartRes());
     af.viewport.setStartSeq(view.getStartSeq());
     af.viewport.setShowAnnotation(view.getShowAnnotation());
@@ -364,8 +360,8 @@ public class Jalview2XML_V1
     af.viewport.setColourText(view.getShowColourText());
     af.viewport.setConservationSelected(view.getConservationSelected());
     af.viewport.setShowJVSuffix(view.getShowFullId());
-    af.viewport.setFont(new java.awt.Font(view.getFontName(),
-                                          view.getFontStyle(), view.getFontSize()));
+    af.viewport.setFont(new java.awt.Font(view.getFontName(), view
+            .getFontStyle(), view.getFontSize()));
     af.alignPanel.fontChanged();
 
     af.viewport.setRenderGaps(view.getRenderGaps());
@@ -410,35 +406,33 @@ public class Jalview2XML_V1
     if (jms.getFeatureSettings() != null)
     {
       af.viewport.featuresDisplayed = new Hashtable();
-      String[] renderOrder = new String[jms.getFeatureSettings().
-          getSettingCount()];
+      String[] renderOrder = new String[jms.getFeatureSettings()
+              .getSettingCount()];
       for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
       {
         Setting setting = jms.getFeatureSettings().getSetting(fs);
 
-        af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.
-            getType(),
-            new java.awt.Color(setting.getColour()));
+        af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
+                setting.getType(), new java.awt.Color(setting.getColour()));
 
         renderOrder[fs] = setting.getType();
 
         if (setting.getDisplay())
         {
-          af.viewport.featuresDisplayed.put(
-              setting.getType(), new Integer(setting.getColour()));
+          af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
+                  setting.getColour()));
         }
       }
-      af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder =
-          renderOrder;
+      af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
     }
 
     af.setMenusFromViewport(af.viewport);
 
-    Desktop.addInternalFrame(af, view.getTitle(),
-                             view.getWidth(), view.getHeight());
+    Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view
+            .getHeight());
 
-    //LOAD TREES
-    ///////////////////////////////////////
+    // LOAD TREES
+    // /////////////////////////////////////
     if (jms.getTreeCount() > 0)
     {
       try
@@ -448,25 +442,22 @@ public class Jalview2XML_V1
 
           Tree tree = jms.getTree(t);
 
-          TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
-              tree.getNewick()), tree.getTitle(),
-                                           tree.getWidth(), tree.getHeight(),
-                                           tree.getXpos(), tree.getYpos());
+          TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(tree
+                  .getNewick()), tree.getTitle(), tree.getWidth(), tree
+                  .getHeight(), tree.getXpos(), tree.getYpos());
 
           tp.fitToWindow.setState(tree.getFitToWindow());
           tp.fitToWindow_actionPerformed(null);
 
           if (tree.getFontName() != null)
           {
-            tp.setTreeFont(new java.awt.Font(tree.getFontName(),
-                                             tree.getFontStyle(),
-                                             tree.getFontSize()));
+            tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
+                    .getFontStyle(), tree.getFontSize()));
           }
           else
           {
-            tp.setTreeFont(new java.awt.Font(view.getFontName(),
-                                             view.getFontStyle(),
-                                             tree.getFontSize()));
+            tp.setTreeFont(new java.awt.Font(view.getFontName(), view
+                    .getFontStyle(), tree.getFontSize()));
           }
 
           tp.showPlaceholders(tree.getMarkUnlinked());
@@ -481,8 +472,7 @@ public class Jalview2XML_V1
           }
         }
 
-      }
-      catch (Exception ex)
+      } catch (Exception ex)
       {
         ex.printStackTrace();
       }
diff --git a/src/jalview/gui/OOMWarning.java b/src/jalview/gui/OOMWarning.java
new file mode 100644
index 0000000..9b69825
--- /dev/null
+++ b/src/jalview/gui/OOMWarning.java
@@ -0,0 +1,79 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.gui;
+
+import java.awt.Component;
+
+public class OOMWarning implements Runnable
+{
+  String action = null;
+
+  String instructions = "";
+
+  Component desktop = null;
+
+  /**
+   * Raise an out of memory error.
+   * 
+   * @param action -
+   *                what was going on when OutOfMemory exception occured.
+   * @param instance -
+   *                Window where the dialog will appear
+   * @param oomex -
+   *                the actual exception - to be written to stderr or debugger.
+   */
+  OOMWarning(String action, OutOfMemoryError oomex, Component instance)
+  {
+    this.action = action;
+    desktop = instance;
+    if (oomex != null)
+    {
+      if (jalview.bin.Cache.log != null)
+      {
+        jalview.bin.Cache.log.error("Out of Memory when " + action, oomex);
+      }
+      else
+      {
+        System.err.println("Out of Memory when " + action);
+        oomex.printStackTrace();
+      }
+    }
+    javax.swing.SwingUtilities.invokeLater(this);
+    System.gc();
+  }
+
+  public OOMWarning(String string, OutOfMemoryError oomerror)
+  {
+    this(string, oomerror, Desktop.desktop);
+  }
+
+  public void run()
+  {
+    javax.swing.JOptionPane
+            .showInternalMessageDialog(
+                    desktop,
+                    "Out of memory when "
+                            + action
+                            + "!!"
+                            + "\nSee help files for increasing Java Virtual Machine memory.",
+                    "Out of memory",
+                    javax.swing.JOptionPane.WARNING_MESSAGE);
+  }
+
+}
diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 04e5f13..6bc630c 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -1,447 +1,458 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.gui;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.image.*;
-import javax.swing.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class OverviewPanel
-    extends JPanel implements Runnable
-{
-  BufferedImage miniMe;
-  AlignViewport av;
-  AlignmentPanel ap;
-  float scalew = 1f;
-  float scaleh = 1f;
-  int width;
-  int sequencesHeight;
-  int graphHeight = 20;
-  int boxX = -1;
-  int boxY = -1;
-  int boxWidth = -1;
-  int boxHeight = -1;
-  boolean resizing = false;
-
-  // Can set different properties in this seqCanvas than
-  // main visible SeqCanvas
-  SequenceRenderer sr;
-  FeatureRenderer fr;
-
-  /**
-   * Creates a new OverviewPanel object.
-   *
-   * @param ap DOCUMENT ME!
-   */
-  public OverviewPanel(AlignmentPanel ap)
-  {
-    this.av = ap.av;
-    this.ap = ap;
-    setLayout(null);
-
-    sr = new SequenceRenderer(av);
-    sr.renderGaps = false;
-    sr.forOverview = true;
-    fr = new FeatureRenderer(ap);
-
-    // scale the initial size of overviewpanel to shape of alignment
-    float initialScale = (float) av.alignment.getWidth() /
-        (float) av.alignment.getHeight();
-
-    if (av.conservation == null)
-    {
-      graphHeight = 0;
-    }
-
-    if (av.alignment.getWidth() > av.alignment.getHeight())
-    {
-      // wider
-      width = 400;
-      sequencesHeight = (int) (400f / initialScale);
-      if (sequencesHeight < 40)
-      {
-        sequencesHeight = 40;
-      }
-    }
-    else
-    {
-      // taller
-      width = (int) (400f * initialScale);
-      sequencesHeight = 300;
-
-      if (width < 120)
-      {
-        width = 120;
-      }
-    }
-
-    addComponentListener(new ComponentAdapter()
-    {
-      public void componentResized(ComponentEvent evt)
-      {
-        if ( (getWidth() != width) ||
-            (getHeight() != (sequencesHeight + graphHeight)))
-        {
-          updateOverviewImage();
-        }
-      }
-    });
-
-    addMouseMotionListener(new MouseMotionAdapter()
-    {
-      public void mouseDragged(MouseEvent evt)
-      {
-        if (!av.wrapAlignment)
-        {
-          boxX = evt.getX();
-          boxY = evt.getY();
-          checkValid();
-        }
-      }
-    });
-
-    addMouseListener(new MouseAdapter()
-    {
-      public void mousePressed(MouseEvent evt)
-      {
-        if (!av.wrapAlignment)
-        {
-          boxX = evt.getX();
-          boxY = evt.getY();
-          checkValid();
-        }
-      }
-    });
-
-    updateOverviewImage();
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  void checkValid()
-  {
-    if (boxY < 0)
-    {
-      boxY = 0;
-    }
-
-    if (boxY > (sequencesHeight - boxHeight))
-    {
-      boxY = sequencesHeight - boxHeight + 1;
-    }
-
-    if (boxX < 0)
-    {
-      boxX = 0;
-    }
-
-    if (boxX > (width - boxWidth))
-    {
-      if (av.hasHiddenColumns)
-      {
-        //Try smallest possible box
-        boxWidth = (int) ( (av.endRes - av.startRes + 1) *
-                          av.getCharWidth() * scalew);
-      }
-      boxX = width - boxWidth;
-    }
-
-    int col = (int) (boxX / scalew / av.getCharWidth());
-    int row = (int) (boxY / scaleh / av.getCharHeight());
-
-    if (av.hasHiddenColumns)
-    {
-      if (!av.getColumnSelection().isVisible(col))
-      {
-        return;
-      }
-
-      col = av.getColumnSelection().findColumnPosition(col);
-    }
-
-    if (av.hasHiddenRows)
-    {
-      row = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(row);
-    }
-
-    ap.setScrollValues(col, row);
-
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  public void updateOverviewImage()
-  {
-    if (resizing)
-    {
-      resizeAgain = true;
-      return;
-    }
-
-    resizing = true;
-
-    if ( (getWidth() > 0) && (getHeight() > 0))
-    {
-      width = getWidth();
-      sequencesHeight = getHeight() - graphHeight;
-    }
-
-    setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
-
-    Thread thread = new Thread(this);
-    thread.start();
-    repaint();
-  }
-
-  // This is set true if the user resizes whilst
-  // the overview is being calculated
-  boolean resizeAgain = false;
-
-  /**
-   * DOCUMENT ME!
-   */
-  public void run()
-  {
-    miniMe = null;
-
-    if (av.showSequenceFeatures)
-    {
-      fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
-    }
-
-    int alwidth = av.alignment.getWidth();
-    int alheight = av.alignment.getHeight()
-        + av.alignment.getHiddenSequences().getSize();
-
-    setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
-
-    int fullsizeWidth = alwidth * av.getCharWidth();
-    int fullsizeHeight = alheight * av.getCharHeight();
-
-    scalew = (float) width / (float) fullsizeWidth;
-    scaleh = (float) sequencesHeight / (float) fullsizeHeight;
-
-    miniMe = new BufferedImage(width, sequencesHeight + graphHeight,
-                               BufferedImage.TYPE_INT_RGB);
-
-    Graphics mg = miniMe.getGraphics();
-    mg.setColor(Color.orange);
-    mg.fillRect(0, 0, width, miniMe.getHeight());
-
-    float sampleCol = (float) alwidth / (float) width;
-    float sampleRow = (float) alheight / (float) sequencesHeight;
-
-    int lastcol = -1, lastrow = -1;
-    int color = Color.white.getRGB();
-    int row, col;
-    jalview.datamodel.SequenceI seq;
-    boolean hiddenRow = false;
-    for (row = 0; row < sequencesHeight; row++)
-    {
-      if ( (int) (row * sampleRow) == lastrow)
-      {
-        //No need to recalculate the colours,
-        //Just copy from the row above
-        for (col = 0; col < width; col++)
-        {
-          miniMe.setRGB(col, row, miniMe.getRGB(col, row - 1));
-        }
-        continue;
-      }
-
-      lastrow = (int) (row * sampleRow);
-
-      hiddenRow = false;
-      if (av.hasHiddenRows)
-      {
-        seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow);
-        if (seq == null)
-        {
-          int index =
-              av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(
-              lastrow);
-
-          seq = av.alignment.getSequenceAt(index);
-        }
-        else
-        {
-          hiddenRow = true;
-        }
-      }
-      else
-      {
-        seq = av.alignment.getSequenceAt(lastrow);
-      }
-
-      if (seq == null)
-      {
-        System.out.println(lastrow + " null");
-        continue;
-      }
-
-      for (col = 0; col < width; col++)
-      {
-        if ( (int) (col * sampleCol) == lastcol &&
-            (int) (row * sampleRow) == lastrow)
-        {
-          miniMe.setRGB(col, row, color);
-          continue;
-        }
-
-        lastcol = (int) (col * sampleCol);
-
-        if (seq.getLength() > lastcol)
-        {
-          color = sr.getResidueBoxColour(
-              seq, lastcol).getRGB();
-
-          if (av.showSequenceFeatures)
-          {
-            color = fr.findFeatureColour(color, seq, lastcol);
-          }
-        }
-        else
-        {
-          color = -1; //White
-        }
-
-        if (hiddenRow ||
-            (av.hasHiddenColumns && !av.getColumnSelection().isVisible(lastcol)))
-        {
-          color = new Color(color).darker().darker().getRGB();
-        }
-
-        miniMe.setRGB(col, row, color);
-
-      }
-    }
-
-    if (av.conservation != null)
-    {
-      for (col = 0; col < width; col++)
-      {
-        lastcol = (int) (col * sampleCol);
-        {
-          mg.translate(col, sequencesHeight);
-          ap.annotationPanel.drawGraph(mg, av.conservation,
-                                       (int) (sampleCol) + 1,
-                                       graphHeight,
-                                       (int) (col * sampleCol),
-                                       (int) (col * sampleCol) + 1);
-          mg.translate( -col, -sequencesHeight);
-        }
-      }
-    }
-    System.gc();
-
-    resizing = false;
-
-    setBoxPosition();
-
-    if (resizeAgain)
-    {
-      resizeAgain = false;
-      updateOverviewImage();
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  public void setBoxPosition()
-  {
-    int fullsizeWidth = av.alignment.getWidth() * av.getCharWidth();
-    int fullsizeHeight = (av.alignment.getHeight()
-                          + av.alignment.getHiddenSequences().getSize()) *
-        av.getCharHeight();
-
-    int startRes = av.getStartRes();
-    int endRes = av.getEndRes();
-
-    if (av.hasHiddenColumns)
-    {
-      startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);
-      endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);
-    }
-
-    int startSeq = av.startSeq;
-    int endSeq = av.endSeq;
-
-    if (av.hasHiddenRows)
-    {
-      startSeq =
-          av.alignment.getHiddenSequences().adjustForHiddenSeqs(startSeq);
-
-      endSeq =
-          av.alignment.getHiddenSequences().adjustForHiddenSeqs(endSeq);
-
-    }
-
-    scalew = (float) width / (float) fullsizeWidth;
-    scaleh = (float) sequencesHeight / (float) fullsizeHeight;
-
-    boxX = (int) (startRes * av.getCharWidth() * scalew);
-    boxY = (int) (startSeq * av.getCharHeight() * scaleh);
-
-    if (av.hasHiddenColumns)
-    {
-      boxWidth = (int) ( (endRes - startRes + 1) * av.getCharWidth() * scalew);
-    }
-    else
-    {
-      boxWidth = (int) ( (endRes - startRes + 1) * av.getCharWidth() * scalew);
-    }
-
-    boxHeight = (int) ( (endSeq - startSeq) * av.getCharHeight() * scaleh);
-
-    repaint();
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param g DOCUMENT ME!
-   */
-  public void paintComponent(Graphics g)
-  {
-    if(resizing)
-    {
-      g.setColor(Color.white);
-      g.fillRect(0,0,getWidth(),getHeight());
-    }
-    else if (miniMe != null)
-    {
-      g.drawImage(miniMe, 0, 0, this);
-    }
-
-    g.setColor(Color.red);
-    g.drawRect(boxX, boxY, boxWidth, boxHeight);
-    g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
-
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.gui;
+
+import java.awt.*;
+import java.awt.event.*;
+import java.awt.image.*;
+import javax.swing.*;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class OverviewPanel extends JPanel implements Runnable
+{
+  BufferedImage miniMe;
+
+  AlignViewport av;
+
+  AlignmentPanel ap;
+
+  float scalew = 1f;
+
+  float scaleh = 1f;
+
+  int width;
+
+  int sequencesHeight;
+
+  int graphHeight = 20;
+
+  int boxX = -1;
+
+  int boxY = -1;
+
+  int boxWidth = -1;
+
+  int boxHeight = -1;
+
+  boolean resizing = false;
+
+  // Can set different properties in this seqCanvas than
+  // main visible SeqCanvas
+  SequenceRenderer sr;
+
+  FeatureRenderer fr;
+
+  /**
+   * Creates a new OverviewPanel object.
+   * 
+   * @param ap
+   *                DOCUMENT ME!
+   */
+  public OverviewPanel(AlignmentPanel ap)
+  {
+    this.av = ap.av;
+    this.ap = ap;
+    setLayout(null);
+
+    sr = new SequenceRenderer(av);
+    sr.renderGaps = false;
+    sr.forOverview = true;
+    fr = new FeatureRenderer(ap);
+
+    // scale the initial size of overviewpanel to shape of alignment
+    float initialScale = (float) av.alignment.getWidth()
+            / (float) av.alignment.getHeight();
+
+    if (av.conservation == null)
+    {
+      graphHeight = 0;
+    }
+
+    if (av.alignment.getWidth() > av.alignment.getHeight())
+    {
+      // wider
+      width = 400;
+      sequencesHeight = (int) (400f / initialScale);
+      if (sequencesHeight < 40)
+      {
+        sequencesHeight = 40;
+      }
+    }
+    else
+    {
+      // taller
+      width = (int) (400f * initialScale);
+      sequencesHeight = 300;
+
+      if (width < 120)
+      {
+        width = 120;
+      }
+    }
+
+    addComponentListener(new ComponentAdapter()
+    {
+      public void componentResized(ComponentEvent evt)
+      {
+        if ((getWidth() != width)
+                || (getHeight() != (sequencesHeight + graphHeight)))
+        {
+          updateOverviewImage();
+        }
+      }
+    });
+
+    addMouseMotionListener(new MouseMotionAdapter()
+    {
+      public void mouseDragged(MouseEvent evt)
+      {
+        if (!av.wrapAlignment)
+        {
+          boxX = evt.getX();
+          boxY = evt.getY();
+          checkValid();
+        }
+      }
+    });
+
+    addMouseListener(new MouseAdapter()
+    {
+      public void mousePressed(MouseEvent evt)
+      {
+        if (!av.wrapAlignment)
+        {
+          boxX = evt.getX();
+          boxY = evt.getY();
+          checkValid();
+        }
+      }
+    });
+
+    updateOverviewImage();
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  void checkValid()
+  {
+    if (boxY < 0)
+    {
+      boxY = 0;
+    }
+
+    if (boxY > (sequencesHeight - boxHeight))
+    {
+      boxY = sequencesHeight - boxHeight + 1;
+    }
+
+    if (boxX < 0)
+    {
+      boxX = 0;
+    }
+
+    if (boxX > (width - boxWidth))
+    {
+      if (av.hasHiddenColumns)
+      {
+        // Try smallest possible box
+        boxWidth = (int) ((av.endRes - av.startRes + 1) * av.getCharWidth() * scalew);
+      }
+      boxX = width - boxWidth;
+    }
+
+    int col = (int) (boxX / scalew / av.getCharWidth());
+    int row = (int) (boxY / scaleh / av.getCharHeight());
+
+    if (av.hasHiddenColumns)
+    {
+      if (!av.getColumnSelection().isVisible(col))
+      {
+        return;
+      }
+
+      col = av.getColumnSelection().findColumnPosition(col);
+    }
+
+    if (av.hasHiddenRows)
+    {
+      row = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(
+              row);
+    }
+
+    ap.setScrollValues(col, row);
+
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void updateOverviewImage()
+  {
+    if (resizing)
+    {
+      resizeAgain = true;
+      return;
+    }
+
+    resizing = true;
+
+    if ((getWidth() > 0) && (getHeight() > 0))
+    {
+      width = getWidth();
+      sequencesHeight = getHeight() - graphHeight;
+    }
+
+    setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
+
+    Thread thread = new Thread(this);
+    thread.start();
+    repaint();
+  }
+
+  // This is set true if the user resizes whilst
+  // the overview is being calculated
+  boolean resizeAgain = false;
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void run()
+  {
+    miniMe = null;
+
+    if (av.showSequenceFeatures)
+    {
+      fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
+    }
+
+    int alwidth = av.alignment.getWidth();
+    int alheight = av.alignment.getHeight()
+            + av.alignment.getHiddenSequences().getSize();
+
+    setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
+
+    int fullsizeWidth = alwidth * av.getCharWidth();
+    int fullsizeHeight = alheight * av.getCharHeight();
+
+    scalew = (float) width / (float) fullsizeWidth;
+    scaleh = (float) sequencesHeight / (float) fullsizeHeight;
+
+    miniMe = new BufferedImage(width, sequencesHeight + graphHeight,
+            BufferedImage.TYPE_INT_RGB);
+
+    Graphics mg = miniMe.getGraphics();
+    mg.setColor(Color.orange);
+    mg.fillRect(0, 0, width, miniMe.getHeight());
+
+    float sampleCol = (float) alwidth / (float) width;
+    float sampleRow = (float) alheight / (float) sequencesHeight;
+
+    int lastcol = -1, lastrow = -1;
+    int color = Color.white.getRGB();
+    int row, col;
+    jalview.datamodel.SequenceI seq;
+    boolean hiddenRow = false;
+    for (row = 0; row < sequencesHeight; row++)
+    {
+      if ((int) (row * sampleRow) == lastrow)
+      {
+        // No need to recalculate the colours,
+        // Just copy from the row above
+        for (col = 0; col < width; col++)
+        {
+          miniMe.setRGB(col, row, miniMe.getRGB(col, row - 1));
+        }
+        continue;
+      }
+
+      lastrow = (int) (row * sampleRow);
+
+      hiddenRow = false;
+      if (av.hasHiddenRows)
+      {
+        seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow);
+        if (seq == null)
+        {
+          int index = av.alignment.getHiddenSequences()
+                  .findIndexWithoutHiddenSeqs(lastrow);
+
+          seq = av.alignment.getSequenceAt(index);
+        }
+        else
+        {
+          hiddenRow = true;
+        }
+      }
+      else
+      {
+        seq = av.alignment.getSequenceAt(lastrow);
+      }
+
+      if (seq == null)
+      {
+        System.out.println(lastrow + " null");
+        continue;
+      }
+
+      for (col = 0; col < width; col++)
+      {
+        if ((int) (col * sampleCol) == lastcol
+                && (int) (row * sampleRow) == lastrow)
+        {
+          miniMe.setRGB(col, row, color);
+          continue;
+        }
+
+        lastcol = (int) (col * sampleCol);
+
+        if (seq.getLength() > lastcol)
+        {
+          color = sr.getResidueBoxColour(seq, lastcol).getRGB();
+
+          if (av.showSequenceFeatures)
+          {
+            color = fr.findFeatureColour(color, seq, lastcol);
+          }
+        }
+        else
+        {
+          color = -1; // White
+        }
+
+        if (hiddenRow
+                || (av.hasHiddenColumns && !av.getColumnSelection()
+                        .isVisible(lastcol)))
+        {
+          color = new Color(color).darker().darker().getRGB();
+        }
+
+        miniMe.setRGB(col, row, color);
+
+      }
+    }
+
+    if (av.conservation != null)
+    {
+      for (col = 0; col < width; col++)
+      {
+        lastcol = (int) (col * sampleCol);
+        {
+          mg.translate(col, sequencesHeight);
+          ap.annotationPanel.drawGraph(mg, av.conservation,
+                  (int) (sampleCol) + 1, graphHeight,
+                  (int) (col * sampleCol), (int) (col * sampleCol) + 1);
+          mg.translate(-col, -sequencesHeight);
+        }
+      }
+    }
+    System.gc();
+
+    resizing = false;
+
+    setBoxPosition();
+
+    if (resizeAgain)
+    {
+      resizeAgain = false;
+      updateOverviewImage();
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void setBoxPosition()
+  {
+    int fullsizeWidth = av.alignment.getWidth() * av.getCharWidth();
+    int fullsizeHeight = (av.alignment.getHeight() + av.alignment
+            .getHiddenSequences().getSize())
+            * av.getCharHeight();
+
+    int startRes = av.getStartRes();
+    int endRes = av.getEndRes();
+
+    if (av.hasHiddenColumns)
+    {
+      startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);
+      endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);
+    }
+
+    int startSeq = av.startSeq;
+    int endSeq = av.endSeq;
+
+    if (av.hasHiddenRows)
+    {
+      startSeq = av.alignment.getHiddenSequences().adjustForHiddenSeqs(
+              startSeq);
+
+      endSeq = av.alignment.getHiddenSequences()
+              .adjustForHiddenSeqs(endSeq);
+
+    }
+
+    scalew = (float) width / (float) fullsizeWidth;
+    scaleh = (float) sequencesHeight / (float) fullsizeHeight;
+
+    boxX = (int) (startRes * av.getCharWidth() * scalew);
+    boxY = (int) (startSeq * av.getCharHeight() * scaleh);
+
+    if (av.hasHiddenColumns)
+    {
+      boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
+    }
+    else
+    {
+      boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
+    }
+
+    boxHeight = (int) ((endSeq - startSeq) * av.getCharHeight() * scaleh);
+
+    repaint();
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param g
+   *                DOCUMENT ME!
+   */
+  public void paintComponent(Graphics g)
+  {
+    if (resizing)
+    {
+      g.setColor(Color.white);
+      g.fillRect(0, 0, getWidth(), getHeight());
+    }
+    else if (miniMe != null)
+    {
+      g.drawImage(miniMe, 0, 0, this);
+    }
+
+    g.setColor(Color.red);
+    g.drawRect(boxX, boxY, boxWidth, boxHeight);
+    g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
+
+  }
+}
diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 06f1b25..b397cf5 100755
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -31,26 +31,33 @@ import jalview.jbgui.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class PCAPanel
-    extends GPCAPanel implements Runnable
+public class PCAPanel extends GPCAPanel implements Runnable
 {
   PCA pca;
+
   int top;
+
   RotatableCanvas rc;
+
   AlignmentPanel ap;
+
   AlignViewport av;
+
   AlignmentView seqstrings;
+
   SequenceI[] seqs;
 
   /**
    * Creates a new PCAPanel object.
-   *
-   * @param av DOCUMENT ME!
-   * @param s DOCUMENT ME!
+   * 
+   * @param av
+   *                DOCUMENT ME!
+   * @param s
+   *                DOCUMENT ME!
    */
   public PCAPanel(AlignmentPanel ap)
   {
@@ -82,18 +89,20 @@ public class PCAPanel
 
     if (!sameLength)
     {
-      JOptionPane.showMessageDialog(Desktop.desktop,
-                                    "The sequences must be aligned before calculating PCA.\n" +
-                                    "Try using the Pad function in the edit menu,\n" +
-                                    "or one of the multiple sequence alignment web services.",
-                                    "Sequences not aligned",
-                                    JOptionPane.WARNING_MESSAGE);
+      JOptionPane
+              .showMessageDialog(
+                      Desktop.desktop,
+                      "The sequences must be aligned before calculating PCA.\n"
+                              + "Try using the Pad function in the edit menu,\n"
+                              + "or one of the multiple sequence alignment web services.",
+                      "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
 
       return;
     }
 
-    Desktop.addInternalFrame(this, "Principal component analysis",
-                             400, 400);
+    Desktop
+            .addInternalFrame(this, "Principal component analysis", 400,
+                    400);
 
     PaintRefresher.Register(this, av.getSequenceSetId());
 
@@ -106,7 +115,7 @@ public class PCAPanel
   public void bgcolour_actionPerformed(ActionEvent e)
   {
     Color col = JColorChooser.showDialog(this, "Select Background Colour",
-                                         rc.bgColour);
+            rc.bgColour);
 
     if (col != null)
     {
@@ -128,7 +137,7 @@ public class PCAPanel
       // Now find the component coordinates
       int ii = 0;
 
-      while ( (ii < seqs.length) && (seqs[ii] != null))
+      while ((ii < seqs.length) && (seqs[ii] != null))
       {
         ii++;
       }
@@ -143,7 +152,7 @@ public class PCAPanel
         }
       }
 
-      //////////////////
+      // ////////////////
       xCombobox.setSelectedIndex(0);
       yCombobox.setSelectedIndex(1);
       zCombobox.setSelectedIndex(2);
@@ -164,17 +173,9 @@ public class PCAPanel
 
       addKeyListener(rc);
 
-    }
-    catch (OutOfMemoryError er)
+    } catch (OutOfMemoryError er)
     {
-      JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                            "Out of memory calculating PCA!!"
-                                            +
-                                            "\nSee help files for increasing Java Virtual Machine memory."
-                                            , "Out of memory",
-                                            JOptionPane.WARNING_MESSAGE);
-      System.out.println("PCAPanel: " + er);
-      System.gc();
+      new OOMWarning("calculating PCA", er);
 
     }
 
@@ -198,7 +199,7 @@ public class PCAPanel
 
     for (int i = 0; i < pca.getM().rows; i++)
     {
-      ( (SequencePoint) rc.points.elementAt(i)).coord = scores[i];
+      ((SequencePoint) rc.points.elementAt(i)).coord = scores[i];
     }
 
     rc.img = null;
@@ -209,8 +210,9 @@ public class PCAPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void xCombobox_actionPerformed(ActionEvent e)
   {
@@ -219,8 +221,9 @@ public class PCAPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void yCombobox_actionPerformed(ActionEvent e)
   {
@@ -229,8 +232,9 @@ public class PCAPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void zCombobox_actionPerformed(ActionEvent e)
   {
@@ -240,8 +244,7 @@ public class PCAPanel
   public void outputValues_actionPerformed(ActionEvent e)
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
-    Desktop.addInternalFrame(cap, "PCA details", 500,
-                             500);
+    Desktop.addInternalFrame(cap, "PCA details", 500, 500);
 
     cap.setText(pca.getDetails());
   }
@@ -259,31 +262,39 @@ public class PCAPanel
 
   public void originalSeqData_actionPerformed(ActionEvent e)
   {
-    // this was cut'n'pasted from the equivalent TreePanel method - we should make this an abstract function of all jalview analysis windows
+    // this was cut'n'pasted from the equivalent TreePanel method - we should
+    // make this an abstract function of all jalview analysis windows
     if (seqstrings == null)
     {
-      jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
+      jalview.bin.Cache.log
+              .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
       return;
     }
-    // decide if av alignment is sufficiently different to original data to warrant a new window to be created
-    // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)
+    // decide if av alignment is sufficiently different to original data to
+    // warrant a new window to be created
+    // create new alignmnt window with hidden regions (unhiding hidden regions
+    // yields unaligned seqs)
     // or create a selection box around columns in alignment view
     // test Alignment(SeqCigar[])
     char gc = '-';
-    try {
+    try
+    {
       // we try to get the associated view's gap character
       // but this may fail if the view was closed...
-      gc = av.
-      getGapCharacter();
-    } catch (Exception ex) {};
+      gc = av.getGapCharacter();
+    } catch (Exception ex)
+    {
+    }
+    ;
     Object[] alAndColsel = seqstrings.getAlignmentAndColumnSelection(gc);
 
     if (alAndColsel != null && alAndColsel[0] != null)
     {
       // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
 
-      Alignment al = new Alignment( (SequenceI[]) alAndColsel[0]);
-      Alignment dataset = (av!=null && av.getAlignment()!=null) ? av.getAlignment().getDataset() : null;
+      Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
+      Alignment dataset = (av != null && av.getAlignment() != null) ? av
+              .getAlignment().getDataset() : null;
       if (dataset != null)
       {
         al.setDataset(dataset);
@@ -292,38 +303,33 @@ public class PCAPanel
       if (true)
       {
         // make a new frame!
-        AlignFrame af = new AlignFrame(al, (ColumnSelection) alAndColsel[1],
-                                       AlignFrame.DEFAULT_WIDTH,
-                                       AlignFrame.DEFAULT_HEIGHT
-            );
+        AlignFrame af = new AlignFrame(al,
+                (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
+                AlignFrame.DEFAULT_HEIGHT);
 
-        //>>>This is a fix for the moment, until a better solution is found!!<<<
+        // >>>This is a fix for the moment, until a better solution is
+        // found!!<<<
         // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
 
-        //           af.addSortByOrderMenuItem(ServiceName + " Ordering",
-        //                                     msaorder);
+        // af.addSortByOrderMenuItem(ServiceName + " Ordering",
+        // msaorder);
 
         Desktop.addInternalFrame(af, "Original Data for " + this.title,
-                                 AlignFrame.DEFAULT_WIDTH,
-                                 AlignFrame.DEFAULT_HEIGHT);
+                AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
       }
     }
-    /*      CutAndPasteTransfer cap = new CutAndPasteTransfer();
-           for (int i = 0; i < seqs.length; i++)
-           {
-             cap.appendText(new jalview.util.Format("%-" + 15 + "s").form(
-      seqs[i].getName()));
-             cap.appendText(" " + seqstrings[i] + "\n");
-
-           }
-
-           Desktop.addInternalFrame(cap, "Original Data",
-               400, 400);
+    /*
+     * CutAndPasteTransfer cap = new CutAndPasteTransfer(); for (int i = 0; i <
+     * seqs.length; i++) { cap.appendText(new jalview.util.Format("%-" + 15 +
+     * "s").form( seqs[i].getName())); cap.appendText(" " + seqstrings[i] +
+     * "\n");
+     *  }
+     * 
+     * Desktop.addInternalFrame(cap, "Original Data", 400, 400);
      */
   }
 
-  class PCAPrinter
-      extends Thread implements Printable
+  class PCAPrinter extends Thread implements Printable
   {
     public void run()
     {
@@ -337,8 +343,7 @@ public class PCAPanel
         try
         {
           printJob.print();
-        }
-        catch (Exception PrintException)
+        } catch (Exception PrintException)
         {
           PrintException.printStackTrace();
         }
@@ -346,9 +351,9 @@ public class PCAPanel
     }
 
     public int print(Graphics pg, PageFormat pf, int pi)
-        throws PrinterException
+            throws PrinterException
     {
-      pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
+      pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
 
       rc.drawBackground(pg, rc.bgColour);
       rc.drawScene(pg);
@@ -370,8 +375,9 @@ public class PCAPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void eps_actionPerformed(ActionEvent e)
   {
@@ -380,8 +386,9 @@ public class PCAPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void png_actionPerformed(ActionEvent e)
   {
@@ -397,19 +404,14 @@ public class PCAPanel
 
     if (type == jalview.util.ImageMaker.PNG)
     {
-      im = new jalview.util.ImageMaker(this,
-                                       jalview.util.ImageMaker.PNG,
-                                       "Make PNG image from PCA",
-                                       width, height,
-                                       null, null);
+      im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
+              "Make PNG image from PCA", width, height, null, null);
     }
     else
     {
-      im = new jalview.util.ImageMaker(this,
-                                       jalview.util.ImageMaker.EPS,
-                                       "Make EPS file from PCA",
-                                       width, height,
-                                       null, this.getTitle());
+      im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
+              "Make EPS file from PCA", width, height, null, this
+                      .getTitle());
     }
 
     if (im.getGraphics() != null)
@@ -431,8 +433,8 @@ public class PCAPanel
 
   void buildAssociatedViewMenu()
   {
-    AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av.
-        getSequenceSetId());
+    AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
+            .getSequenceSetId());
     if (aps.length == 1 && rc.av == aps[0].av)
     {
       associateViewsMenu.setVisible(false);
@@ -441,7 +443,7 @@ public class PCAPanel
 
     associateViewsMenu.setVisible(true);
 
-    if ( (viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
+    if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
     {
       viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
     }
diff --git a/src/jalview/gui/PaintRefresher.java b/src/jalview/gui/PaintRefresher.java
index c6d3b58..19fe4c9 100755
--- a/src/jalview/gui/PaintRefresher.java
+++ b/src/jalview/gui/PaintRefresher.java
@@ -1,243 +1,244 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.gui;
-
-import java.util.*;
-
-import java.awt.*;
-
-import jalview.datamodel.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class PaintRefresher
-{
-  static Hashtable components;
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param comp DOCUMENT ME!
-   * @param al DOCUMENT ME!
-   */
-  public static void Register(Component comp, String seqSetId)
-  {
-    if (components == null)
-    {
-      components = new Hashtable();
-    }
-
-    if (components.containsKey(seqSetId))
-    {
-      Vector comps = (Vector) components.get(seqSetId);
-      if (!comps.contains(comp))
-      {
-        comps.addElement(comp);
-      }
-    }
-    else
-    {
-      Vector vcoms = new Vector();
-      vcoms.addElement(comp);
-      components.put(seqSetId, vcoms);
-    }
-  }
-
-  public static void RemoveComponent(Component comp)
-  {
-    if (components == null)
-    {
-      return;
-    }
-
-    Enumeration en = components.keys();
-    while (en.hasMoreElements())
-    {
-      String id = en.nextElement().toString();
-      Vector comps = (Vector) components.get(id);
-      comps.remove(comp);
-      if (comps.size() == 0)
-      {
-        components.remove(id);
-      }
-    }
-  }
-
-  public static void Refresh(Component source, String id)
-  {
-    Refresh(source, id, false, false);
-  }
-
-  public static void Refresh(Component source,
-                             String id,
-                             boolean alignmentChanged,
-                             boolean validateSequences)
-  {
-    if (components == null)
-    {
-      return;
-    }
-
-    Component comp;
-    Vector comps = (Vector) components.get(id);
-
-    if (comps == null)
-    {
-      return;
-    }
-
-    Enumeration e = comps.elements();
-    while (e.hasMoreElements())
-    {
-      comp = (Component) e.nextElement();
-
-      if (comp == source)
-      {
-        continue;
-      }
-
-      if (validateSequences
-          && comp instanceof AlignmentPanel
-          && source instanceof AlignmentPanel)
-      {
-        validateSequences( ( (AlignmentPanel) source).av.alignment,
-                          ( (AlignmentPanel) comp).av.alignment);
-      }
-
-      if (comp instanceof AlignmentPanel && alignmentChanged)
-      {
-        ( (AlignmentPanel) comp).alignmentChanged();
-      }
-
-      comp.repaint();
-    }
-  }
-
-  static void validateSequences(AlignmentI source, AlignmentI comp)
-  {
-    SequenceI[] a1;
-    if (source.getHiddenSequences().getSize() > 0)
-    {
-      a1 = source.getHiddenSequences().getFullAlignment().getSequencesArray();
-    }
-    else
-    {
-      a1 = source.getSequencesArray();
-    }
-
-    SequenceI[] a2;
-    if (comp.getHiddenSequences().getSize() > 0)
-    {
-      a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();
-    }
-    else
-    {
-      a2 = comp.getSequencesArray();
-    }
-
-    int i, iSize = a1.length, j, jSize = a2.length;
-
-    if (iSize == jSize)
-    {
-      return;
-    }
-
-    boolean exists = false;
-    for (i = 0; i < iSize; i++)
-    {
-      exists = false;
-
-      for (j = 0; j < jSize; j++)
-      {
-        if (a2[j] == a1[i])
-        {
-          exists = true;
-          break;
-        }
-      }
-
-      if (!exists)
-      {
-        if (i < comp.getHeight())
-        {
-          comp.getSequences().insertElementAt(a1[i], i);
-        }
-        else
-        {
-          comp.addSequence(a1[i]);
-        }
-
-        if (comp.getHiddenSequences().getSize() > 0)
-        {
-          a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();
-        }
-        else
-        {
-          a2 = comp.getSequencesArray();
-        }
-
-        jSize = a2.length;
-      }
-    }
-
-    iSize = a1.length;
-    jSize = a2.length;
-
-    for (j = 0; j < jSize; j++)
-    {
-      exists = false;
-      for (i = 0; i < iSize; i++)
-      {
-        if (a2[j] == a1[i])
-        {
-          exists = true;
-          break;
-        }
-      }
-
-      if (!exists)
-      {
-        comp.deleteSequence(a2[j]);
-      }
-    }
-  }
-
-  static AlignmentPanel[] getAssociatedPanels(String id)
-  {
-    Vector comps = (Vector) components.get(id);
-    Vector tmp = new Vector();
-    int i, iSize = comps.size();
-    for (i = 0; i < iSize; i++)
-    {
-      if (comps.elementAt(i) instanceof AlignmentPanel)
-      {
-        tmp.addElement( ( (AlignmentPanel) comps.elementAt(i)));
-      }
-    }
-    AlignmentPanel[] result = new AlignmentPanel[tmp.size()];
-    tmp.toArray(result);
-
-    return result;
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.gui;
+
+import java.util.*;
+
+import java.awt.*;
+
+import jalview.datamodel.*;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class PaintRefresher
+{
+  static Hashtable components;
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param comp
+   *                DOCUMENT ME!
+   * @param al
+   *                DOCUMENT ME!
+   */
+  public static void Register(Component comp, String seqSetId)
+  {
+    if (components == null)
+    {
+      components = new Hashtable();
+    }
+
+    if (components.containsKey(seqSetId))
+    {
+      Vector comps = (Vector) components.get(seqSetId);
+      if (!comps.contains(comp))
+      {
+        comps.addElement(comp);
+      }
+    }
+    else
+    {
+      Vector vcoms = new Vector();
+      vcoms.addElement(comp);
+      components.put(seqSetId, vcoms);
+    }
+  }
+
+  public static void RemoveComponent(Component comp)
+  {
+    if (components == null)
+    {
+      return;
+    }
+
+    Enumeration en = components.keys();
+    while (en.hasMoreElements())
+    {
+      String id = en.nextElement().toString();
+      Vector comps = (Vector) components.get(id);
+      comps.remove(comp);
+      if (comps.size() == 0)
+      {
+        components.remove(id);
+      }
+    }
+  }
+
+  public static void Refresh(Component source, String id)
+  {
+    Refresh(source, id, false, false);
+  }
+
+  public static void Refresh(Component source, String id,
+          boolean alignmentChanged, boolean validateSequences)
+  {
+    if (components == null)
+    {
+      return;
+    }
+
+    Component comp;
+    Vector comps = (Vector) components.get(id);
+
+    if (comps == null)
+    {
+      return;
+    }
+
+    Enumeration e = comps.elements();
+    while (e.hasMoreElements())
+    {
+      comp = (Component) e.nextElement();
+
+      if (comp == source)
+      {
+        continue;
+      }
+
+      if (validateSequences && comp instanceof AlignmentPanel
+              && source instanceof AlignmentPanel)
+      {
+        validateSequences(((AlignmentPanel) source).av.alignment,
+                ((AlignmentPanel) comp).av.alignment);
+      }
+
+      if (comp instanceof AlignmentPanel && alignmentChanged)
+      {
+        ((AlignmentPanel) comp).alignmentChanged();
+      }
+
+      comp.repaint();
+    }
+  }
+
+  static void validateSequences(AlignmentI source, AlignmentI comp)
+  {
+    SequenceI[] a1;
+    if (source.getHiddenSequences().getSize() > 0)
+    {
+      a1 = source.getHiddenSequences().getFullAlignment()
+              .getSequencesArray();
+    }
+    else
+    {
+      a1 = source.getSequencesArray();
+    }
+
+    SequenceI[] a2;
+    if (comp.getHiddenSequences().getSize() > 0)
+    {
+      a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();
+    }
+    else
+    {
+      a2 = comp.getSequencesArray();
+    }
+
+    int i, iSize = a1.length, j, jSize = a2.length;
+
+    if (iSize == jSize)
+    {
+      return;
+    }
+
+    boolean exists = false;
+    for (i = 0; i < iSize; i++)
+    {
+      exists = false;
+
+      for (j = 0; j < jSize; j++)
+      {
+        if (a2[j] == a1[i])
+        {
+          exists = true;
+          break;
+        }
+      }
+
+      if (!exists)
+      {
+        if (i < comp.getHeight())
+        {
+          comp.getSequences().insertElementAt(a1[i], i);
+        }
+        else
+        {
+          comp.addSequence(a1[i]);
+        }
+
+        if (comp.getHiddenSequences().getSize() > 0)
+        {
+          a2 = comp.getHiddenSequences().getFullAlignment()
+                  .getSequencesArray();
+        }
+        else
+        {
+          a2 = comp.getSequencesArray();
+        }
+
+        jSize = a2.length;
+      }
+    }
+
+    iSize = a1.length;
+    jSize = a2.length;
+
+    for (j = 0; j < jSize; j++)
+    {
+      exists = false;
+      for (i = 0; i < iSize; i++)
+      {
+        if (a2[j] == a1[i])
+        {
+          exists = true;
+          break;
+        }
+      }
+
+      if (!exists)
+      {
+        comp.deleteSequence(a2[j]);
+      }
+    }
+  }
+
+  static AlignmentPanel[] getAssociatedPanels(String id)
+  {
+    Vector comps = (Vector) components.get(id);
+    Vector tmp = new Vector();
+    int i, iSize = comps.size();
+    for (i = 0; i < iSize; i++)
+    {
+      if (comps.elementAt(i) instanceof AlignmentPanel)
+      {
+        tmp.addElement(((AlignmentPanel) comps.elementAt(i)));
+      }
+    }
+    AlignmentPanel[] result = new AlignmentPanel[tmp.size()];
+    tmp.toArray(result);
+
+    return result;
+  }
+
+}
diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index 190dcb0..15c8c70 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -28,21 +28,22 @@ import jalview.jbgui.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class PairwiseAlignPanel
-    extends GPairwiseAlignPanel
+public class PairwiseAlignPanel extends GPairwiseAlignPanel
 {
 
   AlignViewport av;
+
   Vector sequences;
 
   /**
    * Creates a new PairwiseAlignPanel object.
-   *
-   * @param av DOCUMENT ME!
+   * 
+   * @param av
+   *                DOCUMENT ME!
    */
   public PairwiseAlignPanel(AlignViewport av)
   {
@@ -63,7 +64,8 @@ public class PairwiseAlignPanel
       seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
     }
 
-    String type = (av.alignment.isNucleotide()) ? AlignSeq.DNA : AlignSeq.PEP;
+    String type = (av.alignment.isNucleotide()) ? AlignSeq.DNA
+            : AlignSeq.PEP;
 
     float[][] scores = new float[seqs.length][seqs.length];
     double totscore = 0;
@@ -76,8 +78,8 @@ public class PairwiseAlignPanel
       for (int j = 0; j < i; j++)
       {
 
-        AlignSeq as = new AlignSeq(seqs[i], seqStrings[i],
-                                   seqs[j], seqStrings[j], type);
+        AlignSeq as = new AlignSeq(seqs[i], seqStrings[i], seqs[j],
+                seqStrings[j], type);
 
         if (as.s1str.length() == 0 || as.s2str.length() == 0)
         {
@@ -88,35 +90,30 @@ public class PairwiseAlignPanel
         as.traceAlignment();
 
         as.printAlignment(System.out);
-        scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;
+        scores[i][j] = (float) as.getMaxScore()
+                / (float) as.getASeq1().length;
         totscore = totscore + scores[i][j];
 
         textarea.append(as.getOutput());
-        seq = new Sequence(as.getS1().getName(),
-                           as.getAStr1(),
-                           as.getS1().getStart(),
-                           as.getS1().getEnd()
-            );
+        seq = new Sequence(as.getS1().getName(), as.getAStr1(), as.getS1()
+                .getStart(), as.getS1().getEnd());
         sequences.add(seq);
 
-        seq = new Sequence(as.getS2().getName(),
-                           as.getAStr2(),
-                           as.getS2().getStart(),
-                           as.getS2().getEnd());
+        seq = new Sequence(as.getS2().getName(), as.getAStr2(), as.getS2()
+                .getStart(), as.getS2().getEnd());
         sequences.add(seq);
       }
     }
 
     if (count > 2)
     {
-      System.out.println(
-          "Pairwise alignment scaled similarity score matrix\n");
+      System.out
+              .println("Pairwise alignment scaled similarity score matrix\n");
 
       for (int i = 0; i < count; i++)
       {
-        jalview.util.Format.print(System.out, "%s \n",
-                                  ("" + i) + " " +
-                                  seqs[i].getName());
+        jalview.util.Format.print(System.out, "%s \n", ("" + i) + " "
+                + seqs[i].getName());
       }
 
       System.out.println("\n");
@@ -125,8 +122,8 @@ public class PairwiseAlignPanel
       {
         for (int j = 0; j < i; j++)
         {
-          jalview.util.Format.print(System.out, "%7.3f",
-                                    scores[i][j] / totscore);
+          jalview.util.Format.print(System.out, "%7.3f", scores[i][j]
+                  / totscore);
         }
       }
 
@@ -136,8 +133,9 @@ public class PairwiseAlignPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void viewInEditorButton_actionPerformed(ActionEvent e)
   {
@@ -149,11 +147,9 @@ public class PairwiseAlignPanel
     }
 
     AlignFrame af = new AlignFrame(new Alignment(seq),
-                                   AlignFrame.DEFAULT_WIDTH,
-                                   AlignFrame.DEFAULT_HEIGHT);
+            AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
 
     Desktop.addInternalFrame(af, "Pairwise Aligned Sequences",
-                             AlignFrame.DEFAULT_WIDTH,
-                             AlignFrame.DEFAULT_HEIGHT);
+            AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
   }
 }
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 056a983..a7e853a 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -34,75 +34,119 @@ import jalview.util.UrlLink;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class PopupMenu
-    extends JPopupMenu
+public class PopupMenu extends JPopupMenu
 {
   JMenu groupMenu = new JMenu();
+
   JMenuItem groupName = new JMenuItem();
+
   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
+
   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
+
   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
-  protected JRadioButtonMenuItem hydrophobicityColour = new
-      JRadioButtonMenuItem();
+
+  protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
+
   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
+
   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
+
   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
+
   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
+
   protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
+
   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
+
   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
+
   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
+
   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
+
   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+
   AlignmentPanel ap;
+
   JMenu sequenceMenu = new JMenu();
+
   JMenuItem sequenceName = new JMenuItem();
+
   Sequence sequence;
+
   JMenuItem unGroupMenuItem = new JMenuItem();
+
   JMenuItem outline = new JMenuItem();
+
   JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
+
   JMenu colourMenu = new JMenu();
+
   JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
+
   JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
+
   JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
+
   JMenu editMenu = new JMenu();
+
   JMenuItem cut = new JMenuItem();
+
   JMenuItem copy = new JMenuItem();
+
   JMenuItem upperCase = new JMenuItem();
+
   JMenuItem lowerCase = new JMenuItem();
+
   JMenuItem toggle = new JMenuItem();
+
   JMenu pdbMenu = new JMenu();
+
   JMenuItem pdbFromFile = new JMenuItem();
+
   JMenuItem enterPDB = new JMenuItem();
+
   JMenuItem discoverPDB = new JMenuItem();
+
   JMenu outputMenu = new JMenu();
+
   JMenuItem sequenceFeature = new JMenuItem();
+
   JMenuItem textColour = new JMenuItem();
+
   JMenu jMenu1 = new JMenu();
+
   JMenu structureMenu = new JMenu();
+
   JMenu viewStructureMenu = new JMenu();
- // JMenu colStructureMenu = new JMenu();
+
+  // JMenu colStructureMenu = new JMenu();
   JMenuItem editSequence = new JMenuItem();
- // JMenuItem annotationMenuItem = new JMenuItem();
+
+  // JMenuItem annotationMenuItem = new JMenuItem();
 
   /**
    * Creates a new PopupMenu object.
-   *
-   * @param ap DOCUMENT ME!
-   * @param seq DOCUMENT ME!
+   * 
+   * @param ap
+   *                DOCUMENT ME!
+   * @param seq
+   *                DOCUMENT ME!
    */
   public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
   {
-    ///////////////////////////////////////////////////////////
+    // /////////////////////////////////////////////////////////
     // If this is activated from the sequence panel, the user may want to
     // edit or annotate a particular residue. Therefore display the residue menu
     //
     // If from the IDPanel, we must display the sequence menu
-    //////////////////////////////////////////////////////////
+    // ////////////////////////////////////////////////////////
     this.ap = ap;
     sequence = seq;
 
@@ -123,8 +167,8 @@ public class PopupMenu
 
     for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
     {
-      JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.WRITEABLE_FORMATS[
-                                     i]);
+      JMenuItem item = new JMenuItem(
+              jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 
       item.addActionListener(new java.awt.event.ActionListener()
       {
@@ -140,8 +184,7 @@ public class PopupMenu
     try
     {
       jbInit();
-    }
-    catch (Exception e)
+    } catch (Exception e)
     {
       e.printStackTrace();
     }
@@ -152,10 +195,10 @@ public class PopupMenu
 
       JMenuItem menuItem;
       if (seq.getDatasetSequence().getPDBId() != null
-          && seq.getDatasetSequence().getPDBId().size()>0)
+              && seq.getDatasetSequence().getPDBId().size() > 0)
       {
-        java.util.Enumeration e = seq.getDatasetSequence().getPDBId().
-            elements();
+        java.util.Enumeration e = seq.getDatasetSequence().getPDBId()
+                .elements();
 
         while (e.hasMoreElements())
         {
@@ -170,48 +213,46 @@ public class PopupMenu
               Vector seqs = new Vector();
               for (int i = 0; i < ap.av.alignment.getHeight(); i++)
               {
-                Vector pdbs = ap.av.alignment.getSequenceAt(i).getDatasetSequence().getPDBId();
-                if(pdbs==null)
+                Vector pdbs = ap.av.alignment.getSequenceAt(i)
+                        .getDatasetSequence().getPDBId();
+                if (pdbs == null)
                   continue;
 
-                for(int p=0; p<pdbs.size(); p++)
+                for (int p = 0; p < pdbs.size(); p++)
                 {
-                  PDBEntry p1 = (PDBEntry)pdbs.elementAt(p);
-                  if(p1.getId().equals(pdb.getId()))
+                  PDBEntry p1 = (PDBEntry) pdbs.elementAt(p);
+                  if (p1.getId().equals(pdb.getId()))
                   {
                     if (!seqs.contains(ap.av.alignment.getSequenceAt(i)))
-                        seqs.addElement(ap.av.alignment.getSequenceAt(i));
+                      seqs.addElement(ap.av.alignment.getSequenceAt(i));
 
-                      continue;
+                    continue;
                   }
                 }
               }
 
-              SequenceI [] seqs2 = new SequenceI[seqs.size()];
+              SequenceI[] seqs2 = new SequenceI[seqs.size()];
               seqs.toArray(seqs2);
 
               new AppJmol(pdb, seqs2, null, ap);
-              //  new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
+              // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
             }
           });
           viewStructureMenu.add(menuItem);
 
-       /*   menuItem = new JMenuItem();
-          menuItem.setText(pdb.getId());
-          menuItem.addActionListener(new java.awt.event.ActionListener()
-          {
-            public void actionPerformed(ActionEvent e)
-            {
-              colourByStructure(pdb.getId());
-            }
-          });
-          colStructureMenu.add(menuItem);*/
+          /*
+           * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());
+           * menuItem.addActionListener(new java.awt.event.ActionListener() {
+           * public void actionPerformed(ActionEvent e) {
+           * colourByStructure(pdb.getId()); } });
+           * colStructureMenu.add(menuItem);
+           */
         }
       }
       else
       {
         structureMenu.remove(viewStructureMenu);
-       // structureMenu.remove(colStructureMenu);
+        // structureMenu.remove(colStructureMenu);
       }
 
       menuItem = new JMenuItem("Hide Sequences");
@@ -225,7 +266,7 @@ public class PopupMenu
       add(menuItem);
 
       if (ap.av.getSelectionGroup() != null
-          && ap.av.getSelectionGroup().getSize() > 1)
+              && ap.av.getSelectionGroup().getSize() > 1)
       {
         menuItem = new JMenuItem("Represent Group with " + seq.getName());
         menuItem.addActionListener(new java.awt.event.ActionListener()
@@ -242,8 +283,8 @@ public class PopupMenu
       {
         final int index = ap.av.alignment.findIndex(seq);
 
-        if (ap.av.adjustForHiddenSeqs(index) -
-            ap.av.adjustForHiddenSeqs(index - 1) > 1)
+        if (ap.av.adjustForHiddenSeqs(index)
+                - ap.av.adjustForHiddenSeqs(index - 1) > 1)
         {
           menuItem = new JMenuItem("Reveal Sequences");
           menuItem.addActionListener(new ActionListener()
@@ -367,12 +408,16 @@ public class PopupMenu
       {
         String link = links.elementAt(i).toString();
         UrlLink urlLink = null;
-        try {
+        try
+        {
           urlLink = new UrlLink(link);
-        } catch (Exception foo) {
-          jalview.bin.Cache.log.error("Exception for URLLink '"+link+"'",foo);
+        } catch (Exception foo)
+        {
+          jalview.bin.Cache.log.error("Exception for URLLink '" + link
+                  + "'", foo);
           continue;
-        };
+        }
+        ;
         if (!urlLink.isValid())
         {
           jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
@@ -383,42 +428,47 @@ public class PopupMenu
         {
 
           // collect matching db-refs
-          DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new String[]{urlLink.getTarget()});
+          DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq
+                  .getDBRef(), new String[]
+          { urlLink.getTarget() });
           // collect id string too
           String id = seq.getName();
-          if (dbr!=null)
+          if (dbr != null)
           {
-            for (int r=0;r<dbr.length; r++)
+            for (int r = 0; r < dbr.length; r++)
             {
-              if (id!=null && dbr[r].getAccessionId().equals(id))
+              if (id != null && dbr[r].getAccessionId().equals(id))
               {
-                // suppress duplicate link creation for the bare sequence ID string with this link
+                // suppress duplicate link creation for the bare sequence ID
+                // string with this link
                 id = null;
               }
               // create Bare ID link for this RUL
-              String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(), true);
-              if (urls!=null)
+              String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
+                      true);
+              if (urls != null)
               {
-                for (int u=0; u<urls.length; u+=2)
+                for (int u = 0; u < urls.length; u += 2)
                 {
-                  addshowLink(linkMenu, label+"|"+urls[u],urls[u+1]); 
+                  addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
                 }
               }
             }
           }
-          if (id!=null)
+          if (id != null)
           {
             // create Bare ID link for this RUL
             String[] urls = urlLink.makeUrls(id, true);
-            if (urls!=null)
+            if (urls != null)
             {
-              for (int u=0; u<urls.length; u+=2)
+              for (int u = 0; u < urls.length; u += 2)
               {
-                addshowLink(linkMenu, label,  urls[u+1]);
+                addshowLink(linkMenu, label, urls[u + 1]);
               }
             }
           }
-        } else
+        }
+        else
         {
           // Add a non-dynamic link
           addshowLink(linkMenu, label, urlLink.getUrl_prefix());
@@ -437,39 +487,43 @@ public class PopupMenu
 
   /**
    * add a show URL menu item to the given linkMenu
+   * 
    * @param linkMenu
-   * @param label - menu label string
-   * @param url - url to open
+   * @param label -
+   *                menu label string
+   * @param url -
+   *                url to open
    */
   private void addshowLink(JMenu linkMenu, String label, final String url)
   {
     JMenuItem item = new JMenuItem(label);
-    item.setToolTipText("open URL: "+url);
+    item.setToolTipText("open URL: " + url);
     item.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        new Thread(new Runnable() {
+        new Thread(new Runnable()
+        {
 
           public void run()
           {
             showLink(url);
           }
-          
+
         }).start();
       }
     });
 
-    linkMenu.add(item);    
+    linkMenu.add(item);
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @throws Exception DOCUMENT ME!
+   * 
+   * @throws Exception
+   *                 DOCUMENT ME!
    */
-  private void jbInit()
-      throws Exception
+  private void jbInit() throws Exception
   {
     groupMenu.setText("Group");
     groupMenu.setText("Selection");
@@ -629,7 +683,7 @@ public class PopupMenu
     jMenu1.setText("Group");
     structureMenu.setText("Structure");
     viewStructureMenu.setText("View Structure");
-  //  colStructureMenu.setText("Colour By Structure");
+    // colStructureMenu.setText("Colour By Structure");
     editSequence.setText("Edit Sequence...");
     editSequence.addActionListener(new ActionListener()
     {
@@ -638,14 +692,12 @@ public class PopupMenu
         editSequence_actionPerformed(actionEvent);
       }
     });
-   /* annotationMenuItem.setText("By Annotation");
-    annotationMenuItem.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        annotationMenuItem_actionPerformed(actionEvent);
-      }
-    });*/
+    /*
+     * annotationMenuItem.setText("By Annotation");
+     * annotationMenuItem.addActionListener(new ActionListener() { public void
+     * actionPerformed(ActionEvent actionEvent) {
+     * annotationMenuItem_actionPerformed(actionEvent); } });
+     */
 
     add(groupMenu);
 
@@ -673,13 +725,12 @@ public class PopupMenu
 
     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
     {
-      java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
-          getUserColourSchemes().keys();
+      java.util.Enumeration userColours = jalview.gui.UserDefinedColours
+              .getUserColourSchemes().keys();
 
       while (userColours.hasMoreElements())
       {
-        JMenuItem item = new JMenuItem(userColours.
-                                       nextElement().toString());
+        JMenuItem item = new JMenuItem(userColours.nextElement().toString());
         item.addActionListener(new ActionListener()
         {
           public void actionPerformed(ActionEvent evt)
@@ -694,7 +745,7 @@ public class PopupMenu
     colourMenu.addSeparator();
     colourMenu.add(abovePIDColour);
     colourMenu.add(conservationMenuItem);
-    //colourMenu.add(annotationMenuItem);
+    // colourMenu.add(annotationMenuItem);
     editMenu.add(copy);
     editMenu.add(cut);
     editMenu.add(editSequence);
@@ -713,7 +764,7 @@ public class PopupMenu
     jMenu1.add(outline);
     structureMenu.add(pdbMenu);
     structureMenu.add(viewStructureMenu);
-   // structureMenu.add(colStructureMenu);
+    // structureMenu.add(colStructureMenu);
     noColourmenuItem.setText("None");
     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
     {
@@ -748,13 +799,14 @@ public class PopupMenu
       }
     });
     hydrophobicityColour.setText("Hydrophobicity");
-    hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        hydrophobicityColour_actionPerformed();
-      }
-    });
+    hydrophobicityColour
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                hydrophobicityColour_actionPerformed();
+              }
+            });
     helixColour.setText("Helix propensity");
     helixColour.addActionListener(new java.awt.event.ActionListener()
     {
@@ -820,13 +872,14 @@ public class PopupMenu
       }
     });
     conservationMenuItem.setText("Conservation");
-    conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        conservationMenuItem_actionPerformed();
-      }
-    });
+    conservationMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                conservationMenuItem_actionPerformed();
+              }
+            });
   }
 
   /**
@@ -841,21 +894,24 @@ public class PopupMenu
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void clustalColour_actionPerformed()
   {
     SequenceGroup sg = getGroup();
-    sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),
-                                     ap.av.alignment.getWidth());
+    sg.cs = new ClustalxColourScheme(sg
+            .getSequences(ap.av.hiddenRepSequences), ap.av.alignment
+            .getWidth());
     refresh();
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void zappoColour_actionPerformed()
   {
@@ -865,8 +921,9 @@ public class PopupMenu
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void taylorColour_actionPerformed()
   {
@@ -876,8 +933,9 @@ public class PopupMenu
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void hydrophobicityColour_actionPerformed()
   {
@@ -887,8 +945,9 @@ public class PopupMenu
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void helixColour_actionPerformed()
   {
@@ -898,8 +957,9 @@ public class PopupMenu
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void strandColour_actionPerformed()
   {
@@ -909,8 +969,9 @@ public class PopupMenu
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void turnColour_actionPerformed()
   {
@@ -920,8 +981,9 @@ public class PopupMenu
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void buriedColour_actionPerformed()
   {
@@ -931,8 +993,9 @@ public class PopupMenu
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void nucleotideMenuItem_actionPerformed()
   {
@@ -942,8 +1005,9 @@ public class PopupMenu
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void abovePIDColour_actionPerformed()
   {
@@ -955,18 +1019,19 @@ public class PopupMenu
 
     if (abovePIDColour.isSelected())
     {
-      sg.cs.setConsensus(AAFrequency.calculate(
-          sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
-          sg.getEndRes() + 1));
+      sg.cs.setConsensus(AAFrequency.calculate(sg
+              .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
+              .getEndRes() + 1));
 
-      int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
-          getGroup().getName());
+      int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
+              .getName());
 
       sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
 
       SliderPanel.showPIDSlider();
     }
-    else // remove PIDColouring
+    else
+    // remove PIDColouring
     {
       sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
     }
@@ -976,8 +1041,9 @@ public class PopupMenu
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void userDefinedColour_actionPerformed(ActionEvent e)
   {
@@ -989,8 +1055,8 @@ public class PopupMenu
     }
     else
     {
-      UserColourScheme udc = (UserColourScheme) UserDefinedColours.
-          getUserColourSchemes().get(e.getActionCommand());
+      UserColourScheme udc = (UserColourScheme) UserDefinedColours
+              .getUserColourSchemes().get(e.getActionCommand());
 
       sg.cs = udc;
     }
@@ -999,24 +1065,25 @@ public class PopupMenu
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void PIDColour_actionPerformed()
   {
     SequenceGroup sg = getGroup();
     sg.cs = new PIDColourScheme();
-    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
-        hiddenRepSequences),
-                                             sg.getStartRes(),
-                                             sg.getEndRes() + 1));
+    sg.cs.setConsensus(AAFrequency.calculate(sg
+            .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
+            .getEndRes() + 1));
     refresh();
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void BLOSUM62Colour_actionPerformed()
   {
@@ -1024,18 +1091,18 @@ public class PopupMenu
 
     sg.cs = new Blosum62ColourScheme();
 
-    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
-        hiddenRepSequences),
-                                             sg.getStartRes(),
-                                             sg.getEndRes() + 1));
+    sg.cs.setConsensus(AAFrequency.calculate(sg
+            .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
+            .getEndRes() + 1));
 
     refresh();
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void noColourmenuItem_actionPerformed()
   {
@@ -1045,8 +1112,9 @@ public class PopupMenu
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void conservationMenuItem_actionPerformed()
   {
@@ -1059,11 +1127,9 @@ public class PopupMenu
     if (conservationMenuItem.isSelected())
     {
       Conservation c = new Conservation("Group",
-                                        ResidueProperties.propHash, 3,
-                                        sg.getSequences(ap.av.
-          hiddenRepSequences),
-                                        sg.getStartRes(),
-                                        sg.getEndRes() + 1);
+              ResidueProperties.propHash, 3, sg
+                      .getSequences(ap.av.hiddenRepSequences), sg
+                      .getStartRes(), sg.getEndRes() + 1);
 
       c.calculate();
       c.verdict(false, ap.av.ConsPercGaps);
@@ -1073,7 +1139,8 @@ public class PopupMenu
       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
       SliderPanel.showConservationSlider();
     }
-    else // remove ConservationColouring
+    else
+    // remove ConservationColouring
     {
       sg.cs.setConservation(null);
     }
@@ -1089,8 +1156,9 @@ public class PopupMenu
       return;
     }
 
-    AnnotationColourGradient acg = new AnnotationColourGradient(
-        sequence.getAnnotation()[0], null, AnnotationColourGradient.NO_THRESHOLD);
+    AnnotationColourGradient acg = new AnnotationColourGradient(sequence
+            .getAnnotation()[0], null,
+            AnnotationColourGradient.NO_THRESHOLD);
 
     acg.predefinedColours = true;
     sg.cs = acg;
@@ -1100,18 +1168,17 @@ public class PopupMenu
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void groupName_actionPerformed()
   {
 
     SequenceGroup sg = getGroup();
-    EditNameDialog dialog = new EditNameDialog(sg.getName(),
-                                               sg.getDescription(),
-                                               "       Group Name ",
-                                               "Group Description ",
-                                               "Edit Group Name/Description");
+    EditNameDialog dialog = new EditNameDialog(sg.getName(), sg
+            .getDescription(), "       Group Name ", "Group Description ",
+            "Edit Group Name/Description");
 
     if (!dialog.accept)
     {
@@ -1124,7 +1191,7 @@ public class PopupMenu
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   SequenceGroup getGroup()
@@ -1141,16 +1208,15 @@ public class PopupMenu
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   void sequenceName_actionPerformed()
   {
-    EditNameDialog dialog = new EditNameDialog(sequence.getName(),
-                                               sequence.getDescription(),
-                                               "       Sequence Name ",
-                                               "Sequence Description ",
-                                               "Edit Sequence Name/Description");
+    EditNameDialog dialog = new EditNameDialog(sequence.getName(), sequence
+            .getDescription(), "       Sequence Name ",
+            "Sequence Description ", "Edit Sequence Name/Description");
 
     if (!dialog.accept)
     {
@@ -1162,9 +1228,9 @@ public class PopupMenu
       if (dialog.getName().indexOf(" ") > -1)
       {
         JOptionPane.showMessageDialog(ap,
-                                      "Spaces have been converted to \"_\"",
-                                      "No spaces allowed in Sequence Name",
-                                      JOptionPane.WARNING_MESSAGE);
+                "Spaces have been converted to \"_\"",
+                "No spaces allowed in Sequence Name",
+                JOptionPane.WARNING_MESSAGE);
       }
 
       sequence.setName(dialog.getName().replace(' ', '_'));
@@ -1173,15 +1239,16 @@ public class PopupMenu
 
     sequence.setDescription(dialog.getDescription());
 
-    ap.av.firePropertyChange("alignment", null,
-                             ap.av.getAlignment().getSequences());
+    ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+            .getSequences());
 
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   void unGroupMenuItem_actionPerformed()
   {
@@ -1193,14 +1260,15 @@ public class PopupMenu
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void outline_actionPerformed()
   {
     SequenceGroup sg = getGroup();
     Color col = JColorChooser.showDialog(this, "Select Outline Colour",
-                                         Color.BLUE);
+            Color.BLUE);
 
     if (col != null)
     {
@@ -1212,8 +1280,9 @@ public class PopupMenu
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void showBoxes_actionPerformed()
   {
@@ -1223,8 +1292,9 @@ public class PopupMenu
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void showText_actionPerformed()
   {
@@ -1234,8 +1304,9 @@ public class PopupMenu
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void showColourText_actionPerformed()
   {
@@ -1248,15 +1319,14 @@ public class PopupMenu
     try
     {
       jalview.util.BrowserLauncher.openURL(url);
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
-      JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                            "Unixers: Couldn't find default web browser."
-                                            +
-          "\nAdd the full path to your browser in Preferences.",
-                                            "Web browser not found",
-                                            JOptionPane.WARNING_MESSAGE);
+      JOptionPane
+              .showInternalMessageDialog(
+                      Desktop.desktop,
+                      "Unixers: Couldn't find default web browser."
+                              + "\nAdd the full path to your browser in Preferences.",
+                      "Web browser not found", JOptionPane.WARNING_MESSAGE);
 
       ex.printStackTrace();
     }
@@ -1268,7 +1338,7 @@ public class PopupMenu
     if (sg == null || sg.getSize() < 1)
     {
       ap.av.hideSequence(new SequenceI[]
-                         {sequence});
+      { sequence });
       return;
     }
 
@@ -1312,8 +1382,8 @@ public class PopupMenu
 
     if (sg != null)
     {
-      int[][] startEnd = ap.av.getVisibleRegionBoundaries(
-          sg.getStartRes(), sg.getEndRes() + 1);
+      int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
+              sg.getEndRes() + 1);
 
       String description;
       int caseChange;
@@ -1334,15 +1404,14 @@ public class PopupMenu
         caseChange = ChangeCaseCommand.TO_LOWER;
       }
 
-      ChangeCaseCommand caseCommand = new ChangeCaseCommand(
-          description, sg.getSequencesAsArray(ap.av.hiddenRepSequences),
-          startEnd, caseChange
-          );
+      ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, sg
+              .getSequencesAsArray(ap.av.hiddenRepSequences), startEnd,
+              caseChange);
 
       ap.alignFrame.addHistoryItem(caseCommand);
 
-      ap.av.firePropertyChange("alignment", null,
-                               ap.av.getAlignment().getSequences());
+      ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+              .getSequences());
 
     }
   }
@@ -1351,36 +1420,33 @@ public class PopupMenu
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
     cap.setForInput(null);
-    Desktop.addInternalFrame(cap,
-                             "Alignment output - " + e.getActionCommand(), 600,
-                             500);
+    Desktop.addInternalFrame(cap, "Alignment output - "
+            + e.getActionCommand(), 600, 500);
 
     String[] omitHidden = null;
 
-    System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens or we simply trust the user wants wysiwig behaviour
+    System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
+                                            // or we simply trust the user wants
+                                            // wysiwig behaviour
     SequenceGroup sg = ap.av.getSelectionGroup();
     ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
     omitHidden = ap.av.getViewAsString(true);
     Alignment oal = new Alignment(ap.av.getSequenceSelection());
     AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation();
-    for (int i=0; i<nala.length; i++)
+    for (int i = 0; i < nala.length; i++)
     {
-      AlignmentAnnotation na =nala[i];
+      AlignmentAnnotation na = nala[i];
       oal.addAnnotation(na);
     }
-    cap.setText(new FormatAdapter().formatSequences(
-            e.getActionCommand(),
-            oal,
-            omitHidden, csel, sg));
-    oal=null;
+    cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
+            oal, omitHidden, csel, sg));
+    oal = null;
   }
 
   public void pdbFromFile_actionPerformed()
   {
-    jalview.io.JalviewFileChooser chooser
-        = new jalview.io.JalviewFileChooser(jalview.bin.Cache.
-                                            getProperty(
-                                                "LAST_DIRECTORY"));
+    jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
+            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new jalview.io.JalviewFileView());
     chooser.setDialogTitle("Select a PDB file");
     chooser.setToolTipText("Load a PDB file");
@@ -1395,15 +1461,16 @@ public class PopupMenu
       try
       {
         MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
-            jalview.io.AppletFormatAdapter.FILE);
+                jalview.io.AppletFormatAdapter.FILE);
 
         if (pdbfile.id == null)
         {
-          String reply = JOptionPane.showInternalInputDialog(
-              Desktop.desktop,
-              "Couldn't find a PDB id in the file supplied."
-              + "Please enter an Id to identify this structure.",
-              "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
+          String reply = JOptionPane
+                  .showInternalInputDialog(
+                          Desktop.desktop,
+                          "Couldn't find a PDB id in the file supplied."
+                                  + "Please enter an Id to identify this structure.",
+                          "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
           if (reply == null)
           {
             return;
@@ -1415,8 +1482,7 @@ public class PopupMenu
         {
           entry.setId(pdbfile.id);
         }
-      }
-      catch (java.io.IOException ex)
+      } catch (java.io.IOException ex)
       {
         ex.printStackTrace();
       }
@@ -1430,32 +1496,31 @@ public class PopupMenu
   public void enterPDB_actionPerformed()
   {
     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
-        "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
+            "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
 
     if (id != null && id.length() > 0)
     {
       PDBEntry entry = new PDBEntry();
       entry.setId(id.toUpperCase());
-      sequence.getDatasetSequence()
-          .addPDBId(entry);
+      sequence.getDatasetSequence().addPDBId(entry);
     }
   }
 
   public void discoverPDB_actionPerformed()
   {
-    
-    final SequenceI[] sequences = 
-      ((ap.av.selectionGroup == null) 
-              ?  new Sequence[]{sequence}
-      : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment));
-    Thread discpdb = new Thread(new Runnable() {
+
+    final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new Sequence[]
+    { sequence }
+            : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment));
+    Thread discpdb = new Thread(new Runnable()
+    {
       public void run()
       {
-        
-        new jalview.ws.DBRefFetcher(sequences,
-                ap.alignFrame).fetchDBRefs(false);
+
+        new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
+                .fetchDBRefs(false);
       }
-      
+
     });
     discpdb.start();
   }
@@ -1477,11 +1542,12 @@ public class PopupMenu
       seqs[i] = sg.getSequenceAt(i).getDatasetSequence();
       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
       int end = sg.findEndRes(sg.getSequenceAt(i));
-      features[i] = new SequenceFeature(null, null, null, start, end, "Jalview");
+      features[i] = new SequenceFeature(null, null, null, start, end,
+              "Jalview");
     }
 
-    if (ap.seqPanel.seqCanvas.getFeatureRenderer()
-        .amendFeatures(seqs, features, true, ap))
+    if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
+            features, true, ap))
     {
       ap.alignFrame.showSeqFeatures.setSelected(true);
       ap.av.setShowSequenceFeatures(true);
@@ -1500,57 +1566,51 @@ public class PopupMenu
 
   public void colourByStructure(String pdbid)
   {
-    Annotation [] anots = jalview.structure.StructureSelectionManager.getStructureSelectionManager()
-        .colourSequenceFromStructure(sequence, pdbid);
+    Annotation[] anots = jalview.structure.StructureSelectionManager
+            .getStructureSelectionManager().colourSequenceFromStructure(
+                    sequence, pdbid);
 
-    AlignmentAnnotation an = new AlignmentAnnotation(
-      "Structure", "Coloured by "+pdbid, anots);
+    AlignmentAnnotation an = new AlignmentAnnotation("Structure",
+            "Coloured by " + pdbid, anots);
 
     ap.av.alignment.addAnnotation(an);
     an.createSequenceMapping(sequence, 0, true);
-    //an.adjustForAlignment();
-    ap.av.alignment.setAnnotationIndex(an,0);
+    // an.adjustForAlignment();
+    ap.av.alignment.setAnnotationIndex(an, 0);
 
     ap.adjustAnnotationHeight();
 
     sequence.addAlignmentAnnotation(an);
 
-    }
+  }
 
   public void editSequence_actionPerformed(ActionEvent actionEvent)
   {
-      SequenceGroup sg = ap.av.getSelectionGroup();
+    SequenceGroup sg = ap.av.getSelectionGroup();
+
+    if (sg != null)
+    {
+      if (sequence == null)
+        sequence = (Sequence) sg.getSequenceAt(0);
+
+      EditNameDialog dialog = new EditNameDialog(sequence
+              .getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1),
+              null, "Edit Sequence ", null, "Edit Sequence");
 
-      if(sg!=null)
+      if (dialog.accept)
       {
-        if (sequence == null)
-          sequence = (Sequence) sg.getSequenceAt(0);
-
-        EditNameDialog dialog = new EditNameDialog(
-            sequence.getSequenceAsString(
-                sg.getStartRes(),
-                sg.getEndRes() + 1),
-            null,
-            "Edit Sequence ",
-            null,
-            "Edit Sequence");
-
-        if (dialog.accept)
-        {
-          EditCommand editCommand = new EditCommand(
-              "Edit Sequences", EditCommand.REPLACE,
-              dialog.getName().replace(' ', ap.av.getGapCharacter()),
-              sg.getSequencesAsArray(ap.av.hiddenRepSequences),
-              sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment
-              );
+        EditCommand editCommand = new EditCommand("Edit Sequences",
+                EditCommand.REPLACE, dialog.getName().replace(' ',
+                        ap.av.getGapCharacter()), sg
+                        .getSequencesAsArray(ap.av.hiddenRepSequences), sg
+                        .getStartRes(), sg.getEndRes() + 1, ap.av.alignment);
 
-          ap.alignFrame.addHistoryItem(editCommand);
+        ap.alignFrame.addHistoryItem(editCommand);
 
-          ap.av.firePropertyChange("alignment", null,
-                                   ap.av.getAlignment().getSequences());
-        }
+        ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+                .getSequences());
       }
+    }
   }
 
-
 }
diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 7226283..bd4c900 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -31,19 +31,23 @@ import jalview.schemes.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class Preferences
-    extends GPreferences
+public class Preferences extends GPreferences
 {
-  /** Holds name and link separated with | character. Sequence ID must be $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$ */
+  /**
+   * Holds name and link separated with | character. Sequence ID must be
+   * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
+   */
   public static Vector sequenceURLLinks;
   static
   {
-    String string = Cache.getDefault("SEQUENCE_LINKS",
-                                     "SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
+    String string = Cache
+            .getDefault(
+                    "SEQUENCE_LINKS",
+                    "SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
     sequenceURLLinks = new Vector();
 
     try
@@ -51,18 +55,17 @@ public class Preferences
       StringTokenizer st = new StringTokenizer(string, "|");
       while (st.hasMoreElements())
       {
-        String name=st.nextToken();
-        String url= st.nextToken();
+        String name = st.nextToken();
+        String url = st.nextToken();
         // check for '|' within a regex
         int rxstart = url.indexOf("$SEQUENCE_ID$");
-        while (rxstart==-1 && url.indexOf("/=$")==-1)
+        while (rxstart == -1 && url.indexOf("/=$") == -1)
         {
           url = url + "|" + st.nextToken();
         }
         sequenceURLLinks.addElement(name + "|" + url);
       }
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       System.out.println(ex + "\nError parsing sequence links");
     }
@@ -118,8 +121,8 @@ public class Preferences
 
     colour.setSelectedItem(string);
 
-    String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()
-        .getAvailableFontFamilyNames();
+    String[] fonts = java.awt.GraphicsEnvironment
+            .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 
     for (int i = 0; i < fonts.length; i++)
     {
@@ -137,7 +140,8 @@ public class Preferences
 
     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
-    fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
+    fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
+            + ""));
 
     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 
@@ -150,9 +154,10 @@ public class Preferences
 
     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 
-    startupCheckbox.setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
+    startupCheckbox
+            .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
-                                                  "http://www.jalview.org/examples/exampleFile_2_3.jar"));
+            "http://www.jalview.org/examples/exampleFile_2_3.jar"));
 
     sortby.addItem("No sort");
     sortby.addItem("Id");
@@ -163,7 +168,7 @@ public class Preferences
     epsRendering.addItem("Lineart");
     epsRendering.addItem("Text");
     epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
-                                                  "Prompt each time"));
+            "Prompt each time"));
 
     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
@@ -175,10 +180,11 @@ public class Preferences
 
     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 
-    autoCalculateConsCheck.setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+    autoCalculateConsCheck.setSelected(Cache.getDefault(
+            "AUTO_CALC_CONSENSUS", true));
     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 
-    /****************************************************
+    /***************************************************************************
      * Set up Connections
      */
     nameLinks = new Vector();
@@ -202,8 +208,7 @@ public class Preferences
     try
     {
       jbInit();
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       ex.printStackTrace();
     }
@@ -212,71 +217,58 @@ public class Preferences
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void ok_actionPerformed(ActionEvent e)
   {
 
-    Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
-                                            Boolean.toString(seqLimit.
-        isSelected()));
-    Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
-                                            Boolean.toString(rightAlign.
-        isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
-                                            Boolean.toString(fullScreen.
-        isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
-                                            Boolean.toString(openoverv.
-        isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
-                                            Boolean.
-                                            toString(annotations.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
-                                            Boolean.
-                                            toString(conservation.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_QUALITY",
-                                            Boolean.toString(quality.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_IDENTITY",
-                                            Boolean.toString(identity.
-        isSelected()));
-
-    Cache.applicationProperties.setProperty("DEFAULT_COLOUR",
-                                            colour.getSelectedItem().toString());
-    Cache.applicationProperties.setProperty("GAP_SYMBOL",
-                                            gapSymbolCB.getSelectedItem().
-                                            toString());
-
-    Cache.applicationProperties.setProperty("FONT_NAME",
-                                            fontNameCB.getSelectedItem().
-                                            toString());
-    Cache.applicationProperties.setProperty("FONT_STYLE",
-                                            fontStyleCB.getSelectedItem().
-                                            toString());
-    Cache.applicationProperties.setProperty("FONT_SIZE",
-                                            fontSizeCB.getSelectedItem().
-                                            toString());
-
-    Cache.applicationProperties.setProperty("ID_ITALICS",
-                                            Boolean.toString(idItalics.
-        isSelected()));
-
-    Cache.applicationProperties.setProperty("ANTI_ALIAS",
-                                            Boolean.toString(smoothFont.
-        isSelected()));
-
-    Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
-                                            Boolean.toString(wrap.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean
+            .toString(seqLimit.isSelected()));
+    Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS", Boolean
+            .toString(rightAlign.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean
+            .toString(fullScreen.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_OVERVIEW", Boolean
+            .toString(openoverv.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean
+            .toString(annotations.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_CONSERVATION", Boolean
+            .toString(conservation.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_QUALITY", Boolean
+            .toString(quality.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_IDENTITY", Boolean
+            .toString(identity.isSelected()));
+
+    Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour
+            .getSelectedItem().toString());
+    Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
+            .getSelectedItem().toString());
+
+    Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
+            .getSelectedItem().toString());
+    Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
+            .getSelectedItem().toString());
+    Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
+            .getSelectedItem().toString());
+
+    Cache.applicationProperties.setProperty("ID_ITALICS", Boolean
+            .toString(idItalics.isSelected()));
+
+    Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean
+            .toString(smoothFont.isSelected()));
+
+    Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", Boolean
+            .toString(wrap.isSelected()));
 
     Cache.applicationProperties.setProperty("STARTUP_FILE",
-                                            startupFileTextfield.getText());
-    Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
-                                            Boolean.
-                                            toString(startupCheckbox.isSelected()));
+            startupFileTextfield.getText());
+    Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE", Boolean
+            .toString(startupCheckbox.isSelected()));
 
-    Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
-                                            sortby.getSelectedItem().toString());
+    Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
+            .getSelectedItem().toString());
 
     if (epsRendering.getSelectedItem().equals("Prompt each time"))
     {
@@ -284,9 +276,8 @@ public class Preferences
     }
     else
     {
-      Cache.applicationProperties.setProperty("EPS_RENDERING",
-                                              epsRendering.getSelectedItem().
-                                              toString());
+      Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering
+              .getSelectedItem().toString());
     }
 
     if (defaultBrowser.getText().trim().length() < 1)
@@ -296,7 +287,7 @@ public class Preferences
     else
     {
       Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
-                                              defaultBrowser.getText());
+              defaultBrowser.getText());
     }
 
     jalview.util.BrowserLauncher.resetBrowser();
@@ -307,23 +298,23 @@ public class Preferences
       sequenceURLLinks = new Vector();
       for (int i = 0; i < nameLinks.size(); i++)
       {
-        sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|" +
-                                    urlLinks.elementAt(i));
+        sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
+                + urlLinks.elementAt(i));
         links.append(sequenceURLLinks.elementAt(i).toString());
         links.append("|");
       }
       // remove last "|"
       links.setLength(links.length() - 1);
-      Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links.toString());
+      Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links
+              .toString());
     }
     else
     {
       Cache.applicationProperties.remove("SEQUENCE_LINKS");
     }
 
-    Cache.applicationProperties.setProperty("USE_PROXY",
-                                            Boolean.toString(useProxy.
-        isSelected()));
+    Cache.applicationProperties.setProperty("USE_PROXY", Boolean
+            .toString(useProxy.isSelected()));
 
     if (proxyServerTB.getText().trim().length() < 1)
     {
@@ -331,8 +322,8 @@ public class Preferences
     }
     else
     {
-      Cache.applicationProperties.setProperty("PROXY_SERVER",
-                                              proxyServerTB.getText());
+      Cache.applicationProperties.setProperty("PROXY_SERVER", proxyServerTB
+              .getText());
     }
 
     if (proxyPortTB.getText().trim().length() < 1)
@@ -341,7 +332,8 @@ public class Preferences
     }
     else
     {
-      Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText());
+      Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB
+              .getText());
     }
 
     if (useProxy.isSelected())
@@ -355,32 +347,28 @@ public class Preferences
       System.setProperty("http.proxyPort", "");
     }
 
-    Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
-                                            Boolean.toString(blcjv.isSelected()));
-    Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
-                                            Boolean.
-                                            toString(clustaljv.isSelected()));
-    Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
-                                            Boolean.toString(fastajv.isSelected()));
-    Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
-                                            Boolean.toString(msfjv.isSelected()));
-    Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
-                                            Boolean.toString(pfamjv.isSelected()));
-    Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
-                                            Boolean.toString(pileupjv.
-        isSelected()));
-    Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
-                                            Boolean.toString(pirjv.isSelected()));
-    Cache.applicationProperties.setProperty("PIR_MODELLER",
-                                            Boolean.toString(modellerOutput.
-        isSelected()));
+    Cache.applicationProperties.setProperty("BLC_JVSUFFIX", Boolean
+            .toString(blcjv.isSelected()));
+    Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean
+            .toString(clustaljv.isSelected()));
+    Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean
+            .toString(fastajv.isSelected()));
+    Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean
+            .toString(msfjv.isSelected()));
+    Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean
+            .toString(pfamjv.isSelected()));
+    Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean
+            .toString(pileupjv.isSelected()));
+    Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean
+            .toString(pirjv.isSelected()));
+    Cache.applicationProperties.setProperty("PIR_MODELLER", Boolean
+            .toString(modellerOutput.isSelected()));
     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 
-    Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
-                                            Boolean.toString(
-        autoCalculateConsCheck.isSelected()));
-    Cache.applicationProperties.setProperty("PAD_GAPS",
-                                            Boolean.toString(padGaps.isSelected()));
+    Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS", Boolean
+            .toString(autoCalculateConsCheck.isSelected()));
+    Cache.applicationProperties.setProperty("PAD_GAPS", Boolean
+            .toString(padGaps.isSelected()));
 
     dasSource.saveProperties(Cache.applicationProperties);
 
@@ -388,8 +376,7 @@ public class Preferences
     try
     {
       frame.setClosed(true);
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
     }
   }
@@ -399,18 +386,12 @@ public class Preferences
    */
   public void startupFileTextfield_mouseClicked()
   {
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-        getProperty(
-            "LAST_DIRECTORY"),
-        new String[]
-        {
-        "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
-        "jar"
-    },
-        new String[]
-        {
-        "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
-    }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+            .getProperty("LAST_DIRECTORY"), new String[]
+    { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "jar" },
+            new String[]
+            { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
+            jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle("Select startup file");
 
@@ -418,33 +399,34 @@ public class Preferences
 
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
-      jalview.bin.Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
-          chooser.getSelectedFormat());
+      jalview.bin.Cache.applicationProperties.setProperty(
+              "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
       startupFileTextfield.setText(chooser.getSelectedFile()
-                                   .getAbsolutePath());
+              .getAbsolutePath());
     }
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void cancel_actionPerformed(ActionEvent e)
   {
     try
     {
       frame.setClosed(true);
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
     }
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void annotations_actionPerformed(ActionEvent e)
   {
@@ -461,10 +443,8 @@ public class Preferences
     while (!valid)
     {
       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
-                                                "New sequence URL link",
-                                                JOptionPane.OK_CANCEL_OPTION
-                                                , -1, null)
-          == JOptionPane.OK_OPTION)
+              "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
+              null) == JOptionPane.OK_OPTION)
       {
         if (link.checkValid())
         {
@@ -489,9 +469,8 @@ public class Preferences
     if (index == -1)
     {
       JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                            "No link selected!"
-                                            , "No link selected",
-                                            JOptionPane.WARNING_MESSAGE);
+              "No link selected!", "No link selected",
+              JOptionPane.WARNING_MESSAGE);
       return;
     }
 
@@ -503,10 +482,8 @@ public class Preferences
     {
 
       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
-                                                "New sequence URL link",
-                                                JOptionPane.OK_CANCEL_OPTION
-                                                , -1, null)
-          == JOptionPane.OK_OPTION)
+              "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
+              null) == JOptionPane.OK_OPTION)
       {
         if (link.checkValid())
         {
@@ -530,9 +507,8 @@ public class Preferences
     if (index == -1)
     {
       JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                            "No link selected!"
-                                            , "No link selected",
-                                            JOptionPane.WARNING_MESSAGE);
+              "No link selected!", "No link selected",
+              JOptionPane.WARNING_MESSAGE);
       return;
     }
     nameLinks.removeElementAt(index);
@@ -560,8 +536,7 @@ public class Preferences
 
   }
 
-  private void jbInit()
-      throws Exception
+  private void jbInit() throws Exception
   {
   }
 }
diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 1e51879..2355b47 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -31,26 +31,33 @@ import jalview.util.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class RedundancyPanel
-    extends GSliderPanel implements Runnable
+public class RedundancyPanel extends GSliderPanel implements Runnable
 {
   AlignFrame af;
+
   AlignmentPanel ap;
+
   Stack historyList = new Stack(); // simpler than synching with alignFrame.
+
   float[] redundancy;
+
   SequenceI[] originalSequences;
+
   JInternalFrame frame;
+
   Vector redundantSeqs;
 
   /**
    * Creates a new RedundancyPanel object.
-   *
-   * @param ap DOCUMENT ME!
-   * @param af DOCUMENT ME!
+   * 
+   * @param ap
+   *                DOCUMENT ME!
+   * @param af
+   *                DOCUMENT ME!
    */
   public RedundancyPanel(final AlignmentPanel ap, AlignFrame af)
   {
@@ -79,26 +86,27 @@ public class RedundancyPanel
     frame = new JInternalFrame();
     frame.setContentPane(this);
     Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
-                             100, false);
+            100, false);
     frame.addInternalFrameListener(new InternalFrameAdapter()
     {
       public void internalFrameClosing(InternalFrameEvent evt)
       {
         ap.idPanel.idCanvas.setHighlighted(null);
       }
-    }
-    );
+    });
 
   }
 
   /**
-   * This is a copy of remove redundancy in jalivew.datamodel.Alignment
-   * except we dont want to remove redundancy, just calculate once
-   * so we can use the slider to dynamically hide redundant sequences
-   *
-   * @param threshold DOCUMENT ME!
-   * @param sel DOCUMENT ME!
-   *
+   * This is a copy of remove redundancy in jalivew.datamodel.Alignment except
+   * we dont want to remove redundancy, just calculate once so we can use the
+   * slider to dynamically hide redundant sequences
+   * 
+   * @param threshold
+   *                DOCUMENT ME!
+   * @param sel
+   *                DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   public void run()
@@ -122,7 +130,7 @@ public class RedundancyPanel
 
     int start, end;
 
-    if ( (sg != null) && (sg.getSize() >= 1))
+    if ((sg != null) && (sg.getSize() >= 1))
     {
       originalSequences = sg.getSequencesInOrder(ap.av.alignment);
       start = sg.getStartRes();
@@ -227,8 +235,9 @@ public class RedundancyPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void applyButton_actionPerformed(ActionEvent e)
   {
@@ -247,7 +256,8 @@ public class RedundancyPanel
       }
     }
 
-    // This has to be done before the restoreHistoryItem method of alignFrame will
+    // This has to be done before the restoreHistoryItem method of alignFrame
+    // will
     // actually restore these sequences.
     if (del.size() > 0)
     {
@@ -264,16 +274,12 @@ public class RedundancyPanel
       }
 
       EditCommand cut = new EditCommand("Remove Redundancy",
-                                        EditCommand.CUT, deleted, 0, width,
-                                        ap.av.alignment);
+              EditCommand.CUT, deleted, 0, width, ap.av.alignment);
 
       for (int i = 0; i < del.size(); i++)
       {
         ap.av.alignment.deleteSequence(deleted[i]);
-        PaintRefresher.Refresh(this,
-                               ap.av.getSequenceSetId(),
-                               true,
-                               true);
+        PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
         if (sg != null)
         {
           sg.deleteSequence(deleted[i], false);
@@ -284,16 +290,17 @@ public class RedundancyPanel
 
       ap.alignFrame.addHistoryItem(cut);
 
-      ap.av.firePropertyChange("alignment", null,
-                               ap.av.getAlignment().getSequences());
+      ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+              .getSequences());
     }
 
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void undoButton_actionPerformed(ActionEvent e)
   {
@@ -316,8 +323,9 @@ public class RedundancyPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void valueField_actionPerformed(ActionEvent e)
   {
@@ -325,8 +333,7 @@ public class RedundancyPanel
     {
       int i = Integer.parseInt(valueField.getText());
       slider.setValue(i);
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       valueField.setText(slider.getValue() + "");
     }
diff --git a/src/jalview/gui/RotatableCanvas.java b/src/jalview/gui/RotatableCanvas.java
index 32c4adc..14cd425 100755
--- a/src/jalview/gui/RotatableCanvas.java
+++ b/src/jalview/gui/RotatableCanvas.java
@@ -1,769 +1,818 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.gui;
-
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-import jalview.datamodel.*;
-import jalview.math.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class RotatableCanvas
-    extends JPanel implements MouseListener,
-    MouseMotionListener, KeyListener
-{
-  RotatableMatrix idmat = new RotatableMatrix(3, 3);
-  RotatableMatrix objmat = new RotatableMatrix(3, 3);
-  RotatableMatrix rotmat = new RotatableMatrix(3, 3);
-
-  //RubberbandRectangle rubberband;
-  boolean drawAxes = true;
-  int omx = 0;
-  int mx = 0;
-  int omy = 0;
-  int my = 0;
-  Image img;
-  Graphics ig;
-  Dimension prefsize;
-  float[] centre = new float[3];
-  float[] width = new float[3];
-  float[] max = new float[3];
-  float[] min = new float[3];
-  float maxwidth;
-  float scale;
-  int npoint;
-  Vector points;
-  float[][] orig;
-  float[][] axes;
-  int startx;
-  int starty;
-  int lastx;
-  int lasty;
-  int rectx1;
-  int recty1;
-  int rectx2;
-  int recty2;
-  float scalefactor = 1;
-  AlignViewport av;
-  AlignmentPanel ap;
-  boolean showLabels = false;
-  Color bgColour = Color.black;
-  boolean applyToAllViews = false;
-
-  //  Controller    controller;
-  public RotatableCanvas(AlignmentPanel ap)
-  {
-    this.av = ap.av;
-    this.ap = ap;
-
-    addMouseWheelListener(new MouseWheelListener()
-    {
-      public void mouseWheelMoved(MouseWheelEvent e)
-      {
-        if (e.getWheelRotation() > 0)
-        {
-          scale = (float) (scale * 1.1);
-          repaint();
-        }
-
-        else
-        {
-          scale = (float) (scale * 0.9);
-          repaint();
-        }
-      }
-    });
-
-  }
-
-  public void showLabels(boolean b)
-  {
-    showLabels = b;
-    repaint();
-  }
-
-  public void setPoints(Vector points, int npoint)
-  {
-    this.points = points;
-    this.npoint = npoint;
-    ToolTipManager.sharedInstance().registerComponent(this);
-    ToolTipManager.sharedInstance().setInitialDelay(0);
-    ToolTipManager.sharedInstance().setDismissDelay(10000);
-
-    prefsize = getPreferredSize();
-    orig = new float[npoint][3];
-
-    for (int i = 0; i < npoint; i++)
-    {
-      SequencePoint sp = (SequencePoint) points.elementAt(i);
-
-      for (int j = 0; j < 3; j++)
-      {
-        orig[i][j] = sp.coord[j];
-      }
-    }
-
-    //Initialize the matrices to identity
-    for (int i = 0; i < 3; i++)
-    {
-      for (int j = 0; j < 3; j++)
-      {
-        if (i != j)
-        {
-          idmat.addElement(i, j, 0);
-          objmat.addElement(i, j, 0);
-          rotmat.addElement(i, j, 0);
-        }
-        else
-        {
-          idmat.addElement(i, j, 0);
-          objmat.addElement(i, j, 0);
-          rotmat.addElement(i, j, 0);
-        }
-      }
-    }
-
-    axes = new float[3][3];
-    initAxes();
-
-    findCentre();
-    findWidth();
-
-    scale = findScale();
-
-    addMouseListener(this);
-
-    addMouseMotionListener(this);
-
-  }
-
-  public void initAxes()
-  {
-    for (int i = 0; i < 3; i++)
-    {
-      for (int j = 0; j < 3; j++)
-      {
-        if (i != j)
-        {
-          axes[i][j] = 0;
-        }
-        else
-        {
-          axes[i][j] = 1;
-        }
-      }
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  public void findWidth()
-  {
-    max = new float[3];
-    min = new float[3];
-
-    max[0] = (float) - 1e30;
-    max[1] = (float) - 1e30;
-    max[2] = (float) - 1e30;
-
-    min[0] = (float) 1e30;
-    min[1] = (float) 1e30;
-    min[2] = (float) 1e30;
-
-    for (int i = 0; i < 3; i++)
-    {
-      for (int j = 0; j < npoint; j++)
-      {
-        SequencePoint sp = (SequencePoint) points.elementAt(j);
-
-        if (sp.coord[i] >= max[i])
-        {
-          max[i] = sp.coord[i];
-        }
-
-        if (sp.coord[i] <= min[i])
-        {
-          min[i] = sp.coord[i];
-        }
-      }
-    }
-
-    //    System.out.println("xmax " + max[0] + " min " + min[0]);
-    //System.out.println("ymax " + max[1] + " min " + min[1]);
-    //System.out.println("zmax " + max[2] + " min " + min[2]);
-    width[0] = Math.abs(max[0] - min[0]);
-    width[1] = Math.abs(max[1] - min[1]);
-    width[2] = Math.abs(max[2] - min[2]);
-
-    maxwidth = width[0];
-
-    if (width[1] > width[0])
-    {
-      maxwidth = width[1];
-    }
-
-    if (width[2] > width[1])
-    {
-      maxwidth = width[2];
-    }
-
-    //System.out.println("Maxwidth = " + maxwidth);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public float findScale()
-  {
-    int dim;
-    int width;
-    int height;
-
-    if (getWidth() != 0)
-    {
-      width = getWidth();
-      height = getHeight();
-    }
-    else
-    {
-      width = prefsize.width;
-      height = prefsize.height;
-    }
-
-    if (width < height)
-    {
-      dim = width;
-    }
-    else
-    {
-      dim = height;
-    }
-
-    return (float) ( (dim * scalefactor) / (2 * maxwidth));
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  public void findCentre()
-  {
-    //Find centre coordinate
-    findWidth();
-
-    centre[0] = (max[0] + min[0]) / 2;
-    centre[1] = (max[1] + min[1]) / 2;
-    centre[2] = (max[2] + min[2]) / 2;
-
-    //    System.out.println("Centre x " + centre[0]);
-    //System.out.println("Centre y " + centre[1]);
-    //System.out.println("Centre z " + centre[2]);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Dimension getPreferredSize()
-  {
-    if (prefsize != null)
-    {
-      return prefsize;
-    }
-    else
-    {
-      return new Dimension(400, 400);
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Dimension getMinimumSize()
-  {
-    return getPreferredSize();
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param g DOCUMENT ME!
-   */
-  public void paintComponent(Graphics g1)
-  {
-
-    Graphics2D g = (Graphics2D) g1;
-
-    g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-                       RenderingHints.VALUE_ANTIALIAS_ON);
-    if (points == null)
-    {
-      g.setFont(new Font("Verdana", Font.PLAIN, 18));
-      g.drawString("Calculating PCA....", 20, getHeight() / 2);
-    }
-    else
-    {
-      //Only create the image at the beginning -
-      if ( (img == null) || (prefsize.width != getWidth()) ||
-          (prefsize.height != getHeight()))
-      {
-        prefsize.width = getWidth();
-        prefsize.height = getHeight();
-
-        scale = findScale();
-
-        //      System.out.println("New scale = " + scale);
-        img = createImage(getWidth(), getHeight());
-        ig = img.getGraphics();
-      }
-
-      drawBackground(ig, bgColour);
-      drawScene(ig);
-
-      if (drawAxes == true)
-      {
-        drawAxes(ig);
-      }
-
-      g.drawImage(img, 0, 0, this);
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param g DOCUMENT ME!
-   */
-  public void drawAxes(Graphics g)
-  {
-
-    g.setColor(Color.yellow);
-
-    for (int i = 0; i < 3; i++)
-    {
-      g.drawLine(getWidth() / 2, getHeight() / 2,
-                 (int) ( (axes[i][0] * scale * max[0]) + (getWidth() / 2)),
-                 (int) ( (axes[i][1] * scale * max[1]) + (getHeight() / 2)));
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param g DOCUMENT ME!
-   * @param col DOCUMENT ME!
-   */
-  public void drawBackground(Graphics g, Color col)
-  {
-    g.setColor(col);
-    g.fillRect(0, 0, prefsize.width, prefsize.height);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param g DOCUMENT ME!
-   */
-  public void drawScene(Graphics g1)
-  {
-
-    Graphics2D g = (Graphics2D) g1;
-
-    g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-                       RenderingHints.VALUE_ANTIALIAS_ON);
-
-    int halfwidth = getWidth() / 2;
-    int halfheight = getHeight() / 2;
-
-    for (int i = 0; i < npoint; i++)
-    {
-      SequencePoint sp = (SequencePoint) points.elementAt(i);
-      int x = (int) ( (float) (sp.coord[0] - centre[0]) * scale) +
-          halfwidth;
-      int y = (int) ( (float) (sp.coord[1] - centre[1]) * scale) +
-          halfheight;
-      float z = sp.coord[1] - centre[2];
-
-      if (av.getSequenceColour(sp.sequence) == Color.black)
-      {
-        g.setColor(Color.white);
-      }
-      else
-      {
-        g.setColor(av.getSequenceColour(sp.sequence));
-      }
-
-      if (av.getSelectionGroup() != null)
-      {
-        if (av.getSelectionGroup().getSequences(null).contains(
-            ( (SequencePoint) points.elementAt(i)).sequence))
-        {
-          g.setColor(Color.gray);
-        }
-      }
-
-      if (z < 0)
-      {
-        g.setColor(g.getColor().darker());
-      }
-
-      g.fillRect(x - 3, y - 3, 6, 6);
-      if (showLabels)
-      {
-        g.setColor(Color.red);
-        g.drawString( ( (SequencePoint) points.elementAt(i)).sequence.
-                     getName(),
-                     x - 3, y - 4);
-      }
-    }
-
-    //    //Now the rectangle
-    //    if (rectx2 != -1 && recty2 != -1) {
-    //      g.setColor(Color.white);
-    //
-    //      g.drawRect(rectx1,recty1,rectx2-rectx1,recty2-recty1);
-    //    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Dimension minimumsize()
-  {
-    return prefsize;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Dimension preferredsize()
-  {
-    return prefsize;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
-   */
-  public void keyTyped(KeyEvent evt)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
-   */
-  public void keyReleased(KeyEvent evt)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
-   */
-  public void keyPressed(KeyEvent evt)
-  {
-    if (evt.getKeyCode() == KeyEvent.VK_UP)
-    {
-      scalefactor = (float) (scalefactor * 1.1);
-      scale = findScale();
-    }
-    else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
-    {
-      scalefactor = (float) (scalefactor * 0.9);
-      scale = findScale();
-    }
-    else if (evt.getKeyChar() == 's')
-    {
-      System.err.println("DEBUG: Rectangle selection"); // log.debug
-
-      if ( (rectx2 != -1) && (recty2 != -1))
-      {
-        rectSelect(rectx1, recty1, rectx2, recty2);
-      }
-    }
-
-    repaint();
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
-   */
-  public void mouseClicked(MouseEvent evt)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
-   */
-  public void mouseEntered(MouseEvent evt)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
-   */
-  public void mouseExited(MouseEvent evt)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
-   */
-  public void mouseReleased(MouseEvent evt)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
-   */
-  public void mousePressed(MouseEvent evt)
-  {
-    int x = evt.getX();
-    int y = evt.getY();
-
-    mx = x;
-    my = y;
-
-    omx = mx;
-    omy = my;
-
-    startx = x;
-    starty = y;
-
-    rectx1 = x;
-    recty1 = y;
-
-    rectx2 = -1;
-    recty2 = -1;
-
-    SequenceI found = findPoint(x, y);
-
-    if (found != null)
-    {
-      AlignmentPanel[] aps = getAssociatedPanels();
-
-      for (int a = 0; a < aps.length; a++)
-      {
-        if (aps[a].av.getSelectionGroup() != null)
-        {
-          aps[a].av.getSelectionGroup().addOrRemove(found, true);
-        }
-        else
-        {
-          aps[a].av.setSelectionGroup(new SequenceGroup());
-          aps[a].av.getSelectionGroup().addOrRemove(found, true);
-          aps[a].av.getSelectionGroup().setEndRes(
-              aps[a].av.alignment.getWidth() - 1);
-        }
-      }
-
-      PaintRefresher.Refresh(this, av.getSequenceSetId());
-    }
-
-    repaint();
-  }
-
-  // private void fireSequenceSelectionEvent(Selection sel) {
-  //   controller.handleSequenceSelectionEvent(new SequenceSelectionEvent(this,sel));
-  //}
-  public void mouseMoved(MouseEvent evt)
-  {
-    SequenceI found = findPoint(evt.getX(), evt.getY());
-
-    if (found != null)
-    {
-      this.setToolTipText(found.getName());
-    }
-    else
-    {
-      this.setToolTipText(null);
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
-   */
-  public void mouseDragged(MouseEvent evt)
-  {
-    mx = evt.getX();
-    my = evt.getY();
-
-    //Check if this is a rectangle drawing drag
-    if ( (evt.getModifiers() & InputEvent.BUTTON2_MASK) != 0)
-    {
-      //      rectx2 = evt.getX();
-      //      recty2 = evt.getY();
-    }
-    else
-    {
-      rotmat.setIdentity();
-
-      rotmat.rotate( (float) (my - omy), 'x');
-      rotmat.rotate( (float) (mx - omx), 'y');
-
-      for (int i = 0; i < npoint; i++)
-      {
-        SequencePoint sp = (SequencePoint) points.elementAt(i);
-        sp.coord[0] -= centre[0];
-        sp.coord[1] -= centre[1];
-        sp.coord[2] -= centre[2];
-
-        //Now apply the rotation matrix
-        sp.coord = rotmat.vectorMultiply(sp.coord);
-
-        //Now translate back again
-        sp.coord[0] += centre[0];
-        sp.coord[1] += centre[1];
-        sp.coord[2] += centre[2];
-      }
-
-      for (int i = 0; i < 3; i++)
-      {
-        axes[i] = rotmat.vectorMultiply(axes[i]);
-      }
-
-      omx = mx;
-      omy = my;
-
-      paint(this.getGraphics());
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param x1 DOCUMENT ME!
-   * @param y1 DOCUMENT ME!
-   * @param x2 DOCUMENT ME!
-   * @param y2 DOCUMENT ME!
-   */
-  public void rectSelect(int x1, int y1, int x2, int y2)
-  {
-    for (int i = 0; i < npoint; i++)
-    {
-      SequencePoint sp = (SequencePoint) points.elementAt(i);
-      int tmp1 = (int) ( ( (sp.coord[0] - centre[0]) * scale) +
-                        ( (float) getWidth() / 2.0));
-      int tmp2 = (int) ( ( (sp.coord[1] - centre[1]) * scale) +
-                        ( (float) getHeight() / 2.0));
-
-      if ( (tmp1 > x1) && (tmp1 < x2) && (tmp2 > y1) && (tmp2 < y2))
-      {
-        if (av != null)
-        {
-          if (!av.getSelectionGroup().getSequences(null).contains(sp.sequence))
-          {
-            av.getSelectionGroup().addSequence(sp.sequence, true);
-          }
-        }
-      }
-    }
-
-    // if (changedSel) {
-    //    fireSequenceSelectionEvent(av.getSelection());
-    // }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param x DOCUMENT ME!
-   * @param y DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public SequenceI findPoint(int x, int y)
-  {
-    int halfwidth = getWidth() / 2;
-    int halfheight = getHeight() / 2;
-
-    int found = -1;
-
-    for (int i = 0; i < npoint; i++)
-    {
-      SequencePoint sp = (SequencePoint) points.elementAt(i);
-      int px = (int) ( (float) (sp.coord[0] - centre[0]) * scale) +
-          halfwidth;
-      int py = (int) ( (float) (sp.coord[1] - centre[1]) * scale) +
-          halfheight;
-
-      if ( (Math.abs(px - x) < 3) && (Math.abs(py - y) < 3))
-      {
-        found = i;
-      }
-    }
-
-    if (found != -1)
-    {
-      return ( (SequencePoint) points.elementAt(found)).sequence;
-    }
-    else
-    {
-      return null;
-    }
-  }
-
-  AlignmentPanel[] getAssociatedPanels()
-  {
-    if (applyToAllViews)
-    {
-      return PaintRefresher.getAssociatedPanels(av.getSequenceSetId());
-    }
-    else
-    {
-      return new AlignmentPanel[]
-          {
-          ap};
-    }
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.gui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+
+import jalview.datamodel.*;
+import jalview.math.*;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class RotatableCanvas extends JPanel implements MouseListener,
+        MouseMotionListener, KeyListener
+{
+  RotatableMatrix idmat = new RotatableMatrix(3, 3);
+
+  RotatableMatrix objmat = new RotatableMatrix(3, 3);
+
+  RotatableMatrix rotmat = new RotatableMatrix(3, 3);
+
+  // RubberbandRectangle rubberband;
+  boolean drawAxes = true;
+
+  int omx = 0;
+
+  int mx = 0;
+
+  int omy = 0;
+
+  int my = 0;
+
+  Image img;
+
+  Graphics ig;
+
+  Dimension prefsize;
+
+  float[] centre = new float[3];
+
+  float[] width = new float[3];
+
+  float[] max = new float[3];
+
+  float[] min = new float[3];
+
+  float maxwidth;
+
+  float scale;
+
+  int npoint;
+
+  Vector points;
+
+  float[][] orig;
+
+  float[][] axes;
+
+  int startx;
+
+  int starty;
+
+  int lastx;
+
+  int lasty;
+
+  int rectx1;
+
+  int recty1;
+
+  int rectx2;
+
+  int recty2;
+
+  float scalefactor = 1;
+
+  AlignViewport av;
+
+  AlignmentPanel ap;
+
+  boolean showLabels = false;
+
+  Color bgColour = Color.black;
+
+  boolean applyToAllViews = false;
+
+  // Controller controller;
+  public RotatableCanvas(AlignmentPanel ap)
+  {
+    this.av = ap.av;
+    this.ap = ap;
+
+    addMouseWheelListener(new MouseWheelListener()
+    {
+      public void mouseWheelMoved(MouseWheelEvent e)
+      {
+        if (e.getWheelRotation() > 0)
+        {
+          scale = (float) (scale * 1.1);
+          repaint();
+        }
+
+        else
+        {
+          scale = (float) (scale * 0.9);
+          repaint();
+        }
+      }
+    });
+
+  }
+
+  public void showLabels(boolean b)
+  {
+    showLabels = b;
+    repaint();
+  }
+
+  public void setPoints(Vector points, int npoint)
+  {
+    this.points = points;
+    this.npoint = npoint;
+    ToolTipManager.sharedInstance().registerComponent(this);
+    ToolTipManager.sharedInstance().setInitialDelay(0);
+    ToolTipManager.sharedInstance().setDismissDelay(10000);
+
+    prefsize = getPreferredSize();
+    orig = new float[npoint][3];
+
+    for (int i = 0; i < npoint; i++)
+    {
+      SequencePoint sp = (SequencePoint) points.elementAt(i);
+
+      for (int j = 0; j < 3; j++)
+      {
+        orig[i][j] = sp.coord[j];
+      }
+    }
+
+    // Initialize the matrices to identity
+    for (int i = 0; i < 3; i++)
+    {
+      for (int j = 0; j < 3; j++)
+      {
+        if (i != j)
+        {
+          idmat.addElement(i, j, 0);
+          objmat.addElement(i, j, 0);
+          rotmat.addElement(i, j, 0);
+        }
+        else
+        {
+          idmat.addElement(i, j, 0);
+          objmat.addElement(i, j, 0);
+          rotmat.addElement(i, j, 0);
+        }
+      }
+    }
+
+    axes = new float[3][3];
+    initAxes();
+
+    findCentre();
+    findWidth();
+
+    scale = findScale();
+
+    addMouseListener(this);
+
+    addMouseMotionListener(this);
+
+  }
+
+  public void initAxes()
+  {
+    for (int i = 0; i < 3; i++)
+    {
+      for (int j = 0; j < 3; j++)
+      {
+        if (i != j)
+        {
+          axes[i][j] = 0;
+        }
+        else
+        {
+          axes[i][j] = 1;
+        }
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void findWidth()
+  {
+    max = new float[3];
+    min = new float[3];
+
+    max[0] = (float) -1e30;
+    max[1] = (float) -1e30;
+    max[2] = (float) -1e30;
+
+    min[0] = (float) 1e30;
+    min[1] = (float) 1e30;
+    min[2] = (float) 1e30;
+
+    for (int i = 0; i < 3; i++)
+    {
+      for (int j = 0; j < npoint; j++)
+      {
+        SequencePoint sp = (SequencePoint) points.elementAt(j);
+
+        if (sp.coord[i] >= max[i])
+        {
+          max[i] = sp.coord[i];
+        }
+
+        if (sp.coord[i] <= min[i])
+        {
+          min[i] = sp.coord[i];
+        }
+      }
+    }
+
+    // System.out.println("xmax " + max[0] + " min " + min[0]);
+    // System.out.println("ymax " + max[1] + " min " + min[1]);
+    // System.out.println("zmax " + max[2] + " min " + min[2]);
+    width[0] = Math.abs(max[0] - min[0]);
+    width[1] = Math.abs(max[1] - min[1]);
+    width[2] = Math.abs(max[2] - min[2]);
+
+    maxwidth = width[0];
+
+    if (width[1] > width[0])
+    {
+      maxwidth = width[1];
+    }
+
+    if (width[2] > width[1])
+    {
+      maxwidth = width[2];
+    }
+
+    // System.out.println("Maxwidth = " + maxwidth);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public float findScale()
+  {
+    int dim;
+    int width;
+    int height;
+
+    if (getWidth() != 0)
+    {
+      width = getWidth();
+      height = getHeight();
+    }
+    else
+    {
+      width = prefsize.width;
+      height = prefsize.height;
+    }
+
+    if (width < height)
+    {
+      dim = width;
+    }
+    else
+    {
+      dim = height;
+    }
+
+    return (float) ((dim * scalefactor) / (2 * maxwidth));
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void findCentre()
+  {
+    // Find centre coordinate
+    findWidth();
+
+    centre[0] = (max[0] + min[0]) / 2;
+    centre[1] = (max[1] + min[1]) / 2;
+    centre[2] = (max[2] + min[2]) / 2;
+
+    // System.out.println("Centre x " + centre[0]);
+    // System.out.println("Centre y " + centre[1]);
+    // System.out.println("Centre z " + centre[2]);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public Dimension getPreferredSize()
+  {
+    if (prefsize != null)
+    {
+      return prefsize;
+    }
+    else
+    {
+      return new Dimension(400, 400);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public Dimension getMinimumSize()
+  {
+    return getPreferredSize();
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param g
+   *                DOCUMENT ME!
+   */
+  public void paintComponent(Graphics g1)
+  {
+
+    Graphics2D g = (Graphics2D) g1;
+
+    g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+            RenderingHints.VALUE_ANTIALIAS_ON);
+    if (points == null)
+    {
+      g.setFont(new Font("Verdana", Font.PLAIN, 18));
+      g.drawString("Calculating PCA....", 20, getHeight() / 2);
+    }
+    else
+    {
+      // Only create the image at the beginning -
+      if ((img == null) || (prefsize.width != getWidth())
+              || (prefsize.height != getHeight()))
+      {
+        prefsize.width = getWidth();
+        prefsize.height = getHeight();
+
+        scale = findScale();
+
+        // System.out.println("New scale = " + scale);
+        img = createImage(getWidth(), getHeight());
+        ig = img.getGraphics();
+      }
+
+      drawBackground(ig, bgColour);
+      drawScene(ig);
+
+      if (drawAxes == true)
+      {
+        drawAxes(ig);
+      }
+
+      g.drawImage(img, 0, 0, this);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param g
+   *                DOCUMENT ME!
+   */
+  public void drawAxes(Graphics g)
+  {
+
+    g.setColor(Color.yellow);
+
+    for (int i = 0; i < 3; i++)
+    {
+      g.drawLine(getWidth() / 2, getHeight() / 2, (int) ((axes[i][0]
+              * scale * max[0]) + (getWidth() / 2)), (int) ((axes[i][1]
+              * scale * max[1]) + (getHeight() / 2)));
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param g
+   *                DOCUMENT ME!
+   * @param col
+   *                DOCUMENT ME!
+   */
+  public void drawBackground(Graphics g, Color col)
+  {
+    g.setColor(col);
+    g.fillRect(0, 0, prefsize.width, prefsize.height);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param g
+   *                DOCUMENT ME!
+   */
+  public void drawScene(Graphics g1)
+  {
+
+    Graphics2D g = (Graphics2D) g1;
+
+    g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+            RenderingHints.VALUE_ANTIALIAS_ON);
+
+    int halfwidth = getWidth() / 2;
+    int halfheight = getHeight() / 2;
+
+    for (int i = 0; i < npoint; i++)
+    {
+      SequencePoint sp = (SequencePoint) points.elementAt(i);
+      int x = (int) ((float) (sp.coord[0] - centre[0]) * scale) + halfwidth;
+      int y = (int) ((float) (sp.coord[1] - centre[1]) * scale)
+              + halfheight;
+      float z = sp.coord[1] - centre[2];
+
+      if (av.getSequenceColour(sp.sequence) == Color.black)
+      {
+        g.setColor(Color.white);
+      }
+      else
+      {
+        g.setColor(av.getSequenceColour(sp.sequence));
+      }
+
+      if (av.getSelectionGroup() != null)
+      {
+        if (av.getSelectionGroup().getSequences(null).contains(
+                ((SequencePoint) points.elementAt(i)).sequence))
+        {
+          g.setColor(Color.gray);
+        }
+      }
+
+      if (z < 0)
+      {
+        g.setColor(g.getColor().darker());
+      }
+
+      g.fillRect(x - 3, y - 3, 6, 6);
+      if (showLabels)
+      {
+        g.setColor(Color.red);
+        g.drawString(((SequencePoint) points.elementAt(i)).sequence
+                .getName(), x - 3, y - 4);
+      }
+    }
+
+    // //Now the rectangle
+    // if (rectx2 != -1 && recty2 != -1) {
+    // g.setColor(Color.white);
+    //
+    // g.drawRect(rectx1,recty1,rectx2-rectx1,recty2-recty1);
+    // }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public Dimension minimumsize()
+  {
+    return prefsize;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public Dimension preferredsize()
+  {
+    return prefsize;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
+   */
+  public void keyTyped(KeyEvent evt)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
+   */
+  public void keyReleased(KeyEvent evt)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
+   */
+  public void keyPressed(KeyEvent evt)
+  {
+    if (evt.getKeyCode() == KeyEvent.VK_UP)
+    {
+      scalefactor = (float) (scalefactor * 1.1);
+      scale = findScale();
+    }
+    else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
+    {
+      scalefactor = (float) (scalefactor * 0.9);
+      scale = findScale();
+    }
+    else if (evt.getKeyChar() == 's')
+    {
+      System.err.println("DEBUG: Rectangle selection"); // log.debug
+
+      if ((rectx2 != -1) && (recty2 != -1))
+      {
+        rectSelect(rectx1, recty1, rectx2, recty2);
+      }
+    }
+
+    repaint();
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
+   */
+  public void mouseClicked(MouseEvent evt)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
+   */
+  public void mouseEntered(MouseEvent evt)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
+   */
+  public void mouseExited(MouseEvent evt)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
+   */
+  public void mouseReleased(MouseEvent evt)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
+   */
+  public void mousePressed(MouseEvent evt)
+  {
+    int x = evt.getX();
+    int y = evt.getY();
+
+    mx = x;
+    my = y;
+
+    omx = mx;
+    omy = my;
+
+    startx = x;
+    starty = y;
+
+    rectx1 = x;
+    recty1 = y;
+
+    rectx2 = -1;
+    recty2 = -1;
+
+    SequenceI found = findPoint(x, y);
+
+    if (found != null)
+    {
+      AlignmentPanel[] aps = getAssociatedPanels();
+
+      for (int a = 0; a < aps.length; a++)
+      {
+        if (aps[a].av.getSelectionGroup() != null)
+        {
+          aps[a].av.getSelectionGroup().addOrRemove(found, true);
+        }
+        else
+        {
+          aps[a].av.setSelectionGroup(new SequenceGroup());
+          aps[a].av.getSelectionGroup().addOrRemove(found, true);
+          aps[a].av.getSelectionGroup().setEndRes(
+                  aps[a].av.alignment.getWidth() - 1);
+        }
+      }
+
+      PaintRefresher.Refresh(this, av.getSequenceSetId());
+    }
+
+    repaint();
+  }
+
+  // private void fireSequenceSelectionEvent(Selection sel) {
+  // controller.handleSequenceSelectionEvent(new
+  // SequenceSelectionEvent(this,sel));
+  // }
+  public void mouseMoved(MouseEvent evt)
+  {
+    SequenceI found = findPoint(evt.getX(), evt.getY());
+
+    if (found != null)
+    {
+      this.setToolTipText(found.getName());
+    }
+    else
+    {
+      this.setToolTipText(null);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
+   */
+  public void mouseDragged(MouseEvent evt)
+  {
+    mx = evt.getX();
+    my = evt.getY();
+
+    // Check if this is a rectangle drawing drag
+    if ((evt.getModifiers() & InputEvent.BUTTON2_MASK) != 0)
+    {
+      // rectx2 = evt.getX();
+      // recty2 = evt.getY();
+    }
+    else
+    {
+      rotmat.setIdentity();
+
+      rotmat.rotate((float) (my - omy), 'x');
+      rotmat.rotate((float) (mx - omx), 'y');
+
+      for (int i = 0; i < npoint; i++)
+      {
+        SequencePoint sp = (SequencePoint) points.elementAt(i);
+        sp.coord[0] -= centre[0];
+        sp.coord[1] -= centre[1];
+        sp.coord[2] -= centre[2];
+
+        // Now apply the rotation matrix
+        sp.coord = rotmat.vectorMultiply(sp.coord);
+
+        // Now translate back again
+        sp.coord[0] += centre[0];
+        sp.coord[1] += centre[1];
+        sp.coord[2] += centre[2];
+      }
+
+      for (int i = 0; i < 3; i++)
+      {
+        axes[i] = rotmat.vectorMultiply(axes[i]);
+      }
+
+      omx = mx;
+      omy = my;
+
+      paint(this.getGraphics());
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param x1
+   *                DOCUMENT ME!
+   * @param y1
+   *                DOCUMENT ME!
+   * @param x2
+   *                DOCUMENT ME!
+   * @param y2
+   *                DOCUMENT ME!
+   */
+  public void rectSelect(int x1, int y1, int x2, int y2)
+  {
+    for (int i = 0; i < npoint; i++)
+    {
+      SequencePoint sp = (SequencePoint) points.elementAt(i);
+      int tmp1 = (int) (((sp.coord[0] - centre[0]) * scale) + ((float) getWidth() / 2.0));
+      int tmp2 = (int) (((sp.coord[1] - centre[1]) * scale) + ((float) getHeight() / 2.0));
+
+      if ((tmp1 > x1) && (tmp1 < x2) && (tmp2 > y1) && (tmp2 < y2))
+      {
+        if (av != null)
+        {
+          if (!av.getSelectionGroup().getSequences(null).contains(
+                  sp.sequence))
+          {
+            av.getSelectionGroup().addSequence(sp.sequence, true);
+          }
+        }
+      }
+    }
+
+    // if (changedSel) {
+    // fireSequenceSelectionEvent(av.getSelection());
+    // }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param x
+   *                DOCUMENT ME!
+   * @param y
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public SequenceI findPoint(int x, int y)
+  {
+    int halfwidth = getWidth() / 2;
+    int halfheight = getHeight() / 2;
+
+    int found = -1;
+
+    for (int i = 0; i < npoint; i++)
+    {
+      SequencePoint sp = (SequencePoint) points.elementAt(i);
+      int px = (int) ((float) (sp.coord[0] - centre[0]) * scale)
+              + halfwidth;
+      int py = (int) ((float) (sp.coord[1] - centre[1]) * scale)
+              + halfheight;
+
+      if ((Math.abs(px - x) < 3) && (Math.abs(py - y) < 3))
+      {
+        found = i;
+      }
+    }
+
+    if (found != -1)
+    {
+      return ((SequencePoint) points.elementAt(found)).sequence;
+    }
+    else
+    {
+      return null;
+    }
+  }
+
+  AlignmentPanel[] getAssociatedPanels()
+  {
+    if (applyToAllViews)
+    {
+      return PaintRefresher.getAssociatedPanels(av.getSequenceSetId());
+    }
+    else
+    {
+      return new AlignmentPanel[]
+      { ap };
+    }
+  }
+}
diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index d8bdba3..4dfb8c8 100755
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -26,22 +26,28 @@ import jalview.datamodel.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class ScalePanel
-    extends JPanel implements MouseMotionListener, MouseListener
+public class ScalePanel extends JPanel implements MouseMotionListener,
+        MouseListener
 {
   protected int offy = 4;
 
   /** DOCUMENT ME!! */
   public int width;
+
   protected AlignViewport av;
+
   AlignmentPanel ap;
+
   boolean stretchingGroup = false;
-  int min; //used by mouseDragged to see if user
-  int max; //used by mouseDragged to see if user
+
+  int min; // used by mouseDragged to see if user
+
+  int max; // used by mouseDragged to see if user
+
   boolean mouseDragging = false;
 
   // wants to delete columns
@@ -56,8 +62,9 @@ public class ScalePanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
    */
   public void mousePressed(MouseEvent evt)
   {
@@ -126,7 +133,8 @@ public class ScalePanel
           {
             av.hideColumns(res, res);
             if (av.getSelectionGroup() != null
-                && av.getSelectionGroup().getSize() == av.alignment.getHeight())
+                    && av.getSelectionGroup().getSize() == av.alignment
+                            .getHeight())
             {
               av.setSelectionGroup(null);
             }
@@ -142,7 +150,8 @@ public class ScalePanel
         pop.show(this, evt.getX(), evt.getY());
       }
     }
-    else // LEFT MOUSE TO SELECT
+    else
+    // LEFT MOUSE TO SELECT
     {
       if (!evt.isControlDown() && !evt.isShiftDown())
       {
@@ -152,13 +161,13 @@ public class ScalePanel
       av.getColumnSelection().addElement(res);
       SequenceGroup sg = new SequenceGroup();
       // try to be as quick as possible
-      SequenceI[] iVec = av.alignment.getSequencesArray(); 
+      SequenceI[] iVec = av.alignment.getSequencesArray();
       for (int i = 0; i < iVec.length; i++)
       {
         sg.addSequence(iVec[i], false);
         iVec[i] = null;
       }
-      iVec=null;
+      iVec = null;
       sg.setStartRes(res);
       sg.setEndRes(res);
       av.setSelectionGroup(sg);
@@ -182,8 +191,9 @@ public class ScalePanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
    */
   public void mouseReleased(MouseEvent evt)
   {
@@ -227,8 +237,9 @@ public class ScalePanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
    */
   public void mouseDragged(MouseEvent evt)
   {
@@ -285,7 +296,7 @@ public class ScalePanel
       {
         col = av.getColumnSelection().adjustForHiddenColumns(i);
 
-        if ( (col < sg.getStartRes()) || (col > sg.getEndRes()))
+        if ((col < sg.getStartRes()) || (col > sg.getEndRes()))
         {
           av.getColumnSelection().removeElement(col);
         }
@@ -316,7 +327,8 @@ public class ScalePanel
   }
 
   public void mouseClicked(MouseEvent evt)
-  {}
+  {
+  }
 
   public void mouseMoved(MouseEvent evt)
   {
@@ -332,13 +344,14 @@ public class ScalePanel
     reveal = null;
     for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
     {
-      int[] region = (int[]) av.getColumnSelection().getHiddenColumns().
-          elementAt(i);
+      int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
+              .elementAt(i);
       if (res + 1 == region[0] || res - 1 == region[1])
       {
         reveal = region;
         ToolTipManager.sharedInstance().registerComponent(this);
-        this.setToolTipText("Reveal Hidden Columns with Right Mouse Button");
+        this
+                .setToolTipText("Reveal Hidden Columns with Right Mouse Button");
         break;
       }
       else
@@ -355,8 +368,9 @@ public class ScalePanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param g DOCUMENT ME!
+   * 
+   * @param g
+   *                DOCUMENT ME!
    */
   public void paintComponent(Graphics g)
   {
@@ -365,7 +379,7 @@ public class ScalePanel
 
   // scalewidth will normally be screenwidth,
   public void drawScale(Graphics g, int startx, int endx, int width,
-                        int height)
+          int height)
   {
     Graphics2D gg = (Graphics2D) g;
     gg.setFont(av.getFont());
@@ -373,15 +387,15 @@ public class ScalePanel
     if (av.antiAlias)
     {
       gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-                          RenderingHints.VALUE_ANTIALIAS_ON);
+              RenderingHints.VALUE_ANTIALIAS_ON);
     }
 
-    //Fill in the background
+    // Fill in the background
     gg.setColor(Color.white);
     gg.fillRect(0, 0, width, height);
     gg.setColor(Color.black);
 
-    //Fill the selected columns
+    // Fill the selected columns
     ColumnSelection cs = av.getColumnSelection();
     gg.setColor(new Color(220, 0, 0));
 
@@ -393,10 +407,10 @@ public class ScalePanel
         sel = av.getColumnSelection().findColumnPosition(sel);
       }
 
-      if ( (sel >= startx) && (sel <= endx))
+      if ((sel >= startx) && (sel <= endx))
       {
-        gg.fillRect( (sel - startx) * av.charWidth, 0, av.charWidth,
-                    getHeight());
+        gg.fillRect((sel - startx) * av.charWidth, 0, av.charWidth,
+                getHeight());
       }
     }
 
@@ -408,7 +422,7 @@ public class ScalePanel
     FontMetrics fm = gg.getFontMetrics(av.getFont());
     int y = av.charHeight - fm.getDescent();
 
-    if ( (scalestartx % 10) == 0)
+    if ((scalestartx % 10) == 0)
     {
       scalestartx += 5;
     }
@@ -418,30 +432,32 @@ public class ScalePanel
 
     for (int i = scalestartx; i < endx; i += 5)
     {
-      if ( (i % 10) == 0)
+      if ((i % 10) == 0)
       {
-        string = String.valueOf(av.getColumnSelection().adjustForHiddenColumns(
-            i));
-        if ( (i - startx - 1) * av.charWidth > maxX)
+        string = String.valueOf(av.getColumnSelection()
+                .adjustForHiddenColumns(i));
+        if ((i - startx - 1) * av.charWidth > maxX)
         {
-          gg.drawString(string,
-                        (i - startx - 1) * av.charWidth, y);
+          gg.drawString(string, (i - startx - 1) * av.charWidth, y);
           maxX = (i - startx + 1) * av.charWidth + fm.stringWidth(string);
         }
 
-        gg.drawLine( (int) ( ( (i - startx - 1) * av.charWidth) +
-                            (av.charWidth / 2)), y + 2,
-                    (int) ( ( (i - startx - 1) * av.charWidth) +
-                           (av.charWidth / 2)),
-                    y + (fm.getDescent() * 2));
+        gg
+                .drawLine(
+                        (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
+                        y + 2,
+                        (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
+                        y + (fm.getDescent() * 2));
 
       }
       else
       {
-        gg.drawLine( (int) ( ( (i - startx - 1) * av.charWidth) +
-                            (av.charWidth / 2)), y + fm.getDescent(),
-                    (int) ( ( (i - startx - 1) * av.charWidth) +
-                           (av.charWidth / 2)), y + (fm.getDescent() * 2));
+        gg
+                .drawLine(
+                        (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
+                        y + fm.getDescent(),
+                        (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
+                        y + (fm.getDescent() * 2));
       }
     }
 
@@ -451,12 +467,12 @@ public class ScalePanel
       int res;
       if (av.getShowHiddenMarkers())
       {
-        for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size();
-             i++)
+        for (int i = 0; i < av.getColumnSelection().getHiddenColumns()
+                .size(); i++)
         {
 
-          res = av.getColumnSelection().findHiddenRegionPosition(i) -
-              startx;
+          res = av.getColumnSelection().findHiddenRegionPosition(i)
+                  - startx;
 
           if (res < 0 || res > endx - scalestartx)
           {
@@ -464,14 +480,11 @@ public class ScalePanel
           }
 
           gg.fillPolygon(new int[]
-                         {res * av.charWidth - av.charHeight / 4,
-                         res * av.charWidth + av.charHeight / 4,
-                         res * av.charWidth},
-                         new int[]
-                         {
-                         y - av.charHeight / 2, y - av.charHeight / 2,
-                         y + 8
-          }, 3);
+          { res * av.charWidth - av.charHeight / 4,
+              res * av.charWidth + av.charHeight / 4, res * av.charWidth },
+                  new int[]
+                  { y - av.charHeight / 2, y - av.charHeight / 2, y + 8 },
+                  3);
 
         }
       }
diff --git a/src/jalview/gui/ScriptWindow.java b/src/jalview/gui/ScriptWindow.java
index 8e69584..9b13847 100644
--- a/src/jalview/gui/ScriptWindow.java
+++ b/src/jalview/gui/ScriptWindow.java
@@ -1,616 +1,730 @@
-/* $RCSfile$
- * $Author$
- * $Date$
- * $Revision$
- *
- * Copyright (C) 2002-2005  The Jmol Development Team
- *
- * Contact: jmol-developers@lists.sf.net
- *
- *  This library is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public
- *  License as published by the Free Software Foundation; either
- *  version 2.1 of the License, or (at your option) any later version.
- *
- *  This library is distributed in the hope that it will be useful,
- *  but WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this library; if not, write to the Free Software
- *  Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
-
- *
- * Modified and added to Jalview by A Waterhouse to extend JInternalFrame
- *
-
- */
-package jalview.gui;
-
-import org.jmol.api.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.text.*;
-import java.util.Vector;
-
-import org.jmol.i18n.GT;
-import org.jmol.util.Logger;
-import org.jmol.util.CommandHistory;
-
-public final class ScriptWindow extends JPanel
-    implements ActionListener, EnterListener{
-
-  private ConsoleTextPane console;
-  private JButton closeButton;
-  private JButton runButton;
-  private JButton haltButton;
-  private JButton clearButton;
-  private JButton historyButton;
-  private JButton stateButton;
-   JmolViewer viewer;
-  AppJmol appJmol;
-
-  public ScriptWindow(AppJmol appJmol)
-  {
-    this.viewer = appJmol.viewer;
-    this.appJmol = appJmol;
-
-
-    setLayout(new BorderLayout());
-
-    console = new ConsoleTextPane(this);
-
-
-    console.setPrompt();
-    add(new JScrollPane(console)
-                         , BorderLayout.CENTER);
-
-    JPanel buttonPanel = new JPanel();
-    add(buttonPanel, BorderLayout.SOUTH);
-
-    runButton = new JButton(GT._("Run"));
-    haltButton = new JButton(GT._("Halt"));
-    runButton.addActionListener(this);
-   // buttonPanel.add(runButton);
-    haltButton.addActionListener(this);
-  //  buttonPanel.add(haltButton);
-    haltButton.setEnabled(false);
-
-    clearButton = new JButton(GT._("Clear"));
-    clearButton.addActionListener(this);
-    buttonPanel.add(clearButton);
-
-    historyButton = new JButton(GT._("History"));
-    historyButton.addActionListener(this);
-    buttonPanel.add(historyButton);
-
-    stateButton = new JButton(GT._("State"));
-    stateButton.addActionListener(this);
-    buttonPanel.add(stateButton);
-
-    closeButton = new JButton(GT._("Close"));
-    closeButton.addActionListener(this);
-    buttonPanel.add(closeButton);
-
-    for(int i=0; i<buttonPanel.getComponentCount(); i++)
-    {
-    //  ((JButton)buttonPanel.getComponent(i))
-    //      .setMargin(new Insets(0, 0, 0, 0));
-    }
-
-  }
-
-  public void sendConsoleEcho(String strEcho) {
-    if (strEcho != null && !isError) {
-
-      console.outputEcho(strEcho);
-
-    }
-    setError(false);
-  }
-
-  boolean isError = false;
-  void setError(boolean TF) {
-    isError = TF;
-    //if (isError)
-      //console.recallCommand(true);
-  }
-
-  public void sendConsoleMessage(String strStatus) {
-    if (strStatus == null) {
-      console.clearContent();
-      console.outputStatus("");
-    } else if (strStatus.indexOf("ERROR:") >= 0) {
-      console.outputError(strStatus);
-      isError = true;
-    } else if (!isError) {
-      console.outputStatus(strStatus);
-    }
-  }
-
-  public void notifyScriptTermination(String strMsg, int msWalltime) {
-    if (strMsg != null && strMsg.indexOf("ERROR") >= 0) {
-      console.outputError(strMsg);
-    }
-    runButton.setEnabled(true);
-    haltButton.setEnabled(false);
-  }
-
-  public void enterPressed() {
-    runButton.doClick(100);
-    //    executeCommand();
-  }
-
-
-  class ExecuteCommandThread extends Thread {
-
-    String strCommand;
-    ExecuteCommandThread (String command) {
-      strCommand = command;
-    }
-
-    public void run() {
-      try {
-        executeCommand(strCommand);
-      } catch (Exception ie) {
-        Logger.debug("execution command interrupted!"+ie);
-      }
-    }
-  }
-
-  ExecuteCommandThread execThread;
-  void executeCommandAsThread(){
-    String strCommand = console.getCommandString().trim();
-    if (strCommand.length() > 0) {
-      execThread = new ExecuteCommandThread(strCommand);
-      execThread.start();
-    }
-  }
-
-  void executeCommand(String strCommand) {
-    boolean doWait;
-    setError(false);
-    console.appendNewline();
-    console.setPrompt();
-    if (strCommand.length() > 0) {
-      String strErrorMessage = null;
-      doWait = (strCommand.indexOf("WAIT ") == 0);
-      if (doWait) { //for testing, mainly
-        // demonstrates using the statusManager system.
-        runButton.setEnabled(false);
-        haltButton.setEnabled(true);
-
-        Vector info = (Vector) viewer
-            .scriptWaitStatus(strCommand.substring(5),
-                "+fileLoaded,+scriptStarted,+scriptStatus,+scriptEcho,+scriptTerminated");
-        runButton.setEnabled(true);
-        haltButton.setEnabled(false);
-        /*
-         * info = [ statusRecortSet0, statusRecortSet1, statusRecortSet2, ...]
-         * statusRecordSet = [ statusRecord0, statusRecord1, statusRecord2, ...]
-         * statusRecord = [int msgPtr, String statusName, int intInfo, String msg]
-         */
-        for (int i = 0; i < info.size(); i++) {
-          Vector statusRecordSet = (Vector) info.get(i);
-          for (int j = 0; j < statusRecordSet.size(); j++) {
-            Vector statusRecord = (Vector) statusRecordSet.get(j);
-            Logger.info("msg#=" + statusRecord.get(0) + " "
-                + statusRecord.get(1) + " intInfo=" + statusRecord.get(2)
-                + " stringInfo=" + statusRecord.get(3));
-          }
-        }
-        console.appendNewline();
-      } else {
-        boolean isScriptExecuting = viewer.isScriptExecuting();
-        if (viewer.checkHalt(strCommand))
-          strErrorMessage = (isScriptExecuting ? "string execution halted with " + strCommand : "no script was executing");
-        else
-          strErrorMessage = "";//viewer.scriptCheck(strCommand);
-        //the problem is that scriptCheck is synchronized, so these might get backed up.
-        if (strErrorMessage != null && strErrorMessage.length() > 0) {
-          console.outputError(strErrorMessage);
-        } else {
-          //runButton.setEnabled(false);
-          haltButton.setEnabled(true);
-          viewer.script(strCommand);
-        }
-      }
-    }
-    console.grabFocus();
-  }
-
-  public void actionPerformed(ActionEvent e) {
-    Object source = e.getSource();
-    if (source == closeButton) {
-      appJmol.showConsole(false);
-    } else if (source == runButton) {
-      executeCommandAsThread();
-    } else if (source == clearButton) {
-      console.clearContent();
-    } else if (source == historyButton) {
-      console.clearContent(viewer.getSetHistory(Integer.MAX_VALUE));
-    } else if (source == stateButton) {
-      console.clearContent(viewer.getStateInfo());
-    } else if (source == haltButton) {
-      viewer.haltScriptExecution();
-    }
-    console.grabFocus(); // always grab the focus (e.g., after clear)
-  }
-}
-
-class ConsoleTextPane extends JTextPane {
-
-  ConsoleDocument consoleDoc;
-  EnterListener enterListener;
-  JmolViewer viewer;
-
-  ConsoleTextPane(ScriptWindow scriptWindow) {
-    super(new ConsoleDocument());
-    consoleDoc = (ConsoleDocument)getDocument();
-    consoleDoc.setConsoleTextPane(this);
-    this.enterListener = (EnterListener) scriptWindow;
-    this.viewer = scriptWindow.viewer;
-  }
-
-  public String getCommandString() {
-    String cmd = consoleDoc.getCommandString();
-    return cmd;
-  }
-
-  public void setPrompt() {
-    consoleDoc.setPrompt();
-  }
-
-  public void appendNewline() {
-    consoleDoc.appendNewline();
-  }
-
-  public void outputError(String strError) {
-    consoleDoc.outputError(strError);
-  }
-
-  public void outputErrorForeground(String strError) {
-    consoleDoc.outputErrorForeground(strError);
-  }
-
-  public void outputEcho(String strEcho) {
-    consoleDoc.outputEcho(strEcho);
-  }
-
-  public void outputStatus(String strStatus) {
-    consoleDoc.outputStatus(strStatus);
-  }
-
-  public void enterPressed() {
-    if (enterListener != null)
-      enterListener.enterPressed();
-  }
-
-  public void clearContent() {
-    clearContent(null);
-  }
-  public void clearContent(String text) {
-    consoleDoc.clearContent();
-    if (text != null)
-      consoleDoc.outputEcho(text);
-    setPrompt();
-  }
-
-   /* (non-Javadoc)
-    * @see java.awt.Component#processKeyEvent(java.awt.event.KeyEvent)
-    */
-
-   /**
-    * Custom key event processing for command 0 implementation.
-    *
-    * Captures key up and key down strokes to call command history
-    * and redefines the same events with control down to allow
-    * caret vertical shift.
-    *
-    * @see java.awt.Component#processKeyEvent(java.awt.event.KeyEvent)
-    */
-   protected void processKeyEvent(KeyEvent ke)
-   {
-      // Id Control key is down, captures events does command
-      // history recall and inhibits caret vertical shift.
-      if (ke.getKeyCode() == KeyEvent.VK_UP
-         && ke.getID() == KeyEvent.KEY_PRESSED
-         && !ke.isControlDown())
-      {
-         recallCommand(true);
-      }
-      else if (
-         ke.getKeyCode() == KeyEvent.VK_DOWN
-            && ke.getID() == KeyEvent.KEY_PRESSED
-            && !ke.isControlDown())
-      {
-         recallCommand(false);
-      }
-      // If Control key is down, redefines the event as if it
-      // where a key up or key down stroke without modifiers.
-      // This allows to move the caret up and down
-      // with no command history recall.
-      else if (
-         (ke.getKeyCode() == KeyEvent.VK_DOWN
-            || ke.getKeyCode() == KeyEvent.VK_UP)
-            && ke.getID() == KeyEvent.KEY_PRESSED
-            && ke.isControlDown())
-      {
-         super
-            .processKeyEvent(new KeyEvent(
-               (Component) ke.getSource(),
-               ke.getID(),
-               ke.getWhen(),
-               0,         // No modifiers
-               ke.getKeyCode(),
-               ke.getKeyChar(),
-               ke.getKeyLocation()));
-      }
-      // Standard processing for other events.
-      else
-      {
-         super.processKeyEvent(ke);
-         //check command for compiler-identifyable syntax issues
-         //this may have to be taken out if people start complaining
-         //that only some of the commands are being checked
-         //that is -- that the script itself is not being fully checked
-
-         //not perfect -- help here?
-         if (ke.getID() == KeyEvent.KEY_RELEASED
-             && (ke.getKeyCode() > KeyEvent.VK_DOWN) || ke.getKeyCode() == KeyEvent.VK_BACK_SPACE)
-           checkCommand();
-      }
-   }
-
-   /**
-   * Recall command history.
-   *
-   * @param up - history up or down
-   */
-   void recallCommand(boolean up) {
-     String cmd = viewer.getSetHistory(up ? -1 : 1);
-    if (cmd == null) {
-      return;
-    }
-    try {
-      if (cmd.endsWith(CommandHistory.ERROR_FLAG)) {
-        cmd = cmd.substring(0, cmd.indexOf(CommandHistory.ERROR_FLAG));
-        consoleDoc.replaceCommand(cmd, true);
-      } else {
-        consoleDoc.replaceCommand(cmd, false);
-      }
-    } catch (BadLocationException e) {
-      e.printStackTrace();
-    }
-  }
-
-   void checkCommand() {
-    String strCommand = consoleDoc.getCommandString();
-    if (strCommand.length() == 0)
-      return;
-    consoleDoc
-        .colorCommand(viewer.scriptCheck(strCommand) == null ? consoleDoc.attUserInput
-            : consoleDoc.attError);
-  }
-
-
-}
-
-class ConsoleDocument extends DefaultStyledDocument {
-
-  ConsoleTextPane consoleTextPane;
-
-  SimpleAttributeSet attError;
-  SimpleAttributeSet attEcho;
-  SimpleAttributeSet attPrompt;
-  SimpleAttributeSet attUserInput;
-  SimpleAttributeSet attStatus;
-
-  ConsoleDocument() {
-    super();
-
-    attError = new SimpleAttributeSet();
-    StyleConstants.setForeground(attError, Color.red);
-
-    attPrompt = new SimpleAttributeSet();
-    StyleConstants.setForeground(attPrompt, Color.magenta);
-
-    attUserInput = new SimpleAttributeSet();
-    StyleConstants.setForeground(attUserInput, Color.black);
-
-    attEcho = new SimpleAttributeSet();
-    StyleConstants.setForeground(attEcho, Color.blue);
-    StyleConstants.setBold(attEcho, true);
-
-    attStatus = new SimpleAttributeSet();
-    StyleConstants.setForeground(attStatus, Color.black);
-    StyleConstants.setItalic(attStatus, true);
-  }
-
-  void setConsoleTextPane(ConsoleTextPane consoleTextPane) {
-    this.consoleTextPane = consoleTextPane;
-  }
-
-  Position positionBeforePrompt; // starts at 0, so first time isn't tracked (at least on Mac OS X)
-  Position positionAfterPrompt;  // immediately after $, so this will track
-  int offsetAfterPrompt;         // only still needed for the insertString override and replaceCommand
-
-  /**
-   * Removes all content of the script window, and add a new prompt.
-   */
-  void clearContent() {
-      try {
-          super.remove(0, getLength());
-      } catch (BadLocationException exception) {
-          System.out.println("Could not clear script window content: " + exception.getMessage());
-      }
-  }
-
-  void setPrompt() {
-    try {
-      super.insertString(getLength(), "$ ", attPrompt);
-      setOffsetPositions();
-      consoleTextPane.setCaretPosition(offsetAfterPrompt);
-    } catch (BadLocationException e) {
-      e.printStackTrace();
-    }
-  }
-
-  void setOffsetPositions() {
-    try {
-      offsetAfterPrompt = getLength();
-      positionBeforePrompt = createPosition(offsetAfterPrompt - 2);
-      // after prompt should be immediately after $ otherwise tracks the end
-      // of the line (and no command will be found) at least on Mac OS X it did.
-      positionAfterPrompt = createPosition(offsetAfterPrompt - 1);
-    } catch (BadLocationException e) {
-      e.printStackTrace();
-    }
-  }
-
-  void setNoPrompt() {
-    try {
-      offsetAfterPrompt = getLength();
-      positionAfterPrompt = positionBeforePrompt = createPosition(offsetAfterPrompt);
-      consoleTextPane.setCaretPosition(offsetAfterPrompt);
-    } catch (BadLocationException e) {
-      e.printStackTrace();
-    }
-  }
-
-  // it looks like the positionBeforePrompt does not track when it started out as 0
-  // and a insertString at location 0 occurs. It may be better to track the
-  // position after the prompt in stead
-  void outputBeforePrompt(String str, SimpleAttributeSet attribute) {
-    try {
-      int pt = consoleTextPane.getCaretPosition();
-      Position caretPosition = createPosition(pt);
-      pt = positionBeforePrompt.getOffset();
-      super.insertString(pt, str+"\n", attribute);
-      setOffsetPositions();
-      pt = caretPosition.getOffset();
-      consoleTextPane.setCaretPosition(pt);
-    } catch (BadLocationException e) {
-      e.printStackTrace();
-    }
-  }
-
-  void outputError(String strError) {
-    outputBeforePrompt(strError, attError);
-  }
-
-  void outputErrorForeground(String strError) {
-    try {
-      super.insertString(getLength(), strError+"\n", attError);
-      consoleTextPane.setCaretPosition(getLength());
-    } catch (BadLocationException e) {
-      e.printStackTrace();
-
-    }
-  }
-
-  void outputEcho(String strEcho) {
-    outputBeforePrompt(strEcho, attEcho);
-  }
-
-  void outputStatus(String strStatus) {
-    outputBeforePrompt(strStatus, attStatus);
-  }
-
-  void appendNewline() {
-    try {
-      super.insertString(getLength(), "\n", attUserInput);
-      consoleTextPane.setCaretPosition(getLength());
-    } catch (BadLocationException e) {
-      e.printStackTrace();
-    }
-  }
-
-  // override the insertString to make sure everything typed ends up at the end
-  // or in the 'command line' using the proper font, and the newline is processed.
-  public void insertString(int offs, String str, AttributeSet a)
-    throws BadLocationException {
-    int ichNewline = str.indexOf('\n');
-    if (ichNewline > 0)
-      str = str.substring(0, ichNewline);
-    if (ichNewline != 0) {
-      if (offs < offsetAfterPrompt) {
-        offs = getLength();
-      }
-      super.insertString(offs, str, a == attError ? a : attUserInput);
-      consoleTextPane.setCaretPosition(offs+str.length());
-    }
-    if (ichNewline >= 0) {
-      consoleTextPane.enterPressed();
-    }
-  }
-
-  String getCommandString() {
-    String strCommand = "";
-    try {
-      int cmdStart = positionAfterPrompt.getOffset();
-      strCommand =  getText(cmdStart, getLength() - cmdStart);
-      while (strCommand.length() > 0 && strCommand.charAt(0) == ' ')
-        strCommand = strCommand.substring(1);
-    } catch (BadLocationException e) {
-      e.printStackTrace();
-    }
-    return strCommand;
-  }
-
-  public void remove(int offs, int len)
-    throws BadLocationException {
-    if (offs < offsetAfterPrompt) {
-      len -= offsetAfterPrompt - offs;
-      if (len <= 0)
-        return;
-      offs = offsetAfterPrompt;
-    }
-    super.remove(offs, len);
-//    consoleTextPane.setCaretPosition(offs);
-  }
-
-  public void replace(int offs, int length, String str, AttributeSet attrs)
-    throws BadLocationException {
-    if (offs < offsetAfterPrompt) {
-      if (offs + length < offsetAfterPrompt) {
-        offs = getLength();
-        length = 0;
-      } else {
-        length -= offsetAfterPrompt - offs;
-        offs = offsetAfterPrompt;
-      }
-    }
-    super.replace(offs, length, str, attrs);
-//    consoleTextPane.setCaretPosition(offs + str.length());
-  }
-
-   /**
-   * Replaces current command on script.
-   *
-   * @param newCommand new command value
-   * @param isError    true to set error color  ends with #??
-   *
-   * @throws BadLocationException
-   */
-  void replaceCommand(String newCommand, boolean isError) throws BadLocationException {
-    if (positionAfterPrompt == positionBeforePrompt)
-      return;
-    replace(offsetAfterPrompt, getLength() - offsetAfterPrompt, newCommand,
-        isError ? attError : attUserInput);
-  }
-
-  void colorCommand(SimpleAttributeSet att) {
-    if (positionAfterPrompt == positionBeforePrompt)
-      return;
-    setCharacterAttributes(offsetAfterPrompt, getLength() - offsetAfterPrompt, att, true);
-  }
-}
-
-interface EnterListener {
-  public void enterPressed();
-}
-
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.gui;
+
+import org.jmol.api.*;
+
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+import javax.swing.text.*;
+import java.util.Vector;
+
+import org.jmol.i18n.GT;
+import org.jmol.util.Logger;
+import org.jmol.util.CommandHistory;
+
+public final class ScriptWindow extends JPanel implements ActionListener,
+        EnterListener
+{
+
+  private ConsoleTextPane console;
+
+  private JButton closeButton;
+
+  private JButton runButton;
+
+  private JButton haltButton;
+
+  private JButton clearButton;
+
+  private JButton historyButton;
+
+  private JButton stateButton;
+
+  JmolViewer viewer;
+
+  AppJmol appJmol;
+
+  public ScriptWindow(AppJmol appJmol)
+  {
+    this.viewer = appJmol.viewer;
+    this.appJmol = appJmol;
+
+    setLayout(new BorderLayout());
+
+    console = new ConsoleTextPane(this);
+
+    console.setPrompt();
+    add(new JScrollPane(console), BorderLayout.CENTER);
+
+    JPanel buttonPanel = new JPanel();
+    add(buttonPanel, BorderLayout.SOUTH);
+
+    runButton = new JButton(GT._("Run"));
+    haltButton = new JButton(GT._("Halt"));
+    runButton.addActionListener(this);
+    // buttonPanel.add(runButton);
+    haltButton.addActionListener(this);
+    // buttonPanel.add(haltButton);
+    haltButton.setEnabled(false);
+
+    clearButton = new JButton(GT._("Clear"));
+    clearButton.addActionListener(this);
+    buttonPanel.add(clearButton);
+
+    historyButton = new JButton(GT._("History"));
+    historyButton.addActionListener(this);
+    buttonPanel.add(historyButton);
+
+    stateButton = new JButton(GT._("State"));
+    stateButton.addActionListener(this);
+    buttonPanel.add(stateButton);
+
+    closeButton = new JButton(GT._("Close"));
+    closeButton.addActionListener(this);
+    buttonPanel.add(closeButton);
+
+    for (int i = 0; i < buttonPanel.getComponentCount(); i++)
+    {
+      // ((JButton)buttonPanel.getComponent(i))
+      // .setMargin(new Insets(0, 0, 0, 0));
+    }
+
+  }
+
+  public void sendConsoleEcho(String strEcho)
+  {
+    if (strEcho != null && !isError)
+    {
+
+      console.outputEcho(strEcho);
+
+    }
+    setError(false);
+  }
+
+  boolean isError = false;
+
+  void setError(boolean TF)
+  {
+    isError = TF;
+    // if (isError)
+    // console.recallCommand(true);
+  }
+
+  public void sendConsoleMessage(String strStatus)
+  {
+    if (strStatus == null)
+    {
+      console.clearContent();
+      console.outputStatus("");
+    }
+    else if (strStatus.indexOf("ERROR:") >= 0)
+    {
+      console.outputError(strStatus);
+      isError = true;
+    }
+    else if (!isError)
+    {
+      console.outputStatus(strStatus);
+    }
+  }
+
+  public void notifyScriptTermination(String strMsg, int msWalltime)
+  {
+    if (strMsg != null && strMsg.indexOf("ERROR") >= 0)
+    {
+      console.outputError(strMsg);
+    }
+    runButton.setEnabled(true);
+    haltButton.setEnabled(false);
+  }
+
+  public void enterPressed()
+  {
+    runButton.doClick(100);
+    // executeCommand();
+  }
+
+  class ExecuteCommandThread extends Thread
+  {
+
+    String strCommand;
+
+    ExecuteCommandThread(String command)
+    {
+      strCommand = command;
+    }
+
+    public void run()
+    {
+      try
+      {
+        executeCommand(strCommand);
+      } catch (Exception ie)
+      {
+        Logger.debug("execution command interrupted!" + ie);
+      }
+    }
+  }
+
+  ExecuteCommandThread execThread;
+
+  void executeCommandAsThread()
+  {
+    String strCommand = console.getCommandString().trim();
+    if (strCommand.length() > 0)
+    {
+      execThread = new ExecuteCommandThread(strCommand);
+      execThread.start();
+    }
+  }
+
+  void executeCommand(String strCommand)
+  {
+    boolean doWait;
+    setError(false);
+    console.appendNewline();
+    console.setPrompt();
+    if (strCommand.length() > 0)
+    {
+      String strErrorMessage = null;
+      doWait = (strCommand.indexOf("WAIT ") == 0);
+      if (doWait)
+      { // for testing, mainly
+        // demonstrates using the statusManager system.
+        runButton.setEnabled(false);
+        haltButton.setEnabled(true);
+
+        Vector info = (Vector) viewer
+                .scriptWaitStatus(strCommand.substring(5),
+                        "+fileLoaded,+scriptStarted,+scriptStatus,+scriptEcho,+scriptTerminated");
+        runButton.setEnabled(true);
+        haltButton.setEnabled(false);
+        /*
+         * info = [ statusRecortSet0, statusRecortSet1, statusRecortSet2, ...]
+         * statusRecordSet = [ statusRecord0, statusRecord1, statusRecord2, ...]
+         * statusRecord = [int msgPtr, String statusName, int intInfo, String
+         * msg]
+         */
+        for (int i = 0; i < info.size(); i++)
+        {
+          Vector statusRecordSet = (Vector) info.get(i);
+          for (int j = 0; j < statusRecordSet.size(); j++)
+          {
+            Vector statusRecord = (Vector) statusRecordSet.get(j);
+            Logger.info("msg#=" + statusRecord.get(0) + " "
+                    + statusRecord.get(1) + " intInfo="
+                    + statusRecord.get(2) + " stringInfo="
+                    + statusRecord.get(3));
+          }
+        }
+        console.appendNewline();
+      }
+      else
+      {
+        boolean isScriptExecuting = viewer.isScriptExecuting();
+        if (viewer.checkHalt(strCommand))
+          strErrorMessage = (isScriptExecuting ? "string execution halted with "
+                  + strCommand
+                  : "no script was executing");
+        else
+          strErrorMessage = "";// viewer.scriptCheck(strCommand);
+        // the problem is that scriptCheck is synchronized, so these might get
+        // backed up.
+        if (strErrorMessage != null && strErrorMessage.length() > 0)
+        {
+          console.outputError(strErrorMessage);
+        }
+        else
+        {
+          // runButton.setEnabled(false);
+          haltButton.setEnabled(true);
+          viewer.script(strCommand);
+        }
+      }
+    }
+    console.grabFocus();
+  }
+
+  public void actionPerformed(ActionEvent e)
+  {
+    Object source = e.getSource();
+    if (source == closeButton)
+    {
+      appJmol.showConsole(false);
+    }
+    else if (source == runButton)
+    {
+      executeCommandAsThread();
+    }
+    else if (source == clearButton)
+    {
+      console.clearContent();
+    }
+    else if (source == historyButton)
+    {
+      console.clearContent(viewer.getSetHistory(Integer.MAX_VALUE));
+    }
+    else if (source == stateButton)
+    {
+      console.clearContent(viewer.getStateInfo());
+    }
+    else if (source == haltButton)
+    {
+      viewer.haltScriptExecution();
+    }
+    console.grabFocus(); // always grab the focus (e.g., after clear)
+  }
+}
+
+class ConsoleTextPane extends JTextPane
+{
+
+  ConsoleDocument consoleDoc;
+
+  EnterListener enterListener;
+
+  JmolViewer viewer;
+
+  ConsoleTextPane(ScriptWindow scriptWindow)
+  {
+    super(new ConsoleDocument());
+    consoleDoc = (ConsoleDocument) getDocument();
+    consoleDoc.setConsoleTextPane(this);
+    this.enterListener = (EnterListener) scriptWindow;
+    this.viewer = scriptWindow.viewer;
+  }
+
+  public String getCommandString()
+  {
+    String cmd = consoleDoc.getCommandString();
+    return cmd;
+  }
+
+  public void setPrompt()
+  {
+    consoleDoc.setPrompt();
+  }
+
+  public void appendNewline()
+  {
+    consoleDoc.appendNewline();
+  }
+
+  public void outputError(String strError)
+  {
+    consoleDoc.outputError(strError);
+  }
+
+  public void outputErrorForeground(String strError)
+  {
+    consoleDoc.outputErrorForeground(strError);
+  }
+
+  public void outputEcho(String strEcho)
+  {
+    consoleDoc.outputEcho(strEcho);
+  }
+
+  public void outputStatus(String strStatus)
+  {
+    consoleDoc.outputStatus(strStatus);
+  }
+
+  public void enterPressed()
+  {
+    if (enterListener != null)
+      enterListener.enterPressed();
+  }
+
+  public void clearContent()
+  {
+    clearContent(null);
+  }
+
+  public void clearContent(String text)
+  {
+    consoleDoc.clearContent();
+    if (text != null)
+      consoleDoc.outputEcho(text);
+    setPrompt();
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see java.awt.Component#processKeyEvent(java.awt.event.KeyEvent)
+   */
+
+  /**
+   * Custom key event processing for command 0 implementation.
+   * 
+   * Captures key up and key down strokes to call command history and redefines
+   * the same events with control down to allow caret vertical shift.
+   * 
+   * @see java.awt.Component#processKeyEvent(java.awt.event.KeyEvent)
+   */
+  protected void processKeyEvent(KeyEvent ke)
+  {
+    // Id Control key is down, captures events does command
+    // history recall and inhibits caret vertical shift.
+    if (ke.getKeyCode() == KeyEvent.VK_UP
+            && ke.getID() == KeyEvent.KEY_PRESSED && !ke.isControlDown())
+    {
+      recallCommand(true);
+    }
+    else if (ke.getKeyCode() == KeyEvent.VK_DOWN
+            && ke.getID() == KeyEvent.KEY_PRESSED && !ke.isControlDown())
+    {
+      recallCommand(false);
+    }
+    // If Control key is down, redefines the event as if it
+    // where a key up or key down stroke without modifiers.
+    // This allows to move the caret up and down
+    // with no command history recall.
+    else if ((ke.getKeyCode() == KeyEvent.VK_DOWN || ke.getKeyCode() == KeyEvent.VK_UP)
+            && ke.getID() == KeyEvent.KEY_PRESSED && ke.isControlDown())
+    {
+      super.processKeyEvent(new KeyEvent((Component) ke.getSource(), ke
+              .getID(), ke.getWhen(), 0, // No modifiers
+              ke.getKeyCode(), ke.getKeyChar(), ke.getKeyLocation()));
+    }
+    // Standard processing for other events.
+    else
+    {
+      super.processKeyEvent(ke);
+      // check command for compiler-identifyable syntax issues
+      // this may have to be taken out if people start complaining
+      // that only some of the commands are being checked
+      // that is -- that the script itself is not being fully checked
+
+      // not perfect -- help here?
+      if (ke.getID() == KeyEvent.KEY_RELEASED
+              && (ke.getKeyCode() > KeyEvent.VK_DOWN)
+              || ke.getKeyCode() == KeyEvent.VK_BACK_SPACE)
+        checkCommand();
+    }
+  }
+
+  /**
+   * Recall command history.
+   * 
+   * @param up -
+   *                history up or down
+   */
+  void recallCommand(boolean up)
+  {
+    String cmd = viewer.getSetHistory(up ? -1 : 1);
+    if (cmd == null)
+    {
+      return;
+    }
+    try
+    {
+      if (cmd.endsWith(CommandHistory.ERROR_FLAG))
+      {
+        cmd = cmd.substring(0, cmd.indexOf(CommandHistory.ERROR_FLAG));
+        consoleDoc.replaceCommand(cmd, true);
+      }
+      else
+      {
+        consoleDoc.replaceCommand(cmd, false);
+      }
+    } catch (BadLocationException e)
+    {
+      e.printStackTrace();
+    }
+  }
+
+  void checkCommand()
+  {
+    String strCommand = consoleDoc.getCommandString();
+    if (strCommand.length() == 0)
+      return;
+    consoleDoc
+            .colorCommand(viewer.scriptCheck(strCommand) == null ? consoleDoc.attUserInput
+                    : consoleDoc.attError);
+  }
+
+}
+
+class ConsoleDocument extends DefaultStyledDocument
+{
+
+  ConsoleTextPane consoleTextPane;
+
+  SimpleAttributeSet attError;
+
+  SimpleAttributeSet attEcho;
+
+  SimpleAttributeSet attPrompt;
+
+  SimpleAttributeSet attUserInput;
+
+  SimpleAttributeSet attStatus;
+
+  ConsoleDocument()
+  {
+    super();
+
+    attError = new SimpleAttributeSet();
+    StyleConstants.setForeground(attError, Color.red);
+
+    attPrompt = new SimpleAttributeSet();
+    StyleConstants.setForeground(attPrompt, Color.magenta);
+
+    attUserInput = new SimpleAttributeSet();
+    StyleConstants.setForeground(attUserInput, Color.black);
+
+    attEcho = new SimpleAttributeSet();
+    StyleConstants.setForeground(attEcho, Color.blue);
+    StyleConstants.setBold(attEcho, true);
+
+    attStatus = new SimpleAttributeSet();
+    StyleConstants.setForeground(attStatus, Color.black);
+    StyleConstants.setItalic(attStatus, true);
+  }
+
+  void setConsoleTextPane(ConsoleTextPane consoleTextPane)
+  {
+    this.consoleTextPane = consoleTextPane;
+  }
+
+  Position positionBeforePrompt; // starts at 0, so first time isn't tracked
+                                  // (at least on Mac OS X)
+
+  Position positionAfterPrompt; // immediately after $, so this will track
+
+  int offsetAfterPrompt; // only still needed for the insertString override and
+                          // replaceCommand
+
+  /**
+   * Removes all content of the script window, and add a new prompt.
+   */
+  void clearContent()
+  {
+    try
+    {
+      super.remove(0, getLength());
+    } catch (BadLocationException exception)
+    {
+      System.out.println("Could not clear script window content: "
+              + exception.getMessage());
+    }
+  }
+
+  void setPrompt()
+  {
+    try
+    {
+      super.insertString(getLength(), "$ ", attPrompt);
+      setOffsetPositions();
+      consoleTextPane.setCaretPosition(offsetAfterPrompt);
+    } catch (BadLocationException e)
+    {
+      e.printStackTrace();
+    }
+  }
+
+  void setOffsetPositions()
+  {
+    try
+    {
+      offsetAfterPrompt = getLength();
+      positionBeforePrompt = createPosition(offsetAfterPrompt - 2);
+      // after prompt should be immediately after $ otherwise tracks the end
+      // of the line (and no command will be found) at least on Mac OS X it did.
+      positionAfterPrompt = createPosition(offsetAfterPrompt - 1);
+    } catch (BadLocationException e)
+    {
+      e.printStackTrace();
+    }
+  }
+
+  void setNoPrompt()
+  {
+    try
+    {
+      offsetAfterPrompt = getLength();
+      positionAfterPrompt = positionBeforePrompt = createPosition(offsetAfterPrompt);
+      consoleTextPane.setCaretPosition(offsetAfterPrompt);
+    } catch (BadLocationException e)
+    {
+      e.printStackTrace();
+    }
+  }
+
+  // it looks like the positionBeforePrompt does not track when it started out
+  // as 0
+  // and a insertString at location 0 occurs. It may be better to track the
+  // position after the prompt in stead
+  void outputBeforePrompt(String str, SimpleAttributeSet attribute)
+  {
+    try
+    {
+      int pt = consoleTextPane.getCaretPosition();
+      Position caretPosition = createPosition(pt);
+      pt = positionBeforePrompt.getOffset();
+      super.insertString(pt, str + "\n", attribute);
+      setOffsetPositions();
+      pt = caretPosition.getOffset();
+      consoleTextPane.setCaretPosition(pt);
+    } catch (BadLocationException e)
+    {
+      e.printStackTrace();
+    }
+  }
+
+  void outputError(String strError)
+  {
+    outputBeforePrompt(strError, attError);
+  }
+
+  void outputErrorForeground(String strError)
+  {
+    try
+    {
+      super.insertString(getLength(), strError + "\n", attError);
+      consoleTextPane.setCaretPosition(getLength());
+    } catch (BadLocationException e)
+    {
+      e.printStackTrace();
+
+    }
+  }
+
+  void outputEcho(String strEcho)
+  {
+    outputBeforePrompt(strEcho, attEcho);
+  }
+
+  void outputStatus(String strStatus)
+  {
+    outputBeforePrompt(strStatus, attStatus);
+  }
+
+  void appendNewline()
+  {
+    try
+    {
+      super.insertString(getLength(), "\n", attUserInput);
+      consoleTextPane.setCaretPosition(getLength());
+    } catch (BadLocationException e)
+    {
+      e.printStackTrace();
+    }
+  }
+
+  // override the insertString to make sure everything typed ends up at the end
+  // or in the 'command line' using the proper font, and the newline is
+  // processed.
+  public void insertString(int offs, String str, AttributeSet a)
+          throws BadLocationException
+  {
+    int ichNewline = str.indexOf('\n');
+    if (ichNewline > 0)
+      str = str.substring(0, ichNewline);
+    if (ichNewline != 0)
+    {
+      if (offs < offsetAfterPrompt)
+      {
+        offs = getLength();
+      }
+      super.insertString(offs, str, a == attError ? a : attUserInput);
+      consoleTextPane.setCaretPosition(offs + str.length());
+    }
+    if (ichNewline >= 0)
+    {
+      consoleTextPane.enterPressed();
+    }
+  }
+
+  String getCommandString()
+  {
+    String strCommand = "";
+    try
+    {
+      int cmdStart = positionAfterPrompt.getOffset();
+      strCommand = getText(cmdStart, getLength() - cmdStart);
+      while (strCommand.length() > 0 && strCommand.charAt(0) == ' ')
+        strCommand = strCommand.substring(1);
+    } catch (BadLocationException e)
+    {
+      e.printStackTrace();
+    }
+    return strCommand;
+  }
+
+  public void remove(int offs, int len) throws BadLocationException
+  {
+    if (offs < offsetAfterPrompt)
+    {
+      len -= offsetAfterPrompt - offs;
+      if (len <= 0)
+        return;
+      offs = offsetAfterPrompt;
+    }
+    super.remove(offs, len);
+    // consoleTextPane.setCaretPosition(offs);
+  }
+
+  public void replace(int offs, int length, String str, AttributeSet attrs)
+          throws BadLocationException
+  {
+    if (offs < offsetAfterPrompt)
+    {
+      if (offs + length < offsetAfterPrompt)
+      {
+        offs = getLength();
+        length = 0;
+      }
+      else
+      {
+        length -= offsetAfterPrompt - offs;
+        offs = offsetAfterPrompt;
+      }
+    }
+    super.replace(offs, length, str, attrs);
+    // consoleTextPane.setCaretPosition(offs + str.length());
+  }
+
+  /**
+   * Replaces current command on script.
+   * 
+   * @param newCommand
+   *                new command value
+   * @param isError
+   *                true to set error color ends with #??
+   * 
+   * @throws BadLocationException
+   */
+  void replaceCommand(String newCommand, boolean isError)
+          throws BadLocationException
+  {
+    if (positionAfterPrompt == positionBeforePrompt)
+      return;
+    replace(offsetAfterPrompt, getLength() - offsetAfterPrompt, newCommand,
+            isError ? attError : attUserInput);
+  }
+
+  void colorCommand(SimpleAttributeSet att)
+  {
+    if (positionAfterPrompt == positionBeforePrompt)
+      return;
+    setCharacterAttributes(offsetAfterPrompt, getLength()
+            - offsetAfterPrompt, att, true);
+  }
+}
+
+interface EnterListener
+{
+  public void enterPressed();
+}
diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index cd7c231..052932b 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -26,32 +26,43 @@ import jalview.datamodel.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class SeqCanvas
-    extends JComponent
+public class SeqCanvas extends JComponent
 {
   final FeatureRenderer fr;
+
   final SequenceRenderer sr;
+
   BufferedImage img;
+
   Graphics2D gg;
+
   int imgWidth;
+
   int imgHeight;
+
   AlignViewport av;
+
   SearchResults searchResults = null;
+
   boolean fastPaint = false;
+
   int LABEL_WEST;
+
   int LABEL_EAST;
 
   int cursorX = 0;
+
   int cursorY = 0;
 
   /**
    * Creates a new SeqCanvas object.
-   *
-   * @param av DOCUMENT ME!
+   * 
+   * @param av
+   *                DOCUMENT ME!
    */
   public SeqCanvas(AlignmentPanel ap)
   {
@@ -73,14 +84,17 @@ public class SeqCanvas
     return fr;
   }
 
-
   /**
    * DOCUMENT ME!
-   *
-   * @param g DOCUMENT ME!
-   * @param startx DOCUMENT ME!
-   * @param endx DOCUMENT ME!
-   * @param ypos DOCUMENT ME!
+   * 
+   * @param g
+   *                DOCUMENT ME!
+   * @param startx
+   *                DOCUMENT ME!
+   * @param endx
+   *                DOCUMENT ME!
+   * @param ypos
+   *                DOCUMENT ME!
    */
   void drawNorthScale(Graphics g, int startx, int endx, int ypos)
   {
@@ -98,22 +112,26 @@ public class SeqCanvas
       }
 
       g.drawString(String.valueOf(value), (i - startx - 1) * av.charWidth,
-                   ypos - (av.charHeight / 2));
+              ypos - (av.charHeight / 2));
 
-      g.drawLine( ( (i - startx - 1) * av.charWidth) + (av.charWidth / 2),
-                 (ypos + 2) - (av.charHeight / 2),
-                 ( (i - startx - 1) * av.charWidth) + (av.charWidth / 2), ypos -
-                 2);
+      g.drawLine(((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
+              (ypos + 2) - (av.charHeight / 2),
+              ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
+              ypos - 2);
     }
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param g DOCUMENT ME!
-   * @param startx DOCUMENT ME!
-   * @param endx DOCUMENT ME!
-   * @param ypos DOCUMENT ME!
+   * 
+   * @param g
+   *                DOCUMENT ME!
+   * @param startx
+   *                DOCUMENT ME!
+   * @param endx
+   *                DOCUMENT ME!
+   * @param ypos
+   *                DOCUMENT ME!
    */
   void drawWestScale(Graphics g, int startx, int endx, int ypos)
   {
@@ -155,21 +173,25 @@ public class SeqCanvas
 
       if (value != -1)
       {
-        int x = LABEL_WEST - fm.stringWidth(String.valueOf(value)) -
-            av.charWidth / 2;
-        g.drawString(value + "", x,
-                     (ypos + (i * av.charHeight)) - (av.charHeight / 5));
+        int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))
+                - av.charWidth / 2;
+        g.drawString(value + "", x, (ypos + (i * av.charHeight))
+                - (av.charHeight / 5));
       }
     }
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param g DOCUMENT ME!
-   * @param startx DOCUMENT ME!
-   * @param endx DOCUMENT ME!
-   * @param ypos DOCUMENT ME!
+   * 
+   * @param g
+   *                DOCUMENT ME!
+   * @param startx
+   *                DOCUMENT ME!
+   * @param endx
+   *                DOCUMENT ME!
+   * @param ypos
+   *                DOCUMENT ME!
    */
   void drawEastScale(Graphics g, int startx, int endx, int ypos)
   {
@@ -204,17 +226,22 @@ public class SeqCanvas
 
       if (value != -1)
       {
-        g.drawString(String.valueOf(value), 0,
-                     (ypos + (i * av.charHeight)) - (av.charHeight / 5));
+        g.drawString(String.valueOf(value), 0, (ypos + (i * av.charHeight))
+                - (av.charHeight / 5));
       }
     }
   }
-  boolean fastpainting=false;
+
+  boolean fastpainting = false;
+
   /**
-   * need to make this thread safe
-   * move alignment rendering in response to slider adjustment
-   * @param horizontal shift along
-   * @param vertical shift up or down in repaint
+   * need to make this thread safe move alignment rendering in response to
+   * slider adjustment
+   * 
+   * @param horizontal
+   *                shift along
+   * @param vertical
+   *                shift up or down in repaint
    */
   public void fastPaint(int horizontal, int vertical)
   {
@@ -222,7 +249,7 @@ public class SeqCanvas
     {
       return;
     }
-    fastpainting=true;
+    fastpainting = true;
     if (gg == null)
     {
       return;
@@ -230,12 +257,9 @@ public class SeqCanvas
 
     fastPaint = true;
 
-    gg.copyArea(horizontal * av.charWidth,
-                vertical * av.charHeight,
-                imgWidth,
-                imgHeight,
-                -horizontal * av.charWidth,
-                -vertical * av.charHeight);
+    gg.copyArea(horizontal * av.charWidth, vertical * av.charHeight,
+            imgWidth, imgHeight, -horizontal * av.charWidth, -vertical
+                    * av.charHeight);
 
     int sr = av.startRes;
     int er = av.endRes;
@@ -279,32 +303,32 @@ public class SeqCanvas
 
     gg.translate(transX, transY);
     drawPanel(gg, sr, er, ss, es, 0);
-    gg.translate( -transX, -transY);
+    gg.translate(-transX, -transY);
 
     repaint();
-    fastpainting=false;
+    fastpainting = false;
   }
 
   /**
-   * Definitions of startx and endx (hopefully):
-   * SMJS This is what I'm working towards!
-   *   startx is the first residue (starting at 0) to display.
-   *   endx   is the last residue to display (starting at 0).
-   *   starty is the first sequence to display (starting at 0).
-   *   endy   is the last sequence to display (starting at 0).
-   * NOTE 1: The av limits are set in setFont in this class and
-   * in the adjustment listener in SeqPanel when the scrollbars move.
+   * Definitions of startx and endx (hopefully): SMJS This is what I'm working
+   * towards! startx is the first residue (starting at 0) to display. endx is
+   * the last residue to display (starting at 0). starty is the first sequence
+   * to display (starting at 0). endy is the last sequence to display (starting
+   * at 0). NOTE 1: The av limits are set in setFont in this class and in the
+   * adjustment listener in SeqPanel when the scrollbars move.
    */
 
   // Set this to false to force a full panel paint
   public void paintComponent(Graphics g)
   {
-    BufferedImage lcimg = img; // take reference since other threads may null img and call later.
+    BufferedImage lcimg = img; // take reference since other threads may null
+                                // img and call later.
     super.paintComponent(g);
 
-    if (lcimg != null && (fastPaint
-                        || (getVisibleRect().width != g.getClipBounds().width)
-                        || (getVisibleRect().height != g.getClipBounds().height)))
+    if (lcimg != null
+            && (fastPaint
+                    || (getVisibleRect().width != g.getClipBounds().width) || (getVisibleRect().height != g
+                    .getClipBounds().height)))
     {
       g.drawImage(lcimg, 0, 0, this);
       fastPaint = false;
@@ -318,37 +342,25 @@ public class SeqCanvas
     imgWidth -= (imgWidth % av.charWidth);
     imgHeight -= (imgHeight % av.charHeight);
 
-    if ( (imgWidth < 1) || (imgHeight < 1))
+    if ((imgWidth < 1) || (imgHeight < 1))
     {
       return;
     }
 
-    if (lcimg == null || imgWidth != lcimg.getWidth() || imgHeight != lcimg.getHeight())
+    if (lcimg == null || imgWidth != lcimg.getWidth()
+            || imgHeight != lcimg.getHeight())
     {
       try
       {
         lcimg = img = new BufferedImage(imgWidth, imgHeight,
-                                BufferedImage.TYPE_INT_RGB);
+                BufferedImage.TYPE_INT_RGB);
         gg = (Graphics2D) img.getGraphics();
         gg.setFont(av.getFont());
-      }
-      catch (OutOfMemoryError er)
+      } catch (OutOfMemoryError er)
       {
         System.gc();
-        System.out.println(er + " making image, SeqCanvas");
-        javax.swing.SwingUtilities.invokeLater(new Runnable()
-        {
-          public void run()
-          {
-            javax.swing.JOptionPane.showInternalMessageDialog(Desktop.
-                desktop,
-                "Out of memory creating alignment image!!"
-                +
-                "\nSee help files for increasing Java Virtual Machine memory."
-                , "Out of memory",
-                javax.swing.JOptionPane.WARNING_MESSAGE);
-          }
-        });
+        System.err.println("SeqCanvas OutOfMemory Redraw Error.\n" + er);
+        new OOMWarning("Creating alignment image for display", er);
 
         return;
       }
@@ -357,7 +369,7 @@ public class SeqCanvas
     if (av.antiAlias)
     {
       gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-                          RenderingHints.VALUE_ANTIALIAS_ON);
+              RenderingHints.VALUE_ANTIALIAS_ON);
     }
 
     gg.setColor(Color.white);
@@ -374,14 +386,14 @@ public class SeqCanvas
 
     g.drawImage(lcimg, 0, 0, this);
 
-
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param cwidth DOCUMENT ME!
-   *
+   * 
+   * @param cwidth
+   *                DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   public int getWrappedCanvasWidth(int cwidth)
@@ -406,6 +418,7 @@ public class SeqCanvas
 
   /**
    * Generates a string of zeroes.
+   * 
    * @return String
    */
   String getMask()
@@ -431,14 +444,18 @@ public class SeqCanvas
 
   /**
    * DOCUMENT ME!
-   *
-   * @param g DOCUMENT ME!
-   * @param canvasWidth DOCUMENT ME!
-   * @param canvasHeight DOCUMENT ME!
-   * @param startRes DOCUMENT ME!
+   * 
+   * @param g
+   *                DOCUMENT ME!
+   * @param canvasWidth
+   *                DOCUMENT ME!
+   * @param canvasHeight
+   *                DOCUMENT ME!
+   * @param startRes
+   *                DOCUMENT ME!
    */
-  public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,
-                               int startRes)
+  public void drawWrappedPanel(Graphics g, int canvasWidth,
+          int canvasHeight, int startRes)
   {
     AlignmentI al = av.getAlignment();
 
@@ -476,7 +493,7 @@ public class SeqCanvas
       maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
     }
 
-    while ( (ypos <= canvasHeight) && (startRes < maxwidth))
+    while ((ypos <= canvasHeight) && (startRes < maxwidth))
     {
       endx = startRes + cWidth - 1;
 
@@ -497,7 +514,7 @@ public class SeqCanvas
       {
         g.translate(canvasWidth - LABEL_EAST, 0);
         drawEastScale(g, startRes, endx, ypos);
-        g.translate( - (canvasWidth - LABEL_EAST), 0);
+        g.translate(-(canvasWidth - LABEL_EAST), 0);
       }
 
       g.translate(LABEL_WEST, 0);
@@ -511,11 +528,11 @@ public class SeqCanvas
       {
         g.setColor(Color.blue);
         int res;
-        for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size();
-             i++)
+        for (int i = 0; i < av.getColumnSelection().getHiddenColumns()
+                .size(); i++)
         {
-          res = av.getColumnSelection().findHiddenRegionPosition(i) -
-              startRes;
+          res = av.getColumnSelection().findHiddenRegionPosition(i)
+                  - startRes;
 
           if (res < 0 || res > endx - startRes)
           {
@@ -523,15 +540,11 @@ public class SeqCanvas
           }
 
           gg.fillPolygon(new int[]
-                         {res * av.charWidth - av.charHeight / 4,
-                         res * av.charWidth + av.charHeight / 4,
-                         res * av.charWidth},
-                         new int[]
-                         {
-                         ypos - (av.charHeight / 2),
-                         ypos - (av.charHeight / 2),
-                         ypos - (av.charHeight / 2) + 8
-          }, 3);
+          { res * av.charWidth - av.charHeight / 4,
+              res * av.charWidth + av.charHeight / 4, res * av.charWidth },
+                  new int[]
+                  { ypos - (av.charHeight / 2), ypos - (av.charHeight / 2),
+                      ypos - (av.charHeight / 2) + 8 }, 3);
 
         }
       }
@@ -546,8 +559,8 @@ public class SeqCanvas
       }
       else
       {
-        g.setClip(0, (int) clip.getBounds().getY(),
-                  cWidth * av.charWidth, (int) clip.getBounds().getHeight());
+        g.setClip(0, (int) clip.getBounds().getY(), cWidth * av.charWidth,
+                (int) clip.getBounds().getHeight());
       }
 
       drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
@@ -560,11 +573,11 @@ public class SeqCanvas
           annotations = new AnnotationPanel(av);
         }
 
-        annotations.drawComponent( (Graphics2D) g, startRes, endx + 1);
+        annotations.drawComponent((Graphics2D) g, startRes, endx + 1);
         g.translate(0, -cHeight - ypos - 3);
       }
       g.setClip(clip);
-      g.translate( -LABEL_WEST, 0);
+      g.translate(-LABEL_WEST, 0);
 
       ypos += cHeight + getAnnotationHeight() + hgap;
 
@@ -573,6 +586,7 @@ public class SeqCanvas
   }
 
   AnnotationPanel annotations;
+
   int getAnnotationHeight()
   {
     if (!av.showAnnotation)
@@ -590,16 +604,22 @@ public class SeqCanvas
 
   /**
    * DOCUMENT ME!
-   *
-   * @param g1 DOCUMENT ME!
-   * @param startRes DOCUMENT ME!
-   * @param endRes DOCUMENT ME!
-   * @param startSeq DOCUMENT ME!
-   * @param endSeq DOCUMENT ME!
-   * @param offset DOCUMENT ME!
+   * 
+   * @param g1
+   *                DOCUMENT ME!
+   * @param startRes
+   *                DOCUMENT ME!
+   * @param endRes
+   *                DOCUMENT ME!
+   * @param startSeq
+   *                DOCUMENT ME!
+   * @param endSeq
+   *                DOCUMENT ME!
+   * @param offset
+   *                DOCUMENT ME!
    */
-  void drawPanel(Graphics g1, int startRes, int endRes,
-                 int startSeq, int endSeq, int offset)
+  void drawPanel(Graphics g1, int startRes, int endRes, int startSeq,
+          int endSeq, int offset)
   {
     if (!av.hasHiddenColumns)
     {
@@ -635,13 +655,14 @@ public class SeqCanvas
         {
           g1.setColor(Color.blue);
 
-          g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth - 1,
-                      0 + offset,
-                      (blockEnd - blockStart + 1) * av.charWidth - 1,
-                      (endSeq - startSeq) * av.charHeight + offset);
+          g1
+                  .drawLine((blockEnd - blockStart + 1) * av.charWidth - 1,
+                          0 + offset, (blockEnd - blockStart + 1)
+                                  * av.charWidth - 1, (endSeq - startSeq)
+                                  * av.charHeight + offset);
         }
 
-        g1.translate( -screenY * av.charWidth, 0);
+        g1.translate(-screenY * av.charWidth, 0);
         screenY += blockEnd - blockStart + 1;
         blockStart = hideEnd + 1;
       }
@@ -652,84 +673,80 @@ public class SeqCanvas
         g1.translate(screenY * av.charWidth, 0);
         draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
 
-        g1.translate( -screenY * av.charWidth, 0);
+        g1.translate(-screenY * av.charWidth, 0);
       }
     }
 
   }
 
-  //int startRes, int endRes, int startSeq, int endSeq, int x, int y,
+  // int startRes, int endRes, int startSeq, int endSeq, int x, int y,
   // int x1, int x2, int y1, int y2, int startx, int starty,
-  void draw(Graphics g,
-            int startRes, int endRes,
-            int startSeq, int endSeq,
-            int offset)
+  void draw(Graphics g, int startRes, int endRes, int startSeq, int endSeq,
+          int offset)
   {
     g.setFont(av.getFont());
     sr.prepare(g, av.renderGaps);
 
     SequenceI nextSeq;
 
-    /// First draw the sequences
-    /////////////////////////////
+    // / First draw the sequences
+    // ///////////////////////////
     for (int i = startSeq; i < endSeq; i++)
     {
       nextSeq = av.alignment.getSequenceAt(i);
 
       sr.drawSequence(nextSeq, av.alignment.findAllGroups(nextSeq),
-                      startRes, endRes,
-                      offset + ( (i - startSeq) * av.charHeight));
+              startRes, endRes, offset + ((i - startSeq) * av.charHeight));
 
       if (av.showSequenceFeatures)
       {
-        fr.drawSequence(g, nextSeq, startRes, endRes,
-                        offset + ( (i - startSeq) * av.charHeight));
+        fr.drawSequence(g, nextSeq, startRes, endRes, offset
+                + ((i - startSeq) * av.charHeight));
       }
 
-      /// Highlight search Results once all sequences have been drawn
-      //////////////////////////////////////////////////////////
+      // / Highlight search Results once all sequences have been drawn
+      // ////////////////////////////////////////////////////////
       if (searchResults != null)
       {
         int[] visibleResults = searchResults.getResults(nextSeq, startRes,
-            endRes);
+                endRes);
         if (visibleResults != null)
         {
           for (int r = 0; r < visibleResults.length; r += 2)
           {
             sr.drawHighlightedText(nextSeq, visibleResults[r],
-                                   visibleResults[r + 1],
-                                   (visibleResults[r] - startRes) *
-                                   av.charWidth,
-                                   offset + ( (i - startSeq) * av.charHeight));
+                    visibleResults[r + 1], (visibleResults[r] - startRes)
+                            * av.charWidth, offset
+                            + ((i - startSeq) * av.charHeight));
           }
         }
       }
 
-      if (av.cursorMode && cursorY == i
-          && cursorX >= startRes && cursorX <= endRes)
+      if (av.cursorMode && cursorY == i && cursorX >= startRes
+              && cursorX <= endRes)
       {
-        sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * av.charWidth,
-                      offset + ( (i - startSeq) * av.charHeight));
+        sr.drawCursor(nextSeq, cursorX,
+                (cursorX - startRes) * av.charWidth, offset
+                        + ((i - startSeq) * av.charHeight));
       }
     }
 
-    if (av.getSelectionGroup() != null || av.alignment.getGroups().size() > 0)
+    if (av.getSelectionGroup() != null
+            || av.alignment.getGroups().size() > 0)
     {
       drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
     }
 
   }
 
-  void drawGroupsBoundaries(Graphics g1,
-                            int startRes, int endRes,
-                            int startSeq, int endSeq,
-                            int offset)
+  void drawGroupsBoundaries(Graphics g1, int startRes, int endRes,
+          int startSeq, int endSeq, int offset)
   {
     Graphics2D g = (Graphics2D) g1;
     //
-    /////////////////////////////////////
+    // ///////////////////////////////////
     // Now outline any areas if necessary
-    /////////////////////////////////////
+    // ///////////////////////////////////
     SequenceGroup group = av.getSelectionGroup();
 
     int sx = -1;
@@ -738,7 +755,7 @@ public class SeqCanvas
     int groupIndex = -1;
     int visWidth = (endRes - startRes + 1) * av.charWidth;
 
-    if ( (group == null) && (av.alignment.getGroups().size() > 0))
+    if ((group == null) && (av.alignment.getGroups().size() > 0))
     {
       group = (SequenceGroup) av.alignment.getGroups().elementAt(0);
       groupIndex = 0;
@@ -757,32 +774,30 @@ public class SeqCanvas
         for (i = startSeq; i < endSeq; i++)
         {
           sx = (group.getStartRes() - startRes) * av.charWidth;
-          sy = offset + ( (i - startSeq) * av.charHeight);
-          ex = ( ( (group.getEndRes() + 1) - group.getStartRes()) *
-                av.charWidth) -
-              1;
+          sy = offset + ((i - startSeq) * av.charHeight);
+          ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) - 1;
 
           if (sx + ex < 0 || sx > visWidth)
           {
             continue;
           }
 
-          if ( (sx <= (endRes - startRes) * av.charWidth) &&
-              group.getSequences(null).
-              contains(av.alignment.getSequenceAt(i)))
+          if ((sx <= (endRes - startRes) * av.charWidth)
+                  && group.getSequences(null).contains(
+                          av.alignment.getSequenceAt(i)))
           {
-            if ( (bottom == -1) &&
-                !group.getSequences(null).contains(
-                    av.alignment.getSequenceAt(i + 1)))
+            if ((bottom == -1)
+                    && !group.getSequences(null).contains(
+                            av.alignment.getSequenceAt(i + 1)))
             {
               bottom = sy + av.charHeight;
             }
 
             if (!inGroup)
             {
-              if ( ( (top == -1) && (i == 0)) ||
-                  !group.getSequences(null).contains(
-                      av.alignment.getSequenceAt(i - 1)))
+              if (((top == -1) && (i == 0))
+                      || !group.getSequences(null).contains(
+                              av.alignment.getSequenceAt(i - 1)))
               {
                 top = sy;
               }
@@ -792,11 +807,9 @@ public class SeqCanvas
 
               if (group == av.getSelectionGroup())
               {
-                g.setStroke(new BasicStroke(1,
-                                            BasicStroke.CAP_BUTT,
-                                            BasicStroke.JOIN_ROUND, 3f,
-                                            new float[]
-                                            {5f, 3f}, 0f));
+                g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT,
+                        BasicStroke.JOIN_ROUND, 3f, new float[]
+                        { 5f, 3f }, 0f));
                 g.setColor(Color.RED);
               }
               else
@@ -855,7 +868,7 @@ public class SeqCanvas
 
         if (inGroup)
         {
-          sy = offset + ( (i - startSeq) * av.charHeight);
+          sy = offset + ((i - startSeq) * av.charHeight);
           if (sx >= 0 && sx < visWidth)
           {
             g.drawLine(sx, oldY, sx, sy);
@@ -905,10 +918,10 @@ public class SeqCanvas
           break;
         }
 
-        group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex);
+        group = (SequenceGroup) av.alignment.getGroups().elementAt(
+                groupIndex);
 
-      }
-      while (groupIndex < av.alignment.getGroups().size());
+      } while (groupIndex < av.alignment.getGroups().size());
 
     }
 
@@ -916,8 +929,9 @@ public class SeqCanvas
 
   /**
    * DOCUMENT ME!
-   *
-   * @param results DOCUMENT ME!
+   * 
+   * @param results
+   *                DOCUMENT ME!
    */
   public void highlightSearchResults(SearchResults results)
   {
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 7d451da..bdfcef4 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -31,13 +31,12 @@ import jalview.structure.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class SeqPanel
-    extends JPanel implements MouseListener,
-    MouseMotionListener, MouseWheelListener, SequenceListener
+public class SeqPanel extends JPanel implements MouseListener,
+        MouseMotionListener, MouseWheelListener, SequenceListener
 
 {
   /** DOCUMENT ME!! */
@@ -45,46 +44,63 @@ public class SeqPanel
 
   /** DOCUMENT ME!! */
   public AlignmentPanel ap;
+
   protected int lastres;
+
   protected int startseq;
+
   protected AlignViewport av;
 
   ScrollThread scrollThread = null;
+
   boolean mouseDragging = false;
+
   boolean editingSeqs = false;
+
   boolean groupEditing = false;
 
-  //////////////////////////////////////////
-  /////Everything below this is for defining the boundary of the rubberband
-  //////////////////////////////////////////
+  // ////////////////////////////////////////
+  // ///Everything below this is for defining the boundary of the rubberband
+  // ////////////////////////////////////////
   int oldSeq = -1;
+
   boolean changeEndSeq = false;
+
   boolean changeStartSeq = false;
+
   boolean changeEndRes = false;
+
   boolean changeStartRes = false;
+
   SequenceGroup stretchGroup = null;
+
   boolean remove = false;
 
   Point lastMousePress;
+
   boolean mouseWheelPressed = false;
+
   StringBuffer keyboardNo1;
+
   StringBuffer keyboardNo2;
 
   java.net.URL linkImageURL;
 
   StringBuffer tooltipText = new StringBuffer("<html>");
+
   String tmpString;
 
   EditCommand editCommand;
 
   StructureSelectionManager ssm;
 
-
   /**
    * Creates a new SeqPanel object.
-   *
-   * @param avp DOCUMENT ME!
-   * @param p DOCUMENT ME!
+   * 
+   * @param avp
+   *                DOCUMENT ME!
+   * @param p
+   *                DOCUMENT ME!
    */
   public SeqPanel(AlignViewport av, AlignmentPanel ap)
   {
@@ -112,7 +128,9 @@ public class SeqPanel
   }
 
   int startWrapBlock = -1;
+
   int wrappedBlock = -1;
+
   int findRes(MouseEvent evt)
   {
     int res = 0;
@@ -127,8 +145,8 @@ public class SeqPanel
         hgap += av.charHeight;
       }
 
-      int cHeight = av.getAlignment().getHeight() * av.charHeight
-          + hgap + seqCanvas.getAnnotationHeight();
+      int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+              + seqCanvas.getAnnotationHeight();
 
       int y = evt.getY();
       y -= hgap;
@@ -173,18 +191,18 @@ public class SeqPanel
         hgap += av.charHeight;
       }
 
-      int cHeight = av.getAlignment().getHeight() * av.charHeight
-          + hgap + seqCanvas.getAnnotationHeight();
+      int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+              + seqCanvas.getAnnotationHeight();
 
       y -= hgap;
 
-      seq = Math.min( (y % cHeight) / av.getCharHeight(),
-                     av.alignment.getHeight() - 1);
+      seq = Math.min((y % cHeight) / av.getCharHeight(), av.alignment
+              .getHeight() - 1);
     }
     else
     {
-      seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(),
-                     av.alignment.getHeight() - 1);
+      seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(),
+              av.alignment.getHeight() - 1);
     }
 
     return seq;
@@ -199,20 +217,21 @@ public class SeqPanel
       for (int i = 0; i < features.length; i++)
       {
         if (av.featuresDisplayed == null
-            || !av.featuresDisplayed.containsKey(features[i].getType()))
+                || !av.featuresDisplayed.containsKey(features[i].getType()))
         {
           continue;
         }
 
         if (features[i].featureGroup != null
-           && seqCanvas.fr.featureGroups!=null
-            && seqCanvas.fr.featureGroups.containsKey(features[i].featureGroup)
-            && !((Boolean)seqCanvas.fr.featureGroups.get(features[i].featureGroup)).booleanValue())
+                && seqCanvas.fr.featureGroups != null
+                && seqCanvas.fr.featureGroups
+                        .containsKey(features[i].featureGroup)
+                && !((Boolean) seqCanvas.fr.featureGroups
+                        .get(features[i].featureGroup)).booleanValue())
           continue;
 
-
-        if ( (features[i].getBegin() <= res) &&
-            (features[i].getEnd() >= res))
+        if ((features[i].getBegin() <= res)
+                && (features[i].getEnd() >= res))
         {
           tmp.addElement(features[i]);
         }
@@ -225,14 +244,13 @@ public class SeqPanel
     return features;
   }
 
-
   void endEditing()
   {
     if (editCommand != null && editCommand.getSize() > 0)
     {
       ap.alignFrame.addHistoryItem(editCommand);
-      av.firePropertyChange("alignment", null,
-                            av.getAlignment().getSequences());
+      av.firePropertyChange("alignment", null, av.getAlignment()
+              .getSequences());
     }
 
     startseq = -1;
@@ -272,12 +290,10 @@ public class SeqPanel
 
   void setCursorPosition()
   {
-    SequenceI sequence =
-        (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
+    SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
+            seqCanvas.cursorY);
 
-    seqCanvas.cursorX = sequence.findIndex(
-        getKeyboardNo1() - 1
-        );
+    seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1() - 1);
     scrollToVisible();
   }
 
@@ -291,14 +307,13 @@ public class SeqPanel
       int maxWidth = av.alignment.getWidth();
 
       while (!av.colSel.isVisible(seqCanvas.cursorX)
-             && seqCanvas.cursorX < maxWidth
-             && seqCanvas.cursorX > 0)
+              && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
       {
         seqCanvas.cursorX += dx;
       }
 
       if (seqCanvas.cursorX >= maxWidth
-          || !av.colSel.isVisible(seqCanvas.cursorX))
+              || !av.colSel.isVisible(seqCanvas.cursorX))
       {
         seqCanvas.cursorX = original;
       }
@@ -344,14 +359,16 @@ public class SeqPanel
       }
       if (!av.wrapAlignment)
       {
-        while (seqCanvas.cursorX < av.colSel.adjustForHiddenColumns(av.startRes))
+        while (seqCanvas.cursorX < av.colSel
+                .adjustForHiddenColumns(av.startRes))
         {
           if (!ap.scrollRight(false))
           {
             break;
           }
         }
-        while (seqCanvas.cursorX > av.colSel.adjustForHiddenColumns(av.endRes))
+        while (seqCanvas.cursorX > av.colSel
+                .adjustForHiddenColumns(av.endRes))
         {
           if (!ap.scrollRight(true))
           {
@@ -361,20 +378,20 @@ public class SeqPanel
       }
     }
     setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
-                     seqCanvas.cursorX, seqCanvas.cursorY);
+            seqCanvas.cursorX, seqCanvas.cursorY);
 
     seqCanvas.repaint();
   }
 
   void setSelectionAreaAtCursor(boolean topLeft)
   {
-    SequenceI sequence =
-        (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
+    SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
+            seqCanvas.cursorY);
 
     if (av.getSelectionGroup() != null)
     {
       SequenceGroup sg = av.selectionGroup;
-      //Find the top and bottom of this group
+      // Find the top and bottom of this group
       int min = av.alignment.getHeight(), max = 0;
       for (int i = 0; i < sg.getSize(); i++)
       {
@@ -501,8 +518,9 @@ public class SeqPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
    */
   public void mouseReleased(MouseEvent evt)
   {
@@ -520,8 +538,9 @@ public class SeqPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
    */
   public void mousePressed(MouseEvent evt)
   {
@@ -533,8 +552,7 @@ public class SeqPanel
       return;
     }
 
-    if (evt.isShiftDown() || evt.isAltDown() ||
-        evt.isControlDown())
+    if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
     {
       if (evt.isAltDown() || evt.isControlDown())
       {
@@ -556,8 +574,8 @@ public class SeqPanel
       return;
     }
 
-    if ( (seq < av.getAlignment().getHeight()) &&
-        (res < av.getAlignment().getSequenceAt(seq).getLength()))
+    if ((seq < av.getAlignment().getHeight())
+            && (res < av.getAlignment().getSequenceAt(seq).getLength()))
     {
       startseq = seq;
       lastres = res;
@@ -572,10 +590,11 @@ public class SeqPanel
   }
 
   String lastMessage;
+
   public void mouseOverSequence(SequenceI sequence, int index, int pos)
   {
-    String tmp = sequence.hashCode()+" "+index+" "+pos;
-    
+    String tmp = sequence.hashCode() + " " + index + " " + pos;
+
     if (lastMessage == null || !lastMessage.equals(tmp))
     {
       // System.err.println("mouseOver Sequence: "+tmp);
@@ -584,22 +603,22 @@ public class SeqPanel
     lastMessage = tmp;
   }
 
-
   public void highlightSequence(SearchResults results)
   {
-      seqCanvas.highlightSearchResults(results);
+    seqCanvas.highlightSearchResults(results);
   }
 
   public void updateColours(SequenceI seq, int index)
   {
     System.out.println("update the seqPanel colours");
-    //repaint();
+    // repaint();
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
    */
   public void mouseMoved(MouseEvent evt)
   {
@@ -626,10 +645,9 @@ public class SeqPanel
     }
 
     pos = setStatusMessage(sequence, res, seq);
-    if (ssm != null && pos>-1)
+    if (ssm != null && pos > -1)
       mouseOverSequence(sequence, res, pos);
 
-
     tooltipText.setLength(6); // Cuts the buffer back to <html>
 
     SequenceGroup[] groups = av.alignment.findAllGroups(sequence);
@@ -644,8 +662,8 @@ public class SeqPanel
             tooltipText.append("<br>");
           }
 
-          if (!groups[g].getName().startsWith("JTreeGroup") &&
-              !groups[g].getName().startsWith("JGroup"))
+          if (!groups[g].getName().startsWith("JTreeGroup")
+                  && !groups[g].getName().startsWith("JGroup"))
           {
             tooltipText.append(groups[g].getName());
           }
@@ -661,8 +679,8 @@ public class SeqPanel
     // use aa to see if the mouse pointer is on a
     if (av.showSequenceFeatures)
     {
-      SequenceFeature[] features = findFeaturesAtRes(
-          sequence.getDatasetSequence(), sequence.findPosition(res));
+      SequenceFeature[] features = findFeaturesAtRes(sequence
+              .getDatasetSequence(), sequence.findPosition(res));
 
       if (features != null)
       {
@@ -671,15 +689,14 @@ public class SeqPanel
           if (features[i].getType().equals("disulfide bond"))
           {
             if (features[i].getBegin() == sequence.findPosition(res)
-                || features[i].getEnd() == sequence.findPosition(res))
+                    || features[i].getEnd() == sequence.findPosition(res))
             {
               if (tooltipText.length() > 6)
               {
                 tooltipText.append("<br>");
               }
-              tooltipText.append("disulfide bond " + features[i].getBegin() +
-                                 ":" +
-                                 features[i].getEnd());
+              tooltipText.append("disulfide bond " + features[i].getBegin()
+                      + ":" + features[i].getEnd());
               if (features[i].links != null)
               {
                 tooltipText.append(" <img src=\"" + linkImageURL + "\">");
@@ -693,15 +710,16 @@ public class SeqPanel
               tooltipText.append("<br>");
             }
 
-            tooltipText.append(features[i].getType() + " " +
-                               features[i].begin);
+            tooltipText.append(features[i].getType() + " "
+                    + features[i].begin);
             if (features[i].begin != features[i].end)
             {
               tooltipText.append(" " + features[i].end);
             }
 
             if (features[i].getDescription() != null
-                && !features[i].description.equals(features[i].getType()))
+                    && !features[i].description.equals(features[i]
+                            .getType()))
             {
               tmpString = features[i].getDescription();
               int startTag = tmpString.toUpperCase().indexOf("<HTML>");
@@ -726,10 +744,11 @@ public class SeqPanel
               }
               else
               {
-                if (tmpString.indexOf("<") > -1 || tmpString.indexOf(">") > -1)
+                if (tmpString.indexOf("<") > -1
+                        || tmpString.indexOf(">") > -1)
                 {
-                  //The description does not specify html is to
-                  //be used, so we must remove < > symbols
+                  // The description does not specify html is to
+                  // be used, so we must remove < > symbols
                   tmpString = tmpString.replaceAll("<", "&lt;");
                   tmpString = tmpString.replaceAll(">", "&gt;");
 
@@ -748,7 +767,8 @@ public class SeqPanel
               String status = features[i].getValue("status").toString();
               if (status.length() > 0)
               {
-                tooltipText.append("; (" + features[i].getValue("status") + ")");
+                tooltipText.append("; (" + features[i].getValue("status")
+                        + ")");
               }
             }
 
@@ -769,33 +789,39 @@ public class SeqPanel
     else
     {
       tooltipText.append("</html>");
-      if (lastTooltip == null || !lastTooltip.equals(tooltipText.toString()))
+      if (lastTooltip == null
+              || !lastTooltip.equals(tooltipText.toString()))
         setToolTipText(tooltipText.toString());
 
       lastTooltip = tooltipText.toString();
     }
 
   }
+
   String lastTooltip;
 
   /**
    * Set status message in alignment panel
-   * @param sequence aligned sequence object
-   * @param res alignment column
-   * @param seq index of sequence in alignment
+   * 
+   * @param sequence
+   *                aligned sequence object
+   * @param res
+   *                alignment column
+   * @param seq
+   *                index of sequence in alignment
    * @return position of res in sequence
    */
   int setStatusMessage(SequenceI sequence, int res, int seq)
   {
-    int pos=-1;
-    StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
-                                         sequence.getName());
+    int pos = -1;
+    StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: "
+            + sequence.getName());
 
     Object obj = null;
     if (av.alignment.isNucleotide())
     {
-      obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
-                                                 "");
+      obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
+              + "");
       if (obj != null)
       {
         text.append(" Nucleotide: ");
@@ -812,11 +838,10 @@ public class SeqPanel
 
     if (obj != null)
     {
-      pos=sequence.findPosition(res);
+      pos = sequence.findPosition(res);
       if (obj != "")
       {
-        text.append(obj + " (" + pos +
-                    ")");
+        text.append(obj + " (" + pos + ")");
       }
     }
     ap.alignFrame.statusBar.setText(text.toString());
@@ -825,8 +850,9 @@ public class SeqPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
    */
   public void mouseDragged(MouseEvent evt)
   {
@@ -834,9 +860,10 @@ public class SeqPanel
     {
       int oldWidth = av.charWidth;
 
-      //Which is bigger, left-right or up-down?
-      if (Math.abs(evt.getY() - lastMousePress.getY())
-          > Math.abs(evt.getX() - lastMousePress.getX()))
+      // Which is bigger, left-right or up-down?
+      if (Math.abs(evt.getY() - lastMousePress.getY()) > Math.abs(evt
+              .getX()
+              - lastMousePress.getX()))
       {
         int fontSize = av.font.getSize();
 
@@ -854,7 +881,9 @@ public class SeqPanel
           fontSize = 1;
         }
 
-        av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
+        av
+                .setFont(new Font(av.font.getName(), av.font.getStyle(),
+                        fontSize));
         av.charWidth = oldWidth;
         ap.fontChanged();
       }
@@ -893,12 +922,12 @@ public class SeqPanel
       res = 0;
     }
 
-    if ( (lastres == -1) || (lastres == res))
+    if ((lastres == -1) || (lastres == res))
     {
       return;
     }
 
-    if ( (res < av.getAlignment().getWidth()) && (res < lastres))
+    if ((res < av.getAlignment().getWidth()) && (res < lastres))
     {
       // dragLeft, delete gap
       editSequence(false, res);
@@ -915,8 +944,6 @@ public class SeqPanel
     }
   }
 
-
-
   synchronized void editSequence(boolean insertGap, int startres)
   {
     int fixedLeft = -1;
@@ -926,11 +953,11 @@ public class SeqPanel
 
     SequenceI seq = av.alignment.getSequenceAt(startseq);
 
-    //No group, but the sequence may represent a group
+    // No group, but the sequence may represent a group
     if (!groupEditing && av.hasHiddenRows)
     {
       if (av.hiddenRepSequences != null
-          && av.hiddenRepSequences.containsKey(seq))
+              && av.hiddenRepSequences.containsKey(seq))
       {
         sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
         groupEditing = true;
@@ -972,18 +999,19 @@ public class SeqPanel
     message.append(Math.abs(startres - lastres) + " gaps.");
     ap.alignFrame.statusBar.setText(message.toString());
 
-    //Are we editing within a selection group?
+    // Are we editing within a selection group?
     if (groupEditing
-        || (sg != null && sg.getSequences(av.hiddenRepSequences).contains(seq)))
+            || (sg != null && sg.getSequences(av.hiddenRepSequences)
+                    .contains(seq)))
     {
       fixedColumns = true;
 
-      //sg might be null as the user may only see 1 sequence,
-      //but the sequence represents a group
+      // sg might be null as the user may only see 1 sequence,
+      // but the sequence represents a group
       if (sg == null)
       {
         if (av.hiddenRepSequences == null
-            || !av.hiddenRepSequences.containsKey(seq))
+                || !av.hiddenRepSequences.containsKey(seq))
         {
           endEditing();
           return;
@@ -994,10 +1022,10 @@ public class SeqPanel
       fixedLeft = sg.getStartRes();
       fixedRight = sg.getEndRes();
 
-      if ( (startres < fixedLeft && lastres >= fixedLeft)
-          || (startres >= fixedLeft && lastres < fixedLeft)
-          || (startres > fixedRight && lastres <= fixedRight)
-          || (startres <= fixedRight && lastres > fixedRight))
+      if ((startres < fixedLeft && lastres >= fixedLeft)
+              || (startres >= fixedLeft && lastres < fixedLeft)
+              || (startres > fixedRight && lastres <= fixedRight)
+              || (startres <= fixedRight && lastres > fixedRight))
       {
         endEditing();
         return;
@@ -1021,15 +1049,15 @@ public class SeqPanel
       int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
       int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
 
-      if ( (insertGap && startres > y1 && lastres < y1)
-          || (!insertGap && startres < y2 && lastres > y2))
+      if ((insertGap && startres > y1 && lastres < y1)
+              || (!insertGap && startres < y2 && lastres > y2))
       {
         endEditing();
         return;
       }
 
-      //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
-      //Selection spans a hidden region
+      // System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
+      // Selection spans a hidden region
       if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
       {
         if (startres >= y2)
@@ -1056,12 +1084,10 @@ public class SeqPanel
       // drag to right
       if (insertGap)
       {
-        //If the user has selected the whole sequence, and is dragging to
+        // If the user has selected the whole sequence, and is dragging to
         // the right, we can still extend the alignment and selectionGroup
-        if (sg.getStartRes() == 0
-            && sg.getEndRes() == fixedRight
-            && sg.getEndRes() == av.alignment.getWidth() - 1
-            )
+        if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
+                && sg.getEndRes() == av.alignment.getWidth() - 1)
         {
           sg.setEndRes(av.alignment.getWidth() + startres - lastres);
           fixedRight = sg.getEndRes();
@@ -1071,9 +1097,7 @@ public class SeqPanel
         // Find the next gap before the end
         // of the visible region boundary
         boolean blank = false;
-        for (fixedRight = fixedRight;
-             fixedRight > lastres;
-             fixedRight--)
+        for (fixedRight = fixedRight; fixedRight > lastres; fixedRight--)
         {
           blank = true;
 
@@ -1081,8 +1105,8 @@ public class SeqPanel
           {
             for (int j = 0; j < startres - lastres; j++)
             {
-              if (!jalview.util.Comparison.isGap(
-                  groupSeqs[g].getCharAt(fixedRight - j)))
+              if (!jalview.util.Comparison.isGap(groupSeqs[g]
+                      .getCharAt(fixedRight - j)))
               {
                 blank = false;
                 break;
@@ -1099,9 +1123,8 @@ public class SeqPanel
         {
           if (sg.getSize() == av.alignment.getHeight())
           {
-            if ( (av.hasHiddenColumns
-                  &&
-                  startres < av.getColumnSelection().getHiddenBoundaryRight(startres)))
+            if ((av.hasHiddenColumns && startres < av.getColumnSelection()
+                    .getHiddenBoundaryRight(startres)))
             {
               endEditing();
               return;
@@ -1116,8 +1139,8 @@ public class SeqPanel
                 alWidth = hwidth;
               }
             }
-            //We can still insert gaps if the selectionGroup
-            //contains all the sequences
+            // We can still insert gaps if the selectionGroup
+            // contains all the sequences
             sg.setEndRes(sg.getEndRes() + startres - lastres);
             fixedRight = alWidth + startres - lastres;
           }
@@ -1132,7 +1155,7 @@ public class SeqPanel
       // drag to left
       else if (!insertGap)
       {
-        /// Are we able to delete?
+        // / Are we able to delete?
         // ie are all columns blank?
 
         for (g = 0; g < groupSize; g++)
@@ -1144,8 +1167,7 @@ public class SeqPanel
               continue;
             }
 
-            if (!jalview.util.Comparison.isGap(
-                groupSeqs[g].getCharAt(j)))
+            if (!jalview.util.Comparison.isGap(groupSeqs[g].getCharAt(j)))
             {
               // Not a gap, block edit not valid
               endEditing();
@@ -1167,11 +1189,8 @@ public class SeqPanel
         }
         else
         {
-          editCommand.appendEdit(EditCommand.INSERT_GAP,
-                                 groupSeqs,
-                                 startres, startres - lastres,
-                                 av.alignment,
-                                 true);
+          editCommand.appendEdit(EditCommand.INSERT_GAP, groupSeqs,
+                  startres, startres - lastres, av.alignment, true);
         }
       }
       else
@@ -1186,16 +1205,14 @@ public class SeqPanel
         }
         else
         {
-          editCommand.appendEdit(EditCommand.DELETE_GAP,
-                                 groupSeqs,
-                                 startres, lastres - startres,
-                                 av.alignment,
-                                 true);
+          editCommand.appendEdit(EditCommand.DELETE_GAP, groupSeqs,
+                  startres, lastres - startres, av.alignment, true);
         }
 
       }
     }
-    else /////Editing a single sequence///////////
+    else
+    // ///Editing a single sequence///////////
     {
       if (insertGap)
       {
@@ -1205,17 +1222,13 @@ public class SeqPanel
           for (int j = lastres; j < startres; j++)
           {
             insertChar(j, new SequenceI[]
-                       {seq}, fixedRight);
+            { seq }, fixedRight);
           }
         }
         else
         {
-          editCommand.appendEdit(EditCommand.INSERT_GAP,
-                                 new SequenceI[]
-                                 {seq},
-                                 lastres, startres - lastres,
-                                 av.alignment,
-                                 true);
+          editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[]
+          { seq }, lastres, startres - lastres, av.alignment, true);
         }
       }
       else
@@ -1231,12 +1244,12 @@ public class SeqPanel
               break;
             }
             deleteChar(startres, new SequenceI[]
-                       {seq}, fixedRight);
+            { seq }, fixedRight);
           }
         }
         else
         {
-          //could be a keyboard edit trying to delete none gaps
+          // could be a keyboard edit trying to delete none gaps
           int max = 0;
           for (int m = startres; m < lastres; m++)
           {
@@ -1249,12 +1262,8 @@ public class SeqPanel
 
           if (max > 0)
           {
-            editCommand.appendEdit(EditCommand.DELETE_GAP,
-                                   new SequenceI[]
-                                   {seq},
-                                   startres, max,
-                                   av.alignment,
-                                   true);
+            editCommand.appendEdit(EditCommand.DELETE_GAP, new SequenceI[]
+            { seq }, startres, max, av.alignment, true);
           }
         }
       }
@@ -1269,14 +1278,14 @@ public class SeqPanel
     int blankColumn = fixedColumn;
     for (int s = 0; s < seq.length; s++)
     {
-      //Find the next gap before the end of the visible region boundary
-      //If lastCol > j, theres a boundary after the gap insertion
+      // Find the next gap before the end of the visible region boundary
+      // If lastCol > j, theres a boundary after the gap insertion
 
       for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
       {
         if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
         {
-          //Theres a space, so break and insert the gap
+          // Theres a space, so break and insert the gap
           break;
         }
       }
@@ -1289,33 +1298,29 @@ public class SeqPanel
       }
     }
 
-    editCommand.appendEdit(EditCommand.DELETE_GAP,
-                           seq,
-                           blankColumn, 1, av.alignment, true);
+    editCommand.appendEdit(EditCommand.DELETE_GAP, seq, blankColumn, 1,
+            av.alignment, true);
 
-    editCommand.appendEdit(EditCommand.INSERT_GAP,
-                           seq,
-                           j, 1, av.alignment,
-                           true);
+    editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1, av.alignment,
+            true);
 
   }
 
   void deleteChar(int j, SequenceI[] seq, int fixedColumn)
   {
 
-    editCommand.appendEdit(EditCommand.DELETE_GAP,
-                           seq,
-                           j, 1, av.alignment, true);
+    editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1, av.alignment,
+            true);
 
-    editCommand.appendEdit(EditCommand.INSERT_GAP,
-                           seq,
-                           fixedColumn, 1, av.alignment, true);
+    editCommand.appendEdit(EditCommand.INSERT_GAP, seq, fixedColumn, 1,
+            av.alignment, true);
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void mouseEntered(MouseEvent e)
   {
@@ -1333,8 +1338,9 @@ public class SeqPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void mouseExited(MouseEvent e)
   {
@@ -1355,30 +1361,26 @@ public class SeqPanel
     if (evt.getClickCount() > 1)
     {
       if (av.getSelectionGroup().getSize() == 1
-          && av.getSelectionGroup().getEndRes()
-          - av.getSelectionGroup().getStartRes() < 2)
+              && av.getSelectionGroup().getEndRes()
+                      - av.getSelectionGroup().getStartRes() < 2)
       {
         av.setSelectionGroup(null);
       }
 
-      SequenceFeature[] features = findFeaturesAtRes(
-          sequence.getDatasetSequence(),
-          sequence.findPosition(findRes(evt))
-          );
+      SequenceFeature[] features = findFeaturesAtRes(sequence
+              .getDatasetSequence(), sequence.findPosition(findRes(evt)));
 
       if (features != null && features.length > 0)
       {
         SearchResults highlight = new SearchResults();
-        highlight.addResult(sequence,
-                            features[0].getBegin(),
-                            features[0].getEnd());
+        highlight.addResult(sequence, features[0].getBegin(), features[0]
+                .getEnd());
         seqCanvas.highlightSearchResults(highlight);
       }
       if (features != null && features.length > 0)
       {
-        seqCanvas.getFeatureRenderer().amendFeatures(
-            new SequenceI[]
-            {sequence}, features, false, ap);
+        seqCanvas.getFeatureRenderer().amendFeatures(new SequenceI[]
+        { sequence }, features, false, ap);
 
         seqCanvas.highlightSearchResults(null);
       }
@@ -1388,20 +1390,21 @@ public class SeqPanel
   public void mouseWheelMoved(MouseWheelEvent e)
   {
     e.consume();
-      if (e.getWheelRotation() > 0)
-      {
-        ap.scrollUp(false);
-      }
-      else
-      {
-        ap.scrollUp(true);
-      }
+    if (e.getWheelRotation() > 0)
+    {
+      ap.scrollUp(false);
+    }
+    else
+    {
+      ap.scrollUp(true);
+    }
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
    */
   public void doMousePressedDefineMode(MouseEvent evt)
   {
@@ -1414,9 +1417,8 @@ public class SeqPanel
     if (av.wrapAlignment && seq > av.alignment.getHeight())
     {
       JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                            "Cannot edit annotations in wrapped view.",
-                                            "Wrapped view - no edit",
-                                            JOptionPane.WARNING_MESSAGE);
+              "Cannot edit annotations in wrapped view.",
+              "Wrapped view - no edit", JOptionPane.WARNING_MESSAGE);
       return;
     }
 
@@ -1427,7 +1429,7 @@ public class SeqPanel
 
     SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
 
-    if ( (sequence == null) || (res > sequence.getLength()))
+    if ((sequence == null) || (res > sequence.getLength()))
     {
       return;
     }
@@ -1438,8 +1440,8 @@ public class SeqPanel
     {
       stretchGroup = av.alignment.findGroup(sequence);
 
-      if ( (stretchGroup != null) && (res > stretchGroup.getStartRes()) &&
-          (res < stretchGroup.getEndRes()))
+      if ((stretchGroup != null) && (res > stretchGroup.getStartRes())
+              && (res < stretchGroup.getEndRes()))
       {
         av.setSelectionGroup(stretchGroup);
       }
@@ -1448,9 +1450,9 @@ public class SeqPanel
         stretchGroup = null;
       }
     }
-    else if (!stretchGroup.getSequences(null).contains(sequence) ||
-             (stretchGroup.getStartRes() > res) ||
-             (stretchGroup.getEndRes() < res))
+    else if (!stretchGroup.getSequences(null).contains(sequence)
+            || (stretchGroup.getStartRes() > res)
+            || (stretchGroup.getEndRes() < res))
     {
       stretchGroup = null;
 
@@ -1460,8 +1462,8 @@ public class SeqPanel
       {
         for (int i = 0; i < allGroups.length; i++)
         {
-          if ( (allGroups[i].getStartRes() <= res) &&
-              (allGroups[i].getEndRes() >= res))
+          if ((allGroups[i].getStartRes() <= res)
+                  && (allGroups[i].getEndRes() >= res))
           {
             stretchGroup = allGroups[i];
             break;
@@ -1475,8 +1477,8 @@ public class SeqPanel
 
     if (javax.swing.SwingUtilities.isRightMouseButton(evt))
     {
-      SequenceFeature [] allFeatures = findFeaturesAtRes(sequence.getDatasetSequence(),
-                                               sequence.findPosition(res));
+      SequenceFeature[] allFeatures = findFeaturesAtRes(sequence
+              .getDatasetSequence(), sequence.findPosition(res));
       Vector links = new Vector();
       for (int i = 0; i < allFeatures.length; i++)
       {
@@ -1504,7 +1506,7 @@ public class SeqPanel
 
     if (stretchGroup == null)
     {
-      //Only if left mouse button do we want to change group sizes
+      // Only if left mouse button do we want to change group sizes
 
       // define a new group here
       SequenceGroup sg = new SequenceGroup();
@@ -1516,23 +1518,22 @@ public class SeqPanel
 
       if (av.getConservationSelected())
       {
-        SliderPanel.setConservationSlider(ap,
-                                          av.getGlobalColourScheme(),
-                                          "Background");
+        SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
+                "Background");
       }
 
       if (av.getAbovePIDThreshold())
       {
         SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
-                                       "Background");
+                "Background");
       }
-      if ( (stretchGroup != null) && (stretchGroup.getEndRes() == res))
+      if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
       {
         // Edit end res position of selected group
         changeEndRes = true;
       }
-      else if ( (stretchGroup != null) &&
-               (stretchGroup.getStartRes() == res))
+      else if ((stretchGroup != null)
+              && (stretchGroup.getStartRes() == res))
       {
         // Edit end res position of selected group
         changeStartRes = true;
@@ -1545,8 +1546,9 @@ public class SeqPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
    */
   public void doMouseReleasedDefineMode(MouseEvent evt)
   {
@@ -1559,28 +1561,28 @@ public class SeqPanel
     {
       if (stretchGroup.cs instanceof ClustalxColourScheme)
       {
-        ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(
-            stretchGroup.getSequences(av.hiddenRepSequences),
-            stretchGroup.getWidth());
+        ((ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup
+                .getSequences(av.hiddenRepSequences), stretchGroup
+                .getWidth());
       }
 
       if (stretchGroup.cs instanceof Blosum62ColourScheme
-          || stretchGroup.cs instanceof PIDColourScheme
-          || stretchGroup.cs.conservationApplied()
-          || stretchGroup.cs.getThreshold() > 0)
+              || stretchGroup.cs instanceof PIDColourScheme
+              || stretchGroup.cs.conservationApplied()
+              || stretchGroup.cs.getThreshold() > 0)
       {
         stretchGroup.recalcConservation();
       }
 
       if (stretchGroup.cs.conservationApplied())
       {
-        SliderPanel.setConservationSlider(ap, stretchGroup.cs,
-                                          stretchGroup.getName());
+        SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup
+                .getName());
       }
       else
       {
-        SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
-                                       stretchGroup.getName());
+        SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup
+                .getName());
       }
       PaintRefresher.Refresh(this, av.getSequenceSetId());
       ap.paintAlignment(true);
@@ -1594,8 +1596,9 @@ public class SeqPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
    */
   public void doMouseDraggedDefineMode(MouseEvent evt)
   {
@@ -1659,7 +1662,7 @@ public class SeqPanel
       dragDirection = -1;
     }
 
-    while ( (y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
+    while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
     {
       // This routine ensures we don't skip any sequences, as the
       // selection is quite slow.
@@ -1729,10 +1732,10 @@ public class SeqPanel
   }
 
   // this class allows scrolling off the bottom of the visible alignment
-  class ScrollThread
-      extends Thread
+  class ScrollThread extends Thread
   {
     MouseEvent evt;
+
     boolean running = false;
 
     public ScrollThread()
@@ -1758,14 +1761,13 @@ public class SeqPanel
       {
         if (evt != null)
         {
-          if (mouseDragging && (evt.getY() < 0) &&
-              (av.getStartSeq() > 0))
+          if (mouseDragging && (evt.getY() < 0) && (av.getStartSeq() > 0))
           {
             running = ap.scrollUp(true);
           }
 
-          if (mouseDragging && (evt.getY() >= getHeight()) &&
-              (av.alignment.getHeight() > av.getEndSeq()))
+          if (mouseDragging && (evt.getY() >= getHeight())
+                  && (av.alignment.getHeight() > av.getEndSeq()))
           {
             running = ap.scrollUp(false);
           }
@@ -1783,8 +1785,7 @@ public class SeqPanel
         try
         {
           Thread.sleep(20);
-        }
-        catch (Exception ex)
+        } catch (Exception ex)
         {
         }
       }
diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index f594554..ccd0f72 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -58,37 +58,42 @@ public class SequenceFetcher extends JPanel implements Runnable
   private static jalview.ws.SequenceFetcher sfetch = null;
 
   private static String dasRegistry = null;
+
   /**
-   * Blocking method that initialises and returns the shared instance of the SequenceFetcher client 
-   * @param guiWindow - where the initialisation delay message should be shown
+   * Blocking method that initialises and returns the shared instance of the
+   * SequenceFetcher client
+   * 
+   * @param guiWindow -
+   *                where the initialisation delay message should be shown
    * @return the singleton instance of the sequence fetcher client
    */
-  public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton(final IProgressIndicator guiWindow) {
+  public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton(
+          final IProgressIndicator guiWindow)
+  {
     if (sfetch == null
             || dasRegistry != DasSourceBrowser.getDasRegistryURL())
     {
       /**
-       * give a visual indication that sequence fetcher construction is
-       * occuring
+       * give a visual indication that sequence fetcher construction is occuring
        */
       if (guiWindow != null)
       {
-        guiWindow.setProgressBar(
-                "Initialising Sequence Database Fetchers", Thread.currentThread()
-                        .hashCode());
+        guiWindow.setProgressBar("Initialising Sequence Database Fetchers",
+                Thread.currentThread().hashCode());
       }
       dasRegistry = DasSourceBrowser.getDasRegistryURL();
       jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
       if (guiWindow != null)
       {
-        guiWindow.setProgressBar(
-                "Initialising Sequence Database Fetchers", Thread.currentThread().hashCode());
+        guiWindow.setProgressBar("Initialising Sequence Database Fetchers",
+                Thread.currentThread().hashCode());
       }
       sfetch = sf;
 
     }
     return sfetch;
   }
+
   public SequenceFetcher(IProgressIndicator guiIndic)
   {
     final IProgressIndicator guiWindow = guiIndic;
@@ -99,20 +104,25 @@ public class SequenceFetcher extends JPanel implements Runnable
 
       public void run()
       {
-        if (getSequenceFetcherSingleton(guiWindow)!=null)
+        if (getSequenceFetcherSingleton(guiWindow) != null)
         {
           us.initGui(guiWindow);
-        } else {
+        }
+        else
+        {
           javax.swing.SwingUtilities.invokeLater(new Runnable()
           {
             public void run()
             {
-              JOptionPane.showInternalMessageDialog(Desktop.desktop, 
-                      "Could not create the sequence fetcher client. Check error logs for details.",
-                      "Couldn't create SequenceFetcher", JOptionPane.ERROR_MESSAGE);
+              JOptionPane
+                      .showInternalMessageDialog(
+                              Desktop.desktop,
+                              "Could not create the sequence fetcher client. Check error logs for details.",
+                              "Couldn't create SequenceFetcher",
+                              JOptionPane.ERROR_MESSAGE);
             }
           });
-          
+
           // raise warning dialog
         }
       }
@@ -395,6 +405,7 @@ public class SequenceFetcher extends JPanel implements Runnable
       e.printStackTrace();
     } catch (OutOfMemoryError e)
     {
+      // resets dialog box - so we don't use OOMwarning here.
       showErrorMessage("Out of Memory when retrieving "
               + textArea.getText()
               + " from "
@@ -407,11 +418,12 @@ public class SequenceFetcher extends JPanel implements Runnable
               + " from " + database.getSelectedItem());
       e.printStackTrace();
     }
-    guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
     if (aresult != null)
     {
       parseResult(aresult, null, null);
     }
+    // only remove visual delay after we finished parsing.
+    guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
     resetDialog();
   }
 
@@ -443,11 +455,10 @@ public class SequenceFetcher extends JPanel implements Runnable
    * for (;si<seqs.length; si++) { newseqs[si] = seqs[si]; seqs[si] = null; } }
    * for (int j=0;j<seqparts.length; si++, j++) { newseqs[si] =
    * seqparts[j].deriveSequence(); // place DBReferences on dataset and refer }
-   * seqs=newseqs;
-   *  } } } else { result.append("# no response for "+qry); } } if (seqs!=null &&
-   * seqs.length>0) { if (parseResult(new Alignment(seqs), null, null)!=null) {
-   * result.append("# Successfully parsed the "+database.getSelectedItem()+"
-   * Queries into an Alignment"); } } } else if
+   * seqs=newseqs; } } } else { result.append("# no response for "+qry); } } if
+   * (seqs!=null && seqs.length>0) { if (parseResult(new Alignment(seqs), null,
+   * null)!=null) { result.append("# Successfully parsed the
+   * "+database.getSelectedItem()+" Queries into an Alignment"); } } } else if
    * (database.getSelectedItem().equals("PDB")) { StringTokenizer qset = new
    * StringTokenizer(textArea.getText(), ";"); String query; SequenceI[] seqs =
    * null; while (qset.hasMoreTokens() && ((query = qset.nextToken())!=null)) {
@@ -465,8 +476,8 @@ public class SequenceFetcher extends JPanel implements Runnable
    * textArea.getText().toUpperCase(), "URL").print() );
    * 
    * if(result.length()>0) { parseResult( result.toString(),
-   * textArea.getText().toUpperCase() ); }
-   *  } catch (java.io.IOException ex) { result = null; } }
+   * textArea.getText().toUpperCase() ); } } catch (java.io.IOException ex) {
+   * result = null; } }
    * 
    * if (result == null || result.length() == 0) { showErrorMessage("Error
    * retrieving " + textArea.getText() + " from " + database.getSelectedItem()); }
@@ -493,8 +504,7 @@ public class SequenceFetcher extends JPanel implements Runnable
    * entry.getProtein().getName().elementAt(0)); }
    * 
    * result.append(name + "\n" + entry.getUniprotSequence().getContent() +
-   * "\n");
-   *  }
+   * "\n"); }
    * 
    * //Then read in the features and apply them to the dataset Alignment al =
    * parseResult(result.toString(), null); for (int i = 0; i < entries.size();
@@ -538,10 +548,10 @@ public class SequenceFetcher extends JPanel implements Runnable
    * Construct the PDBEntry entry.setId(id); if (entry.getProperty() == null)
    * entry.setProperty(new Hashtable()); entry.getProperty().put("chains",
    * pdbchain.id + "=" + sq.getStart() + "-" + sq.getEnd());
-   * sq.getDatasetSequence().addPDBId(entry);
-   *  // Add PDB DB Refs // We make a DBRefEtntry because we have obtained the
-   * PDB file from a verifiable source // JBPNote - PDB DBRefEntry should also
-   * carry the chain and mapping information DBRefEntry dbentry = new
+   * sq.getDatasetSequence().addPDBId(entry); // Add PDB DB Refs // We make a
+   * DBRefEtntry because we have obtained the PDB file from a verifiable source //
+   * JBPNote - PDB DBRefEntry should also carry the chain and mapping
+   * information DBRefEntry dbentry = new
    * DBRefEntry(jalview.datamodel.DBRefSource.PDB, "0", id + pdbchain.id);
    * sq.addDBRef(dbentry); // and add seuqence to the retrieved set
    * result.addElement(sq.deriveSequence()); } }
@@ -599,9 +609,9 @@ public class SequenceFetcher extends JPanel implements Runnable
         if (currentFileFormat != null)
         {
           af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT
-                                                    // FORMAT FOR
-                                                    // NON-FormatAdapter Sourced
-                                                    // Alignments?
+          // FORMAT FOR
+          // NON-FormatAdapter Sourced
+          // Alignments?
         }
 
         if (title == null)
@@ -627,11 +637,11 @@ public class SequenceFetcher extends JPanel implements Runnable
         for (int i = 0; i < al.getHeight(); i++)
         {
           alignFrame.viewport.alignment.addSequence(al.getSequenceAt(i)); // this
-                                                                          // also
-                                                                          // creates
-                                                                          // dataset
-                                                                          // sequence
-                                                                          // entries
+          // also
+          // creates
+          // dataset
+          // sequence
+          // entries
         }
         alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment
                 .getHeight());
diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 70f67d7..a3dd5a6 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -1,434 +1,472 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.gui;
-
-import java.awt.*;
-
-import jalview.datamodel.*;
-import jalview.schemes.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class SequenceRenderer
-{
-  AlignViewport av;
-  FontMetrics fm;
-  boolean renderGaps = true;
-  SequenceGroup currentSequenceGroup = null;
-  SequenceGroup[] allGroups = null;
-  Color resBoxColour;
-  Graphics graphics;
-  boolean monospacedFont;
-  boolean forOverview = false;
-
-  /**
-   * Creates a new SequenceRenderer object.
-   *
-   * @param av DOCUMENT ME!
-   */
-  public SequenceRenderer(AlignViewport av)
-  {
-    this.av = av;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param b DOCUMENT ME!
-   */
-  public void prepare(Graphics g, boolean renderGaps)
-  {
-    graphics = g;
-    fm = g.getFontMetrics();
-
-    // If EPS graphics, stringWidth will be a double, not an int
-    double dwidth = fm.getStringBounds("M", g).getWidth();
-
-    monospacedFont =
-        (dwidth == fm.getStringBounds("|", g).getWidth()
-         && (float) av.charWidth == dwidth);
-
-    this.renderGaps = renderGaps;
-  }
-
-  public Color getResidueBoxColour(SequenceI seq, int i)
-  {
-    allGroups = av.alignment.findAllGroups(seq);
-
-    if (inCurrentSequenceGroup(i))
-    {
-      if (currentSequenceGroup.getDisplayBoxes())
-      {
-        getBoxColour(currentSequenceGroup.cs, seq, i);
-      }
-    }
-    else if (av.getShowBoxes())
-    {
-      getBoxColour(av.globalColourScheme, seq, i);
-    }
-
-    return resBoxColour;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param cs DOCUMENT ME!
-   * @param seq DOCUMENT ME!
-   * @param i DOCUMENT ME!
-   */
-  void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
-  {
-    if (cs != null)
-    {
-      resBoxColour = cs.findColour(seq.getCharAt(i), i);
-    }
-    else if (forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
-    {
-      resBoxColour = Color.lightGray;
-    }
-    else
-    {
-      resBoxColour = Color.white;
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param g DOCUMENT ME!
-   * @param seq DOCUMENT ME!
-   * @param sg DOCUMENT ME!
-   * @param start DOCUMENT ME!
-   * @param end DOCUMENT ME!
-   * @param x1 DOCUMENT ME!
-   * @param y1 DOCUMENT ME!
-   * @param width DOCUMENT ME!
-   * @param height DOCUMENT ME!
-   */
-  public void drawSequence(SequenceI seq, SequenceGroup[] sg,
-                           int start, int end, int y1)
-  {
-    allGroups = sg;
-
-    drawBoxes(seq, start, end, y1);
-
-    if (av.validCharWidth)
-    {
-      drawText(seq, start, end, y1);
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param seq DOCUMENT ME!
-   * @param start DOCUMENT ME!
-   * @param end DOCUMENT ME!
-   * @param x1 DOCUMENT ME!
-   * @param y1 DOCUMENT ME!
-   * @param width DOCUMENT ME!
-   * @param height DOCUMENT ME!
-   */
-  public synchronized void drawBoxes(SequenceI seq, int start, int end, int y1)
-  {
-    int i = start;
-    int length = seq.getLength();
-
-    int curStart = -1;
-    int curWidth = av.charWidth;
-
-    Color tempColour = null;
-
-    while (i <= end)
-    {
-      resBoxColour = Color.white;
-
-      if (i < length)
-      {
-        if (inCurrentSequenceGroup(i))
-        {
-          if (currentSequenceGroup.getDisplayBoxes())
-          {
-            getBoxColour(currentSequenceGroup.cs, seq, i);
-          }
-        }
-        else if (av.getShowBoxes())
-        {
-          getBoxColour(av.globalColourScheme, seq, i);
-        }
-
-      }
-
-      if (resBoxColour != tempColour)
-      {
-        if (tempColour != null)
-        {
-          graphics.fillRect(av.charWidth * (curStart - start), y1,
-                            curWidth, av.charHeight);
-        }
-
-        graphics.setColor(resBoxColour);
-
-        curStart = i;
-        curWidth = av.charWidth;
-        tempColour = resBoxColour;
-      }
-      else
-      {
-        curWidth += av.charWidth;
-      }
-
-      i++;
-    }
-
-    graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,
-                      av.charHeight);
-
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param seq DOCUMENT ME!
-   * @param start DOCUMENT ME!
-   * @param end DOCUMENT ME!
-   * @param x1 DOCUMENT ME!
-   * @param y1 DOCUMENT ME!
-   * @param width DOCUMENT ME!
-   * @param height DOCUMENT ME!
-   */
-  public void drawText(SequenceI seq, int start, int end, int y1)
-  {
-    y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady
-    int charOffset = 0;
-    char s;
-
-    if (end + 1 >= seq.getLength())
-    {
-      end = seq.getLength() - 1;
-    }
-    graphics.setColor(av.textColour);
-
-    if (monospacedFont
-        && av.showText
-        && allGroups.length == 0
-        && !av.getColourText()
-        && av.thresholdTextColour == 0)
-    {
-      if (av.renderGaps)
-      {
-        graphics.drawString(seq.getSequenceAsString(start, end + 1), 0, y1);
-      }
-      else
-      {
-        char gap = av.getGapCharacter();
-        graphics.drawString(seq.getSequenceAsString(start, end + 1).replace(gap,
-            ' '), 0, y1);
-      }
-    }
-    else
-    {
-      boolean getboxColour = false;
-      for (int i = start; i <= end; i++)
-      {
-        graphics.setColor(av.textColour);
-        getboxColour = false;
-        s = seq.getCharAt(i);
-        if (!renderGaps && jalview.util.Comparison.isGap(s))
-        {
-          continue;
-        }
-
-        if (inCurrentSequenceGroup(i))
-        {
-          if (!currentSequenceGroup.getDisplayText())
-          {
-            continue;
-          }
-
-          if (currentSequenceGroup.thresholdTextColour > 0
-              || currentSequenceGroup.getColourText())
-          {
-            getboxColour = true;
-            getBoxColour(currentSequenceGroup.cs, seq, i);
-
-            if (currentSequenceGroup.getColourText())
-            {
-              graphics.setColor(resBoxColour.darker());
-            }
-
-            if (currentSequenceGroup.thresholdTextColour > 0)
-            {
-              if (resBoxColour.getRed() +
-                  resBoxColour.getBlue() +
-                  resBoxColour.getGreen() <
-                  currentSequenceGroup.thresholdTextColour)
-              {
-                graphics.setColor(currentSequenceGroup.textColour2);
-              }
-            }
-          }
-          else
-          {
-            graphics.setColor(currentSequenceGroup.textColour);
-          }
-
-        }
-        else
-        {
-          if (!av.getShowText())
-          {
-            continue;
-          }
-
-          if (av.getColourText())
-          {
-            getboxColour = true;
-            getBoxColour(av.globalColourScheme, seq, i);
-
-            if (av.getShowBoxes())
-            {
-              graphics.setColor(resBoxColour.darker());
-            }
-            else
-            {
-              graphics.setColor(resBoxColour);
-            }
-          }
-
-          if (av.thresholdTextColour > 0)
-          {
-            if (!getboxColour)
-            {
-              getBoxColour(av.globalColourScheme, seq, i);
-            }
-
-            if (resBoxColour.getRed() +
-                resBoxColour.getBlue() +
-                resBoxColour.getGreen() < av.thresholdTextColour)
-            {
-              graphics.setColor(av.textColour2);
-            }
-          }
-
-        }
-
-        charOffset = (av.charWidth - fm.charWidth(s)) / 2;
-        graphics.drawString(String.valueOf(s),
-                            charOffset + av.charWidth * (i - start),
-                            y1);
-
-      }
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param res DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  boolean inCurrentSequenceGroup(int res)
-  {
-    if (allGroups == null)
-    {
-      return false;
-    }
-
-    for (int i = 0; i < allGroups.length; i++)
-    {
-      if ( (allGroups[i].getStartRes() <= res) &&
-          (allGroups[i].getEndRes() >= res))
-      {
-        currentSequenceGroup = allGroups[i];
-
-        return true;
-      }
-    }
-
-    return false;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param seq DOCUMENT ME!
-   * @param start DOCUMENT ME!
-   * @param end DOCUMENT ME!
-   * @param x1 DOCUMENT ME!
-   * @param y1 DOCUMENT ME!
-   * @param width DOCUMENT ME!
-   * @param height DOCUMENT ME!
-   */
-  public void drawHighlightedText(SequenceI seq, int start, int end, int x1,
-                                  int y1)
-  {
-    int pady = av.charHeight / 5;
-    int charOffset = 0;
-    graphics.setColor(Color.BLACK);
-    graphics.fillRect(x1, y1, av.charWidth * (end - start + 1), av.charHeight);
-    graphics.setColor(Color.white);
-
-    char s = '~';
-
-    // Need to find the sequence position here.
-    if (av.validCharWidth)
-    {
-      for (int i = start; i <= end; i++)
-      {
-        if (i < seq.getLength())
-        {
-          s = seq.getCharAt(i);
-        }
-
-        charOffset = (av.charWidth - fm.charWidth(s)) / 2;
-        graphics.drawString(String.valueOf(s),
-                            charOffset + x1 + (av.charWidth * (i - start)),
-                            (y1 + av.charHeight) - pady);
-      }
-    }
-  }
-
-  public void drawCursor(SequenceI seq, int res, int x1, int y1)
-  {
-    int pady = av.charHeight / 5;
-    int charOffset = 0;
-    graphics.setColor(Color.black);
-    graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
-
-    if (av.validCharWidth)
-    {
-      graphics.setColor(Color.white);
-
-      char s = seq.getCharAt(res);
-
-      charOffset = (av.charWidth - fm.charWidth(s)) / 2;
-      graphics.drawString(String.valueOf(s),
-                          charOffset + x1,
-                          (y1 + av.charHeight) - pady);
-    }
-
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.gui;
+
+import java.awt.*;
+
+import jalview.datamodel.*;
+import jalview.schemes.*;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class SequenceRenderer
+{
+  AlignViewport av;
+
+  FontMetrics fm;
+
+  boolean renderGaps = true;
+
+  SequenceGroup currentSequenceGroup = null;
+
+  SequenceGroup[] allGroups = null;
+
+  Color resBoxColour;
+
+  Graphics graphics;
+
+  boolean monospacedFont;
+
+  boolean forOverview = false;
+
+  /**
+   * Creates a new SequenceRenderer object.
+   * 
+   * @param av
+   *                DOCUMENT ME!
+   */
+  public SequenceRenderer(AlignViewport av)
+  {
+    this.av = av;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param b
+   *                DOCUMENT ME!
+   */
+  public void prepare(Graphics g, boolean renderGaps)
+  {
+    graphics = g;
+    fm = g.getFontMetrics();
+
+    // If EPS graphics, stringWidth will be a double, not an int
+    double dwidth = fm.getStringBounds("M", g).getWidth();
+
+    monospacedFont = (dwidth == fm.getStringBounds("|", g).getWidth() && (float) av.charWidth == dwidth);
+
+    this.renderGaps = renderGaps;
+  }
+
+  public Color getResidueBoxColour(SequenceI seq, int i)
+  {
+    allGroups = av.alignment.findAllGroups(seq);
+
+    if (inCurrentSequenceGroup(i))
+    {
+      if (currentSequenceGroup.getDisplayBoxes())
+      {
+        getBoxColour(currentSequenceGroup.cs, seq, i);
+      }
+    }
+    else if (av.getShowBoxes())
+    {
+      getBoxColour(av.globalColourScheme, seq, i);
+    }
+
+    return resBoxColour;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param cs
+   *                DOCUMENT ME!
+   * @param seq
+   *                DOCUMENT ME!
+   * @param i
+   *                DOCUMENT ME!
+   */
+  void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
+  {
+    if (cs != null)
+    {
+      resBoxColour = cs.findColour(seq.getCharAt(i), i);
+    }
+    else if (forOverview
+            && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
+    {
+      resBoxColour = Color.lightGray;
+    }
+    else
+    {
+      resBoxColour = Color.white;
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param g
+   *                DOCUMENT ME!
+   * @param seq
+   *                DOCUMENT ME!
+   * @param sg
+   *                DOCUMENT ME!
+   * @param start
+   *                DOCUMENT ME!
+   * @param end
+   *                DOCUMENT ME!
+   * @param x1
+   *                DOCUMENT ME!
+   * @param y1
+   *                DOCUMENT ME!
+   * @param width
+   *                DOCUMENT ME!
+   * @param height
+   *                DOCUMENT ME!
+   */
+  public void drawSequence(SequenceI seq, SequenceGroup[] sg, int start,
+          int end, int y1)
+  {
+    allGroups = sg;
+
+    drawBoxes(seq, start, end, y1);
+
+    if (av.validCharWidth)
+    {
+      drawText(seq, start, end, y1);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param seq
+   *                DOCUMENT ME!
+   * @param start
+   *                DOCUMENT ME!
+   * @param end
+   *                DOCUMENT ME!
+   * @param x1
+   *                DOCUMENT ME!
+   * @param y1
+   *                DOCUMENT ME!
+   * @param width
+   *                DOCUMENT ME!
+   * @param height
+   *                DOCUMENT ME!
+   */
+  public synchronized void drawBoxes(SequenceI seq, int start, int end,
+          int y1)
+  {
+    int i = start;
+    int length = seq.getLength();
+
+    int curStart = -1;
+    int curWidth = av.charWidth;
+
+    Color tempColour = null;
+
+    while (i <= end)
+    {
+      resBoxColour = Color.white;
+
+      if (i < length)
+      {
+        if (inCurrentSequenceGroup(i))
+        {
+          if (currentSequenceGroup.getDisplayBoxes())
+          {
+            getBoxColour(currentSequenceGroup.cs, seq, i);
+          }
+        }
+        else if (av.getShowBoxes())
+        {
+          getBoxColour(av.globalColourScheme, seq, i);
+        }
+
+      }
+
+      if (resBoxColour != tempColour)
+      {
+        if (tempColour != null)
+        {
+          graphics.fillRect(av.charWidth * (curStart - start), y1,
+                  curWidth, av.charHeight);
+        }
+
+        graphics.setColor(resBoxColour);
+
+        curStart = i;
+        curWidth = av.charWidth;
+        tempColour = resBoxColour;
+      }
+      else
+      {
+        curWidth += av.charWidth;
+      }
+
+      i++;
+    }
+
+    graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,
+            av.charHeight);
+
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param seq
+   *                DOCUMENT ME!
+   * @param start
+   *                DOCUMENT ME!
+   * @param end
+   *                DOCUMENT ME!
+   * @param x1
+   *                DOCUMENT ME!
+   * @param y1
+   *                DOCUMENT ME!
+   * @param width
+   *                DOCUMENT ME!
+   * @param height
+   *                DOCUMENT ME!
+   */
+  public void drawText(SequenceI seq, int start, int end, int y1)
+  {
+    y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady
+    int charOffset = 0;
+    char s;
+
+    if (end + 1 >= seq.getLength())
+    {
+      end = seq.getLength() - 1;
+    }
+    graphics.setColor(av.textColour);
+
+    if (monospacedFont && av.showText && allGroups.length == 0
+            && !av.getColourText() && av.thresholdTextColour == 0)
+    {
+      if (av.renderGaps)
+      {
+        graphics.drawString(seq.getSequenceAsString(start, end + 1), 0, y1);
+      }
+      else
+      {
+        char gap = av.getGapCharacter();
+        graphics.drawString(seq.getSequenceAsString(start, end + 1)
+                .replace(gap, ' '), 0, y1);
+      }
+    }
+    else
+    {
+      boolean getboxColour = false;
+      for (int i = start; i <= end; i++)
+      {
+        graphics.setColor(av.textColour);
+        getboxColour = false;
+        s = seq.getCharAt(i);
+        if (!renderGaps && jalview.util.Comparison.isGap(s))
+        {
+          continue;
+        }
+
+        if (inCurrentSequenceGroup(i))
+        {
+          if (!currentSequenceGroup.getDisplayText())
+          {
+            continue;
+          }
+
+          if (currentSequenceGroup.thresholdTextColour > 0
+                  || currentSequenceGroup.getColourText())
+          {
+            getboxColour = true;
+            getBoxColour(currentSequenceGroup.cs, seq, i);
+
+            if (currentSequenceGroup.getColourText())
+            {
+              graphics.setColor(resBoxColour.darker());
+            }
+
+            if (currentSequenceGroup.thresholdTextColour > 0)
+            {
+              if (resBoxColour.getRed() + resBoxColour.getBlue()
+                      + resBoxColour.getGreen() < currentSequenceGroup.thresholdTextColour)
+              {
+                graphics.setColor(currentSequenceGroup.textColour2);
+              }
+            }
+          }
+          else
+          {
+            graphics.setColor(currentSequenceGroup.textColour);
+          }
+
+        }
+        else
+        {
+          if (!av.getShowText())
+          {
+            continue;
+          }
+
+          if (av.getColourText())
+          {
+            getboxColour = true;
+            getBoxColour(av.globalColourScheme, seq, i);
+
+            if (av.getShowBoxes())
+            {
+              graphics.setColor(resBoxColour.darker());
+            }
+            else
+            {
+              graphics.setColor(resBoxColour);
+            }
+          }
+
+          if (av.thresholdTextColour > 0)
+          {
+            if (!getboxColour)
+            {
+              getBoxColour(av.globalColourScheme, seq, i);
+            }
+
+            if (resBoxColour.getRed() + resBoxColour.getBlue()
+                    + resBoxColour.getGreen() < av.thresholdTextColour)
+            {
+              graphics.setColor(av.textColour2);
+            }
+          }
+
+        }
+
+        charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+        graphics.drawString(String.valueOf(s), charOffset + av.charWidth
+                * (i - start), y1);
+
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param res
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  boolean inCurrentSequenceGroup(int res)
+  {
+    if (allGroups == null)
+    {
+      return false;
+    }
+
+    for (int i = 0; i < allGroups.length; i++)
+    {
+      if ((allGroups[i].getStartRes() <= res)
+              && (allGroups[i].getEndRes() >= res))
+      {
+        currentSequenceGroup = allGroups[i];
+
+        return true;
+      }
+    }
+
+    return false;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param seq
+   *                DOCUMENT ME!
+   * @param start
+   *                DOCUMENT ME!
+   * @param end
+   *                DOCUMENT ME!
+   * @param x1
+   *                DOCUMENT ME!
+   * @param y1
+   *                DOCUMENT ME!
+   * @param width
+   *                DOCUMENT ME!
+   * @param height
+   *                DOCUMENT ME!
+   */
+  public void drawHighlightedText(SequenceI seq, int start, int end,
+          int x1, int y1)
+  {
+    int pady = av.charHeight / 5;
+    int charOffset = 0;
+    graphics.setColor(Color.BLACK);
+    graphics.fillRect(x1, y1, av.charWidth * (end - start + 1),
+            av.charHeight);
+    graphics.setColor(Color.white);
+
+    char s = '~';
+
+    // Need to find the sequence position here.
+    if (av.validCharWidth)
+    {
+      for (int i = start; i <= end; i++)
+      {
+        if (i < seq.getLength())
+        {
+          s = seq.getCharAt(i);
+        }
+
+        charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+        graphics
+                .drawString(String.valueOf(s), charOffset + x1
+                        + (av.charWidth * (i - start)),
+                        (y1 + av.charHeight) - pady);
+      }
+    }
+  }
+
+  public void drawCursor(SequenceI seq, int res, int x1, int y1)
+  {
+    int pady = av.charHeight / 5;
+    int charOffset = 0;
+    graphics.setColor(Color.black);
+    graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
+
+    if (av.validCharWidth)
+    {
+      graphics.setColor(Color.white);
+
+      char s = seq.getCharAt(res);
+
+      charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+      graphics.drawString(String.valueOf(s), charOffset + x1,
+              (y1 + av.charHeight) - pady);
+    }
+
+  }
+}
diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java
index 23b76e3..a200699 100755
--- a/src/jalview/gui/SliderPanel.java
+++ b/src/jalview/gui/SliderPanel.java
@@ -1,359 +1,373 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.gui;
-
-import java.util.*;
-
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.event.*;
-
-import jalview.datamodel.*;
-import jalview.jbgui.*;
-import jalview.schemes.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class SliderPanel
-    extends GSliderPanel
-{
-  static JInternalFrame conservationSlider;
-  static JInternalFrame PIDSlider;
-  AlignmentPanel ap;
-  boolean forConservation = true;
-  ColourSchemeI cs;
-
-  /**
-   * Creates a new SliderPanel object.
-   *
-   * @param ap DOCUMENT ME!
-   * @param value DOCUMENT ME!
-   * @param forConserve DOCUMENT ME!
-   * @param cs DOCUMENT ME!
-   */
-  public SliderPanel(final AlignmentPanel ap, int value, boolean forConserve,
-                     ColourSchemeI cs)
-  {
-    this.ap = ap;
-    this.cs = cs;
-    forConservation = forConserve;
-    undoButton.setVisible(false);
-    applyButton.setVisible(false);
-
-    if (forConservation)
-    {
-      label.setText("Enter value to increase conservation visibility");
-      slider.setMinimum(0);
-      slider.setMaximum(100);
-    }
-    else
-    {
-      label.setText("Enter % identity above which to colour residues");
-      slider.setMinimum(0);
-      slider.setMaximum(100);
-    }
-
-    slider.addChangeListener(new ChangeListener()
-    {
-      public void stateChanged(ChangeEvent evt)
-      {
-        valueField.setText(slider.getValue() + "");
-        valueChanged(slider.getValue());
-      }
-    });
-
-    slider.addMouseListener(new MouseAdapter()
-    {
-      public void mouseReleased(MouseEvent evt)
-      {
-         ap.paintAlignment(true);
-      }
-    });
-
-    slider.setValue(value);
-    valueField.setText(value + "");
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param ap DOCUMENT ME!
-   * @param cs DOCUMENT ME!
-   * @param source DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public static int setConservationSlider(AlignmentPanel ap,
-                                          ColourSchemeI cs, String source)
-  {
-    SliderPanel sp = null;
-
-    if (conservationSlider == null)
-    {
-      sp = new SliderPanel(ap, cs.getConservationInc(), true, cs);
-      conservationSlider = new JInternalFrame();
-      conservationSlider.setContentPane(sp);
-      conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
-    }
-    else
-    {
-      sp = (SliderPanel) conservationSlider.getContentPane();
-      sp.cs = cs;
-    }
-
-    conservationSlider.setTitle("Conservation Colour Increment  (" +
-                                source + ")");
-
-    if (ap.av.alignment.getGroups() != null)
-    {
-      sp.setAllGroupsCheckEnabled(true);
-    }
-    else
-    {
-      sp.setAllGroupsCheckEnabled(false);
-    }
-
-    return sp.getValue();
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  public static void showConservationSlider()
-  {
-    try
-    {
-      PIDSlider.setClosed(true);
-      PIDSlider = null;
-    }
-    catch (Exception ex)
-    {
-    }
-
-    if (!conservationSlider.isVisible())
-    {
-      Desktop.addInternalFrame(conservationSlider,
-                               conservationSlider.getTitle(), 420, 90, false);
-      conservationSlider.addInternalFrameListener(new javax.swing.event.
-                                                  InternalFrameAdapter()
-      {
-        public void internalFrameClosed(
-            javax.swing.event.InternalFrameEvent e)
-        {
-          conservationSlider = null;
-        }
-      });
-      conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param ap DOCUMENT ME!
-   * @param cs DOCUMENT ME!
-   * @param source DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs,
-                                       String source)
-  {
-    SliderPanel pid = null;
-
-    int threshold = cs.getThreshold();
-
-    if (PIDSlider == null)
-    {
-      pid = new SliderPanel(ap, threshold, false, cs);
-      PIDSlider = new JInternalFrame();
-      PIDSlider.setContentPane(pid);
-      PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
-    }
-    else
-    {
-      pid = (SliderPanel) PIDSlider.getContentPane();
-      pid.cs = cs;
-    }
-
-    PIDSlider.setTitle("Percentage Identity Threshold (" + source + ")");
-
-    if (ap.av.alignment.getGroups() != null)
-    {
-      pid.setAllGroupsCheckEnabled(true);
-    }
-    else
-    {
-      pid.setAllGroupsCheckEnabled(false);
-    }
-
-    return pid.getValue();
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  public static void showPIDSlider()
-  {
-    try
-    {
-      conservationSlider.setClosed(true);
-      conservationSlider = null;
-    }
-    catch (Exception ex)
-    {
-    }
-
-    if (!PIDSlider.isVisible())
-    {
-      Desktop.addInternalFrame(PIDSlider, PIDSlider.getTitle(), 420, 90,
-                               false);
-      PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
-      PIDSlider.addInternalFrameListener(new javax.swing.event.
-                                         InternalFrameAdapter()
-      {
-        public void internalFrameClosed(
-            javax.swing.event.InternalFrameEvent e)
-        {
-          PIDSlider = null;
-        }
-      });
-      PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
-   */
-  public void valueChanged(int i)
-  {
-    if (cs == null)
-    {
-      return;
-    }
-
-    ColourSchemeI toChange = null;
-    Vector allGroups = null;
-    int groupIndex = 0;
-
-    if (allGroupsCheck.isSelected())
-    {
-      allGroups = ap.av.alignment.getGroups();
-      groupIndex = allGroups.size() - 1;
-    }
-    else
-    {
-      toChange = cs;
-    }
-
-    while (groupIndex > -1)
-    {
-      if (allGroups != null)
-      {
-        toChange = ( (SequenceGroup) allGroups.get(groupIndex)).cs;
-
-        if (toChange == null)
-        {
-          groupIndex--;
-
-          continue;
-        }
-      }
-
-      if (forConservation)
-      {
-        if (toChange.conservationApplied())
-        {
-          toChange.setConservationInc(i);
-        }
-      }
-      else
-      {
-        toChange.setThreshold(i, ap.av.getIgnoreGapsConsensus());
-      }
-
-      groupIndex--;
-    }
-
-    ap.seqPanel.seqCanvas.repaint();
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param b DOCUMENT ME!
-   */
-  public void setAllGroupsCheckEnabled(boolean b)
-  {
-    allGroupsCheck.setEnabled(b);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  public void valueField_actionPerformed(ActionEvent e)
-  {
-    try
-    {
-      int i = Integer.parseInt(valueField.getText());
-      slider.setValue(i);
-    }
-    catch (NumberFormatException ex)
-    {
-      valueField.setText(slider.getValue() + "");
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param value DOCUMENT ME!
-   */
-  public void setValue(int value)
-  {
-    slider.setValue(value);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public int getValue()
-  {
-    return Integer.parseInt(valueField.getText());
-  }
-
-  public void slider_mouseReleased(MouseEvent e)
-  {
-    if (ap.overviewPanel != null)
-    {
-      ap.overviewPanel.updateOverviewImage();
-    }
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.gui;
+
+import java.util.*;
+
+import java.awt.event.*;
+import javax.swing.*;
+import javax.swing.event.*;
+
+import jalview.datamodel.*;
+import jalview.jbgui.*;
+import jalview.schemes.*;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class SliderPanel extends GSliderPanel
+{
+  static JInternalFrame conservationSlider;
+
+  static JInternalFrame PIDSlider;
+
+  AlignmentPanel ap;
+
+  boolean forConservation = true;
+
+  ColourSchemeI cs;
+
+  /**
+   * Creates a new SliderPanel object.
+   * 
+   * @param ap
+   *                DOCUMENT ME!
+   * @param value
+   *                DOCUMENT ME!
+   * @param forConserve
+   *                DOCUMENT ME!
+   * @param cs
+   *                DOCUMENT ME!
+   */
+  public SliderPanel(final AlignmentPanel ap, int value,
+          boolean forConserve, ColourSchemeI cs)
+  {
+    this.ap = ap;
+    this.cs = cs;
+    forConservation = forConserve;
+    undoButton.setVisible(false);
+    applyButton.setVisible(false);
+
+    if (forConservation)
+    {
+      label.setText("Enter value to increase conservation visibility");
+      slider.setMinimum(0);
+      slider.setMaximum(100);
+    }
+    else
+    {
+      label.setText("Enter % identity above which to colour residues");
+      slider.setMinimum(0);
+      slider.setMaximum(100);
+    }
+
+    slider.addChangeListener(new ChangeListener()
+    {
+      public void stateChanged(ChangeEvent evt)
+      {
+        valueField.setText(slider.getValue() + "");
+        valueChanged(slider.getValue());
+      }
+    });
+
+    slider.addMouseListener(new MouseAdapter()
+    {
+      public void mouseReleased(MouseEvent evt)
+      {
+        ap.paintAlignment(true);
+      }
+    });
+
+    slider.setValue(value);
+    valueField.setText(value + "");
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param ap
+   *                DOCUMENT ME!
+   * @param cs
+   *                DOCUMENT ME!
+   * @param source
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public static int setConservationSlider(AlignmentPanel ap,
+          ColourSchemeI cs, String source)
+  {
+    SliderPanel sp = null;
+
+    if (conservationSlider == null)
+    {
+      sp = new SliderPanel(ap, cs.getConservationInc(), true, cs);
+      conservationSlider = new JInternalFrame();
+      conservationSlider.setContentPane(sp);
+      conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+    }
+    else
+    {
+      sp = (SliderPanel) conservationSlider.getContentPane();
+      sp.cs = cs;
+    }
+
+    conservationSlider.setTitle("Conservation Colour Increment  (" + source
+            + ")");
+
+    if (ap.av.alignment.getGroups() != null)
+    {
+      sp.setAllGroupsCheckEnabled(true);
+    }
+    else
+    {
+      sp.setAllGroupsCheckEnabled(false);
+    }
+
+    return sp.getValue();
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public static void showConservationSlider()
+  {
+    try
+    {
+      PIDSlider.setClosed(true);
+      PIDSlider = null;
+    } catch (Exception ex)
+    {
+    }
+
+    if (!conservationSlider.isVisible())
+    {
+      Desktop.addInternalFrame(conservationSlider, conservationSlider
+              .getTitle(), 420, 90, false);
+      conservationSlider
+              .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+              {
+                public void internalFrameClosed(
+                        javax.swing.event.InternalFrameEvent e)
+                {
+                  conservationSlider = null;
+                }
+              });
+      conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param ap
+   *                DOCUMENT ME!
+   * @param cs
+   *                DOCUMENT ME!
+   * @param source
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs,
+          String source)
+  {
+    SliderPanel pid = null;
+
+    int threshold = cs.getThreshold();
+
+    if (PIDSlider == null)
+    {
+      pid = new SliderPanel(ap, threshold, false, cs);
+      PIDSlider = new JInternalFrame();
+      PIDSlider.setContentPane(pid);
+      PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+    }
+    else
+    {
+      pid = (SliderPanel) PIDSlider.getContentPane();
+      pid.cs = cs;
+    }
+
+    PIDSlider.setTitle("Percentage Identity Threshold (" + source + ")");
+
+    if (ap.av.alignment.getGroups() != null)
+    {
+      pid.setAllGroupsCheckEnabled(true);
+    }
+    else
+    {
+      pid.setAllGroupsCheckEnabled(false);
+    }
+
+    return pid.getValue();
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public static void showPIDSlider()
+  {
+    try
+    {
+      conservationSlider.setClosed(true);
+      conservationSlider = null;
+    } catch (Exception ex)
+    {
+    }
+
+    if (!PIDSlider.isVisible())
+    {
+      Desktop.addInternalFrame(PIDSlider, PIDSlider.getTitle(), 420, 90,
+              false);
+      PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+      PIDSlider
+              .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+              {
+                public void internalFrameClosed(
+                        javax.swing.event.InternalFrameEvent e)
+                {
+                  PIDSlider = null;
+                }
+              });
+      PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param i
+   *                DOCUMENT ME!
+   */
+  public void valueChanged(int i)
+  {
+    if (cs == null)
+    {
+      return;
+    }
+
+    ColourSchemeI toChange = null;
+    Vector allGroups = null;
+    int groupIndex = 0;
+
+    if (allGroupsCheck.isSelected())
+    {
+      allGroups = ap.av.alignment.getGroups();
+      groupIndex = allGroups.size() - 1;
+    }
+    else
+    {
+      toChange = cs;
+    }
+
+    while (groupIndex > -1)
+    {
+      if (allGroups != null)
+      {
+        toChange = ((SequenceGroup) allGroups.get(groupIndex)).cs;
+
+        if (toChange == null)
+        {
+          groupIndex--;
+
+          continue;
+        }
+      }
+
+      if (forConservation)
+      {
+        if (toChange.conservationApplied())
+        {
+          toChange.setConservationInc(i);
+        }
+      }
+      else
+      {
+        toChange.setThreshold(i, ap.av.getIgnoreGapsConsensus());
+      }
+
+      groupIndex--;
+    }
+
+    ap.seqPanel.seqCanvas.repaint();
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param b
+   *                DOCUMENT ME!
+   */
+  public void setAllGroupsCheckEnabled(boolean b)
+  {
+    allGroupsCheck.setEnabled(b);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
+   */
+  public void valueField_actionPerformed(ActionEvent e)
+  {
+    try
+    {
+      int i = Integer.parseInt(valueField.getText());
+      slider.setValue(i);
+    } catch (NumberFormatException ex)
+    {
+      valueField.setText(slider.getValue() + "");
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param value
+   *                DOCUMENT ME!
+   */
+  public void setValue(int value)
+  {
+    slider.setValue(value);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public int getValue()
+  {
+    return Integer.parseInt(valueField.getText());
+  }
+
+  public void slider_mouseReleased(MouseEvent e)
+  {
+    if (ap.overviewPanel != null)
+    {
+      ap.overviewPanel.updateOverviewImage();
+    }
+  }
+
+}
diff --git a/src/jalview/gui/SplashScreen.java b/src/jalview/gui/SplashScreen.java
index b72cc61..6fc4262 100755
--- a/src/jalview/gui/SplashScreen.java
+++ b/src/jalview/gui/SplashScreen.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -24,17 +24,20 @@ import javax.swing.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class SplashScreen
-    extends JPanel implements Runnable
+public class SplashScreen extends JPanel implements Runnable
 {
   boolean visible = true;
+
   JInternalFrame iframe;
+
   Image image;
+
   int fontSize = 11;
+
   int yoffset = 30;
 
   /**
@@ -45,20 +48,22 @@ public class SplashScreen
     Thread t = new Thread(this);
     t.start();
   }
+
   /**
-   * ping the jalview version page then create and display the jalview splashscreen window.
+   * ping the jalview version page then create and display the jalview
+   * splashscreen window.
    */
-  void initSplashScreenWindow() {
+  void initSplashScreenWindow()
+  {
     addMouseListener(new MouseAdapter()
     {
       public void mousePressed(MouseEvent evt)
       {
         try
         {
-          visible=false;
+          visible = false;
           closeSplash();
-        }
-        catch (Exception ex)
+        } catch (Exception ex)
         {
         }
       }
@@ -77,12 +82,10 @@ public class SplashScreen
         mt.waitForID(0);
         Desktop.instance.setIconImage(image);
       }
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
     }
 
-
     iframe = new JInternalFrame();
     iframe.setFrameIcon(null);
     iframe.setClosable(false);
@@ -92,9 +95,8 @@ public class SplashScreen
     Desktop.desktop.add(iframe);
 
     iframe.setVisible(true);
-    iframe.setBounds( (int) ( (Desktop.instance.getWidth() - 750) / 2),
-                      (int) ( (Desktop.instance.getHeight() - 160) / 2),
-                      750, 160);
+    iframe.setBounds((int) ((Desktop.instance.getWidth() - 750) / 2),
+            (int) ((Desktop.instance.getHeight() - 160) / 2), 750, 190);
   }
 
   /**
@@ -104,18 +106,17 @@ public class SplashScreen
   {
     initSplashScreenWindow();
     long startTime = System.currentTimeMillis() / 1000;
-    
+
     while (visible)
     {
       try
       {
         Thread.sleep(1000);
-      }
-      catch (Exception ex)
+      } catch (Exception ex)
       {
       }
 
-      if ( ( (System.currentTimeMillis() / 1000) - startTime) > 5)
+      if (((System.currentTimeMillis() / 1000) - startTime) > 5)
       {
         visible = false;
       }
@@ -135,15 +136,16 @@ public class SplashScreen
     {
 
       iframe.setClosed(true);
+    } catch (Exception ex)
+    {
     }
-    catch (Exception ex)
-    {  }
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param g DOCUMENT ME!
+   * 
+   * @param g
+   *                DOCUMENT ME!
    */
   public void paintComponent(Graphics g)
   {
@@ -159,51 +161,62 @@ public class SplashScreen
 
     int y = yoffset;
 
-    g.drawString("Jalview " + jalview.bin.Cache.getProperty("VERSION"), 50, y);
+    g.drawString("Jalview " + jalview.bin.Cache.getProperty("VERSION"), 50,
+            y);
 
     FontMetrics fm = g.getFontMetrics();
-    int vwidth = fm.stringWidth("Jalview " +
-                                jalview.bin.Cache.getProperty("VERSION"));
+    int vwidth = fm.stringWidth("Jalview "
+            + jalview.bin.Cache.getProperty("VERSION"));
     g.setFont(new Font("Verdana", Font.BOLD, fontSize + 2));
-    g.drawString("Last updated: " +
-                 jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"),
-                 50 + vwidth + 5, y);
-    if (jalview.bin.Cache.getDefault("LATEST_VERSION",
-        "Checking").equals("Checking"))
+    g.drawString("Last updated: "
+            + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"),
+            50 + vwidth + 5, y);
+    if (jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking").equals(
+            "Checking"))
     {
       // Displayed when code version and jnlp version do not match
-      g.drawString("...Checking latest version...",
-                   50, y += fontSize + 10);
+      g.drawString("...Checking latest version...", 50, y += fontSize + 10);
       y += 5;
       g.setColor(Color.black);
     }
-    else if (!jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking").equals(
-        jalview.bin.Cache.getProperty("VERSION")))
+    else if (!jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking")
+            .equals(jalview.bin.Cache.getProperty("VERSION")))
     {
-      if (jalview.bin.Cache.getProperty("VERSION").toLowerCase().indexOf("automated build")==-1)
+      if (jalview.bin.Cache.getProperty("VERSION").toLowerCase().indexOf(
+              "automated build") == -1)
       {
-        // Displayed when code version and jnlp version do not match and code version is not a development build
+        // Displayed when code version and jnlp version do not match and code
+        // version is not a development build
         g.setColor(Color.red);
       }
-      g.drawString(
-              "!! Jalview version "
-              + jalview.bin.Cache.getDefault(
-                      "LATEST_VERSION", "..Checking..")
-                      + " is available for download from http://www.jalview.org !!",
+      g
+              .drawString(
+                      "!! Jalview version "
+                              + jalview.bin.Cache.getDefault(
+                                      "LATEST_VERSION", "..Checking..")
+                              + " is available for download from http://www.jalview.org !!",
                       50, y += fontSize + 10);
       y += 5;
       g.setColor(Color.black);
     }
 
     g.setFont(new Font("Verdana", Font.BOLD, fontSize));
-    g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
-                 50, y += fontSize + 4);
-    g.drawString("Development managed by The Barton Group, University of Dundee.",
-                 50, y += fontSize + 4);
-    g.drawString("If  you use Jalview, please cite: Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004),",
-                 50, y += fontSize + 4);
-    g.drawString(
-        "\"The Jalview Java Alignment Editor\" Bioinformatics,  2004 20; 426-7.",
-        50, y += fontSize + 4);
+    g
+            .drawString(
+                    "Authors: Andrew Waterhouse, Jim Procter, Michele Clamp, James Cuff, Steve Searle,",
+                    50, y += fontSize + 4);
+    g.drawString("David Martin & Geoff Barton.", 60, y += fontSize + 4);
+    g
+            .drawString(
+                    "Development managed by The Barton Group, University of Dundee.",
+                    50, y += fontSize + 4);
+    g
+            .drawString(
+                    "If  you use Jalview, please cite: Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004),",
+                    50, y += fontSize + 4);
+    g
+            .drawString(
+                    "\"The Jalview Java Alignment Editor\" Bioinformatics,  2004 20; 426-7.",
+                    50, y += fontSize + 4);
   }
 }
diff --git a/src/jalview/gui/TextColourChooser.java b/src/jalview/gui/TextColourChooser.java
index 8dd9d49..c0f3916 100644
--- a/src/jalview/gui/TextColourChooser.java
+++ b/src/jalview/gui/TextColourChooser.java
@@ -1,213 +1,209 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.gui;
-
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.event.*;
-
-import jalview.datamodel.*;
-
-public class TextColourChooser
-{
-  AlignmentPanel ap;
-  SequenceGroup sg;
-
-  public void chooseColour(AlignmentPanel ap, SequenceGroup sg)
-  {
-    this.ap = ap;
-    this.sg = sg;
-
-    int original1, original2, originalThreshold;
-    if (sg == null)
-    {
-      original1 = ap.av.textColour.getRGB();
-      original2 = ap.av.textColour2.getRGB();
-      originalThreshold = ap.av.thresholdTextColour;
-    }
-    else
-    {
-      original1 = sg.textColour.getRGB();
-      original2 = sg.textColour2.getRGB();
-      originalThreshold = sg.thresholdTextColour;
-    }
-
-    final JSlider slider = new JSlider(0, 750, originalThreshold);
-    final JPanel col1 = new JPanel();
-    col1.setPreferredSize(new Dimension(40, 20));
-    col1.setBorder(BorderFactory.createEtchedBorder());
-    col1.setToolTipText("Dark Colour");
-    col1.setBackground(new Color(original1));
-    final JPanel col2 = new JPanel();
-    col2.setPreferredSize(new Dimension(40, 20));
-    col2.setBorder(BorderFactory.createEtchedBorder());
-    col2.setToolTipText("Light Colour");
-    col2.setBackground(new Color(original2));
-    final JPanel bigpanel = new JPanel(new BorderLayout());
-    JPanel panel = new JPanel();
-    bigpanel.add(panel, BorderLayout.CENTER);
-    bigpanel.add(new JLabel(
-        "<html><i>Select a dark and light text colour, then set the threshold to"
-        + "<br>switch between colours, based on background colour</i></html>"),
-                 BorderLayout.NORTH);
-    panel.add(col1);
-    panel.add(slider);
-    panel.add(col2);
-
-    col1.addMouseListener(new MouseAdapter()
-    {
-      public void mousePressed(MouseEvent e)
-      {
-        Color col = JColorChooser.showDialog(bigpanel,
-                                             "Select Colour for Text",
-                                             col1.getBackground());
-        if (col != null)
-        {
-          colour1Changed(col);
-          col1.setBackground(col);
-        }
-      }
-    });
-
-    col2.addMouseListener(new MouseAdapter()
-    {
-      public void mousePressed(MouseEvent e)
-      {
-        Color col = JColorChooser.showDialog(bigpanel,
-                                             "Select Colour for Text",
-                                             col2.getBackground());
-        if (col != null)
-        {
-          colour2Changed(col);
-          col2.setBackground(col);
-        }
-      }
-    });
-
-    slider.addChangeListener(new ChangeListener()
-    {
-      public void stateChanged(ChangeEvent evt)
-      {
-        thresholdChanged(slider.getValue());
-      }
-    });
-
-    int reply = JOptionPane.showInternalOptionDialog(
-        ap,
-        bigpanel,
-        "Adjust Foreground Text Colour Threshold",
-        JOptionPane.OK_CANCEL_OPTION,
-        JOptionPane.QUESTION_MESSAGE,
-        null,
-        null, null);
-
-    if (reply == JOptionPane.CANCEL_OPTION)
-    {
-      if (sg == null)
-      {
-        ap.av.textColour = new Color(original1);
-        ap.av.textColour2 = new Color(original2);
-        ap.av.thresholdTextColour = originalThreshold;
-      }
-      else
-      {
-        sg.textColour = new Color(original1);
-        sg.textColour2 = new Color(original2);
-        sg.thresholdTextColour = originalThreshold;
-      }
-    }
-  }
-
-  void colour1Changed(Color col)
-  {
-    if (sg == null)
-    {
-      ap.av.textColour = col;
-      if (ap.av.colourAppliesToAllGroups)
-      {
-        setGroupTextColour();
-      }
-    }
-    else
-    {
-      sg.textColour = col;
-    }
-
-    ap.paintAlignment(true);
-  }
-
-  void colour2Changed(Color col)
-  {
-    if (sg == null)
-    {
-      ap.av.textColour2 = col;
-      if (ap.av.colourAppliesToAllGroups)
-      {
-        setGroupTextColour();
-      }
-    }
-    else
-    {
-      sg.textColour2 = col;
-    }
-
-    ap.paintAlignment(true);
-  }
-
-  void thresholdChanged(int value)
-  {
-    if (sg == null)
-    {
-      ap.av.thresholdTextColour = value;
-      if (ap.av.colourAppliesToAllGroups)
-      {
-        setGroupTextColour();
-      }
-    }
-    else
-    {
-      sg.thresholdTextColour = value;
-    }
-
-    ap.paintAlignment(true);
-  }
-
-  void setGroupTextColour()
-  {
-    if (ap.av.alignment.getGroups() == null)
-    {
-      return;
-    }
-
-    Vector groups = ap.av.alignment.getGroups();
-
-    for (int i = 0; i < groups.size(); i++)
-    {
-      SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-      sg.textColour = ap.av.textColour;
-      sg.textColour2 = ap.av.textColour2;
-      sg.thresholdTextColour = ap.av.thresholdTextColour;
-    }
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.gui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+import javax.swing.event.*;
+
+import jalview.datamodel.*;
+
+public class TextColourChooser
+{
+  AlignmentPanel ap;
+
+  SequenceGroup sg;
+
+  public void chooseColour(AlignmentPanel ap, SequenceGroup sg)
+  {
+    this.ap = ap;
+    this.sg = sg;
+
+    int original1, original2, originalThreshold;
+    if (sg == null)
+    {
+      original1 = ap.av.textColour.getRGB();
+      original2 = ap.av.textColour2.getRGB();
+      originalThreshold = ap.av.thresholdTextColour;
+    }
+    else
+    {
+      original1 = sg.textColour.getRGB();
+      original2 = sg.textColour2.getRGB();
+      originalThreshold = sg.thresholdTextColour;
+    }
+
+    final JSlider slider = new JSlider(0, 750, originalThreshold);
+    final JPanel col1 = new JPanel();
+    col1.setPreferredSize(new Dimension(40, 20));
+    col1.setBorder(BorderFactory.createEtchedBorder());
+    col1.setToolTipText("Dark Colour");
+    col1.setBackground(new Color(original1));
+    final JPanel col2 = new JPanel();
+    col2.setPreferredSize(new Dimension(40, 20));
+    col2.setBorder(BorderFactory.createEtchedBorder());
+    col2.setToolTipText("Light Colour");
+    col2.setBackground(new Color(original2));
+    final JPanel bigpanel = new JPanel(new BorderLayout());
+    JPanel panel = new JPanel();
+    bigpanel.add(panel, BorderLayout.CENTER);
+    bigpanel
+            .add(
+                    new JLabel(
+                            "<html><i>Select a dark and light text colour, then set the threshold to"
+                                    + "<br>switch between colours, based on background colour</i></html>"),
+                    BorderLayout.NORTH);
+    panel.add(col1);
+    panel.add(slider);
+    panel.add(col2);
+
+    col1.addMouseListener(new MouseAdapter()
+    {
+      public void mousePressed(MouseEvent e)
+      {
+        Color col = JColorChooser.showDialog(bigpanel,
+                "Select Colour for Text", col1.getBackground());
+        if (col != null)
+        {
+          colour1Changed(col);
+          col1.setBackground(col);
+        }
+      }
+    });
+
+    col2.addMouseListener(new MouseAdapter()
+    {
+      public void mousePressed(MouseEvent e)
+      {
+        Color col = JColorChooser.showDialog(bigpanel,
+                "Select Colour for Text", col2.getBackground());
+        if (col != null)
+        {
+          colour2Changed(col);
+          col2.setBackground(col);
+        }
+      }
+    });
+
+    slider.addChangeListener(new ChangeListener()
+    {
+      public void stateChanged(ChangeEvent evt)
+      {
+        thresholdChanged(slider.getValue());
+      }
+    });
+
+    int reply = JOptionPane.showInternalOptionDialog(ap, bigpanel,
+            "Adjust Foreground Text Colour Threshold",
+            JOptionPane.OK_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE,
+            null, null, null);
+
+    if (reply == JOptionPane.CANCEL_OPTION)
+    {
+      if (sg == null)
+      {
+        ap.av.textColour = new Color(original1);
+        ap.av.textColour2 = new Color(original2);
+        ap.av.thresholdTextColour = originalThreshold;
+      }
+      else
+      {
+        sg.textColour = new Color(original1);
+        sg.textColour2 = new Color(original2);
+        sg.thresholdTextColour = originalThreshold;
+      }
+    }
+  }
+
+  void colour1Changed(Color col)
+  {
+    if (sg == null)
+    {
+      ap.av.textColour = col;
+      if (ap.av.colourAppliesToAllGroups)
+      {
+        setGroupTextColour();
+      }
+    }
+    else
+    {
+      sg.textColour = col;
+    }
+
+    ap.paintAlignment(true);
+  }
+
+  void colour2Changed(Color col)
+  {
+    if (sg == null)
+    {
+      ap.av.textColour2 = col;
+      if (ap.av.colourAppliesToAllGroups)
+      {
+        setGroupTextColour();
+      }
+    }
+    else
+    {
+      sg.textColour2 = col;
+    }
+
+    ap.paintAlignment(true);
+  }
+
+  void thresholdChanged(int value)
+  {
+    if (sg == null)
+    {
+      ap.av.thresholdTextColour = value;
+      if (ap.av.colourAppliesToAllGroups)
+      {
+        setGroupTextColour();
+      }
+    }
+    else
+    {
+      sg.thresholdTextColour = value;
+    }
+
+    ap.paintAlignment(true);
+  }
+
+  void setGroupTextColour()
+  {
+    if (ap.av.alignment.getGroups() == null)
+    {
+      return;
+    }
+
+    Vector groups = ap.av.alignment.getGroups();
+
+    for (int i = 0; i < groups.size(); i++)
+    {
+      SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+      sg.textColour = ap.av.textColour;
+      sg.textColour2 = ap.av.textColour2;
+      sg.thresholdTextColour = ap.av.thresholdTextColour;
+    }
+  }
+
+}
diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 3407c07..77564aa 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -32,50 +32,69 @@ import jalview.util.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class TreeCanvas
-    extends JPanel implements MouseListener, Runnable,
-    Printable, MouseMotionListener
+public class TreeCanvas extends JPanel implements MouseListener, Runnable,
+        Printable, MouseMotionListener
 {
   /** DOCUMENT ME!! */
   public static final String PLACEHOLDER = " * ";
+
   NJTree tree;
+
   JScrollPane scrollPane;
+
   TreePanel tp;
+
   AlignViewport av;
+
   AlignmentPanel ap;
+
   Font font;
+
   FontMetrics fm;
+
   boolean fitToWindow = true;
+
   boolean showDistances = false;
+
   boolean showBootstrap = false;
+
   boolean markPlaceholders = false;
+
   int offx = 20;
+
   int offy;
+
   float threshold;
+
   String longestName;
+
   int labelLength = -1;
 
   Hashtable nameHash = new Hashtable();
+
   Hashtable nodeHash = new Hashtable();
+
   SequenceNode highlightNode;
 
   boolean applyToAllViews = false;
 
   /**
    * Creates a new TreeCanvas object.
-   *
-   * @param av DOCUMENT ME!
-   * @param tree DOCUMENT ME!
-   * @param scroller DOCUMENT ME!
-   * @param label DOCUMENT ME!
+   * 
+   * @param av
+   *                DOCUMENT ME!
+   * @param tree
+   *                DOCUMENT ME!
+   * @param scroller
+   *                DOCUMENT ME!
+   * @param label
+   *                DOCUMENT ME!
    */
-  public TreeCanvas(TreePanel tp,
-                    AlignmentPanel ap,
-                    JScrollPane scroller)
+  public TreeCanvas(TreePanel tp, AlignmentPanel ap, JScrollPane scroller)
   {
     this.tp = tp;
     this.av = ap.av;
@@ -89,8 +108,9 @@ public class TreeCanvas
 
   /**
    * DOCUMENT ME!
-   *
-   * @param sequence DOCUMENT ME!
+   * 
+   * @param sequence
+   *                DOCUMENT ME!
    */
   public void treeSelectionChanged(SequenceI sequence)
   {
@@ -113,8 +133,9 @@ public class TreeCanvas
 
   /**
    * DOCUMENT ME!
-   *
-   * @param tree DOCUMENT ME!
+   * 
+   * @param tree
+   *                DOCUMENT ME!
    */
   public void setTree(NJTree tree)
   {
@@ -135,11 +156,11 @@ public class TreeCanvas
         has_placeholders = true;
       }
 
-      if (longestName.length() < ( (Sequence) lf.element()).getName()
-          .length())
+      if (longestName.length() < ((Sequence) lf.element()).getName()
+              .length())
       {
-        longestName = TreeCanvas.PLACEHOLDER +
-            ( (Sequence) lf.element()).getName();
+        longestName = TreeCanvas.PLACEHOLDER
+                + ((Sequence) lf.element()).getName();
       }
     }
 
@@ -148,37 +169,44 @@ public class TreeCanvas
 
   /**
    * DOCUMENT ME!
-   *
-   * @param g DOCUMENT ME!
-   * @param node DOCUMENT ME!
-   * @param chunk DOCUMENT ME!
-   * @param scale DOCUMENT ME!
-   * @param width DOCUMENT ME!
-   * @param offx DOCUMENT ME!
-   * @param offy DOCUMENT ME!
+   * 
+   * @param g
+   *                DOCUMENT ME!
+   * @param node
+   *                DOCUMENT ME!
+   * @param chunk
+   *                DOCUMENT ME!
+   * @param scale
+   *                DOCUMENT ME!
+   * @param width
+   *                DOCUMENT ME!
+   * @param offx
+   *                DOCUMENT ME!
+   * @param offy
+   *                DOCUMENT ME!
    */
   public void drawNode(Graphics g, SequenceNode node, float chunk,
-                       float scale, int width, int offx, int offy)
+          float scale, int width, int offx, int offy)
   {
     if (node == null)
     {
       return;
     }
 
-    if ( (node.left() == null) && (node.right() == null))
+    if ((node.left() == null) && (node.right() == null))
     {
       // Drawing leaf node
       float height = node.height;
       float dist = node.dist;
 
-      int xstart = (int) ( (height - dist) * scale) + offx;
+      int xstart = (int) ((height - dist) * scale) + offx;
       int xend = (int) (height * scale) + offx;
 
       int ypos = (int) (node.ycount * chunk) + offy;
 
       if (node.element() instanceof SequenceI)
       {
-        SequenceI seq = (SequenceI) ( (SequenceNode) node).element();
+        SequenceI seq = (SequenceI) ((SequenceNode) node).element();
 
         if (av.getSequenceColour(seq) == Color.white)
         {
@@ -204,7 +232,7 @@ public class TreeCanvas
         nodeLabel = new Format("%-.2f").form(node.dist);
       }
 
-      if (showBootstrap && node.bootstrap>-1)
+      if (showBootstrap && node.bootstrap > -1)
       {
         if (showDistances)
         {
@@ -219,27 +247,28 @@ public class TreeCanvas
         g.drawString(nodeLabel, xstart + 2, ypos - 2);
       }
 
-      String name = (markPlaceholders && node.isPlaceholder())
-          ? (PLACEHOLDER + node.getName()) : node.getName();
+      String name = (markPlaceholders && node.isPlaceholder()) ? (PLACEHOLDER + node
+              .getName())
+              : node.getName();
 
       int charWidth = fm.stringWidth(name) + 3;
       int charHeight = font.getSize();
 
       Rectangle rect = new Rectangle(xend + 10, ypos - charHeight / 2,
-                                     charWidth, charHeight);
+              charWidth, charHeight);
 
-      nameHash.put( (SequenceI) node.element(), rect);
+      nameHash.put((SequenceI) node.element(), rect);
 
       // Colour selected leaves differently
       SequenceGroup selected = av.getSelectionGroup();
 
-      if ( (selected != null) &&
-          selected.getSequences(null).contains( (SequenceI) node.element()))
+      if ((selected != null)
+              && selected.getSequences(null).contains(
+                      (SequenceI) node.element()))
       {
         g.setColor(Color.gray);
 
-        g.fillRect(xend + 10, ypos - charHeight / 2, charWidth,
-                   charHeight);
+        g.fillRect(xend + 10, ypos - charHeight / 2, charWidth, charHeight);
         g.setColor(Color.white);
       }
 
@@ -249,18 +278,18 @@ public class TreeCanvas
     else
     {
       drawNode(g, (SequenceNode) node.left(), chunk, scale, width, offx,
-               offy);
+              offy);
       drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx,
-               offy);
+              offy);
 
       float height = node.height;
       float dist = node.dist;
 
-      int xstart = (int) ( (height - dist) * scale) + offx;
+      int xstart = (int) ((height - dist) * scale) + offx;
       int xend = (int) (height * scale) + offx;
       int ypos = (int) (node.ycount * chunk) + offy;
 
-      g.setColor( ( (SequenceNode) node).color.darker());
+      g.setColor(((SequenceNode) node).color.darker());
 
       // Draw horizontal line
       g.drawLine(xstart, ypos, xend, ypos);
@@ -273,16 +302,16 @@ public class TreeCanvas
         g.fillRect(xend - 2, ypos - 2, 4, 4);
       }
 
-      int ystart = (int) ( ( (SequenceNode) node.left()).ycount * chunk) +
-          offy;
-      int yend = (int) ( ( (SequenceNode) node.right()).ycount * chunk) +
-          offy;
+      int ystart = (int) (((SequenceNode) node.left()).ycount * chunk)
+              + offy;
+      int yend = (int) (((SequenceNode) node.right()).ycount * chunk)
+              + offy;
 
       Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);
       nodeHash.put(node, pos);
 
-      g.drawLine( (int) (height * scale) + offx, ystart,
-                 (int) (height * scale) + offx, yend);
+      g.drawLine((int) (height * scale) + offx, ystart,
+              (int) (height * scale) + offx, yend);
 
       String nodeLabel = "";
 
@@ -291,7 +320,7 @@ public class TreeCanvas
         nodeLabel = new Format("%-.2f").form(node.dist);
       }
 
-      if (showBootstrap && node.bootstrap>-1)
+      if (showBootstrap && node.bootstrap > -1)
       {
         if (showDistances)
         {
@@ -310,10 +339,12 @@ public class TreeCanvas
 
   /**
    * DOCUMENT ME!
-   *
-   * @param x DOCUMENT ME!
-   * @param y DOCUMENT ME!
-   *
+   * 
+   * @param x
+   *                DOCUMENT ME!
+   * @param y
+   *                DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   public Object findElement(int x, int y)
@@ -325,8 +356,8 @@ public class TreeCanvas
       Object ob = keys.nextElement();
       Rectangle rect = (Rectangle) nameHash.get(ob);
 
-      if ( (x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) &&
-          (y <= (rect.y + rect.height)))
+      if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y)
+              && (y <= (rect.y + rect.height)))
       {
         return ob;
       }
@@ -339,8 +370,8 @@ public class TreeCanvas
       Object ob = keys.nextElement();
       Rectangle rect = (Rectangle) nodeHash.get(ob);
 
-      if ( (x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) &&
-          (y <= (rect.y + rect.height)))
+      if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y)
+              && (y <= (rect.y + rect.height)))
       {
         return ob;
       }
@@ -351,8 +382,9 @@ public class TreeCanvas
 
   /**
    * DOCUMENT ME!
-   *
-   * @param pickBox DOCUMENT ME!
+   * 
+   * @param pickBox
+   *                DOCUMENT ME!
    */
   public void pickNodes(Rectangle pickBox)
   {
@@ -361,12 +393,13 @@ public class TreeCanvas
 
     SequenceNode top = tree.getTopNode();
 
-    float wscale = (float) ( (width * .8) - (offx * 2)) / tree.getMaxHeight();
+    float wscale = (float) ((width * .8) - (offx * 2))
+            / tree.getMaxHeight();
 
     if (top.count == 0)
     {
-      top.count = ( (SequenceNode) top.left()).count +
-          ( (SequenceNode) top.right()).count;
+      top.count = ((SequenceNode) top.left()).count
+              + ((SequenceNode) top.right()).count;
     }
 
     float chunk = (float) (height - (offy)) / top.count;
@@ -376,29 +409,36 @@ public class TreeCanvas
 
   /**
    * DOCUMENT ME!
-   *
-   * @param pickBox DOCUMENT ME!
-   * @param node DOCUMENT ME!
-   * @param chunk DOCUMENT ME!
-   * @param scale DOCUMENT ME!
-   * @param width DOCUMENT ME!
-   * @param offx DOCUMENT ME!
-   * @param offy DOCUMENT ME!
+   * 
+   * @param pickBox
+   *                DOCUMENT ME!
+   * @param node
+   *                DOCUMENT ME!
+   * @param chunk
+   *                DOCUMENT ME!
+   * @param scale
+   *                DOCUMENT ME!
+   * @param width
+   *                DOCUMENT ME!
+   * @param offx
+   *                DOCUMENT ME!
+   * @param offy
+   *                DOCUMENT ME!
    */
   public void pickNode(Rectangle pickBox, SequenceNode node, float chunk,
-                       float scale, int width, int offx, int offy)
+          float scale, int width, int offx, int offy)
   {
     if (node == null)
     {
       return;
     }
 
-    if ( (node.left() == null) && (node.right() == null))
+    if ((node.left() == null) && (node.right() == null))
     {
       float height = node.height;
       float dist = node.dist;
 
-      int xstart = (int) ( (height - dist) * scale) + offx;
+      int xstart = (int) ((height - dist) * scale) + offx;
       int xend = (int) (height * scale) + offx;
 
       int ypos = (int) (node.ycount * chunk) + offy;
@@ -420,17 +460,19 @@ public class TreeCanvas
     else
     {
       pickNode(pickBox, (SequenceNode) node.left(), chunk, scale, width,
-               offx, offy);
+              offx, offy);
       pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width,
-               offx, offy);
+              offx, offy);
     }
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param node DOCUMENT ME!
-   * @param c DOCUMENT ME!
+   * 
+   * @param node
+   *                DOCUMENT ME!
+   * @param c
+   *                DOCUMENT ME!
    */
   public void setColor(SequenceNode node, Color c)
   {
@@ -439,7 +481,7 @@ public class TreeCanvas
       return;
     }
 
-    if ( (node.left() == null) && (node.right() == null)) // TODO: internal node
+    if ((node.left() == null) && (node.right() == null)) // TODO: internal node
     {
       node.color = c;
 
@@ -448,15 +490,15 @@ public class TreeCanvas
         AlignmentPanel[] aps = getAssociatedPanels();
         for (int a = 0; a < aps.length; a++)
         {
-          aps[a].av.setSequenceColour( (SequenceI) node.element(), c);
+          aps[a].av.setSequenceColour((SequenceI) node.element(), c);
         }
       }
     }
     else
     {
       node.color = c;
-      setColor( (SequenceNode) node.left(), c);
-      setColor( (SequenceNode) node.right(), c);
+      setColor((SequenceNode) node.left(), c);
+      setColor((SequenceNode) node.right(), c);
     }
   }
 
@@ -482,8 +524,7 @@ public class TreeCanvas
       try
       {
         printJob.print();
-      }
-      catch (Exception PrintException)
+      } catch (Exception PrintException)
       {
         PrintException.printStackTrace();
       }
@@ -492,20 +533,24 @@ public class TreeCanvas
 
   /**
    * DOCUMENT ME!
-   *
-   * @param pg DOCUMENT ME!
-   * @param pf DOCUMENT ME!
-   * @param pi DOCUMENT ME!
-   *
+   * 
+   * @param pg
+   *                DOCUMENT ME!
+   * @param pf
+   *                DOCUMENT ME!
+   * @param pi
+   *                DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
-   *
-   * @throws PrinterException DOCUMENT ME!
+   * 
+   * @throws PrinterException
+   *                 DOCUMENT ME!
    */
   public int print(Graphics pg, PageFormat pf, int pi)
-      throws PrinterException
+          throws PrinterException
   {
     pg.setFont(font);
-    pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
+    pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
 
     int pwidth = (int) pf.getImageableWidth();
     int pheight = (int) pf.getImageableHeight();
@@ -551,8 +596,9 @@ public class TreeCanvas
 
   /**
    * DOCUMENT ME!
-   *
-   * @param g DOCUMENT ME!
+   * 
+   * @param g
+   *                DOCUMENT ME!
    */
   public void paintComponent(Graphics g)
   {
@@ -572,18 +618,18 @@ public class TreeCanvas
         repaint();
       }
 
-      if (fitToWindow ||
-          (!fitToWindow &&
-           (scrollPane.getHeight() > ( (fm.getHeight() * nameHash.size()) +
-                                      offy))))
+      if (fitToWindow
+              || (!fitToWindow && (scrollPane.getHeight() > ((fm
+                      .getHeight() * nameHash.size()) + offy))))
       {
         draw(g, scrollPane.getWidth(), scrollPane.getHeight());
         setPreferredSize(null);
       }
       else
       {
-        setPreferredSize(new Dimension(scrollPane.getWidth(),
-                                       fm.getHeight() * nameHash.size()));
+        setPreferredSize(new Dimension(scrollPane.getWidth(), fm
+                .getHeight()
+                * nameHash.size()));
         draw(g, scrollPane.getWidth(), fm.getHeight() * nameHash.size());
       }
 
@@ -593,8 +639,9 @@ public class TreeCanvas
 
   /**
    * DOCUMENT ME!
-   *
-   * @param fontSize DOCUMENT ME!
+   * 
+   * @param fontSize
+   *                DOCUMENT ME!
    */
   public void setFont(Font font)
   {
@@ -604,16 +651,19 @@ public class TreeCanvas
 
   /**
    * DOCUMENT ME!
-   *
-   * @param g1 DOCUMENT ME!
-   * @param width DOCUMENT ME!
-   * @param height DOCUMENT ME!
+   * 
+   * @param g1
+   *                DOCUMENT ME!
+   * @param width
+   *                DOCUMENT ME!
+   * @param height
+   *                DOCUMENT ME!
    */
   public void draw(Graphics g1, int width, int height)
   {
     Graphics2D g2 = (Graphics2D) g1;
     g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-                        RenderingHints.VALUE_ANTIALIAS_ON);
+            RenderingHints.VALUE_ANTIALIAS_ON);
     g2.setColor(Color.white);
     g2.fillRect(0, 0, width, height);
 
@@ -623,17 +673,17 @@ public class TreeCanvas
 
     fm = g2.getFontMetrics(font);
 
-    labelLength = fm.stringWidth(longestName) + 20; //20 allows for scrollbar
+    labelLength = fm.stringWidth(longestName) + 20; // 20 allows for scrollbar
 
-    float wscale = (float) (width - labelLength - (offx * 2)) /
-        tree.getMaxHeight();
+    float wscale = (float) (width - labelLength - (offx * 2))
+            / tree.getMaxHeight();
 
     SequenceNode top = tree.getTopNode();
 
     if (top.count == 0)
     {
-      top.count = ( (SequenceNode) top.left()).count +
-          ( (SequenceNode) top.right()).count;
+      top.count = ((SequenceNode) top.left()).count
+              + ((SequenceNode) top.right()).count;
     }
 
     float chunk = (float) (height - (offy)) / top.count;
@@ -651,8 +701,7 @@ public class TreeCanvas
         g2.setColor(Color.gray);
       }
 
-      int x = (int) ( (threshold * (float) (getWidth() - labelLength -
-                                            (2 * offx))) + offx);
+      int x = (int) ((threshold * (float) (getWidth() - labelLength - (2 * offx))) + offx);
 
       g2.drawLine(x, 0, x, getHeight());
     }
@@ -660,8 +709,9 @@ public class TreeCanvas
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void mouseReleased(MouseEvent e)
   {
@@ -669,8 +719,9 @@ public class TreeCanvas
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void mouseEntered(MouseEvent e)
   {
@@ -678,8 +729,9 @@ public class TreeCanvas
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void mouseExited(MouseEvent e)
   {
@@ -687,8 +739,9 @@ public class TreeCanvas
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void mouseClicked(MouseEvent evt)
   {
@@ -696,15 +749,14 @@ public class TreeCanvas
     {
       if (SwingUtilities.isRightMouseButton(evt))
       {
-        Color col = JColorChooser.showDialog(this, "Select Sub-Tree Colour",
-                                             highlightNode.color);
-        if (col!=null)
+        Color col = JColorChooser.showDialog(this,
+                "Select Sub-Tree Colour", highlightNode.color);
+        if (col != null)
         {
           setColor(highlightNode, col);
         }
       }
-      else
-      if (evt.getClickCount() > 1)
+      else if (evt.getClickCount() > 1)
       {
         tree.swapNodes(highlightNode);
         tree.reCount(tree.getTopNode());
@@ -717,8 +769,8 @@ public class TreeCanvas
 
         for (int i = 0; i < leaves.size(); i++)
         {
-          SequenceI seq =
-              (SequenceI) ( (SequenceNode) leaves.elementAt(i)).element();
+          SequenceI seq = (SequenceI) ((SequenceNode) leaves.elementAt(i))
+                  .element();
           treeSelectionChanged(seq);
         }
       }
@@ -737,10 +789,9 @@ public class TreeCanvas
     if (ob instanceof SequenceNode)
     {
       highlightNode = (SequenceNode) ob;
-      this.setToolTipText(
-          "<html>Left click to select leaves"
-          + "<br>Double-click to invert leaves"
-          + "<br>Right click to change colour");
+      this.setToolTipText("<html>Left click to select leaves"
+              + "<br>Double-click to invert leaves"
+              + "<br>Right click to change colour");
       repaint();
 
     }
@@ -756,12 +807,14 @@ public class TreeCanvas
   }
 
   public void mouseDragged(MouseEvent ect)
-  {}
+  {
+  }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void mousePressed(MouseEvent e)
   {
@@ -774,18 +827,18 @@ public class TreeCanvas
 
     if (ob instanceof SequenceI)
     {
-      treeSelectionChanged( (Sequence) ob);
+      treeSelectionChanged((Sequence) ob);
       PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
       repaint();
       return;
     }
-    else if (! (ob instanceof SequenceNode))
+    else if (!(ob instanceof SequenceNode))
     {
       // Find threshold
       if (tree.getMaxHeight() != 0)
       {
-        threshold = (float) (x - offx) / (float) (getWidth() -
-                                                  labelLength - (2 * offx));
+        threshold = (float) (x - offx)
+                / (float) (getWidth() - labelLength - (2 * offx));
 
         tree.getGroups().removeAllElements();
         tree.groupNodes(tree.getTopNode(), threshold);
@@ -812,21 +865,19 @@ public class TreeCanvas
   {
     for (int i = 0; i < tree.getGroups().size(); i++)
     {
-      Color col = new Color( (int) (Math.random() * 255),
-                            (int) (Math.random() * 255),
-                            (int) (Math.random() * 255));
-      setColor( (SequenceNode) tree.getGroups().elementAt(i),
-               col.brighter());
+      Color col = new Color((int) (Math.random() * 255), (int) (Math
+              .random() * 255), (int) (Math.random() * 255));
+      setColor((SequenceNode) tree.getGroups().elementAt(i), col.brighter());
 
-      Vector l = tree.findLeaves( (SequenceNode) tree.getGroups()
-                                 .elementAt(i),
-                                 new Vector());
+      Vector l = tree.findLeaves((SequenceNode) tree.getGroups().elementAt(
+              i), new Vector());
 
       Vector sequences = new Vector();
 
       for (int j = 0; j < l.size(); j++)
       {
-        SequenceI s1 = (SequenceI) ( (SequenceNode) l.elementAt(j)).element();
+        SequenceI s1 = (SequenceI) ((SequenceNode) l.elementAt(j))
+                .element();
 
         if (!sequences.contains(s1))
         {
@@ -840,27 +891,23 @@ public class TreeCanvas
       {
         if (av.getGlobalColourScheme() instanceof UserColourScheme)
         {
-          cs = new UserColourScheme(
-              ( (UserColourScheme) av.getGlobalColourScheme()).getColours());
+          cs = new UserColourScheme(((UserColourScheme) av
+                  .getGlobalColourScheme()).getColours());
 
         }
         else
         {
-          cs = ColourSchemeProperty.getColour(sequences,
-                                              av.alignment.getWidth(),
-                                              ColourSchemeProperty.
-                                              getColourName(
-                                                  av.getGlobalColourScheme()));
+          cs = ColourSchemeProperty.getColour(sequences, av.alignment
+                  .getWidth(), ColourSchemeProperty.getColourName(av
+                  .getGlobalColourScheme()));
         }
 
-        cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
-                        av.getIgnoreGapsConsensus());
+        cs.setThreshold(av.getGlobalColourScheme().getThreshold(), av
+                .getIgnoreGapsConsensus());
       }
 
-      SequenceGroup sg = new SequenceGroup(sequences,
-                                           null, cs, true, true, false,
-                                           0,
-                                           av.alignment.getWidth() - 1);
+      SequenceGroup sg = new SequenceGroup(sequences, null, cs, true, true,
+              false, 0, av.alignment.getWidth() - 1);
 
       sg.setName("JTreeGroup:" + sg.hashCode());
       sg.setIdColour(col);
@@ -868,12 +915,11 @@ public class TreeCanvas
       for (int a = 0; a < aps.length; a++)
       {
         if (aps[a].av.getGlobalColourScheme() != null
-            && aps[a].av.getGlobalColourScheme().conservationApplied())
+                && aps[a].av.getGlobalColourScheme().conservationApplied())
         {
           Conservation c = new Conservation("Group",
-                                            ResidueProperties.propHash, 3,
-                                            sg.getSequences(null),
-                                            sg.getStartRes(), sg.getEndRes());
+                  ResidueProperties.propHash, 3, sg.getSequences(null), sg
+                          .getStartRes(), sg.getEndRes());
 
           c.calculate();
           c.verdict(false, aps[a].av.ConsPercGaps);
@@ -888,8 +934,9 @@ public class TreeCanvas
 
   /**
    * DOCUMENT ME!
-   *
-   * @param state DOCUMENT ME!
+   * 
+   * @param state
+   *                DOCUMENT ME!
    */
   public void setShowDistances(boolean state)
   {
@@ -899,8 +946,9 @@ public class TreeCanvas
 
   /**
    * DOCUMENT ME!
-   *
-   * @param state DOCUMENT ME!
+   * 
+   * @param state
+   *                DOCUMENT ME!
    */
   public void setShowBootstrap(boolean state)
   {
@@ -910,8 +958,9 @@ public class TreeCanvas
 
   /**
    * DOCUMENT ME!
-   *
-   * @param state DOCUMENT ME!
+   * 
+   * @param state
+   *                DOCUMENT ME!
    */
   public void setMarkPlaceholders(boolean state)
   {
@@ -928,8 +977,7 @@ public class TreeCanvas
     else
     {
       return new AlignmentPanel[]
-          {
-          ap};
+      { ap };
     }
   }
 }
diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index f85ad9c..d179355 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -36,60 +36,71 @@ import jalview.jbgui.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class TreePanel
-    extends GTreePanel
+public class TreePanel extends GTreePanel
 {
   String type;
+
   String pwtype;
+
   TreeCanvas treeCanvas;
+
   NJTree tree;
+
   AlignViewport av;
 
   /**
    * Creates a new TreePanel object.
-   *
-   * @param av DOCUMENT ME!
-   * @param seqVector DOCUMENT ME!
-   * @param type DOCUMENT ME!
-   * @param pwtype DOCUMENT ME!
-   * @param s DOCUMENT ME!
-   * @param e DOCUMENT ME!
+   * 
+   * @param av
+   *                DOCUMENT ME!
+   * @param seqVector
+   *                DOCUMENT ME!
+   * @param type
+   *                DOCUMENT ME!
+   * @param pwtype
+   *                DOCUMENT ME!
+   * @param s
+   *                DOCUMENT ME!
+   * @param e
+   *                DOCUMENT ME!
    */
   public TreePanel(AlignmentPanel ap, String type, String pwtype)
   {
     super();
     initTreePanel(ap, type, pwtype, null, null);
 
-    // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
+    // We know this tree has distances. JBPNote TODO: prolly should add this as
+    // a userdefined default
     // showDistances(true);
   }
 
   /**
    * Creates a new TreePanel object.
-   *
-   * @param av DOCUMENT ME!
-   * @param seqVector DOCUMENT ME!
-   * @param newtree DOCUMENT ME!
-   * @param type DOCUMENT ME!
-   * @param pwtype DOCUMENT ME!
+   * 
+   * @param av
+   *                DOCUMENT ME!
+   * @param seqVector
+   *                DOCUMENT ME!
+   * @param newtree
+   *                DOCUMENT ME!
+   * @param type
+   *                DOCUMENT ME!
+   * @param pwtype
+   *                DOCUMENT ME!
    */
-  public TreePanel(AlignmentPanel ap,
-                   String type,
-                   String pwtype,
-                   NewickFile newtree)
+  public TreePanel(AlignmentPanel ap, String type, String pwtype,
+          NewickFile newtree)
   {
     super();
     initTreePanel(ap, type, pwtype, newtree, null);
   }
 
-  public TreePanel(AlignmentPanel av,
-                   String type,
-                   String pwtype,
-                   NewickFile newtree, AlignmentView inputData)
+  public TreePanel(AlignmentPanel av, String type, String pwtype,
+          NewickFile newtree, AlignmentView inputData)
   {
     super();
     initTreePanel(av, type, pwtype, newtree, inputData);
@@ -106,7 +117,7 @@ public class TreePanel
   }
 
   void initTreePanel(AlignmentPanel ap, String type, String pwtype,
-                     NewickFile newTree, AlignmentView inputData)
+          NewickFile newTree, AlignmentView inputData)
   {
 
     av = ap.av;
@@ -132,11 +143,13 @@ public class TreePanel
           }
           if (evt.getNewValue() == null)
           {
-            System.out.println("new alignment sequences vector value is null");
+            System.out
+                    .println("new alignment sequences vector value is null");
           }
 
-          tree.UpdatePlaceHolders( (Vector) evt.getNewValue());
-          treeCanvas.nameHash.clear(); // reset the mapping between canvas rectangles and leafnodes
+          tree.UpdatePlaceHolders((Vector) evt.getNewValue());
+          treeCanvas.nameHash.clear(); // reset the mapping between canvas
+                                        // rectangles and leafnodes
           repaint();
         }
       }
@@ -158,8 +171,8 @@ public class TreePanel
 
   void buildAssociatedViewMenu()
   {
-    AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av.
-        getSequenceSetId());
+    AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
+            .getSequenceSetId());
     if (aps.length == 1 && treeCanvas.ap == aps[0])
     {
       associateLeavesMenu.setVisible(false);
@@ -168,7 +181,7 @@ public class TreePanel
 
     associateLeavesMenu.setVisible(true);
 
-    if ( (viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
+    if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
     {
       viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
     }
@@ -212,11 +225,12 @@ public class TreePanel
 
   }
 
-  class TreeLoader
-      extends Thread
+  class TreeLoader extends Thread
   {
     NewickFile newtree;
+
     jalview.datamodel.AlignmentView odata = null;
+
     public TreeLoader(NewickFile newtree)
     {
       this.newtree = newtree;
@@ -236,12 +250,12 @@ public class TreePanel
       {
         if (odata == null)
         {
-          tree = new NJTree(av.alignment.getSequencesArray(),
-                            newtree);
+          tree = new NJTree(av.alignment.getSequencesArray(), newtree);
         }
         else
         {
-          tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);
+          tree = new NJTree(av.alignment.getSequencesArray(), odata,
+                  newtree);
         }
         if (!tree.hasOriginalSequenceData())
         {
@@ -252,7 +266,8 @@ public class TreePanel
       {
         int start, end;
         SequenceI[] seqs;
-        AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup() != null);
+        AlignmentView seqStrings = av.getAlignmentView(av
+                .getSelectionGroup() != null);
         if (av.getSelectionGroup() == null)
         {
           start = 0;
@@ -304,7 +319,7 @@ public class TreePanel
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public NJTree getTree()
@@ -314,8 +329,9 @@ public class TreePanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void textbox_actionPerformed(ActionEvent e)
   {
@@ -343,21 +359,22 @@ public class TreePanel
 
     Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
 
-    jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
+    jalview.io.NewickFile fout = new jalview.io.NewickFile(tree
+            .getTopNode());
     cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
-                           tree.isHasRootDistance()));
+            tree.isHasRootDistance()));
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void saveAsNewick_actionPerformed(ActionEvent e)
   {
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-        getProperty(
-            "LAST_DIRECTORY"));
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+            .getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle("Save tree as newick file");
     chooser.setToolTipText("Save");
@@ -367,21 +384,20 @@ public class TreePanel
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       String choice = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-                                    chooser.getSelectedFile().getParent());
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+              .getSelectedFile().getParent());
 
       try
       {
-        jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
-        String output = fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
-                                   tree.isHasRootDistance());
-        java.io.PrintWriter out = new java.io.PrintWriter(new java.io.
-            FileWriter(
-                choice));
+        jalview.io.NewickFile fout = new jalview.io.NewickFile(tree
+                .getTopNode());
+        String output = fout.print(tree.isHasBootstrap(), tree
+                .isHasDistances(), tree.isHasRootDistance());
+        java.io.PrintWriter out = new java.io.PrintWriter(
+                new java.io.FileWriter(choice));
         out.println(output);
         out.close();
-      }
-      catch (Exception ex)
+      } catch (Exception ex)
       {
         ex.printStackTrace();
       }
@@ -390,12 +406,13 @@ public class TreePanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void printMenu_actionPerformed(ActionEvent e)
   {
-    //Putting in a thread avoids Swing painting problems
+    // Putting in a thread avoids Swing painting problems
     treeCanvas.startPrinting();
   }
 
@@ -403,29 +420,36 @@ public class TreePanel
   {
     if (!tree.hasOriginalSequenceData())
     {
-      jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
+      jalview.bin.Cache.log
+              .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
       return;
     }
-    // decide if av alignment is sufficiently different to original data to warrant a new window to be created
-    // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)
+    // decide if av alignment is sufficiently different to original data to
+    // warrant a new window to be created
+    // create new alignmnt window with hidden regions (unhiding hidden regions
+    // yields unaligned seqs)
     // or create a selection box around columns in alignment view
     // test Alignment(SeqCigar[])
     char gc = '-';
-    try {
+    try
+    {
       // we try to get the associated view's gap character
       // but this may fail if the view was closed...
-      gc = av.
-      getGapCharacter();
-      
-    } catch (Exception ex) {};
+      gc = av.getGapCharacter();
+
+    } catch (Exception ex)
+    {
+    }
+    ;
     Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(gc);
 
     if (alAndColsel != null && alAndColsel[0] != null)
     {
       // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
 
-      Alignment al = new Alignment( (SequenceI[]) alAndColsel[0]);
-      Alignment dataset = (av!=null && av.getAlignment()!=null) ? av.getAlignment().getDataset() : null;
+      Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
+      Alignment dataset = (av != null && av.getAlignment() != null) ? av
+              .getAlignment().getDataset() : null;
       if (dataset != null)
       {
         al.setDataset(dataset);
@@ -434,28 +458,28 @@ public class TreePanel
       if (true)
       {
         // make a new frame!
-        AlignFrame af = new AlignFrame(al, (ColumnSelection) alAndColsel[1],
-                                       AlignFrame.DEFAULT_WIDTH,
-                                       AlignFrame.DEFAULT_HEIGHT
-            );
+        AlignFrame af = new AlignFrame(al,
+                (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
+                AlignFrame.DEFAULT_HEIGHT);
 
-        //>>>This is a fix for the moment, until a better solution is found!!<<<
+        // >>>This is a fix for the moment, until a better solution is
+        // found!!<<<
         // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
 
-        //           af.addSortByOrderMenuItem(ServiceName + " Ordering",
-        //                                     msaorder);
+        // af.addSortByOrderMenuItem(ServiceName + " Ordering",
+        // msaorder);
 
         Desktop.addInternalFrame(af, "Original Data for " + this.title,
-                                 AlignFrame.DEFAULT_WIDTH,
-                                 AlignFrame.DEFAULT_HEIGHT);
+                AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
       }
     }
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void fitToWindow_actionPerformed(ActionEvent e)
   {
@@ -465,8 +489,9 @@ public class TreePanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void font_actionPerformed(ActionEvent e)
   {
@@ -493,8 +518,9 @@ public class TreePanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void distanceMenu_actionPerformed(ActionEvent e)
   {
@@ -503,8 +529,9 @@ public class TreePanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void bootstrapMenu_actionPerformed(ActionEvent e)
   {
@@ -513,8 +540,9 @@ public class TreePanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void placeholdersMenu_actionPerformed(ActionEvent e)
   {
@@ -523,22 +551,22 @@ public class TreePanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void epsTree_actionPerformed(ActionEvent e)
   {
     boolean accurateText = true;
 
     String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
-        "Prompt each time");
+            "Prompt each time");
 
     // If we need to prompt, and if the GUI is visible then
     // Prompt for EPS rendering style
     if (renderStyle.equalsIgnoreCase("Prompt each time")
-        && !
-        (System.getProperty("java.awt.headless") != null
-         && System.getProperty("java.awt.headless").equals("true")))
+            && !(System.getProperty("java.awt.headless") != null && System
+                    .getProperty("java.awt.headless").equals("true")))
     {
       EPSOptions eps = new EPSOptions();
       renderStyle = eps.getValue();
@@ -561,12 +589,9 @@ public class TreePanel
     try
     {
       jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
-          jalview.bin.Cache.getProperty(
-              "LAST_DIRECTORY"), new String[]
-          {"eps"},
-          new String[]
-          {"Encapsulated Postscript"},
-          "Encapsulated Postscript");
+              jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+              { "eps" }, new String[]
+              { "Encapsulated Postscript" }, "Encapsulated Postscript");
       chooser.setFileView(new jalview.io.JalviewFileView());
       chooser.setDialogTitle("Create EPS file from tree");
       chooser.setToolTipText("Save");
@@ -578,12 +603,11 @@ public class TreePanel
         return;
       }
 
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-                                    chooser.getSelectedFile().getParent());
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+              .getSelectedFile().getParent());
 
       FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
-      EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
-                                           height);
+      EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);
 
       pg.setAccurateTextMode(accurateText);
 
@@ -591,8 +615,7 @@ public class TreePanel
 
       pg.flush();
       pg.close();
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       ex.printStackTrace();
     }
@@ -600,8 +623,9 @@ public class TreePanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void pngTree_actionPerformed(ActionEvent e)
   {
@@ -611,12 +635,9 @@ public class TreePanel
     try
     {
       jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
-          jalview.bin.Cache.getProperty(
-              "LAST_DIRECTORY"), new String[]
-          {"png"},
-          new String[]
-          {"Portable network graphics"},
-          "Portable network graphics");
+              jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+              { "png" }, new String[]
+              { "Portable network graphics" }, "Portable network graphics");
 
       chooser.setFileView(new jalview.io.JalviewFileView());
       chooser.setDialogTitle("Create PNG image from tree");
@@ -629,21 +650,20 @@ public class TreePanel
         return;
       }
 
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-                                    chooser.getSelectedFile().getParent());
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+              .getSelectedFile().getParent());
 
       FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
 
       BufferedImage bi = new BufferedImage(width, height,
-                                           BufferedImage.TYPE_INT_RGB);
+              BufferedImage.TYPE_INT_RGB);
       Graphics png = bi.getGraphics();
 
       treeCanvas.draw(png, width, height);
 
       ImageIO.write(bi, "png", out);
       out.close();
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       ex.printStackTrace();
     }
diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 85f35cd..ca1ebf4 100755
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -33,27 +33,36 @@ import jalview.schemes.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class UserDefinedColours
-    extends GUserDefinedColours implements ChangeListener
+public class UserDefinedColours extends GUserDefinedColours implements
+        ChangeListener
 {
   AlignmentPanel ap;
+
   SequenceGroup seqGroup;
+
   Vector selectedButtons;
+
   ColourSchemeI oldColourScheme;
+
   JInternalFrame frame;
+
   AppJmol jmol;
+
   Vector upperCaseButtons;
+
   Vector lowerCaseButtons;
 
   /**
    * Creates a new UserDefinedColours object.
-   *
-   * @param ap DOCUMENT ME!
-   * @param sg DOCUMENT ME!
+   * 
+   * @param ap
+   *                DOCUMENT ME!
+   * @param sg
+   *                DOCUMENT ME!
    */
   public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
   {
@@ -75,8 +84,8 @@ public class UserDefinedColours
 
     if (oldColourScheme instanceof UserColourScheme)
     {
-      schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());
-      if ( ( (UserColourScheme) oldColourScheme).getLowerCaseColours() != null)
+      schemeName.setText(((UserColourScheme) oldColourScheme).getName());
+      if (((UserColourScheme) oldColourScheme).getLowerCaseColours() != null)
       {
         caseSensitive.setSelected(true);
         lcaseColour.setEnabled(true);
@@ -106,7 +115,7 @@ public class UserDefinedColours
 
     if (oldColourScheme instanceof UserColourScheme)
     {
-      schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());
+      schemeName.setText(((UserColourScheme) oldColourScheme).getName());
     }
 
     resetButtonPanel(false);
@@ -152,13 +161,12 @@ public class UserDefinedColours
       }
       else
       {
-        label = ResidueProperties.aa2Triplet.get
-            (ResidueProperties.aa[i]).toString();
+        label = ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i])
+                .toString();
       }
 
-      button = makeButton(label,
-                          ResidueProperties.aa[i],
-                          upperCaseButtons, i);
+      button = makeButton(label, ResidueProperties.aa[i], upperCaseButtons,
+              i);
 
       buttonPanel.add(button);
     }
@@ -188,11 +196,8 @@ public class UserDefinedColours
       {
         int row = i / cols + 1;
         int index = (row * cols) + i;
-        button = makeButton(
-            ResidueProperties.aa[i].toLowerCase(),
-            ResidueProperties.aa[i].toLowerCase(),
-            lowerCaseButtons,
-            i);
+        button = makeButton(ResidueProperties.aa[i].toLowerCase(),
+                ResidueProperties.aa[i].toLowerCase(), lowerCaseButtons, i);
 
         buttonPanel.add(button, index);
       }
@@ -211,8 +216,9 @@ public class UserDefinedColours
 
   /**
    * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
    */
   public void stateChanged(ChangeEvent evt)
   {
@@ -223,8 +229,8 @@ public class UserDefinedColours
       {
         button = (JButton) selectedButtons.elementAt(i);
         button.setBackground(colorChooser.getColor());
-        button.setForeground(button.getBackground().brighter().brighter().
-                             brighter());
+        button.setForeground(button.getBackground().brighter().brighter()
+                .brighter());
       }
       if (button == lcaseColour)
       {
@@ -232,8 +238,8 @@ public class UserDefinedColours
         {
           button = (JButton) lowerCaseButtons.elementAt(i);
           button.setBackground(colorChooser.getColor());
-          button.setForeground(button.getBackground().brighter().brighter().
-                               brighter());
+          button.setForeground(button.getBackground().brighter().brighter()
+                  .brighter());
         }
       }
     }
@@ -241,8 +247,9 @@ public class UserDefinedColours
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void colourButtonPressed(MouseEvent e)
   {
@@ -258,7 +265,8 @@ public class UserDefinedColours
       JButton start, end = (JButton) e.getSource();
       if (selectedButtons.size() > 0)
       {
-        start = (JButton) selectedButtons.elementAt(selectedButtons.size() - 1);
+        start = (JButton) selectedButtons
+                .elementAt(selectedButtons.size() - 1);
       }
       else
       {
@@ -290,7 +298,9 @@ public class UserDefinedColours
         JButton button = (JButton) buttonPanel.getComponent(b);
         if (!selectedButtons.contains(button))
         {
-          button.setForeground(button.getBackground().brighter().brighter());
+          button
+                  .setForeground(button.getBackground().brighter()
+                          .brighter());
           selectedButtons.add(button);
         }
       }
@@ -316,28 +326,30 @@ public class UserDefinedColours
       }
       else
       {
-        pressed.setForeground(pressed.getBackground().brighter().brighter());
+        pressed
+                .setForeground(pressed.getBackground().brighter()
+                        .brighter());
         selectedButtons.addElement(pressed);
       }
     }
 
     if (selectedButtons.size() > 0)
     {
-      colorChooser.setColor( ( (JButton) selectedButtons.elementAt(0)).
-                            getBackground());
+      colorChooser.setColor(((JButton) selectedButtons.elementAt(0))
+              .getBackground());
     }
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param label DOCUMENT ME!
-   * @param aa DOCUMENT ME!
+   * 
+   * @param label
+   *                DOCUMENT ME!
+   * @param aa
+   *                DOCUMENT ME!
    */
-  JButton makeButton(String label,
-                     String aa,
-                     Vector caseSensitiveButtons,
-                     int buttonIndex)
+  JButton makeButton(String label, String aa, Vector caseSensitiveButtons,
+          int buttonIndex)
   {
     final JButton button;
     Color col;
@@ -365,9 +377,9 @@ public class UserDefinedColours
       try
       {
         col = oldColourScheme.findColour(aa.charAt(0), -1);
+      } catch (Exception ex)
+      {
       }
-      catch (Exception ex)
-      {}
     }
 
     if (caseSensitive.isSelected())
@@ -389,8 +401,9 @@ public class UserDefinedColours
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void okButton_actionPerformed(ActionEvent e)
   {
@@ -399,16 +412,16 @@ public class UserDefinedColours
     try
     {
       frame.setClosed(true);
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
     }
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void applyButton_actionPerformed(ActionEvent e)
   {
@@ -464,20 +477,19 @@ public class UserDefinedColours
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void loadbutton_actionPerformed(ActionEvent e)
   {
     upperCaseButtons = new Vector();
     lowerCaseButtons = new Vector();
 
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-        getProperty(
-            "LAST_DIRECTORY"), new String[]
-        {"jc"},
-        new String[]
-        {"Jalview User Colours"}, "Jalview User Colours");
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+            .getProperty("LAST_DIRECTORY"), new String[]
+    { "jc" }, new String[]
+    { "Jalview User Colours" }, "Jalview User Colours");
     chooser.setFileView(new jalview.io.JalviewFileView());
     chooser.setDialogTitle("Load colour scheme");
     chooser.setToolTipText("Load");
@@ -489,11 +501,11 @@ public class UserDefinedColours
       File choice = chooser.getSelectedFile();
       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
       String defaultColours = jalview.bin.Cache.getDefault(
-          "USER_DEFINED_COLOURS",
-          choice.getPath());
+              "USER_DEFINED_COLOURS", choice.getPath());
       if (defaultColours.indexOf(choice.getPath()) == -1)
       {
-        defaultColours = defaultColours.concat("|").concat(choice.getPath());
+        defaultColours = defaultColours.concat("|")
+                .concat(choice.getPath());
       }
 
       jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
@@ -532,7 +544,7 @@ public class UserDefinedColours
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public static UserColourScheme loadDefaultColours()
@@ -565,9 +577,10 @@ public class UserDefinedColours
 
   /**
    * DOCUMENT ME!
-   *
-   * @param file DOCUMENT ME!
-   *
+   * 
+   * @param file
+   *                DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   static UserColourScheme loadColours(String file)
@@ -576,16 +589,15 @@ public class UserDefinedColours
     Color[] newColours = null;
     try
     {
-      InputStreamReader in = new InputStreamReader(new FileInputStream(
-          file), "UTF-8");
+      InputStreamReader in = new InputStreamReader(
+              new FileInputStream(file), "UTF-8");
 
-      jalview.schemabinding.version2.JalviewUserColours jucs
-          = new jalview.schemabinding.version2.JalviewUserColours();
+      jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours();
 
-      org.exolab.castor.xml.Unmarshaller unmar
-          = new org.exolab.castor.xml.Unmarshaller(jucs);
-      jucs = (jalview.schemabinding.version2.JalviewUserColours) unmar.
-          unmarshal(in);
+      org.exolab.castor.xml.Unmarshaller unmar = new org.exolab.castor.xml.Unmarshaller(
+              jucs);
+      jucs = (jalview.schemabinding.version2.JalviewUserColours) unmar
+              .unmarshal(in);
 
       newColours = new Color[24];
 
@@ -599,7 +611,8 @@ public class UserDefinedColours
         name = jucs.getColour(i).getName();
         if (ResidueProperties.aa3Hash.containsKey(name))
         {
-          index = ( (Integer) ResidueProperties.aa3Hash.get(name)).intValue();
+          index = ((Integer) ResidueProperties.aa3Hash.get(name))
+                  .intValue();
         }
         else
         {
@@ -617,13 +630,13 @@ public class UserDefinedColours
             lowerCase = new Color[23];
           }
           caseSensitive = true;
-          lowerCase[index] = new Color(Integer.parseInt(
-              jucs.getColour(i).getRGB(), 16));
+          lowerCase[index] = new Color(Integer.parseInt(jucs.getColour(i)
+                  .getRGB(), 16));
         }
         else
         {
-          newColours[index] = new Color(Integer.parseInt(
-              jucs.getColour(i).getRGB(), 16));
+          newColours[index] = new Color(Integer.parseInt(jucs.getColour(i)
+                  .getRGB(), 16));
         }
       }
 
@@ -637,17 +650,15 @@ public class UserDefinedColours
         }
       }
 
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
-      //Could be Archive Jalview format
+      // Could be Archive Jalview format
       try
       {
         InputStreamReader in = new InputStreamReader(new FileInputStream(
-            file), "UTF-8");
+                file), "UTF-8");
 
-        jalview.binding.JalviewUserColours jucs
-            = new jalview.binding.JalviewUserColours();
+        jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours();
 
         jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);
 
@@ -655,16 +666,15 @@ public class UserDefinedColours
 
         for (int i = 0; i < 24; i++)
         {
-          newColours[i] = new Color(Integer.parseInt(
-              jucs.getColour(i).getRGB(), 16));
+          newColours[i] = new Color(Integer.parseInt(jucs.getColour(i)
+                  .getRGB(), 16));
         }
         if (newColours != null)
         {
           ucs = new UserColourScheme(newColours);
           ucs.setName(jucs.getSchemeName());
         }
-      }
-      catch (Exception ex2)
+      } catch (Exception ex2)
       {
         ex2.printStackTrace();
       }
@@ -680,27 +690,28 @@ public class UserDefinedColours
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void savebutton_actionPerformed(ActionEvent e)
   {
     if (schemeName.getText().trim().length() < 1)
     {
       JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                            "User colour scheme must have a name!",
-                                            "No name for colour scheme",
-                                            JOptionPane.WARNING_MESSAGE);
+              "User colour scheme must have a name!",
+              "No name for colour scheme", JOptionPane.WARNING_MESSAGE);
       return;
     }
 
-    if (userColourSchemes != null &&
-        userColourSchemes.containsKey(schemeName.getText()))
+    if (userColourSchemes != null
+            && userColourSchemes.containsKey(schemeName.getText()))
     {
       int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
-          "Colour scheme " + schemeName.getText() + " exists."
-          + "\nContinue saving colour scheme as " + schemeName.getText() + "?",
-          "Duplicate scheme name", JOptionPane.YES_NO_OPTION);
+              "Colour scheme " + schemeName.getText() + " exists."
+                      + "\nContinue saving colour scheme as "
+                      + schemeName.getText() + "?",
+              "Duplicate scheme name", JOptionPane.YES_NO_OPTION);
       if (reply != JOptionPane.YES_OPTION)
       {
         return;
@@ -708,12 +719,10 @@ public class UserDefinedColours
 
       userColourSchemes.remove(schemeName.getText());
     }
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-        getProperty(
-            "LAST_DIRECTORY"), new String[]
-        {"jc"},
-        new String[]
-        {"Jalview User Colours"}, "Jalview User Colours");
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+            .getProperty("LAST_DIRECTORY"), new String[]
+    { "jc" }, new String[]
+    { "Jalview User Colours" }, "Jalview User Colours");
 
     chooser.setFileView(new jalview.io.JalviewFileView());
     chooser.setDialogTitle("Save colour scheme");
@@ -725,7 +734,7 @@ public class UserDefinedColours
     {
       String choice = chooser.getSelectedFile().getPath();
       String defaultColours = jalview.bin.Cache.getDefault(
-          "USER_DEFINED_COLOURS", choice);
+              "USER_DEFINED_COLOURS", choice);
       if (defaultColours.indexOf(choice) == -1)
       {
         if (defaultColours.length() > 0)
@@ -741,30 +750,27 @@ public class UserDefinedColours
 
       jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
 
-      jalview.schemabinding.version2.JalviewUserColours ucs
-          = new jalview.schemabinding.version2.JalviewUserColours();
+      jalview.schemabinding.version2.JalviewUserColours ucs = new jalview.schemabinding.version2.JalviewUserColours();
 
       ucs.setSchemeName(schemeName.getText());
       try
       {
         PrintWriter out = new PrintWriter(new OutputStreamWriter(
-            new FileOutputStream(choice), "UTF-8"));
+                new FileOutputStream(choice), "UTF-8"));
 
         for (int i = 0; i < buttonPanel.getComponentCount(); i++)
         {
           JButton button = (JButton) buttonPanel.getComponent(i);
-          jalview.schemabinding.version2.Colour col
-              = new jalview.schemabinding.version2.Colour();
+          jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
           col.setName(button.getText());
-          col.setRGB(jalview.util.Format.getHexString(
-              button.getBackground()));
+          col.setRGB(jalview.util.Format.getHexString(button
+                  .getBackground()));
           ucs.addColour(col);
         }
 
         ucs.marshal(out);
         out.close();
-      }
-      catch (Exception ex)
+      } catch (Exception ex)
       {
         ex.printStackTrace();
       }
@@ -773,8 +779,9 @@ public class UserDefinedColours
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void cancelButton_actionPerformed(ActionEvent e)
   {
@@ -799,8 +806,7 @@ public class UserDefinedColours
     try
     {
       frame.setClosed(true);
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
     }
   }
@@ -840,8 +846,7 @@ public class UserDefinedColours
           coloursFound.append(file);
           userColourSchemes.put(ucs.getName(), ucs);
         }
-      }
-      catch (Exception ex)
+      } catch (Exception ex)
       {
         System.out.println("Error loading User ColourFile\n" + ex);
       }
@@ -850,12 +855,13 @@ public class UserDefinedColours
     {
       if (coloursFound.toString().length() > 1)
       {
-        jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
-                                      coloursFound.toString());
+        jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", coloursFound
+                .toString());
       }
       else
       {
-        jalview.bin.Cache.applicationProperties.remove("USER_DEFINED_COLOURS");
+        jalview.bin.Cache.applicationProperties
+                .remove("USER_DEFINED_COLOURS");
       }
     }
   }
@@ -869,8 +875,8 @@ public class UserDefinedColours
     userColourSchemes = new Hashtable();
 
     StringBuffer coloursFound = new StringBuffer();
-    StringTokenizer st = new StringTokenizer(
-        jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|");
+    StringTokenizer st = new StringTokenizer(jalview.bin.Cache
+            .getProperty("USER_DEFINED_COLOURS"), "|");
 
     while (st.hasMoreElements())
     {
@@ -887,8 +893,7 @@ public class UserDefinedColours
           coloursFound.append(file);
           userColourSchemes.put(ucs.getName(), ucs);
         }
-      }
-      catch (Exception ex)
+      } catch (Exception ex)
       {
         System.out.println("Error loading User ColourFile\n" + ex);
       }
@@ -896,12 +901,13 @@ public class UserDefinedColours
 
     if (coloursFound.toString().length() > 1)
     {
-      jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
-                                    coloursFound.toString());
+      jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", coloursFound
+              .toString());
     }
     else
     {
-      jalview.bin.Cache.applicationProperties.remove("USER_DEFINED_COLOURS");
+      jalview.bin.Cache.applicationProperties
+              .remove("USER_DEFINED_COLOURS");
     }
 
   }
diff --git a/src/jalview/gui/UserQuestionnaireCheck.java b/src/jalview/gui/UserQuestionnaireCheck.java
index 0accc9c..8a596ad 100644
--- a/src/jalview/gui/UserQuestionnaireCheck.java
+++ b/src/jalview/gui/UserQuestionnaireCheck.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.gui;
 
 import java.io.*;
@@ -5,24 +23,25 @@ import java.net.*;
 
 import javax.swing.*;
 
-public class UserQuestionnaireCheck
-    implements Runnable
+public class UserQuestionnaireCheck implements Runnable
 {
   /**
    * Implements the client side machinery for detecting a new questionnaire,
-   * checking if the user has responded to an existing one,
-   * and prompting the user for responding to a questionnaire.
-   * This is intended to work with the perl CGI scripts checkresponder.pl and
-   * questionnaire.pl
+   * checking if the user has responded to an existing one, and prompting the
+   * user for responding to a questionnaire. This is intended to work with the
+   * perl CGI scripts checkresponder.pl and questionnaire.pl
    */
   String url = null;
+
   UserQuestionnaireCheck(String url)
   {
     if (url.indexOf("questionnaire.pl") == -1)
     {
-      jalview.bin.Cache.log.error("'" + url +
-          "' is an Invalid URL for the checkForQuestionnaire() method.\n"
-                                  + "This argument is only for questionnaires derived from jalview's questionnaire.pl cgi interface.");
+      jalview.bin.Cache.log
+              .error("'"
+                      + url
+                      + "' is an Invalid URL for the checkForQuestionnaire() method.\n"
+                      + "This argument is only for questionnaires derived from jalview's questionnaire.pl cgi interface.");
     }
     else
     {
@@ -31,16 +50,17 @@ public class UserQuestionnaireCheck
   }
 
   String qid = null, rid = null;
-  private boolean checkresponse(URL qurl)
-      throws Exception
+
+  private boolean checkresponse(URL qurl) throws Exception
   {
     jalview.bin.Cache.log.debug("Checking Response for : " + qurl);
     boolean prompt = false;
-    // see if we have already responsed to this questionnaire or get a new qid/rid pair
-    BufferedReader br = new BufferedReader(new InputStreamReader(qurl.
-        openStream()));
+    // see if we have already responsed to this questionnaire or get a new
+    // qid/rid pair
+    BufferedReader br = new BufferedReader(new InputStreamReader(qurl
+            .openStream()));
     String qresp;
-    while ( (qresp = br.readLine()) != null)
+    while ((qresp = br.readLine()) != null)
     {
       if (qresp.indexOf("NOTYET:") == 0)
       {
@@ -81,21 +101,22 @@ public class UserQuestionnaireCheck
       String lastq = jalview.bin.Cache.getProperty("QUESTIONNAIRE");
       if (lastq == null)
       {
-        prompt = checkresponse(new URL(url + (url.indexOf('?') > -1 ? "&" : "?") +
-                                       "checkresponse=1"));
+        prompt = checkresponse(new URL(url
+                + (url.indexOf('?') > -1 ? "&" : "?") + "checkresponse=1"));
       }
       else
       {
-        String qurl = url + (url.indexOf('?') > -1 ? "&" : "?") +
-            "checkresponse=1";
+        String qurl = url + (url.indexOf('?') > -1 ? "&" : "?")
+                + "checkresponse=1";
         // query the server with the old qid/id pair
-        String qqid = lastq.indexOf(':') > -1 ?
-            lastq.substring(0, lastq.indexOf(':')) : null;
+        String qqid = lastq.indexOf(':') > -1 ? lastq.substring(0, lastq
+                .indexOf(':')) : null;
         if (qqid != null && qqid != "null" && qqid.length() > 0)
         {
           qurl += "&qid=" + qqid;
           qid = qqid;
-          String qrid = lastq.substring(lastq.indexOf(':') + 1); // retrieve old rid
+          String qrid = lastq.substring(lastq.indexOf(':') + 1); // retrieve
+                                                                  // old rid
           if (qrid != null && !qrid.equals("null"))
           {
             rid = qrid;
@@ -112,16 +133,15 @@ public class UserQuestionnaireCheck
       }
       if (prompt)
       {
-        String qurl = url + (url.indexOf('?') > -1 ? "&" : "?") + "qid=" + qid +
-            "&rid=" + rid;
-        jalview.bin.Cache.log.info("Prompting user for questionnaire at " +
-                                   qurl);
+        String qurl = url + (url.indexOf('?') > -1 ? "&" : "?") + "qid="
+                + qid + "&rid=" + rid;
+        jalview.bin.Cache.log.info("Prompting user for questionnaire at "
+                + qurl);
         int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
-            "There is a new Questionnaire available." +
-            "Would you like to complete it now ?\n",
-            "Jalview User Survey",
-            JOptionPane.YES_NO_OPTION,
-            JOptionPane.QUESTION_MESSAGE);
+                "There is a new Questionnaire available."
+                        + "Would you like to complete it now ?\n",
+                "Jalview User Survey", JOptionPane.YES_NO_OPTION,
+                JOptionPane.QUESTION_MESSAGE);
 
         if (reply == JOptionPane.YES_OPTION)
         {
@@ -129,11 +149,10 @@ public class UserQuestionnaireCheck
           jalview.util.BrowserLauncher.openURL(qurl);
         }
       }
-    }
-    catch (Exception e)
+    } catch (Exception e)
     {
-      jalview.bin.Cache.log.warn("When trying to access questionnaire URL " +
-                                 url, e);
+      jalview.bin.Cache.log.warn("When trying to access questionnaire URL "
+              + url, e);
     }
   }
 
diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java
index 121a200..5988bb8 100644
--- a/src/jalview/gui/VamsasApplication.java
+++ b/src/jalview/gui/VamsasApplication.java
@@ -1,5 +1,20 @@
-/**
- *
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
 package jalview.gui;
 
@@ -164,25 +179,31 @@ public class VamsasApplication
 
   private void setVclientConfig()
   {
-    if (vclient==null)
+    if (vclient == null)
     {
       return;
     }
-    try {
+    try
+    {
       if (vclient instanceof uk.ac.vamsas.client.simpleclient.SimpleClient)
       {
-        uk.ac.vamsas.client.simpleclient.SimpleClientConfig cfg = ((uk.ac.vamsas.client.simpleclient.SimpleClient)  vclient).getSimpleClientConfig();
+        uk.ac.vamsas.client.simpleclient.SimpleClientConfig cfg = ((uk.ac.vamsas.client.simpleclient.SimpleClient) vclient)
+                .getSimpleClientConfig();
         cfg._validatemergedroots = false;
-        cfg._validateupdatedroots= true; //we may write rubbish otherwise. 
+        cfg._validateupdatedroots = true; // we may write rubbish otherwise.
       }
-    }
-    catch (Error e)
+    } catch (Error e)
     {
-      Cache.log.warn("Probable SERIOUS VAMSAS client incompatibility - carrying on regardless",e);
-    }
-    catch (Exception e)
+      Cache.log
+              .warn(
+                      "Probable SERIOUS VAMSAS client incompatibility - carrying on regardless",
+                      e);
+    } catch (Exception e)
     {
-      Cache.log.warn("Probable VAMSAS client incompatibility - carrying on regardless",e);
+      Cache.log
+              .warn(
+                      "Probable VAMSAS client incompatibility - carrying on regardless",
+                      e);
     }
   }
 
@@ -223,7 +244,7 @@ public class VamsasApplication
     Cache.log
             .debug("Jalview loading the Vamsas Session for the first time.");
     dealWithDocumentUpdate(false); // we don't push an update out to the
-                                    // document yet.
+    // document yet.
     Cache.log.debug("... finished update for the first time.");
   }
 
@@ -263,17 +284,18 @@ public class VamsasApplication
 
   public void push_update()
   {
-    Thread udthread = new Thread(new Runnable() {
+    Thread udthread = new Thread(new Runnable()
+    {
 
       public void run()
       {
         Cache.log.info("Jalview updating to the Vamsas Session.");
-    
+
         dealWithDocumentUpdate(true);
         /*
          * IClientDocument cdoc=null; try { cdoc = vclient.getClientDocument(); }
-         * catch (Exception e) { Cache.log.error("Failed to get client document for
-         * update."); // RAISE A WARNING DIALOG disableGui(false); return; }
+         * catch (Exception e) { Cache.log.error("Failed to get client document
+         * for update."); // RAISE A WARNING DIALOG disableGui(false); return; }
          * updateVamsasDocument(cdoc); updateJalviewGui();
          * cdoc.setVamsasRoots(cdoc.getVamsasRoots()); // propagate update flags
          * back vclient.updateDocument(cdoc);
@@ -281,7 +303,7 @@ public class VamsasApplication
         Cache.log.info("Jalview finished updating to the Vamsas Session.");
         // TODO Auto-generated method stub
       }
-      
+
     });
     udthread.start();
   }
@@ -342,7 +364,9 @@ public class VamsasApplication
   IdentityHashMap jv2vobj = null;
 
   Hashtable vobj2jv = null;
+
   Hashtable alRedoState = null;
+
   public void updateVamsasDocument(IClientDocument doc)
   {
     ensureJvVamsas();
@@ -482,27 +506,35 @@ public class VamsasApplication
   private void addStoreDocumentHandler()
   {
     final VamsasApplication client = this;
-    vclient.addVorbaEventHandler(uk.ac.vamsas.client.Events.DOCUMENT_REQUESTTOCLOSE, new PropertyChangeListener()
-    {
-      public void propertyChange(PropertyChangeEvent evt)
-      {
-        Cache.log.debug("Asking user if the vamsas session should be stored.");
-        int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
-                "The current VAMSAS session has unsaved data - do you want to save it ?",
-            "VAMSAS Session Shutdown",
-            JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
-        
-            if(reply==JOptionPane.YES_OPTION)
+    vclient.addVorbaEventHandler(
+            uk.ac.vamsas.client.Events.DOCUMENT_REQUESTTOCLOSE,
+            new PropertyChangeListener()
             {
-              Cache.log.debug("Prompting for vamsas store filename.");
-              Desktop.instance.vamsasSave_actionPerformed(null);
-              Cache.log.debug("Finished attempt at storing document.");
-            } 
-            Cache.log.debug("finished dealing with REQUESTTOCLOSE event.");
-      }
-    });
+              public void propertyChange(PropertyChangeEvent evt)
+              {
+                Cache.log
+                        .debug("Asking user if the vamsas session should be stored.");
+                int reply = JOptionPane
+                        .showInternalConfirmDialog(
+                                Desktop.desktop,
+                                "The current VAMSAS session has unsaved data - do you want to save it ?",
+                                "VAMSAS Session Shutdown",
+                                JOptionPane.YES_NO_OPTION,
+                                JOptionPane.QUESTION_MESSAGE);
+
+                if (reply == JOptionPane.YES_OPTION)
+                {
+                  Cache.log.debug("Prompting for vamsas store filename.");
+                  Desktop.instance.vamsasSave_actionPerformed(null);
+                  Cache.log.debug("Finished attempt at storing document.");
+                }
+                Cache.log
+                        .debug("finished dealing with REQUESTTOCLOSE event.");
+              }
+            });
     Cache.log.debug("Added Jalview handler for vamsas document updates.");
   }
+
   public void disableGui(boolean b)
   {
     Desktop.instance.setVamsasUpdate(b);
diff --git a/src/jalview/gui/WebserviceInfo.java b/src/jalview/gui/WebserviceInfo.java
index 5f02c09..a0eeedf 100755
--- a/src/jalview/gui/WebserviceInfo.java
+++ b/src/jalview/gui/WebserviceInfo.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
diff --git a/src/jalview/io/AMSAFile.java b/src/jalview/io/AMSAFile.java
index e7e6d97..569d351 100644
--- a/src/jalview/io/AMSAFile.java
+++ b/src/jalview/io/AMSAFile.java
@@ -1,100 +1,99 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.io;
-
-import jalview.datamodel.*;
-
-public class AMSAFile
-    extends jalview.io.FastaFile
-{
-
-  AlignmentI al;
-  /**
-   * Creates a new AMSAFile object for output.
-   */
-  public AMSAFile(AlignmentI al)
-  {
-    this.al = al;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public String print()
-  {
-    super.print(getSeqsAsArray());
-
-    AlignmentAnnotation aa;
-    if (al.getAlignmentAnnotation() != null)
-    {
-
-      for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
-      {
-        aa = al.getAlignmentAnnotation()[i];
-
-
-        if (aa.autoCalculated || !aa.visible)
-        {
-          continue;
-        }
-
-        out.append(">#_" + aa.label);
-        if (aa.description != null)
-        {
-          out.append(" " + aa.description);
-        }
-
-        out.append("\n");
-
-        int nochunks = Math.min(aa.annotations.length, al.getWidth())
-                        / len + 1;
-
-        for (int j = 0; j < nochunks; j++)
-        {
-          int start = j * len;
-          int end = start + len;
-          if (end > aa.annotations.length)
-          {
-            end = aa.annotations.length;
-          }
-
-          String ch;
-          for (int k = start; k < end; k++)
-          {
-            if (aa.annotations[k] == null)
-            {
-              ch = " ";
-            }
-            else
-            {
-              ch = aa.annotations[k].displayCharacter;
-            }
-
-            out.append(ch);
-
-          }
-          out.append("\n");
-        }
-      }
-    }
-    return out.toString();
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.io;
+
+import jalview.datamodel.*;
+
+public class AMSAFile extends jalview.io.FastaFile
+{
+
+  AlignmentI al;
+
+  /**
+   * Creates a new AMSAFile object for output.
+   */
+  public AMSAFile(AlignmentI al)
+  {
+    this.al = al;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public String print()
+  {
+    super.print(getSeqsAsArray());
+
+    AlignmentAnnotation aa;
+    if (al.getAlignmentAnnotation() != null)
+    {
+
+      for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
+      {
+        aa = al.getAlignmentAnnotation()[i];
+
+        if (aa.autoCalculated || !aa.visible)
+        {
+          continue;
+        }
+
+        out.append(">#_" + aa.label);
+        if (aa.description != null)
+        {
+          out.append(" " + aa.description);
+        }
+
+        out.append("\n");
+
+        int nochunks = Math.min(aa.annotations.length, al.getWidth()) / len
+                + 1;
+
+        for (int j = 0; j < nochunks; j++)
+        {
+          int start = j * len;
+          int end = start + len;
+          if (end > aa.annotations.length)
+          {
+            end = aa.annotations.length;
+          }
+
+          String ch;
+          for (int k = start; k < end; k++)
+          {
+            if (aa.annotations[k] == null)
+            {
+              ch = " ";
+            }
+            else
+            {
+              ch = aa.annotations[k].displayCharacter;
+            }
+
+            out.append(ch);
+
+          }
+          out.append("\n");
+        }
+      }
+    }
+    return out.toString();
+  }
+}
diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 2ad32f0..3ca2563 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -25,29 +25,35 @@ import jalview.datamodel.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
-public abstract class AlignFile
-    extends FileParse
+public abstract class AlignFile extends FileParse
 {
   int noSeqs = 0;
+
   int maxLength = 0;
+
   /**
    * Sequences to be added to form a new alignment.
    */
   protected Vector seqs;
+
   /**
    * annotation to be added to generated alignment object
    */
   protected Vector annotations;
+
   /**
    * Properties to be added to generated alignment object
    */
   protected Hashtable properties;
+
   long start;
+
   long end;
+
   boolean jvSuffix = true;
 
   /**
@@ -59,11 +65,13 @@ public abstract class AlignFile
 
   /**
    * Constructor which parses the data from a file of some specified type.
-   * @param inFile Filename to read from.
-   * @param type   What type of file to read from (File, URL)
+   * 
+   * @param inFile
+   *                Filename to read from.
+   * @param type
+   *                What type of file to read from (File, URL)
    */
-  public AlignFile(String inFile, String type)
-      throws IOException
+  public AlignFile(String inFile, String type) throws IOException
   {
     super(inFile, type);
 
@@ -71,8 +79,11 @@ public abstract class AlignFile
 
     parse();
   }
+
   /**
-   * Attempt to read from the position where some other parsing process left off.
+   * Attempt to read from the position where some other parsing process left
+   * off.
+   * 
    * @param source
    * @throws IOException
    */
@@ -82,6 +93,7 @@ public abstract class AlignFile
     initData();
     parse();
   }
+
   /**
    * Return the seqs Vector
    */
@@ -104,10 +116,11 @@ public abstract class AlignFile
 
     return s;
   }
+
   /**
-   * called by AppletFormatAdapter to generate
-   * an annotated alignment, rather than bare
-   * sequences.
+   * called by AppletFormatAdapter to generate an annotated alignment, rather
+   * than bare sequences.
+   * 
    * @param al
    */
   public void addAnnotations(Alignment al)
@@ -115,21 +128,21 @@ public abstract class AlignFile
     addProperties(al);
     for (int i = 0; i < annotations.size(); i++)
     {
-      al.addAnnotation(
-          (AlignmentAnnotation) annotations.elementAt(i)
-          );
+      al.addAnnotation((AlignmentAnnotation) annotations.elementAt(i));
     }
 
   }
+
   /**
-   * Add any additional information extracted
-   * from the file to the alignment properties.
+   * Add any additional information extracted from the file to the alignment
+   * properties.
+   * 
    * @note implicitly called by addAnnotations()
    * @param al
    */
   public void addProperties(Alignment al)
   {
-    if (properties!=null && properties.size()>0)
+    if (properties != null && properties.size() > 0)
     {
       Enumeration keys = properties.keys();
       Enumeration vals = properties.elements();
@@ -139,36 +152,44 @@ public abstract class AlignFile
       }
     }
   }
+
   /**
-   * Store a non-null key-value pair in a hashtable used to set alignment properties
-   * note: null keys will raise an error, null values will result in the key/value pair being silently ignored.
-   * @param key - non-null key object
-   * @param value - non-null value
+   * Store a non-null key-value pair in a hashtable used to set alignment
+   * properties note: null keys will raise an error, null values will result in
+   * the key/value pair being silently ignored.
+   * 
+   * @param key -
+   *                non-null key object
+   * @param value -
+   *                non-null value
    */
   protected void setAlignmentProperty(Object key, Object value)
   {
-    if (key==null)
+    if (key == null)
     {
-      throw new Error("Implementation error: Cannot have null alignment property key.");
+      throw new Error(
+              "Implementation error: Cannot have null alignment property key.");
     }
-    if (value==null)
+    if (value == null)
     {
       return; // null properties are ignored.
     }
-    if (properties==null)
+    if (properties == null)
     {
       properties = new Hashtable();
     }
     properties.put(key, value);
   }
+
   protected Object getAlignmentProperty(Object key)
   {
-    if (properties!=null && key!=null)
+    if (properties != null && key != null)
     {
       return properties.get(key);
     }
     return null;
   }
+
   /**
    * Initialise objects to store sequence data in.
    */
@@ -180,8 +201,9 @@ public abstract class AlignFile
 
   /**
    * DOCUMENT ME!
-   *
-   * @param s DOCUMENT ME!
+   * 
+   * @param s
+   *                DOCUMENT ME!
    */
   protected void setSeqs(SequenceI[] s)
   {
@@ -196,8 +218,7 @@ public abstract class AlignFile
   /**
    * This method must be implemented to parse the contents of the file.
    */
-  public abstract void parse()
-      throws IOException;
+  public abstract void parse() throws IOException;
 
   /**
    * Print out in alignment file format the Sequences in the seqs Vector.
@@ -211,7 +232,7 @@ public abstract class AlignFile
 
   /**
    * A general parser for ids.
-   *
+   * 
    * @String id Id to be parsed
    */
   Sequence parseId(String id)
@@ -233,20 +254,20 @@ public abstract class AlignFile
   }
 
   /**
-   * Creates the output id.
-   * Adds prefix Uniprot format source|id
-   * And suffix Jalview /start-end
-   *
+   * Creates the output id. Adds prefix Uniprot format source|id And suffix
+   * Jalview /start-end
+   * 
    * @String id Id to be parsed
    */
   String printId(SequenceI seq)
   {
     return seq.getDisplayId(jvSuffix);
   }
+
   /**
    * vector of String[] treeName, newickString pairs
    */
-  Vector newickStrings=null;
+  Vector newickStrings = null;
 
   protected void addNewickTree(String treeName, String newickString)
   {
@@ -254,12 +275,13 @@ public abstract class AlignFile
     {
       newickStrings = new Vector();
     }
-    newickStrings.addElement(new String[] { treeName, newickString});
+    newickStrings.addElement(new String[]
+    { treeName, newickString });
   }
 
   protected int getTreeCount()
   {
-    if (newickStrings==null)
+    if (newickStrings == null)
     {
       return 0;
     }
diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 288ce2f..1bc5eff 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.io;
 
 import java.io.*;
@@ -29,34 +28,39 @@ import jalview.schemes.*;
 
 public class AnnotationFile
 {
-  StringBuffer text = new StringBuffer(
-      "JALVIEW_ANNOTATION\n"
-      + "# Created: "
-      + new java.util.Date() + "\n\n");
+  StringBuffer text = new StringBuffer("JALVIEW_ANNOTATION\n"
+          + "# Created: " + new java.util.Date() + "\n\n");
+
   /**
-   * convenience method for pre-2.4 feature files which have no view, hidden columns or hidden row keywords.
+   * convenience method for pre-2.4 feature files which have no view, hidden
+   * columns or hidden row keywords.
+   * 
    * @param annotations
    * @param groups
    * @param properties
    * @return feature file as a string.
    */
   public String printAnnotations(AlignmentAnnotation[] annotations,
-                                 Vector groups,
-                                 Hashtable properties)
+          Vector groups, Hashtable properties)
   {
-    return printAnnotations(annotations, groups,
-            properties, null);
+    return printAnnotations(annotations, groups, properties, null);
 
   }
+
   /**
-   * hold all the information about a particular view definition
-   * read from or written out in an annotations file.
+   * hold all the information about a particular view definition read from or
+   * written out in an annotations file.
    */
-  public class ViewDef {
+  public class ViewDef
+  {
     public String viewname;
+
     public HiddenSequences hidseqs;
+
     public ColumnSelection hiddencols;
+
     public Vector visibleGroups;
+
     public ViewDef(String viewname, HiddenSequences hidseqs,
             ColumnSelection hiddencols)
     {
@@ -65,9 +69,9 @@ public class AnnotationFile
       this.hiddencols = hiddencols;
     }
   }
+
   public String printAnnotations(AlignmentAnnotation[] annotations,
-          Vector groups,
-          Hashtable properties, ViewDef[] views)
+          Vector groups, Hashtable properties, ViewDef[] views)
   {
     if (annotations != null)
     {
@@ -128,13 +132,16 @@ public class AnnotationFile
 
           if (row.getThreshold() != null)
           {
-            graphLine.append("GRAPHLINE\t"
-                             + row.label + "\t"
-                             + row.getThreshold().value + "\t"
-                             + row.getThreshold().label + "\t"
-                             + jalview.util.Format.getHexString(
-                                 row.getThreshold().colour) + "\n"
-                );
+            graphLine
+                    .append("GRAPHLINE\t"
+                            + row.label
+                            + "\t"
+                            + row.getThreshold().value
+                            + "\t"
+                            + row.getThreshold().label
+                            + "\t"
+                            + jalview.util.Format.getHexString(row
+                                    .getThreshold().colour) + "\n");
           }
 
           if (row.graphGroup > -1)
@@ -142,8 +149,7 @@ public class AnnotationFile
             String key = String.valueOf(row.graphGroup);
             if (graphGroup.containsKey(key))
             {
-              graphGroup.put(key, graphGroup.get(key)
-                             + "\t" + row.label);
+              graphGroup.put(key, graphGroup.get(key) + "\t" + row.label);
             }
             else
             {
@@ -158,10 +164,11 @@ public class AnnotationFile
           text.append(row.description + "\t");
         }
 
-        for (int j = 0; row.annotations!=null && j < row.annotations.length; j++)
+        for (int j = 0; row.annotations != null
+                && j < row.annotations.length; j++)
         {
-          if (refSeq != null &&
-              jalview.util.Comparison.isGap(refSeq.getCharAt(j)))
+          if (refSeq != null
+                  && jalview.util.Comparison.isGap(refSeq.getCharAt(j)))
           {
             continue;
           }
@@ -174,9 +181,9 @@ public class AnnotationFile
               text.append(comma + row.annotations[j].secondaryStructure);
               comma = ",";
             }
-            if (row.annotations[j].displayCharacter!=null
-                && row.annotations[j].displayCharacter.length() > 0
-                && !row.annotations[j].displayCharacter.equals(" "))
+            if (row.annotations[j].displayCharacter != null
+                    && row.annotations[j].displayCharacter.length() > 0
+                    && !row.annotations[j].displayCharacter.equals(" "))
             {
               text.append(comma + row.annotations[j].displayCharacter);
               comma = ",";
@@ -184,39 +191,41 @@ public class AnnotationFile
 
             if (row.annotations[j] != null)
             {
-              if(color!=null && !color.equals(row.annotations[j].colour))
+              if (color != null && !color.equals(row.annotations[j].colour))
               {
                 oneColour = false;
               }
 
               color = row.annotations[j].colour;
-              if (row.annotations[j].value != 0f && row.annotations[j].value!=Float.NaN) 
+              if (row.annotations[j].value != 0f
+                      && row.annotations[j].value != Float.NaN)
               {
                 text.append(comma + row.annotations[j].value);
               }
             }
 
-            if(row.annotations[j].colour!=null
-               && row.annotations[j].colour!=java.awt.Color.black)
+            if (row.annotations[j].colour != null
+                    && row.annotations[j].colour != java.awt.Color.black)
             {
-              text.append(comma+"["+
-                          jalview.util.Format.getHexString(
-                          row.annotations[j].colour)+"]");
+              text.append(comma
+                      + "["
+                      + jalview.util.Format
+                              .getHexString(row.annotations[j].colour)
+                      + "]");
             }
           }
           text.append("|");
         }
 
-        if(row.hasScore())
-          text.append("\t"+row.score);
+        if (row.hasScore())
+          text.append("\t" + row.score);
 
         text.append("\n");
 
         if (color != null && color != java.awt.Color.black && oneColour)
         {
-          colours.append("COLOUR\t"
-                         + row.label + "\t"
-                         + jalview.util.Format.getHexString(color) + "\n");
+          colours.append("COLOUR\t" + row.label + "\t"
+                  + jalview.util.Format.getHexString(color) + "\n");
         }
 
       }
@@ -241,18 +250,18 @@ public class AnnotationFile
       printGroups(groups);
     }
 
-    if(properties!=null)
+    if (properties != null)
     {
       text.append("\n\nALIGNMENT");
       Enumeration en = properties.keys();
-      while(en.hasMoreElements())
+      while (en.hasMoreElements())
       {
         String key = en.nextElement().toString();
-        text.append("\t"+key+"="+properties.get(key));
+        text.append("\t" + key + "=" + properties.get(key));
       }
 
     }
-    
+
     return text.toString();
   }
 
@@ -262,10 +271,9 @@ public class AnnotationFile
     for (int i = 0; i < sequenceGroups.size(); i++)
     {
       sg = (SequenceGroup) sequenceGroups.elementAt(i);
-      text.append("SEQUENCE_GROUP\t"
-                  + sg.getName() + "\t"
-                  + (sg.getStartRes() + 1) + "\t"
-                  + (sg.getEndRes() + 1) + "\t" + "-1\t");
+      text.append("SEQUENCE_GROUP\t" + sg.getName() + "\t"
+              + (sg.getStartRes() + 1) + "\t" + (sg.getEndRes() + 1) + "\t"
+              + "-1\t");
       for (int s = 0; s < sg.getSize(); s++)
       {
         text.append(sg.getSequenceAt(s).getName() + "\t");
@@ -279,8 +287,8 @@ public class AnnotationFile
       }
       if (sg.cs != null)
       {
-        text.append("colour=" + ColourSchemeProperty.getColourName(sg.cs) +
-                    "\t");
+        text.append("colour=" + ColourSchemeProperty.getColourName(sg.cs)
+                + "\t");
         if (sg.cs.getThreshold() != 0)
         {
           text.append("pidThreshold=" + sg.cs.getThreshold());
@@ -290,9 +298,9 @@ public class AnnotationFile
           text.append("consThreshold=" + sg.cs.getConservationInc() + "\t");
         }
       }
-      text.append("outlineColour=" +
-                  jalview.util.Format.getHexString(sg.getOutlineColour()) +
-                  "\t");
+      text.append("outlineColour="
+              + jalview.util.Format.getHexString(sg.getOutlineColour())
+              + "\t");
 
       text.append("displayBoxes=" + sg.getDisplayBoxes() + "\t");
       text.append("displayText=" + sg.getDisplayText() + "\t");
@@ -300,21 +308,22 @@ public class AnnotationFile
 
       if (sg.textColour != java.awt.Color.black)
       {
-        text.append("textCol1=" +
-                    jalview.util.Format.getHexString(sg.textColour) + "\t");
+        text.append("textCol1="
+                + jalview.util.Format.getHexString(sg.textColour) + "\t");
       }
       if (sg.textColour2 != java.awt.Color.white)
       {
-        text.append("textCol2=" +
-                    jalview.util.Format.getHexString(sg.textColour2) + "\t");
+        text.append("textCol2="
+                + jalview.util.Format.getHexString(sg.textColour2) + "\t");
       }
       if (sg.thresholdTextColour != 0)
       {
         text.append("textColThreshold=" + sg.thresholdTextColour);
       }
-      if (sg.idColour!=null)
+      if (sg.idColour != null)
       {
-        text.append("idColour="+jalview.util.Format.getHexString(sg.idColour)+"\t");
+        text.append("idColour="
+                + jalview.util.Format.getHexString(sg.idColour) + "\t");
       }
 
       text.append("\n\n");
@@ -323,10 +332,11 @@ public class AnnotationFile
   }
 
   SequenceI refSeq = null;
+
   String refSeqId = null;
-  public boolean readAnnotationFile(AlignmentI al,
-                                    String file,
-                                    String protocol)
+
+  public boolean readAnnotationFile(AlignmentI al, String file,
+          String protocol)
   {
     try
     {
@@ -370,7 +380,7 @@ public class AnnotationFile
 
       // First confirm this is an Annotation file
       boolean jvAnnotationFile = false;
-      while ( (line = in.readLine()) != null)
+      while ((line = in.readLine()) != null)
       {
         if (line.indexOf("#") == 0)
         {
@@ -390,11 +400,11 @@ public class AnnotationFile
         return false;
       }
 
-      while ( (line = in.readLine()) != null)
+      while ((line = in.readLine()) != null)
       {
         if (line.indexOf("#") == 0
-            || line.indexOf("JALVIEW_ANNOTATION") > -1
-            || line.length() == 0)
+                || line.indexOf("JALVIEW_ANNOTATION") > -1
+                || line.length() == 0)
         {
           continue;
         }
@@ -423,30 +433,31 @@ public class AnnotationFile
         {
           if (st.hasMoreTokens())
           {
-            refSeq = al.findName(refSeqId=st.nextToken());
-          if (refSeq==null)
-          {
-            refSeqId=null;
-          }
-          try
-          {
-            refSeqIndex = Integer.parseInt(st.nextToken());
-            if (refSeqIndex < 1)
+            refSeq = al.findName(refSeqId = st.nextToken());
+            if (refSeq == null)
+            {
+              refSeqId = null;
+            }
+            try
+            {
+              refSeqIndex = Integer.parseInt(st.nextToken());
+              if (refSeqIndex < 1)
+              {
+                refSeqIndex = 1;
+                System.out
+                        .println("WARNING: SEQUENCE_REF index must be > 0 in AnnotationFile");
+              }
+            } catch (Exception ex)
             {
               refSeqIndex = 1;
-              System.out.println(
-                  "WARNING: SEQUENCE_REF index must be > 0 in AnnotationFile");
             }
           }
-          catch (Exception ex)
+          else
           {
-            refSeqIndex = 1;
-          }
-          } else {
             refSeq = null;
             refSeqId = null;
           }
-          continue ;
+          continue;
         }
 
         else if (token.equalsIgnoreCase("SEQUENCE_GROUP"))
@@ -461,12 +472,12 @@ public class AnnotationFile
           continue;
         }
 
-        else if( token.equalsIgnoreCase("BELOW_ALIGNMENT"))
+        else if (token.equalsIgnoreCase("BELOW_ALIGNMENT"))
         {
           setBelowAlignment(al, st);
           continue;
         }
-        else if( token.equalsIgnoreCase("ALIGNMENT"))
+        else if (token.equalsIgnoreCase("ALIGNMENT"))
         {
           addAlignmentDetails(al, st);
           continue;
@@ -475,47 +486,46 @@ public class AnnotationFile
         graphStyle = AlignmentAnnotation.getGraphValueFromString(token);
         label = st.nextToken();
 
-
         index = 0;
         annotations = new Annotation[alWidth];
         description = null;
         float score = Float.NaN;
 
-        if(st.hasMoreTokens())
+        if (st.hasMoreTokens())
         {
           line = st.nextToken();
 
-          if (line.indexOf("|") ==-1)
+          if (line.indexOf("|") == -1)
           {
             description = line;
             if (st.hasMoreTokens())
               line = st.nextToken();
           }
 
-          if(st.hasMoreTokens())
+          if (st.hasMoreTokens())
           {
-            //This must be the score
+            // This must be the score
             score = Float.valueOf(st.nextToken()).floatValue();
           }
 
           st = new StringTokenizer(line, "|", true);
 
-
           boolean emptyColumn = true;
-          boolean onlyOneElement = (st.countTokens()==1);
+          boolean onlyOneElement = (st.countTokens() == 1);
 
           while (st.hasMoreElements() && index < alWidth)
           {
             token = st.nextToken().trim();
 
-            if(onlyOneElement)
+            if (onlyOneElement)
             {
               try
               {
                 score = Float.valueOf(token).floatValue();
                 break;
+              } catch (NumberFormatException ex)
+              {
               }
-              catch(NumberFormatException ex){}
             }
 
             if (token.equals("|"))
@@ -536,43 +546,43 @@ public class AnnotationFile
 
         }
 
-        annotation = new AlignmentAnnotation(label,
-                                             description,
-                                             (index==0) ? null : annotations,
-                                             0,
-                                             0,
-                                             graphStyle);
+        annotation = new AlignmentAnnotation(label, description,
+                (index == 0) ? null : annotations, 0, 0, graphStyle);
 
         annotation.score = score;
 
         if (refSeq != null)
         {
-          annotation.belowAlignment=false;
-          do {
+          annotation.belowAlignment = false;
+          do
+          {
             // copy before we do any mapping business.
-            // TODO: verify that undo/redo with 1:many sequence associated annotations can be undone correctly
+            // TODO: verify that undo/redo with 1:many sequence associated
+            // annotations can be undone correctly
             AlignmentAnnotation ann = new AlignmentAnnotation(annotation);
             annotation.createSequenceMapping(refSeq, refSeqIndex, false);
             annotation.adjustForAlignment();
             refSeq.addAlignmentAnnotation(annotation);
             al.addAnnotation(annotation);
             al.setAnnotationIndex(annotation,
-                                al.getAlignmentAnnotation().length - existingAnnotations -
-                                1);
+                    al.getAlignmentAnnotation().length
+                            - existingAnnotations - 1);
             // and recover our virgin copy to use again if necessary.
             annotation = ann;
-            
-          } while (refSeqId!=null && (refSeq=al.findName(refSeq, refSeqId, true))!=null);
-        } else {
+
+          } while (refSeqId != null
+                  && (refSeq = al.findName(refSeq, refSeqId, true)) != null);
+        }
+        else
+        {
           al.addAnnotation(annotation);
           al.setAnnotationIndex(annotation,
-                              al.getAlignmentAnnotation().length - existingAnnotations -
-                              1);
+                  al.getAlignmentAnnotation().length - existingAnnotations
+                          - 1);
         }
       }
 
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       ex.printStackTrace();
       System.out.println("Problem reading annotation file: " + ex);
@@ -588,17 +598,17 @@ public class AnnotationFile
     float value = 0;
     boolean parsedValue = false;
 
-    //find colour here
+    // find colour here
     java.awt.Color colour = null;
-    int i=string.indexOf("[");
-    int j=string.indexOf("]");
-    if(i>-1 && j>-1)
+    int i = string.indexOf("[");
+    int j = string.indexOf("]");
+    if (i > -1 && j > -1)
     {
       UserColourScheme ucs = new UserColourScheme();
 
-      colour = ucs.getColourFromString(string.substring(i+1,j));
+      colour = ucs.getColourFromString(string.substring(i + 1, j));
 
-      string = string.substring(0,i)+string.substring(j+1);
+      string = string.substring(0, i) + string.substring(j + 1);
     }
 
     StringTokenizer st = new StringTokenizer(string, ",");
@@ -619,9 +629,9 @@ public class AnnotationFile
           value = new Float(token).floatValue();
           parsedValue = true;
           continue;
+        } catch (NumberFormatException ex)
+        {
         }
-        catch (NumberFormatException ex)
-        {}
       }
 
       if (token.equals("H") || token.equals("E"))
@@ -641,23 +651,19 @@ public class AnnotationFile
 
     }
 
-    if (displayChar!=null
-        && displayChar.length() > 1
-        &&  desc!=null
-        && desc.length() == 1)
+    if (displayChar != null && displayChar.length() > 1 && desc != null
+            && desc.length() == 1)
     {
       String tmp = displayChar;
       displayChar = desc;
       desc = tmp;
     }
     /*
-     * In principle, this code will ensure that the Annotation element generated is renderable by any of the applet or application rendering code
-     * but instead we check for null strings when the display character is rendered. 
-    if (displayChar==null)
-    {
-      displayChar="";
-    }
-    */
+     * In principle, this code will ensure that the Annotation element generated
+     * is renderable by any of the applet or application rendering code but
+     * instead we check for null strings when the display character is rendered.
+     * if (displayChar==null) { displayChar=""; }
+     */
     Annotation anot = new Annotation(displayChar, desc, ss, value);
 
     anot.colour = colour;
@@ -689,7 +695,7 @@ public class AnnotationFile
   {
     int graphGroup = -1;
     String group = st.nextToken();
-    //First make sure we are not overwriting the graphIndex
+    // First make sure we are not overwriting the graphIndex
     for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
     {
       if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))
@@ -700,7 +706,7 @@ public class AnnotationFile
       }
     }
 
-    //Now update groups
+    // Now update groups
     while (st.hasMoreTokens())
     {
       group = st.nextToken();
@@ -791,13 +797,13 @@ public class AnnotationFile
         }
         else
         {
-          sg.addSequence(al.getSequenceAt(Integer.parseInt(tmp) - 1), false);
+          sg
+                  .addSequence(al.getSequenceAt(Integer.parseInt(tmp) - 1),
+                          false);
         }
       }
     }
 
-
-
     if (refSeq != null)
     {
       sg.setStartRes(refSeq.findIndex(sg.getStartRes() + 1) - 1);
@@ -813,9 +819,9 @@ public class AnnotationFile
   void addProperties(AlignmentI al, StringTokenizer st)
   {
 
-    //So far we have only added groups to the annotationHash,
-    //the idea is in the future properties can be added to
-    //alignments, other annotations etc
+    // So far we have only added groups to the annotationHash,
+    // the idea is in the future properties can be added to
+    // alignments, other annotations etc
     if (al.getGroups() == null)
     {
       return;
@@ -866,10 +872,8 @@ public class AnnotationFile
         {
           sg.cs.setConservationInc(Integer.parseInt(value));
           Conservation c = new Conservation("Group",
-                                            ResidueProperties.propHash, 3,
-                                            sg.getSequences(null),
-                                            sg.getStartRes(),
-                                            sg.getEndRes() + 1);
+                  ResidueProperties.propHash, 3, sg.getSequences(null), sg
+                          .getStartRes(), sg.getEndRes() + 1);
 
           c.calculate();
           c.verdict(false, 25);
@@ -908,11 +912,12 @@ public class AnnotationFile
         else if (key.equalsIgnoreCase("idColour"))
         {
           // consider warning if colour doesn't resolve to a real colour
-          sg.setIdColour((def = new UserColourScheme(value)).findColour('A'));
+          sg.setIdColour((def = new UserColourScheme(value))
+                  .findColour('A'));
         }
         sg.recalcConservation();
       }
-      if (sg.cs==null)
+      if (sg.cs == null)
       {
         sg.cs = def;
       }
@@ -923,13 +928,13 @@ public class AnnotationFile
   {
     String token;
     AlignmentAnnotation aa;
-    while(st.hasMoreTokens())
+    while (st.hasMoreTokens())
     {
       token = st.nextToken();
-      for(int i=0; i<al.getAlignmentAnnotation().length; i++)
+      for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
       {
         aa = al.getAlignmentAnnotation()[i];
-        if(aa.sequenceRef==refSeq && aa.label.equals(token))
+        if (aa.sequenceRef == refSeq && aa.label.equals(token))
         {
           aa.belowAlignment = true;
         }
@@ -945,35 +950,40 @@ public class AnnotationFile
       keyValue = st.nextToken();
       key = keyValue.substring(0, keyValue.indexOf("="));
       value = keyValue.substring(keyValue.indexOf("=") + 1);
-      al.setProperty(key,value);
+      al.setProperty(key, value);
     }
   }
 
   /**
-   * Write annotations as a CSV file of the form 'label, value, value, ...' for each row.
+   * Write annotations as a CSV file of the form 'label, value, value, ...' for
+   * each row.
+   * 
    * @param annotations
    * @return CSV file as a string.
    */
   public String printCSVAnnotations(AlignmentAnnotation[] annotations)
   {
     StringBuffer sp = new StringBuffer();
-    for (int i=0; i<annotations.length; i++)
+    for (int i = 0; i < annotations.length; i++)
     {
       String atos = annotations[i].toString();
       int p = 0;
-      do {
+      do
+      {
         int cp = atos.indexOf("\n", p);
         sp.append(annotations[i].label);
         sp.append(",");
-        if (cp>p)
+        if (cp > p)
+        {
+          sp.append(atos.substring(p, cp + 1));
+        }
+        else
         {
-          sp.append(atos.substring(p, cp+1));
-        } else {
           sp.append(atos.substring(p));
           sp.append("\n");
         }
-        p = cp+1;
-      } while (p>0);
+        p = cp + 1;
+      } while (p > 0);
     }
     return sp.toString();
   }
diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index c7b0575..e5fc584 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -23,108 +23,122 @@ import java.io.File;
 import jalview.datamodel.*;
 
 /**
- * A low level class for alignment and feature IO
- * with alignment formatting methods used by both applet 
- * and application for generating flat alignment files.
- * It also holds the lists of magic format names
- * that the applet and application will allow the user to read or write files with.
- *
+ * A low level class for alignment and feature IO with alignment formatting
+ * methods used by both applet and application for generating flat alignment
+ * files. It also holds the lists of magic format names that the applet and
+ * application will allow the user to read or write files with.
+ * 
  * @author $author$
  * @version $Revision$
  */
 public class AppletFormatAdapter
 {
-  /** 
-   * List of valid format strings used in the isValidFormat method 
+  /**
+   * List of valid format strings used in the isValidFormat method
    */
   public static final String[] READABLE_FORMATS = new String[]
-      {
-      "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", "PDB", "JnetFile"
-  };
+  { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
+      "PDB", "JnetFile" };
+
   /**
-   * List of valid format strings for use by callers of the formatSequences method
+   * List of valid format strings for use by callers of the formatSequences
+   * method
    */
   public static final String[] WRITEABLE_FORMATS = new String[]
-      {
-      "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM" , "AMSA"
-  };
+  { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA" };
+
   /**
-   * List of extensions corresponding to file format types 
-   * in WRITABLE_FNAMES that are writable by the
-   * application.
+   * List of extensions corresponding to file format types in WRITABLE_FNAMES
+   * that are writable by the application.
    */
   public static final String[] WRITABLE_EXTENSIONS = new String[]
-        { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc","amsa","jar" };
+  { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar" };
+
   /**
-   * List of writable formats by the application. Order must
-   * correspond with the WRITABLE_EXTENSIONS list of formats.
+   * List of writable formats by the application. Order must correspond with the
+   * WRITABLE_EXTENSIONS list of formats.
    */
   public static final String[] WRITABLE_FNAMES = new String[]
-        { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview" };
+  { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview" };
 
   /**
    * List of readable format file extensions by application in order
-   * corresponding to READABLE_FNAMES 
+   * corresponding to READABLE_FNAMES
    */
-  public static final String[] READABLE_EXTENSIONS =         new String[]
-        {
-        "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
-        "amsa","jar"
-    };
+  public static final String[] READABLE_EXTENSIONS = new String[]
+  { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar" };
+
   /**
-   * List of readable formats by application in order
-   * corresponding to READABLE_EXTENSIONS
+   * List of readable formats by application in order corresponding to
+   * READABLE_EXTENSIONS
    */
-  public static final String[] READABLE_FNAMES =         new String[]
-        {
-        "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA","Jalview"
-    };
-        
+  public static final String[] READABLE_FNAMES = new String[]
+  { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview" };
+
   public static String INVALID_CHARACTERS = "Contains invalid characters";
+
   // TODO: make these messages dynamic
-  public static String SUPPORTED_FORMATS = "Formats currently supported are\n" +
-    prettyPrint(READABLE_FORMATS);
+  public static String SUPPORTED_FORMATS = "Formats currently supported are\n"
+          + prettyPrint(READABLE_FORMATS);
+
   /**
    * 
    * @param els
    * @return grammatically correct(ish) list consisting of els elements.
    */
-  public static String prettyPrint(String[] els) {
+  public static String prettyPrint(String[] els)
+  {
     StringBuffer list = new StringBuffer();
-    for (int i=0,iSize=els.length-1; i<iSize;i++)
+    for (int i = 0, iSize = els.length - 1; i < iSize; i++)
     {
       list.append(els[i]);
       list.append(",");
     }
-    list.append(" and "+els[els.length-1]+".");
+    list.append(" and " + els[els.length - 1] + ".");
     return list.toString();
   }
+
   public static String FILE = "File";
+
   public static String URL = "URL";
+
   public static String PASTE = "Paste";
+
   public static String CLASSLOADER = "ClassLoader";
 
   AlignFile afile = null;
+
   String inFile;
+
   /**
    * check that this format is valid for reading
-   * @param format a format string to be compared with READABLE_FORMATS
+   * 
+   * @param format
+   *                a format string to be compared with READABLE_FORMATS
    * @return true if format is readable
    */
   public static final boolean isValidFormat(String format)
   {
     return isValidFormat(format, false);
   }
+
   /**
    * validate format is valid for IO
-   * @param format a format string to be compared with either READABLE_FORMATS or WRITEABLE_FORMATS
-   * @param forwriting when true, format is checked for containment in WRITEABLE_FORMATS
+   * 
+   * @param format
+   *                a format string to be compared with either READABLE_FORMATS
+   *                or WRITEABLE_FORMATS
+   * @param forwriting
+   *                when true, format is checked for containment in
+   *                WRITEABLE_FORMATS
    * @return true if format is valid
    */
-  public static final boolean isValidFormat(String format, boolean forwriting)
+  public static final boolean isValidFormat(String format,
+          boolean forwriting)
   {
     boolean valid = false;
-    String[] format_list = (forwriting) ? WRITEABLE_FORMATS : READABLE_FORMATS;
+    String[] format_list = (forwriting) ? WRITEABLE_FORMATS
+            : READABLE_FORMATS;
     for (int i = 0; i < format_list.length; i++)
     {
       if (format_list[i].equalsIgnoreCase(format))
@@ -135,20 +149,24 @@ public class AppletFormatAdapter
 
     return valid;
   }
-  
+
   /**
    * Constructs the correct filetype parser for a characterised datasource
-   *
-   * @param inFile data/data location
-   * @param type type of datasource
-   * @param format File format of data provided by datasource
-   *
+   * 
+   * @param inFile
+   *                data/data location
+   * @param type
+   *                type of datasource
+   * @param format
+   *                File format of data provided by datasource
+   * 
    * @return DOCUMENT ME!
    */
   public Alignment readFile(String inFile, String type, String format)
-      throws java.io.IOException
+          throws java.io.IOException
   {
-    // TODO: generalise mapping between format string and io. class instances using Constructor.invoke reflection
+    // TODO: generalise mapping between format string and io. class instances
+    // using Constructor.invoke reflection
     this.inFile = inFile;
     try
     {
@@ -183,7 +201,7 @@ public class AppletFormatAdapter
       else if (format.equals("JnetFile"))
       {
         afile = new JPredFile(inFile, type);
-        ( (JPredFile) afile).removeNonSequences();
+        ((JPredFile) afile).removeNonSequences();
       }
       else if (format.equals("PDB"))
       {
@@ -199,15 +217,14 @@ public class AppletFormatAdapter
       afile.addAnnotations(al);
 
       return al;
-    }
-    catch (Exception e)
+    } catch (Exception e)
     {
       e.printStackTrace();
-      System.err.println("Failed to read alignment using the '" + format +
-                         "' reader.\n" + e);
+      System.err.println("Failed to read alignment using the '" + format
+              + "' reader.\n" + e);
 
-      if (e.getMessage() != null &&
-          e.getMessage().startsWith(INVALID_CHARACTERS))
+      if (e.getMessage() != null
+              && e.getMessage().startsWith(INVALID_CHARACTERS))
       {
         throw new java.io.IOException(e.getMessage());
       }
@@ -223,8 +240,7 @@ public class AppletFormatAdapter
           afile.addAnnotations(al);
           return al;
 
-        }
-        catch (Exception ex)
+        } catch (Exception ex)
         {
           if (ex.toString().startsWith(INVALID_CHARACTERS))
           {
@@ -239,19 +255,24 @@ public class AppletFormatAdapter
       throw new java.io.IOException(SUPPORTED_FORMATS);
     }
   }
+
   /**
    * Constructs the correct filetype parser for an already open datasource
-   *
-   * @param source an existing datasource
-   * @param format File format of data that will be provided by datasource
-   *
+   * 
+   * @param source
+   *                an existing datasource
+   * @param format
+   *                File format of data that will be provided by datasource
+   * 
    * @return DOCUMENT ME!
    */
   public Alignment readFromFile(FileParse source, String format)
-      throws java.io.IOException
+          throws java.io.IOException
   {
-    // TODO: generalise mapping between format string and io. class instances using Constructor.invoke reflection
-    // This is exactly the same as the readFile method except we substitute 'inFile, type' with 'source'
+    // TODO: generalise mapping between format string and io. class instances
+    // using Constructor.invoke reflection
+    // This is exactly the same as the readFile method except we substitute
+    // 'inFile, type' with 'source'
     this.inFile = source.getInFile();
     String type = source.type;
     try
@@ -287,7 +308,7 @@ public class AppletFormatAdapter
       else if (format.equals("JnetFile"))
       {
         afile = new JPredFile(source);
-        ( (JPredFile) afile).removeNonSequences();
+        ((JPredFile) afile).removeNonSequences();
       }
       else if (format.equals("PDB"))
       {
@@ -303,15 +324,14 @@ public class AppletFormatAdapter
       afile.addAnnotations(al);
 
       return al;
-    }
-    catch (Exception e)
+    } catch (Exception e)
     {
       e.printStackTrace();
-      System.err.println("Failed to read alignment using the '" + format +
-                         "' reader.\n" + e);
+      System.err.println("Failed to read alignment using the '" + format
+              + "' reader.\n" + e);
 
-      if (e.getMessage() != null &&
-          e.getMessage().startsWith(INVALID_CHARACTERS))
+      if (e.getMessage() != null
+              && e.getMessage().startsWith(INVALID_CHARACTERS))
       {
         throw new java.io.IOException(e.getMessage());
       }
@@ -327,8 +347,7 @@ public class AppletFormatAdapter
           afile.addAnnotations(al);
           return al;
 
-        }
-        catch (Exception ex)
+        } catch (Exception ex)
         {
           if (ex.toString().startsWith(INVALID_CHARACTERS))
           {
@@ -343,19 +362,22 @@ public class AppletFormatAdapter
       throw new java.io.IOException(SUPPORTED_FORMATS);
     }
   }
-  
+
   /**
    * Construct an output class for an alignment in a particular filetype
-   *
-   * @param format string name of alignment format 
-   * @param alignment the alignment to be written out
-   * @param jvsuffix passed to AlnFile class controls whether /START-END is added to sequence names
-   *
+   * 
+   * @param format
+   *                string name of alignment format
+   * @param alignment
+   *                the alignment to be written out
+   * @param jvsuffix
+   *                passed to AlnFile class controls whether /START-END is added
+   *                to sequence names
+   * 
    * @return alignment flat file contents
    */
-  public String formatSequences(String format,
-                                AlignmentI alignment,
-                                boolean jvsuffix)
+  public String formatSequences(String format, AlignmentI alignment,
+          boolean jvsuffix)
   {
     try
     {
@@ -396,8 +418,11 @@ public class AppletFormatAdapter
       else if (format.equalsIgnoreCase("AMSA"))
       {
         afile = new AMSAFile(alignment);
-      } else {
-        throw new Exception("Implementation error: Unknown file format string");
+      }
+      else
+      {
+        throw new Exception(
+                "Implementation error: Unknown file format string");
       }
 
       afile.addJVSuffix(jvsuffix);
@@ -405,53 +430,64 @@ public class AppletFormatAdapter
       afile.setSeqs(alignment.getSequencesArray());
 
       return afile.print();
-    }
-    catch (Exception e)
+    } catch (Exception e)
     {
-      System.err.println("Failed to write alignment as a '" + format +
-                         "' file\n");
+      System.err.println("Failed to write alignment as a '" + format
+              + "' file\n");
       e.printStackTrace();
     }
 
     return null;
   }
+
   public static void main(String[] args)
   {
-    int i=0;
-    while (i<args.length)
+    int i = 0;
+    while (i < args.length)
     {
       File f = new File(args[i]);
       if (f.exists())
       {
-        try {
-          System.out.println("Reading file: "+f);
+        try
+        {
+          System.out.println("Reading file: " + f);
           AppletFormatAdapter afa = new AppletFormatAdapter();
           Runtime r = Runtime.getRuntime();
           System.gc();
-          long memf = -r.totalMemory()+r.freeMemory();
+          long memf = -r.totalMemory() + r.freeMemory();
           long t1 = -System.currentTimeMillis();
-          Alignment al = afa.readFile(args[i], FILE, new IdentifyFile().Identify(args[i], FILE));
-          t1 +=System.currentTimeMillis();
+          Alignment al = afa.readFile(args[i], FILE, new IdentifyFile()
+                  .Identify(args[i], FILE));
+          t1 += System.currentTimeMillis();
           System.gc();
-          memf += r.totalMemory()-r.freeMemory();
-          if (al!=null)
+          memf += r.totalMemory() - r.freeMemory();
+          if (al != null)
+          {
+            System.out.println("Alignment contains " + al.getHeight()
+                    + " sequences and " + al.getWidth() + " columns.");
+          }
+          else
           {
-            System.out.println("Alignment contains "+al.getHeight()+" sequences and "+al.getWidth()+" columns.");
-          } else {
             System.out.println("Couldn't read alignment");
           }
-          System.out.println("Read took "+(t1/1000.0)+" seconds.");
-          System.out.println("Difference between free memory now and before is "+(memf/(1024.0*1024.0)*1.0)+" MB");
-          
+          System.out.println("Read took " + (t1 / 1000.0) + " seconds.");
+          System.out
+                  .println("Difference between free memory now and before is "
+                          + (memf / (1024.0 * 1024.0) * 1.0) + " MB");
+
         } catch (Exception e)
         {
-          System.err.println("Exception when dealing with "+i+"'th argument: "+args[i]+"\n"+e);
+          System.err.println("Exception when dealing with " + i
+                  + "'th argument: " + args[i] + "\n" + e);
         }
-      } else {
-          System.err.println("Ignoring argument '"+args[i]+"' ("+i+"'th)- not a readable file.");
+      }
+      else
+      {
+        System.err.println("Ignoring argument '" + args[i] + "' (" + i
+                + "'th)- not a readable file.");
       }
       i++;
     }
-    
+
   }
 }
diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java
index fa6f8e2..9b5b3e5 100755
--- a/src/jalview/io/BLCFile.java
+++ b/src/jalview/io/BLCFile.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -25,12 +25,11 @@ import jalview.datamodel.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class BLCFile
-extends AlignFile
+public class BLCFile extends AlignFile
 {
   Vector titles;
 
@@ -43,17 +42,20 @@ extends AlignFile
 
   /**
    * Creates a new BLCFile object.
-   *
-   * @param inFile DOCUMENT ME!
-   * @param type DOCUMENT ME!
-   *
-   * @throws IOException DOCUMENT ME!
+   * 
+   * @param inFile
+   *                DOCUMENT ME!
+   * @param type
+   *                DOCUMENT ME!
+   * 
+   * @throws IOException
+   *                 DOCUMENT ME!
    */
-  public BLCFile(String inFile, String type)
-  throws IOException
+  public BLCFile(String inFile, String type) throws IOException
   {
     super(inFile, type);
   }
+
   public BLCFile(FileParse source) throws IOException
   {
     super(source);
@@ -67,45 +69,50 @@ extends AlignFile
     super.initData();
     titles = new Vector();
   }
+
   /**
-   * Control the number of block iterations to skip before returning.
-   * set to 0 to read first block file entry only
-   * set to -1 to read last block file entry only
-   * set to greater than zero to skip at most that many entries before parsing
+   * Control the number of block iterations to skip before returning. set to 0
+   * to read first block file entry only set to -1 to read last block file entry
+   * only set to greater than zero to skip at most that many entries before
+   * parsing
    */
-  int iterationSkips=0;
+  int iterationSkips = 0;
+
   /**
-   * The iteration number for the alignment actually parsed from the blc file 
+   * The iteration number for the alignment actually parsed from the blc file
    */
-  int iterationCount=0;
+  int iterationCount = 0;
 
   /**
    * DOCUMENT ME!
    */
-  public void parse()
-  throws IOException
+  public void parse() throws IOException
   {
-    StringBuffer headerLines=new StringBuffer();
+    StringBuffer headerLines = new StringBuffer();
     int numHeaderLines = 0; // number of lines appended.
-    StringBuffer[] seqstrings=null;
-    if (suffix!=null) {
-      try {
-        iterationSkips = Integer.parseInt(suffix); 
-      } catch (NumberFormatException e) {
+    StringBuffer[] seqstrings = null;
+    if (suffix != null)
+    {
+      try
+      {
+        iterationSkips = Integer.parseInt(suffix);
+      } catch (NumberFormatException e)
+      {
         iterationSkips = 0; // first
       }
     }
 
     String line = null;
 
-    do {
+    do
+    {
       boolean idsFound = false;
       boolean newids = false;
-        // search for ID header.
+      // search for ID header.
       do
       {
         line = nextLine();
-        if (line==null)
+        if (line == null)
           break;
         // seek end of ids
         if (line.indexOf("*") > -1)
@@ -114,31 +121,33 @@ extends AlignFile
 
           break;
         }
-        
+
         int abracket = line.indexOf(">");
 
         if (abracket > -1)
         {
 
-          if (iterationCount>0 && !newids) {
+          if (iterationCount > 0 && !newids)
+          {
             // we have a new set of IDs to record.
             newids = true;
-            seqs.removeAllElements(); 
+            seqs.removeAllElements();
           }
 
           line = line.substring(abracket + 1);
 
           Sequence seq = parseId(line);
           seqs.addElement(seq);
-        } else {
+        }
+        else
+        {
           // header lines - keep them for the alignment comments.
           headerLines.append(line);
           headerLines.append("\n");
           numHeaderLines++;
         }
-      }
-      while (!idsFound);
-      if (line==null)
+      } while (!idsFound);
+      if (line == null)
         break; // end of file.
       int starCol = line.indexOf("*");
       seqstrings = new StringBuffer[seqs.size()];
@@ -151,9 +160,10 @@ extends AlignFile
         }
       }
 
-      try {
+      try
+      {
         line = nextLine();
-        while (line!=null && line.indexOf("*") == -1)
+        while (line != null && line.indexOf("*") == -1)
         {
           for (int i = 0; i < seqs.size(); i++)
           {
@@ -164,33 +174,38 @@ extends AlignFile
           }
           line = nextLine();
         }
-      } catch (IOException e) {
-        if (iterationCount==0) {
-          throw(e); // otherwise we've just run out of iterations.
-        } else {
-          iterationSkips=0;
+      } catch (IOException e)
+      {
+        if (iterationCount == 0)
+        {
+          throw (e); // otherwise we've just run out of iterations.
+        }
+        else
+        {
+          iterationSkips = 0;
         }
       }
       iterationCount++;
-    } while (--iterationSkips!=-1);
-    
+    } while (--iterationSkips != -1);
+
     for (int i = 0; i < seqs.size(); i++)
     {
       Sequence newSeq = (Sequence) seqs.elementAt(i);
 
       newSeq.setSequence(seqstrings[i].toString());
     }
-    if (seqs.size()>0)
+    if (seqs.size() > 0)
     {
-      if (headerLines.length()>1+numHeaderLines) // could see if buffer is just whitespace or not. 
+      if (headerLines.length() > 1 + numHeaderLines) // could see if buffer is
+                                                      // just whitespace or not.
         setAlignmentProperty("Comments", headerLines.toString());
-      setAlignmentProperty("iteration", ""+iterationCount);
+      setAlignmentProperty("iteration", "" + iterationCount);
     }
   }
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public String print()
@@ -200,25 +215,25 @@ extends AlignFile
 
   /**
    * DOCUMENT ME!
-   *
-   * @param s DOCUMENT ME!
-   *
+   * 
+   * @param s
+   *                DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   public String print(SequenceI[] s)
   {
     StringBuffer out = new StringBuffer();
     /**
-     * A general parser for ids. Will look for dbrefs in
-     * Uniprot format source|id
-     * And also Jalview /start-end
-     *
+     * A general parser for ids. Will look for dbrefs in Uniprot format
+     * source|id And also Jalview /start-end
+     * 
      * @String id Id to be parsed
      */
     int i = 0;
     int max = -1;
 
-    while ( (i < s.length) && (s[i] != null))
+    while ((i < s.length) && (s[i] != null))
     {
       out.append(">" + printId(s[i]));
       if (s[i].getDescription() != null)
@@ -242,7 +257,7 @@ extends AlignFile
     {
       i = 0;
 
-      while ( (i < s.length) && (s[i] != null))
+      while ((i < s.length) && (s[i] != null))
       {
         if (s[i].getSequence().length > j)
         {
diff --git a/src/jalview/io/ClansFile.java b/src/jalview/io/ClansFile.java
index ee709e5..696ccb2 100644
--- a/src/jalview/io/ClansFile.java
+++ b/src/jalview/io/ClansFile.java
@@ -1,7 +1,25 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.io;
 
 /**
- * Read or write a CLANS style score matrix file. 
+ * Read or write a CLANS style score matrix file.
  */
 
 public class ClansFile extends FileParse
diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index d62d185..f46e3ad 100755
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -24,30 +24,29 @@ import java.util.*;
 import jalview.datamodel.*;
 import jalview.util.*;
 
-public class ClustalFile
-    extends AlignFile
+public class ClustalFile extends AlignFile
 {
 
   public ClustalFile()
   {
   }
 
-  public ClustalFile(String inFile, String type)
-      throws IOException
+  public ClustalFile(String inFile, String type) throws IOException
   {
     super(inFile, type);
   }
+
   public ClustalFile(FileParse source) throws IOException
   {
     super(source);
   }
+
   public void initData()
   {
     super.initData();
   }
 
-  public void parse()
-      throws IOException
+  public void parse() throws IOException
   {
     int i = 0;
     boolean flag = false;
@@ -60,7 +59,7 @@ public class ClustalFile
 
     try
     {
-      while ( (line = nextLine()) != null)
+      while ((line = nextLine()) != null)
       {
         if (line.indexOf(" ") != 0)
         {
@@ -88,7 +87,7 @@ public class ClustalFile
                   seqhash.put(id, tempseq);
                 }
 
-                if (! (headers.contains(id)))
+                if (!(headers.contains(id)))
                 {
                   headers.addElement(id);
                 }
@@ -106,8 +105,7 @@ public class ClustalFile
           }
         }
       }
-    }
-    catch (IOException e)
+    } catch (IOException e)
     {
       System.err.println("Exception parsing clustal file " + e);
       e.printStackTrace();
@@ -117,29 +115,29 @@ public class ClustalFile
     {
       this.noSeqs = headers.size();
 
-      //Add sequences to the hash
+      // Add sequences to the hash
       for (i = 0; i < headers.size(); i++)
       {
         if (seqhash.get(headers.elementAt(i)) != null)
         {
           if (maxLength < seqhash.get(headers.elementAt(i)).toString()
-              .length())
+                  .length())
           {
             maxLength = seqhash.get(headers.elementAt(i)).toString()
-                .length();
+                    .length();
           }
 
           Sequence newSeq = parseId(headers.elementAt(i).toString());
-          newSeq.setSequence(seqhash.get(headers.elementAt(i).toString()).
-                             toString());
+          newSeq.setSequence(seqhash.get(headers.elementAt(i).toString())
+                  .toString());
 
           seqs.addElement(newSeq);
         }
         else
         {
-          System.err.println(
-              "Clustal File Reader: Can't find sequence for " +
-              headers.elementAt(i));
+          System.err
+                  .println("Clustal File Reader: Can't find sequence for "
+                          + headers.elementAt(i));
         }
       }
     }
@@ -159,7 +157,7 @@ public class ClustalFile
 
     int i = 0;
 
-    while ( (i < s.length) && (s[i] != null))
+    while ((i < s.length) && (s[i] != null))
     {
       String tmp = printId(s[i]);
 
@@ -190,15 +188,17 @@ public class ClustalFile
     {
       int j = 0;
 
-      while ( (j < s.length) && (s[j] != null))
+      while ((j < s.length) && (s[j] != null))
       {
-        out.append(new Format("%-" + maxid + "s").form(printId(s[j]) + " "));
+        out
+                .append(new Format("%-" + maxid + "s").form(printId(s[j])
+                        + " "));
 
         int start = i * len;
         int end = start + len;
 
-        if ( (end < s[j].getSequence().length) &&
-            (start < s[j].getSequence().length))
+        if ((end < s[j].getSequence().length)
+                && (start < s[j].getSequence().length))
         {
           out.append(s[j].getSequenceAsString(start, end));
         }
diff --git a/src/jalview/io/DBRefFile.java b/src/jalview/io/DBRefFile.java
index f43a2a6..9ebc661 100644
--- a/src/jalview/io/DBRefFile.java
+++ b/src/jalview/io/DBRefFile.java
@@ -1,10 +1,28 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.io;
 
 import java.io.IOException;
+
 /**
- * jalview flatfile for io of sequence ID mapping data
- * DATABASE\t<nickname>\t<name>\t<version>... properties?jdbc, url, handler
- * DBREF<seqID>\tDBID\taccno\t|seqstart,seqend,start,end...|\t|dbstart,dbend,...|
+ * jalview flatfile for io of sequence ID mapping data DATABASE\t<nickname>\t<name>\t<version>...
+ * properties?jdbc, url, handler DBREF<seqID>\tDBID\taccno\t|seqstart,seqend,start,end...|\t|dbstart,dbend,...|
  * 
  */
 public class DBRefFile extends AlignFile
diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java
index 1cb016c..2ee715d 100755
--- a/src/jalview/io/FastaFile.java
+++ b/src/jalview/io/FastaFile.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -24,12 +24,11 @@ import jalview.datamodel.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class FastaFile
-    extends AlignFile
+public class FastaFile extends AlignFile
 {
   /**
    * Length of a sequence line
@@ -47,14 +46,16 @@ public class FastaFile
 
   /**
    * Creates a new FastaFile object.
-   *
-   * @param inFile DOCUMENT ME!
-   * @param type DOCUMENT ME!
-   *
-   * @throws IOException DOCUMENT ME!
+   * 
+   * @param inFile
+   *                DOCUMENT ME!
+   * @param type
+   *                DOCUMENT ME!
+   * 
+   * @throws IOException
+   *                 DOCUMENT ME!
    */
-  public FastaFile(String inFile, String type)
-      throws IOException
+  public FastaFile(String inFile, String type) throws IOException
   {
     super(inFile, type);
   }
@@ -66,11 +67,11 @@ public class FastaFile
 
   /**
    * DOCUMENT ME!
-   *
-   * @throws IOException DOCUMENT ME!
+   * 
+   * @throws IOException
+   *                 DOCUMENT ME!
    */
-  public void parse()
-      throws IOException
+  public void parse() throws IOException
   {
     StringBuffer sb = new StringBuffer();
     boolean firstLine = true;
@@ -80,7 +81,7 @@ public class FastaFile
 
     boolean annotation = false;
 
-    while ( (line = nextLine()) != null)
+    while ((line = nextLine()) != null)
     {
       line = line.trim();
       if (line.length() > 0)
@@ -96,12 +97,10 @@ public class FastaFile
               for (int i = 0; i < sb.length(); i++)
               {
                 anots[i] = new Annotation(anotString.substring(i, i + 1),
-                                          null,
-                                          ' ', 0);
+                        null, ' ', 0);
               }
-              AlignmentAnnotation aa = new AlignmentAnnotation(
-                  seq.getName().substring(2), seq.getDescription(),
-                  anots);
+              AlignmentAnnotation aa = new AlignmentAnnotation(seq
+                      .getName().substring(2), seq.getDescription(), anots);
 
               annotations.addElement(aa);
             }
@@ -144,13 +143,11 @@ public class FastaFile
       String anotString = sb.toString();
       for (int i = 0; i < sb.length(); i++)
       {
-        anots[i] = new Annotation(anotString.substring(i, i + 1),
-                                  null,
-                                  ' ', 0);
+        anots[i] = new Annotation(anotString.substring(i, i + 1), null,
+                ' ', 0);
       }
-      AlignmentAnnotation aa = new AlignmentAnnotation(
-          seq.getName().substring(2), seq.getDescription(),
-          anots);
+      AlignmentAnnotation aa = new AlignmentAnnotation(seq.getName()
+              .substring(2), seq.getDescription(), anots);
 
       annotations.addElement(aa);
     }
@@ -163,9 +160,9 @@ public class FastaFile
   }
 
   /**
-   * called by AppletFormatAdapter to generate
-   * an annotated alignment, rather than bare
-   * sequences.
+   * called by AppletFormatAdapter to generate an annotated alignment, rather
+   * than bare sequences.
+   * 
    * @param al
    */
   public void addAnnotations(Alignment al)
@@ -173,21 +170,25 @@ public class FastaFile
     addProperties(al);
     for (int i = 0; i < annotations.size(); i++)
     {
-      AlignmentAnnotation aa = (AlignmentAnnotation) annotations.elementAt(i);
+      AlignmentAnnotation aa = (AlignmentAnnotation) annotations
+              .elementAt(i);
       aa.setPadGaps(true, al.getGapCharacter());
-      al.addAnnotation( aa );
+      al.addAnnotation(aa);
     }
   }
 
-
   /**
    * DOCUMENT ME!
-   *
-   * @param s DOCUMENT ME!
-   * @param len DOCUMENT ME!
-   * @param gaps DOCUMENT ME!
-   * @param displayId DOCUMENT ME!
-   *
+   * 
+   * @param s
+   *                DOCUMENT ME!
+   * @param len
+   *                DOCUMENT ME!
+   * @param gaps
+   *                DOCUMENT ME!
+   * @param displayId
+   *                DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   public String print(SequenceI[] s)
@@ -195,7 +196,7 @@ public class FastaFile
     out = new StringBuffer();
     int i = 0;
 
-    while ( (i < s.length) && (s[i] != null))
+    while ((i < s.length) && (s[i] != null))
     {
       out.append(">" + printId(s[i]));
       if (s[i].getDescription() != null)
@@ -218,7 +219,8 @@ public class FastaFile
         }
         else if (start < s[i].getLength())
         {
-          out.append(s[i].getSequenceAsString(start, s[i].getLength()) + "\n");
+          out.append(s[i].getSequenceAsString(start, s[i].getLength())
+                  + "\n");
         }
       }
 
@@ -230,7 +232,7 @@ public class FastaFile
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public String print()
diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index 3e0314a..462ee22 100755
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -148,7 +148,7 @@ public class FeaturesFile extends AlignFile
           }
           continue;
         }
-        String seqId="";
+        String seqId = "";
         while (st.hasMoreElements())
         {
 
@@ -205,7 +205,7 @@ public class FeaturesFile extends AlignFile
               }
 
               seq.addSequenceFeature(sf);
-              while ((seq=align.findName(seq, seqId, true))!=null)
+              while ((seq = align.findName(seq, seqId, true)) != null)
               {
                 seq.addSequenceFeature(new SequenceFeature(sf));
               }
@@ -234,12 +234,12 @@ public class FeaturesFile extends AlignFile
 
           if (!token.equals("ID_NOT_SPECIFIED"))
           {
-            seq = align.findName(seqId=token, true);
+            seq = align.findName(seqId = token, true);
             st.nextToken();
           }
           else
           {
-            seqId=null;
+            seqId = null;
             try
             {
               index = Integer.parseInt(st.nextToken());
@@ -285,7 +285,8 @@ public class FeaturesFile extends AlignFile
 
           seq.addSequenceFeature(sf);
 
-          while (seqId!=null && (seq=align.findName(seq, seqId, false))!=null)
+          while (seqId != null
+                  && (seq = align.findName(seq, seqId, false)) != null)
           {
             seq.addSequenceFeature(new SequenceFeature(sf));
           }
@@ -379,12 +380,15 @@ public class FeaturesFile extends AlignFile
 
   }
 
-/**
- * generate a features file for seqs
- * @param seqs source of sequence features
- * @param visible hash of feature types and colours 
- * @return features file contents
- */
+  /**
+   * generate a features file for seqs
+   * 
+   * @param seqs
+   *                source of sequence features
+   * @param visible
+   *                hash of feature types and colours
+   * @return features file contents
+   */
   public String printJalviewFormat(SequenceI[] seqs, Hashtable visible)
   {
     return printJalviewFormat(seqs, visible, true);
@@ -392,9 +396,13 @@ public class FeaturesFile extends AlignFile
 
   /**
    * generate a features file for seqs with colours from visible (if any)
-   * @param seqs        source of features
-   * @param visible     hash of Colours for each feature type
-   * @param visOnly     when true only feature types in 'visible' will be output
+   * 
+   * @param seqs
+   *                source of features
+   * @param visible
+   *                hash of Colours for each feature type
+   * @param visOnly
+   *                when true only feature types in 'visible' will be output
    * @return features file contents
    */
   public String printJalviewFormat(SequenceI[] seqs, Hashtable visible,
@@ -409,7 +417,8 @@ public class FeaturesFile extends AlignFile
     }
     if (visible != null && visOnly)
     {
-      // write feature colours only if we're given them and we are generating viewed features
+      // write feature colours only if we're given them and we are generating
+      // viewed features
       Enumeration en = visible.keys();
       String type;
       int color;
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 584840e..6cb1212 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.io;
 
 import java.util.*;
@@ -47,15 +46,20 @@ public class FileLoader implements Runnable
   long memused;
 
   boolean raiseGUI = true;
+
   /**
-   * default constructor always raised errors in GUI dialog boxes 
+   * default constructor always raised errors in GUI dialog boxes
    */
-  public FileLoader() {
+  public FileLoader()
+  {
     this(true);
   }
+
   /**
-   * construct a Fileloader that may raise errors non-interactively 
-   * @param raiseGUI true if errors are to be raised as GUI dialog boxes
+   * construct a Fileloader that may raise errors non-interactively
+   * 
+   * @param raiseGUI
+   *                true if errors are to be raised as GUI dialog boxes
    */
   public FileLoader(boolean raiseGUI)
   {
@@ -236,7 +240,10 @@ public class FileLoader implements Runnable
       if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage())
       {
         System.gc();
-        memused = (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // free memory before load
+        memused = (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // free
+                                                                          // memory
+                                                                          // before
+                                                                          // load
       }
       loadtime = -System.currentTimeMillis();
       Alignment al = null;
@@ -351,10 +358,9 @@ public class FileLoader implements Runnable
 
       updateRecentlyOpened();
 
-    }
-    catch (Exception er)
+    } catch (Exception er)
     {
-      System.err.println("Exception whilst opening file '"+file);
+      System.err.println("Exception whilst opening file '" + file);
       er.printStackTrace();
       if (raiseGUI)
       {
@@ -362,20 +368,15 @@ public class FileLoader implements Runnable
         {
           public void run()
           {
-            javax.swing.JOptionPane
-                    .showInternalMessageDialog(
-                            Desktop.desktop,
-                            "Encountered problems opening "
-                                    + file
-                                    + "!!"
-                                    , "File open error",
-                            javax.swing.JOptionPane.WARNING_MESSAGE);
+            javax.swing.JOptionPane.showInternalMessageDialog(
+                    Desktop.desktop, "Encountered problems opening " + file
+                            + "!!", "File open error",
+                    javax.swing.JOptionPane.WARNING_MESSAGE);
           }
         });
       }
       alignFrame = null;
-    }
-    catch (OutOfMemoryError er)
+    } catch (OutOfMemoryError er)
     {
 
       er.printStackTrace();
@@ -398,15 +399,19 @@ public class FileLoader implements Runnable
           }
         });
       }
-      else
-      {
-        System.err.println("Out of memory loading file " + file + "!!");
-      }
+      System.err.println("Out of memory loading file " + file + "!!");
+
     }
     loadtime += System.currentTimeMillis();
-
+    // TODO: Estimate percentage of memory used by a newly loaded alignment -
+    // warn if more memory will be needed to work with it
     // System.gc();
-    memused = memused - (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // difference in free memory after load
+    memused = memused
+            - (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // difference
+                                                                      // in free
+                                                                      // memory
+                                                                      // after
+                                                                      // load
     if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage())
     {
       if (alignFrame != null)
@@ -417,11 +422,15 @@ public class FileLoader implements Runnable
                 + (loadtime / 1000.0) + "s, took an additional "
                 + (1.0 * memused / (1024.0 * 1024.0)) + " MB ("
                 + al.getHeight() + " seqs by " + al.getWidth() + " cols)");
-      } else {
-        // report that we didn't load anything probably due to an out of memory error
-        System.out.println("Failed to load '"+title+"' in "
+      }
+      else
+      {
+        // report that we didn't load anything probably due to an out of memory
+        // error
+        System.out.println("Failed to load '" + title + "' in "
                 + (loadtime / 1000.0) + "s, took an additional "
-                + (1.0 * memused / (1024.0 * 1024.0)) + " MB (alignment is null)");
+                + (1.0 * memused / (1024.0 * 1024.0))
+                + " MB (alignment is null)");
       }
     }
     // remove the visual delay indicator
diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 04a673c..cca8ace 100755
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -20,46 +20,60 @@ package jalview.io;
 
 import java.io.*;
 import java.net.*;
-/** 
- * implements a random access wrapper around a particular datasource, for passing to
- * identifyFile and AlignFile objects.
+
+/**
+ * implements a random access wrapper around a particular datasource, for
+ * passing to identifyFile and AlignFile objects.
  */
 public class FileParse
 {
-  public File inFile=null;
-  public int index = 1; // sequence counter for FileParse object created from same data source
+  public File inFile = null;
+
+  public int index = 1; // sequence counter for FileParse object created from
+                        // same data source
+
   protected char suffixSeparator = '#';
+
   /**
-   * '#' separated string tagged on to end of filename 
-   * or url that was clipped off to resolve to valid filename
+   * '#' separated string tagged on to end of filename or url that was clipped
+   * off to resolve to valid filename
    */
-  protected String suffix=null; 
-  protected String type=null;
-  protected BufferedReader dataIn=null;
-  protected String errormessage="UNITIALISED SOURCE";
-  protected boolean error=true;
-  protected String warningMessage=null;
+  protected String suffix = null;
+
+  protected String type = null;
+
+  protected BufferedReader dataIn = null;
+
+  protected String errormessage = "UNITIALISED SOURCE";
+
+  protected boolean error = true;
+
+  protected String warningMessage = null;
+
   /**
    * size of readahead buffer used for when initial stream position is marked.
    */
-  final int READAHEAD_LIMIT=2048;
+  final int READAHEAD_LIMIT = 2048;
+
   public FileParse()
   {
   }
+
   /**
-   * Create a new FileParse instance reading from the same datasource starting at the current position.
-   * WARNING! Subsequent reads from either object will affect the read position of the other, but not
-   * the error state.
+   * Create a new FileParse instance reading from the same datasource starting
+   * at the current position. WARNING! Subsequent reads from either object will
+   * affect the read position of the other, but not the error state.
    * 
    * @param from
    */
   public FileParse(FileParse from) throws IOException
   {
-    if (from==null)
+    if (from == null)
     {
-      throw new Error("Implementation error. Null FileParse in copy constructor");
+      throw new Error(
+              "Implementation error. Null FileParse in copy constructor");
     }
-    if (from==this)
+    if (from == this)
       return;
     index = ++from.index;
     inFile = from.inFile;
@@ -69,118 +83,147 @@ public class FileParse
     error = false; // reset any error condition.
     type = from.type;
     dataIn = from.dataIn;
-    if (dataIn!=null)
+    if (dataIn != null)
     {
       mark();
     }
   }
+
   /**
-   * Attempt to open a file as a datasource.
-   * Sets error and errormessage if fileStr was invalid.
+   * Attempt to open a file as a datasource. Sets error and errormessage if
+   * fileStr was invalid.
+   * 
    * @param fileStr
    * @return this.error (true if the source was invalid)
    */
-  private boolean checkFileSource(String fileStr) throws IOException {
-    error=false;
+  private boolean checkFileSource(String fileStr) throws IOException
+  {
+    error = false;
     this.inFile = new File(fileStr);
     // check to see if it's a Jar file in disguise.
-    if (!inFile.exists()) {
+    if (!inFile.exists())
+    {
       errormessage = "FILE NOT FOUND";
-      error=true;
+      error = true;
     }
-    if (!inFile.canRead()) {
+    if (!inFile.canRead())
+    {
       errormessage = "FILE CANNOT BE OPENED FOR READING";
-      error=true;
+      error = true;
     }
-    if (inFile.isDirectory()) {
-      // this is really a 'complex' filetype - but we don't handle directory reads yet.
+    if (inFile.isDirectory())
+    {
+      // this is really a 'complex' filetype - but we don't handle directory
+      // reads yet.
       errormessage = "FILE IS A DIRECTORY";
-      error=true;
+      error = true;
     }
-    if (!error) {
+    if (!error)
+    {
       dataIn = new BufferedReader(new FileReader(fileStr));
     }
     return error;
   }
-  private boolean checkURLSource(String fileStr) throws IOException, MalformedURLException
+
+  private boolean checkURLSource(String fileStr) throws IOException,
+          MalformedURLException
   {
     errormessage = "URL NOT FOUND";
     URL url = new URL(fileStr);
     dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
     return false;
   }
+
   /**
-   * sets the suffix string (if any) and returns remainder (if suffix was detected) 
+   * sets the suffix string (if any) and returns remainder (if suffix was
+   * detected)
+   * 
    * @param fileStr
    * @return truncated fileStr or null
    */
-  private String extractSuffix(String fileStr) {
+  private String extractSuffix(String fileStr)
+  {
     // first check that there wasn't a suffix string tagged on.
     int sfpos = fileStr.lastIndexOf(suffixSeparator);
-    if (sfpos>-1 && sfpos<fileStr.length()-1) {
-      suffix = fileStr.substring(sfpos+1);
+    if (sfpos > -1 && sfpos < fileStr.length() - 1)
+    {
+      suffix = fileStr.substring(sfpos + 1);
       // System.err.println("DEBUG: Found Suffix:"+suffix);
-      return fileStr.substring(0,sfpos);
+      return fileStr.substring(0, sfpos);
     }
     return null;
   }
+
   /**
-   * Create a datasource for input to Jalview.
-   * See AppletFormatAdapter for the types of sources that are handled.
-   * @param fileStr - datasource locator/content
-   * @param type - protocol of source 
+   * Create a datasource for input to Jalview. See AppletFormatAdapter for the
+   * types of sources that are handled.
+   * 
+   * @param fileStr -
+   *                datasource locator/content
+   * @param type -
+   *                protocol of source
    * @throws MalformedURLException
    * @throws IOException
    */
   public FileParse(String fileStr, String type)
-      throws MalformedURLException, IOException
+          throws MalformedURLException, IOException
   {
     this.type = type;
-    error=false;
+    error = false;
 
     if (type.equals(AppletFormatAdapter.FILE))
     {
-      if (checkFileSource(fileStr)) {  
+      if (checkFileSource(fileStr))
+      {
         String suffixLess = extractSuffix(fileStr);
-        if (suffixLess!=null)
+        if (suffixLess != null)
         {
           if (checkFileSource(suffixLess))
           {
-            throw new IOException("Problem opening "+inFile+" (also tried "+suffixLess+") : "+errormessage);
+            throw new IOException("Problem opening " + inFile
+                    + " (also tried " + suffixLess + ") : " + errormessage);
           }
-        } else
+        }
+        else
         {
-          throw new IOException("Problem opening "+inFile+" : "+errormessage);
+          throw new IOException("Problem opening " + inFile + " : "
+                  + errormessage);
         }
       }
     }
     else if (type.equals(AppletFormatAdapter.URL))
     {
-      try {
-      try {
-        checkURLSource(fileStr);
-        if (suffixSeparator=='#')
-          extractSuffix(fileStr); // URL lref is stored for later reference.
-      } catch (IOException e) {
-        String suffixLess = extractSuffix(fileStr);
-        if (suffixLess==null)
+      try
+      {
+        try
         {
-          throw(e);
-        } else {
-          try {
-            checkURLSource(suffixLess);
+          checkURLSource(fileStr);
+          if (suffixSeparator == '#')
+            extractSuffix(fileStr); // URL lref is stored for later reference.
+        } catch (IOException e)
+        {
+          String suffixLess = extractSuffix(fileStr);
+          if (suffixLess == null)
+          {
+            throw (e);
           }
-          catch (IOException e2) {
-            errormessage = "BAD URL WITH OR WITHOUT SUFFIX";
-            throw(e); // just pass back original - everything was wrong.
+          else
+          {
+            try
+            {
+              checkURLSource(suffixLess);
+            } catch (IOException e2)
+            {
+              errormessage = "BAD URL WITH OR WITHOUT SUFFIX";
+              throw (e); // just pass back original - everything was wrong.
+            }
           }
         }
-      }
-      }
-      catch (Exception e)
+      } catch (Exception e)
       {
-        errormessage = "CANNOT ACCESS DATA AT URL '"+fileStr+"' ("+e.getMessage()+")";
-        error=true;
+        errormessage = "CANNOT ACCESS DATA AT URL '" + fileStr + "' ("
+                + e.getMessage() + ")";
+        error = true;
       }
     }
     else if (type.equals(AppletFormatAdapter.PASTE))
@@ -191,106 +234,131 @@ public class FileParse
     else if (type.equals(AppletFormatAdapter.CLASSLOADER))
     {
       errormessage = "RESOURCE CANNOT BE LOCATED";
-      java.io.InputStream is = getClass().getResourceAsStream("/" + fileStr);
-      if (is==null) {
+      java.io.InputStream is = getClass()
+              .getResourceAsStream("/" + fileStr);
+      if (is == null)
+      {
         String suffixLess = extractSuffix(fileStr);
-        if (suffixLess!=null)
+        if (suffixLess != null)
           is = getClass().getResourceAsStream("/" + suffixLess);
       }
       if (is != null)
       {
         dataIn = new BufferedReader(new java.io.InputStreamReader(is));
-      } else {
+      }
+      else
+      {
         error = true;
       }
     }
-    if (dataIn==null)
+    else
+    {
+      errormessage = "PROBABLE IMPLEMENTATION ERROR : Datasource Type given as '"
+              + (type != null ? type : "null") + "'";
+      error = true;
+    }
+    if (dataIn == null || error)
     {
       // pass up the reason why we have no source to read from
-      throw new IOException("Failed to read data from source:\n"+errormessage);
+      throw new IOException("Failed to read data from source:\n"
+              + errormessage);
     }
-    error=false;
+    error = false;
     dataIn.mark(READAHEAD_LIMIT);
   }
+
   /**
-   * mark the current position in the source as start
-   * for the purposes of it being analysed by IdentifyFile().identify
+   * mark the current position in the source as start for the purposes of it
+   * being analysed by IdentifyFile().identify
+   * 
    * @throws IOException
    */
   public void mark() throws IOException
   {
-    if (dataIn!=null)
+    if (dataIn != null)
     {
       dataIn.mark(READAHEAD_LIMIT);
-    } else {
+    }
+    else
+    {
       throw new IOException("Unitialised Source Stream");
     }
   }
-  public String nextLine()
-      throws IOException
+
+  public String nextLine() throws IOException
   {
     if (!error)
       return dataIn.readLine();
-    throw new IOException("Invalid Source Stream:"+errormessage);
+    throw new IOException("Invalid Source Stream:" + errormessage);
   }
 
   public boolean isValid()
   {
     return !error;
   }
+
   /**
-   * closes the datasource and tidies up.
-   * source will be left in an error state
+   * closes the datasource and tidies up. source will be left in an error state
    */
   public void close() throws IOException
   {
-    errormessage="EXCEPTION ON CLOSE";
-    error=true;
+    errormessage = "EXCEPTION ON CLOSE";
+    error = true;
     dataIn.close();
-    dataIn=null;
-    errormessage="SOURCE IS CLOSED";
+    dataIn = null;
+    errormessage = "SOURCE IS CLOSED";
   }
+
   /**
    * rewinds the datasource the beginning.
-   *
+   * 
    */
   public void reset() throws IOException
   {
-    if (dataIn!=null && !error) {
+    if (dataIn != null && !error)
+    {
       dataIn.reset();
-    } else {
-      throw new IOException("Implementation Error: Reset called for invalid source.");
+    }
+    else
+    {
+      throw new IOException(
+              "Implementation Error: Reset called for invalid source.");
     }
   }
+
   /**
    * 
    * @return true if there is a warning for the user
    */
-  public boolean hasWarningMessage() {
-    return (warningMessage!=null && warningMessage.length()>0);
+  public boolean hasWarningMessage()
+  {
+    return (warningMessage != null && warningMessage.length() > 0);
   }
+
   /**
    * 
    * @return empty string or warning message about file that was just parsed.
    */
-  public String getWarningMessage() {
+  public String getWarningMessage()
+  {
     return warningMessage;
   }
+
   public String getInFile()
   {
-    if (inFile!=null)
+    if (inFile != null)
     {
-      return inFile.getAbsolutePath()+" ("+index+")";
+      return inFile.getAbsolutePath() + " (" + index + ")";
     }
     else
     {
-      return "From Paste + ("+index+")";
+      return "From Paste + (" + index + ")";
     }
   }
-  
+
   public Reader getReader() throws IOException
   {
-    if (dataIn!=null && dataIn.ready())
+    if (dataIn != null && dataIn.ready())
     {
       return dataIn;
     }
diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 983d02e..17a5c68 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -21,40 +21,39 @@ package jalview.io;
 import jalview.datamodel.*;
 
 /**
- * Additional formatting methods used by the application
- * in a number of places. 
- *
+ * Additional formatting methods used by the application in a number of places.
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class FormatAdapter
-    extends AppletFormatAdapter
+public class FormatAdapter extends AppletFormatAdapter
 {
-  
-  public String formatSequences(String format,
-                                SequenceI[] seqs,
-                                String[] omitHiddenColumns)
+
+  public String formatSequences(String format, SequenceI[] seqs,
+          String[] omitHiddenColumns)
   {
 
     return formatSequences(format, replaceStrings(seqs, omitHiddenColumns));
   }
 
   /**
-   * create sequences with each seuqence string replaced with the one given in omitHiddenCOlumns
+   * create sequences with each seuqence string replaced with the one given in
+   * omitHiddenCOlumns
+   * 
    * @param seqs
    * @param omitHiddenColumns
    * @return new sequences
    */
-  public SequenceI[] replaceStrings(SequenceI[] seqs, String[] omitHiddenColumns)
+  public SequenceI[] replaceStrings(SequenceI[] seqs,
+          String[] omitHiddenColumns)
   {
     if (omitHiddenColumns != null)
     {
       SequenceI[] tmp = new SequenceI[seqs.length];
       for (int i = 0; i < seqs.length; i++)
       {
-        tmp[i] = new Sequence(
-            seqs[i].getName(), omitHiddenColumns[i],
-            seqs[i].getStart(), seqs[i].getEnd());
+        tmp[i] = new Sequence(seqs[i].getName(), omitHiddenColumns[i],
+                seqs[i].getStart(), seqs[i].getEnd());
         tmp[i].setDescription(seqs[i].getDescription());
       }
       seqs = tmp;
@@ -64,14 +63,17 @@ public class FormatAdapter
 
   /**
    * Format a vector of sequences as a flat alignment file.
-   *
-   * @param format Format string as givien in the AppletFormatAdaptor list (exact match to name of class implementing file io for that format)
-   * @param seqs vector of sequences to write
-   *
+   * 
+   * @param format
+   *                Format string as givien in the AppletFormatAdaptor list
+   *                (exact match to name of class implementing file io for that
+   *                format)
+   * @param seqs
+   *                vector of sequences to write
+   * 
    * @return String containing sequences in desired format
    */
-  public String formatSequences(String format,
-                                SequenceI[] seqs)
+  public String formatSequences(String format, SequenceI[] seqs)
   {
 
     try
@@ -81,109 +83,127 @@ public class FormatAdapter
       if (format.equalsIgnoreCase("FASTA"))
       {
         afile = new FastaFile();
-        afile.addJVSuffix(
-            jalview.bin.Cache.getDefault("FASTA_JVSUFFIX", true));
+        afile.addJVSuffix(jalview.bin.Cache.getDefault("FASTA_JVSUFFIX",
+                true));
       }
       else if (format.equalsIgnoreCase("MSF"))
       {
         afile = new MSFfile();
-        afile.addJVSuffix(
-            jalview.bin.Cache.getDefault("MSF_JVSUFFIX", true));
+        afile.addJVSuffix(jalview.bin.Cache
+                .getDefault("MSF_JVSUFFIX", true));
       }
       else if (format.equalsIgnoreCase("PileUp"))
       {
         afile = new PileUpfile();
-        afile.addJVSuffix(
-            jalview.bin.Cache.getDefault("PILEUP_JVSUFFIX", true));
+        afile.addJVSuffix(jalview.bin.Cache.getDefault("PILEUP_JVSUFFIX",
+                true));
       }
       else if (format.equalsIgnoreCase("CLUSTAL"))
       {
         afile = new ClustalFile();
-        afile.addJVSuffix(
-            jalview.bin.Cache.getDefault("CLUSTAL_JVSUFFIX", true));
+        afile.addJVSuffix(jalview.bin.Cache.getDefault("CLUSTAL_JVSUFFIX",
+                true));
       }
       else if (format.equalsIgnoreCase("BLC"))
       {
         afile = new BLCFile();
-        afile.addJVSuffix(
-            jalview.bin.Cache.getDefault("BLC_JVSUFFIX", true));
+        afile.addJVSuffix(jalview.bin.Cache
+                .getDefault("BLC_JVSUFFIX", true));
       }
       else if (format.equalsIgnoreCase("PIR"))
       {
         afile = new PIRFile();
-        afile.addJVSuffix(
-            jalview.bin.Cache.getDefault("PIR_JVSUFFIX", true));
+        afile.addJVSuffix(jalview.bin.Cache
+                .getDefault("PIR_JVSUFFIX", true));
       }
       else if (format.equalsIgnoreCase("PFAM"))
       {
         afile = new PfamFile();
-        afile.addJVSuffix(
-            jalview.bin.Cache.getDefault("PFAM_JVSUFFIX", true));
+        afile.addJVSuffix(jalview.bin.Cache.getDefault("PFAM_JVSUFFIX",
+                true));
       }
-      /* amsa is not supported by this function - it requires an alignment rather than a sequence vector
-      else if (format.equalsIgnoreCase("AMSA"))
-      {
-        afile = new AMSAFile();
-        afile.addJVSuffix(
-            jalview.bin.Cache.getDefault("AMSA_JVSUFFIX", true));
-      }*/
+      /*
+       * amsa is not supported by this function - it requires an alignment
+       * rather than a sequence vector else if (format.equalsIgnoreCase("AMSA")) {
+       * afile = new AMSAFile(); afile.addJVSuffix(
+       * jalview.bin.Cache.getDefault("AMSA_JVSUFFIX", true)); }
+       */
 
       afile.setSeqs(seqs);
 
       return afile.print();
-    }
-    catch (Exception e)
+    } catch (Exception e)
     {
-      System.err.println("Failed to write alignment as a '" + format +
-                         "' file\n");
+      System.err.println("Failed to write alignment as a '" + format
+              + "' file\n");
       e.printStackTrace();
     }
 
     return null;
   }
+
   public boolean getCacheSuffixDefault(String format)
   {
     if (isValidFormat(format))
-      return jalview.bin.Cache.getDefault(format.toUpperCase()+"_JVSUFFIX", true);
+      return jalview.bin.Cache.getDefault(format.toUpperCase()
+              + "_JVSUFFIX", true);
     return false;
   }
-  public String formatSequences(String format, AlignmentI alignment, String[] omitHidden, ColumnSelection colSel)
+
+  public String formatSequences(String format, AlignmentI alignment,
+          String[] omitHidden, ColumnSelection colSel)
   {
-    return formatSequences(format, alignment, omitHidden, getCacheSuffixDefault(format), colSel, null);
+    return formatSequences(format, alignment, omitHidden,
+            getCacheSuffixDefault(format), colSel, null);
   }
-  public String formatSequences(String format, AlignmentI alignment, String[] omitHidden, ColumnSelection colSel, SequenceGroup sgp)
+
+  public String formatSequences(String format, AlignmentI alignment,
+          String[] omitHidden, ColumnSelection colSel, SequenceGroup sgp)
   {
-    return formatSequences(format, alignment, omitHidden, getCacheSuffixDefault(format), colSel, sgp);
+    return formatSequences(format, alignment, omitHidden,
+            getCacheSuffixDefault(format), colSel, sgp);
   }
-    /**
-   * hack function to replace seuqences with visible sequence strings before generating a
-   * string of the alignment in the given format.
+
+  /**
+   * hack function to replace seuqences with visible sequence strings before
+   * generating a string of the alignment in the given format.
+   * 
    * @param format
-     * @param alignment
-     * @param omitHidden sequence strings to write out in order of sequences in alignment
-     * @param colSel defines hidden columns that are edited out of annotation 
+   * @param alignment
+   * @param omitHidden
+   *                sequence strings to write out in order of sequences in
+   *                alignment
+   * @param colSel
+   *                defines hidden columns that are edited out of annotation
    * @return string representation of the alignment formatted as format
    */
-  public String formatSequences(String format, AlignmentI alignment, String[] omitHidden, boolean suffix, ColumnSelection colSel)
+  public String formatSequences(String format, AlignmentI alignment,
+          String[] omitHidden, boolean suffix, ColumnSelection colSel)
   {
-    return formatSequences(format, alignment, omitHidden, suffix, colSel, null);
+    return formatSequences(format, alignment, omitHidden, suffix, colSel,
+            null);
   }
 
-  public String formatSequences(String format, AlignmentI alignment, String[] omitHidden, boolean suffix, 
-          ColumnSelection colSel, jalview.datamodel.SequenceGroup selgp)
+  public String formatSequences(String format, AlignmentI alignment,
+          String[] omitHidden, boolean suffix, ColumnSelection colSel,
+          jalview.datamodel.SequenceGroup selgp)
   {
-    if (omitHidden!=null)
+    if (omitHidden != null)
     {
       // 
-      Alignment alv = new Alignment(replaceStrings(alignment.getSequencesArray(), omitHidden));
+      Alignment alv = new Alignment(replaceStrings(alignment
+              .getSequencesArray(), omitHidden));
       AlignmentAnnotation[] ala = alignment.getAlignmentAnnotation();
-      for (int i=0; i<ala.length; i++)
+      for (int i = 0; i < ala.length; i++)
       {
         AlignmentAnnotation na = new AlignmentAnnotation(ala[i]);
-        if (selgp!=null)
+        if (selgp != null)
+        {
+          colSel.makeVisibleAnnotation(selgp.getStartRes(), selgp
+                  .getEndRes(), na);
+        }
+        else
         {
-          colSel.makeVisibleAnnotation(selgp.getStartRes(),selgp.getEndRes(), na);
-        } else {
           colSel.makeVisibleAnnotation(na);
         }
         alv.addAnnotation(na);
diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java
index 8406f3d..3d2a148 100755
--- a/src/jalview/io/HTMLOutput.java
+++ b/src/jalview/io/HTMLOutput.java
@@ -1,389 +1,384 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.io;
-
-import java.io.*;
-
-import java.awt.*;
-
-import jalview.datamodel.*;
-import jalview.gui.*;
-
-public class HTMLOutput
-{
-  AlignViewport av;
-  SequenceRenderer sr;
-  FeatureRenderer fr;
-  Color color;
-
-  public HTMLOutput(AlignmentPanel ap, SequenceRenderer sr, FeatureRenderer fr1)
-  {
-    this.av = ap.av;
-    this.sr = sr;
-
-    fr = new FeatureRenderer(ap);
-    fr.transferSettings(fr1);
-
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-        getProperty(
-            "LAST_DIRECTORY"), new String[]
-        {"html"},
-        new String[]
-        {"HTML files"}, "HTML files");
-
-    chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle("Save as HTML");
-    chooser.setToolTipText("Save");
-
-    int value = chooser.showSaveDialog(null);
-
-    if (value == JalviewFileChooser.APPROVE_OPTION)
-    {
-      String choice = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-                                    chooser.getSelectedFile().getParent());
-
-      try
-      {
-        PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
-            choice));
-        out.println("<HTML>");
-        out.println("<style type=\"text/css\">");
-        out.println("<!--");
-        out.print("td {font-family: \"" + av.getFont().getFamily() +
-                  "\", \"" + av.getFont().getName() + "\", mono; " +
-                  "font-size: " + av.getFont().getSize() + "px; ");
-
-        if (av.getFont().getStyle() == Font.BOLD)
-        {
-          out.print("font-weight: BOLD; ");
-        }
-
-        if (av.getFont().getStyle() == Font.ITALIC)
-        {
-          out.print("font-style: italic; ");
-        }
-
-        out.println("text-align: center; }");
-
-        out.println("-->");
-        out.println("</style>");
-        out.println("<BODY>");
-
-        if (av.getWrapAlignment())
-        {
-          drawWrappedAlignment(out);
-        }
-        else
-        {
-          drawUnwrappedAlignment(out);
-        }
-
-        out.println("\n</body>\n</html>");
-        out.close();
-        jalview.util.BrowserLauncher.openURL("file:///" + choice);
-      }
-      catch (Exception ex)
-      {
-        ex.printStackTrace();
-      }
-    }
-  }
-
-  void drawUnwrappedAlignment(PrintWriter out)
-  {
-    out.println("<table border=\"1\"><tr><td>\n");
-    out.println(
-        "<table border=\"0\"  cellpadding=\"0\" cellspacing=\"0\">\n");
-
-    //////////////
-    SequenceI seq;
-    AlignmentI alignment = av.getAlignment();
-
-    // draws the top row, the measure rule
-    out.println("<tr><td colspan=\"6\"></td>");
-
-    int i = 0;
-
-    for (i = 10; i < (alignment.getWidth() - 10); i += 10)
-    {
-      out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
-    }
-
-    out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i +
-                "<br>|</td>");
-    out.println("</tr>");
-
-    for (i = 0; i < alignment.getHeight(); i++)
-    {
-      seq = alignment.getSequenceAt(i);
-
-      String id = seq.getDisplayId(av.getShowJVSuffix());
-
-      out.println("<tr><td nowrap>" + id +
-                  "&nbsp;&nbsp;</td>");
-
-      for (int res = 0; res < seq.getLength(); res++)
-      {
-        if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
-        {
-          color = sr.getResidueBoxColour(seq, res);
-
-          color = fr.findFeatureColour(color, seq, res);
-        }
-        else
-        {
-          color = Color.white;
-        }
-
-        if (color.getRGB() < -1)
-        {
-          out.println("<td bgcolor=\"#" +
-                      jalview.util.Format.getHexString(color) + "\">" +
-                      seq.getCharAt(res) + "</td>");
-        }
-        else
-        {
-          out.println("<td>" + seq.getCharAt(res) + "</td>");
-        }
-      }
-
-      out.println("</tr>");
-    }
-
-    //////////////
-    out.println("</table>");
-    out.println("</td></tr></table>");
-  }
-
-  void drawWrappedAlignment(PrintWriter out)
-  {
-    ////////////////////////////////////
-    /// How many sequences and residues can we fit on a printable page?
-    AlignmentI al = av.getAlignment();
-    SequenceI seq;
-    String r;
-    String g;
-    String b;
-
-    out.println("<table border=\"1\"><tr><td>\n");
-    out.println(
-        "<table border=\"0\"  cellpadding=\"0\" cellspacing=\"0\">\n");
-
-    for (int startRes = 0; startRes < al.getWidth();
-         startRes += av.getWrappedWidth())
-    {
-      int endRes = startRes + av.getWrappedWidth();
-
-      if (endRes > al.getWidth())
-      {
-        endRes = al.getWidth();
-      }
-
-      if (av.getScaleAboveWrapped())
-      {
-        out.println("<tr>");
-
-        if (av.getScaleLeftWrapped())
-        {
-          out.println("<td colspan=\"7\">&nbsp;</td>");
-        }
-        else
-        {
-          out.println("<td colspan=\"6\">&nbsp;</td>");
-        }
-
-        for (int i = startRes + 10; i < endRes; i += 10)
-        {
-          out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
-        }
-
-        out.println("</tr>");
-      }
-
-      int startPos, endPos;
-      for (int s = 0; s < al.getHeight(); s++)
-      {
-        out.println("<tr>");
-        seq = al.getSequenceAt(s);
-
-        startPos = seq.findPosition(startRes);
-        endPos = seq.findPosition(endRes) - 1;
-
-        String id = seq.getDisplayId(av.getShowJVSuffix());
-
-        out.println("<td nowrap>" + id +
-                    "&nbsp;&nbsp;</td>");
-
-        if (av.getScaleLeftWrapped())
-        {
-          if (startPos > seq.getEnd() || endPos == 0)
-          {
-            out.println("<td nowrap>&nbsp;</td>");
-          }
-          else
-          {
-            out.println("<td nowrap>" + startPos +
-                        "&nbsp;&nbsp;</td>");
-          }
-        }
-
-        for (int res = startRes; res < endRes; res++)
-        {
-          if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
-          {
-            color = sr.getResidueBoxColour(seq, res);
-
-            color = fr.findFeatureColour(color, seq, res);
-          }
-          else
-          {
-            color = Color.white;
-          }
-
-          if (color.getRGB() < -1)
-          {
-            out.println("<td bgcolor=\"#" +
-                        jalview.util.Format.getHexString(color) + "\">" +
-                        seq.getCharAt(res) + "</td>");
-          }
-          else
-          {
-            out.println("<td>" + seq.getCharAt(res) + "</td>");
-          }
-
-        }
-
-        if (av.getScaleRightWrapped() &&
-            endRes < startRes + av.getWrappedWidth())
-        {
-          out.println("<td colspan=\"" +
-                      (startRes + av.getWrappedWidth() - endRes) + "\">"
-                      + "&nbsp;&nbsp;</td>");
-        }
-
-        if (av.getScaleRightWrapped() && startPos < endPos)
-        {
-          out.println("<td nowrap>&nbsp;" + endPos +
-                      "&nbsp;&nbsp;</td>");
-        }
-
-        out.println("</tr>");
-      }
-
-      if (endRes < al.getWidth())
-      {
-        out.println("<tr><td height=\"5\"></td></tr>");
-      }
-    }
-
-    out.println("</table>");
-    out.println("</table>");
-  }
-
-  public static String getImageMapHTML()
-  {
-    return new String(
-        "<html>\n"
-        + "<head>\n"
-        + "<script language=\"JavaScript\">\n"
-        + "var ns4 = document.layers;\n"
-        + "var ns6 = document.getElementById && !document.all;\n"
-        + "var ie4 = document.all;\n"
-        + "offsetX = 0;\n"
-        + "offsetY = 20;\n"
-        + "var toolTipSTYLE=\"\";\n"
-        + "function initToolTips()\n"
-        + "{\n"
-        + "  if(ns4||ns6||ie4)\n"
-        + "  {\n"
-        + "    if(ns4) toolTipSTYLE = document.toolTipLayer;\n"
-        + "    else if(ns6) toolTipSTYLE = document.getElementById(\"toolTipLayer\").style;\n"
-        + "    else if(ie4) toolTipSTYLE = document.all.toolTipLayer.style;\n"
-        + "    if(ns4) document.captureEvents(Event.MOUSEMOVE);\n"
-        + "    else\n"
-        + "    {\n"
-        + "      toolTipSTYLE.visibility = \"visible\";\n"
-        + "      toolTipSTYLE.display = \"none\";\n"
-        + "    }\n"
-        + "    document.onmousemove = moveToMouseLoc;\n"
-        + "  }\n"
-        + "}\n"
-        + "function toolTip(msg, fg, bg)\n"
-        + "{\n"
-        + "  if(toolTip.arguments.length < 1) // hide\n"
-        + "  {\n"
-        + "    if(ns4) toolTipSTYLE.visibility = \"hidden\";\n"
-        + "    else toolTipSTYLE.display = \"none\";\n"
-        + "  }\n"
-        + "  else // show\n"
-        + "  {\n"
-        + "    if(!fg) fg = \"#555555\";\n"
-        + "    if(!bg) bg = \"#FFFFFF\";\n"
-        + "    var content =\n"
-        + "    '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + fg + '\"><td>' +\n"
-        + "    '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + bg + \n"
-        +
-        "    '\"><td align=\"center\"><font face=\"sans-serif\" color=\"' + fg +\n"
-        + "    '\" size=\"-2\">&nbsp;' + msg +\n"
-        + "    '&nbsp;</font></td></table></td></table>';\n"
-        + "    if(ns4)\n"
-        + "    {\n"
-        + "      toolTipSTYLE.document.write(content);\n"
-        + "      toolTipSTYLE.document.close();\n"
-        + "      toolTipSTYLE.visibility = \"visible\";\n"
-        + "    }\n"
-        + "    if(ns6)\n"
-        + "    {\n"
-        +
-        "      document.getElementById(\"toolTipLayer\").innerHTML = content;\n"
-        + "      toolTipSTYLE.display='block'\n"
-        + "    }\n"
-        + "    if(ie4)\n"
-        + "    {\n"
-        + "      document.all(\"toolTipLayer\").innerHTML=content;\n"
-        + "      toolTipSTYLE.display='block'\n"
-        + "    }\n"
-        + "  }\n"
-        + "}\n"
-        + "function moveToMouseLoc(e)\n"
-        + "{\n"
-        + "  if(ns4||ns6)\n"
-        + "  {\n"
-        + "    x = e.pageX;\n"
-        + "    y = e.pageY;\n"
-        + "  }\n"
-        + "  else\n"
-        + "  {\n"
-        + "    x = event.x + document.body.scrollLeft;\n"
-        + "    y = event.y + document.body.scrollTop;\n"
-        + "  }\n"
-        + "  toolTipSTYLE.left = x + offsetX;\n"
-        + "  toolTipSTYLE.top = y + offsetY;\n"
-        + "  return true;\n"
-        + "}\n"
-        + "</script>\n"
-        + "</head>\n"
-        + "<body>\n"
-        + "<div id=\"toolTipLayer\" style=\"position:absolute; visibility: hidden\"></div>\n"
-        + "<script language=\"JavaScript\"><!--\n"
-        + "initToolTips(); //--></script>\n");
-
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.io;
+
+import java.io.*;
+
+import java.awt.*;
+
+import jalview.datamodel.*;
+import jalview.gui.*;
+
+public class HTMLOutput
+{
+  AlignViewport av;
+
+  SequenceRenderer sr;
+
+  FeatureRenderer fr;
+
+  Color color;
+
+  public HTMLOutput(AlignmentPanel ap, SequenceRenderer sr,
+          FeatureRenderer fr1)
+  {
+    this.av = ap.av;
+    this.sr = sr;
+
+    fr = new FeatureRenderer(ap);
+    fr.transferSettings(fr1);
+
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+            .getProperty("LAST_DIRECTORY"), new String[]
+    { "html" }, new String[]
+    { "HTML files" }, "HTML files");
+
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle("Save as HTML");
+    chooser.setToolTipText("Save");
+
+    int value = chooser.showSaveDialog(null);
+
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      String choice = chooser.getSelectedFile().getPath();
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+              .getSelectedFile().getParent());
+
+      try
+      {
+        PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
+                choice));
+        out.println("<HTML>");
+        out.println("<style type=\"text/css\">");
+        out.println("<!--");
+        out.print("td {font-family: \"" + av.getFont().getFamily()
+                + "\", \"" + av.getFont().getName() + "\", mono; "
+                + "font-size: " + av.getFont().getSize() + "px; ");
+
+        if (av.getFont().getStyle() == Font.BOLD)
+        {
+          out.print("font-weight: BOLD; ");
+        }
+
+        if (av.getFont().getStyle() == Font.ITALIC)
+        {
+          out.print("font-style: italic; ");
+        }
+
+        out.println("text-align: center; }");
+
+        out.println("-->");
+        out.println("</style>");
+        out.println("<BODY>");
+
+        if (av.getWrapAlignment())
+        {
+          drawWrappedAlignment(out);
+        }
+        else
+        {
+          drawUnwrappedAlignment(out);
+        }
+
+        out.println("\n</body>\n</html>");
+        out.close();
+        jalview.util.BrowserLauncher.openURL("file:///" + choice);
+      } catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
+    }
+  }
+
+  void drawUnwrappedAlignment(PrintWriter out)
+  {
+    out.println("<table border=\"1\"><tr><td>\n");
+    out
+            .println("<table border=\"0\"  cellpadding=\"0\" cellspacing=\"0\">\n");
+
+    // ////////////
+    SequenceI seq;
+    AlignmentI alignment = av.getAlignment();
+
+    // draws the top row, the measure rule
+    out.println("<tr><td colspan=\"6\"></td>");
+
+    int i = 0;
+
+    for (i = 10; i < (alignment.getWidth() - 10); i += 10)
+    {
+      out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
+    }
+
+    out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i
+            + "<br>|</td>");
+    out.println("</tr>");
+
+    for (i = 0; i < alignment.getHeight(); i++)
+    {
+      seq = alignment.getSequenceAt(i);
+
+      String id = seq.getDisplayId(av.getShowJVSuffix());
+
+      out.println("<tr><td nowrap>" + id + "&nbsp;&nbsp;</td>");
+
+      for (int res = 0; res < seq.getLength(); res++)
+      {
+        if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
+        {
+          color = sr.getResidueBoxColour(seq, res);
+
+          color = fr.findFeatureColour(color, seq, res);
+        }
+        else
+        {
+          color = Color.white;
+        }
+
+        if (color.getRGB() < -1)
+        {
+          out.println("<td bgcolor=\"#"
+                  + jalview.util.Format.getHexString(color) + "\">"
+                  + seq.getCharAt(res) + "</td>");
+        }
+        else
+        {
+          out.println("<td>" + seq.getCharAt(res) + "</td>");
+        }
+      }
+
+      out.println("</tr>");
+    }
+
+    // ////////////
+    out.println("</table>");
+    out.println("</td></tr></table>");
+  }
+
+  void drawWrappedAlignment(PrintWriter out)
+  {
+    // //////////////////////////////////
+    // / How many sequences and residues can we fit on a printable page?
+    AlignmentI al = av.getAlignment();
+    SequenceI seq;
+    String r;
+    String g;
+    String b;
+
+    out.println("<table border=\"1\"><tr><td>\n");
+    out
+            .println("<table border=\"0\"  cellpadding=\"0\" cellspacing=\"0\">\n");
+
+    for (int startRes = 0; startRes < al.getWidth(); startRes += av
+            .getWrappedWidth())
+    {
+      int endRes = startRes + av.getWrappedWidth();
+
+      if (endRes > al.getWidth())
+      {
+        endRes = al.getWidth();
+      }
+
+      if (av.getScaleAboveWrapped())
+      {
+        out.println("<tr>");
+
+        if (av.getScaleLeftWrapped())
+        {
+          out.println("<td colspan=\"7\">&nbsp;</td>");
+        }
+        else
+        {
+          out.println("<td colspan=\"6\">&nbsp;</td>");
+        }
+
+        for (int i = startRes + 10; i < endRes; i += 10)
+        {
+          out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
+        }
+
+        out.println("</tr>");
+      }
+
+      int startPos, endPos;
+      for (int s = 0; s < al.getHeight(); s++)
+      {
+        out.println("<tr>");
+        seq = al.getSequenceAt(s);
+
+        startPos = seq.findPosition(startRes);
+        endPos = seq.findPosition(endRes) - 1;
+
+        String id = seq.getDisplayId(av.getShowJVSuffix());
+
+        out.println("<td nowrap>" + id + "&nbsp;&nbsp;</td>");
+
+        if (av.getScaleLeftWrapped())
+        {
+          if (startPos > seq.getEnd() || endPos == 0)
+          {
+            out.println("<td nowrap>&nbsp;</td>");
+          }
+          else
+          {
+            out.println("<td nowrap>" + startPos + "&nbsp;&nbsp;</td>");
+          }
+        }
+
+        for (int res = startRes; res < endRes; res++)
+        {
+          if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
+          {
+            color = sr.getResidueBoxColour(seq, res);
+
+            color = fr.findFeatureColour(color, seq, res);
+          }
+          else
+          {
+            color = Color.white;
+          }
+
+          if (color.getRGB() < -1)
+          {
+            out.println("<td bgcolor=\"#"
+                    + jalview.util.Format.getHexString(color) + "\">"
+                    + seq.getCharAt(res) + "</td>");
+          }
+          else
+          {
+            out.println("<td>" + seq.getCharAt(res) + "</td>");
+          }
+
+        }
+
+        if (av.getScaleRightWrapped()
+                && endRes < startRes + av.getWrappedWidth())
+        {
+          out.println("<td colspan=\""
+                  + (startRes + av.getWrappedWidth() - endRes) + "\">"
+                  + "&nbsp;&nbsp;</td>");
+        }
+
+        if (av.getScaleRightWrapped() && startPos < endPos)
+        {
+          out.println("<td nowrap>&nbsp;" + endPos + "&nbsp;&nbsp;</td>");
+        }
+
+        out.println("</tr>");
+      }
+
+      if (endRes < al.getWidth())
+      {
+        out.println("<tr><td height=\"5\"></td></tr>");
+      }
+    }
+
+    out.println("</table>");
+    out.println("</table>");
+  }
+
+  public static String getImageMapHTML()
+  {
+    return new String(
+            "<html>\n"
+                    + "<head>\n"
+                    + "<script language=\"JavaScript\">\n"
+                    + "var ns4 = document.layers;\n"
+                    + "var ns6 = document.getElementById && !document.all;\n"
+                    + "var ie4 = document.all;\n"
+                    + "offsetX = 0;\n"
+                    + "offsetY = 20;\n"
+                    + "var toolTipSTYLE=\"\";\n"
+                    + "function initToolTips()\n"
+                    + "{\n"
+                    + "  if(ns4||ns6||ie4)\n"
+                    + "  {\n"
+                    + "    if(ns4) toolTipSTYLE = document.toolTipLayer;\n"
+                    + "    else if(ns6) toolTipSTYLE = document.getElementById(\"toolTipLayer\").style;\n"
+                    + "    else if(ie4) toolTipSTYLE = document.all.toolTipLayer.style;\n"
+                    + "    if(ns4) document.captureEvents(Event.MOUSEMOVE);\n"
+                    + "    else\n"
+                    + "    {\n"
+                    + "      toolTipSTYLE.visibility = \"visible\";\n"
+                    + "      toolTipSTYLE.display = \"none\";\n"
+                    + "    }\n"
+                    + "    document.onmousemove = moveToMouseLoc;\n"
+                    + "  }\n"
+                    + "}\n"
+                    + "function toolTip(msg, fg, bg)\n"
+                    + "{\n"
+                    + "  if(toolTip.arguments.length < 1) // hide\n"
+                    + "  {\n"
+                    + "    if(ns4) toolTipSTYLE.visibility = \"hidden\";\n"
+                    + "    else toolTipSTYLE.display = \"none\";\n"
+                    + "  }\n"
+                    + "  else // show\n"
+                    + "  {\n"
+                    + "    if(!fg) fg = \"#555555\";\n"
+                    + "    if(!bg) bg = \"#FFFFFF\";\n"
+                    + "    var content =\n"
+                    + "    '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + fg + '\"><td>' +\n"
+                    + "    '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + bg + \n"
+                    + "    '\"><td align=\"center\"><font face=\"sans-serif\" color=\"' + fg +\n"
+                    + "    '\" size=\"-2\">&nbsp;' + msg +\n"
+                    + "    '&nbsp;</font></td></table></td></table>';\n"
+                    + "    if(ns4)\n"
+                    + "    {\n"
+                    + "      toolTipSTYLE.document.write(content);\n"
+                    + "      toolTipSTYLE.document.close();\n"
+                    + "      toolTipSTYLE.visibility = \"visible\";\n"
+                    + "    }\n"
+                    + "    if(ns6)\n"
+                    + "    {\n"
+                    + "      document.getElementById(\"toolTipLayer\").innerHTML = content;\n"
+                    + "      toolTipSTYLE.display='block'\n"
+                    + "    }\n"
+                    + "    if(ie4)\n"
+                    + "    {\n"
+                    + "      document.all(\"toolTipLayer\").innerHTML=content;\n"
+                    + "      toolTipSTYLE.display='block'\n"
+                    + "    }\n"
+                    + "  }\n"
+                    + "}\n"
+                    + "function moveToMouseLoc(e)\n"
+                    + "{\n"
+                    + "  if(ns4||ns6)\n"
+                    + "  {\n"
+                    + "    x = e.pageX;\n"
+                    + "    y = e.pageY;\n"
+                    + "  }\n"
+                    + "  else\n"
+                    + "  {\n"
+                    + "    x = event.x + document.body.scrollLeft;\n"
+                    + "    y = event.y + document.body.scrollTop;\n"
+                    + "  }\n"
+                    + "  toolTipSTYLE.left = x + offsetX;\n"
+                    + "  toolTipSTYLE.top = y + offsetY;\n"
+                    + "  return true;\n"
+                    + "}\n"
+                    + "</script>\n"
+                    + "</head>\n"
+                    + "<body>\n"
+                    + "<div id=\"toolTipLayer\" style=\"position:absolute; visibility: hidden\"></div>\n"
+                    + "<script language=\"JavaScript\"><!--\n"
+                    + "initToolTips(); //--></script>\n");
+
+  }
+}
diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 46899da..f1f51b1 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -23,90 +23,111 @@ import java.net.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
 public class IdentifyFile
 {
   /**
-   * Identify a datasource's file content. 
-   * @note Do not use this method
-   * for stream sources - create a FileParse object instead. 
-   *
-   * @param file DOCUMENT ME!
-   * @param protocol DOCUMENT ME! 
+   * Identify a datasource's file content.
+   * 
+   * @note Do not use this method for stream sources - create a FileParse object
+   *       instead.
+   * 
+   * @param file
+   *                DOCUMENT ME!
+   * @param protocol
+   *                DOCUMENT ME!
    * @return ID String
    */
   public String Identify(String file, String protocol)
   {
     String emessage = "UNIDENTIFIED FILE PARSING ERROR";
     FileParse parser = null;
-    try {
+    try
+    {
       parser = new FileParse(file, protocol);
-      if (parser.isValid()) {
+      if (parser.isValid())
+      {
         return Identify(parser);
       }
-    } catch (Exception e) {
+    } catch (Exception e)
+    {
       System.err.println("Error whilst identifying");
       e.printStackTrace(System.err);
       emessage = e.getMessage();
     }
-    if (parser!=null)
+    if (parser != null)
       return parser.errormessage;
     return emessage;
   }
-  public String Identify(FileParse source) {
-    return Identify(source, true); // preserves original behaviour prior to version 2.3
+
+  public String Identify(FileParse source)
+  {
+    return Identify(source, true); // preserves original behaviour prior to
+                                    // version 2.3
   }
+
   /**
-   * Identify contents of source, closing it or resetting source to start afterwards.
+   * Identify contents of source, closing it or resetting source to start
+   * afterwards.
+   * 
    * @param source
    * @param closeSource
    * @return filetype string
    */
-  public String Identify(FileParse source, boolean closeSource) {
+  public String Identify(FileParse source, boolean closeSource)
+  {
     String reply = "PFAM";
     String data;
-    int length=0;
-    boolean lineswereskipped=false;
-    boolean isBinary = false; // true if length is non-zero and non-printable characters are encountered
-    try {
+    int length = 0;
+    boolean lineswereskipped = false;
+    boolean isBinary = false; // true if length is non-zero and non-printable
+                              // characters are encountered
+    try
+    {
       if (!closeSource)
       {
         source.mark();
       }
-      while ( (data = source.nextLine()) != null)
+      while ((data = source.nextLine()) != null)
       {
-        length+=data.length();
+        length += data.length();
         if (!lineswereskipped)
         {
-          for (int i=0;!isBinary && i<data.length(); i++)
+          for (int i = 0; !isBinary && i < data.length(); i++)
           {
             char c = data.charAt(i);
-            isBinary = (c<32 && c!='\t' && c!='\n' && c!='\r' && c!=5 && c!=27); // nominal binary character filter excluding CR, LF, tab,DEL and ^E for certain blast ids 
+            isBinary = (c < 32 && c != '\t' && c != '\n' && c != '\r'
+                    && c != 5 && c != 27); // nominal binary character filter
+                                            // excluding CR, LF, tab,DEL and ^E
+                                            // for certain blast ids
           }
         }
         if (isBinary)
         {
-          // jar files are special - since they contain all sorts of random characters.
-          if (source.inFile!=null) 
+          // jar files are special - since they contain all sorts of random
+          // characters.
+          if (source.inFile != null)
           {
-              String fileStr=source.inFile.getName();
-              // possibly a Jalview archive. 
-              if (fileStr.lastIndexOf(".jar")>-1 || fileStr.lastIndexOf(".zip")>-1) 
-              {
-                reply = "Jalview";
-              }
-          } 
-          if (!lineswereskipped && data.startsWith("PK")) {
-            reply="Jalview"; // archive.
+            String fileStr = source.inFile.getName();
+            // possibly a Jalview archive.
+            if (fileStr.lastIndexOf(".jar") > -1
+                    || fileStr.lastIndexOf(".zip") > -1)
+            {
+              reply = "Jalview";
+            }
+          }
+          if (!lineswereskipped && data.startsWith("PK"))
+          {
+            reply = "Jalview"; // archive.
             break;
           }
         }
         data = data.toUpperCase();
 
-        if ( (data.indexOf("# STOCKHOLM") > -1))
+        if ((data.indexOf("# STOCKHOLM") > -1))
         {
           reply = "STH";
 
@@ -115,7 +136,7 @@ public class IdentifyFile
 
         if ((data.length() < 1) || (data.indexOf("#") == 0))
         {
-          lineswereskipped=true;
+          lineswereskipped = true;
           continue;
         }
 
@@ -126,10 +147,9 @@ public class IdentifyFile
           break;
         }
 
-        if ( (data.indexOf("//") == 0) ||
-            ( (data.indexOf("!!") > -1) &&
-             (data.indexOf("!!") < data.indexOf(
-                 "_MULTIPLE_ALIGNMENT "))))
+        if ((data.indexOf("//") == 0)
+                || ((data.indexOf("!!") > -1) && (data.indexOf("!!") < data
+                        .indexOf("_MULTIPLE_ALIGNMENT "))))
         {
           reply = "MSF";
 
@@ -141,8 +161,7 @@ public class IdentifyFile
 
           break;
         }
-        else if ( (data.indexOf(">P1;") > -1) ||
-                 (data.indexOf(">DL;") > -1))
+        else if ((data.indexOf(">P1;") > -1) || (data.indexOf(">DL;") > -1))
         {
           reply = "PIR";
 
@@ -159,67 +178,74 @@ public class IdentifyFile
           }
           else
           {
-            //Is this a single line BLC file?
+            // Is this a single line BLC file?
             source.nextLine();
             String data2 = source.nextLine();
-            if (data2 != null
-                && data.indexOf("*") > -1
-                && data.indexOf("*") == data2.indexOf("*"))
+            if (data2 != null && data.indexOf("*") > -1
+                    && data.indexOf("*") == data2.indexOf("*"))
             {
               reply = "BLC";
             }
             else
             {
-                reply = "FASTA";
-                // TODO : AMSA File is indicated if there is annotation in the FASTA file - but FASTA will automatically generate this at the mo.
+              reply = "FASTA";
+              // TODO : AMSA File is indicated if there is annotation in the
+              // FASTA file - but FASTA will automatically generate this at the
+              // mo.
             }
           }
           break;
         }
-        else if (data.indexOf("HEADER") == 0 ||
-                 data.indexOf("ATOM") == 0)
+        else if (data.indexOf("HEADER") == 0 || data.indexOf("ATOM") == 0)
         {
           reply = "PDB";
           break;
         }
-        else if (!lineswereskipped 
-                && data.charAt(0)!='*' 
-                  && data.charAt(0)!=' ' 
-                    && data.indexOf(":") < data.indexOf(",")) //  && data.indexOf(",")<data.indexOf(",", data.indexOf(",")))
+        else if (!lineswereskipped && data.charAt(0) != '*'
+                && data.charAt(0) != ' '
+                && data.indexOf(":") < data.indexOf(",")) // &&
+                                                          // data.indexOf(",")<data.indexOf(",",
+                                                          // data.indexOf(",")))
         {
           // file looks like a concise JNet file
           reply = "JnetFile";
           break;
         }
-        
-        lineswereskipped=true; // this means there was some junk before any key file signature  
+
+        lineswereskipped = true; // this means there was some junk before any
+                                  // key file signature
       }
-      if (closeSource) {
+      if (closeSource)
+      {
         source.close();
-      } else {
+      }
+      else
+      {
         source.reset(); // so the file can be parsed from the beginning again.
       }
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       System.err.println("File Identification failed!\n" + ex);
       return source.errormessage;
     }
-    if (length==0)
+    if (length == 0)
     {
-      System.err.println("File Identification failed! - Empty file was read.");
+      System.err
+              .println("File Identification failed! - Empty file was read.");
       return "EMPTY DATA FILE";
     }
     return reply;
   }
-  public static void main(String[] args) {
-    for (int i=0; args!=null && i<args.length; i++)
+
+  public static void main(String[] args)
+  {
+    for (int i = 0; args != null && i < args.length; i++)
     {
       IdentifyFile ider = new IdentifyFile();
       String type = ider.Identify(args[i], AppletFormatAdapter.FILE);
-      System.out.println("Type of "+args[i]+" is "+type);
+      System.out.println("Type of " + args[i] + " is " + type);
     }
-    if (args==null || args.length==0)
+    if (args == null || args.length == 0)
     {
       System.err.println("Usage: <Filename> [<Filename> ...]");
     }
diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index dfe1ecf..1e1b8bf 100755
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 /**
  * PredFile.java
  * JalviewX / Vamsas Project
@@ -30,47 +29,59 @@ import java.util.*;
 import jalview.datamodel.*;
 
 /**
- * Parser for the JPred/JNet concise format. This is a series of CSV lines,
- * each line is either a sequence (QUERY), a sequence profile (align;), or
- * jnet prediction annotation (anything else). 
- * Automagic translation happens for annotation called 'JNETPRED' (translated to Secondary Structure Prediction), or 'JNETCONF' (translates to 'Prediction Confidence').
- * Numeric scores are differentiated from symbolic by being parseable into a float vector. They are put in Scores.
- * Symscores gets the others.
- * JNetAnnotationMaker translates the data parsed by this object into annotation on an alignment. It is automatically called
- * but can be used to transfer the annotation onto a sequence in another alignment (and insert gaps where necessary)
+ * Parser for the JPred/JNet concise format. This is a series of CSV lines, each
+ * line is either a sequence (QUERY), a sequence profile (align;), or jnet
+ * prediction annotation (anything else). Automagic translation happens for
+ * annotation called 'JNETPRED' (translated to Secondary Structure Prediction),
+ * or 'JNETCONF' (translates to 'Prediction Confidence'). Numeric scores are
+ * differentiated from symbolic by being parseable into a float vector. They are
+ * put in Scores. Symscores gets the others. JNetAnnotationMaker translates the
+ * data parsed by this object into annotation on an alignment. It is
+ * automatically called but can be used to transfer the annotation onto a
+ * sequence in another alignment (and insert gaps where necessary)
+ * 
  * @author jprocter
  * @version $Revision$
  */
-public class JPredFile
-    extends AlignFile
+public class JPredFile extends AlignFile
 {
   Vector ids;
+
   Vector conf;
+
   Hashtable Scores; // Hash of names and score vectors
-  Hashtable Symscores; // indexes of symbol annotation properties in sequenceI vector
+
+  Hashtable Symscores; // indexes of symbol annotation properties in sequenceI
+                        // vector
+
   private int QuerySeqPosition;
 
   /**
    * Creates a new JPredFile object.
-   *
-   * @param inFile DOCUMENT ME!
-   * @param type DOCUMENT ME!
-   *
-   * @throws IOException DOCUMENT ME!
+   * 
+   * @param inFile
+   *                DOCUMENT ME!
+   * @param type
+   *                DOCUMENT ME!
+   * 
+   * @throws IOException
+   *                 DOCUMENT ME!
    */
-  public JPredFile(String inFile, String type)
-      throws IOException
+  public JPredFile(String inFile, String type) throws IOException
   {
     super(inFile, type);
   }
+
   public JPredFile(FileParse source) throws IOException
   {
     super(source);
   }
+
   /**
    * DOCUMENT ME!
-   *
-   * @param QuerySeqPosition DOCUMENT ME!
+   * 
+   * @param QuerySeqPosition
+   *                DOCUMENT ME!
    */
   public void setQuerySeqPosition(int QuerySeqPosition)
   {
@@ -79,7 +90,7 @@ public class JPredFile
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public int getQuerySeqPosition()
@@ -89,7 +100,7 @@ public class JPredFile
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public Hashtable getScores()
@@ -99,7 +110,7 @@ public class JPredFile
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public Hashtable getSymscores()
@@ -121,8 +132,7 @@ public class JPredFile
   /**
    * parse a JPred concise file into a sequence-alignment like object.
    */
-  public void parse()
-      throws IOException
+  public void parse() throws IOException
   {
     // JBPNote log.System.out.println("all read in ");
     String line;
@@ -133,7 +143,7 @@ public class JPredFile
     Vector ids = new Vector();
     Hashtable Symscores = new Hashtable();
 
-    while ( (line = nextLine()) != null)
+    while ((line = nextLine()) != null)
     {
       // Concise format allows no comments or non comma-formatted data
       StringTokenizer str = new StringTokenizer(line, ":");
@@ -186,28 +196,27 @@ public class JPredFile
             ascore = symbols.nextToken();
 
             Float score = new Float(ascore);
-            scores.addElement( (Object) score);
+            scores.addElement((Object) score);
           }
 
           Scores.put(id, scores);
-        }
-        catch (Exception e)
+        } catch (Exception e)
         {
           // or just keep them as strings
           i = scores.size();
 
           for (int j = 0; j < i; j++)
           {
-            scores.setElementAt(
-                (Object) ( (Float) scores.elementAt(j)).toString(), j);
+            scores.setElementAt((Object) ((Float) scores.elementAt(j))
+                    .toString(), j);
           }
 
-          scores.addElement( (Object) ascore);
+          scores.addElement((Object) ascore);
 
           while (symbols.hasMoreTokens())
           {
             ascore = symbols.nextToken();
-            scores.addElement( (Object) ascore);
+            scores.addElement((Object) ascore);
           }
 
           Scores.put(id, scores);
@@ -246,7 +255,7 @@ public class JPredFile
             name = id.substring(id.indexOf(";") + 1) + "_" + ++i;
           }
 
-          if (QuerySeqPosition==-1)
+          if (QuerySeqPosition == -1)
             QuerySeqPosition = ids.size();
           ids.addElement(name);
           noSeqs++;
@@ -260,17 +269,15 @@ public class JPredFile
 
           seq_entries.addElement(newseq.toString());
           ids.addElement(id);
-          Symscores.put( (Object) id,
-                        (Object)new Integer(ids.size() - 1));
+          Symscores.put((Object) id, (Object) new Integer(ids.size() - 1));
         }
       }
     }
-    /* leave it to the parser user to actually check this.
-             if (noSeqs < 1)
-             {
-        throw new IOException(
-            "JpredFile Parser: No sequence in the prediction!");
-             }*/
+    /*
+     * leave it to the parser user to actually check this. if (noSeqs < 1) {
+     * throw new IOException( "JpredFile Parser: No sequence in the
+     * prediction!"); }
+     */
 
     maxLength = seq_entries.elementAt(0).toString().length();
 
@@ -278,48 +285,54 @@ public class JPredFile
     {
       // Add all sequence like objects
       Sequence newSeq = new Sequence(ids.elementAt(i).toString(),
-                                     seq_entries.elementAt(i).toString(), 1,
-                                     seq_entries.elementAt(i).toString().length());
+              seq_entries.elementAt(i).toString(), 1, seq_entries
+                      .elementAt(i).toString().length());
 
       if (maxLength != seq_entries.elementAt(i).toString().length())
       {
-        throw new IOException("JPredConcise: Entry (" +
-                              ids.elementAt(i).toString() +
-                              ") has an unexpected number of columns");
+        throw new IOException("JPredConcise: Entry ("
+                + ids.elementAt(i).toString()
+                + ") has an unexpected number of columns");
       }
 
-      if ((newSeq.getName().startsWith("QUERY") || newSeq.getName().startsWith("align;"))&&
-          (QuerySeqPosition == -1))
+      if ((newSeq.getName().startsWith("QUERY") || newSeq.getName()
+              .startsWith("align;"))
+              && (QuerySeqPosition == -1))
       {
         QuerySeqPosition = seqs.size();
       }
 
       seqs.addElement(newSeq);
     }
-    if (seqs.size()>0)
+    if (seqs.size() > 0)
     {
-      // try to make annotation for a prediction only input (default if no alignment is given)
+      // try to make annotation for a prediction only input (default if no
+      // alignment is given)
       Alignment tal = new Alignment(this.getSeqsAsArray());
-      try {
-        JnetAnnotationMaker.add_annotation(this, tal, QuerySeqPosition, true);
+      try
+      {
+        JnetAnnotationMaker.add_annotation(this, tal, QuerySeqPosition,
+                true);
       } catch (Exception e)
       {
         tal = null;
-        IOException ex = new IOException("Couldn't parse concise annotation for prediction profile.\n"+e);
+        IOException ex = new IOException(
+                "Couldn't parse concise annotation for prediction profile.\n"
+                        + e);
         throw ex;
       }
       this.annotations = new Vector();
       AlignmentAnnotation[] aan = tal.getAlignmentAnnotation();
-      for (int aai = 0; aan!=null && aai<aan.length; aai++)
+      for (int aai = 0; aan != null && aai < aan.length; aai++)
       {
         annotations.addElement(aan[aai]);
       }
-    } 
+    }
   }
 
   /**
    * print
-   *
+   * 
    * @return String
    */
   public String print()
@@ -329,8 +342,9 @@ public class JPredFile
 
   /**
    * DOCUMENT ME!
-   *
-   * @param args DOCUMENT ME!
+   * 
+   * @param args
+   *                DOCUMENT ME!
    */
   public static void main(String[] args)
   {
@@ -340,13 +354,12 @@ public class JPredFile
 
       for (int i = 0; i < blc.seqs.size(); i++)
       {
-        System.out.println( ( (Sequence) blc.seqs.elementAt(i)).getName() +
-                           "\n" +
-                           ( (Sequence) blc.seqs.elementAt(i)).getSequenceAsString() +
-                           "\n");
+        System.out.println(((Sequence) blc.seqs.elementAt(i)).getName()
+                + "\n"
+                + ((Sequence) blc.seqs.elementAt(i)).getSequenceAsString()
+                + "\n");
       }
-    }
-    catch (java.io.IOException e)
+    } catch (java.io.IOException e)
     {
       System.err.println("Exception " + e);
       // e.printStackTrace(); not java 1.1 compatible!
@@ -354,6 +367,7 @@ public class JPredFile
   }
 
   Vector annotSeqs = null;
+
   /**
    * removeNonSequences
    */
@@ -391,46 +405,26 @@ public class JPredFile
 }
 
 /*
- StringBuffer out = new StringBuffer();
-
- out.append("START PRED\n");
- for (int i = 0; i < s[0].sequence.length(); i++)
- {
-  out.append(s[0].sequence.substring(i, i + 1) + " ");
-  out.append(s[1].sequence.substring(i, i + 1) + " ");
-  out.append(s[1].score[0].elementAt(i) + " ");
-  out.append(s[1].score[1].elementAt(i) + " ");
-  out.append(s[1].score[2].elementAt(i) + " ");
-  out.append(s[1].score[3].elementAt(i) + " ");
-
-  out.append("\n");
- }
- out.append("END PRED\n");
- return out.toString();
- }
-
-    public static void main(String[] args)
- {
-  try
-  {
-    BLCFile blc = new BLCFile(args[0], "File");
-    DrawableSequence[] s = new DrawableSequence[blc.seqs.size()];
-    for (int i = 0; i < blc.seqs.size(); i++)
-    {
-      s[i] = new DrawableSequence( (Sequence) blc.seqs.elementAt(i));
-    }
-    String out = BLCFile.print(s);
-
-    AlignFrame af = new AlignFrame(null, s);
-    af.resize(700, 500);
-    af.show();
-    System.out.println(out);
-  }
-  catch (java.io.IOException e)
-  {
-    System.out.println("Exception " + e);
-  }
- }
-
- }
+ * StringBuffer out = new StringBuffer();
+ * 
+ * out.append("START PRED\n"); for (int i = 0; i < s[0].sequence.length(); i++) {
+ * out.append(s[0].sequence.substring(i, i + 1) + " ");
+ * out.append(s[1].sequence.substring(i, i + 1) + " ");
+ * out.append(s[1].score[0].elementAt(i) + " ");
+ * out.append(s[1].score[1].elementAt(i) + " ");
+ * out.append(s[1].score[2].elementAt(i) + " ");
+ * out.append(s[1].score[3].elementAt(i) + " ");
+ * 
+ * out.append("\n"); } out.append("END PRED\n"); return out.toString(); }
+ * 
+ * public static void main(String[] args) { try { BLCFile blc = new
+ * BLCFile(args[0], "File"); DrawableSequence[] s = new
+ * DrawableSequence[blc.seqs.size()]; for (int i = 0; i < blc.seqs.size(); i++) {
+ * s[i] = new DrawableSequence( (Sequence) blc.seqs.elementAt(i)); } String out =
+ * BLCFile.print(s);
+ * 
+ * AlignFrame af = new AlignFrame(null, s); af.resize(700, 500); af.show();
+ * System.out.println(out); } catch (java.io.IOException e) {
+ * System.out.println("Exception " + e); } }
+ *  }
  */
diff --git a/src/jalview/io/JalviewFileChooser.java b/src/jalview/io/JalviewFileChooser.java
index 465b8a3..b381d62 100755
--- a/src/jalview/io/JalviewFileChooser.java
+++ b/src/jalview/io/JalviewFileChooser.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 //////////////////////////////////////////////////////////////////
 package jalview.io;
 
@@ -26,16 +25,17 @@ import java.util.*;
 import java.awt.*;
 import java.awt.event.*;
 import javax.swing.*;
+
 /**
  * Enhanced file chooser dialog box.
  * 
- * NOTE: bug on Windows systems when filechooser opened on directory to view files with colons in title.
+ * NOTE: bug on Windows systems when filechooser opened on directory to view
+ * files with colons in title.
  * 
  * @author AMW
- *
+ * 
  */
-public class JalviewFileChooser
-    extends JFileChooser
+public class JalviewFileChooser extends JFileChooser
 {
   public JalviewFileChooser(String dir)
   {
@@ -45,47 +45,41 @@ public class JalviewFileChooser
 
   private static File safePath(String dir)
   {
-    if (dir==null)
-    { return null;
+    if (dir == null)
+    {
+      return null;
     }
-     
+
     File f = new File(dir);
-    if (f.getName().indexOf(':')>-1)
+    if (f.getName().indexOf(':') > -1)
     {
       return null;
     }
     return f;
   }
 
-  public JalviewFileChooser(String dir,
-                            String[] suffix,
-                            String[] desc,
-                            String selected,
-                            boolean selectAll)
+  public JalviewFileChooser(String dir, String[] suffix, String[] desc,
+          String selected, boolean selectAll)
   {
     super(safePath(dir));
     init(suffix, desc, selected, selectAll);
   }
 
-  public JalviewFileChooser(String dir,
-                            String[] suffix,
-                            String[] desc,
-                            String selected)
+  public JalviewFileChooser(String dir, String[] suffix, String[] desc,
+          String selected)
   {
     super(safePath(dir));
     init(suffix, desc, selected, true);
   }
 
-  void init(String[] suffix,
-            String[] desc,
-            String selected,
-            boolean selectAll)
+  void init(String[] suffix, String[] desc, String selected,
+          boolean selectAll)
   {
 
     JalviewFileFilter chosen = null;
 
-    //SelectAllFilter needs to be set first before adding further
-    //file filters to fix bug on Mac OSX
+    // SelectAllFilter needs to be set first before adding further
+    // file filters to fix bug on Mac OSX
     setAcceptAllFileFilterUsed(selectAll);
 
     for (int i = 0; i < suffix.length; i++)
@@ -93,7 +87,7 @@ public class JalviewFileChooser
       JalviewFileFilter jvf = new JalviewFileFilter(suffix[i], desc[i]);
       addChoosableFileFilter(jvf);
 
-      if ( (selected != null) && selected.equalsIgnoreCase(desc[i]))
+      if ((selected != null) && selected.equalsIgnoreCase(desc[i]))
       {
         chosen = jvf;
       }
@@ -115,11 +109,10 @@ public class JalviewFileChooser
     {
       if (getUI() instanceof javax.swing.plaf.basic.BasicFileChooserUI)
       {
-        final javax.swing.plaf.basic.BasicFileChooserUI ui = (javax.swing.plaf.
-            basic.BasicFileChooserUI) getUI();
+        final javax.swing.plaf.basic.BasicFileChooserUI ui = (javax.swing.plaf.basic.BasicFileChooserUI) getUI();
         final String name = ui.getFileName().trim();
 
-        if ( (name == null) || (name.length() == 0))
+        if ((name == null) || (name.length() == 0))
         {
           return;
         }
@@ -129,15 +122,14 @@ public class JalviewFileChooser
           public void run()
           {
             String currentName = ui.getFileName();
-            if ( (currentName == null) || (currentName.length() == 0))
+            if ((currentName == null) || (currentName.length() == 0))
             {
               ui.setFileName(name);
             }
           }
         });
       }
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       ex.printStackTrace();
       // Some platforms do not have BasicFileChooserUI
@@ -185,8 +177,7 @@ public class JalviewFileChooser
     return format;
   }
 
-  public int showSaveDialog(Component parent)
-      throws HeadlessException
+  public int showSaveDialog(Component parent) throws HeadlessException
   {
     this.setAccessory(null);
 
@@ -200,19 +191,19 @@ public class JalviewFileChooser
 
       if (!jvf.accept(getSelectedFile()))
       {
-        String withExtension = getSelectedFile() + "." +
-            jvf.getAcceptableExtension();
+        String withExtension = getSelectedFile() + "."
+                + jvf.getAcceptableExtension();
         setSelectedFile(new File(withExtension));
       }
     }
-    // TODO: ENSURE THAT FILES SAVED WITH A ':' IN THE NAME ARE REFUSED AND THE USER PROMPTED FOR A NEW FILENAME
-    if ( (ret == JalviewFileChooser.APPROVE_OPTION) &&
-        getSelectedFile().exists())
+    // TODO: ENSURE THAT FILES SAVED WITH A ':' IN THE NAME ARE REFUSED AND THE
+    // USER PROMPTED FOR A NEW FILENAME
+    if ((ret == JalviewFileChooser.APPROVE_OPTION)
+            && getSelectedFile().exists())
     {
       int confirm = JOptionPane.showConfirmDialog(parent,
-                                                  "Overwrite existing file?",
-                                                  "File exists",
-                                                  JOptionPane.YES_NO_OPTION);
+              "Overwrite existing file?", "File exists",
+              JOptionPane.YES_NO_OPTION);
 
       if (confirm != JOptionPane.YES_OPTION)
       {
@@ -230,7 +221,7 @@ public class JalviewFileChooser
     File file = new File(selection);
     if (getFileFilter() instanceof JalviewFileFilter)
     {
-      JalviewFileFilter jvf = (JalviewFileFilter)this.getFileFilter();
+      JalviewFileFilter jvf = (JalviewFileFilter) this.getFileFilter();
 
       if (!jvf.accept(file))
       {
@@ -241,10 +232,10 @@ public class JalviewFileChooser
     setSelectedFile(file);
   }
 
-  class RecentlyOpened
-      extends JPanel
+  class RecentlyOpened extends JPanel
   {
     JList list;
+
     public RecentlyOpened()
     {
       String historyItems = jalview.bin.Cache.getProperty("RECENT_FILE");
@@ -275,7 +266,9 @@ public class JalviewFileChooser
         }
       });
 
-      this.setBorder(new javax.swing.border.TitledBorder("Recently Opened"));
+      this
+              .setBorder(new javax.swing.border.TitledBorder(
+                      "Recently Opened"));
 
       final JScrollPane scroller = new JScrollPane(list);
       scroller.setPreferredSize(new Dimension(130, 200));
@@ -286,7 +279,7 @@ public class JalviewFileChooser
         public void run()
         {
           scroller.getHorizontalScrollBar().setValue(
-              scroller.getHorizontalScrollBar().getMaximum());
+                  scroller.getHorizontalScrollBar().getMaximum());
         }
       });
 
diff --git a/src/jalview/io/JalviewFileFilter.java b/src/jalview/io/JalviewFileFilter.java
index fd8bcd3..7178aae 100755
--- a/src/jalview/io/JalviewFileFilter.java
+++ b/src/jalview/io/JalviewFileFilter.java
@@ -1,172 +1,173 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.io;
-
-import java.io.*;
-import java.util.*;
-
-import javax.swing.filechooser.FileFilter;
-
-public class JalviewFileFilter
-    extends FileFilter
-{
-  public static Hashtable suffixHash = new Hashtable();
-  private Hashtable filters = null;
-  private String description = "no description";
-  private String fullDescription = "full description";
-  private boolean useExtensionsInDescription = true;
-
-  public JalviewFileFilter(String extension, String description)
-  {
-    StringTokenizer st = new StringTokenizer(extension, ",");
-
-    while (st.hasMoreElements())
-    {
-      addExtension(st.nextToken().trim());
-    }
-
-    setDescription(description);
-  }
-
-  public JalviewFileFilter(String[] filts)
-  {
-    this(filts, null);
-  }
-
-  public JalviewFileFilter(String[] filts, String description)
-  {
-    for (int i = 0; i < filts.length; i++)
-    {
-      // add filters one by one
-      addExtension(filts[i]);
-    }
-
-    if (description != null)
-    {
-      setDescription(description);
-    }
-  }
-
-  public String getAcceptableExtension()
-  {
-    return filters.keys().nextElement().toString();
-  }
-
-  // takes account of the fact that database is a directory
-  public boolean accept(File f)
-  {
-    if (f != null)
-    {
-      String extension = getExtension(f);
-
-      if (f.isDirectory())
-      {
-        return true;
-      }
-
-      if ( (extension != null) && (filters.get(getExtension(f)) != null))
-      {
-        return true;
-      }
-    }
-
-    return false;
-  }
-
-  public String getExtension(File f)
-  {
-    if (f != null)
-    {
-      String filename = f.getName();
-      int i = filename.lastIndexOf('.');
-
-      if ( (i > 0) && (i < (filename.length() - 1)))
-      {
-        return filename.substring(i + 1).toLowerCase();
-      }
-
-      ;
-    }
-
-    return "";
-  }
-
-  public void addExtension(String extension)
-  {
-    if (filters == null)
-    {
-      filters = new Hashtable(5);
-    }
-
-    filters.put(extension.toLowerCase(), this);
-    fullDescription = null;
-  }
-
-  public String getDescription()
-  {
-    if (fullDescription == null)
-    {
-      if ( (description == null) || isExtensionListInDescription())
-      {
-        fullDescription = (description == null) ? "(" : (description +
-            " (");
-
-        // build the description from the extension list
-        Enumeration extensions = filters.keys();
-
-        if (extensions != null)
-        {
-          fullDescription += ("." +
-                              (String) extensions.nextElement());
-
-          while (extensions.hasMoreElements())
-          {
-            fullDescription += (", " +
-                                (String) extensions.nextElement());
-          }
-        }
-
-        fullDescription += ")";
-      }
-      else
-      {
-        fullDescription = description;
-      }
-    }
-
-    return fullDescription;
-  }
-
-  public void setDescription(String description)
-  {
-    this.description = description;
-    fullDescription = null;
-  }
-
-  public void setExtensionListInDescription(boolean b)
-  {
-    useExtensionsInDescription = b;
-    fullDescription = null;
-  }
-
-  public boolean isExtensionListInDescription()
-  {
-    return useExtensionsInDescription;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.io;
+
+import java.io.*;
+import java.util.*;
+
+import javax.swing.filechooser.FileFilter;
+
+public class JalviewFileFilter extends FileFilter
+{
+  public static Hashtable suffixHash = new Hashtable();
+
+  private Hashtable filters = null;
+
+  private String description = "no description";
+
+  private String fullDescription = "full description";
+
+  private boolean useExtensionsInDescription = true;
+
+  public JalviewFileFilter(String extension, String description)
+  {
+    StringTokenizer st = new StringTokenizer(extension, ",");
+
+    while (st.hasMoreElements())
+    {
+      addExtension(st.nextToken().trim());
+    }
+
+    setDescription(description);
+  }
+
+  public JalviewFileFilter(String[] filts)
+  {
+    this(filts, null);
+  }
+
+  public JalviewFileFilter(String[] filts, String description)
+  {
+    for (int i = 0; i < filts.length; i++)
+    {
+      // add filters one by one
+      addExtension(filts[i]);
+    }
+
+    if (description != null)
+    {
+      setDescription(description);
+    }
+  }
+
+  public String getAcceptableExtension()
+  {
+    return filters.keys().nextElement().toString();
+  }
+
+  // takes account of the fact that database is a directory
+  public boolean accept(File f)
+  {
+    if (f != null)
+    {
+      String extension = getExtension(f);
+
+      if (f.isDirectory())
+      {
+        return true;
+      }
+
+      if ((extension != null) && (filters.get(getExtension(f)) != null))
+      {
+        return true;
+      }
+    }
+
+    return false;
+  }
+
+  public String getExtension(File f)
+  {
+    if (f != null)
+    {
+      String filename = f.getName();
+      int i = filename.lastIndexOf('.');
+
+      if ((i > 0) && (i < (filename.length() - 1)))
+      {
+        return filename.substring(i + 1).toLowerCase();
+      }
+
+      ;
+    }
+
+    return "";
+  }
+
+  public void addExtension(String extension)
+  {
+    if (filters == null)
+    {
+      filters = new Hashtable(5);
+    }
+
+    filters.put(extension.toLowerCase(), this);
+    fullDescription = null;
+  }
+
+  public String getDescription()
+  {
+    if (fullDescription == null)
+    {
+      if ((description == null) || isExtensionListInDescription())
+      {
+        fullDescription = (description == null) ? "("
+                : (description + " (");
+
+        // build the description from the extension list
+        Enumeration extensions = filters.keys();
+
+        if (extensions != null)
+        {
+          fullDescription += ("." + (String) extensions.nextElement());
+
+          while (extensions.hasMoreElements())
+          {
+            fullDescription += (", " + (String) extensions.nextElement());
+          }
+        }
+
+        fullDescription += ")";
+      }
+      else
+      {
+        fullDescription = description;
+      }
+    }
+
+    return fullDescription;
+  }
+
+  public void setDescription(String description)
+  {
+    this.description = description;
+    fullDescription = null;
+  }
+
+  public void setExtensionListInDescription(boolean b)
+  {
+    useExtensionsInDescription = b;
+    fullDescription = null;
+  }
+
+  public boolean isExtensionListInDescription()
+  {
+    return useExtensionsInDescription;
+  }
+}
diff --git a/src/jalview/io/JalviewFileView.java b/src/jalview/io/JalviewFileView.java
index b32cbb6..d09b200 100755
--- a/src/jalview/io/JalviewFileView.java
+++ b/src/jalview/io/JalviewFileView.java
@@ -1,111 +1,111 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.io;
-
-import java.io.*;
-import java.util.*;
-
-import javax.swing.*;
-import javax.swing.filechooser.*;
-
-public class JalviewFileView
-    extends FileView
-{
-  static Hashtable alignSuffix = new Hashtable();
-
-  static
-  {
-    alignSuffix.put("fasta", "Fasta file");
-    alignSuffix.put("fa", "Fasta file");
-    alignSuffix.put("fastq", "Fasta file");
-    alignSuffix.put("blc", "BLC file");
-    alignSuffix.put("msf", "MSF file");
-    alignSuffix.put("pfam", "PFAM file");
-    alignSuffix.put("aln", "Clustal file");
-    alignSuffix.put("pir", "PIR file");
-    alignSuffix.put("jar", "Jalview file");
-  }
-
-  public String getTypeDescription(File f)
-  {
-    String extension = getExtension(f);
-    String type = null;
-
-    if (extension != null)
-    {
-      if (alignSuffix.containsKey(extension))
-      {
-        type = alignSuffix.get(extension).toString();
-      }
-    }
-
-    return type;
-  }
-
-  public Icon getIcon(File f)
-  {
-    String extension = getExtension(f);
-    Icon icon = null;
-
-    if (extension != null)
-    {
-      if (alignSuffix.containsKey(extension))
-      {
-        icon = createImageIcon("/images/file.png");
-      }
-    }
-
-    return icon;
-  }
-
-  /*
-   * Get the extension of a file.
-   */
-  public static String getExtension(File f)
-  {
-    String ext = null;
-    String s = f.getName();
-    int i = s.lastIndexOf('.');
-
-    if ( (i > 0) && (i < (s.length() - 1)))
-    {
-      ext = s.substring(i + 1).toLowerCase();
-    }
-
-    return ext;
-  }
-
-  /** Returns an ImageIcon, or null if the path was invalid. */
-  protected static ImageIcon createImageIcon(String path)
-  {
-    java.net.URL imgURL = JalviewFileView.class.getResource(path);
-
-    if (imgURL != null)
-    {
-      return new ImageIcon(imgURL);
-    }
-    else
-    {
-      System.err.println(
-          "JalviewFileView.createImageIcon: Couldn't find file: " + path);
-
-      return null;
-    }
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.io;
+
+import java.io.*;
+import java.util.*;
+
+import javax.swing.*;
+import javax.swing.filechooser.*;
+
+public class JalviewFileView extends FileView
+{
+  static Hashtable alignSuffix = new Hashtable();
+
+  static
+  {
+    alignSuffix.put("fasta", "Fasta file");
+    alignSuffix.put("fa", "Fasta file");
+    alignSuffix.put("fastq", "Fasta file");
+    alignSuffix.put("blc", "BLC file");
+    alignSuffix.put("msf", "MSF file");
+    alignSuffix.put("pfam", "PFAM file");
+    alignSuffix.put("aln", "Clustal file");
+    alignSuffix.put("pir", "PIR file");
+    alignSuffix.put("jar", "Jalview file");
+  }
+
+  public String getTypeDescription(File f)
+  {
+    String extension = getExtension(f);
+    String type = null;
+
+    if (extension != null)
+    {
+      if (alignSuffix.containsKey(extension))
+      {
+        type = alignSuffix.get(extension).toString();
+      }
+    }
+
+    return type;
+  }
+
+  public Icon getIcon(File f)
+  {
+    String extension = getExtension(f);
+    Icon icon = null;
+
+    if (extension != null)
+    {
+      if (alignSuffix.containsKey(extension))
+      {
+        icon = createImageIcon("/images/file.png");
+      }
+    }
+
+    return icon;
+  }
+
+  /*
+   * Get the extension of a file.
+   */
+  public static String getExtension(File f)
+  {
+    String ext = null;
+    String s = f.getName();
+    int i = s.lastIndexOf('.');
+
+    if ((i > 0) && (i < (s.length() - 1)))
+    {
+      ext = s.substring(i + 1).toLowerCase();
+    }
+
+    return ext;
+  }
+
+  /** Returns an ImageIcon, or null if the path was invalid. */
+  protected static ImageIcon createImageIcon(String path)
+  {
+    java.net.URL imgURL = JalviewFileView.class.getResource(path);
+
+    if (imgURL != null)
+    {
+      return new ImageIcon(imgURL);
+    }
+    else
+    {
+      System.err
+              .println("JalviewFileView.createImageIcon: Couldn't find file: "
+                      + path);
+
+      return null;
+    }
+  }
+}
diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java
index bb34548..993737b 100755
--- a/src/jalview/io/JnetAnnotationMaker.java
+++ b/src/jalview/io/JnetAnnotationMaker.java
@@ -1,21 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/
+ */
 package jalview.io;
 
 import jalview.datamodel.*;
@@ -23,23 +23,30 @@ import jalview.datamodel.*;
 public class JnetAnnotationMaker
 {
   public static void add_annotation(JPredFile prediction, AlignmentI al,
-                                    int firstSeq, boolean noMsa)
-      throws Exception
+          int firstSeq, boolean noMsa) throws Exception
   {
-    JnetAnnotationMaker.add_annotation(prediction, al, firstSeq, noMsa, (int[])null);
+    JnetAnnotationMaker.add_annotation(prediction, al, firstSeq, noMsa,
+            (int[]) null);
   }
 
   /**
    * adds the annotation parsed by prediction to al.
-   * @param prediction JPredFile
-   * @param al AlignmentI
-   * @param firstSeq int the index of the sequence to attach the annotation to (usually zero)
-   * @param noMsa boolean
-   * @param delMap mapping from columns in JPredFile prediction to residue number in al.getSequence(firstSeq)
+   * 
+   * @param prediction
+   *                JPredFile
+   * @param al
+   *                AlignmentI
+   * @param firstSeq
+   *                int the index of the sequence to attach the annotation to
+   *                (usually zero)
+   * @param noMsa
+   *                boolean
+   * @param delMap
+   *                mapping from columns in JPredFile prediction to residue
+   *                number in al.getSequence(firstSeq)
    */
   public static void add_annotation(JPredFile prediction, AlignmentI al,
-                                    int firstSeq, boolean noMsa, int[] delMap)
-      throws Exception
+          int firstSeq, boolean noMsa, int[] delMap) throws Exception
   {
     int i = 0;
     SequenceI[] preds = prediction.getSeqsAsArray();
@@ -48,16 +55,16 @@ public class JnetAnnotationMaker
     SequenceI seqRef = al.getSequenceAt(firstSeq);
     int width = preds[0].getSequence().length;
     int[] gapmap = al.getSequenceAt(firstSeq).gapMap();
-    if ( (delMap != null && delMap.length > width) ||
-        (delMap == null && gapmap.length != width))
+    if ((delMap != null && delMap.length > width)
+            || (delMap == null && gapmap.length != width))
     {
-      throw (new Exception(
-          "Number of residues in " + (delMap == null ? "" : " mapped ") +
-          "supposed query sequence ('" +
-          al.getSequenceAt(firstSeq).getName() + "'\n" +
-          al.getSequenceAt(firstSeq).getSequenceAsString() +
-          ")\ndiffer from number of prediction sites in prediction (" + width +
-          ")"));
+      throw (new Exception("Number of residues in "
+              + (delMap == null ? "" : " mapped ")
+              + "supposed query sequence ('"
+              + al.getSequenceAt(firstSeq).getName() + "'\n"
+              + al.getSequenceAt(firstSeq).getSequenceAsString()
+              + ")\ndiffer from number of prediction sites in prediction ("
+              + width + ")"));
     }
 
     AlignmentAnnotation annot;
@@ -73,25 +80,24 @@ public class JnetAnnotationMaker
     {
       String id = preds[i].getName().toUpperCase();
 
-      if (id.startsWith("LUPAS") || id.startsWith("JNET") ||
-          id.startsWith("JPRED"))
+      if (id.startsWith("LUPAS") || id.startsWith("JNET")
+              || id.startsWith("JPRED"))
       {
         annotations = new Annotation[al.getWidth()];
-        /*        if (delMap!=null) {
-          for (int j=0; j<annotations.length; j++)
-            annotations[j] = new Annotation("","",'',0);
-                 }
+        /*
+         * if (delMap!=null) { for (int j=0; j<annotations.length; j++)
+         * annotations[j] = new Annotation("","",'',0); }
          */
-        if (id.equals("JNETPRED") || id.equals("JNETPSSM") ||
-            id.equals("JNETFREQ") || id.equals("JNETHMM") ||
-            id.equals("JNETALIGN") || id.equals("JPRED"))
+        if (id.equals("JNETPRED") || id.equals("JNETPSSM")
+                || id.equals("JNETFREQ") || id.equals("JNETHMM")
+                || id.equals("JNETALIGN") || id.equals("JPRED"))
         {
           if (delMap == null)
           {
             for (int j = 0; j < width; j++)
             {
-              annotations[gapmap[j]] = new Annotation("", "",
-                  preds[i].getCharAt(j), 0);
+              annotations[gapmap[j]] = new Annotation("", "", preds[i]
+                      .getCharAt(j), 0);
             }
           }
           else
@@ -99,7 +105,7 @@ public class JnetAnnotationMaker
             for (int j = 0; j < width; j++)
             {
               annotations[gapmap[delMap[j]]] = new Annotation("", "",
-                  preds[i].getCharAt(j), 0);
+                      preds[i].getCharAt(j), 0);
             }
           }
         }
@@ -109,23 +115,21 @@ public class JnetAnnotationMaker
           {
             for (int j = 0; j < width; j++)
             {
-              float value = new Float(preds[i].getCharAt(
-                  j) + "").floatValue();
-              annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(
-                  j) + "", "", preds[i].getCharAt(j),
-                  value);
+              float value = new Float(preds[i].getCharAt(j) + "")
+                      .floatValue();
+              annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(j)
+                      + "", "", preds[i].getCharAt(j), value);
             }
           }
           else
           {
             for (int j = 0; j < width; j++)
             {
-              float value = new Float(preds[i].getCharAt(
-                  j) + "").floatValue();
-              annotations[gapmap[delMap[j]]] = new Annotation(preds[i].
-                  getCharAt(
-                      j) + "", "", preds[i].getCharAt(j),
-                  value);
+              float value = new Float(preds[i].getCharAt(j) + "")
+                      .floatValue();
+              annotations[gapmap[delMap[j]]] = new Annotation(preds[i]
+                      .getCharAt(j)
+                      + "", "", preds[i].getCharAt(j), value);
             }
           }
         }
@@ -135,17 +139,17 @@ public class JnetAnnotationMaker
           {
             for (int j = 0; j < width; j++)
             {
-              annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(
-                  j) + "", "", ' ', 0);
+              annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(j)
+                      + "", "", ' ', 0);
             }
           }
           else
           {
             for (int j = 0; j < width; j++)
             {
-              annotations[gapmap[delMap[j]]] = new Annotation(preds[i].
-                  getCharAt(
-                      j) + "", "", ' ', 0);
+              annotations[gapmap[delMap[j]]] = new Annotation(preds[i]
+                      .getCharAt(j)
+                      + "", "", ' ', 0);
             }
           }
         }
@@ -153,14 +157,13 @@ public class JnetAnnotationMaker
         if (id.equals("JNETCONF"))
         {
           annot = new AlignmentAnnotation(preds[i].getName(),
-                                          "JNet Output", annotations, 0f,
-                                          10f,
-                                          AlignmentAnnotation.BAR_GRAPH);
+                  "JNet Output", annotations, 0f, 10f,
+                  AlignmentAnnotation.BAR_GRAPH);
         }
         else
         {
           annot = new AlignmentAnnotation(preds[i].getName(),
-                                          "JNet Output", annotations);
+                  "JNet Output", annotations);
         }
 
         if (seqRef != null)
@@ -170,9 +173,8 @@ public class JnetAnnotationMaker
         }
 
         al.addAnnotation(annot);
-        al.setAnnotationIndex(annot,
-                              al.getAlignmentAnnotation().
-                              length - existingAnnotations - 1);
+        al.setAnnotationIndex(annot, al.getAlignmentAnnotation().length
+                - existingAnnotations - 1);
 
         if (noMsa)
         {
@@ -183,16 +185,17 @@ public class JnetAnnotationMaker
       i++;
     }
 
-    //Hashtable scores = prediction.getScores();
-
-    /*  addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPH"),
-                          "JnetpropH", "Jnet Helix Propensity", 0f,1f,1);
-
-      addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPB"),
-     "JnetpropB", "Jnet Beta Sheet Propensity", 0f,1f,1);
-
-      addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPC"),
-                          "JnetpropC", "Jnet Coil Propensity", 0f,1f,1);
+    // Hashtable scores = prediction.getScores();
+
+    /*
+     * addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPH"),
+     * "JnetpropH", "Jnet Helix Propensity", 0f,1f,1);
+     * 
+     * addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPB"),
+     * "JnetpropB", "Jnet Beta Sheet Propensity", 0f,1f,1);
+     * 
+     * addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPC"),
+     * "JnetpropC", "Jnet Coil Propensity", 0f,1f,1);
      */
 
   }
diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index e2d3704..73d0f0f 100755
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -26,12 +26,11 @@ import jalview.util.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class MSFfile
-    extends AlignFile
+public class MSFfile extends AlignFile
 {
 
   /**
@@ -43,14 +42,16 @@ public class MSFfile
 
   /**
    * Creates a new MSFfile object.
-   *
-   * @param inFile DOCUMENT ME!
-   * @param type DOCUMENT ME!
-   *
-   * @throws IOException DOCUMENT ME!
+   * 
+   * @param inFile
+   *                DOCUMENT ME!
+   * @param type
+   *                DOCUMENT ME!
+   * 
+   * @throws IOException
+   *                 DOCUMENT ME!
    */
-  public MSFfile(String inFile, String type)
-      throws IOException
+  public MSFfile(String inFile, String type) throws IOException
   {
     super(inFile, type);
   }
@@ -59,15 +60,15 @@ public class MSFfile
   {
     super(source);
   }
-{
+
+  {
     // TODO Auto-generated constructor stub
   }
 
   /**
    * DOCUMENT ME!
    */
-  public void parse()
-      throws IOException
+  public void parse() throws IOException
   {
     int i = 0;
     boolean seqFlag = false;
@@ -78,7 +79,7 @@ public class MSFfile
 
     try
     {
-      while ( (line = nextLine()) != null)
+      while ((line = nextLine()) != null)
       {
         StringTokenizer str = new StringTokenizer(line);
 
@@ -86,28 +87,28 @@ public class MSFfile
         {
           String inStr = str.nextToken();
 
-          //If line has header information add to the headers vector
+          // If line has header information add to the headers vector
           if (inStr.indexOf("Name:") != -1)
           {
             key = str.nextToken();
             headers.addElement(key);
           }
 
-          //if line has // set SeqFlag to 1 so we know sequences are coming
+          // if line has // set SeqFlag to 1 so we know sequences are coming
           if (inStr.indexOf("//") != -1)
           {
             seqFlag = true;
           }
 
-          //Process lines as sequence lines if seqFlag is set
-          if ( (inStr.indexOf("//") == -1) && (seqFlag == true))
+          // Process lines as sequence lines if seqFlag is set
+          if ((inStr.indexOf("//") == -1) && (seqFlag == true))
           {
-            //seqeunce id is the first field
+            // seqeunce id is the first field
             key = inStr;
 
             StringBuffer tempseq;
 
-            //Get sequence from hash if it exists
+            // Get sequence from hash if it exists
             if (seqhash.containsKey(key))
             {
               tempseq = (StringBuffer) seqhash.get(key);
@@ -118,17 +119,16 @@ public class MSFfile
               seqhash.put(key, tempseq);
             }
 
-            //loop through the rest of the words
+            // loop through the rest of the words
             while (str.hasMoreTokens())
             {
-              //append the word to the sequence
+              // append the word to the sequence
               tempseq.append(str.nextToken());
             }
           }
         }
       }
-    }
-    catch (IOException e)
+    } catch (IOException e)
     {
       System.err.println("Exception parsing MSFFile " + e);
       e.printStackTrace();
@@ -136,7 +136,7 @@ public class MSFfile
 
     this.noSeqs = headers.size();
 
-    //Add sequences to the hash
+    // Add sequences to the hash
     for (i = 0; i < headers.size(); i++)
     {
       if (seqhash.get(headers.elementAt(i)) != null)
@@ -160,17 +160,18 @@ public class MSFfile
       }
       else
       {
-        System.err.println("MSFFile Parser: Can't find sequence for " +
-                           headers.elementAt(i));
+        System.err.println("MSFFile Parser: Can't find sequence for "
+                + headers.elementAt(i));
       }
     }
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param seq DOCUMENT ME!
-   *
+   * 
+   * @param seq
+   *                DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   public int checkSum(String seq)
@@ -188,8 +189,7 @@ public class MSFfile
         {
           check += (i % 57 + 1) * value;
         }
-      }
-      catch (Exception e)
+      } catch (Exception e)
       {
         System.err.println("Exception during MSF Checksum calculation");
         e.printStackTrace();
@@ -201,10 +201,12 @@ public class MSFfile
 
   /**
    * DOCUMENT ME!
-   *
-   * @param s DOCUMENT ME!
-   * @param is_NA DOCUMENT ME!
-   *
+   * 
+   * @param s
+   *                DOCUMENT ME!
+   * @param is_NA
+   *                DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   public String print(SequenceI[] seqs)
@@ -214,18 +216,19 @@ public class MSFfile
 
     SequenceI[] s = new SequenceI[seqs.length];
 
-    StringBuffer out = new StringBuffer("!!" + (is_NA ? "NA" : "AA") +
-                                        "_MULTIPLE_ALIGNMENT 1.0\n\n"); // TODO: JBPNote : Jalview doesn't remember NA or AA yet.
+    StringBuffer out = new StringBuffer("!!" + (is_NA ? "NA" : "AA")
+            + "_MULTIPLE_ALIGNMENT 1.0\n\n"); // TODO: JBPNote : Jalview doesn't
+                                              // remember NA or AA yet.
 
     int max = 0;
     int maxid = 0;
     int i = 0;
 
-    while ( (i < seqs.length) && (seqs[i] != null))
+    while ((i < seqs.length) && (seqs[i] != null))
     {
       // Replace all internal gaps with . and external spaces with ~
-      s[i] = new Sequence(seqs[i].getName(),
-                          seqs[i].getSequenceAsString().replace('-', '.'));
+      s[i] = new Sequence(seqs[i].getName(), seqs[i].getSequenceAsString()
+              .replace('-', '.'));
 
       StringBuffer sb = new StringBuffer();
       sb.append(s[i].getSequence());
@@ -264,10 +267,10 @@ public class MSFfile
       i++;
     }
 
-    Format maxLenpad = new Format("%" + (new String("" + max)).length() +
-                                  "d");
-    Format maxChkpad = new Format("%" + (new String("1" + max)).length() +
-                                  "d");
+    Format maxLenpad = new Format("%" + (new String("" + max)).length()
+            + "d");
+    Format maxChkpad = new Format("%" + (new String("1" + max)).length()
+            + "d");
     i = 0;
 
     int bigChecksum = 0;
@@ -280,23 +283,22 @@ public class MSFfile
     }
 
     long maxNB = 0;
-    out.append("   MSF: " + s[0].getSequence().length + "   Type: " +
-               (is_NA ? "N" : "P") + "    Check:  " + (bigChecksum % 10000) +
-               "   ..\n\n\n");
+    out.append("   MSF: " + s[0].getSequence().length + "   Type: "
+            + (is_NA ? "N" : "P") + "    Check:  " + (bigChecksum % 10000)
+            + "   ..\n\n\n");
 
     String[] nameBlock = new String[s.length];
     String[] idBlock = new String[s.length];
 
     i = 0;
-    while ( (i < s.length) && (s[i] != null))
+    while ((i < s.length) && (s[i] != null))
     {
 
       nameBlock[i] = new String("  Name: " + printId(s[i]) + " ");
 
-      idBlock[i] = new String("Len: " +
-                              maxLenpad.form(s[i].getSequence().length) +
-                              "  Check: " +
-                              maxChkpad.form(checksums[i]) + "  Weight: 1.00\n");
+      idBlock[i] = new String("Len: "
+              + maxLenpad.form(s[i].getSequence().length) + "  Check: "
+              + maxChkpad.form(checksums[i]) + "  Weight: 1.00\n");
 
       if (s[i].getName().length() > maxid)
       {
@@ -335,7 +337,7 @@ public class MSFfile
 
     int nochunks = (max / len) + 1;
 
-    if ( (max % len) == 0)
+    if ((max % len) == 0)
     {
       nochunks--;
     }
@@ -344,7 +346,7 @@ public class MSFfile
     {
       int j = 0;
 
-      while ( (j < s.length) && (s[j] != null))
+      while ((j < s.length) && (s[j] != null))
       {
         String name = printId(s[j]);
 
@@ -355,8 +357,8 @@ public class MSFfile
           int start = (i * 50) + (k * 10);
           int end = start + 10;
 
-          if ( (end < s[j].getSequence().length) &&
-              (start < s[j].getSequence().length))
+          if ((end < s[j].getSequence().length)
+                  && (start < s[j].getSequence().length))
           {
             out.append(s[j].getSequence(start, end));
 
@@ -397,7 +399,7 @@ public class MSFfile
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public String print()
diff --git a/src/jalview/io/MatrixFile.java b/src/jalview/io/MatrixFile.java
index 5b9e79f..011eda3 100644
--- a/src/jalview/io/MatrixFile.java
+++ b/src/jalview/io/MatrixFile.java
@@ -1,22 +1,35 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.io;
 
 import java.io.IOException;
 
 /**
- * IO for asymmetric matrix with arbitrary dimension
- * with labels, as displayed by PCA viewer.
- * Form is: tab separated entity defs
- * header line
- * TITLE\ttitle
- * DESC\tdesc
- * PROPERTY\t<id or empty for whole matrix>\tname\ttype\tvalue
+ * IO for asymmetric matrix with arbitrary dimension with labels, as displayed
+ * by PCA viewer. Form is: tab separated entity defs header line TITLE\ttitle
+ * DESC\tdesc PROPERTY\t<id or empty for whole matrix>\tname\ttype\tvalue
  * ROW\tRow i label (ID)/tPrinciple text/tprinciple description/t...
- * COLUMN\t(similar, optional)..
- * ..
- * <float>\t<float>...(column-wise data for row i)
+ * COLUMN\t(similar, optional).. .. <float>\t<float>...(column-wise data for
+ * row i)
  */
- 
+
 public class MatrixFile extends FileParse
-{ 
-  
+{
+
 }
diff --git a/src/jalview/io/ModellerDescription.java b/src/jalview/io/ModellerDescription.java
index fa6ef6d..e4483a5 100755
--- a/src/jalview/io/ModellerDescription.java
+++ b/src/jalview/io/ModellerDescription.java
@@ -1,391 +1,408 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.io;
-
-import jalview.datamodel.*;
-
-public class ModellerDescription
-{
-  /**
-   * Translates between a String containing a set of colon-separated values
-   * on a single line, and sequence start/end and other properties.
-   * See PIRFile IO for its use.
-   */
-  final String[] seqTypes =
-      {
-      "sequence", "structure", "structureX", "structureN"};
-  final String[] Fields =
-      {
-      "objectType", "objectId",
-      "startField", "startCode",
-      "endField", "endCode",
-      "description1", "description2",
-      "resolutionField", "tailField"};
-  final int TYPE = 0;
-  final int LOCALID = 1;
-  final int START = 2;
-  final int START_CHAIN = 3;
-  final int END = 4;
-  final int END_CHAIN = 5;
-  final int DESCRIPTION1 = 6;
-  final int DESCRIPTION2 = 7;
-  final int RESOLUTION = 8;
-  final int TAIL = 9;
-
-  /**
-   * 0 is free text or empty
-   * 1 is something that parses to an integer, or \@
-   */
-  final int Types[] =
-      {
-      0, 0, 1, 0, 1, 0, 0, 0, 0, 0
-  };
-  final char Padding[] =
-      {
-      ' ', ' ', ' ', '.', ' ', '.', '.', '.', '.', '.'
-  };
-
-  java.util.Hashtable fields = new java.util.Hashtable();
-  ModellerDescription()
-  {
-    fields.put(Fields[TAIL], "");
-  }
-
-  class resCode
-  {
-    Integer val;
-    String field;
-    resCode(String f, Integer v)
-    {
-      val = v;
-      field = f;
-    }
-
-    resCode(int v)
-    {
-      val = new Integer(v);
-      field = val.toString();
-    }
-  };
-
-  private resCode validResidueCode(String field)
-  {
-    Integer val = null;
-    com.stevesoft.pat.Regex r = new com.stevesoft.pat.Regex(
-        "\\s*((([-0-9]+).?)|FIRST|LAST|@)");
-
-    if (!r.search(field))
-    {
-      return null; // invalid
-    }
-    String value = r.stringMatched(3);
-    if (value == null)
-    {
-      value = r.stringMatched(1);
-    }
-    // jalview.bin.Cache.log.debug("from '" + field + "' matched '" + value +
-    //                             "'");
-    try
-    {
-      val = Integer.valueOf(value);
-      return new resCode(field, val); // successful numeric extraction
-    }
-    catch (Exception e)
-    {
-    }
-    return new resCode(field, null);
-  }
-
-  private java.util.Hashtable parseDescription(String desc)
-  {
-    java.util.Hashtable fields = new java.util.Hashtable();
-    java.util.StringTokenizer st = new java.util.StringTokenizer(desc, ":");
-    String field;
-    int type = -1;
-    if (st.countTokens() > 0)
-    {
-      // parse colon-fields
-      int i = 0;
-      field = st.nextToken(":");
-      do
-      {
-        if (seqTypes[i].equalsIgnoreCase(field))
-        {
-          break;
-        }
-      }
-      while (++i < seqTypes.length);
-
-      if (i < seqTypes.length)
-      {
-        // valid seqType for modeller
-        type = i;
-        i = 1; // continue parsing fields
-        while (i < TAIL && st.hasMoreTokens())
-        {
-          if ( (field = st.nextToken(":")) != null)
-          {
-            // validate residue field value
-            if (Types[i] == 1)
-            {
-              resCode val = validResidueCode(field);
-              if (val != null)
-              {
-                fields.put(new String(Fields[i] + "num"), val);
-              }
-              else
-              {
-                //      jalview.bin.Cache.log.debug(
-                //           "Ignoring non-Modeller description: invalid integer-like field '" + field + "'");
-                type = -1; /* invalid field! - throw the FieldSet away */
-              }
-              ;
-            }
-            fields.put(Fields[i++], field);
-          }
-        }
-        if (i == TAIL)
-        {
-          // slurp remaining fields
-          while (st.hasMoreTokens())
-          {
-            field += ":" + st.nextToken(":");
-          }
-          fields.put(Fields[TAIL], field);
-        }
-      }
-    }
-    if (type == -1)
-    {
-      // object is not a proper ModellerPIR object
-      fields = new java.util.Hashtable();
-      fields.put(Fields[TAIL], new String(desc));
-    }
-    else
-    {
-      fields.put(Fields[TYPE], seqTypes[type]);
-    }
-    return fields;
-  }
-
-  ModellerDescription(String desc)
-  {
-    if (desc == null)
-    {
-      desc = "";
-    }
-    fields = parseDescription(desc);
-  }
-
-  void setStartCode(int v)
-  {
-    resCode r;
-    fields.put(Fields[START] + "num", r = new resCode(v));
-    fields.put(Fields[START], r.field);
-  }
-
-  void setEndCode(int v)
-  {
-    resCode r;
-    fields.put(Fields[END] + "num", r = new resCode(v));
-    fields.put(Fields[END], r.field);
-  }
-
-  /**
-   * make a possibly updated modeller field line for the sequence object
-   * @param seq SequenceI
-   */
-  ModellerDescription(SequenceI seq)
-  {
-
-    if (seq.getDescription() != null)
-    {
-      fields = parseDescription(seq.getDescription());
-    }
-
-    if (isModellerFieldset())
-    {
-      // Set start and end before we update the type (in the case of a synthesized field set)
-      if (getStartNum() != seq.getStart() && getStartCode().val != null)
-      {
-        setStartCode(seq.getStart());
-      }
-
-      if (getEndNum() != seq.getEnd() && getStartCode().val != null)
-      {
-        setEndCode(seq.getEnd());
-      }
-    }
-    else
-    {
-      // synthesize fields
-      setStartCode(seq.getStart());
-      setEndCode(seq.getEnd());
-      fields.put(Fields[LOCALID], seq.getName()); // this may be overwritten below...
-      // type - decide based on evidence of PDB database references - this also sets the local reference field
-      int t = 0; // sequence
-      if (seq.getDatasetSequence() != null &&
-          seq.getDatasetSequence().getDBRef() != null)
-      {
-        jalview.datamodel.DBRefEntry[] dbr = seq.getDatasetSequence().getDBRef();
-        int i, j;
-        for (i = 0, j = dbr.length; i < j; i++)
-        {
-          if (dbr[i] != null)
-          {
-            // JBPNote PDB dbRefEntry needs properties to propagate onto ModellerField
-            // JBPNote Need to get info from the user about whether the sequence is the one being modelled, or if it is a template.
-            if (dbr[i].getSource().equals(jalview.datamodel.DBRefSource.PDB))
-            {
-              fields.put(Fields[LOCALID], dbr[i].getAccessionId());
-              t = 2;
-              break;
-            }
-          }
-        }
-      }
-      fields.put(Fields[TYPE], seqTypes[t]);
-    }
-
-  }
-
-  /**
-   * Indicate if fields parsed to a modeller-like colon-separated value line
-   * @return boolean
-   */
-  boolean isModellerFieldset()
-  {
-    return (fields.containsKey(Fields[TYPE]));
-  }
-
-  String getDescriptionLine()
-  {
-    String desc = "";
-    int lastfield = Fields.length - 1;
-
-    if (isModellerFieldset())
-    {
-      String value;
-      // try to write a minimal modeller field set, so..
-
-      // find the last valid field in the entry
-
-      for (; lastfield > 6; lastfield--)
-      {
-        if (fields.containsKey(Fields[lastfield]))
-        {
-          break;
-        }
-      }
-
-      for (int i = 0; i < lastfield; i++)
-      {
-        value = (String) fields.get(Fields[i]);
-        if (value != null && value.length() > 0)
-        {
-          desc += ( (String) fields.get(Fields[i])) + ":";
-        }
-        else
-        {
-          desc += Padding[i] + ":";
-        }
-      }
-    }
-    // just return the last field if no others were defined.
-    if (fields.containsKey(Fields[lastfield]))
-    {
-      desc += (String) fields.get(Fields[lastfield]);
-    }
-    else
-    {
-      desc += ".";
-    }
-    return desc;
-  }
-
-  int getStartNum()
-  {
-    int start = 0;
-    resCode val = getStartCode();
-    if (val.val != null)
-    {
-      return val.val.intValue();
-    }
-    return start;
-  }
-
-  resCode getStartCode()
-  {
-    if (isModellerFieldset() && fields.containsKey(Fields[START] + "num"))
-    {
-      return (resCode) fields.get(Fields[START] + "num");
-    }
-    return null;
-  }
-
-  resCode getEndCode()
-  {
-    if (isModellerFieldset() && fields.containsKey(Fields[END] + "num"))
-    {
-      return (resCode) fields.get(Fields[END] + "num");
-    }
-    return null;
-  }
-
-  int getEndNum()
-  {
-    int end = 0;
-    resCode val = getEndCode();
-    if (val.val != null)
-    {
-      return val.val.intValue();
-    }
-    return end;
-  }
-
-  /**
-   * returns true if sequence object was modifed with a valid modellerField set
-   * @param newSeq SequenceI
-   * @return boolean
-   */
-  boolean updateSequenceI(SequenceI newSeq)
-  {
-    if (isModellerFieldset())
-    {
-      if (getStartCode().val != null)
-      {
-        newSeq.setStart(getStartNum());
-      }
-      else
-      {
-        newSeq.setStart(1);
-      }
-      if (getEndCode().val != null)
-      {
-        newSeq.setEnd(getEndNum());
-      }
-      else
-      {
-        newSeq.setEnd(newSeq.getStart() + newSeq.getLength());
-      }
-      return true;
-    }
-    return false;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.io;
+
+import jalview.datamodel.*;
+
+public class ModellerDescription
+{
+  /**
+   * Translates between a String containing a set of colon-separated values on a
+   * single line, and sequence start/end and other properties. See PIRFile IO
+   * for its use.
+   */
+  final String[] seqTypes =
+  { "sequence", "structure", "structureX", "structureN" };
+
+  final String[] Fields =
+  { "objectType", "objectId", "startField", "startCode", "endField",
+      "endCode", "description1", "description2", "resolutionField",
+      "tailField" };
+
+  final int TYPE = 0;
+
+  final int LOCALID = 1;
+
+  final int START = 2;
+
+  final int START_CHAIN = 3;
+
+  final int END = 4;
+
+  final int END_CHAIN = 5;
+
+  final int DESCRIPTION1 = 6;
+
+  final int DESCRIPTION2 = 7;
+
+  final int RESOLUTION = 8;
+
+  final int TAIL = 9;
+
+  /**
+   * 0 is free text or empty 1 is something that parses to an integer, or \@
+   */
+  final int Types[] =
+  { 0, 0, 1, 0, 1, 0, 0, 0, 0, 0 };
+
+  final char Padding[] =
+  { ' ', ' ', ' ', '.', ' ', '.', '.', '.', '.', '.' };
+
+  java.util.Hashtable fields = new java.util.Hashtable();
+
+  ModellerDescription()
+  {
+    fields.put(Fields[TAIL], "");
+  }
+
+  class resCode
+  {
+    Integer val;
+
+    String field;
+
+    resCode(String f, Integer v)
+    {
+      val = v;
+      field = f;
+    }
+
+    resCode(int v)
+    {
+      val = new Integer(v);
+      field = val.toString();
+    }
+  };
+
+  private resCode validResidueCode(String field)
+  {
+    Integer val = null;
+    com.stevesoft.pat.Regex r = new com.stevesoft.pat.Regex(
+            "\\s*((([-0-9]+).?)|FIRST|LAST|@)");
+
+    if (!r.search(field))
+    {
+      return null; // invalid
+    }
+    String value = r.stringMatched(3);
+    if (value == null)
+    {
+      value = r.stringMatched(1);
+    }
+    // jalview.bin.Cache.log.debug("from '" + field + "' matched '" + value +
+    // "'");
+    try
+    {
+      val = Integer.valueOf(value);
+      return new resCode(field, val); // successful numeric extraction
+    } catch (Exception e)
+    {
+    }
+    return new resCode(field, null);
+  }
+
+  private java.util.Hashtable parseDescription(String desc)
+  {
+    java.util.Hashtable fields = new java.util.Hashtable();
+    java.util.StringTokenizer st = new java.util.StringTokenizer(desc, ":");
+    String field;
+    int type = -1;
+    if (st.countTokens() > 0)
+    {
+      // parse colon-fields
+      int i = 0;
+      field = st.nextToken(":");
+      do
+      {
+        if (seqTypes[i].equalsIgnoreCase(field))
+        {
+          break;
+        }
+      } while (++i < seqTypes.length);
+
+      if (i < seqTypes.length)
+      {
+        // valid seqType for modeller
+        type = i;
+        i = 1; // continue parsing fields
+        while (i < TAIL && st.hasMoreTokens())
+        {
+          if ((field = st.nextToken(":")) != null)
+          {
+            // validate residue field value
+            if (Types[i] == 1)
+            {
+              resCode val = validResidueCode(field);
+              if (val != null)
+              {
+                fields.put(new String(Fields[i] + "num"), val);
+              }
+              else
+              {
+                // jalview.bin.Cache.log.debug(
+                // "Ignoring non-Modeller description: invalid integer-like
+                // field '" + field + "'");
+                type = -1; /* invalid field! - throw the FieldSet away */
+              }
+              ;
+            }
+            fields.put(Fields[i++], field);
+          }
+        }
+        if (i == TAIL)
+        {
+          // slurp remaining fields
+          while (st.hasMoreTokens())
+          {
+            field += ":" + st.nextToken(":");
+          }
+          fields.put(Fields[TAIL], field);
+        }
+      }
+    }
+    if (type == -1)
+    {
+      // object is not a proper ModellerPIR object
+      fields = new java.util.Hashtable();
+      fields.put(Fields[TAIL], new String(desc));
+    }
+    else
+    {
+      fields.put(Fields[TYPE], seqTypes[type]);
+    }
+    return fields;
+  }
+
+  ModellerDescription(String desc)
+  {
+    if (desc == null)
+    {
+      desc = "";
+    }
+    fields = parseDescription(desc);
+  }
+
+  void setStartCode(int v)
+  {
+    resCode r;
+    fields.put(Fields[START] + "num", r = new resCode(v));
+    fields.put(Fields[START], r.field);
+  }
+
+  void setEndCode(int v)
+  {
+    resCode r;
+    fields.put(Fields[END] + "num", r = new resCode(v));
+    fields.put(Fields[END], r.field);
+  }
+
+  /**
+   * make a possibly updated modeller field line for the sequence object
+   * 
+   * @param seq
+   *                SequenceI
+   */
+  ModellerDescription(SequenceI seq)
+  {
+
+    if (seq.getDescription() != null)
+    {
+      fields = parseDescription(seq.getDescription());
+    }
+
+    if (isModellerFieldset())
+    {
+      // Set start and end before we update the type (in the case of a
+      // synthesized field set)
+      if (getStartNum() != seq.getStart() && getStartCode().val != null)
+      {
+        setStartCode(seq.getStart());
+      }
+
+      if (getEndNum() != seq.getEnd() && getStartCode().val != null)
+      {
+        setEndCode(seq.getEnd());
+      }
+    }
+    else
+    {
+      // synthesize fields
+      setStartCode(seq.getStart());
+      setEndCode(seq.getEnd());
+      fields.put(Fields[LOCALID], seq.getName()); // this may be overwritten
+                                                  // below...
+      // type - decide based on evidence of PDB database references - this also
+      // sets the local reference field
+      int t = 0; // sequence
+      if (seq.getDatasetSequence() != null
+              && seq.getDatasetSequence().getDBRef() != null)
+      {
+        jalview.datamodel.DBRefEntry[] dbr = seq.getDatasetSequence()
+                .getDBRef();
+        int i, j;
+        for (i = 0, j = dbr.length; i < j; i++)
+        {
+          if (dbr[i] != null)
+          {
+            // JBPNote PDB dbRefEntry needs properties to propagate onto
+            // ModellerField
+            // JBPNote Need to get info from the user about whether the sequence
+            // is the one being modelled, or if it is a template.
+            if (dbr[i].getSource()
+                    .equals(jalview.datamodel.DBRefSource.PDB))
+            {
+              fields.put(Fields[LOCALID], dbr[i].getAccessionId());
+              t = 2;
+              break;
+            }
+          }
+        }
+      }
+      fields.put(Fields[TYPE], seqTypes[t]);
+    }
+
+  }
+
+  /**
+   * Indicate if fields parsed to a modeller-like colon-separated value line
+   * 
+   * @return boolean
+   */
+  boolean isModellerFieldset()
+  {
+    return (fields.containsKey(Fields[TYPE]));
+  }
+
+  String getDescriptionLine()
+  {
+    String desc = "";
+    int lastfield = Fields.length - 1;
+
+    if (isModellerFieldset())
+    {
+      String value;
+      // try to write a minimal modeller field set, so..
+
+      // find the last valid field in the entry
+
+      for (; lastfield > 6; lastfield--)
+      {
+        if (fields.containsKey(Fields[lastfield]))
+        {
+          break;
+        }
+      }
+
+      for (int i = 0; i < lastfield; i++)
+      {
+        value = (String) fields.get(Fields[i]);
+        if (value != null && value.length() > 0)
+        {
+          desc += ((String) fields.get(Fields[i])) + ":";
+        }
+        else
+        {
+          desc += Padding[i] + ":";
+        }
+      }
+    }
+    // just return the last field if no others were defined.
+    if (fields.containsKey(Fields[lastfield]))
+    {
+      desc += (String) fields.get(Fields[lastfield]);
+    }
+    else
+    {
+      desc += ".";
+    }
+    return desc;
+  }
+
+  int getStartNum()
+  {
+    int start = 0;
+    resCode val = getStartCode();
+    if (val.val != null)
+    {
+      return val.val.intValue();
+    }
+    return start;
+  }
+
+  resCode getStartCode()
+  {
+    if (isModellerFieldset() && fields.containsKey(Fields[START] + "num"))
+    {
+      return (resCode) fields.get(Fields[START] + "num");
+    }
+    return null;
+  }
+
+  resCode getEndCode()
+  {
+    if (isModellerFieldset() && fields.containsKey(Fields[END] + "num"))
+    {
+      return (resCode) fields.get(Fields[END] + "num");
+    }
+    return null;
+  }
+
+  int getEndNum()
+  {
+    int end = 0;
+    resCode val = getEndCode();
+    if (val.val != null)
+    {
+      return val.val.intValue();
+    }
+    return end;
+  }
+
+  /**
+   * returns true if sequence object was modifed with a valid modellerField set
+   * 
+   * @param newSeq
+   *                SequenceI
+   * @return boolean
+   */
+  boolean updateSequenceI(SequenceI newSeq)
+  {
+    if (isModellerFieldset())
+    {
+      if (getStartCode().val != null)
+      {
+        newSeq.setStart(getStartNum());
+      }
+      else
+      {
+        newSeq.setStart(1);
+      }
+      if (getEndCode().val != null)
+      {
+        newSeq.setEnd(getEndNum());
+      }
+      else
+      {
+        newSeq.setEnd(newSeq.getStart() + newSeq.getLength());
+      }
+      return true;
+    }
+    return false;
+  }
+}
diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index 9a7f6fb..8dc2389 100755
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 // NewickFile.java
 // Tree I/O
 // http://evolution.genetics.washington.edu/phylip/newick_doc.html
@@ -84,12 +83,12 @@ public class NewickFile extends FileParse
 
   private com.stevesoft.pat.Regex[] NodeSafeName = new com.stevesoft.pat.Regex[]
   { new com.stevesoft.pat.Regex().perlCode("m/[\\[,:'()]/"), // test for
-                                                              // requiring
-                                                              // quotes
+      // requiring
+      // quotes
       new com.stevesoft.pat.Regex().perlCode("s/'/''/"), // escaping quote
-                                                          // characters
+      // characters
       new com.stevesoft.pat.Regex().perlCode("s/\\/w/_/") // unqoted whitespace
-                                                          // transformation
+  // transformation
   };
 
   char QuoteChar = '\'';
@@ -280,14 +279,14 @@ public class NewickFile extends FileParse
     String commentString2 = null; // comments after simple node props
 
     float DefDistance = (float) 0.001; // @param Default distance for a node -
-                                        // very very small
+    // very very small
     int DefBootstrap = -1; // @param Default bootstrap for a node
 
     float distance = DefDistance;
     int bootstrap = DefBootstrap;
 
     boolean ascending = false; // flag indicating that we are leaving the
-                                // current node
+    // current node
 
     com.stevesoft.pat.Regex majorsyms = new com.stevesoft.pat.Regex(
             "[(\\['),;]");
@@ -430,7 +429,7 @@ public class NewickFile extends FileParse
         if (uqnodename.search(fstring)
                 && ((uqnodename.matchedFrom(1) == 0) || (fstring
                         .charAt(uqnodename.matchedFrom(1) - 1) != ':'))) // JBPNote
-                                                                          // HACK!
+        // HACK!
         {
           if (nodename == null)
           {
@@ -506,8 +505,8 @@ public class NewickFile extends FileParse
           if (c == realroot)
           {
             RootHasDistance = nodehasdistance; // JBPNote This is really
-                                                // UGLY!!! Ensure root node gets
-                                                // its given distance
+            // UGLY!!! Ensure root node gets
+            // its given distance
           }
           parseNHXNodeProps(c, commentString2);
           commentString2 = null;
@@ -585,7 +584,7 @@ public class NewickFile extends FileParse
         nodename = null;
         distance = DefDistance;
         bootstrap = DefBootstrap;
-        commentString2=null;
+        commentString2 = null;
       }
       if (nextcp == 0)
       {
@@ -630,39 +629,40 @@ public class NewickFile extends FileParse
     // tree is output
     if (commentString != null && commentString.startsWith("&&NHX"))
     {
-      StringTokenizer st = new StringTokenizer(commentString.substring(5),":");
+      StringTokenizer st = new StringTokenizer(commentString.substring(5),
+              ":");
       while (st.hasMoreTokens())
       {
         String tok = st.nextToken();
-        int colpos=tok.indexOf("=");
+        int colpos = tok.indexOf("=");
 
-        if (colpos>-1)
+        if (colpos > -1)
         {
           String code = tok.substring(0, colpos);
-          String value = tok.substring(colpos+1);
-          try {
+          String value = tok.substring(colpos + 1);
+          try
+          {
             // parse out code/value pairs
             if (code.toLowerCase().equals("b"))
             {
-              int v=-1;
+              int v = -1;
               Float iv = new Float(value);
               v = iv.intValue(); // jalview only does integer bootstraps
-                                  // currently
+              // currently
               c.setBootstrap(v);
               HasBootstrap = true;
             }
             // more codes here.
-          }
-          catch (Exception e)
+          } catch (Exception e)
           {
-            System.err.println("Couldn't parse code '"+code+"' = '"+value+"'");
+            System.err.println("Couldn't parse code '" + code + "' = '"
+                    + value + "'");
             e.printStackTrace(System.err);
           }
         }
       }
     }
-        
-      
+
   }
 
   /**
diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index b18b8f4..4c10abe 100755
--- a/src/jalview/io/PIRFile.java
+++ b/src/jalview/io/PIRFile.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -23,38 +23,37 @@ import java.util.*;
 
 import jalview.datamodel.*;
 
-public class PIRFile
-    extends AlignFile
+public class PIRFile extends AlignFile
 {
   public static boolean useModellerOutput = false;
 
-  Vector words = new Vector(); //Stores the words in a line after splitting
+  Vector words = new Vector(); // Stores the words in a line after splitting
 
   public PIRFile()
   {
   }
 
-  public PIRFile(String inFile, String type)
-      throws IOException
+  public PIRFile(String inFile, String type) throws IOException
   {
     super(inFile, type);
   }
+
   public PIRFile(FileParse source) throws IOException
   {
     super(source);
   }
-  public void parse()
-      throws IOException
+
+  public void parse() throws IOException
   {
     StringBuffer sequence;
     String line = null;
     ModellerDescription md;
 
-    while ( (line = nextLine()) != null)
+    while ((line = nextLine()) != null)
     {
       if (line.length() == 0)
       {
-        //System.out.println("blank line");
+        // System.out.println("blank line");
         continue;
       }
       if (line.indexOf("C;") == 0 || line.indexOf("#") == 0)
@@ -92,8 +91,7 @@ public class PIRFile
 
         seqs.addElement(newSeq);
 
-        md = new ModellerDescription(newSeq.
-                                     getDescription());
+        md = new ModellerDescription(newSeq.getDescription());
         md.updateSequenceI(newSeq);
       }
     }
@@ -112,7 +110,7 @@ public class PIRFile
     int i = 0;
     ModellerDescription md;
 
-    while ( (i < s.length) && (s[i] != null))
+    while ((i < s.length) && (s[i] != null))
     {
       String seq = s[i].getSequenceAsString();
       seq = seq + "*";
@@ -133,8 +131,8 @@ public class PIRFile
         out.append(">N1;" + s[i].getName() + "\n");
         if (s[i].getDescription() == null)
         {
-          out.append(s[i].getName() + " " +
-                     (s[i].getEnd() - s[i].getStart() + 1));
+          out.append(s[i].getName() + " "
+                  + (s[i].getEnd() - s[i].getStart() + 1));
           out.append(is_NA ? " bases\n" : " residues\n");
         }
         else
@@ -160,9 +158,10 @@ public class PIRFile
           }
           else
           {
-            out.append(s[i].getName() + " "
-                       + (s[i].getEnd() - s[i].getStart() + 1)
-                       + " residues\n");
+            out
+                    .append(s[i].getName() + " "
+                            + (s[i].getEnd() - s[i].getStart() + 1)
+                            + " residues\n");
           }
         }
       }
diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java
index 2b0bf13..223e7a4 100755
--- a/src/jalview/io/PfamFile.java
+++ b/src/jalview/io/PfamFile.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -24,30 +24,29 @@ import java.util.*;
 import jalview.datamodel.*;
 import jalview.util.*;
 
-public class PfamFile
-    extends AlignFile
+public class PfamFile extends AlignFile
 {
 
   public PfamFile()
   {
   }
 
-  public PfamFile(String inFile, String type)
-      throws IOException
+  public PfamFile(String inFile, String type) throws IOException
   {
     super(inFile, type);
   }
+
   public PfamFile(FileParse source) throws IOException
   {
     super(source);
   }
+
   public void initData()
   {
     super.initData();
   }
 
-  public void parse()
-      throws IOException
+  public void parse() throws IOException
   {
     int i = 0;
     String line;
@@ -55,7 +54,7 @@ public class PfamFile
     Hashtable seqhash = new Hashtable();
     Vector headers = new Vector();
 
-    while ( (line = nextLine()) != null)
+    while ((line = nextLine()) != null)
     {
       if (line.indexOf(" ") != 0)
       {
@@ -80,7 +79,7 @@ public class PfamFile
               seqhash.put(id, tempseq);
             }
 
-            if (! (headers.contains(id)))
+            if (!(headers.contains(id)))
             {
               headers.addElement(id);
             }
@@ -103,21 +102,20 @@ public class PfamFile
       if (seqhash.get(headers.elementAt(i)) != null)
       {
         if (maxLength < seqhash.get(headers.elementAt(i)).toString()
-            .length())
+                .length())
         {
-          maxLength = seqhash.get(headers.elementAt(i)).toString()
-              .length();
+          maxLength = seqhash.get(headers.elementAt(i)).toString().length();
         }
 
         Sequence newSeq = parseId(headers.elementAt(i).toString());
-        newSeq.setSequence(seqhash.get(headers.elementAt(i).toString()).
-                           toString());
+        newSeq.setSequence(seqhash.get(headers.elementAt(i).toString())
+                .toString());
         seqs.addElement(newSeq);
       }
       else
       {
-        System.err.println("PFAM File reader: Can't find sequence for " +
-                           headers.elementAt(i));
+        System.err.println("PFAM File reader: Can't find sequence for "
+                + headers.elementAt(i));
       }
     }
   }
@@ -131,7 +129,7 @@ public class PfamFile
 
     int i = 0;
 
-    while ( (i < s.length) && (s[i] != null))
+    while ((i < s.length) && (s[i] != null))
     {
       String tmp = printId(s[i]);
 
@@ -155,7 +153,7 @@ public class PfamFile
 
     int j = 0;
 
-    while ( (j < s.length) && (s[j] != null))
+    while ((j < s.length) && (s[j] != null))
     {
       out.append(new Format("%-" + maxid + "s").form(printId(s[j]) + " "));
 
diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index cd46541..947d982 100755
--- a/src/jalview/io/PileUpfile.java
+++ b/src/jalview/io/PileUpfile.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -19,23 +19,26 @@
 package jalview.io;
 
 /**
- * <p>Title: </p>
- *  PileUpfile
- * <p>Description: </p>
- *
- *  Read and write PileUp style MSF Files.
- *  This used to be the MSFFile class, and was written according to the EBI's idea
- *  of a subset of the MSF alignment format. But, that was updated to reflect current
- *  GCG style IO fashion, as found in Emboss (thanks David Martin!)
- *
- **/
+ * <p>
+ * Title:
+ * </p>
+ * PileUpfile
+ * <p>
+ * Description:
+ * </p>
+ * 
+ * Read and write PileUp style MSF Files. This used to be the MSFFile class, and
+ * was written according to the EBI's idea of a subset of the MSF alignment
+ * format. But, that was updated to reflect current GCG style IO fashion, as
+ * found in Emboss (thanks David Martin!)
+ * 
+ */
 import java.io.*;
 
 import jalview.datamodel.*;
 import jalview.util.*;
 
-public class PileUpfile
-    extends MSFfile
+public class PileUpfile extends MSFfile
 {
 
   /**
@@ -47,24 +50,28 @@ public class PileUpfile
 
   /**
    * Creates a new MSFfile object.
-   *
-   * @param inFile DOCUMENT ME!
-   * @param type DOCUMENT ME!
-   *
-   * @throws IOException DOCUMENT ME!
+   * 
+   * @param inFile
+   *                DOCUMENT ME!
+   * @param type
+   *                DOCUMENT ME!
+   * 
+   * @throws IOException
+   *                 DOCUMENT ME!
    */
-  public PileUpfile(String inFile, String type)
-      throws IOException
+  public PileUpfile(String inFile, String type) throws IOException
   {
     super(inFile, type);
   }
+
   public PileUpfile(FileParse source) throws IOException
   {
     super(source);
   }
+
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public String print()
@@ -89,17 +96,16 @@ public class PileUpfile
       i++;
     }
 
-    out.append("   MSF: " + s[0].getSequence().length +
-               "   Type: P    Check:  " + bigChecksum % 10000 + "   ..\n\n\n");
+    out.append("   MSF: " + s[0].getSequence().length
+            + "   Type: P    Check:  " + bigChecksum % 10000
+            + "   ..\n\n\n");
 
     i = 0;
-    while ( (i < s.length) && (s[i] != null))
+    while ((i < s.length) && (s[i] != null))
     {
       String seq = s[i].getSequenceAsString();
-      out.append(" Name: " + printId(s[i]) +
-                 " oo  Len:  " +
-                 seq.length() + "  Check:  " + checksums[i] +
-                 "  Weight:  1.00\n");
+      out.append(" Name: " + printId(s[i]) + " oo  Len:  " + seq.length()
+              + "  Check:  " + checksums[i] + "  Weight:  1.00\n");
 
       if (seq.length() > max)
       {
@@ -126,7 +132,7 @@ public class PileUpfile
 
     int nochunks = (max / len) + 1;
 
-    if ( (max % len) == 0)
+    if ((max % len) == 0)
     {
       nochunks--;
     }
@@ -135,7 +141,7 @@ public class PileUpfile
     {
       int j = 0;
 
-      while ( (j < s.length) && (s[j] != null))
+      while ((j < s.length) && (s[j] != null))
       {
         String name = printId(s[j]);
 
@@ -146,8 +152,8 @@ public class PileUpfile
           int start = (i * 50) + (k * 10);
           int end = start + 10;
 
-          if ( (end < s[j].getSequence().length) &&
-              (start < s[j].getSequence().length))
+          if ((end < s[j].getSequence().length)
+                  && (start < s[j].getSequence().length))
           {
             out.append(s[j].getSequence(start, end));
 
diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index ccbe818..2183f2d 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -30,13 +30,13 @@ import jalview.datamodel.*;
 // import org.apache.log4j.*;
 
 /**
- * This class is supposed to parse a Stockholm format file into Jalview
- * There are TODOs in this class: we do not know what the database source and
- * version is for the file when parsing the #GS= AC tag which associates accessions
- * with sequences. 
- * Database references are also not parsed correctly: a separate reference string
- * parser must be added to parse the database reference form into Jalview's local
- * representation.
+ * This class is supposed to parse a Stockholm format file into Jalview There
+ * are TODOs in this class: we do not know what the database source and version
+ * is for the file when parsing the #GS= AC tag which associates accessions with
+ * sequences. Database references are also not parsed correctly: a separate
+ * reference string parser must be added to parse the database reference form
+ * into Jalview's local representation.
+ * 
  * @author bsb at sanger.ac.uk
  * @version 0.3 + jalview mods
  * 
@@ -53,10 +53,12 @@ public class StockholmFile extends AlignFile
   {
     super(inFile, type);
   }
+
   public StockholmFile(FileParse source) throws IOException
   {
     super(source);
   }
+
   public void initData()
   {
     super.initData();
@@ -67,7 +69,7 @@ public class StockholmFile extends AlignFile
    * be passed at construction time
    * 
    * @throws IOException
-   *           If there is an error with the input file
+   *                 If there is an error with the input file
    */
   public void parse() throws IOException
   {
@@ -99,7 +101,7 @@ public class StockholmFile extends AlignFile
     // We define some Regexes here that will be used regularily later
     rend = new Regex("\\/\\/"); // Find the end of an alignment
     p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in
-                                                // id/from/to
+    // id/from/to
     s = new Regex("(\\S+)\\s+(\\S*)\\s+(.*)"); // Parses annotation subtype
     r = new Regex("#=(G[FSRC]?)\\s+(.*)"); // Finds any annotation line
     x = new Regex("(\\S+)\\s+(\\S+)"); // split id from sequence
@@ -168,7 +170,7 @@ public class StockholmFile extends AlignFile
               String src = dbr.substring(0, dbr.indexOf(";"));
               String acn = dbr.substring(dbr.indexOf(";") + 1);
               jalview.util.DBRefUtils.parseToDbRef(seqO, src, "0", acn);
-              //seqO.addDBRef(dbref);
+              // seqO.addDBRef(dbref);
             }
           }
           Hashtable features = null;
@@ -204,9 +206,15 @@ public class StockholmFile extends AlignFile
                 for (int k = 0; k < byChar.length; k++)
                 {
                   char c = byChar[k];
-                  if (!(c == ' ' || c == '_' || c == '-' || c == '.')) // PFAM uses '.' for feature background
+                  if (!(c == ' ' || c == '_' || c == '-' || c == '.')) // PFAM
+                                                                        // uses
+                                                                        // '.'
+                                                                        // for
+                                                                        // feature
+                                                                        // background
                   {
-                    int new_pos = posmap[k]; // look up nearest seqeunce position to this column
+                    int new_pos = posmap[k]; // look up nearest seqeunce
+                                              // position to this column
                     SequenceFeature feat = new SequenceFeature(type, desc,
                             new_pos, new_pos, 0f, null);
 
@@ -216,10 +224,10 @@ public class StockholmFile extends AlignFile
               }
 
             }
-            
+
           }
           // garbage collect
-          
+
           // logger.debug("Adding seq " + acc + " from " + start + " to " + end
           // + ": " + seq);
           this.seqs.addElement(seqO);
@@ -379,13 +387,15 @@ public class StockholmFile extends AlignFile
             String seq = new String(s.stringMatched(3));
             String description = null;
             // Check for additional information about the current annotation
-            // We use a simple  string tokenizer here for speed
-            StringTokenizer sep = new StringTokenizer(seq," \t");
+            // We use a simple string tokenizer here for speed
+            StringTokenizer sep = new StringTokenizer(seq, " \t");
             description = sep.nextToken();
             if (sep.hasMoreTokens())
             {
               seq = sep.nextToken();
-            } else {
+            }
+            else
+            {
               seq = description;
               description = new String();
             }
@@ -442,7 +452,9 @@ public class StockholmFile extends AlignFile
           }
           else
           {
-            System.err.println("Warning - couldn't parse sequence annotation row line:\n"+line);
+            System.err
+                    .println("Warning - couldn't parse sequence annotation row line:\n"
+                            + line);
             // throw new IOException("Error parsing " + line);
           }
         }
@@ -480,7 +492,8 @@ public class StockholmFile extends AlignFile
     {
       String pos = annots.substring(i, i + 1);
       Annotation ann;
-      ann = new Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not be written out 
+      ann = new Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not
+                                              // be written out
       if (ss)
       {
         ann.secondaryStructure = jalview.schemes.ResidueProperties
@@ -491,7 +504,7 @@ public class StockholmFile extends AlignFile
         }
         else
         {
-          ann.displayCharacter = " "+ann.displayCharacter;
+          ann.displayCharacter = " " + ann.displayCharacter;
         }
       }
 
diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index 1964c2f..c2031cc 100644
--- a/src/jalview/io/VamsasAppDatastore.java
+++ b/src/jalview/io/VamsasAppDatastore.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.io;
 
 import jalview.bin.Cache;
@@ -351,7 +350,7 @@ public class VamsasAppDatastore
             }
           }
         }
-        if (sq.getDatasetSequence()==null && sq.getDBRef() != null)
+        if (sq.getDatasetSequence() == null && sq.getDBRef() != null)
         {
           // only sync database references for dataset sequences
           DBRefEntry[] entries = sq.getDBRef();
@@ -379,22 +378,22 @@ public class VamsasAppDatastore
       // ////////////////////////////////////////////
       if (!av.getAlignment().isAligned())
         return; // TODO: trees could be written - but for the moment we just
-                // skip
+      // skip
       // ////////////////////////////////////////////
       // Save the Alignments
 
       Alignment alignment = (Alignment) getjv2vObj(av.getSequenceSetId()); // bind
-                                                                            // to
-                                                                            // the
-                                                                            // value
-                                                                            // used
-                                                                            // to
-                                                                            // associate
-                                                                            // different
-                                                                            // views
-                                                                            // to
-                                                                            // same
-                                                                            // alignment
+      // to
+      // the
+      // value
+      // used
+      // to
+      // associate
+      // different
+      // views
+      // to
+      // same
+      // alignment
 
       if (alignment == null)
       {
@@ -456,20 +455,20 @@ public class VamsasAppDatastore
             {
               // info in the undo
               addProvenance(alignment.getProvenance(), "Edited"); // TODO:
-                                                                  // insert
-                                                                  // something
-                                                                  // sensible
-                                                                  // here again
+              // insert
+              // something
+              // sensible
+              // here again
             }
             else
             {
               // info in the undo
               addProvenance(alignment.getProvenance(), "Attributes Edited"); // TODO:
-                                                                              // insert
-                                                                              // something
-                                                                              // sensible
-                                                                              // here
-                                                                              // again
+              // insert
+              // something
+              // sensible
+              // here
+              // again
             }
           }
           if (alismod)
@@ -2047,9 +2046,9 @@ public class VamsasAppDatastore
         if (type == 0)
         {
           type = jalview.datamodel.AlignmentAnnotation.BAR_GRAPH; // default
-                                                                  // type of
-                                                                  // value
-                                                                  // annotation
+          // type of
+          // value
+          // annotation
           if (has[HASHPHOB])
           {
             // no hints - so we ensure HPHOB display is like this.
@@ -2148,7 +2147,7 @@ public class VamsasAppDatastore
       }
       if (annotation.getModifiable() == null
               || annotation.getModifiable().length() == 0) // TODO: USE VAMSAS
-                                                            // LIBRARY OBJECT
+      // LIBRARY OBJECT
       // LOCK METHODS)
       {
         jan.editable = true;
@@ -2159,12 +2158,12 @@ public class VamsasAppDatastore
                 && annotation.getGroup().length() > 0)
         {
           jan.graphGroup = Integer.parseInt(annotation.getGroup()); // TODO:
-                                                                    // group
-                                                                    // similarly
-                                                                    // named
-                                                                    // annotation
-                                                                    // together
-                                                                    // ?
+          // group
+          // similarly
+          // named
+          // annotation
+          // together
+          // ?
         }
       } catch (Exception e)
       {
diff --git a/src/jalview/io/WSWUBlastClient.java b/src/jalview/io/WSWUBlastClient.java
index 1d42620..ad291db 100755
--- a/src/jalview/io/WSWUBlastClient.java
+++ b/src/jalview/io/WSWUBlastClient.java
@@ -1,303 +1,306 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.io;
-
-import java.util.*;
-
-import javax.swing.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import uk.ac.ebi.www.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class WSWUBlastClient
-{
-  AlignmentPanel ap;
-  AlignmentI al;
-  CutAndPasteTransfer output = new CutAndPasteTransfer();
-  int jobsRunning = 0;
-
-  Vector suggestedIds = new Vector();
-  /**
-   * Creates a new WSWUBlastClient object.
-   *
-   * @param al DOCUMENT ME!
-   * @param ids DOCUMENT ME!
-   */
-  public WSWUBlastClient(AlignmentPanel ap, AlignmentI al, ArrayList ids)
-  {
-    this.ap = ap;
-    this.al = al;
-    output.setText(
-        "To display sequence features an exact Uniprot id with 100% sequence identity match must be entered."
-        + "\nIn order to display these features, try changing the names of your sequences to the ids suggested below."
-        + "\n\nRunning WSWUBlast at EBI."
-        + "\nPlease quote Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R."
-        +
-        "\nSOAP-based services provided by the European Bioinformatics Institute."
-        + "\nNucleic Acids Res. 33(1):W25-W28 (2005));");
-
-    Desktop.addInternalFrame(output,
-                             "BLASTing for unidentified sequences ", 800, 300);
-
-    for (int i = 0; i < ids.size(); i++)
-    {
-      Sequence sequence = (Sequence) ids.get(i);
-      System.out.println(sequence.getName());
-
-      BlastThread thread = new BlastThread(sequence);
-      thread.start();
-      jobsRunning++;
-    }
-
-    ImageTwirler thread = new ImageTwirler();
-    thread.start();
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param id1 DOCUMENT ME!
-   * @param res DOCUMENT ME!
-   */
-  void parseResult(Sequence seq, String res)
-  {
-    StringTokenizer st = new StringTokenizer(res, "\n");
-    String data;
-    String id2;
-    int maxFound = 90;
-    StringBuffer buffer = new StringBuffer("\n\n" + seq.getName() + " :");
-
-    while (st.hasMoreTokens())
-    {
-      data = st.nextToken();
-
-      if (data.indexOf(">UNIPROT") > -1)
-      {
-        int index = data.indexOf(">UNIPROT") + 9;
-        id2 = data.substring(index, data.indexOf(" ", index));
-
-        boolean identitiesFound = false;
-        while (!identitiesFound)
-        {
-          data = st.nextToken();
-
-          if (data.indexOf("Identities") > -1)
-          {
-            identitiesFound = true;
-
-            int value = Integer.parseInt(data.substring(data.indexOf(
-                "(") + 1,
-                data.indexOf("%")));
-
-            if (value >= maxFound)
-            {
-              maxFound = value;
-              buffer.append(" " + id2 + " " + value + "%; ");
-              suggestedIds.addElement(new Object[]
-                                      {seq, id2});
-            }
-          }
-        }
-      }
-    }
-
-    output.appendText(buffer.toString());
-  }
-
-  void updateIds()
-  {
-    // This must be outside the run() body as java 1.5
-    // will not return any value from the OptionPane to the expired thread.
-    int reply = JOptionPane.showConfirmDialog(
-        Desktop.desktop, "Automatically update suggested ids?",
-        "Auto replace sequence ids", JOptionPane.YES_NO_OPTION);
-
-    if (reply == JOptionPane.YES_OPTION)
-    {
-      Enumeration keys = suggestedIds.elements();
-      while (keys.hasMoreElements())
-      {
-        Object[] object = (Object[]) keys.nextElement();
-
-        Sequence oldseq = (Sequence) object[0];
-
-        oldseq.setName(object[1].toString());
-
-        // Oldseq is actually in the dataset, we must find the
-        // Visible seq and change its name also.
-        for (int i = 0; i < al.getHeight(); i++)
-        {
-          if (al.getSequenceAt(i).getDatasetSequence() == oldseq)
-          {
-            al.getSequenceAt(i).setName(oldseq.getName());
-            break;
-          }
-        }
-
-        DBRefEntry[] entries = oldseq.getDBRef();
-        if (entries != null)
-        {
-          oldseq.addDBRef(new jalview.datamodel.
-                          DBRefEntry(jalview.datamodel.DBRefSource.UNIPROT,
-                                     "0",
-                                     entries[0].getAccessionId()));
-        }
-      }
-    }
-    ap.paintAlignment(true);
-
-  }
-
-  class ImageTwirler
-      extends Thread
-  {
-    ImageIcon[] imageIcon;
-    int imageIndex = 0;
-
-    public ImageTwirler()
-    {
-      imageIcon = new ImageIcon[9];
-
-      for (int i = 0; i < 9; i++)
-      {
-        java.net.URL url = getClass().getResource("/images/dna" +
-                                                  (i + 1) + ".gif");
-
-        if (url != null)
-        {
-          imageIcon[i] = new ImageIcon(url);
-        }
-      }
-    }
-
-    public void run()
-    {
-      while (jobsRunning > 0)
-      {
-        try
-        {
-          Thread.sleep(100);
-          imageIndex++;
-          imageIndex %= 9;
-          output.setFrameIcon(imageIcon[imageIndex]);
-          output.setTitle("BLASTing for unidentified sequences - " +
-                          jobsRunning + " jobs running.");
-        }
-        catch (Exception ex)
-        {
-        }
-      }
-
-      if (jobsRunning == 0)
-      {
-        updateIds();
-      }
-    }
-  }
-
-  class BlastThread
-      extends Thread
-  {
-    Sequence sequence;
-    String jobid;
-    boolean jobComplete = false;
-
-    BlastThread(Sequence sequence)
-    {
-      System.out.println("blasting for: " + sequence.getName());
-      this.sequence = sequence;
-    }
-
-    public void run()
-    {
-      StartJob();
-
-      while (!jobComplete)
-      {
-        try
-        {
-          WSWUBlastService service = new WSWUBlastServiceLocator();
-          WSWUBlast wublast = service.getWSWUBlast();
-          WSFile[] results = wublast.getResults(jobid);
-
-          if (results != null)
-          {
-            String result = new String(wublast.poll(jobid, "tooloutput"));
-            parseResult(sequence, result);
-            jobComplete = true;
-            jobsRunning--;
-          }
-          else
-          {
-            Thread.sleep(10000);
-            System.out.println("WSWuBlastClient: I'm alive " +
-                               sequence.getName() + " " + jobid); // log.debug
-          }
-        }
-        catch (Exception ex)
-        {
-        }
-      }
-    }
-
-    void StartJob()
-    {
-      InputParams params = new InputParams();
-
-      params.setProgram("blastp");
-      params.setDatabase("uniprot");
-      params.setMatrix("pam10");
-
-      params.setNumal(5);
-      params.setSensitivity("low");
-      params.setSort("totalscore");
-      params.setOutformat("txt");
-      params.setAsync(true);
-
-      try
-      {
-        Data inputs[] = new Data[1];
-        Data input = new Data();
-        input.setType("sequence");
-        input.setContent(AlignSeq.extractGaps("-. ",
-                                              sequence.getSequenceAsString()));
-        inputs[0] = input;
-
-        WSWUBlastService service = new WSWUBlastServiceLocator();
-        WSWUBlast wublast = service.getWSWUBlast();
-        jobid = wublast.runWUBlast(params, inputs);
-      }
-      catch (Exception exp)
-      {
-        jobComplete = true;
-        jobsRunning--;
-        System.err.println("WSWUBlastClient error:\n" + exp.toString());
-        exp.printStackTrace();
-      }
-    }
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.io;
+
+import java.util.*;
+
+import javax.swing.*;
+
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.gui.*;
+import uk.ac.ebi.www.*;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class WSWUBlastClient
+{
+  AlignmentPanel ap;
+
+  AlignmentI al;
+
+  CutAndPasteTransfer output = new CutAndPasteTransfer();
+
+  int jobsRunning = 0;
+
+  Vector suggestedIds = new Vector();
+
+  /**
+   * Creates a new WSWUBlastClient object.
+   * 
+   * @param al
+   *                DOCUMENT ME!
+   * @param ids
+   *                DOCUMENT ME!
+   */
+  public WSWUBlastClient(AlignmentPanel ap, AlignmentI al, ArrayList ids)
+  {
+    this.ap = ap;
+    this.al = al;
+    output
+            .setText("To display sequence features an exact Uniprot id with 100% sequence identity match must be entered."
+                    + "\nIn order to display these features, try changing the names of your sequences to the ids suggested below."
+                    + "\n\nRunning WSWUBlast at EBI."
+                    + "\nPlease quote Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R."
+                    + "\nSOAP-based services provided by the European Bioinformatics Institute."
+                    + "\nNucleic Acids Res. 33(1):W25-W28 (2005));");
+
+    Desktop.addInternalFrame(output,
+            "BLASTing for unidentified sequences ", 800, 300);
+
+    for (int i = 0; i < ids.size(); i++)
+    {
+      Sequence sequence = (Sequence) ids.get(i);
+      System.out.println(sequence.getName());
+
+      BlastThread thread = new BlastThread(sequence);
+      thread.start();
+      jobsRunning++;
+    }
+
+    ImageTwirler thread = new ImageTwirler();
+    thread.start();
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param id1
+   *                DOCUMENT ME!
+   * @param res
+   *                DOCUMENT ME!
+   */
+  void parseResult(Sequence seq, String res)
+  {
+    StringTokenizer st = new StringTokenizer(res, "\n");
+    String data;
+    String id2;
+    int maxFound = 90;
+    StringBuffer buffer = new StringBuffer("\n\n" + seq.getName() + " :");
+
+    while (st.hasMoreTokens())
+    {
+      data = st.nextToken();
+
+      if (data.indexOf(">UNIPROT") > -1)
+      {
+        int index = data.indexOf(">UNIPROT") + 9;
+        id2 = data.substring(index, data.indexOf(" ", index));
+
+        boolean identitiesFound = false;
+        while (!identitiesFound)
+        {
+          data = st.nextToken();
+
+          if (data.indexOf("Identities") > -1)
+          {
+            identitiesFound = true;
+
+            int value = Integer.parseInt(data.substring(
+                    data.indexOf("(") + 1, data.indexOf("%")));
+
+            if (value >= maxFound)
+            {
+              maxFound = value;
+              buffer.append(" " + id2 + " " + value + "%; ");
+              suggestedIds.addElement(new Object[]
+              { seq, id2 });
+            }
+          }
+        }
+      }
+    }
+
+    output.appendText(buffer.toString());
+  }
+
+  void updateIds()
+  {
+    // This must be outside the run() body as java 1.5
+    // will not return any value from the OptionPane to the expired thread.
+    int reply = JOptionPane.showConfirmDialog(Desktop.desktop,
+            "Automatically update suggested ids?",
+            "Auto replace sequence ids", JOptionPane.YES_NO_OPTION);
+
+    if (reply == JOptionPane.YES_OPTION)
+    {
+      Enumeration keys = suggestedIds.elements();
+      while (keys.hasMoreElements())
+      {
+        Object[] object = (Object[]) keys.nextElement();
+
+        Sequence oldseq = (Sequence) object[0];
+
+        oldseq.setName(object[1].toString());
+
+        // Oldseq is actually in the dataset, we must find the
+        // Visible seq and change its name also.
+        for (int i = 0; i < al.getHeight(); i++)
+        {
+          if (al.getSequenceAt(i).getDatasetSequence() == oldseq)
+          {
+            al.getSequenceAt(i).setName(oldseq.getName());
+            break;
+          }
+        }
+
+        DBRefEntry[] entries = oldseq.getDBRef();
+        if (entries != null)
+        {
+          oldseq.addDBRef(new jalview.datamodel.DBRefEntry(
+                  jalview.datamodel.DBRefSource.UNIPROT, "0", entries[0]
+                          .getAccessionId()));
+        }
+      }
+    }
+    ap.paintAlignment(true);
+
+  }
+
+  class ImageTwirler extends Thread
+  {
+    ImageIcon[] imageIcon;
+
+    int imageIndex = 0;
+
+    public ImageTwirler()
+    {
+      imageIcon = new ImageIcon[9];
+
+      for (int i = 0; i < 9; i++)
+      {
+        java.net.URL url = getClass().getResource(
+                "/images/dna" + (i + 1) + ".gif");
+
+        if (url != null)
+        {
+          imageIcon[i] = new ImageIcon(url);
+        }
+      }
+    }
+
+    public void run()
+    {
+      while (jobsRunning > 0)
+      {
+        try
+        {
+          Thread.sleep(100);
+          imageIndex++;
+          imageIndex %= 9;
+          output.setFrameIcon(imageIcon[imageIndex]);
+          output.setTitle("BLASTing for unidentified sequences - "
+                  + jobsRunning + " jobs running.");
+        } catch (Exception ex)
+        {
+        }
+      }
+
+      if (jobsRunning == 0)
+      {
+        updateIds();
+      }
+    }
+  }
+
+  class BlastThread extends Thread
+  {
+    Sequence sequence;
+
+    String jobid;
+
+    boolean jobComplete = false;
+
+    BlastThread(Sequence sequence)
+    {
+      System.out.println("blasting for: " + sequence.getName());
+      this.sequence = sequence;
+    }
+
+    public void run()
+    {
+      StartJob();
+
+      while (!jobComplete)
+      {
+        try
+        {
+          WSWUBlastService service = new WSWUBlastServiceLocator();
+          WSWUBlast wublast = service.getWSWUBlast();
+          WSFile[] results = wublast.getResults(jobid);
+
+          if (results != null)
+          {
+            String result = new String(wublast.poll(jobid, "tooloutput"));
+            parseResult(sequence, result);
+            jobComplete = true;
+            jobsRunning--;
+          }
+          else
+          {
+            Thread.sleep(10000);
+            System.out.println("WSWuBlastClient: I'm alive "
+                    + sequence.getName() + " " + jobid); // log.debug
+          }
+        } catch (Exception ex)
+        {
+        }
+      }
+    }
+
+    void StartJob()
+    {
+      InputParams params = new InputParams();
+
+      params.setProgram("blastp");
+      params.setDatabase("uniprot");
+      params.setMatrix("pam10");
+
+      params.setNumal(5);
+      params.setSensitivity("low");
+      params.setSort("totalscore");
+      params.setOutformat("txt");
+      params.setAsync(true);
+
+      try
+      {
+        Data inputs[] = new Data[1];
+        Data input = new Data();
+        input.setType("sequence");
+        input.setContent(AlignSeq.extractGaps("-. ", sequence
+                .getSequenceAsString()));
+        inputs[0] = input;
+
+        WSWUBlastService service = new WSWUBlastServiceLocator();
+        WSWUBlast wublast = service.getWSWUBlast();
+        jobid = wublast.runWUBlast(params, inputs);
+      } catch (Exception exp)
+      {
+        jobComplete = true;
+        jobsRunning--;
+        System.err.println("WSWUBlastClient error:\n" + exp.toString());
+        exp.printStackTrace();
+      }
+    }
+  }
+}
diff --git a/src/jalview/io/vamsas/DatastoreItem.java b/src/jalview/io/vamsas/DatastoreItem.java
index 4cc540d..42e494f 100644
--- a/src/jalview/io/vamsas/DatastoreItem.java
+++ b/src/jalview/io/vamsas/DatastoreItem.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.io.vamsas;
 
 import jalview.bin.Cache;
@@ -18,8 +36,9 @@ import uk.ac.vamsas.objects.core.Seg;
 
 /**
  * Holds all the common machinery for binding objects to vamsas objects
+ * 
  * @author JimP
- *
+ * 
  */
 public class DatastoreItem
 {
@@ -33,6 +52,7 @@ public class DatastoreItem
   Hashtable vobj2jv;
 
   IdentityHashMap jv2vobj;
+
   /**
    * @return the Vobject bound to Jalview datamodel object
    */
@@ -40,30 +60,31 @@ public class DatastoreItem
   {
     if (jv2vobj.containsKey(jvobj))
     {
-      return cdoc.getObject( (VorbaId) jv2vobj.get(jvobj));
+      return cdoc.getObject((VorbaId) jv2vobj.get(jvobj));
     }
     if (Cache.log.isDebugEnabled())
     {
-      Cache.log.debug("Returning null VorbaID binding for jalview object "+jvobj);
+      Cache.log.debug("Returning null VorbaID binding for jalview object "
+              + jvobj);
     }
     return null;
   }
 
   /**
-   *
+   * 
    * @param vobj
    * @return Jalview datamodel object bound to the vamsas document object
    */
   protected Object getvObj2jv(uk.ac.vamsas.client.Vobject vobj)
   {
-    if (vobj2jv==null)
+    if (vobj2jv == null)
       return null;
     VorbaId id = vobj.getVorbaId();
     if (id == null)
     {
       id = cdoc.registerObject(vobj);
       Cache.log
-          .debug("Registering new object and returning null for getvObj2jv");
+              .debug("Registering new object and returning null for getvObj2jv");
       return null;
     }
     if (vobj2jv.containsKey(vobj.getVorbaId()))
@@ -79,53 +100,67 @@ public class DatastoreItem
     if (id == null)
     {
       id = cdoc.registerObject(vobj);
-      if (id == null || vobj.getVorbaId() == null || cdoc.getObject(id)!=vobj)
+      if (id == null || vobj.getVorbaId() == null
+              || cdoc.getObject(id) != vobj)
       {
-        Cache.log.error("Failed to get id for " +
-                        (vobj.isRegisterable() ? "registerable" :
-                         "unregisterable") + " object " + vobj);
+        Cache.log.error("Failed to get id for "
+                + (vobj.isRegisterable() ? "registerable"
+                        : "unregisterable") + " object " + vobj);
       }
     }
 
-    if (vobj2jv.containsKey(vobj.getVorbaId()) &&
-        ! ( (VorbaId) vobj2jv.get(vobj.getVorbaId())).equals(jvobj))
+    if (vobj2jv.containsKey(vobj.getVorbaId())
+            && !((VorbaId) vobj2jv.get(vobj.getVorbaId())).equals(jvobj))
     {
-      Cache.log.debug("Warning? Overwriting existing vamsas id binding for " +
-                      vobj.getVorbaId(),
-                      new Exception("Overwriting vamsas id binding."));
+      Cache.log.debug(
+              "Warning? Overwriting existing vamsas id binding for "
+                      + vobj.getVorbaId(), new Exception(
+                      "Overwriting vamsas id binding."));
     }
-    else if (jv2vobj.containsKey(jvobj) &&
-             ! ( (VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId()))
+    else if (jv2vobj.containsKey(jvobj)
+            && !((VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId()))
     {
       Cache.log.debug(
-          "Warning? Overwriting existing jalview object binding for " + jvobj,
-          new Exception("Overwriting jalview object binding."));
+              "Warning? Overwriting existing jalview object binding for "
+                      + jvobj, new Exception(
+                      "Overwriting jalview object binding."));
     }
-    /* Cache.log.error("Attempt to make conflicting object binding! "+vobj+" id " +vobj.getVorbaId()+" already bound to "+getvObj2jv(vobj)+" and "+jvobj+" already bound to "+getjv2vObj(jvobj),new Exception("Excessive call to bindjvvobj"));
-         }*/
+    /*
+     * Cache.log.error("Attempt to make conflicting object binding! "+vobj+" id "
+     * +vobj.getVorbaId()+" already bound to "+getvObj2jv(vobj)+" and "+jvobj+"
+     * already bound to "+getjv2vObj(jvobj),new Exception("Excessive call to
+     * bindjvvobj")); }
+     */
     // we just update the hash's regardless!
-    Cache.log.debug("Binding "+vobj.getVorbaId()+" to "+jvobj);
+    Cache.log.debug("Binding " + vobj.getVorbaId() + " to " + jvobj);
     vobj2jv.put(vobj.getVorbaId(), jvobj);
     // JBPNote - better implementing a hybrid invertible hash.
     jv2vobj.put(jvobj, vobj.getVorbaId());
   }
 
-  public DatastoreItem() {
+  public DatastoreItem()
+  {
     super();
   }
+
   public DatastoreItem(VamsasAppDatastore datastore)
   {
     this();
     initDatastoreItem(datastore);
     // TODO Auto-generated constructor stub
   }
+
   VamsasAppDatastore datastore = null;
+
   public void initDatastoreItem(VamsasAppDatastore ds)
   {
     datastore = ds;
-    initDatastoreItem(ds.getProvEntry(), ds.getClientDocument(), ds.getVamsasObjectBinding(), ds.getJvObjectBinding());
+    initDatastoreItem(ds.getProvEntry(), ds.getClientDocument(), ds
+            .getVamsasObjectBinding(), ds.getJvObjectBinding());
   }
-  public void initDatastoreItem(Entry provEntry, IClientDocument cdoc, Hashtable vobj2jv, IdentityHashMap jv2vobj)
+
+  public void initDatastoreItem(Entry provEntry, IClientDocument cdoc,
+          Hashtable vobj2jv, IdentityHashMap jv2vobj)
   {
     this.provEntry = provEntry;
     this.cdoc = cdoc;
@@ -135,7 +170,7 @@ public class DatastoreItem
 
   protected boolean isModifiable(String modifiable)
   {
-    return modifiable==null; // TODO: USE VAMSAS LIBRARY OBJECT LOCK METHODS)
+    return modifiable == null; // TODO: USE VAMSAS LIBRARY OBJECT LOCK METHODS)
   }
 
   protected Vector getjv2vObjs(Vector alsq)
@@ -148,14 +183,17 @@ public class DatastoreItem
     }
     return vObjs;
   }
+
   // utility functions
   /**
    * get start<end range of segment, adjusting for inclusivity flag and
    * polarity.
-   *
+   * 
    * @param visSeg
-   * @param ensureDirection when true - always ensure start is less than end.
-   * @return int[] { start, end, direction} where direction==1 for range running from end to start.
+   * @param ensureDirection
+   *                when true - always ensure start is less than end.
+   * @return int[] { start, end, direction} where direction==1 for range running
+   *         from end to start.
    */
   public int[] getSegRange(Seg visSeg, boolean ensureDirection)
   {
@@ -173,28 +211,29 @@ public class DatastoreItem
       start = t;
     }
     return new int[]
-        {
-        start, end, pol < 0 ? 1 : 0};
+    { start, end, pol < 0 ? 1 : 0 };
   }
+
   /**
    * provenance bits
    */
-  protected jalview.datamodel.Provenance getJalviewProvenance(Provenance prov)
+  protected jalview.datamodel.Provenance getJalviewProvenance(
+          Provenance prov)
   {
     // TODO: fix App and Action entries and check use of provenance in jalview.
     jalview.datamodel.Provenance jprov = new jalview.datamodel.Provenance();
     for (int i = 0; i < prov.getEntryCount(); i++)
     {
-      jprov.addEntry(prov.getEntry(i).getUser(), prov.getEntry(i).getAction(),
-                     prov.getEntry(i).getDate(),
-                     prov.getEntry(i).getId());
+      jprov.addEntry(prov.getEntry(i).getUser(), prov.getEntry(i)
+              .getAction(), prov.getEntry(i).getDate(), prov.getEntry(i)
+              .getId());
     }
 
     return jprov;
   }
 
   /**
-   *
+   * 
    * @return default initial provenance list for a Jalview created vamsas
    *         object.
    */
diff --git a/src/jalview/io/vamsas/Dbref.java b/src/jalview/io/vamsas/Dbref.java
index c4d72c3..e8fedac 100644
--- a/src/jalview/io/vamsas/Dbref.java
+++ b/src/jalview/io/vamsas/Dbref.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.io.vamsas;
 
 import jalview.datamodel.DBRefEntry;
@@ -10,32 +28,43 @@ import jalview.io.VamsasAppDatastore;
 public class Dbref extends Rangetype
 {
   jalview.datamodel.SequenceI sq = null;
+
   uk.ac.vamsas.objects.core.Sequence sequence = null;
+
   DbRef dbref = null;
-  DBRefEntry dbentry=null;
-  public Dbref(VamsasAppDatastore datastore, DBRefEntry dbentry, jalview.datamodel.SequenceI sq2, uk.ac.vamsas.objects.core.Sequence sequence2)
+
+  DBRefEntry dbentry = null;
+
+  public Dbref(VamsasAppDatastore datastore, DBRefEntry dbentry,
+          jalview.datamodel.SequenceI sq2,
+          uk.ac.vamsas.objects.core.Sequence sequence2)
   {
     super(datastore);
     dbref = (DbRef) getjv2vObj(dbentry);
     sq = sq2;
     sequence = sequence2;
     this.dbentry = dbentry;
-    if (dbref==null)
+    if (dbref == null)
     {
       add();
-    } else {
+    }
+    else
+    {
       if (dbref.isUpdated())
       {
         conflict();
-      } else {
+      }
+      else
+      {
         update();
       }
-        
+
     }
-    
+
   }
 
-  public Dbref(VamsasAppDatastore datastore, DbRef ref, Sequence vdseq, SequenceI dsseq)
+  public Dbref(VamsasAppDatastore datastore, DbRef ref, Sequence vdseq,
+          SequenceI dsseq)
   {
     super(datastore);
     dbref = ref;
@@ -45,7 +74,9 @@ public class Dbref extends Rangetype
     if (dbentry == null)
     {
       addFromDocument();
-    } else {
+    }
+    else
+    {
       if (dbref.isUpdated())
       {
         update();
@@ -58,38 +89,47 @@ public class Dbref extends Rangetype
     // TODO: verify and update dbrefs in vamsas document
     // there will be trouble when a dataset sequence is modified to
     // contain more residues than were originally referenced - we must
-    // then make a number of dataset sequence entries - this info is already stored 
-    jalview.bin.Cache.log.debug("TODO verify update of dataset sequence database references.");
+    // then make a number of dataset sequence entries - this info is already
+    // stored
+    jalview.bin.Cache.log
+            .debug("TODO verify update of dataset sequence database references.");
   }
 
   private void conflict()
   {
-    jalview.bin.Cache.log.debug("Conflict in dbentry update for "+dbref.getAccessionId()+dbref.getSource()+" "+dbref.getVorbaId());
+    jalview.bin.Cache.log.debug("Conflict in dbentry update for "
+            + dbref.getAccessionId() + dbref.getSource() + " "
+            + dbref.getVorbaId());
     // TODO Auto-generated method stub
-    
+
   }
+
   private void addFromDocument()
   {
     // add new dbref
-    sq.addDBRef(dbentry = new jalview.datamodel.DBRefEntry
-            (
-                    dbref.getSource().toString(),
-                 dbref.getVersion().toString(),
-                 dbref.getAccessionId().toString()));
-    if (dbref.getMapCount()>0)
+    sq.addDBRef(dbentry = new jalview.datamodel.DBRefEntry(dbref
+            .getSource().toString(), dbref.getVersion().toString(), dbref
+            .getAccessionId().toString()));
+    if (dbref.getMapCount() > 0)
     {
       // TODO: Jalview ignores all the other maps
-      if (dbref.getMapCount()>1)
+      if (dbref.getMapCount() > 1)
       {
-        jalview.bin.Cache.log.debug("Ignoring additional mappings on DbRef: "+dbentry.getSource()+":"+dbentry.getAccessionId());
+        jalview.bin.Cache.log
+                .debug("Ignoring additional mappings on DbRef: "
+                        + dbentry.getSource() + ":"
+                        + dbentry.getAccessionId());
       }
-      jalview.datamodel.Mapping mp = new jalview.datamodel.Mapping(parsemapType(dbref.getMap(0)));
+      jalview.datamodel.Mapping mp = new jalview.datamodel.Mapping(
+              parsemapType(dbref.getMap(0)));
       dbentry.setMap(mp);
     }
-    // TODO: jalview ignores links and properties because it doesn't know what to do with them.
-    
+    // TODO: jalview ignores links and properties because it doesn't know what
+    // to do with them.
+
     bindjvvobj(dbentry, dbref);
   }
+
   private void add()
   {
     DbRef dbref = new DbRef();
@@ -97,16 +137,19 @@ public class Dbref extends Rangetype
     dbref.setAccessionId(dbentry.getAccessionId());
     dbref.setSource(dbentry.getSource());
     dbref.setVersion(dbentry.getVersion());
-    if (dbentry.getMap()!=null)
+    if (dbentry.getMap() != null)
     {
       jalview.datamodel.Mapping mp = dbentry.getMap();
-      if (mp.getMap()!=null)
+      if (mp.getMap() != null)
       {
         Map vMap = new Map();
         initMapType(vMap, mp.getMap(), true);
         dbref.addMap(vMap);
-      } else {
-        jalview.bin.Cache.log.debug("Ignoring mapless DbRef.Map "+dbentry.getSrcAccString());
+      }
+      else
+      {
+        jalview.bin.Cache.log.debug("Ignoring mapless DbRef.Map "
+                + dbentry.getSrcAccString());
       }
     }
     sequence.addDbRef(dbref);
diff --git a/src/jalview/io/vamsas/LocalDocSyncObject.java b/src/jalview/io/vamsas/LocalDocSyncObject.java
index bfc2123..2c9eddc 100644
--- a/src/jalview/io/vamsas/LocalDocSyncObject.java
+++ b/src/jalview/io/vamsas/LocalDocSyncObject.java
@@ -1,80 +1,118 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.io.vamsas;
 
 import uk.ac.vamsas.client.Vobject;
 
 /**
- * Implement the basic logic for synchronising changes to or from the Vamsas Document
+ * Implement the basic logic for synchronising changes to or from the Vamsas
+ * Document
+ * 
  * @author JimP
  */
 public abstract class LocalDocSyncObject extends DatastoreItem
 {
   /**
    * 
-   * @return null or the local object that is being worked on. 
+   * @return null or the local object that is being worked on.
    */
   public abstract Object getLObject();
+
   /**
    * 
    * @return null or the document object that is being worked on
    */
   public abstract Vobject getVObject();
-  
+
   /**
    * endpoint for synchronize when all opreations are finished.
    */
   public abstract void nextObject();
+
   /**
-   * called if the local object can be safely updated from the bound document object.
+   * called if the local object can be safely updated from the bound document
+   * object.
    */
   public abstract void updateFromDoc();
+
   /**
-   * called if the associated document object can be safely updated with the local changes
+   * called if the associated document object can be safely updated with the
+   * local changes
    */
   public abstract void updateToDoc();
+
   /**
    * @return true if the local object is modified
    */
   public abstract boolean locallyModified();
+
   /**
    * 
    * @return true if the bound document object is modified
    */
   public abstract boolean documentModified();
+
   /**
    * 
-   * @return true if the document object is locked  w.r.t. this object's update.
+   * @return true if the document object is locked w.r.t. this object's update.
    */
   public abstract boolean documentObjectLocked();
+
   /**
    * 
-   * @return a new datastore item instance which binds the local object to a new document object 
+   * @return a new datastore item instance which binds the local object to a new
+   *         document object
    */
-  public abstract LocalDocSyncObject newDocumentObject(); // could make this constructor(Lobject)
+  public abstract LocalDocSyncObject newDocumentObject(); // could make this
+                                                          // constructor(Lobject)
+
   /**
    * 
-   * @return a new datastore item instance which binds the document object to a new local object. 
+   * @return a new datastore item instance which binds the document object to a
+   *         new local object.
    */
-  public abstract LocalDocSyncObject newLocalObject(); // make this constructor(Vobject)
+  public abstract LocalDocSyncObject newLocalObject(); // make this
+                                                        // constructor(Vobject)
+
   /**
    * apply the update/commit logic as defined in the vamsas paper
-   * @param documentIsUpdated true if a document update event is being handled  
+   * 
+   * @param documentIsUpdated
+   *                true if a document update event is being handled
    */
-  public void synchronize(boolean documentIsUpdated) {
+  public void synchronize(boolean documentIsUpdated)
+  {
     Object Lobject = getLObject();
     Vobject Vobject = getVObject();
-    if (Lobject==null)
+    if (Lobject == null)
     {
       // no local binding for document object
       newLocalObject().synchronize(documentIsUpdated);
       return;
     }
-    if (Vobject==null)
+    if (Vobject == null)
     {
       // no document binding for local object
       newDocumentObject().synchronize(documentIsUpdated);
     }
     // Check binding is valid
-    if (getjv2vObj(Lobject)!=Vobject)
+    if (getjv2vObj(Lobject) != Vobject)
     {
       // no local binding for document object
       newLocalObject().synchronize(documentIsUpdated);
diff --git a/src/jalview/io/vamsas/Rangetype.java b/src/jalview/io/vamsas/Rangetype.java
index b7e6f79..2686e85 100644
--- a/src/jalview/io/vamsas/Rangetype.java
+++ b/src/jalview/io/vamsas/Rangetype.java
@@ -1,6 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.io.vamsas;
 
-
 import java.util.Vector;
 
 import uk.ac.vamsas.objects.core.Local;
@@ -27,8 +44,9 @@ public class Rangetype extends DatastoreItem
 
   /**
    * get real bounds of a RangeType's specification. start and end are an
-   * inclusive range within which all segments and positions lie.
-   * TODO: refactor to vamsas utils
+   * inclusive range within which all segments and positions lie. TODO: refactor
+   * to vamsas utils
+   * 
    * @param dseta
    * @return int[] { start, end}
    */
@@ -39,7 +57,8 @@ public class Rangetype extends DatastoreItem
       int[] se = null;
       if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
       {
-        throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+        throw new Error(
+                "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
       }
       if (dseta.getSegCount() > 0)
       {
@@ -59,11 +78,11 @@ public class Rangetype extends DatastoreItem
       }
       if (dseta.getPosCount() > 0)
       {
-        // could do a polarity for pos range too. and pass back indication of discontinuities.
+        // could do a polarity for pos range too. and pass back indication of
+        // discontinuities.
         int pos = dseta.getPos(0).getI();
         se = new int[]
-            {
-            pos, pos};
+        { pos, pos };
         for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
         {
           pos = dseta.getPos(p).getI();
@@ -83,7 +102,9 @@ public class Rangetype extends DatastoreItem
   }
 
   /**
-   * map from a rangeType's internal frame to the referenced object's coordinate frame.
+   * map from a rangeType's internal frame to the referenced object's coordinate
+   * frame.
+   * 
    * @param dseta
    * @return int [] { ref(pos)...} for all pos in rangeType's frame.
    */
@@ -95,7 +116,8 @@ public class Rangetype extends DatastoreItem
       int[] se = null;
       if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
       {
-        throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+        throw new Error(
+                "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
       }
       if (dseta.getSegCount() > 0)
       {
@@ -112,7 +134,7 @@ public class Rangetype extends DatastoreItem
       else if (dseta.getPosCount() > 0)
       {
         int pos = dseta.getPos(0).getI();
-  
+
         for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
         {
           pos = dseta.getPos(p).getI();
@@ -125,7 +147,7 @@ public class Rangetype extends DatastoreItem
       int[] range = new int[posList.size()];
       for (int i = 0; i < range.length; i++)
       {
-        range[i] = ( (Integer) posList.elementAt(i)).intValue();
+        range[i] = ((Integer) posList.elementAt(i)).intValue();
       }
       posList.clear();
       return range;
@@ -135,14 +157,15 @@ public class Rangetype extends DatastoreItem
 
   protected int[] getIntervals(RangeType range)
   {
-    int[] intervals=null;
+    int[] intervals = null;
     Vector posList = new Vector();
     if (range != null)
     {
       int[] se = null;
       if (range.getSegCount() > 0 && range.getPosCount() > 0)
       {
-        throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+        throw new Error(
+                "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
       }
       if (range.getSegCount() > 0)
       {
@@ -156,7 +179,7 @@ public class Rangetype extends DatastoreItem
       else if (range.getPosCount() > 0)
       {
         int pos = range.getPos(0).getI();
-  
+
         for (int p = 0, pSize = range.getPosCount(); p < pSize; p++)
         {
           pos = range.getPos(p).getI();
@@ -167,28 +190,30 @@ public class Rangetype extends DatastoreItem
     }
     if (posList != null && posList.size() > 0)
     {
-      intervals=new int[posList.size()];
+      intervals = new int[posList.size()];
       java.util.Enumeration e = posList.elements();
-      int i=0;
+      int i = 0;
       while (e.hasMoreElements())
       {
-        intervals[i++] = ((Integer)e.nextElement()).intValue();
+        intervals[i++] = ((Integer) e.nextElement()).intValue();
       }
     }
     return intervals;
   }
+
   /**
    * initialise a range type object from a set of start/end inclusive intervals
+   * 
    * @param mrt
    * @param range
    */
   protected void initRangeType(RangeType mrt, int[] range)
   {
-    for (int i=0; i<range.length; i+=2)
+    for (int i = 0; i < range.length; i += 2)
     {
       Seg vSeg = new Seg();
       vSeg.setStart(range[i]);
-      vSeg.setEnd(range[i+1]);
+      vSeg.setEnd(range[i + 1]);
       vSeg.setInclusive(true);
       mrt.addSeg(vSeg);
     }
@@ -196,75 +221,97 @@ public class Rangetype extends DatastoreItem
 
   /**
    * 
-   * @param maprange where the from range is the local mapped range, and the to range is the 'mapped' range in the MapRangeType
-   * @param default unit for local
-   * @param default unit for mapped
+   * @param maprange
+   *                where the from range is the local mapped range, and the to
+   *                range is the 'mapped' range in the MapRangeType
+   * @param default
+   *                unit for local
+   * @param default
+   *                unit for mapped
    * @return MapList
    */
-  protected jalview.util.MapList parsemapType(MapType maprange, int localu, int mappedu)
+  protected jalview.util.MapList parsemapType(MapType maprange, int localu,
+          int mappedu)
   {
     jalview.util.MapList ml = null;
     int[] localRange = getIntervals(maprange.getLocal());
     int[] mappedRange = getIntervals(maprange.getMapped());
-    long lu = maprange.getLocal().hasUnit() ? maprange.getLocal().getUnit() : localu;
-    long mu = maprange.getMapped().hasUnit() ? maprange.getMapped().getUnit() : mappedu;
-    ml = new jalview.util.MapList(localRange, mappedRange, (int)lu, (int)mu);
+    long lu = maprange.getLocal().hasUnit() ? maprange.getLocal().getUnit()
+            : localu;
+    long mu = maprange.getMapped().hasUnit() ? maprange.getMapped()
+            .getUnit() : mappedu;
+    ml = new jalview.util.MapList(localRange, mappedRange, (int) lu,
+            (int) mu);
     return ml;
   }
+
   protected jalview.util.MapList parsemapType(MapType map)
   {
     if (!map.getLocal().hasUnit() || map.getMapped().hasUnit())
     {
-      jalview.bin.Cache.log.warn("using default mapping length of 1:1 for map "
-              +(map.isRegistered() ? map.getVorbaId().toString() : ("<no Id registered> "+map.toString())));
+      jalview.bin.Cache.log
+              .warn("using default mapping length of 1:1 for map "
+                      + (map.isRegistered() ? map.getVorbaId().toString()
+                              : ("<no Id registered> " + map.toString())));
     }
-    return parsemapType(map, 1, 1); 
+    return parsemapType(map, 1, 1);
   }
 
   /**
    * initialise a MapType object from a MapList object.
+   * 
    * @param maprange
    * @param ml
    * @param setUnits
    */
-  protected void initMapType(MapType maprange, jalview.util.MapList ml, boolean setUnits)
+  protected void initMapType(MapType maprange, jalview.util.MapList ml,
+          boolean setUnits)
   {
     initMapType(maprange, ml, setUnits, false);
   }
+
   /**
    * 
    * @param maprange
    * @param ml
    * @param setUnits
-   * @param reverse - reverse MapList mapping for Local and Mapped ranges and units 
+   * @param reverse -
+   *                reverse MapList mapping for Local and Mapped ranges and
+   *                units
    */
-  protected void initMapType(MapType maprange, jalview.util.MapList ml, boolean setUnits, boolean reverse)
+  protected void initMapType(MapType maprange, jalview.util.MapList ml,
+          boolean setUnits, boolean reverse)
   {
-    if (ml==null)
+    if (ml == null)
     {
-      throw new Error("Implementation error. MapList is null for initMapType.");
+      throw new Error(
+              "Implementation error. MapList is null for initMapType.");
     }
     maprange.setLocal(new Local());
     maprange.setMapped(new Mapped());
     if (!reverse)
-      {
+    {
       initRangeType(maprange.getLocal(), ml.getFromRanges());
       initRangeType(maprange.getMapped(), ml.getToRanges());
-      } else {
-        initRangeType(maprange.getLocal(), ml.getToRanges());
-        initRangeType(maprange.getMapped(), ml.getFromRanges());
-      }
+    }
+    else
+    {
+      initRangeType(maprange.getLocal(), ml.getToRanges());
+      initRangeType(maprange.getMapped(), ml.getFromRanges());
+    }
     if (setUnits)
     {
       if (!reverse)
-      { 
+      {
         maprange.getLocal().setUnit(ml.getFromRatio());
         maprange.getMapped().setUnit(ml.getToRatio());
-      } else {
+      }
+      else
+      {
         maprange.getLocal().setUnit(ml.getToRatio());
         maprange.getMapped().setUnit(ml.getFromRatio());
       }
     }
   }
 
-}
\ No newline at end of file
+}
diff --git a/src/jalview/io/vamsas/Sequencemapping.java b/src/jalview/io/vamsas/Sequencemapping.java
index 8c73992..de4a01e 100644
--- a/src/jalview/io/vamsas/Sequencemapping.java
+++ b/src/jalview/io/vamsas/Sequencemapping.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.io.vamsas;
 
 import java.util.Vector;
@@ -18,20 +36,24 @@ import uk.ac.vamsas.objects.core.SequenceType;
 
 public class Sequencemapping extends Rangetype
 {
-  public Sequencemapping(VamsasAppDatastore datastore, SequenceMapping sequenceMapping)
+  public Sequencemapping(VamsasAppDatastore datastore,
+          SequenceMapping sequenceMapping)
   {
     super(datastore);
     Object mjvmapping = getvObj2jv(sequenceMapping);
-    if (mjvmapping==null)
+    if (mjvmapping == null)
     {
       add(sequenceMapping);
-    } else {
+    }
+    else
+    {
       if (sequenceMapping.isUpdated())
       {
         update((jalview.util.MapList) mjvmapping, sequenceMapping);
       }
     }
   }
+
   /**
    * create or update a vamsas sequence mapping corresponding to a jalview
    * Mapping between two dataset sequences
@@ -41,96 +63,121 @@ public class Sequencemapping extends Rangetype
    * @param from
    * @param ds
    */
-  public Sequencemapping(VamsasAppDatastore datastore, jalview.datamodel.Mapping mjvmapping, uk.ac.vamsas.objects.core.SequenceType from, uk.ac.vamsas.objects.core.DataSet ds)
+  public Sequencemapping(VamsasAppDatastore datastore,
+          jalview.datamodel.Mapping mjvmapping,
+          uk.ac.vamsas.objects.core.SequenceType from,
+          uk.ac.vamsas.objects.core.DataSet ds)
   {
     super(datastore);
     SequenceMapping sequenceMapping = (SequenceMapping) getjv2vObj(mjvmapping);
-    if (sequenceMapping==null)
+    if (sequenceMapping == null)
     {
       add(mjvmapping, from, ds);
-    } else {
-      if (from!=null && sequenceMapping.getLoc()!=from)
+    }
+    else
+    {
+      if (from != null && sequenceMapping.getLoc() != from)
       {
-        jalview.bin.Cache.log.warn("Probable IMPLEMENTATION ERROR: "+from+" doesn't match the local mapping sequence.");
+        jalview.bin.Cache.log.warn("Probable IMPLEMENTATION ERROR: " + from
+                + " doesn't match the local mapping sequence.");
       }
-      if (ds!=null && sequenceMapping.is__stored_in_document() && sequenceMapping.getV_parent()!=ds)
+      if (ds != null && sequenceMapping.is__stored_in_document()
+              && sequenceMapping.getV_parent() != ds)
       {
-        jalview.bin.Cache.log.warn("Probable IMPLEMENTATION ERROR: "+ds+" doesn't match the parent of the bound sequence mapping object.");
+        jalview.bin.Cache.log
+                .warn("Probable IMPLEMENTATION ERROR: "
+                        + ds
+                        + " doesn't match the parent of the bound sequence mapping object.");
       }
       if (sequenceMapping.isUpdated())
-      { 
+      {
         conflict(mjvmapping, sequenceMapping);
-      } else {
+      }
+      else
+      {
         update(mjvmapping, sequenceMapping);
       }
     }
   }
+
   private void conflict(Mapping mjvmapping, SequenceMapping sequenceMapping)
   {
-    System.err.println("Conflict in update of sequenceMapping "+sequenceMapping.getVorbaId());
+    System.err.println("Conflict in update of sequenceMapping "
+            + sequenceMapping.getVorbaId());
   }
-  private void add(Mapping mjvmapping, uk.ac.vamsas.objects.core.SequenceType from, DataSet ds)
+
+  private void add(Mapping mjvmapping,
+          uk.ac.vamsas.objects.core.SequenceType from, DataSet ds)
   {
     SequenceI jvto = mjvmapping.getTo();
-    while (jvto.getDatasetSequence()!=null)
+    while (jvto.getDatasetSequence() != null)
     {
       jvto = jvto.getDatasetSequence();
     }
     SequenceType to = (SequenceType) getjv2vObj(jvto);
-    if (to==null)
+    if (to == null)
     {
-      jalview.bin.Cache.log.warn("NONFATAL - do a second update: Ignoring Forward Reference to seuqence not yet bound to vamsas seuqence object");
+      jalview.bin.Cache.log
+              .warn("NONFATAL - do a second update: Ignoring Forward Reference to seuqence not yet bound to vamsas seuqence object");
       return;
-    } 
+    }
     SequenceMapping sequenceMapping = new SequenceMapping();
     sequenceMapping.setLoc(from);
     sequenceMapping.setMap(to);
-    boolean dnaToProt=false,sense=false;
+    boolean dnaToProt = false, sense = false;
     // ensure that we create a mapping with the correct sense
-    if (((Sequence) sequenceMapping.getLoc())
-            .getDictionary()
-            .equals(uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
+    if (((Sequence) sequenceMapping.getLoc()).getDictionary().equals(
+            uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
     {
-      if (((Sequence) sequenceMapping.getMap())
-              .getDictionary()
-              .equals(uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA))
+      if (((Sequence) sequenceMapping.getMap()).getDictionary().equals(
+              uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA))
       {
-        dnaToProt=true;
-        sense=true;
-      } 
-    } else {
-      if (((Sequence) sequenceMapping.getMap())
-              .getDictionary()
-              .equals(uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
+        dnaToProt = true;
+        sense = true;
+      }
+    }
+    else
+    {
+      if (((Sequence) sequenceMapping.getMap()).getDictionary().equals(
+              uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
       {
-        dnaToProt=true;
-        sense=false;
-      } 
+        dnaToProt = true;
+        sense = false;
+      }
     }
 
     if (!dnaToProt)
     {
-      jalview.bin.Cache.log.warn("Ignoring Mapping - don't support protein to protein mapping in vamsas document yet.");
+      jalview.bin.Cache.log
+              .warn("Ignoring Mapping - don't support protein to protein mapping in vamsas document yet.");
       return;
     }
-    if (ds==null)
+    if (ds == null)
     {
       // locate dataset for storage of SequenceMapping
       if (sense)
       {
-        ds = (DataSet) ((uk.ac.vamsas.client.Vobject) sequenceMapping.getLoc()).getV_parent();
-      } else {
-        ds = (DataSet) ((uk.ac.vamsas.client.Vobject) sequenceMapping.getMap()).getV_parent();
-      } 
+        ds = (DataSet) ((uk.ac.vamsas.client.Vobject) sequenceMapping
+                .getLoc()).getV_parent();
+      }
+      else
+      {
+        ds = (DataSet) ((uk.ac.vamsas.client.Vobject) sequenceMapping
+                .getMap()).getV_parent();
+      }
     }
     if (sense)
     {
       this.initMapType(sequenceMapping, mjvmapping.getMap(), true);
-    } else {
-      this.initMapType(sequenceMapping, mjvmapping.getMap().getInverse(), true);
+    }
+    else
+    {
+      this.initMapType(sequenceMapping, mjvmapping.getMap().getInverse(),
+              true);
     }
     ds.addSequenceMapping(sequenceMapping);
-    sequenceMapping.setProvenance(this.dummyProvenance("user defined coding region translation")); // TODO:
+    sequenceMapping.setProvenance(this
+            .dummyProvenance("user defined coding region translation")); // TODO:
     // correctly
     // construct
     // provenance
@@ -141,16 +188,24 @@ public class Sequencemapping extends Rangetype
     // mapping
     bindjvvobj(mjvmapping, sequenceMapping);
 
-    jalview.bin.Cache.log.debug("Successfully created mapping "+sequenceMapping.getVorbaId());
+    jalview.bin.Cache.log.debug("Successfully created mapping "
+            + sequenceMapping.getVorbaId());
   }
-  private void update(jalview.util.MapList mjvmapping, SequenceMapping sequenceMapping)
+
+  private void update(jalview.util.MapList mjvmapping,
+          SequenceMapping sequenceMapping)
   {
-    jalview.bin.Cache.log.error("Not implemented: Jalview Update Alcodon Mapping:TODO!"); 
+    jalview.bin.Cache.log
+            .error("Not implemented: Jalview Update Alcodon Mapping:TODO!");
   }
-  private void update(jalview.datamodel.Mapping mjvmapping, SequenceMapping sequenceMapping)
+
+  private void update(jalview.datamodel.Mapping mjvmapping,
+          SequenceMapping sequenceMapping)
   {
-    jalview.bin.Cache.log.error("Not implemented: Jalview Update Sequence DBRef Mapping"); 
+    jalview.bin.Cache.log
+            .error("Not implemented: Jalview Update Sequence DBRef Mapping");
   }
+
   /**
    * limitations: Currently, jalview only deals with mappings between dataset
    * sequences, and even then, only between those that map from DNA to Protein.
@@ -160,22 +215,28 @@ public class Sequencemapping extends Rangetype
   private void add(SequenceMapping sequenceMapping)
   {
     Object mobj;
-    SequenceI from=null,to=null;
-    boolean dnaToProt=false,sense=false;
-    Sequence sdloc=null, sdmap=null;
+    SequenceI from = null, to = null;
+    boolean dnaToProt = false, sense = false;
+    Sequence sdloc = null, sdmap = null;
     if (sequenceMapping.getLoc() instanceof AlignmentSequence)
     {
-      sdloc = (Sequence) ((AlignmentSequence) sequenceMapping.getLoc()).getRefid();
-    } else {
+      sdloc = (Sequence) ((AlignmentSequence) sequenceMapping.getLoc())
+              .getRefid();
+    }
+    else
+    {
       sdloc = ((Sequence) sequenceMapping.getLoc());
     }
     if (sequenceMapping.getMap() instanceof AlignmentSequence)
     {
-      sdmap = (Sequence) ((AlignmentSequence) sequenceMapping.getMap()).getRefid();
-    } else {
+      sdmap = (Sequence) ((AlignmentSequence) sequenceMapping.getMap())
+              .getRefid();
+    }
+    else
+    {
       sdmap = ((Sequence) sequenceMapping.getMap());
     }
-    if (sdloc==null || sdmap == null)
+    if (sdloc == null || sdmap == null)
     {
       jalview.bin.Cache.log.info("Ignoring non sequence-sequence mapping");
       return;
@@ -193,135 +254,163 @@ public class Sequencemapping extends Rangetype
     if (from == null || to == null)
     {
 
-      jalview.bin.Cache.log.error("Probable Vamsas implementation error : unbound dataset sequences involved in a mapping are being parsed!");
+      jalview.bin.Cache.log
+              .error("Probable Vamsas implementation error : unbound dataset sequences involved in a mapping are being parsed!");
       return;
-    } 
+    }
 
-    if (sdloc.getDictionary()
-            .equals(uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
+    if (sdloc.getDictionary().equals(
+            uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
     {
-      if (sdmap.getDictionary()
-              .equals(uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA))
+      if (sdmap.getDictionary().equals(
+              uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA))
       {
-        dnaToProt=true;
-        sense=true;
-      } 
+        dnaToProt = true;
+        sense = true;
+      }
       // else {
 
       // }
-    } else {
-      if (sdmap.getDictionary()
-              .equals(uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
+    }
+    else
+    {
+      if (sdmap.getDictionary().equals(
+              uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
       {
-        dnaToProt=true;
-        sense=false;
-      } 
+        dnaToProt = true;
+        sense = false;
+      }
     }
     // create mapping storage object and make each dataset alignment reference
     // it.
-    jalview.datamodel.AlignmentI dsLoc = (jalview.datamodel.AlignmentI) getvObj2jv(sdloc.getV_parent());
-    jalview.datamodel.AlignmentI dsMap = (jalview.datamodel.AlignmentI) getvObj2jv(sdmap.getV_parent());
+    jalview.datamodel.AlignmentI dsLoc = (jalview.datamodel.AlignmentI) getvObj2jv(sdloc
+            .getV_parent());
+    jalview.datamodel.AlignmentI dsMap = (jalview.datamodel.AlignmentI) getvObj2jv(sdmap
+            .getV_parent());
     AlignedCodonFrame afc = new AlignedCodonFrame(0);
 
-    if (dsLoc!=null && dsLoc!=dsMap)
+    if (dsLoc != null && dsLoc != dsMap)
     {
       dsLoc.addCodonFrame(afc);
     }
-    if (dsMap!=null)
+    if (dsMap != null)
     {
       dsMap.addCodonFrame(afc);
     }
     // create and add the new mapping to (each) dataset's codonFrame
 
-    jalview.util.MapList mapping = null; 
+    jalview.util.MapList mapping = null;
     if (!sense)
     {
       mapping = this.parsemapType(sequenceMapping, 1, 3); // invert sense
-      mapping = new jalview.util.MapList(mapping.getToRanges(), mapping.getFromRanges(), mapping.getToRatio(), mapping.getFromRatio());
+      mapping = new jalview.util.MapList(mapping.getToRanges(), mapping
+              .getFromRanges(), mapping.getToRatio(), mapping
+              .getFromRatio());
       afc.addMap(to, from, mapping);
-    } else {
+    }
+    else
+    {
       mapping = this.parsemapType(sequenceMapping, 3, 1); // correct sense
       afc.addMap(from, to, mapping);
     }
     bindjvvobj(mapping, sequenceMapping);
-    jalview.structure.StructureSelectionManager.getStructureSelectionManager().addMappings(new AlignedCodonFrame[] { afc });
+    jalview.structure.StructureSelectionManager
+            .getStructureSelectionManager().addMappings(
+                    new AlignedCodonFrame[]
+                    { afc });
     // Try to link up any conjugate database references in the two sequences
-    // matchConjugateDBRefs(from, to,  mapping);
+    // matchConjugateDBRefs(from, to, mapping);
     // Try to propagate any dbrefs across this mapping.
 
   }
+
   /**
-   * Complete any 'to' references in jalview.datamodel.Mapping objects associated with conjugate DBRefEntry under given mapping  
-   * @param from sequence corresponding to from reference for sequence mapping
-   * @param to sequence correspondeing to to reference for sequence mapping
-   * @param smap maplist parsed in same sense as from and to
+   * Complete any 'to' references in jalview.datamodel.Mapping objects
+   * associated with conjugate DBRefEntry under given mapping
+   * 
+   * @param from
+   *                sequence corresponding to from reference for sequence
+   *                mapping
+   * @param to
+   *                sequence correspondeing to to reference for sequence mapping
+   * @param smap
+   *                maplist parsed in same sense as from and to
    */
   private void matchConjugateDBRefs(SequenceI from, SequenceI to,
           jalview.util.MapList smap)
   {
-    if (from.getDBRef()==null && to.getDBRef()==null)
+    if (from.getDBRef() == null && to.getDBRef() == null)
     {
       if (jalview.bin.Cache.log.isDebugEnabled())
       {
-        jalview.bin.Cache.log.debug("Not matching conjugate refs for "+from.getName()+" and "+to.getName());
+        jalview.bin.Cache.log.debug("Not matching conjugate refs for "
+                + from.getName() + " and " + to.getName());
       }
-      return; 
+      return;
     }
     if (jalview.bin.Cache.log.isDebugEnabled())
     {
-      jalview.bin.Cache.log.debug("Matching conjugate refs for "+from.getName()+" and "+to.getName());
+      jalview.bin.Cache.log.debug("Matching conjugate refs for "
+              + from.getName() + " and " + to.getName());
     }
     jalview.datamodel.DBRefEntry[] fdb = from.getDBRef();
-    jalview.datamodel.DBRefEntry[] tdb = new jalview.datamodel.DBRefEntry[to.getDBRef().length];
+    jalview.datamodel.DBRefEntry[] tdb = new jalview.datamodel.DBRefEntry[to
+            .getDBRef().length];
     int tdblen = to.getDBRef().length;
     System.arraycopy(to.getDBRef(), 0, tdb, 0, tdblen);
     Vector matched = new Vector();
     jalview.util.MapList smapI = smap.getInverse();
-    for (int f=0;f<fdb.length; f++)
+    for (int f = 0; f < fdb.length; f++)
     {
       jalview.datamodel.DBRefEntry fe = fdb[f];
       jalview.datamodel.Mapping fmp = fe.getMap();
-      boolean fmpnnl = fmp!=null;
+      boolean fmpnnl = fmp != null;
       // if (fmpnnl && fmp.getTo()!=null)
-      //{
-      //  jalview.bin.Cache.log.debug("Not overwriting existing To reference in "+fe);
-      //  continue;
-      //}
+      // {
+      // jalview.bin.Cache.log.debug("Not overwriting existing To reference in
+      // "+fe);
+      // continue;
+      // }
       // smap from maps from fe.local to fe.map
-      boolean smapfromlocal2fe = (fmpnnl) ? smap.equals(fmp.getMap()) : false;
+      boolean smapfromlocal2fe = (fmpnnl) ? smap.equals(fmp.getMap())
+              : false;
       // smap from maps from fe.map to fe.local.
-      boolean smapfromfemap2local = (fmpnnl) ? smapI.equals(fmp.getMap()) : false;
-      for (int t=0; t<tdblen; t++)
+      boolean smapfromfemap2local = (fmpnnl) ? smapI.equals(fmp.getMap())
+              : false;
+      for (int t = 0; t < tdblen; t++)
       {
         jalview.datamodel.DBRefEntry te = tdb[t];
-        if (te!=null)
+        if (te != null)
         {
           if (fe.getSource().equals(te.getSource())
-              && fe.getAccessionId().equals(te.getAccessionId()))
+                  && fe.getAccessionId().equals(te.getAccessionId()))
           {
             jalview.datamodel.Mapping tmp = te.getMap();
-            boolean tmpnnl = tmp!=null;
-            if (tmpnnl && tmp.getTo()!=null)
+            boolean tmpnnl = tmp != null;
+            if (tmpnnl && tmp.getTo() != null)
             {
-              
+
             }
             // smap to maps from te.local to te.map
-            boolean smaptolocal2tm = (tmpnnl) ? smap.equals(tmp.getMap()) : false;
+            boolean smaptolocal2tm = (tmpnnl) ? smap.equals(tmp.getMap())
+                    : false;
             // smap to maps from te.map to te.local
-            boolean smaptotemap2local = (tmpnnl) ? smapI.equals(fmp.getMap()) : false;
+            boolean smaptotemap2local = (tmpnnl) ? smapI.equals(fmp
+                    .getMap()) : false;
             if (smapfromlocal2fe && smaptotemap2local)
             {
               // smap implies mapping from to to from
               fmp.setTo(to);
               tmp.setTo(from);
-            } else 
-              if (smapfromfemap2local && smaptolocal2tm) {
-                fmp.setTo(to);
-              }
             }
-            
+            else if (smapfromfemap2local && smaptolocal2tm)
+            {
+              fmp.setTo(to);
+            }
+          }
+
         }
       }
     }
-    }
-}
\ No newline at end of file
+  }
+}
diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java
index eb4af4a..fd9294b 100644
--- a/src/jalview/io/vamsas/Tree.java
+++ b/src/jalview/io/vamsas/Tree.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.io.vamsas;
 
 import java.io.IOException;
@@ -168,7 +186,7 @@ public class Tree extends DatastoreItem
       prov.getEntry(0).getParam(0).setName("treeType");
       prov.getEntry(0).getParam(0).setType("utf8");
       prov.getEntry(0).getParam(0).setContent("NJ"); // TODO: type of tree is a
-                                                      // general parameter
+      // general parameter
       int ranges[] = tp.getTree().seqData.getVisibleContigs();
       // VisibleContigs are with respect to alignment coordinates. Still need
       // offsets
@@ -226,21 +244,23 @@ public class Tree extends DatastoreItem
    * 
    * Update jalview newick representation with TreeNode map
    * 
-   * @param tp the treepanel that this tree is bound to.
+   * @param tp
+   *                the treepanel that this tree is bound to.
    */
   public void UpdateSequenceTreeMap(TreePanel tp)
   {
     if (tp == null || tree == null)
       return;
     Vector leaves = new Vector();
-    if (tp.getTree()==null)
+    if (tp.getTree() == null)
     {
-      Cache.log.warn("Not updating SequenceTreeMap for "+tree.getVorbaId());
+      Cache.log.warn("Not updating SequenceTreeMap for "
+              + tree.getVorbaId());
       return;
     }
     tp.getTree().findLeaves(tp.getTree().getTopNode(), leaves);
     Treenode[] tn = tree.getTreenode(); // todo: select nodes for this
-                                        // particular tree
+    // particular tree
     int sz = tn.length;
     int i = 0;
 
@@ -292,7 +312,7 @@ public class Tree extends DatastoreItem
    * construct treenode mappings for mapped sequences
    * 
    * @param ntree
-   * @param newick 
+   * @param newick
    * @return
    */
   public Treenode[] makeTreeNodes(NJTree ntree, Newick newick)
@@ -430,7 +450,7 @@ public class Tree extends DatastoreItem
    * referenced in input data has already been associated with jalview objects.
    * 
    * @param tp
-   * @param alignFrame 
+   * @param alignFrame
    * @return Object[] { AlignmentView, AlignmentI - reference alignment for
    *         input }
    */
@@ -454,7 +474,8 @@ public class Tree extends DatastoreItem
         // is this the whole alignment or a specific set of sequences ?
         if (vInput.getObjRefCount() == 0)
         {
-          if (tree.getV_parent()!=null && tree.getV_parent() instanceof uk.ac.vamsas.objects.core.Alignment)
+          if (tree.getV_parent() != null
+                  && tree.getV_parent() instanceof uk.ac.vamsas.objects.core.Alignment)
           {
             javport = getViewport(tree.getV_parent());
             jal = javport.getAlignment();
@@ -475,7 +496,8 @@ public class Tree extends DatastoreItem
           else if (vInput.getObjRef(0) instanceof uk.ac.vamsas.objects.core.AlignmentSequence)
           {
             // recover an AlignmentView for the input data
-            javport = getViewport(((Vobject) vInput.getObjRef(0)).getV_parent());
+            javport = getViewport(((Vobject) vInput.getObjRef(0))
+                    .getV_parent());
             jal = javport.getAlignment();
             jalview.datamodel.SequenceI[] seqs = new jalview.datamodel.SequenceI[vInput
                     .getObjRefCount()];
@@ -557,7 +579,7 @@ public class Tree extends DatastoreItem
   {
     try
     {
-      if (ntree==null)
+      if (ntree == null)
       {
         return false;
       }
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 1bc0b72..a12a74f 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -26,131 +26,250 @@ import javax.swing.event.*;
 
 import jalview.schemes.*;
 
-public class GAlignFrame
-    extends JInternalFrame
+public class GAlignFrame extends JInternalFrame
 {
   protected JMenuBar alignFrameMenuBar = new JMenuBar();
+
   protected JMenu fileMenu = new JMenu();
+
   protected JMenuItem closeMenuItem = new JMenuItem();
+
   protected JMenu editMenu = new JMenu();
+
   protected JMenu viewMenu = new JMenu();
+
   protected JMenu colourMenu = new JMenu();
+
   protected JMenu calculateMenu = new JMenu();
+
   protected JMenu webService = new JMenu();
+
   protected JMenuItem webServiceNoServices;
+
   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
+
   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
+
   protected JMenuItem invertSequenceMenuItem = new JMenuItem();
+
   protected JMenuItem remove2LeftMenuItem = new JMenuItem();
+
   protected JMenuItem remove2RightMenuItem = new JMenuItem();
+
   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
+
   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
+
   public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
+
   public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
+
   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
+
   protected JMenuItem sortIDMenuItem = new JMenuItem();
+
   protected JMenuItem sortGroupMenuItem = new JMenuItem();
+
   protected JMenu sortByAnnotScore = new JMenu();
+
   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
+
   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
+
   protected JMenuItem PCAMenuItem = new JMenuItem();
+
   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
+
   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
+
   BorderLayout borderLayout1 = new BorderLayout();
+
   public JLabel statusBar = new JLabel();
+
   protected JMenuItem saveAs = new JMenuItem();
+
   protected JMenu outputTextboxMenu = new JMenu();
+
   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
+
   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
+
   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
-  protected JRadioButtonMenuItem hydrophobicityColour = new
-      JRadioButtonMenuItem();
+
+  protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
+
   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
+
   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
+
   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
+
   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
+
   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
+
   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
+
   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
+
   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
+
   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
+
   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
+
   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
+
   JMenuItem htmlMenuItem = new JMenuItem();
+
   JMenuItem overviewMenuItem = new JMenuItem();
+
   protected JMenuItem undoMenuItem = new JMenuItem();
+
   protected JMenuItem redoMenuItem = new JMenuItem();
+
   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+
   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
+
   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
+
   JMenuItem printMenuItem = new JMenuItem();
+
   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
+
   JMenuItem findMenuItem = new JMenuItem();
+
   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
+
   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
+
   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
+
   JMenuItem deleteGroups = new JMenuItem();
+
   JMenuItem delete = new JMenuItem();
+
   JMenuItem copy = new JMenuItem();
+
   JMenuItem cut = new JMenuItem();
+
   JMenu pasteMenu = new JMenu();
+
   JMenuItem pasteNew = new JMenuItem();
+
   JMenuItem pasteThis = new JMenuItem();
+
   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
+
   JMenuItem createPNG = new JMenuItem();
+
   protected JMenuItem font = new JMenuItem();
+
   public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
+
   JMenuItem epsFile = new JMenuItem();
+
   JMenuItem LoadtreeMenuItem = new JMenuItem();
+
   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
+
   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
+
   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
+
   protected JMenuItem modifyPID = new JMenuItem();
+
   protected JMenuItem modifyConservation = new JMenuItem();
+
   protected JMenu sortByTreeMenu = new JMenu();
+
   protected JMenu sort = new JMenu();
+
   JMenu calculate = new JMenu();
+
   JMenu jMenu2 = new JMenu();
+
   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
+
   protected ButtonGroup colours = new ButtonGroup();
+
   JMenuItem vamsasStore = new JMenuItem();
+
   protected JMenuItem showTranslation = new JMenuItem();
+
   protected JMenuItem extractScores = new JMenuItem();
+
   protected JMenu showProducts = new JMenu();
+
   public JMenuItem featureSettings = new JMenuItem();
+
   JMenuItem fetchSequence = new JMenuItem();
+
   JMenuItem annotationColour = new JMenuItem();
+
   JMenuItem associatedData = new JMenuItem();
+
   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
+
   JMenu addSequenceMenu = new JMenu();
+
   JMenuItem addFromFile = new JMenuItem();
+
   JMenuItem addFromText = new JMenuItem();
+
   JMenuItem addFromURL = new JMenuItem();
+
   JMenuItem exportAnnotations = new JMenuItem();
+
   JMenuItem exportFeatures = new JMenuItem();
+
   protected JPanel statusPanel = new JPanel();
+
   GridLayout gridLayout1 = new GridLayout();
+
   JMenu jMenu3 = new JMenu();
+
   JMenuItem showAllSeqs = new JMenuItem();
+
   JMenuItem showAllColumns = new JMenuItem();
+
   JMenu hideMenu = new JMenu();
+
   JMenuItem hideSelSequences = new JMenuItem();
+
   JMenuItem hideSelColumns = new JMenuItem();
+
   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
+
   JMenuItem invertColSel = new JMenuItem();
+
   protected JTabbedPane tabbedPane = new JTabbedPane();
+
   JMenuItem save = new JMenuItem();
+
   protected JMenuItem reload = new JMenuItem();
+
   JMenuItem newView = new JMenuItem();
+
   JMenuItem textColour = new JMenuItem();
+
   JMenu formatMenu = new JMenu();
+
   JMenu selectMenu = new JMenu();
+
   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
+
   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
+
   protected JMenuItem gatherViews = new JMenuItem();
+
   protected JMenuItem expandViews = new JMenuItem();
+
   JMenuItem pageSetup = new JMenuItem();
+
   JMenuItem alignmentProperties = new JMenuItem();
+
   public GAlignFrame()
   {
     try
@@ -161,8 +280,8 @@ public class GAlignFrame
       // dynamically fill save as menu with available formats
       for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
       {
-        JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.
-                                       WRITEABLE_FORMATS[i]);
+        JMenuItem item = new JMenuItem(
+                jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 
         item.addActionListener(new java.awt.event.ActionListener()
         {
@@ -174,8 +293,7 @@ public class GAlignFrame
 
         outputTextboxMenu.add(item);
       }
-    }
-    catch (Exception e)
+    } catch (Exception e)
     {
     }
 
@@ -193,32 +311,33 @@ public class GAlignFrame
 
     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
     {
-      java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
-          getUserColourSchemes().keys();
+      java.util.Enumeration userColours = jalview.gui.UserDefinedColours
+              .getUserColourSchemes().keys();
 
       while (userColours.hasMoreElements())
       {
         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
-            userColours.
-            nextElement().toString());
+                userColours.nextElement().toString());
         radioItem.setName("USER_DEFINED");
         radioItem.addMouseListener(new MouseAdapter()
         {
           public void mousePressed(MouseEvent evt)
           {
-            if (evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
+            if (evt.isControlDown()
+                    || SwingUtilities.isRightMouseButton(evt))
             {
-              radioItem.removeActionListener(radioItem.getActionListeners()[0]);
-
-              int option = JOptionPane.showInternalConfirmDialog(jalview.gui.
-                  Desktop.desktop,
-                  "Remove from default list?",
-                  "Remove user defined colour",
-                  JOptionPane.YES_NO_OPTION);
+              radioItem
+                      .removeActionListener(radioItem.getActionListeners()[0]);
+
+              int option = JOptionPane.showInternalConfirmDialog(
+                      jalview.gui.Desktop.desktop,
+                      "Remove from default list?",
+                      "Remove user defined colour",
+                      JOptionPane.YES_NO_OPTION);
               if (option == JOptionPane.YES_OPTION)
               {
-                jalview.gui.UserDefinedColours.removeColourFromDefaults(
-                    radioItem.getText());
+                jalview.gui.UserDefinedColours
+                        .removeColourFromDefaults(radioItem.getText());
                 colourMenu.remove(radioItem);
               }
               else
@@ -259,7 +378,8 @@ public class GAlignFrame
     colours.add(BLOSUM62Colour);
     colours.add(nucleotideColour);
 
-    setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
+    setColourSelected(jalview.bin.Cache
+            .getDefault("DEFAULT_COLOUR", "None"));
 
   }
 
@@ -268,85 +388,85 @@ public class GAlignFrame
 
     if (defaultColour != null)
     {
-      int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
+      int index = ColourSchemeProperty
+              .getColourIndexFromName(defaultColour);
 
       switch (index)
       {
-        case ColourSchemeProperty.NONE:
-          noColourmenuItem.setSelected(true);
-          break;
-        case ColourSchemeProperty.CLUSTAL:
-          clustalColour.setSelected(true);
+      case ColourSchemeProperty.NONE:
+        noColourmenuItem.setSelected(true);
+        break;
+      case ColourSchemeProperty.CLUSTAL:
+        clustalColour.setSelected(true);
 
-          break;
+        break;
 
-        case ColourSchemeProperty.BLOSUM:
-          BLOSUM62Colour.setSelected(true);
+      case ColourSchemeProperty.BLOSUM:
+        BLOSUM62Colour.setSelected(true);
 
-          break;
+        break;
 
-        case ColourSchemeProperty.PID:
-          PIDColour.setSelected(true);
+      case ColourSchemeProperty.PID:
+        PIDColour.setSelected(true);
 
-          break;
+        break;
 
-        case ColourSchemeProperty.ZAPPO:
-          zappoColour.setSelected(true);
+      case ColourSchemeProperty.ZAPPO:
+        zappoColour.setSelected(true);
 
-          break;
+        break;
 
-        case ColourSchemeProperty.TAYLOR:
-          taylorColour.setSelected(true);
-          break;
+      case ColourSchemeProperty.TAYLOR:
+        taylorColour.setSelected(true);
+        break;
 
-        case ColourSchemeProperty.HYDROPHOBIC:
-          hydrophobicityColour.setSelected(true);
+      case ColourSchemeProperty.HYDROPHOBIC:
+        hydrophobicityColour.setSelected(true);
 
-          break;
+        break;
 
-        case ColourSchemeProperty.HELIX:
-          helixColour.setSelected(true);
+      case ColourSchemeProperty.HELIX:
+        helixColour.setSelected(true);
 
-          break;
+        break;
 
-        case ColourSchemeProperty.STRAND:
-          strandColour.setSelected(true);
+      case ColourSchemeProperty.STRAND:
+        strandColour.setSelected(true);
 
-          break;
+        break;
 
-        case ColourSchemeProperty.TURN:
-          turnColour.setSelected(true);
+      case ColourSchemeProperty.TURN:
+        turnColour.setSelected(true);
 
-          break;
+        break;
 
-        case ColourSchemeProperty.BURIED:
-          buriedColour.setSelected(true);
+      case ColourSchemeProperty.BURIED:
+        buriedColour.setSelected(true);
 
-          break;
+        break;
 
-        case ColourSchemeProperty.NUCLEOTIDE:
-          nucleotideColour.setSelected(true);
+      case ColourSchemeProperty.NUCLEOTIDE:
+        nucleotideColour.setSelected(true);
 
-          break;
+        break;
 
-        case ColourSchemeProperty.USER_DEFINED:
-          userDefinedColour.setSelected(true);
+      case ColourSchemeProperty.USER_DEFINED:
+        userDefinedColour.setSelected(true);
 
-          break;
+        break;
       }
     }
 
   }
 
-  private void jbInit()
-      throws Exception
+  private void jbInit() throws Exception
   {
     fileMenu.setText("File");
     saveAs.setText("Save As...");
-    saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
-        KeyEvent.VK_S,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |
-        java.awt.event.KeyEvent.SHIFT_MASK, false));
+    saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask()
+                    | java.awt.event.KeyEvent.SHIFT_MASK, false));
     saveAs.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -355,8 +475,9 @@ public class GAlignFrame
       }
     });
     closeMenuItem.setText("Close");
-    closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
-        event.KeyEvent.VK_W, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask(), false));
     closeMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -370,86 +491,89 @@ public class GAlignFrame
     calculateMenu.setText("Calculate");
     webService.setText("Web Service");
     selectAllSequenceMenuItem.setText("Select All");
-    selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-        java.awt.event.KeyEvent.VK_A,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    selectAllSequenceMenuItem.addActionListener(new java.awt.event.
-                                                ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        selectAllSequenceMenuItem_actionPerformed(e);
-      }
-    });
+    selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
+            .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
+                    .getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    selectAllSequenceMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                selectAllSequenceMenuItem_actionPerformed(e);
+              }
+            });
     deselectAllSequenceMenuItem.setText("Deselect All");
-    deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
-                                               getKeyStroke(
-        java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
-    deselectAllSequenceMenuItem.addActionListener(new java.awt.event.
-                                                  ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        deselectAllSequenceMenuItem_actionPerformed(e);
-      }
-    });
+    deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
+            .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
+    deselectAllSequenceMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                deselectAllSequenceMenuItem_actionPerformed(e);
+              }
+            });
     invertSequenceMenuItem.setText("Invert Sequence Selection");
-    invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-        java.awt.event.KeyEvent.VK_I,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        invertSequenceMenuItem_actionPerformed(e);
-      }
-    });
+    invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
+            .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
+                    .getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    invertSequenceMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                invertSequenceMenuItem_actionPerformed(e);
+              }
+            });
     remove2LeftMenuItem.setText("Remove Left");
-    remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
-        awt.event.KeyEvent.VK_L,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        remove2LeftMenuItem_actionPerformed(e);
-      }
-    });
+    remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask(), false));
+    remove2LeftMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                remove2LeftMenuItem_actionPerformed(e);
+              }
+            });
     remove2RightMenuItem.setText("Remove Right");
-    remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
-        awt.event.KeyEvent.VK_R,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        remove2RightMenuItem_actionPerformed(e);
-      }
-    });
+    remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask(), false));
+    remove2RightMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                remove2RightMenuItem_actionPerformed(e);
+              }
+            });
     removeGappedColumnMenuItem.setText("Remove Empty Columns");
-    removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke.
-                                              getKeyStroke(java.awt.event.
-        KeyEvent.VK_E, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    removeGappedColumnMenuItem.addActionListener(new java.awt.event.
-                                                 ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        removeGappedColumnMenuItem_actionPerformed(e);
-      }
-    });
+    removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
+            .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
+                    .getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    removeGappedColumnMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                removeGappedColumnMenuItem_actionPerformed(e);
+              }
+            });
     removeAllGapsMenuItem.setText("Remove All Gaps");
-    removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-        java.awt.event.KeyEvent.VK_E,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |
-        java.awt.event.KeyEvent.SHIFT_MASK, false));
-    removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        removeAllGapsMenuItem_actionPerformed(e);
-      }
-    });
+    removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
+            .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
+                    .getDefaultToolkit().getMenuShortcutKeyMask()
+                    | java.awt.event.KeyEvent.SHIFT_MASK, false));
+    removeAllGapsMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                removeAllGapsMenuItem_actionPerformed(e);
+              }
+            });
     viewBoxesMenuItem.setText("Boxes");
     viewBoxesMenuItem.setState(true);
     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
@@ -469,13 +593,14 @@ public class GAlignFrame
       }
     });
     sortPairwiseMenuItem.setText("by Pairwise Identity");
-    sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        sortPairwiseMenuItem_actionPerformed(e);
-      }
-    });
+    sortPairwiseMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                sortPairwiseMenuItem_actionPerformed(e);
+              }
+            });
     sortIDMenuItem.setText("by ID");
     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
@@ -493,26 +618,26 @@ public class GAlignFrame
       }
     });
     removeRedundancyMenuItem.setText("Remove Redundancy...");
-    removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-        java.awt.event.KeyEvent.VK_D,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    removeRedundancyMenuItem.addActionListener(new java.awt.event.
-                                               ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        removeRedundancyMenuItem_actionPerformed(e);
-      }
-    });
+    removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
+            .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
+                    .getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    removeRedundancyMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                removeRedundancyMenuItem_actionPerformed(e);
+              }
+            });
     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
-    pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.
-                                                ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        pairwiseAlignmentMenuItem_actionPerformed(e);
-      }
-    });
+    pairwiseAlignmentMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                pairwiseAlignmentMenuItem_actionPerformed(e);
+              }
+            });
     PCAMenuItem.setText("Principal Component Analysis");
     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
@@ -521,24 +646,25 @@ public class GAlignFrame
         PCAMenuItem_actionPerformed(e);
       }
     });
-    averageDistanceTreeMenuItem.setText(
-        "Average Distance Using % Identity");
-    averageDistanceTreeMenuItem.addActionListener(new java.awt.event.
-                                                  ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        averageDistanceTreeMenuItem_actionPerformed(e);
-      }
-    });
+    averageDistanceTreeMenuItem
+            .setText("Average Distance Using % Identity");
+    averageDistanceTreeMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                averageDistanceTreeMenuItem_actionPerformed(e);
+              }
+            });
     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
-    neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        neighbourTreeMenuItem_actionPerformed(e);
-      }
-    });
+    neighbourTreeMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                neighbourTreeMenuItem_actionPerformed(e);
+              }
+            });
     this.getContentPane().setLayout(borderLayout1);
     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
     statusBar.setBackground(Color.white);
@@ -572,13 +698,14 @@ public class GAlignFrame
       }
     });
     hydrophobicityColour.setText("Hydrophobicity");
-    hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        hydrophobicityColour_actionPerformed(e);
-      }
-    });
+    hydrophobicityColour
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                hydrophobicityColour_actionPerformed(e);
+              }
+            });
     helixColour.setText("Helix Propensity");
     helixColour.addActionListener(new java.awt.event.ActionListener()
     {
@@ -635,43 +762,45 @@ public class GAlignFrame
         BLOSUM62Colour_actionPerformed(e);
       }
     });
-    avDistanceTreeBlosumMenuItem.setText(
-        "Average Distance Using BLOSUM62");
-    avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.
-        ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        avTreeBlosumMenuItem_actionPerformed(e);
-      }
-    });
+    avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
+    avDistanceTreeBlosumMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                avTreeBlosumMenuItem_actionPerformed(e);
+              }
+            });
     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
-    njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        njTreeBlosumMenuItem_actionPerformed(e);
-      }
-    });
+    njTreeBlosumMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                njTreeBlosumMenuItem_actionPerformed(e);
+              }
+            });
     annotationPanelMenuItem.setActionCommand("");
     annotationPanelMenuItem.setText("Show Annotations");
     annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
-        "SHOW_ANNOTATIONS", true));
-    annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        annotationPanelMenuItem_actionPerformed(e);
-      }
-    });
+            "SHOW_ANNOTATIONS", true));
+    annotationPanelMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                annotationPanelMenuItem_actionPerformed(e);
+              }
+            });
     colourTextMenuItem.setText("Colour Text");
-    colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        colourTextMenuItem_actionPerformed(e);
-      }
-    });
+    colourTextMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                colourTextMenuItem_actionPerformed(e);
+              }
+            });
     htmlMenuItem.setText("HTML");
     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
@@ -691,8 +820,8 @@ public class GAlignFrame
     undoMenuItem.setEnabled(false);
     undoMenuItem.setText("Undo");
     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-        java.awt.event.KeyEvent.VK_Z,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+            java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask(), false));
     undoMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -702,8 +831,9 @@ public class GAlignFrame
     });
     redoMenuItem.setEnabled(false);
     redoMenuItem.setText("Redo");
-    redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
-        event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask(), false));
     redoMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -712,13 +842,14 @@ public class GAlignFrame
       }
     });
     conservationMenuItem.setText("By Conservation");
-    conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        conservationMenuItem_actionPerformed(e);
-      }
-    });
+    conservationMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                conservationMenuItem_actionPerformed(e);
+              }
+            });
     noColourmenuItem.setText("None");
     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
     {
@@ -736,8 +867,9 @@ public class GAlignFrame
       }
     });
     printMenuItem.setText("Print ...");
-    printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
-        event.KeyEvent.VK_P, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask(), false));
     printMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -747,17 +879,18 @@ public class GAlignFrame
     });
     renderGapsMenuItem.setText("Show Gaps");
     renderGapsMenuItem.setState(true);
-    renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        renderGapsMenuItem_actionPerformed(e);
-      }
-    });
+    renderGapsMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                renderGapsMenuItem_actionPerformed(e);
+              }
+            });
     findMenuItem.setText("Find...");
     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-        java.awt.event.KeyEvent.VK_F,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+            java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask(), false));
     findMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -790,8 +923,9 @@ public class GAlignFrame
       }
     });
     deleteGroups.setText("Undefine groups");
-    deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
-        event.KeyEvent.VK_U, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask(), false));
     deleteGroups.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -801,8 +935,8 @@ public class GAlignFrame
     });
     copy.setText("Copy");
     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-        java.awt.event.KeyEvent.VK_C,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+            java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask(), false));
 
     copy.addActionListener(new java.awt.event.ActionListener()
     {
@@ -813,8 +947,8 @@ public class GAlignFrame
     });
     cut.setText("Cut");
     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-        java.awt.event.KeyEvent.VK_X,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+            java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask(), false));
     cut.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -823,8 +957,8 @@ public class GAlignFrame
       }
     });
     delete.setText("Delete");
-    delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
-        KeyEvent.VK_BACK_SPACE, 0, false));
+    delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
     delete.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -835,9 +969,9 @@ public class GAlignFrame
     pasteMenu.setText("Paste");
     pasteNew.setText("To New Alignment");
     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-        java.awt.event.KeyEvent.VK_V,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |
-        java.awt.event.KeyEvent.SHIFT_MASK, false));
+            java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask()
+                    | java.awt.event.KeyEvent.SHIFT_MASK, false));
     pasteNew.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -847,8 +981,8 @@ public class GAlignFrame
     });
     pasteThis.setText("Add To This Alignment");
     pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-        java.awt.event.KeyEvent.VK_V,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+            java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask(), false));
     pasteThis.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -940,14 +1074,15 @@ public class GAlignFrame
     centreColumnLabelsMenuItem.setVisible(true);
     centreColumnLabelsMenuItem.setState(false);
     centreColumnLabelsMenuItem.setText("Centre Column Labels");
-    centreColumnLabelsMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        centreColumnLabels_actionPerformed(e);
-      }
-    });
-    
+    centreColumnLabelsMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                centreColumnLabels_actionPerformed(e);
+              }
+            });
+
     modifyPID.setText("Modify Identity Threshold...");
     modifyPID.addActionListener(new java.awt.event.ActionListener()
     {
@@ -957,13 +1092,14 @@ public class GAlignFrame
       }
     });
     modifyConservation.setText("Modify Conservation Threshold...");
-    modifyConservation.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        modifyConservation_actionPerformed(e);
-      }
-    });
+    modifyConservation
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                modifyConservation_actionPerformed(e);
+              }
+            });
     sortByTreeMenu.setText("By Tree Order");
     sort.setText("Sort");
     sort.addMenuListener(new MenuListener()
@@ -983,30 +1119,30 @@ public class GAlignFrame
     });
     sortByAnnotScore.setText("by Score");
     sort.add(sortByAnnotScore);
-    sortByAnnotScore.addMenuListener(
-            new javax.swing.event.MenuListener() {
-              
-                public void menuCanceled(MenuEvent e)
-                {
-                }
+    sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
+    {
 
-                public void menuDeselected(MenuEvent e)
-                {
-                }
+      public void menuCanceled(MenuEvent e)
+      {
+      }
 
-                public void menuSelected(MenuEvent e)
-                {
-                  buildSortByAnnotationScoresMenu();
-                }
-              }
-              );
+      public void menuDeselected(MenuEvent e)
+      {
+      }
+
+      public void menuSelected(MenuEvent e)
+      {
+        buildSortByAnnotationScoresMenu();
+      }
+    });
     sortByAnnotScore.setVisible(false);
-    
+
     calculate.setText("Calculate Tree");
 
     jMenu2.setText("Export Image");
     padGapsMenuitem.setText("Pad Gaps");
-    padGapsMenuitem.setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
+    padGapsMenuitem.setState(jalview.bin.Cache
+            .getDefault("PAD_GAPS", false));
     padGapsMenuitem.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1039,16 +1175,15 @@ public class GAlignFrame
         extractScores_actionPerformed(e);
       }
     });
-    extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based score extraction
+    extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
+                                    // score extraction
     showProducts.setText("Get Cross References");
-    /*showProducts.addActionListener(new ActionListener()
-    {
-
-      public void actionPerformed(ActionEvent e)
-      {
-        showProducts_actionPerformed(e);
-      }
-    });*/
+    /*
+     * showProducts.addActionListener(new ActionListener() {
+     * 
+     * public void actionPerformed(ActionEvent e) {
+     * showProducts_actionPerformed(e); } });
+     */
     featureSettings.setText("Feature Settings...");
     featureSettings.addActionListener(new ActionListener()
     {
@@ -1083,7 +1218,8 @@ public class GAlignFrame
       }
     });
     autoCalculate.setText("Autocalculate Consensus");
-    autoCalculate.setState(jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+    autoCalculate.setState(jalview.bin.Cache.getDefault(
+            "AUTO_CALC_CONSENSUS", true));
     autoCalculate.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1176,11 +1312,10 @@ public class GAlignFrame
       }
     });
     invertColSel.setText("Invert Column Selection");
-    invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
-        event.KeyEvent.VK_I,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
-        | java.awt.event.KeyEvent.ALT_MASK,
-        false));
+    invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask()
+                    | java.awt.event.KeyEvent.ALT_MASK, false));
     invertColSel.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1212,8 +1347,9 @@ public class GAlignFrame
       }
     });
     save.setText("Save");
-    save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
-        KeyEvent.VK_S, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask(), false));
     save.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1231,8 +1367,9 @@ public class GAlignFrame
       }
     });
     newView.setText("New View");
-    newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
-        KeyEvent.VK_T, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask(), false));
     newView.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1241,8 +1378,7 @@ public class GAlignFrame
       }
     });
     tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
-                              +
-        "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
+            + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
     textColour.setText("Colour Text ...");
     textColour.addActionListener(new ActionListener()
     {
@@ -1263,8 +1399,8 @@ public class GAlignFrame
     });
     gatherViews.setEnabled(false);
     gatherViews.setText("Gather Views");
-    gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
-        event.KeyEvent.VK_G, 0, false));
+    gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_G, 0, false));
     gatherViews.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1274,8 +1410,8 @@ public class GAlignFrame
     });
     expandViews.setEnabled(false);
     expandViews.setText("Expand Views");
-    expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
-        event.KeyEvent.VK_X, 0, false));
+    expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_X, 0, false));
     expandViews.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1894,7 +2030,7 @@ public class GAlignFrame
   {
 
   }
-  
+
   public void pageSetup_actionPerformed(ActionEvent e)
   {
 
diff --git a/src/jalview/jbgui/GAlignmentPanel.java b/src/jalview/jbgui/GAlignmentPanel.java
index f8b91c4..cc3d68f 100755
--- a/src/jalview/jbgui/GAlignmentPanel.java
+++ b/src/jalview/jbgui/GAlignmentPanel.java
@@ -1,108 +1,126 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.jbgui;
-
-import java.awt.*;
-import javax.swing.*;
-import javax.swing.border.*;
-
-public class GAlignmentPanel
-    extends JPanel
-{
-  protected JPanel sequenceHolderPanel = new JPanel();
-  protected JScrollBar vscroll = new JScrollBar();
-  protected JScrollBar hscroll = new JScrollBar();
-  protected JPanel seqPanelHolder = new JPanel();
-  BorderLayout borderLayout1 = new BorderLayout();
-  BorderLayout borderLayout3 = new BorderLayout();
-  protected JPanel scalePanelHolder = new JPanel();
-  protected JPanel idPanelHolder = new JPanel();
-  BorderLayout borderLayout5 = new BorderLayout();
-  protected JPanel idSpaceFillerPanel1 = new JPanel();
-  public JPanel annotationSpaceFillerHolder = new JPanel();
-  BorderLayout borderLayout6 = new BorderLayout();
-  ButtonGroup buttonGroup1 = new ButtonGroup();
-  BorderLayout borderLayout7 = new BorderLayout();
-  JPanel hscrollHolder = new JPanel();
-  BorderLayout borderLayout10 = new BorderLayout();
-  protected JPanel hscrollFillerPanel = new JPanel();
-  BorderLayout borderLayout11 = new BorderLayout();
-  public JScrollPane annotationScroller = new JScrollPane();
-  Border border1;
-  BorderLayout borderLayout4 = new BorderLayout();
-
-  public GAlignmentPanel()
-  {
-    try
-    {
-      jbInit();
-    }
-    catch (Exception e)
-    {
-      e.printStackTrace();
-    }
-  }
-
-  private void jbInit()
-      throws Exception
-  {
-    border1 = BorderFactory.createLineBorder(Color.gray, 1);
-    idPanelHolder.setBorder(null);
-    idPanelHolder.setPreferredSize(new Dimension(70, 10));
-    this.setLayout(borderLayout7);
-    sequenceHolderPanel.setMaximumSize(new Dimension(2147483647, 2147483647));
-    sequenceHolderPanel.setMinimumSize(new Dimension(150, 150));
-    sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
-    sequenceHolderPanel.setLayout(borderLayout3);
-    seqPanelHolder.setLayout(borderLayout1);
-    scalePanelHolder.setBackground(Color.white);
-    scalePanelHolder.setMinimumSize(new Dimension(10, 80));
-    scalePanelHolder.setPreferredSize(new Dimension(10, 30));
-    scalePanelHolder.setLayout(borderLayout6);
-    idPanelHolder.setLayout(borderLayout5);
-    idSpaceFillerPanel1.setBackground(Color.white);
-    idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
-    idSpaceFillerPanel1.setLayout(borderLayout11);
-    annotationSpaceFillerHolder.setBackground(Color.white);
-    annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
-    annotationSpaceFillerHolder.setLayout(borderLayout4);
-    hscroll.setOrientation(JScrollBar.HORIZONTAL);
-    hscrollHolder.setLayout(borderLayout10);
-    hscrollFillerPanel.setBackground(Color.white);
-    hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
-    hscrollHolder.setBackground(Color.white);
-    annotationScroller.setBorder(null);
-    annotationScroller.setPreferredSize(new Dimension(10, 80));
-    this.setPreferredSize(new Dimension(220, 166));
-
-    sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);
-    sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);
-    seqPanelHolder.add(vscroll, BorderLayout.EAST);
-    sequenceHolderPanel.add(annotationScroller, BorderLayout.SOUTH);
-
-    //  jPanel3.add(secondaryPanelHolder,  BorderLayout.SOUTH);
-    this.add(idPanelHolder, BorderLayout.WEST);
-    idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);
-    idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);
-    this.add(hscrollHolder, BorderLayout.SOUTH);
-    hscrollHolder.add(hscroll, BorderLayout.CENTER);
-    hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);
-    this.add(sequenceHolderPanel, BorderLayout.CENTER);
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.jbgui;
+
+import java.awt.*;
+import javax.swing.*;
+import javax.swing.border.*;
+
+public class GAlignmentPanel extends JPanel
+{
+  protected JPanel sequenceHolderPanel = new JPanel();
+
+  protected JScrollBar vscroll = new JScrollBar();
+
+  protected JScrollBar hscroll = new JScrollBar();
+
+  protected JPanel seqPanelHolder = new JPanel();
+
+  BorderLayout borderLayout1 = new BorderLayout();
+
+  BorderLayout borderLayout3 = new BorderLayout();
+
+  protected JPanel scalePanelHolder = new JPanel();
+
+  protected JPanel idPanelHolder = new JPanel();
+
+  BorderLayout borderLayout5 = new BorderLayout();
+
+  protected JPanel idSpaceFillerPanel1 = new JPanel();
+
+  public JPanel annotationSpaceFillerHolder = new JPanel();
+
+  BorderLayout borderLayout6 = new BorderLayout();
+
+  ButtonGroup buttonGroup1 = new ButtonGroup();
+
+  BorderLayout borderLayout7 = new BorderLayout();
+
+  JPanel hscrollHolder = new JPanel();
+
+  BorderLayout borderLayout10 = new BorderLayout();
+
+  protected JPanel hscrollFillerPanel = new JPanel();
+
+  BorderLayout borderLayout11 = new BorderLayout();
+
+  public JScrollPane annotationScroller = new JScrollPane();
+
+  Border border1;
+
+  BorderLayout borderLayout4 = new BorderLayout();
+
+  public GAlignmentPanel()
+  {
+    try
+    {
+      jbInit();
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+  }
+
+  private void jbInit() throws Exception
+  {
+    border1 = BorderFactory.createLineBorder(Color.gray, 1);
+    idPanelHolder.setBorder(null);
+    idPanelHolder.setPreferredSize(new Dimension(70, 10));
+    this.setLayout(borderLayout7);
+    sequenceHolderPanel
+            .setMaximumSize(new Dimension(2147483647, 2147483647));
+    sequenceHolderPanel.setMinimumSize(new Dimension(150, 150));
+    sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
+    sequenceHolderPanel.setLayout(borderLayout3);
+    seqPanelHolder.setLayout(borderLayout1);
+    scalePanelHolder.setBackground(Color.white);
+    scalePanelHolder.setMinimumSize(new Dimension(10, 80));
+    scalePanelHolder.setPreferredSize(new Dimension(10, 30));
+    scalePanelHolder.setLayout(borderLayout6);
+    idPanelHolder.setLayout(borderLayout5);
+    idSpaceFillerPanel1.setBackground(Color.white);
+    idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
+    idSpaceFillerPanel1.setLayout(borderLayout11);
+    annotationSpaceFillerHolder.setBackground(Color.white);
+    annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
+    annotationSpaceFillerHolder.setLayout(borderLayout4);
+    hscroll.setOrientation(JScrollBar.HORIZONTAL);
+    hscrollHolder.setLayout(borderLayout10);
+    hscrollFillerPanel.setBackground(Color.white);
+    hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
+    hscrollHolder.setBackground(Color.white);
+    annotationScroller.setBorder(null);
+    annotationScroller.setPreferredSize(new Dimension(10, 80));
+    this.setPreferredSize(new Dimension(220, 166));
+
+    sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);
+    sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);
+    seqPanelHolder.add(vscroll, BorderLayout.EAST);
+    sequenceHolderPanel.add(annotationScroller, BorderLayout.SOUTH);
+
+    // jPanel3.add(secondaryPanelHolder, BorderLayout.SOUTH);
+    this.add(idPanelHolder, BorderLayout.WEST);
+    idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);
+    idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);
+    this.add(hscrollHolder, BorderLayout.SOUTH);
+    hscrollHolder.add(hscroll, BorderLayout.CENTER);
+    hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);
+    this.add(sequenceHolderPanel, BorderLayout.CENTER);
+  }
+}
diff --git a/src/jalview/jbgui/GCutAndPasteTransfer.java b/src/jalview/jbgui/GCutAndPasteTransfer.java
index c19db0e..2697e1c 100755
--- a/src/jalview/jbgui/GCutAndPasteTransfer.java
+++ b/src/jalview/jbgui/GCutAndPasteTransfer.java
@@ -1,212 +1,232 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.jbgui;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class GCutAndPasteTransfer
-    extends JInternalFrame
-{
-  protected JTextArea textarea = new JTextArea();
-  protected JScrollPane scrollPane = new JScrollPane();
-  BorderLayout borderLayout1 = new BorderLayout();
-  JMenuBar editMenubar = new JMenuBar();
-  JMenu editMenu = new JMenu();
-  JMenuItem copyItem = new JMenuItem();
-  JMenuItem pasteMenu = new JMenuItem();
-  BorderLayout borderLayout2 = new BorderLayout();
-  protected JPanel inputButtonPanel = new JPanel();
-  protected JButton ok = new JButton();
-  JButton cancel = new JButton();
-  JMenuItem selectAll = new JMenuItem();
-  JMenu jMenu1 = new JMenu();
-  JMenuItem save = new JMenuItem();
-
-  /**
-   * Creates a new GCutAndPasteTransfer object.
-   */
-  public GCutAndPasteTransfer()
-  {
-    try
-    {
-      setJMenuBar(editMenubar);
-      jbInit();
-    }
-    catch (Exception e)
-    {
-      e.printStackTrace();
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @throws Exception DOCUMENT ME!
-   */
-  private void jbInit()
-      throws Exception
-  {
-    scrollPane.setBorder(null);
-    ok.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    ok.setText("New Window");
-    ok.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        ok_actionPerformed(e);
-      }
-    });
-    cancel.setText("Close");
-    cancel.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        cancel_actionPerformed(e);
-      }
-    });
-    textarea.setBorder(null);
-
-    selectAll.setText("Select All");
-    selectAll.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
-        KeyEvent.VK_A, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    selectAll.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        selectAll_actionPerformed(e);
-      }
-    });
-    jMenu1.setText("File");
-    save.setText("Save");
-    save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
-        KeyEvent.VK_S, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    save.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        save_actionPerformed(e);
-      }
-    });
-    copyItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
-        KeyEvent.VK_C, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    pasteMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
-        KeyEvent.VK_V, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    editMenubar.add(jMenu1);
-    editMenubar.add(editMenu);
-    textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 12));
-    textarea.addMouseListener(new java.awt.event.MouseAdapter()
-    {
-      public void mousePressed(MouseEvent e)
-      {
-        textarea_mousePressed(e);
-      }
-    });
-    editMenu.setText("Edit");
-    pasteMenu.setText("Paste");
-    pasteMenu.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        pasteMenu_actionPerformed(e);
-      }
-    });
-    copyItem.setText("Copy");
-    copyItem.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        copyItem_actionPerformed(e);
-      }
-    });
-    this.getContentPane().setLayout(borderLayout2);
-    scrollPane.setBorder(null);
-    scrollPane.getViewport().add(textarea, null);
-    editMenu.add(selectAll);
-    editMenu.add(copyItem);
-    editMenu.add(pasteMenu);
-    this.getContentPane().add(scrollPane, java.awt.BorderLayout.CENTER);
-    inputButtonPanel.add(ok);
-    inputButtonPanel.add(cancel);
-    jMenu1.add(save);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  public void textarea_mousePressed(MouseEvent e)
-  {
-
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  public void copyItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  public void pasteMenu_actionPerformed(ActionEvent e)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  public void ok_actionPerformed(ActionEvent e)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  public void cancel_actionPerformed(ActionEvent e)
-  {
-  }
-
-  public void selectAll_actionPerformed(ActionEvent e)
-  {
-    textarea.selectAll();
-  }
-
-  public void save_actionPerformed(ActionEvent e)
-  {
-
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.jbgui;
+
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class GCutAndPasteTransfer extends JInternalFrame
+{
+  protected JTextArea textarea = new JTextArea();
+
+  protected JScrollPane scrollPane = new JScrollPane();
+
+  BorderLayout borderLayout1 = new BorderLayout();
+
+  JMenuBar editMenubar = new JMenuBar();
+
+  JMenu editMenu = new JMenu();
+
+  JMenuItem copyItem = new JMenuItem();
+
+  JMenuItem pasteMenu = new JMenuItem();
+
+  BorderLayout borderLayout2 = new BorderLayout();
+
+  protected JPanel inputButtonPanel = new JPanel();
+
+  protected JButton ok = new JButton();
+
+  JButton cancel = new JButton();
+
+  JMenuItem selectAll = new JMenuItem();
+
+  JMenu jMenu1 = new JMenu();
+
+  JMenuItem save = new JMenuItem();
+
+  /**
+   * Creates a new GCutAndPasteTransfer object.
+   */
+  public GCutAndPasteTransfer()
+  {
+    try
+    {
+      setJMenuBar(editMenubar);
+      jbInit();
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @throws Exception
+   *                 DOCUMENT ME!
+   */
+  private void jbInit() throws Exception
+  {
+    scrollPane.setBorder(null);
+    ok.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    ok.setText("New Window");
+    ok.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        ok_actionPerformed(e);
+      }
+    });
+    cancel.setText("Close");
+    cancel.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        cancel_actionPerformed(e);
+      }
+    });
+    textarea.setBorder(null);
+
+    selectAll.setText("Select All");
+    selectAll.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_A, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask(), false));
+    selectAll.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        selectAll_actionPerformed(e);
+      }
+    });
+    jMenu1.setText("File");
+    save.setText("Save");
+    save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask(), false));
+    save.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        save_actionPerformed(e);
+      }
+    });
+    copyItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask(), false));
+    pasteMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask(), false));
+    editMenubar.add(jMenu1);
+    editMenubar.add(editMenu);
+    textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 12));
+    textarea.addMouseListener(new java.awt.event.MouseAdapter()
+    {
+      public void mousePressed(MouseEvent e)
+      {
+        textarea_mousePressed(e);
+      }
+    });
+    editMenu.setText("Edit");
+    pasteMenu.setText("Paste");
+    pasteMenu.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        pasteMenu_actionPerformed(e);
+      }
+    });
+    copyItem.setText("Copy");
+    copyItem.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        copyItem_actionPerformed(e);
+      }
+    });
+    this.getContentPane().setLayout(borderLayout2);
+    scrollPane.setBorder(null);
+    scrollPane.getViewport().add(textarea, null);
+    editMenu.add(selectAll);
+    editMenu.add(copyItem);
+    editMenu.add(pasteMenu);
+    this.getContentPane().add(scrollPane, java.awt.BorderLayout.CENTER);
+    inputButtonPanel.add(ok);
+    inputButtonPanel.add(cancel);
+    jMenu1.add(save);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
+   */
+  public void textarea_mousePressed(MouseEvent e)
+  {
+
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
+   */
+  public void copyItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
+   */
+  public void pasteMenu_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
+   */
+  public void ok_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
+   */
+  public void cancel_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void selectAll_actionPerformed(ActionEvent e)
+  {
+    textarea.selectAll();
+  }
+
+  public void save_actionPerformed(ActionEvent e)
+  {
+
+  }
+}
diff --git a/src/jalview/jbgui/GDasSourceBrowser.java b/src/jalview/jbgui/GDasSourceBrowser.java
index d4f6d1d..625e2c4 100755
--- a/src/jalview/jbgui/GDasSourceBrowser.java
+++ b/src/jalview/jbgui/GDasSourceBrowser.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -24,23 +24,20 @@ import javax.swing.*;
 import javax.swing.border.*;
 import javax.swing.event.*;
 
-public class GDasSourceBrowser
-    extends JPanel
+public class GDasSourceBrowser extends JPanel
 {
   public GDasSourceBrowser()
   {
     try
     {
       jbInit();
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       ex.printStackTrace();
     }
   }
 
-  private void jbInit()
-      throws Exception
+  private void jbInit() throws Exception
   {
     this.setLayout(gridBagLayout1);
     refresh.setText("Refresh Available Sources");
@@ -82,9 +79,12 @@ public class GDasSourceBrowser
     jScrollPane2.setBorder(titledBorder3);
     jScrollPane3.setBorder(titledBorder4);
     jScrollPane4.setBorder(titledBorder5);
-    titledBorder2.setTitleFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
-    titledBorder3.setTitleFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
-    titledBorder4.setTitleFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+    titledBorder2
+            .setTitleFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+    titledBorder3
+            .setTitleFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+    titledBorder4
+            .setTitleFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
     filter1.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
     filter2.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
     filter3.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
@@ -110,68 +110,84 @@ public class GDasSourceBrowser
     jPanel1.add(addLocal, null);
     jPanel1.add(progressBar, null);
     jScrollPane2.getViewport().add(filter1);
-    this.add(jPanel1, new GridBagConstraints(0, 3, 3, 1, 1.0, 1.0
-                                             , GridBagConstraints.CENTER,
-                                             GridBagConstraints.HORIZONTAL,
-                                             new Insets(0, 0, 0, 0), 0, 0));
-    this.add(fullDetailsScrollpane, new GridBagConstraints(1, 0, 2, 1, 1.0, 1.0
-        , GridBagConstraints.CENTER, GridBagConstraints.BOTH,
-        new Insets(3, 0, 0, 3), 240, 130));
-    this.add(scrollPane, new GridBagConstraints(0, 0, 1, 1, 1.0, 1.0
-                                                , GridBagConstraints.CENTER,
-                                                GridBagConstraints.BOTH,
-                                                new Insets(3, 2, 0, 0), 150,
-                                                130));
+    this.add(jPanel1, new GridBagConstraints(0, 3, 3, 1, 1.0, 1.0,
+            GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
+            new Insets(0, 0, 0, 0), 0, 0));
+    this.add(fullDetailsScrollpane, new GridBagConstraints(1, 0, 2, 1, 1.0,
+            1.0, GridBagConstraints.CENTER, GridBagConstraints.BOTH,
+            new Insets(3, 0, 0, 3), 240, 130));
+    this.add(scrollPane, new GridBagConstraints(0, 0, 1, 1, 1.0, 1.0,
+            GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
+                    3, 2, 0, 0), 150, 130));
     jPanel2.add(registryLabel, java.awt.BorderLayout.WEST);
     jPanel2.add(registryURL, java.awt.BorderLayout.CENTER);
     jPanel2.add(reset, java.awt.BorderLayout.EAST);
-    this.add(jPanel2, new GridBagConstraints(0, 2, 3, 1, 0.0, 0.0
-                                             , GridBagConstraints.CENTER,
-                                             GridBagConstraints.HORIZONTAL,
-                                             new Insets(5, 10, 0, 10), 339, 0));
-    this.add(jScrollPane2, new GridBagConstraints(0, 1, 1, 1, 1.0, 1.0
-                                                  , GridBagConstraints.CENTER,
-                                                  GridBagConstraints.BOTH,
-                                                  new Insets(0, 0, 0, 60), 80,
-                                                  60));
-    this.add(jScrollPane4, new GridBagConstraints(2, 1, 1, 1, 1.0, 1.0
-                                                  , GridBagConstraints.CENTER,
-                                                  GridBagConstraints.BOTH,
-                                                  new Insets(0, -80, 0, 0), 80,
-                                                  60));
-    this.add(jScrollPane3, new GridBagConstraints(1, 1, 1, 1, 1.0, 1.0
-                                                  , GridBagConstraints.CENTER,
-                                                  GridBagConstraints.BOTH,
-                                                  new Insets(0, -60, 0, 80), 80,
-                                                  60));
+    this.add(jPanel2, new GridBagConstraints(0, 2, 3, 1, 0.0, 0.0,
+            GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
+            new Insets(5, 10, 0, 10), 339, 0));
+    this.add(jScrollPane2, new GridBagConstraints(0, 1, 1, 1, 1.0, 1.0,
+            GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
+                    0, 0, 0, 60), 80, 60));
+    this.add(jScrollPane4, new GridBagConstraints(2, 1, 1, 1, 1.0, 1.0,
+            GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
+                    0, -80, 0, 0), 80, 60));
+    this.add(jScrollPane3, new GridBagConstraints(1, 1, 1, 1, 1.0, 1.0,
+            GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
+                    0, -60, 0, 80), 80, 60));
   }
 
   protected JTable table = new JTable();
+
   protected JEditorPane fullDetails = new JEditorPane("text/html", "");
+
   TitledBorder titledBorder1 = new TitledBorder("Available DAS Sources");
+
   protected JButton refresh = new JButton();
+
   protected JProgressBar progressBar = new JProgressBar();
+
   protected JScrollPane scrollPane = new JScrollPane();
+
   TitledBorder titledBorder2 = new TitledBorder("Full Details");
+
   protected JScrollPane fullDetailsScrollpane = new JScrollPane();
+
   protected JList filter1 = new JList();
+
   protected JList filter2 = new JList();
+
   protected JList filter3 = new JList();
+
   JScrollPane jScrollPane2 = new JScrollPane();
+
   JScrollPane jScrollPane3 = new JScrollPane();
+
   JScrollPane jScrollPane4 = new JScrollPane();
+
   protected JTextField registryURL = new JTextField();
+
   protected JLabel registryLabel = new JLabel();
+
   protected JButton addLocal = new JButton();
+
   JPanel jPanel1 = new JPanel();
+
   FlowLayout flowLayout1 = new FlowLayout();
+
   GridBagLayout gridBagLayout1 = new GridBagLayout();
+
   TitledBorder titledBorder3 = new TitledBorder("Authority:");
+
   TitledBorder titledBorder4 = new TitledBorder("Type:");
+
   TitledBorder titledBorder5 = new TitledBorder("Label:");
+
   JButton reset = new JButton();
+
   JPanel jPanel2 = new JPanel();
+
   BorderLayout borderLayout1 = new BorderLayout();
+
   public void refresh_actionPerformed(ActionEvent e)
   {
 
@@ -186,8 +202,7 @@ public class GDasSourceBrowser
       {
         jalview.util.BrowserLauncher.openURL(e.getURL().toString());
       }
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       System.out.println(e.getURL());
       ex.printStackTrace();
diff --git a/src/jalview/jbgui/GDesktop.java b/src/jalview/jbgui/GDesktop.java
index aa86809..a8e2ef5 100755
--- a/src/jalview/jbgui/GDesktop.java
+++ b/src/jalview/jbgui/GDesktop.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -25,40 +25,66 @@ import javax.swing.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class GDesktop
-    extends JFrame
+public class GDesktop extends JFrame
 {
   protected static JMenu windowMenu = new JMenu();
+
   JMenuBar desktopMenubar = new JMenuBar();
+
   JMenu FileMenu = new JMenu();
+
   JMenu HelpMenu = new JMenu();
+
   protected JMenu VamsasMenu = new JMenu();
+
   protected JMenu VamsasStMenu = new JMenu();
+
   JMenuItem inputLocalFileMenuItem = new JMenuItem();
+
   JMenuItem inputURLMenuItem = new JMenuItem();
+
   JMenuItem inputTextboxMenuItem = new JMenuItem();
+
   JMenuItem quit = new JMenuItem();
+
   JMenuItem aboutMenuItem = new JMenuItem();
+
   JMenuItem documentationMenuItem = new JMenuItem();
+
   FlowLayout flowLayout1 = new FlowLayout();
+
   protected JMenu toolsMenu = new JMenu();
+
   JMenuItem preferences = new JMenuItem();
+
   JMenuItem saveState = new JMenuItem();
+
   JMenuItem loadState = new JMenuItem();
+
   JMenu inputMenu = new JMenu();
+
   protected JMenuItem vamsasStart = new JMenuItem();
+
   protected JMenuItem vamsasImport = new JMenuItem();
+
   protected JMenuItem vamsasSave = new JMenuItem();
+
   JMenuItem inputSequence = new JMenuItem();
+
   protected JMenuItem vamsasStop = new JMenuItem();
+
   JMenuItem closeAll = new JMenuItem();
+
   JMenuItem raiseRelated = new JMenuItem();
+
   JMenuItem minimizeAssociated = new JMenuItem();
+
   protected JCheckBoxMenuItem showMemusage = new JCheckBoxMenuItem();
+
   JMenuItem garbageCollect = new JMenuItem();
 
   /**
@@ -70,8 +96,7 @@ public class GDesktop
     {
       jbInit();
       this.setJMenuBar(desktopMenubar);
-    }
-    catch (Exception e)
+    } catch (Exception e)
     {
       e.printStackTrace();
     }
@@ -92,11 +117,11 @@ public class GDesktop
 
   /**
    * DOCUMENT ME!
-   *
-   * @throws Exception DOCUMENT ME!
+   * 
+   * @throws Exception
+   *                 DOCUMENT ME!
    */
-  private void jbInit()
-      throws Exception
+  private void jbInit() throws Exception
   {
     FileMenu.setText("File");
     HelpMenu.setText("Help");
@@ -105,16 +130,17 @@ public class GDesktop
     VamsasStMenu.setText("Connect to");
     VamsasStMenu.setToolTipText("Join an existing vamsas session");
     inputLocalFileMenuItem.setText("from File");
-    inputLocalFileMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-        java.awt.event.KeyEvent.VK_O,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    inputLocalFileMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        inputLocalFileMenuItem_actionPerformed(null);
-      }
-    });
+    inputLocalFileMenuItem.setAccelerator(javax.swing.KeyStroke
+            .getKeyStroke(java.awt.event.KeyEvent.VK_O, Toolkit
+                    .getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    inputLocalFileMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                inputLocalFileMenuItem_actionPerformed(null);
+              }
+            });
     inputURLMenuItem.setText("from URL");
     inputURLMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
@@ -124,13 +150,14 @@ public class GDesktop
       }
     });
     inputTextboxMenuItem.setText("from Textbox");
-    inputTextboxMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        inputTextboxMenuItem_actionPerformed(null);
-      }
-    });
+    inputTextboxMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                inputTextboxMenuItem_actionPerformed(null);
+              }
+            });
     quit.setText("Quit");
     quit.addActionListener(new java.awt.event.ActionListener()
     {
@@ -148,15 +175,16 @@ public class GDesktop
       }
     });
     documentationMenuItem.setText("Documentation");
-    documentationMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-        java.awt.event.KeyEvent.VK_F1, 0, false));
-    documentationMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        documentationMenuItem_actionPerformed(e);
-      }
-    });
+    documentationMenuItem.setAccelerator(javax.swing.KeyStroke
+            .getKeyStroke(java.awt.event.KeyEvent.VK_F1, 0, false));
+    documentationMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                documentationMenuItem_actionPerformed(e);
+              }
+            });
     this.getContentPane().setLayout(flowLayout1);
     windowMenu.setText("Window");
     preferences.setText("Preferences...");
@@ -300,19 +328,19 @@ public class GDesktop
     windowMenu.add(raiseRelated);
     windowMenu.add(minimizeAssociated);
     windowMenu.addSeparator();
-    //    inputMenu.add(vamsasLoad);
+    // inputMenu.add(vamsasLoad);
   }
 
   protected void showMemusage_actionPerformed(ActionEvent e)
   {
     // TODO Auto-generated method stub
-    
+
   }
 
   protected void garbageCollect_actionPerformed(ActionEvent e)
   {
     // TODO Auto-generated method stub
-    
+
   }
 
   protected void vamsasStMenu_actionPerformed()
@@ -325,30 +353,34 @@ public class GDesktop
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
-  protected void inputLocalFileMenuItem_actionPerformed(jalview.gui.
-      AlignViewport av)
+  protected void inputLocalFileMenuItem_actionPerformed(
+          jalview.gui.AlignViewport av)
   {
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
-  protected void inputURLMenuItem_actionPerformed(jalview.gui.AlignViewport av)
+  protected void inputURLMenuItem_actionPerformed(
+          jalview.gui.AlignViewport av)
   {
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
-  protected void inputTextboxMenuItem_actionPerformed(jalview.gui.AlignViewport
-      av)
+  protected void inputTextboxMenuItem_actionPerformed(
+          jalview.gui.AlignViewport av)
   {
   }
 
@@ -361,8 +393,9 @@ public class GDesktop
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void aboutMenuItem_actionPerformed(ActionEvent e)
   {
@@ -370,8 +403,9 @@ public class GDesktop
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void documentationMenuItem_actionPerformed(ActionEvent e)
   {
@@ -379,8 +413,9 @@ public class GDesktop
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void SaveState_actionPerformed(ActionEvent e)
   {
@@ -388,8 +423,9 @@ public class GDesktop
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void preferences_actionPerformed(ActionEvent e)
   {
@@ -397,8 +433,9 @@ public class GDesktop
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void saveState_actionPerformed(ActionEvent e)
   {
@@ -406,8 +443,9 @@ public class GDesktop
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void loadState_actionPerformed(ActionEvent e)
   {
@@ -415,8 +453,9 @@ public class GDesktop
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void loadJalviewAlign_actionPerformed(ActionEvent e)
   {
diff --git a/src/jalview/jbgui/GFinder.java b/src/jalview/jbgui/GFinder.java
index 9d72d26..6444582 100755
--- a/src/jalview/jbgui/GFinder.java
+++ b/src/jalview/jbgui/GFinder.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -26,38 +26,50 @@ import javax.swing.event.*;
 import jalview.datamodel.*;
 import jalview.io.*;
 
-public class GFinder
-    extends JPanel
+public class GFinder extends JPanel
 {
   JLabel jLabel1 = new JLabel();
+
   protected JButton findAll = new JButton();
+
   protected JButton findNext = new JButton();
+
   JPanel jPanel1 = new JPanel();
+
   GridLayout gridLayout1 = new GridLayout();
+
   protected JButton createNewGroup = new JButton();
+
   JScrollPane jScrollPane1 = new JScrollPane();
+
   protected JTextArea textfield = new JTextArea();
+
   BorderLayout borderLayout1 = new BorderLayout();
+
   JPanel jPanel2 = new JPanel();
+
   JPanel jPanel3 = new JPanel();
+
   JPanel jPanel4 = new JPanel();
+
   BorderLayout borderLayout2 = new BorderLayout();
+
   JPanel jPanel6 = new JPanel();
+
   protected JCheckBox caseSensitive = new JCheckBox();
+
   public GFinder()
   {
     try
     {
       jbInit();
-    }
-    catch (Exception e)
+    } catch (Exception e)
     {
       e.printStackTrace();
     }
   }
 
-  private void jbInit()
-      throws Exception
+  private void jbInit() throws Exception
   {
     jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
     jLabel1.setText("Find");
@@ -168,14 +180,14 @@ public class GFinder
           try
           {
             al = new FormatAdapter().readFile(str, "Paste", "FASTA");
+          } catch (Exception ex)
+          {
           }
-          catch (Exception ex)
-          {}
           if (al != null && al.getHeight() > 0)
           {
             str = jalview.analysis.AlignSeq.extractGaps(
-                jalview.util.Comparison.GapChars,
-                al.getSequenceAt(0).getSequenceAsString());
+                    jalview.util.Comparison.GapChars, al.getSequenceAt(0)
+                            .getSequenceAsString());
 
             textfield.setText(str);
           }
diff --git a/src/jalview/jbgui/GFontChooser.java b/src/jalview/jbgui/GFontChooser.java
index 6c04561..a30293a 100755
--- a/src/jalview/jbgui/GFontChooser.java
+++ b/src/jalview/jbgui/GFontChooser.java
@@ -1,252 +1,274 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.jbgui;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class GFontChooser
-    extends JPanel
-{
-  JLabel jLabel1 = new JLabel();
-  protected JComboBox fontSize = new JComboBox();
-  protected JComboBox fontStyle = new JComboBox();
-  JLabel jLabel2 = new JLabel();
-  JLabel jLabel3 = new JLabel();
-  protected JComboBox fontName = new JComboBox();
-  JButton ok = new JButton();
-  JButton cancel = new JButton();
-  JPanel jPanel1 = new JPanel();
-  JPanel jPanel2 = new JPanel();
-  JPanel jPanel3 = new JPanel();
-  BorderLayout borderLayout1 = new BorderLayout();
-  BorderLayout borderLayout2 = new BorderLayout();
-  BorderLayout borderLayout3 = new BorderLayout();
-  protected JButton defaultButton = new JButton();
-  protected JCheckBox smoothFont = new JCheckBox();
-  BorderLayout borderLayout4 = new BorderLayout();
-  protected JCheckBox monospaced = new JCheckBox();
-  JPanel jPanel4 = new JPanel();
-
-  /**
-   * Creates a new GFontChooser object.
-   */
-  public GFontChooser()
-  {
-    try
-    {
-      jbInit();
-    }
-    catch (Exception e)
-    {
-      e.printStackTrace();
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @throws Exception DOCUMENT ME!
-   */
-  private void jbInit()
-      throws Exception
-  {
-    jLabel1.setFont(new java.awt.Font("Verdana", 0, 11));
-    jLabel1.setHorizontalAlignment(SwingConstants.RIGHT);
-    jLabel1.setText("Font: ");
-    jLabel1.setVerticalTextPosition(javax.swing.SwingConstants.CENTER);
-    this.setLayout(null);
-    fontSize.setFont(new java.awt.Font("Verdana", 0, 11));
-    fontSize.setOpaque(false);
-    fontSize.setPreferredSize(new Dimension(50, 21));
-    fontSize.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        fontSize_actionPerformed(e);
-      }
-    });
-    fontStyle.setFont(new java.awt.Font("Verdana", 0, 11));
-    fontStyle.setOpaque(false);
-    fontStyle.setPreferredSize(new Dimension(90, 21));
-    fontStyle.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        fontStyle_actionPerformed(e);
-      }
-    });
-    jLabel2.setFont(new java.awt.Font("Verdana", 0, 11));
-    jLabel2.setHorizontalAlignment(SwingConstants.RIGHT);
-    jLabel2.setText("Size: ");
-    jLabel2.setVerticalTextPosition(javax.swing.SwingConstants.CENTER);
-    jLabel3.setFont(new java.awt.Font("Verdana", 0, 11));
-    jLabel3.setHorizontalAlignment(SwingConstants.RIGHT);
-    jLabel3.setText("Style: ");
-    jLabel3.setVerticalTextPosition(javax.swing.SwingConstants.CENTER);
-    fontName.setFont(new java.awt.Font("Verdana", 0, 11));
-    fontName.setMaximumSize(new Dimension(32767, 32767));
-    fontName.setMinimumSize(new Dimension(300, 21));
-    fontName.setOpaque(false);
-    fontName.setPreferredSize(new Dimension(180, 21));
-    fontName.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        fontName_actionPerformed(e);
-      }
-    });
-    ok.setFont(new java.awt.Font("Verdana", 0, 11));
-    ok.setText("OK");
-    ok.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        ok_actionPerformed(e);
-      }
-    });
-    cancel.setFont(new java.awt.Font("Verdana", 0, 11));
-    cancel.setText("Cancel");
-    cancel.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        cancel_actionPerformed(e);
-      }
-    });
-    this.setBackground(Color.white);
-    jPanel1.setOpaque(false);
-    jPanel1.setBounds(new Rectangle(5, 6, 308, 23));
-    jPanel1.setLayout(borderLayout1);
-    jPanel2.setOpaque(false);
-    jPanel2.setBounds(new Rectangle(5, 37, 128, 21));
-    jPanel2.setLayout(borderLayout3);
-    jPanel3.setOpaque(false);
-    jPanel3.setBounds(new Rectangle(174, 38, 134, 21));
-    jPanel3.setLayout(borderLayout2);
-    defaultButton.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    defaultButton.setText("Set as Default");
-    defaultButton.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        defaultButton_actionPerformed(e);
-      }
-    });
-    smoothFont.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    smoothFont.setOpaque(false);
-    smoothFont.setText("Anti-alias Fonts (Slower to render)");
-    smoothFont.setBounds(new Rectangle(41, 65, 223, 23));
-    smoothFont.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        smoothFont_actionPerformed(e);
-      }
-    });
-    monospaced.setEnabled(false);
-    monospaced.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    monospaced.setOpaque(false);
-    monospaced.setToolTipText("Monospaced fonts are faster to render");
-    monospaced.setText("Monospaced");
-    jPanel4.setOpaque(false);
-    jPanel4.setBounds(new Rectangle(24, 92, 259, 35));
-    jPanel1.add(jLabel1, BorderLayout.WEST);
-    jPanel1.add(fontName, BorderLayout.CENTER);
-    jPanel1.add(monospaced, java.awt.BorderLayout.EAST);
-    this.add(jPanel3, null);
-    this.add(jPanel2, null);
-    jPanel2.add(fontSize, java.awt.BorderLayout.CENTER);
-    jPanel2.add(jLabel2, java.awt.BorderLayout.WEST);
-    jPanel4.add(defaultButton);
-    jPanel4.add(ok);
-    jPanel4.add(cancel);
-    this.add(smoothFont);
-    this.add(jPanel4);
-    jPanel3.add(jLabel3, java.awt.BorderLayout.WEST);
-    jPanel3.add(fontStyle, java.awt.BorderLayout.CENTER);
-    this.add(jPanel1, null);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void ok_actionPerformed(ActionEvent e)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void cancel_actionPerformed(ActionEvent e)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void fontName_actionPerformed(ActionEvent e)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void fontSize_actionPerformed(ActionEvent e)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void fontStyle_actionPerformed(ActionEvent e)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  public void defaultButton_actionPerformed(ActionEvent e)
-  {
-  }
-
-  public void smoothFont_actionPerformed(ActionEvent e)
-  {
-
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.jbgui;
+
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class GFontChooser extends JPanel
+{
+  JLabel jLabel1 = new JLabel();
+
+  protected JComboBox fontSize = new JComboBox();
+
+  protected JComboBox fontStyle = new JComboBox();
+
+  JLabel jLabel2 = new JLabel();
+
+  JLabel jLabel3 = new JLabel();
+
+  protected JComboBox fontName = new JComboBox();
+
+  JButton ok = new JButton();
+
+  JButton cancel = new JButton();
+
+  JPanel jPanel1 = new JPanel();
+
+  JPanel jPanel2 = new JPanel();
+
+  JPanel jPanel3 = new JPanel();
+
+  BorderLayout borderLayout1 = new BorderLayout();
+
+  BorderLayout borderLayout2 = new BorderLayout();
+
+  BorderLayout borderLayout3 = new BorderLayout();
+
+  protected JButton defaultButton = new JButton();
+
+  protected JCheckBox smoothFont = new JCheckBox();
+
+  BorderLayout borderLayout4 = new BorderLayout();
+
+  protected JCheckBox monospaced = new JCheckBox();
+
+  JPanel jPanel4 = new JPanel();
+
+  /**
+   * Creates a new GFontChooser object.
+   */
+  public GFontChooser()
+  {
+    try
+    {
+      jbInit();
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @throws Exception
+   *                 DOCUMENT ME!
+   */
+  private void jbInit() throws Exception
+  {
+    jLabel1.setFont(new java.awt.Font("Verdana", 0, 11));
+    jLabel1.setHorizontalAlignment(SwingConstants.RIGHT);
+    jLabel1.setText("Font: ");
+    jLabel1.setVerticalTextPosition(javax.swing.SwingConstants.CENTER);
+    this.setLayout(null);
+    fontSize.setFont(new java.awt.Font("Verdana", 0, 11));
+    fontSize.setOpaque(false);
+    fontSize.setPreferredSize(new Dimension(50, 21));
+    fontSize.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        fontSize_actionPerformed(e);
+      }
+    });
+    fontStyle.setFont(new java.awt.Font("Verdana", 0, 11));
+    fontStyle.setOpaque(false);
+    fontStyle.setPreferredSize(new Dimension(90, 21));
+    fontStyle.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        fontStyle_actionPerformed(e);
+      }
+    });
+    jLabel2.setFont(new java.awt.Font("Verdana", 0, 11));
+    jLabel2.setHorizontalAlignment(SwingConstants.RIGHT);
+    jLabel2.setText("Size: ");
+    jLabel2.setVerticalTextPosition(javax.swing.SwingConstants.CENTER);
+    jLabel3.setFont(new java.awt.Font("Verdana", 0, 11));
+    jLabel3.setHorizontalAlignment(SwingConstants.RIGHT);
+    jLabel3.setText("Style: ");
+    jLabel3.setVerticalTextPosition(javax.swing.SwingConstants.CENTER);
+    fontName.setFont(new java.awt.Font("Verdana", 0, 11));
+    fontName.setMaximumSize(new Dimension(32767, 32767));
+    fontName.setMinimumSize(new Dimension(300, 21));
+    fontName.setOpaque(false);
+    fontName.setPreferredSize(new Dimension(180, 21));
+    fontName.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        fontName_actionPerformed(e);
+      }
+    });
+    ok.setFont(new java.awt.Font("Verdana", 0, 11));
+    ok.setText("OK");
+    ok.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        ok_actionPerformed(e);
+      }
+    });
+    cancel.setFont(new java.awt.Font("Verdana", 0, 11));
+    cancel.setText("Cancel");
+    cancel.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        cancel_actionPerformed(e);
+      }
+    });
+    this.setBackground(Color.white);
+    jPanel1.setOpaque(false);
+    jPanel1.setBounds(new Rectangle(5, 6, 308, 23));
+    jPanel1.setLayout(borderLayout1);
+    jPanel2.setOpaque(false);
+    jPanel2.setBounds(new Rectangle(5, 37, 128, 21));
+    jPanel2.setLayout(borderLayout3);
+    jPanel3.setOpaque(false);
+    jPanel3.setBounds(new Rectangle(174, 38, 134, 21));
+    jPanel3.setLayout(borderLayout2);
+    defaultButton.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    defaultButton.setText("Set as Default");
+    defaultButton.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        defaultButton_actionPerformed(e);
+      }
+    });
+    smoothFont.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    smoothFont.setOpaque(false);
+    smoothFont.setText("Anti-alias Fonts (Slower to render)");
+    smoothFont.setBounds(new Rectangle(41, 65, 223, 23));
+    smoothFont.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        smoothFont_actionPerformed(e);
+      }
+    });
+    monospaced.setEnabled(false);
+    monospaced.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    monospaced.setOpaque(false);
+    monospaced.setToolTipText("Monospaced fonts are faster to render");
+    monospaced.setText("Monospaced");
+    jPanel4.setOpaque(false);
+    jPanel4.setBounds(new Rectangle(24, 92, 259, 35));
+    jPanel1.add(jLabel1, BorderLayout.WEST);
+    jPanel1.add(fontName, BorderLayout.CENTER);
+    jPanel1.add(monospaced, java.awt.BorderLayout.EAST);
+    this.add(jPanel3, null);
+    this.add(jPanel2, null);
+    jPanel2.add(fontSize, java.awt.BorderLayout.CENTER);
+    jPanel2.add(jLabel2, java.awt.BorderLayout.WEST);
+    jPanel4.add(defaultButton);
+    jPanel4.add(ok);
+    jPanel4.add(cancel);
+    this.add(smoothFont);
+    this.add(jPanel4);
+    jPanel3.add(jLabel3, java.awt.BorderLayout.WEST);
+    jPanel3.add(fontStyle, java.awt.BorderLayout.CENTER);
+    this.add(jPanel1, null);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
+   */
+  protected void ok_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
+   */
+  protected void cancel_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
+   */
+  protected void fontName_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
+   */
+  protected void fontSize_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
+   */
+  protected void fontStyle_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
+   */
+  public void defaultButton_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void smoothFont_actionPerformed(ActionEvent e)
+  {
+
+  }
+}
diff --git a/src/jalview/jbgui/GPCAPanel.java b/src/jalview/jbgui/GPCAPanel.java
index 5c17ba7..6ad36e8 100755
--- a/src/jalview/jbgui/GPCAPanel.java
+++ b/src/jalview/jbgui/GPCAPanel.java
@@ -1,255 +1,272 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.jbgui;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.event.*;
-
-public class GPCAPanel
-    extends JInternalFrame
-{
-  JPanel jPanel2 = new JPanel();
-  JLabel jLabel1 = new JLabel();
-  JLabel jLabel2 = new JLabel();
-  JLabel jLabel3 = new JLabel();
-  protected JComboBox xCombobox = new JComboBox();
-  protected JComboBox yCombobox = new JComboBox();
-  protected JComboBox zCombobox = new JComboBox();
-  FlowLayout flowLayout1 = new FlowLayout();
-  BorderLayout borderLayout1 = new BorderLayout();
-  JMenuBar jMenuBar1 = new JMenuBar();
-  JMenu fileMenu = new JMenu();
-  JMenu saveMenu = new JMenu();
-  JMenuItem eps = new JMenuItem();
-  JMenuItem png = new JMenuItem();
-  JMenuItem print = new JMenuItem();
-  JMenuItem outputValues = new JMenuItem();
-  protected JMenu viewMenu = new JMenu();
-  protected JCheckBoxMenuItem showLabels = new JCheckBoxMenuItem();
-  JMenuItem bgcolour = new JMenuItem();
-  JMenuItem originalSeqData = new JMenuItem();
-  protected JMenu associateViewsMenu = new JMenu();
-
-  public GPCAPanel()
-  {
-    try
-    {
-      jbInit();
-    }
-    catch (Exception e)
-    {
-      e.printStackTrace();
-    }
-
-    for (int i = 1; i < 8; i++)
-    {
-      xCombobox.addItem("dim " + i);
-      yCombobox.addItem("dim " + i);
-      zCombobox.addItem("dim " + i);
-    }
-
-    setJMenuBar(jMenuBar1);
-  }
-
-  private void jbInit()
-      throws Exception
-  {
-    this.getContentPane().setLayout(borderLayout1);
-    jPanel2.setLayout(flowLayout1);
-    jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
-    jLabel1.setText("x=");
-    jLabel2.setFont(new java.awt.Font("Verdana", 0, 12));
-    jLabel2.setText("y=");
-    jLabel3.setFont(new java.awt.Font("Verdana", 0, 12));
-    jLabel3.setText("z=");
-    jPanel2.setBackground(Color.white);
-    jPanel2.setBorder(null);
-    zCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
-    zCombobox.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        zCombobox_actionPerformed(e);
-      }
-    });
-    yCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
-    yCombobox.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        yCombobox_actionPerformed(e);
-      }
-    });
-    xCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
-    xCombobox.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        xCombobox_actionPerformed(e);
-      }
-    });
-    fileMenu.setText("File");
-    saveMenu.setText("Save as");
-    eps.setText("EPS");
-    eps.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        eps_actionPerformed(e);
-      }
-    });
-    png.setText("PNG");
-    png.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        png_actionPerformed(e);
-      }
-    });
-    outputValues.setText("Output Values...");
-    outputValues.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        outputValues_actionPerformed(e);
-      }
-    });
-    print.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        print_actionPerformed(e);
-      }
-    });
-    viewMenu.setText("View");
-    viewMenu.addMenuListener(new MenuListener()
-    {
-      public void menuSelected(MenuEvent e)
-      {
-        viewMenu_menuSelected();
-      }
-
-      public void menuDeselected(MenuEvent e)
-      {
-      }
-
-      public void menuCanceled(MenuEvent e)
-      {
-      }
-    });
-    showLabels.setText("Show Labels");
-    showLabels.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        showLabels_actionPerformed(e);
-      }
-    });
-    print.setText("Print");
-    bgcolour.setText("Background Colour...");
-    bgcolour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        bgcolour_actionPerformed(e);
-      }
-    });
-    originalSeqData.setText("Input Data...");
-    originalSeqData.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        originalSeqData_actionPerformed(e);
-      }
-    });
-    associateViewsMenu.setText("Associate Nodes With");
-    this.getContentPane().add(jPanel2, BorderLayout.SOUTH);
-    jPanel2.add(jLabel1, null);
-    jPanel2.add(xCombobox, null);
-    jPanel2.add(jLabel2, null);
-    jPanel2.add(yCombobox, null);
-    jPanel2.add(jLabel3, null);
-    jPanel2.add(zCombobox, null);
-    jMenuBar1.add(fileMenu);
-    jMenuBar1.add(viewMenu);
-    fileMenu.add(saveMenu);
-    fileMenu.add(outputValues);
-    fileMenu.add(print);
-    fileMenu.add(originalSeqData);
-    saveMenu.add(eps);
-    saveMenu.add(png);
-    viewMenu.add(showLabels);
-    viewMenu.add(bgcolour);
-    viewMenu.add(associateViewsMenu);
-  }
-
-  protected void xCombobox_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void yCombobox_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void zCombobox_actionPerformed(ActionEvent e)
-  {
-  }
-
-  public void eps_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void png_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void outputValues_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void print_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void showLabels_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void bgcolour_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void originalSeqData_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void viewMenu_menuSelected()
-  {
-
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.jbgui;
+
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+import javax.swing.event.*;
+
+public class GPCAPanel extends JInternalFrame
+{
+  JPanel jPanel2 = new JPanel();
+
+  JLabel jLabel1 = new JLabel();
+
+  JLabel jLabel2 = new JLabel();
+
+  JLabel jLabel3 = new JLabel();
+
+  protected JComboBox xCombobox = new JComboBox();
+
+  protected JComboBox yCombobox = new JComboBox();
+
+  protected JComboBox zCombobox = new JComboBox();
+
+  FlowLayout flowLayout1 = new FlowLayout();
+
+  BorderLayout borderLayout1 = new BorderLayout();
+
+  JMenuBar jMenuBar1 = new JMenuBar();
+
+  JMenu fileMenu = new JMenu();
+
+  JMenu saveMenu = new JMenu();
+
+  JMenuItem eps = new JMenuItem();
+
+  JMenuItem png = new JMenuItem();
+
+  JMenuItem print = new JMenuItem();
+
+  JMenuItem outputValues = new JMenuItem();
+
+  protected JMenu viewMenu = new JMenu();
+
+  protected JCheckBoxMenuItem showLabels = new JCheckBoxMenuItem();
+
+  JMenuItem bgcolour = new JMenuItem();
+
+  JMenuItem originalSeqData = new JMenuItem();
+
+  protected JMenu associateViewsMenu = new JMenu();
+
+  public GPCAPanel()
+  {
+    try
+    {
+      jbInit();
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+
+    for (int i = 1; i < 8; i++)
+    {
+      xCombobox.addItem("dim " + i);
+      yCombobox.addItem("dim " + i);
+      zCombobox.addItem("dim " + i);
+    }
+
+    setJMenuBar(jMenuBar1);
+  }
+
+  private void jbInit() throws Exception
+  {
+    this.getContentPane().setLayout(borderLayout1);
+    jPanel2.setLayout(flowLayout1);
+    jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
+    jLabel1.setText("x=");
+    jLabel2.setFont(new java.awt.Font("Verdana", 0, 12));
+    jLabel2.setText("y=");
+    jLabel3.setFont(new java.awt.Font("Verdana", 0, 12));
+    jLabel3.setText("z=");
+    jPanel2.setBackground(Color.white);
+    jPanel2.setBorder(null);
+    zCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
+    zCombobox.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        zCombobox_actionPerformed(e);
+      }
+    });
+    yCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
+    yCombobox.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        yCombobox_actionPerformed(e);
+      }
+    });
+    xCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
+    xCombobox.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        xCombobox_actionPerformed(e);
+      }
+    });
+    fileMenu.setText("File");
+    saveMenu.setText("Save as");
+    eps.setText("EPS");
+    eps.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        eps_actionPerformed(e);
+      }
+    });
+    png.setText("PNG");
+    png.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        png_actionPerformed(e);
+      }
+    });
+    outputValues.setText("Output Values...");
+    outputValues.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        outputValues_actionPerformed(e);
+      }
+    });
+    print.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        print_actionPerformed(e);
+      }
+    });
+    viewMenu.setText("View");
+    viewMenu.addMenuListener(new MenuListener()
+    {
+      public void menuSelected(MenuEvent e)
+      {
+        viewMenu_menuSelected();
+      }
+
+      public void menuDeselected(MenuEvent e)
+      {
+      }
+
+      public void menuCanceled(MenuEvent e)
+      {
+      }
+    });
+    showLabels.setText("Show Labels");
+    showLabels.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        showLabels_actionPerformed(e);
+      }
+    });
+    print.setText("Print");
+    bgcolour.setText("Background Colour...");
+    bgcolour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        bgcolour_actionPerformed(e);
+      }
+    });
+    originalSeqData.setText("Input Data...");
+    originalSeqData.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        originalSeqData_actionPerformed(e);
+      }
+    });
+    associateViewsMenu.setText("Associate Nodes With");
+    this.getContentPane().add(jPanel2, BorderLayout.SOUTH);
+    jPanel2.add(jLabel1, null);
+    jPanel2.add(xCombobox, null);
+    jPanel2.add(jLabel2, null);
+    jPanel2.add(yCombobox, null);
+    jPanel2.add(jLabel3, null);
+    jPanel2.add(zCombobox, null);
+    jMenuBar1.add(fileMenu);
+    jMenuBar1.add(viewMenu);
+    fileMenu.add(saveMenu);
+    fileMenu.add(outputValues);
+    fileMenu.add(print);
+    fileMenu.add(originalSeqData);
+    saveMenu.add(eps);
+    saveMenu.add(png);
+    viewMenu.add(showLabels);
+    viewMenu.add(bgcolour);
+    viewMenu.add(associateViewsMenu);
+  }
+
+  protected void xCombobox_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void yCombobox_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void zCombobox_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void eps_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void png_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void outputValues_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void print_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void showLabels_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void bgcolour_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void originalSeqData_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void viewMenu_menuSelected()
+  {
+
+  }
+}
diff --git a/src/jalview/jbgui/GPairwiseAlignPanel.java b/src/jalview/jbgui/GPairwiseAlignPanel.java
index f690a21..b4e6321 100755
--- a/src/jalview/jbgui/GPairwiseAlignPanel.java
+++ b/src/jalview/jbgui/GPairwiseAlignPanel.java
@@ -1,90 +1,94 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.jbgui;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class GPairwiseAlignPanel
-    extends JPanel
-{
-  protected JScrollPane scrollPane = new JScrollPane();
-  protected JTextArea textarea = new JTextArea();
-  protected JButton viewInEditorButton = new JButton();
-  JPanel jPanel1 = new JPanel();
-  BorderLayout borderLayout1 = new BorderLayout();
-
-  /**
-   * Creates a new GPairwiseAlignPanel object.
-   */
-  public GPairwiseAlignPanel()
-  {
-    try
-    {
-      jbInit();
-    }
-    catch (Exception e)
-    {
-      e.printStackTrace();
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @throws Exception DOCUMENT ME!
-   */
-  private void jbInit()
-      throws Exception
-  {
-    this.setLayout(borderLayout1);
-    textarea.setFont(new java.awt.Font("Monospaced", 0, 12));
-    textarea.setText("");
-    textarea.setWrapStyleWord(false);
-    viewInEditorButton.setFont(new java.awt.Font("Verdana", 0, 12));
-    viewInEditorButton.setText("View in alignment editor");
-    viewInEditorButton.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        viewInEditorButton_actionPerformed(e);
-      }
-    });
-    this.add(scrollPane, BorderLayout.CENTER);
-    scrollPane.getViewport().add(textarea, null);
-    this.add(jPanel1, BorderLayout.SOUTH);
-    jPanel1.add(viewInEditorButton, null);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void viewInEditorButton_actionPerformed(ActionEvent e)
-  {
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.jbgui;
+
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class GPairwiseAlignPanel extends JPanel
+{
+  protected JScrollPane scrollPane = new JScrollPane();
+
+  protected JTextArea textarea = new JTextArea();
+
+  protected JButton viewInEditorButton = new JButton();
+
+  JPanel jPanel1 = new JPanel();
+
+  BorderLayout borderLayout1 = new BorderLayout();
+
+  /**
+   * Creates a new GPairwiseAlignPanel object.
+   */
+  public GPairwiseAlignPanel()
+  {
+    try
+    {
+      jbInit();
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @throws Exception
+   *                 DOCUMENT ME!
+   */
+  private void jbInit() throws Exception
+  {
+    this.setLayout(borderLayout1);
+    textarea.setFont(new java.awt.Font("Monospaced", 0, 12));
+    textarea.setText("");
+    textarea.setWrapStyleWord(false);
+    viewInEditorButton.setFont(new java.awt.Font("Verdana", 0, 12));
+    viewInEditorButton.setText("View in alignment editor");
+    viewInEditorButton
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                viewInEditorButton_actionPerformed(e);
+              }
+            });
+    this.add(scrollPane, BorderLayout.CENTER);
+    scrollPane.getViewport().add(textarea, null);
+    this.add(jPanel1, BorderLayout.SOUTH);
+    jPanel1.add(viewInEditorButton, null);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
+   */
+  protected void viewInEditorButton_actionPerformed(ActionEvent e)
+  {
+  }
+}
diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index 842ade9..e28581f 100755
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -1,565 +1,642 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.jbgui;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.border.*;
-import javax.swing.event.*;
-import java.awt.Rectangle;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class GPreferences
-    extends JPanel
-{
-  JTabbedPane tabbedPane = new JTabbedPane();
-
-  JButton ok = new JButton();
-  JButton cancel = new JButton();
-  JPanel okCancelPanel = new JPanel();
-  BorderLayout borderLayout1 = new BorderLayout();
-  protected JCheckBox quality = new JCheckBox();
-  JPanel visualTab = new JPanel();
-  protected JCheckBox fullScreen = new JCheckBox();
-  protected JCheckBox conservation = new JCheckBox();
-  protected JCheckBox identity = new JCheckBox();
-  protected JCheckBox annotations = new JCheckBox();
-  JLabel gapLabel = new JLabel();
-  protected JComboBox colour = new JComboBox();
-  JLabel colourLabel = new JLabel();
-  JLabel fontLabel = new JLabel();
-  protected JComboBox fontSizeCB = new JComboBox();
-  protected JComboBox fontStyleCB = new JComboBox();
-  protected JComboBox fontNameCB = new JComboBox();
-  protected JComboBox gapSymbolCB = new JComboBox();
-  protected JCheckBox startupCheckbox = new JCheckBox();
-  protected JTextField startupFileTextfield = new JTextField();
-  JPanel connectTab = new JPanel();
-  JLabel serverLabel = new JLabel();
-  protected JList linkURLList = new JList();
-  protected JTextField proxyServerTB = new JTextField();
-  protected JTextField proxyPortTB = new JTextField();
-  JLabel portLabel = new JLabel();
-  JLabel browserLabel = new JLabel();
-  protected JTextField defaultBrowser = new JTextField();
-  JButton newLink = new JButton();
-  JButton editLink = new JButton();
-  JButton deleteLink = new JButton();
-  JScrollPane linkScrollPane = new JScrollPane();
-  JPanel linkPanel = new JPanel();
-  BorderLayout borderLayout2 = new BorderLayout();
-  JPanel editLinkButtons = new JPanel();
-  GridLayout gridLayout1 = new GridLayout();
-  protected JList linkNameList = new JList();
-  JPanel linkPanel2 = new JPanel();
-  BorderLayout borderLayout3 = new BorderLayout();
-  protected JCheckBox useProxy = new JCheckBox();
-  JPanel jPanel1 = new JPanel();
-  TitledBorder titledBorder1 = new TitledBorder("Proxy Server");
-  TitledBorder titledBorder2 = new TitledBorder("File Output");
-  GridBagLayout gridBagLayout2 = new GridBagLayout();
-  GridBagLayout gridBagLayout1 = new GridBagLayout();
-  GridBagLayout gridBagLayout3 = new GridBagLayout();
-  protected JComboBox sortby = new JComboBox();
-  JLabel sortLabel = new JLabel();
-  JPanel jPanel2 = new JPanel();
-  GridLayout gridLayout2 = new GridLayout();
-  JPanel jPanel3 = new JPanel();
-  JPanel exportTab = new JPanel();
-  JLabel epsLabel = new JLabel();
-  protected JComboBox epsRendering = new JComboBox();
-  JLabel jLabel1 = new JLabel();
-  protected JCheckBox blcjv = new JCheckBox();
-  protected JCheckBox pileupjv = new JCheckBox();
-  protected JCheckBox clustaljv = new JCheckBox();
-  protected JCheckBox msfjv = new JCheckBox();
-  protected JCheckBox fastajv = new JCheckBox();
-  protected JCheckBox pfamjv = new JCheckBox();
-  FlowLayout flowLayout1 = new FlowLayout();
-  protected JCheckBox pirjv = new JCheckBox();
-  JPanel jPanel11 = new JPanel();
-  Font verdana11 = new java.awt.Font("Verdana", Font.PLAIN, 11);
-  protected JCheckBox seqLimit = new JCheckBox();
-  GridLayout gridLayout3 = new GridLayout();
-  protected JCheckBox smoothFont = new JCheckBox();
-  JPanel calcTab = new JPanel();
-  protected JCheckBox autoCalculateConsCheck = new JCheckBox();
-  protected JCheckBox padGaps = new JCheckBox();
-  protected JCheckBox modellerOutput = new JCheckBox();
-  protected JPanel dasPanel = new JPanel();
-  BorderLayout borderLayout4 = new BorderLayout();
-  protected JCheckBox wrap = new JCheckBox();
-  protected JCheckBox rightAlign = new JCheckBox();
-  protected JCheckBox idItalics = new JCheckBox();
-  protected JCheckBox openoverv = new JCheckBox();
-  /**
-   * Creates a new GPreferences object.
-   */
-  public GPreferences()
-  {
-    try
-    {
-      jbInit();
-    }
-    catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @throws Exception DOCUMENT ME!
-   */
-  private void jbInit()
-      throws Exception
-  {
-    this.setLayout(borderLayout1);
-    ok.setText("OK");
-    ok.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        ok_actionPerformed(e);
-      }
-    });
-    cancel.setText("Cancel");
-    cancel.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        cancel_actionPerformed(e);
-      }
-    });
-    quality.setEnabled(false);
-    quality.setFont(verdana11);
-    quality.setHorizontalAlignment(SwingConstants.RIGHT);
-    quality.setHorizontalTextPosition(SwingConstants.LEFT);
-    quality.setSelected(true);
-    quality.setText("Quality");
-    visualTab.setBorder(new TitledBorder("Open new alignment"));
-    visualTab.setLayout(null);
-    fullScreen.setFont(verdana11);
-    fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
-    fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
-    fullScreen.setText("Maximise Window");
-    conservation.setEnabled(false);
-    conservation.setFont(verdana11);
-    conservation.setHorizontalAlignment(SwingConstants.RIGHT);
-    conservation.setHorizontalTextPosition(SwingConstants.LEFT);
-    conservation.setSelected(true);
-    conservation.setText("Conservation");
-    identity.setEnabled(false);
-    identity.setFont(verdana11);
-    identity.setHorizontalAlignment(SwingConstants.RIGHT);
-    identity.setHorizontalTextPosition(SwingConstants.LEFT);
-    identity.setSelected(true);
-    identity.setText("Consensus");
-    annotations.setFont(verdana11);
-    annotations.setHorizontalAlignment(SwingConstants.RIGHT);
-    annotations.setHorizontalTextPosition(SwingConstants.LEFT);
-    annotations.setSelected(true);
-    annotations.setText("Show Annotations");
-    annotations.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        annotations_actionPerformed(e);
-      }
-    });
-    gapLabel.setFont(verdana11);
-    gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
-    gapLabel.setText("Gap Symbol ");
-    colour.setFont(verdana11);
-    colour.setBounds(new Rectangle(172, 225, 155, 21));
-    colourLabel.setFont(verdana11);
-    colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
-    colourLabel.setText("Colour ");
-    fontLabel.setFont(verdana11);
-    fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
-    fontLabel.setText("Font ");
-    fontSizeCB.setFont(verdana11);
-    fontSizeCB.setBounds(new Rectangle(319, 111, 49, 21));
-    fontStyleCB.setFont(verdana11);
-    fontStyleCB.setBounds(new Rectangle(367, 111, 70, 21));
-    fontNameCB.setFont(verdana11);
-    fontNameCB.setBounds(new Rectangle(172, 111, 147, 21));
-    gapSymbolCB.setFont(verdana11);
-    gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 21));
-    startupCheckbox.setText("Open file");
-    startupCheckbox.setFont(verdana11);
-    startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
-    startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
-    startupCheckbox.setSelected(true);
-    startupFileTextfield.setFont(verdana11);
-    startupFileTextfield.setBounds(new Rectangle(172, 273, 270, 20));
-    startupFileTextfield.addMouseListener(new MouseAdapter()
-    {
-      public void mouseClicked(MouseEvent e)
-      {
-        if (e.getClickCount() > 1)
-        {
-          startupFileTextfield_mouseClicked();
-        }
-      }
-    });
-
-    connectTab.setLayout(gridBagLayout3);
-    serverLabel.setText("Address");
-    serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
-    serverLabel.setFont(verdana11);
-    proxyServerTB.setFont(verdana11);
-    proxyPortTB.setFont(verdana11);
-    portLabel.setFont(verdana11);
-    portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
-    portLabel.setText("Port");
-    browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
-    browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
-    browserLabel.setText("Default Browser (Unix)");
-    defaultBrowser.setFont(verdana11);
-    defaultBrowser.setText("");
-    newLink.setText("New");
-    newLink.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        newLink_actionPerformed(e);
-      }
-    });
-    editLink.setText("Edit");
-    editLink.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        editLink_actionPerformed(e);
-      }
-    });
-    deleteLink.setText("Delete");
-    deleteLink.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        deleteLink_actionPerformed(e);
-      }
-    });
-
-    linkURLList.addListSelectionListener(new ListSelectionListener()
-    {
-      public void valueChanged(ListSelectionEvent e)
-      {
-        int index = linkURLList.getSelectedIndex();
-        linkNameList.setSelectedIndex(index);
-      }
-    });
-
-    linkNameList.addListSelectionListener(new ListSelectionListener()
-    {
-      public void valueChanged(ListSelectionEvent e)
-      {
-        int index = linkNameList.getSelectedIndex();
-        linkURLList.setSelectedIndex(index);
-      }
-    });
-
-    linkScrollPane.setBorder(null);
-    linkPanel.setBorder(new TitledBorder("URL link from Sequence ID"));
-    linkPanel.setLayout(borderLayout2);
-    editLinkButtons.setLayout(gridLayout1);
-    gridLayout1.setRows(3);
-    linkNameList.setFont(verdana11);
-    linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
-    linkPanel2.setLayout(borderLayout3);
-    linkURLList.setFont(verdana11);
-    linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
-
-    defaultBrowser.addMouseListener(new MouseAdapter()
-    {
-      public void mouseClicked(MouseEvent e)
-      {
-        if (e.getClickCount() > 1)
-        {
-          defaultBrowser_mouseClicked(e);
-        }
-      }
-    });
-    useProxy.setFont(verdana11);
-    useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
-    useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
-    useProxy.setText("Use a proxy server");
-    useProxy.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        useProxy_actionPerformed();
-      }
-    });
-    jPanel1.setBorder(titledBorder1);
-    jPanel1.setLayout(gridBagLayout1);
-    sortby.setFont(verdana11);
-    sortby.setBounds(new Rectangle(172, 249, 155, 21));
-    sortLabel.setFont(verdana11);
-    sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
-    sortLabel.setText("Sort by ");
-    jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
-    jPanel2.setLayout(gridLayout2);
-    gridLayout2.setRows(12);
-    jPanel3.setBounds(new Rectangle(173, 35, 274, 26));
-    exportTab.setLayout(null);
-    epsLabel.setFont(verdana11);
-    epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
-    epsLabel.setText("EPS Rendering Style");
-    epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
-    epsRendering.setFont(verdana11);
-    epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
-    jLabel1.setFont(verdana11);
-    jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
-    jLabel1.setText("Append /start-end (/15-380)");
-    jLabel1.setFont(verdana11);
-    fastajv.setFont(verdana11);
-    fastajv.setHorizontalAlignment(SwingConstants.LEFT);
-    clustaljv.setText("Clustal     ");
-    blcjv.setText("BLC     ");
-    fastajv.setText("Fasta     ");
-    msfjv.setText("MSF     ");
-    pfamjv.setText("PFAM     ");
-    pileupjv.setText("Pileup     ");
-    msfjv.setFont(verdana11);
-    msfjv.setHorizontalAlignment(SwingConstants.LEFT);
-    pirjv.setText("PIR     ");
-    jPanel11.setFont(verdana11);
-    jPanel11.setBorder(titledBorder2);
-    jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
-    jPanel11.setLayout(gridLayout3);
-    blcjv.setFont(verdana11);
-    blcjv.setHorizontalAlignment(SwingConstants.LEFT);
-    clustaljv.setFont(verdana11);
-    clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
-    pfamjv.setFont(verdana11);
-    pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
-    pileupjv.setFont(verdana11);
-    pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
-    pirjv.setFont(verdana11);
-    pirjv.setHorizontalAlignment(SwingConstants.LEFT);
-    seqLimit.setFont(verdana11);
-    seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
-    seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
-    seqLimit.setText("Full Sequence Id");
-    gridLayout3.setRows(8);
-    smoothFont.setFont(verdana11);
-    smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
-    smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
-    smoothFont.setText("Smooth Font");
-    calcTab.setLayout(null);
-    autoCalculateConsCheck.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    autoCalculateConsCheck.setText("AutoCalculate Consensus");
-    autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
-    padGaps.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    padGaps.setText("Pad gaps when editing");
-    padGaps.setBounds(new Rectangle(22, 94, 168, 23));
-    modellerOutput.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    modellerOutput.setText("Use Modeller Output");
-    modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
-    dasPanel.setLayout(borderLayout4);
-    wrap.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    wrap.setHorizontalAlignment(SwingConstants.TRAILING);
-    wrap.setHorizontalTextPosition(SwingConstants.LEADING);
-    wrap.setText("Wrap Alignment");
-    rightAlign.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    rightAlign.setForeground(Color.black);
-    rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
-    rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
-    rightAlign.setText("Right Align Ids");
-    idItalics.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
-    idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
-    idItalics.setText("Sequence Name Italics");
-    openoverv.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    openoverv.setActionCommand("Open Overview");
-    openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
-    openoverv.setHorizontalTextPosition(SwingConstants.LEADING);
-    openoverv.setText("Open Overview Window");
-    openoverv.setBounds(new Rectangle(169, 17, 200, 23));
-    jPanel2.add(fullScreen);
-    jPanel2.add(annotations);
-    jPanel2.add(seqLimit);
-    jPanel2.add(rightAlign);
-    jPanel2.add(fontLabel);
-    jPanel2.add(idItalics);
-    jPanel2.add(smoothFont);
-    jPanel2.add(wrap);
-    jPanel2.add(gapLabel);
-    jPanel2.add(colourLabel);
-    jPanel2.add(sortLabel);
-    jPanel2.add(startupCheckbox);
-    visualTab.add(openoverv);
-    visualTab.add(startupFileTextfield);
-    visualTab.add(sortby);
-    visualTab.add(colour);
-    visualTab.add(gapSymbolCB);
-    visualTab.add(jPanel3);
-    visualTab.add(fontNameCB);
-    visualTab.add(fontSizeCB);
-    visualTab.add(fontStyleCB);
-    jPanel3.add(conservation);
-    jPanel3.add(identity);
-    jPanel3.add(quality);
-    visualTab.add(jPanel2);
-    linkPanel.add(editLinkButtons, BorderLayout.EAST);
-    editLinkButtons.add(newLink, null);
-    editLinkButtons.add(editLink, null);
-    editLinkButtons.add(deleteLink, null);
-    linkPanel.add(linkScrollPane, BorderLayout.CENTER);
-    linkScrollPane.getViewport().add(linkPanel2, null);
-    linkPanel2.add(linkURLList, BorderLayout.CENTER);
-    linkPanel2.add(linkNameList, BorderLayout.WEST);
-    okCancelPanel.add(ok);
-    okCancelPanel.add(cancel);
-    this.add(tabbedPane, java.awt.BorderLayout.CENTER);
-
-    this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
-    jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0
-        , GridBagConstraints.WEST, GridBagConstraints.NONE,
-        new Insets(0, 2, 4, 0), 5, 0));
-    jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0
-                                                  , GridBagConstraints.WEST,
-                                                  GridBagConstraints.NONE,
-                                                  new Insets(0, 0, 4, 0), 11, 6));
-    connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0
-        , GridBagConstraints.CENTER, GridBagConstraints.BOTH,
-        new Insets(16, 0, 0, 12), 359, -17));
-    connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0
-        , GridBagConstraints.CENTER, GridBagConstraints.BOTH,
-        new Insets(21, 0, 35, 12), 4, 6));
-    connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0
-        , GridBagConstraints.WEST, GridBagConstraints.NONE,
-        new Insets(16, 0, 0, 0), 5, 1));
-    jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0
-        , GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
-        new Insets(0, 2, 4, 2), 54, 1));
-    jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0
-        , GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
-        new Insets(0, 2, 4, 0), 263, 1));
-    connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0
-        , GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
-        new Insets(15, 0, 0, 15), 307, 1));
-
-    jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0
-                                                 , GridBagConstraints.WEST,
-                                                 GridBagConstraints.NONE,
-                                                 new Insets(0, 2, 5, 185), 2,
-                                                 -4));
-    DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
-    dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
-    gapSymbolCB.setRenderer(dlcr);
-
-    tabbedPane.add(visualTab, "Visual");
-    tabbedPane.add(connectTab, "Connections");
-    tabbedPane.add(exportTab, "Output");
-    jPanel11.add(jLabel1);
-    jPanel11.add(blcjv);
-    jPanel11.add(clustaljv);
-    jPanel11.add(fastajv);
-    jPanel11.add(msfjv);
-    jPanel11.add(pfamjv);
-    jPanel11.add(pileupjv);
-    jPanel11.add(pirjv);
-    exportTab.add(modellerOutput);
-    tabbedPane.add(calcTab, "Editing");
-    calcTab.add(autoCalculateConsCheck);
-    calcTab.add(padGaps);
-    tabbedPane.add(dasPanel, "DAS Settings");
-
-    exportTab.add(epsLabel);
-    exportTab.add(epsRendering);
-    exportTab.add(jPanel11);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  public void ok_actionPerformed(ActionEvent e)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  public void cancel_actionPerformed(ActionEvent e)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  public void annotations_actionPerformed(ActionEvent e)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  public void startupFileTextfield_mouseClicked()
-  {
-  }
-
-  public void newLink_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void editLink_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void deleteLink_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void defaultBrowser_mouseClicked(MouseEvent e)
-  {
-
-  }
-
-  public void linkURLList_keyTyped(KeyEvent e)
-  {
-
-  }
-
-  public void useProxy_actionPerformed()
-  {
-    proxyServerTB.setEnabled(useProxy.isSelected());
-    proxyPortTB.setEnabled(useProxy.isSelected());
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.jbgui;
+
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+import javax.swing.border.*;
+import javax.swing.event.*;
+import java.awt.Rectangle;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class GPreferences extends JPanel
+{
+  JTabbedPane tabbedPane = new JTabbedPane();
+
+  JButton ok = new JButton();
+
+  JButton cancel = new JButton();
+
+  JPanel okCancelPanel = new JPanel();
+
+  BorderLayout borderLayout1 = new BorderLayout();
+
+  protected JCheckBox quality = new JCheckBox();
+
+  JPanel visualTab = new JPanel();
+
+  protected JCheckBox fullScreen = new JCheckBox();
+
+  protected JCheckBox conservation = new JCheckBox();
+
+  protected JCheckBox identity = new JCheckBox();
+
+  protected JCheckBox annotations = new JCheckBox();
+
+  JLabel gapLabel = new JLabel();
+
+  protected JComboBox colour = new JComboBox();
+
+  JLabel colourLabel = new JLabel();
+
+  JLabel fontLabel = new JLabel();
+
+  protected JComboBox fontSizeCB = new JComboBox();
+
+  protected JComboBox fontStyleCB = new JComboBox();
+
+  protected JComboBox fontNameCB = new JComboBox();
+
+  protected JComboBox gapSymbolCB = new JComboBox();
+
+  protected JCheckBox startupCheckbox = new JCheckBox();
+
+  protected JTextField startupFileTextfield = new JTextField();
+
+  JPanel connectTab = new JPanel();
+
+  JLabel serverLabel = new JLabel();
+
+  protected JList linkURLList = new JList();
+
+  protected JTextField proxyServerTB = new JTextField();
+
+  protected JTextField proxyPortTB = new JTextField();
+
+  JLabel portLabel = new JLabel();
+
+  JLabel browserLabel = new JLabel();
+
+  protected JTextField defaultBrowser = new JTextField();
+
+  JButton newLink = new JButton();
+
+  JButton editLink = new JButton();
+
+  JButton deleteLink = new JButton();
+
+  JScrollPane linkScrollPane = new JScrollPane();
+
+  JPanel linkPanel = new JPanel();
+
+  BorderLayout borderLayout2 = new BorderLayout();
+
+  JPanel editLinkButtons = new JPanel();
+
+  GridLayout gridLayout1 = new GridLayout();
+
+  protected JList linkNameList = new JList();
+
+  JPanel linkPanel2 = new JPanel();
+
+  BorderLayout borderLayout3 = new BorderLayout();
+
+  protected JCheckBox useProxy = new JCheckBox();
+
+  JPanel jPanel1 = new JPanel();
+
+  TitledBorder titledBorder1 = new TitledBorder("Proxy Server");
+
+  TitledBorder titledBorder2 = new TitledBorder("File Output");
+
+  GridBagLayout gridBagLayout2 = new GridBagLayout();
+
+  GridBagLayout gridBagLayout1 = new GridBagLayout();
+
+  GridBagLayout gridBagLayout3 = new GridBagLayout();
+
+  protected JComboBox sortby = new JComboBox();
+
+  JLabel sortLabel = new JLabel();
+
+  JPanel jPanel2 = new JPanel();
+
+  GridLayout gridLayout2 = new GridLayout();
+
+  JPanel jPanel3 = new JPanel();
+
+  JPanel exportTab = new JPanel();
+
+  JLabel epsLabel = new JLabel();
+
+  protected JComboBox epsRendering = new JComboBox();
+
+  JLabel jLabel1 = new JLabel();
+
+  protected JCheckBox blcjv = new JCheckBox();
+
+  protected JCheckBox pileupjv = new JCheckBox();
+
+  protected JCheckBox clustaljv = new JCheckBox();
+
+  protected JCheckBox msfjv = new JCheckBox();
+
+  protected JCheckBox fastajv = new JCheckBox();
+
+  protected JCheckBox pfamjv = new JCheckBox();
+
+  FlowLayout flowLayout1 = new FlowLayout();
+
+  protected JCheckBox pirjv = new JCheckBox();
+
+  JPanel jPanel11 = new JPanel();
+
+  Font verdana11 = new java.awt.Font("Verdana", Font.PLAIN, 11);
+
+  protected JCheckBox seqLimit = new JCheckBox();
+
+  GridLayout gridLayout3 = new GridLayout();
+
+  protected JCheckBox smoothFont = new JCheckBox();
+
+  JPanel calcTab = new JPanel();
+
+  protected JCheckBox autoCalculateConsCheck = new JCheckBox();
+
+  protected JCheckBox padGaps = new JCheckBox();
+
+  protected JCheckBox modellerOutput = new JCheckBox();
+
+  protected JPanel dasPanel = new JPanel();
+
+  BorderLayout borderLayout4 = new BorderLayout();
+
+  protected JCheckBox wrap = new JCheckBox();
+
+  protected JCheckBox rightAlign = new JCheckBox();
+
+  protected JCheckBox idItalics = new JCheckBox();
+
+  protected JCheckBox openoverv = new JCheckBox();
+
+  /**
+   * Creates a new GPreferences object.
+   */
+  public GPreferences()
+  {
+    try
+    {
+      jbInit();
+    } catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @throws Exception
+   *                 DOCUMENT ME!
+   */
+  private void jbInit() throws Exception
+  {
+    this.setLayout(borderLayout1);
+    ok.setText("OK");
+    ok.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        ok_actionPerformed(e);
+      }
+    });
+    cancel.setText("Cancel");
+    cancel.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        cancel_actionPerformed(e);
+      }
+    });
+    quality.setEnabled(false);
+    quality.setFont(verdana11);
+    quality.setHorizontalAlignment(SwingConstants.RIGHT);
+    quality.setHorizontalTextPosition(SwingConstants.LEFT);
+    quality.setSelected(true);
+    quality.setText("Quality");
+    visualTab.setBorder(new TitledBorder("Open new alignment"));
+    visualTab.setLayout(null);
+    fullScreen.setFont(verdana11);
+    fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
+    fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
+    fullScreen.setText("Maximise Window");
+    conservation.setEnabled(false);
+    conservation.setFont(verdana11);
+    conservation.setHorizontalAlignment(SwingConstants.RIGHT);
+    conservation.setHorizontalTextPosition(SwingConstants.LEFT);
+    conservation.setSelected(true);
+    conservation.setText("Conservation");
+    identity.setEnabled(false);
+    identity.setFont(verdana11);
+    identity.setHorizontalAlignment(SwingConstants.RIGHT);
+    identity.setHorizontalTextPosition(SwingConstants.LEFT);
+    identity.setSelected(true);
+    identity.setText("Consensus");
+    annotations.setFont(verdana11);
+    annotations.setHorizontalAlignment(SwingConstants.RIGHT);
+    annotations.setHorizontalTextPosition(SwingConstants.LEFT);
+    annotations.setSelected(true);
+    annotations.setText("Show Annotations");
+    annotations.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        annotations_actionPerformed(e);
+      }
+    });
+    gapLabel.setFont(verdana11);
+    gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+    gapLabel.setText("Gap Symbol ");
+    colour.setFont(verdana11);
+    colour.setBounds(new Rectangle(172, 225, 155, 21));
+    colourLabel.setFont(verdana11);
+    colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+    colourLabel.setText("Colour ");
+    fontLabel.setFont(verdana11);
+    fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+    fontLabel.setText("Font ");
+    fontSizeCB.setFont(verdana11);
+    fontSizeCB.setBounds(new Rectangle(319, 111, 49, 21));
+    fontStyleCB.setFont(verdana11);
+    fontStyleCB.setBounds(new Rectangle(367, 111, 70, 21));
+    fontNameCB.setFont(verdana11);
+    fontNameCB.setBounds(new Rectangle(172, 111, 147, 21));
+    gapSymbolCB.setFont(verdana11);
+    gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 21));
+    startupCheckbox.setText("Open file");
+    startupCheckbox.setFont(verdana11);
+    startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
+    startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
+    startupCheckbox.setSelected(true);
+    startupFileTextfield.setFont(verdana11);
+    startupFileTextfield.setBounds(new Rectangle(172, 273, 270, 20));
+    startupFileTextfield.addMouseListener(new MouseAdapter()
+    {
+      public void mouseClicked(MouseEvent e)
+      {
+        if (e.getClickCount() > 1)
+        {
+          startupFileTextfield_mouseClicked();
+        }
+      }
+    });
+
+    connectTab.setLayout(gridBagLayout3);
+    serverLabel.setText("Address");
+    serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+    serverLabel.setFont(verdana11);
+    proxyServerTB.setFont(verdana11);
+    proxyPortTB.setFont(verdana11);
+    portLabel.setFont(verdana11);
+    portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+    portLabel.setText("Port");
+    browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
+    browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
+    browserLabel.setText("Default Browser (Unix)");
+    defaultBrowser.setFont(verdana11);
+    defaultBrowser.setText("");
+    newLink.setText("New");
+    newLink.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        newLink_actionPerformed(e);
+      }
+    });
+    editLink.setText("Edit");
+    editLink.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        editLink_actionPerformed(e);
+      }
+    });
+    deleteLink.setText("Delete");
+    deleteLink.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        deleteLink_actionPerformed(e);
+      }
+    });
+
+    linkURLList.addListSelectionListener(new ListSelectionListener()
+    {
+      public void valueChanged(ListSelectionEvent e)
+      {
+        int index = linkURLList.getSelectedIndex();
+        linkNameList.setSelectedIndex(index);
+      }
+    });
+
+    linkNameList.addListSelectionListener(new ListSelectionListener()
+    {
+      public void valueChanged(ListSelectionEvent e)
+      {
+        int index = linkNameList.getSelectedIndex();
+        linkURLList.setSelectedIndex(index);
+      }
+    });
+
+    linkScrollPane.setBorder(null);
+    linkPanel.setBorder(new TitledBorder("URL link from Sequence ID"));
+    linkPanel.setLayout(borderLayout2);
+    editLinkButtons.setLayout(gridLayout1);
+    gridLayout1.setRows(3);
+    linkNameList.setFont(verdana11);
+    linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+    linkPanel2.setLayout(borderLayout3);
+    linkURLList.setFont(verdana11);
+    linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+
+    defaultBrowser.addMouseListener(new MouseAdapter()
+    {
+      public void mouseClicked(MouseEvent e)
+      {
+        if (e.getClickCount() > 1)
+        {
+          defaultBrowser_mouseClicked(e);
+        }
+      }
+    });
+    useProxy.setFont(verdana11);
+    useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
+    useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
+    useProxy.setText("Use a proxy server");
+    useProxy.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        useProxy_actionPerformed();
+      }
+    });
+    jPanel1.setBorder(titledBorder1);
+    jPanel1.setLayout(gridBagLayout1);
+    sortby.setFont(verdana11);
+    sortby.setBounds(new Rectangle(172, 249, 155, 21));
+    sortLabel.setFont(verdana11);
+    sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+    sortLabel.setText("Sort by ");
+    jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
+    jPanel2.setLayout(gridLayout2);
+    gridLayout2.setRows(12);
+    jPanel3.setBounds(new Rectangle(173, 35, 274, 26));
+    exportTab.setLayout(null);
+    epsLabel.setFont(verdana11);
+    epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+    epsLabel.setText("EPS Rendering Style");
+    epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
+    epsRendering.setFont(verdana11);
+    epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
+    jLabel1.setFont(verdana11);
+    jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
+    jLabel1.setText("Append /start-end (/15-380)");
+    jLabel1.setFont(verdana11);
+    fastajv.setFont(verdana11);
+    fastajv.setHorizontalAlignment(SwingConstants.LEFT);
+    clustaljv.setText("Clustal     ");
+    blcjv.setText("BLC     ");
+    fastajv.setText("Fasta     ");
+    msfjv.setText("MSF     ");
+    pfamjv.setText("PFAM     ");
+    pileupjv.setText("Pileup     ");
+    msfjv.setFont(verdana11);
+    msfjv.setHorizontalAlignment(SwingConstants.LEFT);
+    pirjv.setText("PIR     ");
+    jPanel11.setFont(verdana11);
+    jPanel11.setBorder(titledBorder2);
+    jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
+    jPanel11.setLayout(gridLayout3);
+    blcjv.setFont(verdana11);
+    blcjv.setHorizontalAlignment(SwingConstants.LEFT);
+    clustaljv.setFont(verdana11);
+    clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
+    pfamjv.setFont(verdana11);
+    pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
+    pileupjv.setFont(verdana11);
+    pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
+    pirjv.setFont(verdana11);
+    pirjv.setHorizontalAlignment(SwingConstants.LEFT);
+    seqLimit.setFont(verdana11);
+    seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
+    seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
+    seqLimit.setText("Full Sequence Id");
+    gridLayout3.setRows(8);
+    smoothFont.setFont(verdana11);
+    smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
+    smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
+    smoothFont.setText("Smooth Font");
+    calcTab.setLayout(null);
+    autoCalculateConsCheck.setFont(new java.awt.Font("Verdana", Font.PLAIN,
+            11));
+    autoCalculateConsCheck.setText("AutoCalculate Consensus");
+    autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
+    padGaps.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    padGaps.setText("Pad gaps when editing");
+    padGaps.setBounds(new Rectangle(22, 94, 168, 23));
+    modellerOutput.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    modellerOutput.setText("Use Modeller Output");
+    modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
+    dasPanel.setLayout(borderLayout4);
+    wrap.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    wrap.setHorizontalAlignment(SwingConstants.TRAILING);
+    wrap.setHorizontalTextPosition(SwingConstants.LEADING);
+    wrap.setText("Wrap Alignment");
+    rightAlign.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    rightAlign.setForeground(Color.black);
+    rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
+    rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
+    rightAlign.setText("Right Align Ids");
+    idItalics.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
+    idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
+    idItalics.setText("Sequence Name Italics");
+    openoverv.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    openoverv.setActionCommand("Open Overview");
+    openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
+    openoverv.setHorizontalTextPosition(SwingConstants.LEADING);
+    openoverv.setText("Open Overview Window");
+    openoverv.setBounds(new Rectangle(169, 17, 200, 23));
+    jPanel2.add(fullScreen);
+    jPanel2.add(annotations);
+    jPanel2.add(seqLimit);
+    jPanel2.add(rightAlign);
+    jPanel2.add(fontLabel);
+    jPanel2.add(idItalics);
+    jPanel2.add(smoothFont);
+    jPanel2.add(wrap);
+    jPanel2.add(gapLabel);
+    jPanel2.add(colourLabel);
+    jPanel2.add(sortLabel);
+    jPanel2.add(startupCheckbox);
+    visualTab.add(openoverv);
+    visualTab.add(startupFileTextfield);
+    visualTab.add(sortby);
+    visualTab.add(colour);
+    visualTab.add(gapSymbolCB);
+    visualTab.add(jPanel3);
+    visualTab.add(fontNameCB);
+    visualTab.add(fontSizeCB);
+    visualTab.add(fontStyleCB);
+    jPanel3.add(conservation);
+    jPanel3.add(identity);
+    jPanel3.add(quality);
+    visualTab.add(jPanel2);
+    linkPanel.add(editLinkButtons, BorderLayout.EAST);
+    editLinkButtons.add(newLink, null);
+    editLinkButtons.add(editLink, null);
+    editLinkButtons.add(deleteLink, null);
+    linkPanel.add(linkScrollPane, BorderLayout.CENTER);
+    linkScrollPane.getViewport().add(linkPanel2, null);
+    linkPanel2.add(linkURLList, BorderLayout.CENTER);
+    linkPanel2.add(linkNameList, BorderLayout.WEST);
+    okCancelPanel.add(ok);
+    okCancelPanel.add(cancel);
+    this.add(tabbedPane, java.awt.BorderLayout.CENTER);
+
+    this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
+    jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
+            GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
+                    2, 4, 0), 5, 0));
+    jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
+            GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
+                    0, 4, 0), 11, 6));
+    connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
+            GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
+                    16, 0, 0, 12), 359, -17));
+    connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
+            GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
+                    21, 0, 35, 12), 4, 6));
+    connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
+            0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
+            new Insets(16, 0, 0, 0), 5, 1));
+    jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
+            GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+            new Insets(0, 2, 4, 2), 54, 1));
+    jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
+            GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+            new Insets(0, 2, 4, 0), 263, 1));
+    connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
+            0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+            new Insets(15, 0, 0, 15), 307, 1));
+
+    jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
+            GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
+                    2, 5, 185), 2, -4));
+    DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
+    dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
+    gapSymbolCB.setRenderer(dlcr);
+
+    tabbedPane.add(visualTab, "Visual");
+    tabbedPane.add(connectTab, "Connections");
+    tabbedPane.add(exportTab, "Output");
+    jPanel11.add(jLabel1);
+    jPanel11.add(blcjv);
+    jPanel11.add(clustaljv);
+    jPanel11.add(fastajv);
+    jPanel11.add(msfjv);
+    jPanel11.add(pfamjv);
+    jPanel11.add(pileupjv);
+    jPanel11.add(pirjv);
+    exportTab.add(modellerOutput);
+    tabbedPane.add(calcTab, "Editing");
+    calcTab.add(autoCalculateConsCheck);
+    calcTab.add(padGaps);
+    tabbedPane.add(dasPanel, "DAS Settings");
+
+    exportTab.add(epsLabel);
+    exportTab.add(epsRendering);
+    exportTab.add(jPanel11);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
+   */
+  public void ok_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
+   */
+  public void cancel_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
+   */
+  public void annotations_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void startupFileTextfield_mouseClicked()
+  {
+  }
+
+  public void newLink_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void editLink_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void deleteLink_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void defaultBrowser_mouseClicked(MouseEvent e)
+  {
+
+  }
+
+  public void linkURLList_keyTyped(KeyEvent e)
+  {
+
+  }
+
+  public void useProxy_actionPerformed()
+  {
+    proxyServerTB.setEnabled(useProxy.isSelected());
+    proxyPortTB.setEnabled(useProxy.isSelected());
+  }
+
+}
diff --git a/src/jalview/jbgui/GSequenceLink.java b/src/jalview/jbgui/GSequenceLink.java
index 40d00be..b412f6c 100755
--- a/src/jalview/jbgui/GSequenceLink.java
+++ b/src/jalview/jbgui/GSequenceLink.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -24,23 +24,20 @@ import java.awt.*;
 import java.awt.event.*;
 import javax.swing.*;
 
-public class GSequenceLink
-    extends Panel
+public class GSequenceLink extends Panel
 {
   public GSequenceLink()
   {
     try
     {
       jbInit();
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       ex.printStackTrace();
     }
   }
 
-  private void jbInit()
-      throws Exception
+  private void jbInit() throws Exception
   {
     this.setLayout(gridBagLayout1);
     nameTB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
@@ -84,10 +81,9 @@ public class GSequenceLink
     jPanel1.add(jLabel2);
     jPanel1.add(jLabel3);
     jPanel1.add(jLabel4);
-    this.add(jPanel1, new GridBagConstraints(0, 0, 1, 1, 1.0, 1.0
-                                             , GridBagConstraints.CENTER,
-                                             GridBagConstraints.BOTH,
-                                             new Insets(5, 4, 6, 5), 390, 130));
+    this.add(jPanel1, new GridBagConstraints(0, 0, 1, 1, 1.0, 1.0,
+            GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
+                    5, 4, 6, 5), 390, 130));
   }
 
   public void setName(String name)
@@ -112,27 +108,36 @@ public class GSequenceLink
 
   public boolean checkValid()
   {
-    UrlLink ul = new UrlLink("foo|"+urlTB.getText().trim());
-    if (ul.isValid()&&ul.isDynamic())
+    UrlLink ul = new UrlLink("foo|" + urlTB.getText().trim());
+    if (ul.isValid() && ul.isDynamic())
     {
       return true;
     }
-    
-    JOptionPane.showInternalMessageDialog(jalview.gui.Desktop.desktop,
-            "Sequence URL must contain $SEQUENCE_ID$ or a regex $SEQUENCE_ID=/<regex>/=$",
-            "URL not valid",
-            JOptionPane.WARNING_MESSAGE);
+
+    JOptionPane
+            .showInternalMessageDialog(
+                    jalview.gui.Desktop.desktop,
+                    "Sequence URL must contain $SEQUENCE_ID$ or a regex $SEQUENCE_ID=/<regex>/=$",
+                    "URL not valid", JOptionPane.WARNING_MESSAGE);
     return false;
   }
 
   JTextField nameTB = new JTextField();
+
   JTextField urlTB = new JTextField();
+
   JLabel jLabel1 = new JLabel();
+
   JLabel jLabel2 = new JLabel();
+
   JLabel jLabel3 = new JLabel();
+
   JLabel jLabel4 = new JLabel();
+
   JPanel jPanel1 = new JPanel();
+
   GridBagLayout gridBagLayout1 = new GridBagLayout();
+
   public void nameTB_keyTyped(KeyEvent e)
   {
     if (e.getKeyChar() == '|')
@@ -144,10 +149,10 @@ public class GSequenceLink
   public void urlTB_keyTyped(KeyEvent e)
   {
     // URLLink object validation takes care of incorrect regexes.
-    //if (e.getKeyChar() == '|' || e.getKeyChar() == ' ')
-    //{
-    //  e.consume();
-   // }
+    // if (e.getKeyChar() == '|' || e.getKeyChar() == ' ')
+    // {
+    // e.consume();
+    // }
 
   }
 }
diff --git a/src/jalview/jbgui/GSliderPanel.java b/src/jalview/jbgui/GSliderPanel.java
index 568c66a..e8df12d 100755
--- a/src/jalview/jbgui/GSliderPanel.java
+++ b/src/jalview/jbgui/GSliderPanel.java
@@ -1,194 +1,208 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.jbgui;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class GSliderPanel
-    extends JPanel
-{
-  // this is used for conservation colours, PID colours and redundancy threshold
-  protected JSlider slider = new JSlider();
-  protected JTextField valueField = new JTextField();
-  protected JLabel label = new JLabel();
-  protected JPanel southPanel = new JPanel();
-  GridLayout gridLayout1 = new GridLayout();
-  JPanel jPanel2 = new JPanel();
-  protected JButton applyButton = new JButton();
-  protected JButton undoButton = new JButton();
-  FlowLayout flowLayout1 = new FlowLayout();
-  protected JCheckBox allGroupsCheck = new JCheckBox();
-  BorderLayout borderLayout1 = new BorderLayout();
-  JPanel jPanel1 = new JPanel();
-  BorderLayout borderLayout2 = new BorderLayout();
-
-  /**
-   * Creates a new GSliderPanel object.
-   */
-  public GSliderPanel()
-  {
-    try
-    {
-      jbInit();
-    }
-    catch (Exception e)
-    {
-      e.printStackTrace();
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @throws Exception DOCUMENT ME!
-   */
-  private void jbInit()
-      throws Exception
-  {
-    this.setLayout(gridLayout1);
-    slider.setMajorTickSpacing(10);
-    slider.setMinorTickSpacing(1);
-    slider.setPaintTicks(true);
-    slider.setBackground(Color.white);
-    slider.setFont(new java.awt.Font("Verdana", 0, 11));
-    slider.setDoubleBuffered(true);
-    slider.addMouseListener(new MouseAdapter()
-    {
-      public void mouseReleased(MouseEvent e)
-      {
-        slider_mouseReleased(e);
-      }
-    });
-    valueField.setFont(new java.awt.Font("Verdana", 0, 11));
-    valueField.setMinimumSize(new Dimension(6, 14));
-    valueField.setPreferredSize(new Dimension(50, 12));
-    valueField.setText("");
-    valueField.setHorizontalAlignment(SwingConstants.CENTER);
-    valueField.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        valueField_actionPerformed(e);
-      }
-    });
-    label.setFont(new java.awt.Font("Verdana", 0, 11));
-    label.setOpaque(false);
-    label.setHorizontalAlignment(SwingConstants.CENTER);
-    label.setText("set this label text");
-    southPanel.setLayout(borderLayout1);
-    gridLayout1.setRows(2);
-    jPanel2.setLayout(flowLayout1);
-    applyButton.setFont(new java.awt.Font("Verdana", 0, 11));
-    applyButton.setOpaque(false);
-    applyButton.setText("Apply");
-    applyButton.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        applyButton_actionPerformed(e);
-      }
-    });
-    undoButton.setEnabled(false);
-    undoButton.setFont(new java.awt.Font("Verdana", 0, 11));
-    undoButton.setOpaque(false);
-    undoButton.setText("Undo");
-    undoButton.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        undoButton_actionPerformed(e);
-      }
-    });
-    allGroupsCheck.setEnabled(false);
-    allGroupsCheck.setFont(new java.awt.Font("Verdana", 0, 11));
-    allGroupsCheck.setOpaque(false);
-    allGroupsCheck.setText("Apply to all Groups");
-    allGroupsCheck.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        allGroupsCheck_actionPerformed(e);
-      }
-    });
-    this.setBackground(Color.white);
-    this.setPreferredSize(new Dimension(415, 84));
-    jPanel2.setOpaque(false);
-    southPanel.setOpaque(false);
-    jPanel1.setLayout(borderLayout2);
-    jPanel1.setOpaque(false);
-    this.add(jPanel2, null);
-    jPanel2.add(label, null);
-    jPanel2.add(applyButton, null);
-    jPanel2.add(undoButton, null);
-    this.add(southPanel, null);
-    southPanel.add(jPanel1, java.awt.BorderLayout.EAST);
-    southPanel.add(slider, java.awt.BorderLayout.CENTER);
-    jPanel1.add(valueField, java.awt.BorderLayout.CENTER);
-    jPanel1.add(allGroupsCheck, java.awt.BorderLayout.EAST);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void valueField_actionPerformed(ActionEvent e)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void applyButton_actionPerformed(ActionEvent e)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void undoButton_actionPerformed(ActionEvent e)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void allGroupsCheck_actionPerformed(ActionEvent e)
-  {
-  }
-
-  public void slider_mouseReleased(MouseEvent e)
-  {
-
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.jbgui;
+
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class GSliderPanel extends JPanel
+{
+  // this is used for conservation colours, PID colours and redundancy threshold
+  protected JSlider slider = new JSlider();
+
+  protected JTextField valueField = new JTextField();
+
+  protected JLabel label = new JLabel();
+
+  protected JPanel southPanel = new JPanel();
+
+  GridLayout gridLayout1 = new GridLayout();
+
+  JPanel jPanel2 = new JPanel();
+
+  protected JButton applyButton = new JButton();
+
+  protected JButton undoButton = new JButton();
+
+  FlowLayout flowLayout1 = new FlowLayout();
+
+  protected JCheckBox allGroupsCheck = new JCheckBox();
+
+  BorderLayout borderLayout1 = new BorderLayout();
+
+  JPanel jPanel1 = new JPanel();
+
+  BorderLayout borderLayout2 = new BorderLayout();
+
+  /**
+   * Creates a new GSliderPanel object.
+   */
+  public GSliderPanel()
+  {
+    try
+    {
+      jbInit();
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @throws Exception
+   *                 DOCUMENT ME!
+   */
+  private void jbInit() throws Exception
+  {
+    this.setLayout(gridLayout1);
+    slider.setMajorTickSpacing(10);
+    slider.setMinorTickSpacing(1);
+    slider.setPaintTicks(true);
+    slider.setBackground(Color.white);
+    slider.setFont(new java.awt.Font("Verdana", 0, 11));
+    slider.setDoubleBuffered(true);
+    slider.addMouseListener(new MouseAdapter()
+    {
+      public void mouseReleased(MouseEvent e)
+      {
+        slider_mouseReleased(e);
+      }
+    });
+    valueField.setFont(new java.awt.Font("Verdana", 0, 11));
+    valueField.setMinimumSize(new Dimension(6, 14));
+    valueField.setPreferredSize(new Dimension(50, 12));
+    valueField.setText("");
+    valueField.setHorizontalAlignment(SwingConstants.CENTER);
+    valueField.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        valueField_actionPerformed(e);
+      }
+    });
+    label.setFont(new java.awt.Font("Verdana", 0, 11));
+    label.setOpaque(false);
+    label.setHorizontalAlignment(SwingConstants.CENTER);
+    label.setText("set this label text");
+    southPanel.setLayout(borderLayout1);
+    gridLayout1.setRows(2);
+    jPanel2.setLayout(flowLayout1);
+    applyButton.setFont(new java.awt.Font("Verdana", 0, 11));
+    applyButton.setOpaque(false);
+    applyButton.setText("Apply");
+    applyButton.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        applyButton_actionPerformed(e);
+      }
+    });
+    undoButton.setEnabled(false);
+    undoButton.setFont(new java.awt.Font("Verdana", 0, 11));
+    undoButton.setOpaque(false);
+    undoButton.setText("Undo");
+    undoButton.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        undoButton_actionPerformed(e);
+      }
+    });
+    allGroupsCheck.setEnabled(false);
+    allGroupsCheck.setFont(new java.awt.Font("Verdana", 0, 11));
+    allGroupsCheck.setOpaque(false);
+    allGroupsCheck.setText("Apply to all Groups");
+    allGroupsCheck.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        allGroupsCheck_actionPerformed(e);
+      }
+    });
+    this.setBackground(Color.white);
+    this.setPreferredSize(new Dimension(415, 84));
+    jPanel2.setOpaque(false);
+    southPanel.setOpaque(false);
+    jPanel1.setLayout(borderLayout2);
+    jPanel1.setOpaque(false);
+    this.add(jPanel2, null);
+    jPanel2.add(label, null);
+    jPanel2.add(applyButton, null);
+    jPanel2.add(undoButton, null);
+    this.add(southPanel, null);
+    southPanel.add(jPanel1, java.awt.BorderLayout.EAST);
+    southPanel.add(slider, java.awt.BorderLayout.CENTER);
+    jPanel1.add(valueField, java.awt.BorderLayout.CENTER);
+    jPanel1.add(allGroupsCheck, java.awt.BorderLayout.EAST);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
+   */
+  protected void valueField_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
+   */
+  protected void applyButton_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
+   */
+  protected void undoButton_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
+   */
+  protected void allGroupsCheck_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void slider_mouseReleased(MouseEvent e)
+  {
+
+  }
+}
diff --git a/src/jalview/jbgui/GStructureViewer.java b/src/jalview/jbgui/GStructureViewer.java
index 10e0b9b..d2bebc3 100644
--- a/src/jalview/jbgui/GStructureViewer.java
+++ b/src/jalview/jbgui/GStructureViewer.java
@@ -1,322 +1,344 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.jbgui;
-
-import javax.swing.*;
-import java.awt.event.ActionListener;
-import java.awt.event.ActionEvent;
-
-public class GStructureViewer  extends JInternalFrame
-{
-  public GStructureViewer()
-  {
-    try
-    {
-      jbInit();
-    }
-    catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
-  }
-
-  private void jbInit()
-      throws Exception
-  {
-    this.setJMenuBar(menuBar);
-    fileMenu.setText("File");
-    savemenu.setActionCommand("Save Image");
-    savemenu.setText("Save As");
-    pdbFile.setText("PDB File");
-    pdbFile.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        pdbFile_actionPerformed(actionEvent);
-      }
-    });
-    png.setText("PNG");
-    png.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        png_actionPerformed(actionEvent);
-      }
-    });
-    eps.setText("EPS");
-    eps.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        eps_actionPerformed(actionEvent);
-      }
-    });
-    viewMapping.setText("View Mapping");
-    viewMapping.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        viewMapping_actionPerformed(actionEvent);
-      }
-    });
-    viewMenu.setText("View");
-    chainMenu.setText("Show Chain");
-    colourMenu.setText("Colours");
-    backGround.setText("Background Colour...");
-    backGround.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        backGround_actionPerformed(actionEvent);
-      }
-    });
-    seqColour.setSelected(true);
-    seqColour.setText("By Sequence");
-    seqColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        seqColour_actionPerformed(actionEvent);
-      }
-    });
-    chainColour.setText("By Chain");
-    chainColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        chainColour_actionPerformed(actionEvent);
-      }
-    });
-    chargeColour.setText("Charge & Cysteine");
-    chargeColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        chargeColour_actionPerformed(actionEvent);
-      }
-    });
-    zappoColour.setText("Zappo");
-    zappoColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        zappoColour_actionPerformed(actionEvent);
-      }
-    });
-    taylorColour.setText("Taylor");
-    taylorColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        taylorColour_actionPerformed(actionEvent);
-      }
-    });
-    hydroColour.setText("Hydro");
-    hydroColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        hydroColour_actionPerformed(actionEvent);
-      }
-    });
-    strandColour.setText("Strand");
-    strandColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        strandColour_actionPerformed(actionEvent);
-      }
-    });
-    helixColour.setText("Helix Propensity");
-    helixColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        helixColour_actionPerformed(actionEvent);
-      }
-    });
-    turnColour.setText("Turn Propensity");
-    turnColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        turnColour_actionPerformed(actionEvent);
-      }
-    });
-    buriedColour.setText("Buried Index");
-    buriedColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        buriedColour_actionPerformed(actionEvent);
-      }
-    });
-    userColour.setText("User Defined ...");
-    userColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        userColour_actionPerformed(actionEvent);
-      }
-    });
-    helpMenu.setText("Help");
-    jmolHelp.setText("Jmol Help");
-    jmolHelp.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        jmolHelp_actionPerformed(actionEvent);
-      }
-    });
-    menuBar.add(fileMenu);
-    menuBar.add(viewMenu);
-    menuBar.add(colourMenu);
-    menuBar.add(helpMenu);
-    fileMenu.add(savemenu);
-    fileMenu.add(viewMapping);
-    savemenu.add(pdbFile);
-    savemenu.add(png);
-    savemenu.add(eps);
-    viewMenu.add(chainMenu);
-    colourMenu.add(seqColour);
-    colourMenu.add(chainColour);
-    colourMenu.add(chargeColour);
-    colourMenu.add(zappoColour);
-    colourMenu.add(taylorColour);
-    colourMenu.add(hydroColour);
-    colourMenu.add(helixColour);
-    colourMenu.add(strandColour);
-    colourMenu.add(turnColour);
-    colourMenu.add(buriedColour);
-    colourMenu.add(userColour);
-    colourMenu.add(backGround);
-    helpMenu.add(jmolHelp);
-  }
-
-  JMenuBar menuBar = new JMenuBar();
-  JMenu fileMenu = new JMenu();
-  JMenu savemenu = new JMenu();
-  JMenuItem pdbFile = new JMenuItem();
-  JMenuItem png = new JMenuItem();
-  JMenuItem eps = new JMenuItem();
-  JMenuItem viewMapping = new JMenuItem();
-  JMenu viewMenu = new JMenu();
-  protected JMenu chainMenu = new JMenu();
-  JMenu jMenu1 = new JMenu();
-  JMenu colourMenu = new JMenu();
-  JMenuItem backGround = new JMenuItem();
-  protected JCheckBoxMenuItem seqColour = new JCheckBoxMenuItem();
-  JMenuItem chainColour = new JMenuItem();
-  JMenuItem chargeColour = new JMenuItem();
-  JMenuItem zappoColour = new JMenuItem();
-  JMenuItem taylorColour = new JMenuItem();
-  JMenuItem hydroColour = new JMenuItem();
-  JMenuItem strandColour = new JMenuItem();
-  JMenuItem helixColour = new JMenuItem();
-  JMenuItem turnColour = new JMenuItem();
-  JMenuItem buriedColour = new JMenuItem();
-  JMenuItem userColour = new JMenuItem();
-  JMenu helpMenu = new JMenu();
-  JMenuItem jmolHelp = new JMenuItem();
-  public void pdbFile_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void png_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void eps_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void viewMapping_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void seqColour_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void chainColour_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void chargeColour_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void zappoColour_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void taylorColour_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void hydroColour_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void helixColour_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void strandColour_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void turnColour_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void buriedColour_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void userColour_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void backGround_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void jmolHelp_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.jbgui;
+
+import javax.swing.*;
+import java.awt.event.ActionListener;
+import java.awt.event.ActionEvent;
+
+public class GStructureViewer extends JInternalFrame
+{
+  public GStructureViewer()
+  {
+    try
+    {
+      jbInit();
+    } catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
+
+  private void jbInit() throws Exception
+  {
+    this.setJMenuBar(menuBar);
+    fileMenu.setText("File");
+    savemenu.setActionCommand("Save Image");
+    savemenu.setText("Save As");
+    pdbFile.setText("PDB File");
+    pdbFile.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        pdbFile_actionPerformed(actionEvent);
+      }
+    });
+    png.setText("PNG");
+    png.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        png_actionPerformed(actionEvent);
+      }
+    });
+    eps.setText("EPS");
+    eps.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        eps_actionPerformed(actionEvent);
+      }
+    });
+    viewMapping.setText("View Mapping");
+    viewMapping.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        viewMapping_actionPerformed(actionEvent);
+      }
+    });
+    viewMenu.setText("View");
+    chainMenu.setText("Show Chain");
+    colourMenu.setText("Colours");
+    backGround.setText("Background Colour...");
+    backGround.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        backGround_actionPerformed(actionEvent);
+      }
+    });
+    seqColour.setSelected(true);
+    seqColour.setText("By Sequence");
+    seqColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        seqColour_actionPerformed(actionEvent);
+      }
+    });
+    chainColour.setText("By Chain");
+    chainColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        chainColour_actionPerformed(actionEvent);
+      }
+    });
+    chargeColour.setText("Charge & Cysteine");
+    chargeColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        chargeColour_actionPerformed(actionEvent);
+      }
+    });
+    zappoColour.setText("Zappo");
+    zappoColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        zappoColour_actionPerformed(actionEvent);
+      }
+    });
+    taylorColour.setText("Taylor");
+    taylorColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        taylorColour_actionPerformed(actionEvent);
+      }
+    });
+    hydroColour.setText("Hydro");
+    hydroColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        hydroColour_actionPerformed(actionEvent);
+      }
+    });
+    strandColour.setText("Strand");
+    strandColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        strandColour_actionPerformed(actionEvent);
+      }
+    });
+    helixColour.setText("Helix Propensity");
+    helixColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        helixColour_actionPerformed(actionEvent);
+      }
+    });
+    turnColour.setText("Turn Propensity");
+    turnColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        turnColour_actionPerformed(actionEvent);
+      }
+    });
+    buriedColour.setText("Buried Index");
+    buriedColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        buriedColour_actionPerformed(actionEvent);
+      }
+    });
+    userColour.setText("User Defined ...");
+    userColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        userColour_actionPerformed(actionEvent);
+      }
+    });
+    helpMenu.setText("Help");
+    jmolHelp.setText("Jmol Help");
+    jmolHelp.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        jmolHelp_actionPerformed(actionEvent);
+      }
+    });
+    menuBar.add(fileMenu);
+    menuBar.add(viewMenu);
+    menuBar.add(colourMenu);
+    menuBar.add(helpMenu);
+    fileMenu.add(savemenu);
+    fileMenu.add(viewMapping);
+    savemenu.add(pdbFile);
+    savemenu.add(png);
+    savemenu.add(eps);
+    viewMenu.add(chainMenu);
+    colourMenu.add(seqColour);
+    colourMenu.add(chainColour);
+    colourMenu.add(chargeColour);
+    colourMenu.add(zappoColour);
+    colourMenu.add(taylorColour);
+    colourMenu.add(hydroColour);
+    colourMenu.add(helixColour);
+    colourMenu.add(strandColour);
+    colourMenu.add(turnColour);
+    colourMenu.add(buriedColour);
+    colourMenu.add(userColour);
+    colourMenu.add(backGround);
+    helpMenu.add(jmolHelp);
+  }
+
+  JMenuBar menuBar = new JMenuBar();
+
+  JMenu fileMenu = new JMenu();
+
+  JMenu savemenu = new JMenu();
+
+  JMenuItem pdbFile = new JMenuItem();
+
+  JMenuItem png = new JMenuItem();
+
+  JMenuItem eps = new JMenuItem();
+
+  JMenuItem viewMapping = new JMenuItem();
+
+  JMenu viewMenu = new JMenu();
+
+  protected JMenu chainMenu = new JMenu();
+
+  JMenu jMenu1 = new JMenu();
+
+  JMenu colourMenu = new JMenu();
+
+  JMenuItem backGround = new JMenuItem();
+
+  protected JCheckBoxMenuItem seqColour = new JCheckBoxMenuItem();
+
+  JMenuItem chainColour = new JMenuItem();
+
+  JMenuItem chargeColour = new JMenuItem();
+
+  JMenuItem zappoColour = new JMenuItem();
+
+  JMenuItem taylorColour = new JMenuItem();
+
+  JMenuItem hydroColour = new JMenuItem();
+
+  JMenuItem strandColour = new JMenuItem();
+
+  JMenuItem helixColour = new JMenuItem();
+
+  JMenuItem turnColour = new JMenuItem();
+
+  JMenuItem buriedColour = new JMenuItem();
+
+  JMenuItem userColour = new JMenuItem();
+
+  JMenu helpMenu = new JMenu();
+
+  JMenuItem jmolHelp = new JMenuItem();
+
+  public void pdbFile_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void png_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void eps_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void viewMapping_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void seqColour_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void chainColour_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void chargeColour_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void zappoColour_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void taylorColour_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void hydroColour_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void helixColour_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void strandColour_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void turnColour_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void buriedColour_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void userColour_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void backGround_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void jmolHelp_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+}
diff --git a/src/jalview/jbgui/GTreePanel.java b/src/jalview/jbgui/GTreePanel.java
index 5d3b8b8..d6677f4 100755
--- a/src/jalview/jbgui/GTreePanel.java
+++ b/src/jalview/jbgui/GTreePanel.java
@@ -1,248 +1,263 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.jbgui;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.event.*;
-
-public class GTreePanel
-    extends JInternalFrame
-{
-  BorderLayout borderLayout1 = new BorderLayout();
-  public JScrollPane scrollPane = new JScrollPane();
-  JMenuBar jMenuBar1 = new JMenuBar();
-  JMenu fileMenu = new JMenu();
-  JMenuItem saveAsNewick = new JMenuItem();
-  JMenuItem printMenu = new JMenuItem();
-  protected JMenu viewMenu = new JMenu();
-  public JMenuItem font = new JMenuItem();
-  public JCheckBoxMenuItem bootstrapMenu = new JCheckBoxMenuItem();
-  public JCheckBoxMenuItem distanceMenu = new JCheckBoxMenuItem();
-  public JCheckBoxMenuItem fitToWindow = new JCheckBoxMenuItem();
-  public JCheckBoxMenuItem placeholdersMenu = new JCheckBoxMenuItem();
-  JMenuItem pngTree = new JMenuItem();
-  JMenuItem epsTree = new JMenuItem();
-  JMenu saveAsMenu = new JMenu();
-  JMenuItem textbox = new JMenuItem();
-  public JMenuItem originalSeqData = new JMenuItem();
-  protected JMenu associateLeavesMenu = new JMenu();
-  public GTreePanel()
-  {
-    try
-    {
-      jbInit();
-      this.setJMenuBar(jMenuBar1);
-    }
-    catch (Exception e)
-    {
-      e.printStackTrace();
-    }
-  }
-
-  private void jbInit()
-      throws Exception
-  {
-    this.getContentPane().setLayout(borderLayout1);
-    this.setBackground(Color.white);
-    this.setFont(new java.awt.Font("Verdana", 0, 12));
-    scrollPane.setOpaque(false);
-    fileMenu.setText("File");
-    saveAsNewick.setText("Newick Format");
-    saveAsNewick.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        saveAsNewick_actionPerformed(e);
-      }
-    });
-    printMenu.setText("Print");
-    printMenu.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        printMenu_actionPerformed(e);
-      }
-    });
-    viewMenu.setText("View");
-    viewMenu.addMenuListener(new MenuListener()
-    {
-      public void menuSelected(MenuEvent e)
-      {
-        viewMenu_menuSelected();
-      }
-
-      public void menuDeselected(MenuEvent e)
-      {
-      }
-
-      public void menuCanceled(MenuEvent e)
-      {
-      }
-    });
-    font.setText("Font...");
-    font.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        font_actionPerformed(e);
-      }
-    });
-    bootstrapMenu.setText("Show Bootstrap Values");
-    bootstrapMenu.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        bootstrapMenu_actionPerformed(e);
-      }
-    });
-    distanceMenu.setText("Show Distances");
-    distanceMenu.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        distanceMenu_actionPerformed(e);
-      }
-    });
-    fitToWindow.setSelected(true);
-    fitToWindow.setText("Fit To Window");
-    fitToWindow.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        fitToWindow_actionPerformed(e);
-      }
-    });
-    epsTree.setText("EPS");
-    epsTree.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        epsTree_actionPerformed(e);
-      }
-    });
-    pngTree.setText("PNG");
-    pngTree.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        pngTree_actionPerformed(e);
-      }
-    });
-    saveAsMenu.setText("Save as");
-    placeholdersMenu.setToolTipText(
-        "Marks leaves of tree not associated with a sequence");
-    placeholdersMenu.setText("Mark Unlinked Leaves");
-    placeholdersMenu.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        placeholdersMenu_actionPerformed(e);
-      }
-    });
-    textbox.setText("Output to Textbox...");
-    textbox.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        textbox_actionPerformed(e);
-      }
-    });
-    originalSeqData.setText("Input Data...");
-    originalSeqData.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        originalSeqData_actionPerformed(e);
-      }
-    });
-    associateLeavesMenu.setText("Associate Leaves With");
-    this.getContentPane().add(scrollPane, BorderLayout.CENTER);
-    jMenuBar1.add(fileMenu);
-    jMenuBar1.add(viewMenu);
-    fileMenu.add(saveAsMenu);
-    fileMenu.add(textbox);
-    fileMenu.add(printMenu);
-    fileMenu.add(originalSeqData);
-    viewMenu.add(fitToWindow);
-    viewMenu.add(font);
-    viewMenu.add(distanceMenu);
-    viewMenu.add(bootstrapMenu);
-    viewMenu.add(placeholdersMenu);
-    viewMenu.add(associateLeavesMenu);
-    saveAsMenu.add(saveAsNewick);
-    saveAsMenu.add(epsTree);
-    saveAsMenu.add(pngTree);
-  }
-
-  public void printMenu_actionPerformed(ActionEvent e)
-  {
-  }
-
-  public void font_actionPerformed(ActionEvent e)
-  {
-  }
-
-  public void distanceMenu_actionPerformed(ActionEvent e)
-  {
-  }
-
-  public void bootstrapMenu_actionPerformed(ActionEvent e)
-  {
-  }
-
-  public void fitToWindow_actionPerformed(ActionEvent e)
-  {
-  }
-
-  public void pngTree_actionPerformed(ActionEvent e)
-  {
-  }
-
-  public void epsTree_actionPerformed(ActionEvent e)
-  {
-  }
-
-  public void saveAsNewick_actionPerformed(ActionEvent e)
-  {
-  }
-
-  public void placeholdersMenu_actionPerformed(ActionEvent e)
-  {
-  }
-
-  public void textbox_actionPerformed(ActionEvent e)
-  {
-  }
-
-  public void fullid_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void originalSeqData_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void viewMenu_menuSelected()
-  {
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.jbgui;
+
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+import javax.swing.event.*;
+
+public class GTreePanel extends JInternalFrame
+{
+  BorderLayout borderLayout1 = new BorderLayout();
+
+  public JScrollPane scrollPane = new JScrollPane();
+
+  JMenuBar jMenuBar1 = new JMenuBar();
+
+  JMenu fileMenu = new JMenu();
+
+  JMenuItem saveAsNewick = new JMenuItem();
+
+  JMenuItem printMenu = new JMenuItem();
+
+  protected JMenu viewMenu = new JMenu();
+
+  public JMenuItem font = new JMenuItem();
+
+  public JCheckBoxMenuItem bootstrapMenu = new JCheckBoxMenuItem();
+
+  public JCheckBoxMenuItem distanceMenu = new JCheckBoxMenuItem();
+
+  public JCheckBoxMenuItem fitToWindow = new JCheckBoxMenuItem();
+
+  public JCheckBoxMenuItem placeholdersMenu = new JCheckBoxMenuItem();
+
+  JMenuItem pngTree = new JMenuItem();
+
+  JMenuItem epsTree = new JMenuItem();
+
+  JMenu saveAsMenu = new JMenu();
+
+  JMenuItem textbox = new JMenuItem();
+
+  public JMenuItem originalSeqData = new JMenuItem();
+
+  protected JMenu associateLeavesMenu = new JMenu();
+
+  public GTreePanel()
+  {
+    try
+    {
+      jbInit();
+      this.setJMenuBar(jMenuBar1);
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+  }
+
+  private void jbInit() throws Exception
+  {
+    this.getContentPane().setLayout(borderLayout1);
+    this.setBackground(Color.white);
+    this.setFont(new java.awt.Font("Verdana", 0, 12));
+    scrollPane.setOpaque(false);
+    fileMenu.setText("File");
+    saveAsNewick.setText("Newick Format");
+    saveAsNewick.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        saveAsNewick_actionPerformed(e);
+      }
+    });
+    printMenu.setText("Print");
+    printMenu.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        printMenu_actionPerformed(e);
+      }
+    });
+    viewMenu.setText("View");
+    viewMenu.addMenuListener(new MenuListener()
+    {
+      public void menuSelected(MenuEvent e)
+      {
+        viewMenu_menuSelected();
+      }
+
+      public void menuDeselected(MenuEvent e)
+      {
+      }
+
+      public void menuCanceled(MenuEvent e)
+      {
+      }
+    });
+    font.setText("Font...");
+    font.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        font_actionPerformed(e);
+      }
+    });
+    bootstrapMenu.setText("Show Bootstrap Values");
+    bootstrapMenu.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        bootstrapMenu_actionPerformed(e);
+      }
+    });
+    distanceMenu.setText("Show Distances");
+    distanceMenu.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        distanceMenu_actionPerformed(e);
+      }
+    });
+    fitToWindow.setSelected(true);
+    fitToWindow.setText("Fit To Window");
+    fitToWindow.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        fitToWindow_actionPerformed(e);
+      }
+    });
+    epsTree.setText("EPS");
+    epsTree.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        epsTree_actionPerformed(e);
+      }
+    });
+    pngTree.setText("PNG");
+    pngTree.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        pngTree_actionPerformed(e);
+      }
+    });
+    saveAsMenu.setText("Save as");
+    placeholdersMenu
+            .setToolTipText("Marks leaves of tree not associated with a sequence");
+    placeholdersMenu.setText("Mark Unlinked Leaves");
+    placeholdersMenu.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        placeholdersMenu_actionPerformed(e);
+      }
+    });
+    textbox.setText("Output to Textbox...");
+    textbox.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        textbox_actionPerformed(e);
+      }
+    });
+    originalSeqData.setText("Input Data...");
+    originalSeqData.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        originalSeqData_actionPerformed(e);
+      }
+    });
+    associateLeavesMenu.setText("Associate Leaves With");
+    this.getContentPane().add(scrollPane, BorderLayout.CENTER);
+    jMenuBar1.add(fileMenu);
+    jMenuBar1.add(viewMenu);
+    fileMenu.add(saveAsMenu);
+    fileMenu.add(textbox);
+    fileMenu.add(printMenu);
+    fileMenu.add(originalSeqData);
+    viewMenu.add(fitToWindow);
+    viewMenu.add(font);
+    viewMenu.add(distanceMenu);
+    viewMenu.add(bootstrapMenu);
+    viewMenu.add(placeholdersMenu);
+    viewMenu.add(associateLeavesMenu);
+    saveAsMenu.add(saveAsNewick);
+    saveAsMenu.add(epsTree);
+    saveAsMenu.add(pngTree);
+  }
+
+  public void printMenu_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void font_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void distanceMenu_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void bootstrapMenu_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void fitToWindow_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void pngTree_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void epsTree_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void saveAsNewick_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void placeholdersMenu_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void textbox_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void fullid_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void originalSeqData_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void viewMenu_menuSelected()
+  {
+  }
+}
diff --git a/src/jalview/jbgui/GUserDefinedColours.java b/src/jalview/jbgui/GUserDefinedColours.java
index 1801152..70a75e4 100755
--- a/src/jalview/jbgui/GUserDefinedColours.java
+++ b/src/jalview/jbgui/GUserDefinedColours.java
@@ -1,253 +1,283 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.jbgui;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class GUserDefinedColours
-    extends JPanel
-{
-  protected JColorChooser colorChooser = new JColorChooser();
-  protected JPanel buttonPanel = new JPanel();
-  protected GridLayout gridLayout = new GridLayout();
-  JPanel lowerPanel = new JPanel();
-  protected JButton okButton = new JButton();
-  protected JButton applyButton = new JButton();
-  protected JButton loadbutton = new JButton();
-  protected JButton savebutton = new JButton();
-  protected JButton cancelButton = new JButton();
-  JPanel namePanel = new JPanel();
-  JLabel jLabel1 = new JLabel();
-  protected JTextField schemeName = new JTextField();
-  BorderLayout borderLayout1 = new BorderLayout();
-  JPanel panel1 = new JPanel();
-  JPanel okCancelPanel = new JPanel();
-  JPanel saveLoadPanel = new JPanel();
-  BorderLayout borderLayout3 = new BorderLayout();
-  GridBagLayout gridBagLayout1 = new GridBagLayout();
-  BorderLayout borderLayout2 = new BorderLayout();
-  FlowLayout flowLayout1 = new FlowLayout();
-  BorderLayout borderLayout4 = new BorderLayout();
-  JPanel jPanel4 = new JPanel();
-  BorderLayout borderLayout5 = new BorderLayout();
-  JLabel label = new JLabel();
-  protected JPanel casePanel = new JPanel();
-  protected JCheckBox caseSensitive = new JCheckBox();
-  protected JButton lcaseColour = new JButton();
-  /**
-   * Creates a new GUserDefinedColours object.
-   */
-  public GUserDefinedColours()
-  {
-    try
-    {
-      jbInit();
-    }
-    catch (Exception e)
-    {
-      e.printStackTrace();
-    }
-
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @throws Exception DOCUMENT ME!
-   */
-  private void jbInit()
-      throws Exception
-  {
-    this.setLayout(borderLayout4);
-    buttonPanel.setLayout(gridLayout);
-    gridLayout.setColumns(4);
-    gridLayout.setRows(5);
-    okButton.setFont(new java.awt.Font("Verdana", 0, 11));
-    okButton.setText("OK");
-    okButton.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        okButton_actionPerformed(e);
-      }
-    });
-    applyButton.setFont(new java.awt.Font("Verdana", 0, 11));
-    applyButton.setText("Apply");
-    applyButton.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        applyButton_actionPerformed(e);
-      }
-    });
-    loadbutton.setFont(new java.awt.Font("Verdana", 0, 11));
-    loadbutton.setText("Load scheme");
-    loadbutton.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        loadbutton_actionPerformed(e);
-      }
-    });
-    savebutton.setFont(new java.awt.Font("Verdana", 0, 11));
-    savebutton.setText("Save scheme");
-    savebutton.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        savebutton_actionPerformed(e);
-      }
-    });
-    cancelButton.setFont(new java.awt.Font("Verdana", 0, 11));
-    cancelButton.setText("Cancel");
-    cancelButton.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        cancelButton_actionPerformed(e);
-      }
-    });
-    this.setBackground(new Color(212, 208, 223));
-    lowerPanel.setOpaque(false);
-    lowerPanel.setLayout(borderLayout3);
-    colorChooser.setOpaque(false);
-    jLabel1.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    jLabel1.setText("Name");
-    namePanel.setMinimumSize(new Dimension(300, 31));
-    namePanel.setOpaque(false);
-    namePanel.setPreferredSize(new Dimension(240, 25));
-    namePanel.setLayout(borderLayout1);
-    schemeName.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    schemeName.setPreferredSize(new Dimension(105, 21));
-    schemeName.setText("");
-    schemeName.setHorizontalAlignment(SwingConstants.CENTER);
-    panel1.setLayout(flowLayout1);
-    panel1.setOpaque(false);
-    okCancelPanel.setOpaque(false);
-    saveLoadPanel.setOpaque(false);
-    jPanel4.setLayout(borderLayout5);
-    label.setFont(new java.awt.Font("Verdana", Font.ITALIC, 10));
-    label.setOpaque(false);
-    label.setPreferredSize(new Dimension(260, 34));
-    label.setText(
-        "<html>Save your colour scheme with a unique name and it will be added " +
-        "to the Colour menu.</html>");
-    caseSensitive.setText("Case Sensitive");
-    caseSensitive.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        caseSensitive_actionPerformed(e);
-      }
-    });
-    lcaseColour.setText("Lower Case Colour");
-    lcaseColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        lcaseColour_actionPerformed(e);
-      }
-    });
-
-    saveLoadPanel.add(savebutton);
-    saveLoadPanel.add(loadbutton);
-    okCancelPanel.add(applyButton);
-    okCancelPanel.add(okButton);
-    okCancelPanel.add(cancelButton);
-    lowerPanel.add(saveLoadPanel, java.awt.BorderLayout.NORTH);
-    lowerPanel.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
-
-    namePanel.add(schemeName, java.awt.BorderLayout.CENTER);
-    namePanel.add(jLabel1, java.awt.BorderLayout.WEST);
-    panel1.add(namePanel, null);
-    panel1.add(buttonPanel, null);
-    panel1.add(casePanel);
-    casePanel.add(caseSensitive);
-    casePanel.add(lcaseColour);
-    panel1.add(lowerPanel, null);
-    panel1.add(label);
-
-    jPanel4.add(panel1, java.awt.BorderLayout.CENTER);
-    this.add(jPanel4, java.awt.BorderLayout.CENTER);
-    this.add(colorChooser, java.awt.BorderLayout.EAST);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void okButton_actionPerformed(ActionEvent e)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void applyButton_actionPerformed(ActionEvent e)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void loadbutton_actionPerformed(ActionEvent e)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void savebutton_actionPerformed(ActionEvent e)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void cancelButton_actionPerformed(ActionEvent e)
-  {
-  }
-
-  public void caseSensitive_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void lcaseColour_actionPerformed(ActionEvent e)
-  {
-
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.jbgui;
+
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class GUserDefinedColours extends JPanel
+{
+  protected JColorChooser colorChooser = new JColorChooser();
+
+  protected JPanel buttonPanel = new JPanel();
+
+  protected GridLayout gridLayout = new GridLayout();
+
+  JPanel lowerPanel = new JPanel();
+
+  protected JButton okButton = new JButton();
+
+  protected JButton applyButton = new JButton();
+
+  protected JButton loadbutton = new JButton();
+
+  protected JButton savebutton = new JButton();
+
+  protected JButton cancelButton = new JButton();
+
+  JPanel namePanel = new JPanel();
+
+  JLabel jLabel1 = new JLabel();
+
+  protected JTextField schemeName = new JTextField();
+
+  BorderLayout borderLayout1 = new BorderLayout();
+
+  JPanel panel1 = new JPanel();
+
+  JPanel okCancelPanel = new JPanel();
+
+  JPanel saveLoadPanel = new JPanel();
+
+  BorderLayout borderLayout3 = new BorderLayout();
+
+  GridBagLayout gridBagLayout1 = new GridBagLayout();
+
+  BorderLayout borderLayout2 = new BorderLayout();
+
+  FlowLayout flowLayout1 = new FlowLayout();
+
+  BorderLayout borderLayout4 = new BorderLayout();
+
+  JPanel jPanel4 = new JPanel();
+
+  BorderLayout borderLayout5 = new BorderLayout();
+
+  JLabel label = new JLabel();
+
+  protected JPanel casePanel = new JPanel();
+
+  protected JCheckBox caseSensitive = new JCheckBox();
+
+  protected JButton lcaseColour = new JButton();
+
+  /**
+   * Creates a new GUserDefinedColours object.
+   */
+  public GUserDefinedColours()
+  {
+    try
+    {
+      jbInit();
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @throws Exception
+   *                 DOCUMENT ME!
+   */
+  private void jbInit() throws Exception
+  {
+    this.setLayout(borderLayout4);
+    buttonPanel.setLayout(gridLayout);
+    gridLayout.setColumns(4);
+    gridLayout.setRows(5);
+    okButton.setFont(new java.awt.Font("Verdana", 0, 11));
+    okButton.setText("OK");
+    okButton.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        okButton_actionPerformed(e);
+      }
+    });
+    applyButton.setFont(new java.awt.Font("Verdana", 0, 11));
+    applyButton.setText("Apply");
+    applyButton.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        applyButton_actionPerformed(e);
+      }
+    });
+    loadbutton.setFont(new java.awt.Font("Verdana", 0, 11));
+    loadbutton.setText("Load scheme");
+    loadbutton.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        loadbutton_actionPerformed(e);
+      }
+    });
+    savebutton.setFont(new java.awt.Font("Verdana", 0, 11));
+    savebutton.setText("Save scheme");
+    savebutton.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        savebutton_actionPerformed(e);
+      }
+    });
+    cancelButton.setFont(new java.awt.Font("Verdana", 0, 11));
+    cancelButton.setText("Cancel");
+    cancelButton.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        cancelButton_actionPerformed(e);
+      }
+    });
+    this.setBackground(new Color(212, 208, 223));
+    lowerPanel.setOpaque(false);
+    lowerPanel.setLayout(borderLayout3);
+    colorChooser.setOpaque(false);
+    jLabel1.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    jLabel1.setText("Name");
+    namePanel.setMinimumSize(new Dimension(300, 31));
+    namePanel.setOpaque(false);
+    namePanel.setPreferredSize(new Dimension(240, 25));
+    namePanel.setLayout(borderLayout1);
+    schemeName.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    schemeName.setPreferredSize(new Dimension(105, 21));
+    schemeName.setText("");
+    schemeName.setHorizontalAlignment(SwingConstants.CENTER);
+    panel1.setLayout(flowLayout1);
+    panel1.setOpaque(false);
+    okCancelPanel.setOpaque(false);
+    saveLoadPanel.setOpaque(false);
+    jPanel4.setLayout(borderLayout5);
+    label.setFont(new java.awt.Font("Verdana", Font.ITALIC, 10));
+    label.setOpaque(false);
+    label.setPreferredSize(new Dimension(260, 34));
+    label
+            .setText("<html>Save your colour scheme with a unique name and it will be added "
+                    + "to the Colour menu.</html>");
+    caseSensitive.setText("Case Sensitive");
+    caseSensitive.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        caseSensitive_actionPerformed(e);
+      }
+    });
+    lcaseColour.setText("Lower Case Colour");
+    lcaseColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        lcaseColour_actionPerformed(e);
+      }
+    });
+
+    saveLoadPanel.add(savebutton);
+    saveLoadPanel.add(loadbutton);
+    okCancelPanel.add(applyButton);
+    okCancelPanel.add(okButton);
+    okCancelPanel.add(cancelButton);
+    lowerPanel.add(saveLoadPanel, java.awt.BorderLayout.NORTH);
+    lowerPanel.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
+
+    namePanel.add(schemeName, java.awt.BorderLayout.CENTER);
+    namePanel.add(jLabel1, java.awt.BorderLayout.WEST);
+    panel1.add(namePanel, null);
+    panel1.add(buttonPanel, null);
+    panel1.add(casePanel);
+    casePanel.add(caseSensitive);
+    casePanel.add(lcaseColour);
+    panel1.add(lowerPanel, null);
+    panel1.add(label);
+
+    jPanel4.add(panel1, java.awt.BorderLayout.CENTER);
+    this.add(jPanel4, java.awt.BorderLayout.CENTER);
+    this.add(colorChooser, java.awt.BorderLayout.EAST);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
+   */
+  protected void okButton_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
+   */
+  protected void applyButton_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
+   */
+  protected void loadbutton_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
+   */
+  protected void savebutton_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
+   */
+  protected void cancelButton_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void caseSensitive_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void lcaseColour_actionPerformed(ActionEvent e)
+  {
+
+  }
+}
diff --git a/src/jalview/jbgui/GWebserviceInfo.java b/src/jalview/jbgui/GWebserviceInfo.java
index ca68115..89c5bf2 100755
--- a/src/jalview/jbgui/GWebserviceInfo.java
+++ b/src/jalview/jbgui/GWebserviceInfo.java
@@ -1,115 +1,125 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.jbgui;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class GWebserviceInfo
-    extends JPanel
-{
-  protected JTextArea infoText = new JTextArea();
-  JScrollPane jScrollPane1 = new JScrollPane();
-  JPanel jPanel1 = new JPanel();
-  BorderLayout borderLayout1 = new BorderLayout();
-  BorderLayout borderLayout2 = new BorderLayout();
-  protected JPanel titlePanel = new JPanel();
-  BorderLayout borderLayout3 = new BorderLayout();
-  protected JPanel buttonPanel = new JPanel();
-  public JButton cancel = new JButton();
-  public JButton showResultsNewFrame = new JButton();
-  public JButton mergeResults = new JButton();
-  GridBagLayout gridBagLayout1 = new GridBagLayout();
-  /**
-   * Creates a new GWebserviceInfo object.
-   */
-  public GWebserviceInfo()
-  {
-    try
-    {
-      jbInit();
-    }
-    catch (Exception e)
-    {
-      e.printStackTrace();
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @throws Exception DOCUMENT ME!
-   */
-  private void jbInit()
-      throws Exception
-  {
-    infoText.setFont(new java.awt.Font("Verdana", 0, 10));
-    infoText.setBorder(null);
-    infoText.setEditable(false);
-    infoText.setText("");
-    infoText.setLineWrap(true);
-    infoText.setWrapStyleWord(true);
-    this.setLayout(borderLayout1);
-    jPanel1.setLayout(borderLayout2);
-    titlePanel.setBackground(Color.white);
-    titlePanel.setPreferredSize(new Dimension(0, 60));
-    titlePanel.setLayout(borderLayout3);
-    jScrollPane1.setBorder(null);
-    jScrollPane1.setPreferredSize(new Dimension(400, 70));
-    cancel.setFont(new java.awt.Font("Verdana", 0, 11));
-    cancel.setText("Cancel");
-    cancel.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        cancel_actionPerformed(e);
-      }
-    });
-    buttonPanel.setLayout(gridBagLayout1);
-    buttonPanel.setOpaque(false);
-    showResultsNewFrame.setText("New Window");
-    mergeResults.setText("Merge Results");
-    this.setBackground(Color.white);
-    this.add(jPanel1, BorderLayout.NORTH);
-    jPanel1.add(jScrollPane1, BorderLayout.CENTER);
-    jScrollPane1.getViewport().add(infoText, null);
-    jPanel1.add(titlePanel, BorderLayout.NORTH);
-    titlePanel.add(buttonPanel, BorderLayout.EAST);
-    buttonPanel.add(cancel, new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0
-        , GridBagConstraints.CENTER,
-        GridBagConstraints.NONE,
-        new Insets(19, 6, 16, 4), 0, 0));
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void cancel_actionPerformed(ActionEvent e)
-  {
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.jbgui;
+
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class GWebserviceInfo extends JPanel
+{
+  protected JTextArea infoText = new JTextArea();
+
+  JScrollPane jScrollPane1 = new JScrollPane();
+
+  JPanel jPanel1 = new JPanel();
+
+  BorderLayout borderLayout1 = new BorderLayout();
+
+  BorderLayout borderLayout2 = new BorderLayout();
+
+  protected JPanel titlePanel = new JPanel();
+
+  BorderLayout borderLayout3 = new BorderLayout();
+
+  protected JPanel buttonPanel = new JPanel();
+
+  public JButton cancel = new JButton();
+
+  public JButton showResultsNewFrame = new JButton();
+
+  public JButton mergeResults = new JButton();
+
+  GridBagLayout gridBagLayout1 = new GridBagLayout();
+
+  /**
+   * Creates a new GWebserviceInfo object.
+   */
+  public GWebserviceInfo()
+  {
+    try
+    {
+      jbInit();
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @throws Exception
+   *                 DOCUMENT ME!
+   */
+  private void jbInit() throws Exception
+  {
+    infoText.setFont(new java.awt.Font("Verdana", 0, 10));
+    infoText.setBorder(null);
+    infoText.setEditable(false);
+    infoText.setText("");
+    infoText.setLineWrap(true);
+    infoText.setWrapStyleWord(true);
+    this.setLayout(borderLayout1);
+    jPanel1.setLayout(borderLayout2);
+    titlePanel.setBackground(Color.white);
+    titlePanel.setPreferredSize(new Dimension(0, 60));
+    titlePanel.setLayout(borderLayout3);
+    jScrollPane1.setBorder(null);
+    jScrollPane1.setPreferredSize(new Dimension(400, 70));
+    cancel.setFont(new java.awt.Font("Verdana", 0, 11));
+    cancel.setText("Cancel");
+    cancel.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        cancel_actionPerformed(e);
+      }
+    });
+    buttonPanel.setLayout(gridBagLayout1);
+    buttonPanel.setOpaque(false);
+    showResultsNewFrame.setText("New Window");
+    mergeResults.setText("Merge Results");
+    this.setBackground(Color.white);
+    this.add(jPanel1, BorderLayout.NORTH);
+    jPanel1.add(jScrollPane1, BorderLayout.CENTER);
+    jScrollPane1.getViewport().add(infoText, null);
+    jPanel1.add(titlePanel, BorderLayout.NORTH);
+    titlePanel.add(buttonPanel, BorderLayout.EAST);
+    buttonPanel.add(cancel, new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0,
+            GridBagConstraints.CENTER, GridBagConstraints.NONE, new Insets(
+                    19, 6, 16, 4), 0, 0));
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
+   */
+  protected void cancel_actionPerformed(ActionEvent e)
+  {
+  }
+}
diff --git a/src/jalview/math/Matrix.java b/src/jalview/math/Matrix.java
index 2f79875..5baf47c 100755
--- a/src/jalview/math/Matrix.java
+++ b/src/jalview/math/Matrix.java
@@ -1,851 +1,857 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.math;
-
-import java.io.*;
-
-import jalview.util.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class Matrix
-{
-  /**
-   * SMJSPUBLIC
-   */
-  public double[][] value;
-
-  /** DOCUMENT ME!! */
-  public int rows;
-
-  /** DOCUMENT ME!! */
-  public int cols;
-
-  /** DOCUMENT ME!! */
-  public double[] d; // Diagonal
-
-  /** DOCUMENT ME!! */
-  public double[] e; // off diagonal
-
-  /**
-   * Creates a new Matrix object.
-   *
-   * @param value DOCUMENT ME!
-   * @param rows DOCUMENT ME!
-   * @param cols DOCUMENT ME!
-   */
-  public Matrix(double[][] value, int rows, int cols)
-  {
-    this.rows = rows;
-    this.cols = cols;
-    this.value = value;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Matrix transpose()
-  {
-    double[][] out = new double[cols][rows];
-
-    for (int i = 0; i < cols; i++)
-    {
-      for (int j = 0; j < rows; j++)
-      {
-        out[i][j] = value[j][i];
-      }
-    }
-
-    return new Matrix(out, cols, rows);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param ps DOCUMENT ME!
-   */
-  public void print(PrintStream ps)
-  {
-    for (int i = 0; i < rows; i++)
-    {
-      for (int j = 0; j < cols; j++)
-      {
-        Format.print(ps, "%8.2f", value[i][j]);
-      }
-
-      ps.println();
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param in DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Matrix preMultiply(Matrix in)
-  {
-    double[][] tmp = new double[in.rows][this.cols];
-
-    for (int i = 0; i < in.rows; i++)
-    {
-      for (int j = 0; j < this.cols; j++)
-      {
-        tmp[i][j] = 0.0;
-
-        for (int k = 0; k < in.cols; k++)
-        {
-          tmp[i][j] += (in.value[i][k] * this.value[k][j]);
-        }
-      }
-    }
-
-    return new Matrix(tmp, in.rows, this.cols);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param in DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public double[] vectorPostMultiply(double[] in)
-  {
-    double[] out = new double[in.length];
-
-    for (int i = 0; i < in.length; i++)
-    {
-      out[i] = 0.0;
-
-      for (int k = 0; k < in.length; k++)
-      {
-        out[i] += (value[i][k] * in[k]);
-      }
-    }
-
-    return out;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param in DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Matrix postMultiply(Matrix in)
-  {
-    double[][] out = new double[this.rows][in.cols];
-
-    for (int i = 0; i < this.rows; i++)
-    {
-      for (int j = 0; j < in.cols; j++)
-      {
-        out[i][j] = 0.0;
-
-        for (int k = 0; k < rows; k++)
-        {
-          out[i][j] = out[i][j] + (value[i][k] * in.value[k][j]);
-        }
-      }
-    }
-
-    return new Matrix(out, this.cols, in.rows);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Matrix copy()
-  {
-    double[][] newmat = new double[rows][cols];
-
-    for (int i = 0; i < rows; i++)
-    {
-      for (int j = 0; j < cols; j++)
-      {
-        newmat[i][j] = value[i][j];
-      }
-    }
-
-    return new Matrix(newmat, rows, cols);
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  public void tred()
-  {
-    int n = rows;
-    int l;
-    int k;
-    int j;
-    int i;
-
-    double scale;
-    double hh;
-    double h;
-    double g;
-    double f;
-
-    this.d = new double[rows];
-    this.e = new double[rows];
-
-    for (i = n; i >= 2; i--)
-    {
-      l = i - 1;
-      h = 0.0;
-      scale = 0.0;
-
-      if (l > 1)
-      {
-        for (k = 1; k <= l; k++)
-        {
-          scale += Math.abs(value[i - 1][k - 1]);
-        }
-
-        if (scale == 0.0)
-        {
-          e[i - 1] = value[i - 1][l - 1];
-        }
-        else
-        {
-          for (k = 1; k <= l; k++)
-          {
-            value[i - 1][k - 1] /= scale;
-            h += (value[i - 1][k - 1] * value[i - 1][k - 1]);
-          }
-
-          f = value[i - 1][l - 1];
-
-          if (f > 0)
-          {
-            g = -1.0 * Math.sqrt(h);
-          }
-          else
-          {
-            g = Math.sqrt(h);
-          }
-
-          e[i - 1] = scale * g;
-          h -= (f * g);
-          value[i - 1][l - 1] = f - g;
-          f = 0.0;
-
-          for (j = 1; j <= l; j++)
-          {
-            value[j - 1][i - 1] = value[i - 1][j - 1] / h;
-            g = 0.0;
-
-            for (k = 1; k <= j; k++)
-            {
-              g += (value[j - 1][k - 1] * value[i - 1][k - 1]);
-            }
-
-            for (k = j + 1; k <= l; k++)
-            {
-              g += (value[k - 1][j - 1] * value[i - 1][k - 1]);
-            }
-
-            e[j - 1] = g / h;
-            f += (e[j - 1] * value[i - 1][j - 1]);
-          }
-
-          hh = f / (h + h);
-
-          for (j = 1; j <= l; j++)
-          {
-            f = value[i - 1][j - 1];
-            g = e[j - 1] - (hh * f);
-            e[j - 1] = g;
-
-            for (k = 1; k <= j; k++)
-            {
-              value[j - 1][k - 1] -= ( (f * e[k - 1]) +
-                                      (g * value[i - 1][k - 1]));
-            }
-          }
-        }
-      }
-      else
-      {
-        e[i - 1] = value[i - 1][l - 1];
-      }
-
-      d[i - 1] = h;
-    }
-
-    d[0] = 0.0;
-    e[0] = 0.0;
-
-    for (i = 1; i <= n; i++)
-    {
-      l = i - 1;
-
-      if (d[i - 1] != 0.0)
-      {
-        for (j = 1; j <= l; j++)
-        {
-          g = 0.0;
-
-          for (k = 1; k <= l; k++)
-          {
-            g += (value[i - 1][k - 1] * value[k - 1][j - 1]);
-          }
-
-          for (k = 1; k <= l; k++)
-          {
-            value[k - 1][j - 1] -= (g * value[k - 1][i - 1]);
-          }
-        }
-      }
-
-      d[i - 1] = value[i - 1][i - 1];
-      value[i - 1][i - 1] = 1.0;
-
-      for (j = 1; j <= l; j++)
-      {
-        value[j - 1][i - 1] = 0.0;
-        value[i - 1][j - 1] = 0.0;
-      }
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  public void tqli()
-  {
-    int n = rows;
-
-    int m;
-    int l;
-    int iter;
-    int i;
-    int k;
-    double s;
-    double r;
-    double p;
-    ;
-
-    double g;
-    double f;
-    double dd;
-    double c;
-    double b;
-
-    for (i = 2; i <= n; i++)
-    {
-      e[i - 2] = e[i - 1];
-    }
-
-    e[n - 1] = 0.0;
-
-    for (l = 1; l <= n; l++)
-    {
-      iter = 0;
-
-      do
-      {
-        for (m = l; m <= (n - 1); m++)
-        {
-          dd = Math.abs(d[m - 1]) + Math.abs(d[m]);
-
-          if ( (Math.abs(e[m - 1]) + dd) == dd)
-          {
-            break;
-          }
-        }
-
-        if (m != l)
-        {
-          iter++;
-
-          if (iter == 30)
-          {
-            System.err.print("Too many iterations in tqli");
-            System.exit(0); // JBPNote - should this really be here ???
-          }
-          else
-          {
-            //	    System.out.println("Iteration " + iter);
-          }
-
-          g = (d[l] - d[l - 1]) / (2.0 * e[l - 1]);
-          r = Math.sqrt( (g * g) + 1.0);
-          g = d[m - 1] - d[l - 1] + (e[l - 1] / (g + sign(r, g)));
-          c = 1.0;
-          s = c;
-          p = 0.0;
-
-          for (i = m - 1; i >= l; i--)
-          {
-            f = s * e[i - 1];
-            b = c * e[i - 1];
-
-            if (Math.abs(f) >= Math.abs(g))
-            {
-              c = g / f;
-              r = Math.sqrt( (c * c) + 1.0);
-              e[i] = f * r;
-              s = 1.0 / r;
-              c *= s;
-            }
-            else
-            {
-              s = f / g;
-              r = Math.sqrt( (s * s) + 1.0);
-              e[i] = g * r;
-              c = 1.0 / r;
-              s *= c;
-            }
-
-            g = d[i] - p;
-            r = ( (d[i - 1] - g) * s) + (2.0 * c * b);
-            p = s * r;
-            d[i] = g + p;
-            g = (c * r) - b;
-
-            for (k = 1; k <= n; k++)
-            {
-              f = value[k - 1][i];
-              value[k - 1][i] = (s * value[k - 1][i - 1]) +
-                  (c * f);
-              value[k - 1][i - 1] = (c * value[k - 1][i - 1]) -
-                  (s * f);
-            }
-          }
-
-          d[l - 1] = d[l - 1] - p;
-          e[l - 1] = g;
-          e[m - 1] = 0.0;
-        }
-      }
-      while (m != l);
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  public void tred2()
-  {
-    int n = rows;
-    int l;
-    int k;
-    int j;
-    int i;
-
-    double scale;
-    double hh;
-    double h;
-    double g;
-    double f;
-
-    this.d = new double[rows];
-    this.e = new double[rows];
-
-    for (i = n - 1; i >= 1; i--)
-    {
-      l = i - 1;
-      h = 0.0;
-      scale = 0.0;
-
-      if (l > 0)
-      {
-        for (k = 0; k < l; k++)
-        {
-          scale += Math.abs(value[i][k]);
-        }
-
-        if (scale == 0.0)
-        {
-          e[i] = value[i][l];
-        }
-        else
-        {
-          for (k = 0; k < l; k++)
-          {
-            value[i][k] /= scale;
-            h += (value[i][k] * value[i][k]);
-          }
-
-          f = value[i][l];
-
-          if (f > 0)
-          {
-            g = -1.0 * Math.sqrt(h);
-          }
-          else
-          {
-            g = Math.sqrt(h);
-          }
-
-          e[i] = scale * g;
-          h -= (f * g);
-          value[i][l] = f - g;
-          f = 0.0;
-
-          for (j = 0; j < l; j++)
-          {
-            value[j][i] = value[i][j] / h;
-            g = 0.0;
-
-            for (k = 0; k < j; k++)
-            {
-              g += (value[j][k] * value[i][k]);
-            }
-
-            for (k = j; k < l; k++)
-            {
-              g += (value[k][j] * value[i][k]);
-            }
-
-            e[j] = g / h;
-            f += (e[j] * value[i][j]);
-          }
-
-          hh = f / (h + h);
-
-          for (j = 0; j < l; j++)
-          {
-            f = value[i][j];
-            g = e[j] - (hh * f);
-            e[j] = g;
-
-            for (k = 0; k < j; k++)
-            {
-              value[j][k] -= ( (f * e[k]) + (g * value[i][k]));
-            }
-          }
-        }
-      }
-      else
-      {
-        e[i] = value[i][l];
-      }
-
-      d[i] = h;
-    }
-
-    d[0] = 0.0;
-    e[0] = 0.0;
-
-    for (i = 0; i < n; i++)
-    {
-      l = i - 1;
-
-      if (d[i] != 0.0)
-      {
-        for (j = 0; j < l; j++)
-        {
-          g = 0.0;
-
-          for (k = 0; k < l; k++)
-          {
-            g += (value[i][k] * value[k][j]);
-          }
-
-          for (k = 0; k < l; k++)
-          {
-            value[k][j] -= (g * value[k][i]);
-          }
-        }
-      }
-
-      d[i] = value[i][i];
-      value[i][i] = 1.0;
-
-      for (j = 0; j < l; j++)
-      {
-        value[j][i] = 0.0;
-        value[i][j] = 0.0;
-      }
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  public void tqli2()
-  {
-    int n = rows;
-
-    int m;
-    int l;
-    int iter;
-    int i;
-    int k;
-    double s;
-    double r;
-    double p;
-    ;
-
-    double g;
-    double f;
-    double dd;
-    double c;
-    double b;
-
-    for (i = 2; i <= n; i++)
-    {
-      e[i - 2] = e[i - 1];
-    }
-
-    e[n - 1] = 0.0;
-
-    for (l = 1; l <= n; l++)
-    {
-      iter = 0;
-
-      do
-      {
-        for (m = l; m <= (n - 1); m++)
-        {
-          dd = Math.abs(d[m - 1]) + Math.abs(d[m]);
-
-          if ( (Math.abs(e[m - 1]) + dd) == dd)
-          {
-            break;
-          }
-        }
-
-        if (m != l)
-        {
-          iter++;
-
-          if (iter == 30)
-          {
-            System.err.print("Too many iterations in tqli");
-            System.exit(0); // JBPNote - same as above - not a graceful exit!
-          }
-          else
-          {
-            //	    System.out.println("Iteration " + iter);
-          }
-
-          g = (d[l] - d[l - 1]) / (2.0 * e[l - 1]);
-          r = Math.sqrt( (g * g) + 1.0);
-          g = d[m - 1] - d[l - 1] + (e[l - 1] / (g + sign(r, g)));
-          c = 1.0;
-          s = c;
-          p = 0.0;
-
-          for (i = m - 1; i >= l; i--)
-          {
-            f = s * e[i - 1];
-            b = c * e[i - 1];
-
-            if (Math.abs(f) >= Math.abs(g))
-            {
-              c = g / f;
-              r = Math.sqrt( (c * c) + 1.0);
-              e[i] = f * r;
-              s = 1.0 / r;
-              c *= s;
-            }
-            else
-            {
-              s = f / g;
-              r = Math.sqrt( (s * s) + 1.0);
-              e[i] = g * r;
-              c = 1.0 / r;
-              s *= c;
-            }
-
-            g = d[i] - p;
-            r = ( (d[i - 1] - g) * s) + (2.0 * c * b);
-            p = s * r;
-            d[i] = g + p;
-            g = (c * r) - b;
-
-            for (k = 1; k <= n; k++)
-            {
-              f = value[k - 1][i];
-              value[k - 1][i] = (s * value[k - 1][i - 1]) +
-                  (c * f);
-              value[k - 1][i - 1] = (c * value[k - 1][i - 1]) -
-                  (s * f);
-            }
-          }
-
-          d[l - 1] = d[l - 1] - p;
-          e[l - 1] = g;
-          e[m - 1] = 0.0;
-        }
-      }
-      while (m != l);
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param a DOCUMENT ME!
-   * @param b DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public double sign(double a, double b)
-  {
-    if (b < 0)
-    {
-      return -Math.abs(a);
-    }
-    else
-    {
-      return Math.abs(a);
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param n DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public double[] getColumn(int n)
-  {
-    double[] out = new double[rows];
-
-    for (int i = 0; i < rows; i++)
-    {
-      out[i] = value[i][n];
-    }
-
-    return out;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param ps DOCUMENT ME!
-   */
-  public void printD(PrintStream ps)
-  {
-    for (int j = 0; j < rows; j++)
-    {
-      Format.print(ps, "%15.4e", d[j]);
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param ps DOCUMENT ME!
-   */
-  public void printE(PrintStream ps)
-  {
-    for (int j = 0; j < rows; j++)
-    {
-      Format.print(ps, "%15.4e", e[j]);
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param args DOCUMENT ME!
-   */
-  public static void main(String[] args)
-  {
-    int n = Integer.parseInt(args[0]);
-    double[][] in = new double[n][n];
-
-    for (int i = 0; i < n; i++)
-    {
-      for (int j = 0; j < n; j++)
-      {
-        in[i][j] = (double) Math.random();
-      }
-    }
-
-    Matrix origmat = new Matrix(in, n, n);
-
-    //    System.out.println(" --- Original matrix ---- ");
-    ///    origmat.print(System.out);
-    //System.out.println();
-    //System.out.println(" --- transpose matrix ---- ");
-    Matrix trans = origmat.transpose();
-
-    //trans.print(System.out);
-    //System.out.println();
-    //System.out.println(" --- OrigT * Orig ---- ");
-    Matrix symm = trans.postMultiply(origmat);
-
-    //symm.print(System.out);
-    //System.out.println();
-    // Copy the symmetric matrix for later
-    //Matrix origsymm = symm.copy();
-
-    // This produces the tridiagonal transformation matrix
-    //long tstart = System.currentTimeMillis();
-    symm.tred();
-
-    //long tend = System.currentTimeMillis();
-
-    //System.out.println("Time take for tred = " + (tend-tstart) + "ms");
-    //System.out.println(" ---Tridiag transform matrix ---");
-    //symm.print(System.out);
-    //System.out.println();
-    //System.out.println(" --- D vector ---");
-    //symm.printD(System.out);
-    //System.out.println();
-    //System.out.println(" --- E vector ---");
-    //symm.printE(System.out);
-    //System.out.println();
-    // Now produce the diagonalization matrix
-    //tstart = System.currentTimeMillis();
-    symm.tqli();
-    //tend = System.currentTimeMillis();
-
-    //System.out.println("Time take for tqli = " + (tend-tstart) + " ms");
-    //System.out.println(" --- New diagonalization matrix ---");
-    //symm.print(System.out);
-    //System.out.println();
-    //System.out.println(" --- D vector ---");
-    //symm.printD(System.out);
-    //System.out.println();
-    //System.out.println(" --- E vector ---");
-    //symm.printE(System.out);
-    //System.out.println();
-    //System.out.println(" --- First eigenvector --- ");
-    //double[] eigenv = symm.getColumn(0);
-    //for (int i=0; i < eigenv.length;i++) {
-    //  Format.print(System.out,"%15.4f",eigenv[i]);
-    // }
-    //System.out.println();
-    //double[] neigenv = origsymm.vectorPostMultiply(eigenv);
-    //for (int i=0; i < neigenv.length;i++) {
-    //  Format.print(System.out,"%15.4f",neigenv[i]/symm.d[0]);
-    //}
-    //System.out.println();
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.math;
+
+import java.io.*;
+
+import jalview.util.*;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class Matrix
+{
+  /**
+   * SMJSPUBLIC
+   */
+  public double[][] value;
+
+  /** DOCUMENT ME!! */
+  public int rows;
+
+  /** DOCUMENT ME!! */
+  public int cols;
+
+  /** DOCUMENT ME!! */
+  public double[] d; // Diagonal
+
+  /** DOCUMENT ME!! */
+  public double[] e; // off diagonal
+
+  /**
+   * Creates a new Matrix object.
+   * 
+   * @param value
+   *                DOCUMENT ME!
+   * @param rows
+   *                DOCUMENT ME!
+   * @param cols
+   *                DOCUMENT ME!
+   */
+  public Matrix(double[][] value, int rows, int cols)
+  {
+    this.rows = rows;
+    this.cols = cols;
+    this.value = value;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public Matrix transpose()
+  {
+    double[][] out = new double[cols][rows];
+
+    for (int i = 0; i < cols; i++)
+    {
+      for (int j = 0; j < rows; j++)
+      {
+        out[i][j] = value[j][i];
+      }
+    }
+
+    return new Matrix(out, cols, rows);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param ps
+   *                DOCUMENT ME!
+   */
+  public void print(PrintStream ps)
+  {
+    for (int i = 0; i < rows; i++)
+    {
+      for (int j = 0; j < cols; j++)
+      {
+        Format.print(ps, "%8.2f", value[i][j]);
+      }
+
+      ps.println();
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param in
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public Matrix preMultiply(Matrix in)
+  {
+    double[][] tmp = new double[in.rows][this.cols];
+
+    for (int i = 0; i < in.rows; i++)
+    {
+      for (int j = 0; j < this.cols; j++)
+      {
+        tmp[i][j] = 0.0;
+
+        for (int k = 0; k < in.cols; k++)
+        {
+          tmp[i][j] += (in.value[i][k] * this.value[k][j]);
+        }
+      }
+    }
+
+    return new Matrix(tmp, in.rows, this.cols);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param in
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public double[] vectorPostMultiply(double[] in)
+  {
+    double[] out = new double[in.length];
+
+    for (int i = 0; i < in.length; i++)
+    {
+      out[i] = 0.0;
+
+      for (int k = 0; k < in.length; k++)
+      {
+        out[i] += (value[i][k] * in[k]);
+      }
+    }
+
+    return out;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param in
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public Matrix postMultiply(Matrix in)
+  {
+    double[][] out = new double[this.rows][in.cols];
+
+    for (int i = 0; i < this.rows; i++)
+    {
+      for (int j = 0; j < in.cols; j++)
+      {
+        out[i][j] = 0.0;
+
+        for (int k = 0; k < rows; k++)
+        {
+          out[i][j] = out[i][j] + (value[i][k] * in.value[k][j]);
+        }
+      }
+    }
+
+    return new Matrix(out, this.cols, in.rows);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public Matrix copy()
+  {
+    double[][] newmat = new double[rows][cols];
+
+    for (int i = 0; i < rows; i++)
+    {
+      for (int j = 0; j < cols; j++)
+      {
+        newmat[i][j] = value[i][j];
+      }
+    }
+
+    return new Matrix(newmat, rows, cols);
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void tred()
+  {
+    int n = rows;
+    int l;
+    int k;
+    int j;
+    int i;
+
+    double scale;
+    double hh;
+    double h;
+    double g;
+    double f;
+
+    this.d = new double[rows];
+    this.e = new double[rows];
+
+    for (i = n; i >= 2; i--)
+    {
+      l = i - 1;
+      h = 0.0;
+      scale = 0.0;
+
+      if (l > 1)
+      {
+        for (k = 1; k <= l; k++)
+        {
+          scale += Math.abs(value[i - 1][k - 1]);
+        }
+
+        if (scale == 0.0)
+        {
+          e[i - 1] = value[i - 1][l - 1];
+        }
+        else
+        {
+          for (k = 1; k <= l; k++)
+          {
+            value[i - 1][k - 1] /= scale;
+            h += (value[i - 1][k - 1] * value[i - 1][k - 1]);
+          }
+
+          f = value[i - 1][l - 1];
+
+          if (f > 0)
+          {
+            g = -1.0 * Math.sqrt(h);
+          }
+          else
+          {
+            g = Math.sqrt(h);
+          }
+
+          e[i - 1] = scale * g;
+          h -= (f * g);
+          value[i - 1][l - 1] = f - g;
+          f = 0.0;
+
+          for (j = 1; j <= l; j++)
+          {
+            value[j - 1][i - 1] = value[i - 1][j - 1] / h;
+            g = 0.0;
+
+            for (k = 1; k <= j; k++)
+            {
+              g += (value[j - 1][k - 1] * value[i - 1][k - 1]);
+            }
+
+            for (k = j + 1; k <= l; k++)
+            {
+              g += (value[k - 1][j - 1] * value[i - 1][k - 1]);
+            }
+
+            e[j - 1] = g / h;
+            f += (e[j - 1] * value[i - 1][j - 1]);
+          }
+
+          hh = f / (h + h);
+
+          for (j = 1; j <= l; j++)
+          {
+            f = value[i - 1][j - 1];
+            g = e[j - 1] - (hh * f);
+            e[j - 1] = g;
+
+            for (k = 1; k <= j; k++)
+            {
+              value[j - 1][k - 1] -= ((f * e[k - 1]) + (g * value[i - 1][k - 1]));
+            }
+          }
+        }
+      }
+      else
+      {
+        e[i - 1] = value[i - 1][l - 1];
+      }
+
+      d[i - 1] = h;
+    }
+
+    d[0] = 0.0;
+    e[0] = 0.0;
+
+    for (i = 1; i <= n; i++)
+    {
+      l = i - 1;
+
+      if (d[i - 1] != 0.0)
+      {
+        for (j = 1; j <= l; j++)
+        {
+          g = 0.0;
+
+          for (k = 1; k <= l; k++)
+          {
+            g += (value[i - 1][k - 1] * value[k - 1][j - 1]);
+          }
+
+          for (k = 1; k <= l; k++)
+          {
+            value[k - 1][j - 1] -= (g * value[k - 1][i - 1]);
+          }
+        }
+      }
+
+      d[i - 1] = value[i - 1][i - 1];
+      value[i - 1][i - 1] = 1.0;
+
+      for (j = 1; j <= l; j++)
+      {
+        value[j - 1][i - 1] = 0.0;
+        value[i - 1][j - 1] = 0.0;
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void tqli()
+  {
+    int n = rows;
+
+    int m;
+    int l;
+    int iter;
+    int i;
+    int k;
+    double s;
+    double r;
+    double p;
+    ;
+
+    double g;
+    double f;
+    double dd;
+    double c;
+    double b;
+
+    for (i = 2; i <= n; i++)
+    {
+      e[i - 2] = e[i - 1];
+    }
+
+    e[n - 1] = 0.0;
+
+    for (l = 1; l <= n; l++)
+    {
+      iter = 0;
+
+      do
+      {
+        for (m = l; m <= (n - 1); m++)
+        {
+          dd = Math.abs(d[m - 1]) + Math.abs(d[m]);
+
+          if ((Math.abs(e[m - 1]) + dd) == dd)
+          {
+            break;
+          }
+        }
+
+        if (m != l)
+        {
+          iter++;
+
+          if (iter == 30)
+          {
+            System.err.print("Too many iterations in tqli");
+            System.exit(0); // JBPNote - should this really be here ???
+          }
+          else
+          {
+            // System.out.println("Iteration " + iter);
+          }
+
+          g = (d[l] - d[l - 1]) / (2.0 * e[l - 1]);
+          r = Math.sqrt((g * g) + 1.0);
+          g = d[m - 1] - d[l - 1] + (e[l - 1] / (g + sign(r, g)));
+          c = 1.0;
+          s = c;
+          p = 0.0;
+
+          for (i = m - 1; i >= l; i--)
+          {
+            f = s * e[i - 1];
+            b = c * e[i - 1];
+
+            if (Math.abs(f) >= Math.abs(g))
+            {
+              c = g / f;
+              r = Math.sqrt((c * c) + 1.0);
+              e[i] = f * r;
+              s = 1.0 / r;
+              c *= s;
+            }
+            else
+            {
+              s = f / g;
+              r = Math.sqrt((s * s) + 1.0);
+              e[i] = g * r;
+              c = 1.0 / r;
+              s *= c;
+            }
+
+            g = d[i] - p;
+            r = ((d[i - 1] - g) * s) + (2.0 * c * b);
+            p = s * r;
+            d[i] = g + p;
+            g = (c * r) - b;
+
+            for (k = 1; k <= n; k++)
+            {
+              f = value[k - 1][i];
+              value[k - 1][i] = (s * value[k - 1][i - 1]) + (c * f);
+              value[k - 1][i - 1] = (c * value[k - 1][i - 1]) - (s * f);
+            }
+          }
+
+          d[l - 1] = d[l - 1] - p;
+          e[l - 1] = g;
+          e[m - 1] = 0.0;
+        }
+      } while (m != l);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void tred2()
+  {
+    int n = rows;
+    int l;
+    int k;
+    int j;
+    int i;
+
+    double scale;
+    double hh;
+    double h;
+    double g;
+    double f;
+
+    this.d = new double[rows];
+    this.e = new double[rows];
+
+    for (i = n - 1; i >= 1; i--)
+    {
+      l = i - 1;
+      h = 0.0;
+      scale = 0.0;
+
+      if (l > 0)
+      {
+        for (k = 0; k < l; k++)
+        {
+          scale += Math.abs(value[i][k]);
+        }
+
+        if (scale == 0.0)
+        {
+          e[i] = value[i][l];
+        }
+        else
+        {
+          for (k = 0; k < l; k++)
+          {
+            value[i][k] /= scale;
+            h += (value[i][k] * value[i][k]);
+          }
+
+          f = value[i][l];
+
+          if (f > 0)
+          {
+            g = -1.0 * Math.sqrt(h);
+          }
+          else
+          {
+            g = Math.sqrt(h);
+          }
+
+          e[i] = scale * g;
+          h -= (f * g);
+          value[i][l] = f - g;
+          f = 0.0;
+
+          for (j = 0; j < l; j++)
+          {
+            value[j][i] = value[i][j] / h;
+            g = 0.0;
+
+            for (k = 0; k < j; k++)
+            {
+              g += (value[j][k] * value[i][k]);
+            }
+
+            for (k = j; k < l; k++)
+            {
+              g += (value[k][j] * value[i][k]);
+            }
+
+            e[j] = g / h;
+            f += (e[j] * value[i][j]);
+          }
+
+          hh = f / (h + h);
+
+          for (j = 0; j < l; j++)
+          {
+            f = value[i][j];
+            g = e[j] - (hh * f);
+            e[j] = g;
+
+            for (k = 0; k < j; k++)
+            {
+              value[j][k] -= ((f * e[k]) + (g * value[i][k]));
+            }
+          }
+        }
+      }
+      else
+      {
+        e[i] = value[i][l];
+      }
+
+      d[i] = h;
+    }
+
+    d[0] = 0.0;
+    e[0] = 0.0;
+
+    for (i = 0; i < n; i++)
+    {
+      l = i - 1;
+
+      if (d[i] != 0.0)
+      {
+        for (j = 0; j < l; j++)
+        {
+          g = 0.0;
+
+          for (k = 0; k < l; k++)
+          {
+            g += (value[i][k] * value[k][j]);
+          }
+
+          for (k = 0; k < l; k++)
+          {
+            value[k][j] -= (g * value[k][i]);
+          }
+        }
+      }
+
+      d[i] = value[i][i];
+      value[i][i] = 1.0;
+
+      for (j = 0; j < l; j++)
+      {
+        value[j][i] = 0.0;
+        value[i][j] = 0.0;
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void tqli2()
+  {
+    int n = rows;
+
+    int m;
+    int l;
+    int iter;
+    int i;
+    int k;
+    double s;
+    double r;
+    double p;
+    ;
+
+    double g;
+    double f;
+    double dd;
+    double c;
+    double b;
+
+    for (i = 2; i <= n; i++)
+    {
+      e[i - 2] = e[i - 1];
+    }
+
+    e[n - 1] = 0.0;
+
+    for (l = 1; l <= n; l++)
+    {
+      iter = 0;
+
+      do
+      {
+        for (m = l; m <= (n - 1); m++)
+        {
+          dd = Math.abs(d[m - 1]) + Math.abs(d[m]);
+
+          if ((Math.abs(e[m - 1]) + dd) == dd)
+          {
+            break;
+          }
+        }
+
+        if (m != l)
+        {
+          iter++;
+
+          if (iter == 30)
+          {
+            System.err.print("Too many iterations in tqli");
+            System.exit(0); // JBPNote - same as above - not a graceful exit!
+          }
+          else
+          {
+            // System.out.println("Iteration " + iter);
+          }
+
+          g = (d[l] - d[l - 1]) / (2.0 * e[l - 1]);
+          r = Math.sqrt((g * g) + 1.0);
+          g = d[m - 1] - d[l - 1] + (e[l - 1] / (g + sign(r, g)));
+          c = 1.0;
+          s = c;
+          p = 0.0;
+
+          for (i = m - 1; i >= l; i--)
+          {
+            f = s * e[i - 1];
+            b = c * e[i - 1];
+
+            if (Math.abs(f) >= Math.abs(g))
+            {
+              c = g / f;
+              r = Math.sqrt((c * c) + 1.0);
+              e[i] = f * r;
+              s = 1.0 / r;
+              c *= s;
+            }
+            else
+            {
+              s = f / g;
+              r = Math.sqrt((s * s) + 1.0);
+              e[i] = g * r;
+              c = 1.0 / r;
+              s *= c;
+            }
+
+            g = d[i] - p;
+            r = ((d[i - 1] - g) * s) + (2.0 * c * b);
+            p = s * r;
+            d[i] = g + p;
+            g = (c * r) - b;
+
+            for (k = 1; k <= n; k++)
+            {
+              f = value[k - 1][i];
+              value[k - 1][i] = (s * value[k - 1][i - 1]) + (c * f);
+              value[k - 1][i - 1] = (c * value[k - 1][i - 1]) - (s * f);
+            }
+          }
+
+          d[l - 1] = d[l - 1] - p;
+          e[l - 1] = g;
+          e[m - 1] = 0.0;
+        }
+      } while (m != l);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param a
+   *                DOCUMENT ME!
+   * @param b
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public double sign(double a, double b)
+  {
+    if (b < 0)
+    {
+      return -Math.abs(a);
+    }
+    else
+    {
+      return Math.abs(a);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param n
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public double[] getColumn(int n)
+  {
+    double[] out = new double[rows];
+
+    for (int i = 0; i < rows; i++)
+    {
+      out[i] = value[i][n];
+    }
+
+    return out;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param ps
+   *                DOCUMENT ME!
+   */
+  public void printD(PrintStream ps)
+  {
+    for (int j = 0; j < rows; j++)
+    {
+      Format.print(ps, "%15.4e", d[j]);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param ps
+   *                DOCUMENT ME!
+   */
+  public void printE(PrintStream ps)
+  {
+    for (int j = 0; j < rows; j++)
+    {
+      Format.print(ps, "%15.4e", e[j]);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param args
+   *                DOCUMENT ME!
+   */
+  public static void main(String[] args)
+  {
+    int n = Integer.parseInt(args[0]);
+    double[][] in = new double[n][n];
+
+    for (int i = 0; i < n; i++)
+    {
+      for (int j = 0; j < n; j++)
+      {
+        in[i][j] = (double) Math.random();
+      }
+    }
+
+    Matrix origmat = new Matrix(in, n, n);
+
+    // System.out.println(" --- Original matrix ---- ");
+    // / origmat.print(System.out);
+    // System.out.println();
+    // System.out.println(" --- transpose matrix ---- ");
+    Matrix trans = origmat.transpose();
+
+    // trans.print(System.out);
+    // System.out.println();
+    // System.out.println(" --- OrigT * Orig ---- ");
+    Matrix symm = trans.postMultiply(origmat);
+
+    // symm.print(System.out);
+    // System.out.println();
+    // Copy the symmetric matrix for later
+    // Matrix origsymm = symm.copy();
+
+    // This produces the tridiagonal transformation matrix
+    // long tstart = System.currentTimeMillis();
+    symm.tred();
+
+    // long tend = System.currentTimeMillis();
+
+    // System.out.println("Time take for tred = " + (tend-tstart) + "ms");
+    // System.out.println(" ---Tridiag transform matrix ---");
+    // symm.print(System.out);
+    // System.out.println();
+    // System.out.println(" --- D vector ---");
+    // symm.printD(System.out);
+    // System.out.println();
+    // System.out.println(" --- E vector ---");
+    // symm.printE(System.out);
+    // System.out.println();
+    // Now produce the diagonalization matrix
+    // tstart = System.currentTimeMillis();
+    symm.tqli();
+    // tend = System.currentTimeMillis();
+
+    // System.out.println("Time take for tqli = " + (tend-tstart) + " ms");
+    // System.out.println(" --- New diagonalization matrix ---");
+    // symm.print(System.out);
+    // System.out.println();
+    // System.out.println(" --- D vector ---");
+    // symm.printD(System.out);
+    // System.out.println();
+    // System.out.println(" --- E vector ---");
+    // symm.printE(System.out);
+    // System.out.println();
+    // System.out.println(" --- First eigenvector --- ");
+    // double[] eigenv = symm.getColumn(0);
+    // for (int i=0; i < eigenv.length;i++) {
+    // Format.print(System.out,"%15.4f",eigenv[i]);
+    // }
+    // System.out.println();
+    // double[] neigenv = origsymm.vectorPostMultiply(eigenv);
+    // for (int i=0; i < neigenv.length;i++) {
+    // Format.print(System.out,"%15.4f",neigenv[i]/symm.d[0]);
+    // }
+    // System.out.println();
+  }
+}
diff --git a/src/jalview/math/RotatableMatrix.java b/src/jalview/math/RotatableMatrix.java
index eff8dea..3487c6d 100755
--- a/src/jalview/math/RotatableMatrix.java
+++ b/src/jalview/math/RotatableMatrix.java
@@ -1,331 +1,344 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.math;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class RotatableMatrix
-{
-  float[][] matrix;
-  float[] temp;
-  float[][] rot;
-
-  /**
-   * Creates a new RotatableMatrix object.
-   *
-   * @param rows DOCUMENT ME!
-   * @param cols DOCUMENT ME!
-   */
-  public RotatableMatrix(int rows, int cols)
-  {
-    matrix = new float[rows][cols];
-
-    temp = new float[3];
-
-    rot = new float[3][3];
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
-   * @param j DOCUMENT ME!
-   * @param value DOCUMENT ME!
-   */
-  public void addElement(int i, int j, float value)
-  {
-    matrix[i][j] = value;
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  public void print()
-  {
-    System.out.println(matrix[0][0] + " " + matrix[0][1] + " " +
-                       matrix[0][2]);
-
-    System.out.println(matrix[1][0] + " " + matrix[1][1] + " " +
-                       matrix[1][2]);
-
-    System.out.println(matrix[2][0] + " " + matrix[2][1] + " " +
-                       matrix[2][2]);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param degrees DOCUMENT ME!
-   * @param axis DOCUMENT ME!
-   */
-  public void rotate(float degrees, char axis)
-  {
-    float costheta = (float) Math.cos( (degrees * Math.PI) / (float) 180.0);
-
-    float sintheta = (float) Math.sin( (degrees * Math.PI) / (float) 180.0);
-
-    if (axis == 'z')
-    {
-      rot[0][0] = (float) costheta;
-
-      rot[0][1] = (float) - sintheta;
-
-      rot[0][2] = (float) 0.0;
-
-      rot[1][0] = (float) sintheta;
-
-      rot[1][1] = (float) costheta;
-
-      rot[1][2] = (float) 0.0;
-
-      rot[2][0] = (float) 0.0;
-
-      rot[2][1] = (float) 0.0;
-
-      rot[2][2] = (float) 1.0;
-
-      preMultiply(rot);
-    }
-
-    if (axis == 'x')
-    {
-      rot[0][0] = (float) 1.0;
-
-      rot[0][1] = (float) 0.0;
-
-      rot[0][2] = (float) 0.0;
-
-      rot[1][0] = (float) 0.0;
-
-      rot[1][1] = (float) costheta;
-
-      rot[1][2] = (float) sintheta;
-
-      rot[2][0] = (float) 0.0;
-
-      rot[2][1] = (float) - sintheta;
-
-      rot[2][2] = (float) costheta;
-
-      preMultiply(rot);
-    }
-
-    if (axis == 'y')
-    {
-      rot[0][0] = (float) costheta;
-
-      rot[0][1] = (float) 0.0;
-
-      rot[0][2] = (float) - sintheta;
-
-      rot[1][0] = (float) 0.0;
-
-      rot[1][1] = (float) 1.0;
-
-      rot[1][2] = (float) 0.0;
-
-      rot[2][0] = (float) sintheta;
-
-      rot[2][1] = (float) 0.0;
-
-      rot[2][2] = (float) costheta;
-
-      preMultiply(rot);
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param vect DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public float[] vectorMultiply(float[] vect)
-  {
-    temp[0] = vect[0];
-
-    temp[1] = vect[1];
-
-    temp[2] = vect[2];
-
-    for (int i = 0; i < 3; i++)
-    {
-      temp[i] = (matrix[i][0] * vect[0]) + (matrix[i][1] * vect[1]) +
-          (matrix[i][2] * vect[2]);
-    }
-
-    vect[0] = temp[0];
-
-    vect[1] = temp[1];
-
-    vect[2] = temp[2];
-
-    return vect;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param mat DOCUMENT ME!
-   */
-  public void preMultiply(float[][] mat)
-  {
-    float[][] tmp = new float[3][3];
-
-    for (int i = 0; i < 3; i++)
-    {
-      for (int j = 0; j < 3; j++)
-      {
-        tmp[i][j] = (mat[i][0] * matrix[0][j]) +
-            (mat[i][1] * matrix[1][j]) + (mat[i][2] * matrix[2][j]);
-      }
-    }
-
-    for (int i = 0; i < 3; i++)
-    {
-      for (int j = 0; j < 3; j++)
-      {
-        matrix[i][j] = tmp[i][j];
-      }
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param mat DOCUMENT ME!
-   */
-  public void postMultiply(float[][] mat)
-  {
-    float[][] tmp = new float[3][3];
-
-    for (int i = 0; i < 3; i++)
-    {
-      for (int j = 0; j < 3; j++)
-      {
-        tmp[i][j] = (matrix[i][0] * mat[0][j]) +
-            (matrix[i][1] * mat[1][j]) + (matrix[i][2] * mat[2][j]);
-      }
-    }
-
-    for (int i = 0; i < 3; i++)
-    {
-      for (int j = 0; j < 3; j++)
-      {
-        matrix[i][j] = tmp[i][j];
-      }
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param args DOCUMENT ME!
-   */
-  public static void main(String[] args)
-  {
-    RotatableMatrix m = new RotatableMatrix(3, 3);
-
-    m.addElement(0, 0, 1);
-
-    m.addElement(0, 1, 0);
-
-    m.addElement(0, 2, 0);
-
-    m.addElement(1, 0, 0);
-
-    m.addElement(1, 1, 2);
-
-    m.addElement(1, 2, 0);
-
-    m.addElement(2, 0, 0);
-
-    m.addElement(2, 1, 0);
-
-    m.addElement(2, 2, 1);
-
-    m.print();
-
-    RotatableMatrix n = new RotatableMatrix(3, 3);
-
-    n.addElement(0, 0, 2);
-
-    n.addElement(0, 1, 1);
-
-    n.addElement(0, 2, 1);
-
-    n.addElement(1, 0, 2);
-
-    n.addElement(1, 1, 1);
-
-    n.addElement(1, 2, 1);
-
-    n.addElement(2, 0, 2);
-
-    n.addElement(2, 1, 1);
-
-    n.addElement(2, 2, 1);
-
-    n.print();
-
-    //m.postMultiply(n.matrix);
-    //m.print();
-    //     m.rotate(45,'z',new RotatableMatrix(3,3));
-    float[] vect = new float[3];
-
-    vect[0] = 2;
-
-    vect[1] = 4;
-
-    vect[2] = 6;
-
-    vect = m.vectorMultiply(vect);
-
-    System.out.println(vect[0] + " " + vect[1] + " " + vect[2]);
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  public void setIdentity()
-  {
-    matrix[0][0] = (float) 1.0;
-
-    matrix[1][1] = (float) 1.0;
-
-    matrix[2][2] = (float) 1.0;
-
-    matrix[0][1] = (float) 0.0;
-
-    matrix[0][2] = (float) 0.0;
-
-    matrix[1][0] = (float) 0.0;
-
-    matrix[1][2] = (float) 0.0;
-
-    matrix[2][0] = (float) 0.0;
-
-    matrix[2][1] = (float) 0.0;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.math;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class RotatableMatrix
+{
+  float[][] matrix;
+
+  float[] temp;
+
+  float[][] rot;
+
+  /**
+   * Creates a new RotatableMatrix object.
+   * 
+   * @param rows
+   *                DOCUMENT ME!
+   * @param cols
+   *                DOCUMENT ME!
+   */
+  public RotatableMatrix(int rows, int cols)
+  {
+    matrix = new float[rows][cols];
+
+    temp = new float[3];
+
+    rot = new float[3][3];
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param i
+   *                DOCUMENT ME!
+   * @param j
+   *                DOCUMENT ME!
+   * @param value
+   *                DOCUMENT ME!
+   */
+  public void addElement(int i, int j, float value)
+  {
+    matrix[i][j] = value;
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void print()
+  {
+    System.out.println(matrix[0][0] + " " + matrix[0][1] + " "
+            + matrix[0][2]);
+
+    System.out.println(matrix[1][0] + " " + matrix[1][1] + " "
+            + matrix[1][2]);
+
+    System.out.println(matrix[2][0] + " " + matrix[2][1] + " "
+            + matrix[2][2]);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param degrees
+   *                DOCUMENT ME!
+   * @param axis
+   *                DOCUMENT ME!
+   */
+  public void rotate(float degrees, char axis)
+  {
+    float costheta = (float) Math.cos((degrees * Math.PI) / (float) 180.0);
+
+    float sintheta = (float) Math.sin((degrees * Math.PI) / (float) 180.0);
+
+    if (axis == 'z')
+    {
+      rot[0][0] = (float) costheta;
+
+      rot[0][1] = (float) -sintheta;
+
+      rot[0][2] = (float) 0.0;
+
+      rot[1][0] = (float) sintheta;
+
+      rot[1][1] = (float) costheta;
+
+      rot[1][2] = (float) 0.0;
+
+      rot[2][0] = (float) 0.0;
+
+      rot[2][1] = (float) 0.0;
+
+      rot[2][2] = (float) 1.0;
+
+      preMultiply(rot);
+    }
+
+    if (axis == 'x')
+    {
+      rot[0][0] = (float) 1.0;
+
+      rot[0][1] = (float) 0.0;
+
+      rot[0][2] = (float) 0.0;
+
+      rot[1][0] = (float) 0.0;
+
+      rot[1][1] = (float) costheta;
+
+      rot[1][2] = (float) sintheta;
+
+      rot[2][0] = (float) 0.0;
+
+      rot[2][1] = (float) -sintheta;
+
+      rot[2][2] = (float) costheta;
+
+      preMultiply(rot);
+    }
+
+    if (axis == 'y')
+    {
+      rot[0][0] = (float) costheta;
+
+      rot[0][1] = (float) 0.0;
+
+      rot[0][2] = (float) -sintheta;
+
+      rot[1][0] = (float) 0.0;
+
+      rot[1][1] = (float) 1.0;
+
+      rot[1][2] = (float) 0.0;
+
+      rot[2][0] = (float) sintheta;
+
+      rot[2][1] = (float) 0.0;
+
+      rot[2][2] = (float) costheta;
+
+      preMultiply(rot);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param vect
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public float[] vectorMultiply(float[] vect)
+  {
+    temp[0] = vect[0];
+
+    temp[1] = vect[1];
+
+    temp[2] = vect[2];
+
+    for (int i = 0; i < 3; i++)
+    {
+      temp[i] = (matrix[i][0] * vect[0]) + (matrix[i][1] * vect[1])
+              + (matrix[i][2] * vect[2]);
+    }
+
+    vect[0] = temp[0];
+
+    vect[1] = temp[1];
+
+    vect[2] = temp[2];
+
+    return vect;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param mat
+   *                DOCUMENT ME!
+   */
+  public void preMultiply(float[][] mat)
+  {
+    float[][] tmp = new float[3][3];
+
+    for (int i = 0; i < 3; i++)
+    {
+      for (int j = 0; j < 3; j++)
+      {
+        tmp[i][j] = (mat[i][0] * matrix[0][j]) + (mat[i][1] * matrix[1][j])
+                + (mat[i][2] * matrix[2][j]);
+      }
+    }
+
+    for (int i = 0; i < 3; i++)
+    {
+      for (int j = 0; j < 3; j++)
+      {
+        matrix[i][j] = tmp[i][j];
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param mat
+   *                DOCUMENT ME!
+   */
+  public void postMultiply(float[][] mat)
+  {
+    float[][] tmp = new float[3][3];
+
+    for (int i = 0; i < 3; i++)
+    {
+      for (int j = 0; j < 3; j++)
+      {
+        tmp[i][j] = (matrix[i][0] * mat[0][j]) + (matrix[i][1] * mat[1][j])
+                + (matrix[i][2] * mat[2][j]);
+      }
+    }
+
+    for (int i = 0; i < 3; i++)
+    {
+      for (int j = 0; j < 3; j++)
+      {
+        matrix[i][j] = tmp[i][j];
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param args
+   *                DOCUMENT ME!
+   */
+  public static void main(String[] args)
+  {
+    RotatableMatrix m = new RotatableMatrix(3, 3);
+
+    m.addElement(0, 0, 1);
+
+    m.addElement(0, 1, 0);
+
+    m.addElement(0, 2, 0);
+
+    m.addElement(1, 0, 0);
+
+    m.addElement(1, 1, 2);
+
+    m.addElement(1, 2, 0);
+
+    m.addElement(2, 0, 0);
+
+    m.addElement(2, 1, 0);
+
+    m.addElement(2, 2, 1);
+
+    m.print();
+
+    RotatableMatrix n = new RotatableMatrix(3, 3);
+
+    n.addElement(0, 0, 2);
+
+    n.addElement(0, 1, 1);
+
+    n.addElement(0, 2, 1);
+
+    n.addElement(1, 0, 2);
+
+    n.addElement(1, 1, 1);
+
+    n.addElement(1, 2, 1);
+
+    n.addElement(2, 0, 2);
+
+    n.addElement(2, 1, 1);
+
+    n.addElement(2, 2, 1);
+
+    n.print();
+
+    // m.postMultiply(n.matrix);
+    // m.print();
+    // m.rotate(45,'z',new RotatableMatrix(3,3));
+    float[] vect = new float[3];
+
+    vect[0] = 2;
+
+    vect[1] = 4;
+
+    vect[2] = 6;
+
+    vect = m.vectorMultiply(vect);
+
+    System.out.println(vect[0] + " " + vect[1] + " " + vect[2]);
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void setIdentity()
+  {
+    matrix[0][0] = (float) 1.0;
+
+    matrix[1][1] = (float) 1.0;
+
+    matrix[2][2] = (float) 1.0;
+
+    matrix[0][1] = (float) 0.0;
+
+    matrix[0][2] = (float) 0.0;
+
+    matrix[1][0] = (float) 0.0;
+
+    matrix[1][2] = (float) 0.0;
+
+    matrix[2][0] = (float) 0.0;
+
+    matrix[2][1] = (float) 0.0;
+  }
+}
diff --git a/src/jalview/schemabinding/version2/AlcodMap.java b/src/jalview/schemabinding/version2/AlcodMap.java
index f43acd6..117ebcd 100644
--- a/src/jalview/schemabinding/version2/AlcodMap.java
+++ b/src/jalview/schemabinding/version2/AlcodMap.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,166 +30,178 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class AlcodMap implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * internal jalview id for the dnasq for this mapping.
-     *  
-     */
-    private java.lang.String _dnasq;
-
-    /**
-     * a Mapping entry and an associated protein sequence
-     *  
-     */
-    private jalview.schemabinding.version2.Mapping _mapping;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public AlcodMap() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'dnasq'. The field 'dnasq' has
-     * the following description: internal jalview id for the dnasq
-     * for this mapping.
-     *  
-     * 
-     * @return the value of field 'Dnasq'.
-     */
-    public java.lang.String getDnasq(
-    ) {
-        return this._dnasq;
-    }
-
-    /**
-     * Returns the value of field 'mapping'. The field 'mapping'
-     * has the following description: a Mapping entry and an
-     * associated protein sequence
-     *  
-     * 
-     * @return the value of field 'Mapping'.
-     */
-    public jalview.schemabinding.version2.Mapping getMapping(
-    ) {
-        return this._mapping;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'dnasq'. The field 'dnasq' has the
-     * following description: internal jalview id for the dnasq for
-     * this mapping.
-     *  
-     * 
-     * @param dnasq the value of field 'dnasq'.
-     */
-    public void setDnasq(
-            final java.lang.String dnasq) {
-        this._dnasq = dnasq;
-    }
-
-    /**
-     * Sets the value of field 'mapping'. The field 'mapping' has
-     * the following description: a Mapping entry and an associated
-     * protein sequence
-     *  
-     * 
-     * @param mapping the value of field 'mapping'.
-     */
-    public void setMapping(
-            final jalview.schemabinding.version2.Mapping mapping) {
-        this._mapping = mapping;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.AlcodMap
-     */
-    public static jalview.schemabinding.version2.AlcodMap unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.AlcodMap) Unmarshaller.unmarshal(jalview.schemabinding.version2.AlcodMap.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class AlcodMap implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * internal jalview id for the dnasq for this mapping.
+   * 
+   */
+  private java.lang.String _dnasq;
+
+  /**
+   * a Mapping entry and an associated protein sequence
+   * 
+   */
+  private jalview.schemabinding.version2.Mapping _mapping;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public AlcodMap()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Returns the value of field 'dnasq'. The field 'dnasq' has the following
+   * description: internal jalview id for the dnasq for this mapping.
+   * 
+   * 
+   * @return the value of field 'Dnasq'.
+   */
+  public java.lang.String getDnasq()
+  {
+    return this._dnasq;
+  }
+
+  /**
+   * Returns the value of field 'mapping'. The field 'mapping' has the following
+   * description: a Mapping entry and an associated protein sequence
+   * 
+   * 
+   * @return the value of field 'Mapping'.
+   */
+  public jalview.schemabinding.version2.Mapping getMapping()
+  {
+    return this._mapping;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'dnasq'. The field 'dnasq' has the following
+   * description: internal jalview id for the dnasq for this mapping.
+   * 
+   * 
+   * @param dnasq
+   *                the value of field 'dnasq'.
+   */
+  public void setDnasq(final java.lang.String dnasq)
+  {
+    this._dnasq = dnasq;
+  }
+
+  /**
+   * Sets the value of field 'mapping'. The field 'mapping' has the following
+   * description: a Mapping entry and an associated protein sequence
+   * 
+   * 
+   * @param mapping
+   *                the value of field 'mapping'.
+   */
+  public void setMapping(
+          final jalview.schemabinding.version2.Mapping mapping)
+  {
+    this._mapping = mapping;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.AlcodMap
+   */
+  public static jalview.schemabinding.version2.AlcodMap unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.AlcodMap) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.AlcodMap.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/Alcodon.java b/src/jalview/schemabinding/version2/Alcodon.java
index cffbd9a..165bad0 100644
--- a/src/jalview/schemabinding/version2/Alcodon.java
+++ b/src/jalview/schemabinding/version2/Alcodon.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,245 +30,261 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Alcodon implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _pos1.
-     */
-    private long _pos1;
-
-    /**
-     * keeps track of state for field: _pos1
-     */
-    private boolean _has_pos1;
-
-    /**
-     * Field _pos2.
-     */
-    private long _pos2;
-
-    /**
-     * keeps track of state for field: _pos2
-     */
-    private boolean _has_pos2;
-
-    /**
-     * Field _pos3.
-     */
-    private long _pos3;
-
-    /**
-     * keeps track of state for field: _pos3
-     */
-    private boolean _has_pos3;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Alcodon() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     */
-    public void deletePos1(
-    ) {
-        this._has_pos1= false;
-    }
-
-    /**
-     */
-    public void deletePos2(
-    ) {
-        this._has_pos2= false;
-    }
-
-    /**
-     */
-    public void deletePos3(
-    ) {
-        this._has_pos3= false;
-    }
-
-    /**
-     * Returns the value of field 'pos1'.
-     * 
-     * @return the value of field 'Pos1'.
-     */
-    public long getPos1(
-    ) {
-        return this._pos1;
-    }
-
-    /**
-     * Returns the value of field 'pos2'.
-     * 
-     * @return the value of field 'Pos2'.
-     */
-    public long getPos2(
-    ) {
-        return this._pos2;
-    }
-
-    /**
-     * Returns the value of field 'pos3'.
-     * 
-     * @return the value of field 'Pos3'.
-     */
-    public long getPos3(
-    ) {
-        return this._pos3;
-    }
-
-    /**
-     * Method hasPos1.
-     * 
-     * @return true if at least one Pos1 has been added
-     */
-    public boolean hasPos1(
-    ) {
-        return this._has_pos1;
-    }
-
-    /**
-     * Method hasPos2.
-     * 
-     * @return true if at least one Pos2 has been added
-     */
-    public boolean hasPos2(
-    ) {
-        return this._has_pos2;
-    }
-
-    /**
-     * Method hasPos3.
-     * 
-     * @return true if at least one Pos3 has been added
-     */
-    public boolean hasPos3(
-    ) {
-        return this._has_pos3;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'pos1'.
-     * 
-     * @param pos1 the value of field 'pos1'.
-     */
-    public void setPos1(
-            final long pos1) {
-        this._pos1 = pos1;
-        this._has_pos1 = true;
-    }
-
-    /**
-     * Sets the value of field 'pos2'.
-     * 
-     * @param pos2 the value of field 'pos2'.
-     */
-    public void setPos2(
-            final long pos2) {
-        this._pos2 = pos2;
-        this._has_pos2 = true;
-    }
-
-    /**
-     * Sets the value of field 'pos3'.
-     * 
-     * @param pos3 the value of field 'pos3'.
-     */
-    public void setPos3(
-            final long pos3) {
-        this._pos3 = pos3;
-        this._has_pos3 = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.schemabinding.version2.Alcodo
-     */
-    public static jalview.schemabinding.version2.Alcodon unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.Alcodon) Unmarshaller.unmarshal(jalview.schemabinding.version2.Alcodon.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class Alcodon implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _pos1.
+   */
+  private long _pos1;
+
+  /**
+   * keeps track of state for field: _pos1
+   */
+  private boolean _has_pos1;
+
+  /**
+   * Field _pos2.
+   */
+  private long _pos2;
+
+  /**
+   * keeps track of state for field: _pos2
+   */
+  private boolean _has_pos2;
+
+  /**
+   * Field _pos3.
+   */
+  private long _pos3;
+
+  /**
+   * keeps track of state for field: _pos3
+   */
+  private boolean _has_pos3;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Alcodon()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   */
+  public void deletePos1()
+  {
+    this._has_pos1 = false;
+  }
+
+  /**
+   */
+  public void deletePos2()
+  {
+    this._has_pos2 = false;
+  }
+
+  /**
+   */
+  public void deletePos3()
+  {
+    this._has_pos3 = false;
+  }
+
+  /**
+   * Returns the value of field 'pos1'.
+   * 
+   * @return the value of field 'Pos1'.
+   */
+  public long getPos1()
+  {
+    return this._pos1;
+  }
+
+  /**
+   * Returns the value of field 'pos2'.
+   * 
+   * @return the value of field 'Pos2'.
+   */
+  public long getPos2()
+  {
+    return this._pos2;
+  }
+
+  /**
+   * Returns the value of field 'pos3'.
+   * 
+   * @return the value of field 'Pos3'.
+   */
+  public long getPos3()
+  {
+    return this._pos3;
+  }
+
+  /**
+   * Method hasPos1.
+   * 
+   * @return true if at least one Pos1 has been added
+   */
+  public boolean hasPos1()
+  {
+    return this._has_pos1;
+  }
+
+  /**
+   * Method hasPos2.
+   * 
+   * @return true if at least one Pos2 has been added
+   */
+  public boolean hasPos2()
+  {
+    return this._has_pos2;
+  }
+
+  /**
+   * Method hasPos3.
+   * 
+   * @return true if at least one Pos3 has been added
+   */
+  public boolean hasPos3()
+  {
+    return this._has_pos3;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'pos1'.
+   * 
+   * @param pos1
+   *                the value of field 'pos1'.
+   */
+  public void setPos1(final long pos1)
+  {
+    this._pos1 = pos1;
+    this._has_pos1 = true;
+  }
+
+  /**
+   * Sets the value of field 'pos2'.
+   * 
+   * @param pos2
+   *                the value of field 'pos2'.
+   */
+  public void setPos2(final long pos2)
+  {
+    this._pos2 = pos2;
+    this._has_pos2 = true;
+  }
+
+  /**
+   * Sets the value of field 'pos3'.
+   * 
+   * @param pos3
+   *                the value of field 'pos3'.
+   */
+  public void setPos3(final long pos3)
+  {
+    this._pos3 = pos3;
+    this._has_pos3 = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.Alcodo
+   */
+  public static jalview.schemabinding.version2.Alcodon unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.Alcodon) Unmarshaller.unmarshal(
+            jalview.schemabinding.version2.Alcodon.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/AlcodonFrame.java b/src/jalview/schemabinding/version2/AlcodonFrame.java
index b8b2a41..5b7b55d 100644
--- a/src/jalview/schemabinding/version2/AlcodonFrame.java
+++ b/src/jalview/schemabinding/version2/AlcodonFrame.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,414 +30,452 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class AlcodonFrame implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _alcodonList.
-     */
-    private java.util.Vector _alcodonList;
-
-    /**
-     * Field _alcodMapList.
-     */
-    private java.util.Vector _alcodMapList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public AlcodonFrame() {
-        super();
-        this._alcodonList = new java.util.Vector();
-        this._alcodMapList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vAlcodMap
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addAlcodMap(
-            final jalview.schemabinding.version2.AlcodMap vAlcodMap)
-    throws java.lang.IndexOutOfBoundsException {
-        this._alcodMapList.addElement(vAlcodMap);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vAlcodMap
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addAlcodMap(
-            final int index,
-            final jalview.schemabinding.version2.AlcodMap vAlcodMap)
-    throws java.lang.IndexOutOfBoundsException {
-        this._alcodMapList.add(index, vAlcodMap);
-    }
-
-    /**
-     * 
-     * 
-     * @param vAlcodon
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addAlcodon(
-            final jalview.schemabinding.version2.Alcodon vAlcodon)
-    throws java.lang.IndexOutOfBoundsException {
-        this._alcodonList.addElement(vAlcodon);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vAlcodon
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addAlcodon(
-            final int index,
-            final jalview.schemabinding.version2.Alcodon vAlcodon)
-    throws java.lang.IndexOutOfBoundsException {
-        this._alcodonList.add(index, vAlcodon);
-    }
-
-    /**
-     * Method enumerateAlcodMap.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.AlcodMap elements
-     */
-    public java.util.Enumeration enumerateAlcodMap(
-    ) {
-        return this._alcodMapList.elements();
-    }
-
-    /**
-     * Method enumerateAlcodon.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.Alcodon elements
-     */
-    public java.util.Enumeration enumerateAlcodon(
-    ) {
-        return this._alcodonList.elements();
-    }
-
-    /**
-     * Method getAlcodMap.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.AlcodMap at the given index
-     */
-    public jalview.schemabinding.version2.AlcodMap getAlcodMap(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._alcodMapList.size()) {
-            throw new IndexOutOfBoundsException("getAlcodMap: Index value '" + index + "' not in range [0.." + (this._alcodMapList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.AlcodMap) _alcodMapList.get(index);
-    }
-
-    /**
-     * Method getAlcodMap.Returns the contents of the collection in
-     * an Array.  <p>Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we <i>know</i>
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.AlcodMap[] getAlcodMap(
-    ) {
-        jalview.schemabinding.version2.AlcodMap[] array = new jalview.schemabinding.version2.AlcodMap[0];
-        return (jalview.schemabinding.version2.AlcodMap[]) this._alcodMapList.toArray(array);
+public class AlcodonFrame implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _alcodonList.
+   */
+  private java.util.Vector _alcodonList;
+
+  /**
+   * Field _alcodMapList.
+   */
+  private java.util.Vector _alcodMapList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public AlcodonFrame()
+  {
+    super();
+    this._alcodonList = new java.util.Vector();
+    this._alcodMapList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vAlcodMap
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addAlcodMap(
+          final jalview.schemabinding.version2.AlcodMap vAlcodMap)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._alcodMapList.addElement(vAlcodMap);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAlcodMap
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addAlcodMap(final int index,
+          final jalview.schemabinding.version2.AlcodMap vAlcodMap)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._alcodMapList.add(index, vAlcodMap);
+  }
+
+  /**
+   * 
+   * 
+   * @param vAlcodon
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addAlcodon(
+          final jalview.schemabinding.version2.Alcodon vAlcodon)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._alcodonList.addElement(vAlcodon);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAlcodon
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addAlcodon(final int index,
+          final jalview.schemabinding.version2.Alcodon vAlcodon)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._alcodonList.add(index, vAlcodon);
+  }
+
+  /**
+   * Method enumerateAlcodMap.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.AlcodMap
+   *         elements
+   */
+  public java.util.Enumeration enumerateAlcodMap()
+  {
+    return this._alcodMapList.elements();
+  }
+
+  /**
+   * Method enumerateAlcodon.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.Alcodon
+   *         elements
+   */
+  public java.util.Enumeration enumerateAlcodon()
+  {
+    return this._alcodonList.elements();
+  }
+
+  /**
+   * Method getAlcodMap.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.AlcodMap at the
+   *         given index
+   */
+  public jalview.schemabinding.version2.AlcodMap getAlcodMap(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._alcodMapList.size())
+    {
+      throw new IndexOutOfBoundsException("getAlcodMap: Index value '"
+              + index + "' not in range [0.."
+              + (this._alcodMapList.size() - 1) + "]");
     }
 
-    /**
-     * Method getAlcodMapCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getAlcodMapCount(
-    ) {
-        return this._alcodMapList.size();
+    return (jalview.schemabinding.version2.AlcodMap) _alcodMapList
+            .get(index);
+  }
+
+  /**
+   * Method getAlcodMap.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.AlcodMap[] getAlcodMap()
+  {
+    jalview.schemabinding.version2.AlcodMap[] array = new jalview.schemabinding.version2.AlcodMap[0];
+    return (jalview.schemabinding.version2.AlcodMap[]) this._alcodMapList
+            .toArray(array);
+  }
+
+  /**
+   * Method getAlcodMapCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getAlcodMapCount()
+  {
+    return this._alcodMapList.size();
+  }
+
+  /**
+   * Method getAlcodon.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.Alcodon at the
+   *         given index
+   */
+  public jalview.schemabinding.version2.Alcodon getAlcodon(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._alcodonList.size())
+    {
+      throw new IndexOutOfBoundsException("getAlcodon: Index value '"
+              + index + "' not in range [0.."
+              + (this._alcodonList.size() - 1) + "]");
     }
 
-    /**
-     * Method getAlcodon.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.Alcodon at the given index
-     */
-    public jalview.schemabinding.version2.Alcodon getAlcodon(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._alcodonList.size()) {
-            throw new IndexOutOfBoundsException("getAlcodon: Index value '" + index + "' not in range [0.." + (this._alcodonList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.Alcodon) _alcodonList.get(index);
+    return (jalview.schemabinding.version2.Alcodon) _alcodonList.get(index);
+  }
+
+  /**
+   * Method getAlcodon.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.Alcodon[] getAlcodon()
+  {
+    jalview.schemabinding.version2.Alcodon[] array = new jalview.schemabinding.version2.Alcodon[0];
+    return (jalview.schemabinding.version2.Alcodon[]) this._alcodonList
+            .toArray(array);
+  }
+
+  /**
+   * Method getAlcodonCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getAlcodonCount()
+  {
+    return this._alcodonList.size();
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
-
-    /**
-     * Method getAlcodon.Returns the contents of the collection in
-     * an Array.  <p>Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we <i>know</i>
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.Alcodon[] getAlcodon(
-    ) {
-        jalview.schemabinding.version2.Alcodon[] array = new jalview.schemabinding.version2.Alcodon[0];
-        return (jalview.schemabinding.version2.Alcodon[]) this._alcodonList.toArray(array);
-    }
-
-    /**
-     * Method getAlcodonCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getAlcodonCount(
-    ) {
-        return this._alcodonList.size();
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Method removeAlcodMap.
-     * 
-     * @param vAlcodMap
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeAlcodMap(
-            final jalview.schemabinding.version2.AlcodMap vAlcodMap) {
-        boolean removed = _alcodMapList.remove(vAlcodMap);
-        return removed;
-    }
-
-    /**
-     * Method removeAlcodMapAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.AlcodMap removeAlcodMapAt(
-            final int index) {
-        java.lang.Object obj = this._alcodMapList.remove(index);
-        return (jalview.schemabinding.version2.AlcodMap) obj;
-    }
-
-    /**
-     * Method removeAlcodon.
-     * 
-     * @param vAlcodon
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeAlcodon(
-            final jalview.schemabinding.version2.Alcodon vAlcodon) {
-        boolean removed = _alcodonList.remove(vAlcodon);
-        return removed;
-    }
-
-    /**
-     * Method removeAlcodonAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.Alcodon removeAlcodonAt(
-            final int index) {
-        java.lang.Object obj = this._alcodonList.remove(index);
-        return (jalview.schemabinding.version2.Alcodon) obj;
-    }
-
-    /**
-     */
-    public void removeAllAlcodMap(
-    ) {
-        this._alcodMapList.clear();
-    }
-
-    /**
-     */
-    public void removeAllAlcodon(
-    ) {
-        this._alcodonList.clear();
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Method removeAlcodMap.
+   * 
+   * @param vAlcodMap
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeAlcodMap(
+          final jalview.schemabinding.version2.AlcodMap vAlcodMap)
+  {
+    boolean removed = _alcodMapList.remove(vAlcodMap);
+    return removed;
+  }
+
+  /**
+   * Method removeAlcodMapAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.AlcodMap removeAlcodMapAt(
+          final int index)
+  {
+    java.lang.Object obj = this._alcodMapList.remove(index);
+    return (jalview.schemabinding.version2.AlcodMap) obj;
+  }
+
+  /**
+   * Method removeAlcodon.
+   * 
+   * @param vAlcodon
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeAlcodon(
+          final jalview.schemabinding.version2.Alcodon vAlcodon)
+  {
+    boolean removed = _alcodonList.remove(vAlcodon);
+    return removed;
+  }
+
+  /**
+   * Method removeAlcodonAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.Alcodon removeAlcodonAt(
+          final int index)
+  {
+    java.lang.Object obj = this._alcodonList.remove(index);
+    return (jalview.schemabinding.version2.Alcodon) obj;
+  }
+
+  /**
+   */
+  public void removeAllAlcodMap()
+  {
+    this._alcodMapList.clear();
+  }
+
+  /**
+   */
+  public void removeAllAlcodon()
+  {
+    this._alcodonList.clear();
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAlcodMap
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setAlcodMap(final int index,
+          final jalview.schemabinding.version2.AlcodMap vAlcodMap)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._alcodMapList.size())
+    {
+      throw new IndexOutOfBoundsException("setAlcodMap: Index value '"
+              + index + "' not in range [0.."
+              + (this._alcodMapList.size() - 1) + "]");
     }
 
-    /**
-     * 
-     * 
-     * @param index
-     * @param vAlcodMap
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setAlcodMap(
-            final int index,
-            final jalview.schemabinding.version2.AlcodMap vAlcodMap)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._alcodMapList.size()) {
-            throw new IndexOutOfBoundsException("setAlcodMap: Index value '" + index + "' not in range [0.." + (this._alcodMapList.size() - 1) + "]");
-        }
-        
-        this._alcodMapList.set(index, vAlcodMap);
+    this._alcodMapList.set(index, vAlcodMap);
+  }
+
+  /**
+   * 
+   * 
+   * @param vAlcodMapArray
+   */
+  public void setAlcodMap(
+          final jalview.schemabinding.version2.AlcodMap[] vAlcodMapArray)
+  {
+    // -- copy array
+    _alcodMapList.clear();
+
+    for (int i = 0; i < vAlcodMapArray.length; i++)
+    {
+      this._alcodMapList.add(vAlcodMapArray[i]);
     }
-
-    /**
-     * 
-     * 
-     * @param vAlcodMapArray
-     */
-    public void setAlcodMap(
-            final jalview.schemabinding.version2.AlcodMap[] vAlcodMapArray) {
-        //-- copy array
-        _alcodMapList.clear();
-        
-        for (int i = 0; i < vAlcodMapArray.length; i++) {
-                this._alcodMapList.add(vAlcodMapArray[i]);
-        }
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vAlcodon
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setAlcodon(
-            final int index,
-            final jalview.schemabinding.version2.Alcodon vAlcodon)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._alcodonList.size()) {
-            throw new IndexOutOfBoundsException("setAlcodon: Index value '" + index + "' not in range [0.." + (this._alcodonList.size() - 1) + "]");
-        }
-        
-        this._alcodonList.set(index, vAlcodon);
-    }
-
-    /**
-     * 
-     * 
-     * @param vAlcodonArray
-     */
-    public void setAlcodon(
-            final jalview.schemabinding.version2.Alcodon[] vAlcodonArray) {
-        //-- copy array
-        _alcodonList.clear();
-        
-        for (int i = 0; i < vAlcodonArray.length; i++) {
-                this._alcodonList.add(vAlcodonArray[i]);
-        }
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.AlcodonFrame
-     */
-    public static jalview.schemabinding.version2.AlcodonFrame unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.AlcodonFrame) Unmarshaller.unmarshal(jalview.schemabinding.version2.AlcodonFrame.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAlcodon
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setAlcodon(final int index,
+          final jalview.schemabinding.version2.Alcodon vAlcodon)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._alcodonList.size())
+    {
+      throw new IndexOutOfBoundsException("setAlcodon: Index value '"
+              + index + "' not in range [0.."
+              + (this._alcodonList.size() - 1) + "]");
     }
 
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+    this._alcodonList.set(index, vAlcodon);
+  }
+
+  /**
+   * 
+   * 
+   * @param vAlcodonArray
+   */
+  public void setAlcodon(
+          final jalview.schemabinding.version2.Alcodon[] vAlcodonArray)
+  {
+    // -- copy array
+    _alcodonList.clear();
+
+    for (int i = 0; i < vAlcodonArray.length; i++)
+    {
+      this._alcodonList.add(vAlcodonArray[i]);
     }
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.AlcodonFrame
+   */
+  public static jalview.schemabinding.version2.AlcodonFrame unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.AlcodonFrame) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.AlcodonFrame.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/Annotation.java b/src/jalview/schemabinding/version2/Annotation.java
index 9ee76e3..bf36492 100755
--- a/src/jalview/schemabinding/version2/Annotation.java
+++ b/src/jalview/schemabinding/version2/Annotation.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,751 +30,793 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Annotation implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _graph.
-     */
-    private boolean _graph;
-
-    /**
-     * keeps track of state for field: _graph
-     */
-    private boolean _has_graph;
-
-    /**
-     * Field _graphType.
-     */
-    private int _graphType;
-
-    /**
-     * keeps track of state for field: _graphType
-     */
-    private boolean _has_graphType;
-
-    /**
-     * Field _sequenceRef.
-     */
-    private java.lang.String _sequenceRef;
-
-    /**
-     * Field _graphColour.
-     */
-    private int _graphColour;
-
-    /**
-     * keeps track of state for field: _graphColour
-     */
-    private boolean _has_graphColour;
-
-    /**
-     * Field _graphGroup.
-     */
-    private int _graphGroup;
-
-    /**
-     * keeps track of state for field: _graphGroup
-     */
-    private boolean _has_graphGroup;
-
-    /**
-     * Field _id.
-     */
-    private java.lang.String _id;
-
-    /**
-     * Field _scoreOnly.
-     */
-    private boolean _scoreOnly = false;
-
-    /**
-     * keeps track of state for field: _scoreOnly
-     */
-    private boolean _has_scoreOnly;
-
-    /**
-     * Field _score.
-     */
-    private double _score;
-
-    /**
-     * keeps track of state for field: _score
-     */
-    private boolean _has_score;
-
-    /**
-     * Field _visible.
-     */
-    private boolean _visible;
-
-    /**
-     * keeps track of state for field: _visible
-     */
-    private boolean _has_visible;
-
-    /**
-     * Field _annotationElementList.
-     */
-    private java.util.Vector _annotationElementList;
-
-    /**
-     * Field _label.
-     */
-    private java.lang.String _label;
-
-    /**
-     * Field _description.
-     */
-    private java.lang.String _description;
-
-    /**
-     * Field _thresholdLine.
-     */
-    private jalview.schemabinding.version2.ThresholdLine _thresholdLine;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Annotation() {
-        super();
-        this._annotationElementList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vAnnotationElement
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addAnnotationElement(
-            final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
-    throws java.lang.IndexOutOfBoundsException {
-        this._annotationElementList.addElement(vAnnotationElement);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vAnnotationElement
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addAnnotationElement(
-            final int index,
-            final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
-    throws java.lang.IndexOutOfBoundsException {
-        this._annotationElementList.add(index, vAnnotationElement);
-    }
-
-    /**
-     */
-    public void deleteGraph(
-    ) {
-        this._has_graph= false;
-    }
-
-    /**
-     */
-    public void deleteGraphColour(
-    ) {
-        this._has_graphColour= false;
-    }
-
-    /**
-     */
-    public void deleteGraphGroup(
-    ) {
-        this._has_graphGroup= false;
-    }
-
-    /**
-     */
-    public void deleteGraphType(
-    ) {
-        this._has_graphType= false;
-    }
-
-    /**
-     */
-    public void deleteScore(
-    ) {
-        this._has_score= false;
-    }
-
-    /**
-     */
-    public void deleteScoreOnly(
-    ) {
-        this._has_scoreOnly= false;
-    }
-
-    /**
-     */
-    public void deleteVisible(
-    ) {
-        this._has_visible= false;
-    }
-
-    /**
-     * Method enumerateAnnotationElement.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.AnnotationElement elements
-     */
-    public java.util.Enumeration enumerateAnnotationElement(
-    ) {
-        return this._annotationElementList.elements();
-    }
-
-    /**
-     * Method getAnnotationElement.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.AnnotationElement at the
-     * given index
-     */
-    public jalview.schemabinding.version2.AnnotationElement getAnnotationElement(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._annotationElementList.size()) {
-            throw new IndexOutOfBoundsException("getAnnotationElement: Index value '" + index + "' not in range [0.." + (this._annotationElementList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.AnnotationElement) _annotationElementList.get(index);
-    }
-
-    /**
-     * Method getAnnotationElement.Returns the contents of the
-     * collection in an Array.  <p>Note:  Just in case the
-     * collection contents are changing in another thread, we pass
-     * a 0-length Array of the correct type into the API call. 
-     * This way we <i>know</i> that the Array returned is of
-     * exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.AnnotationElement[] getAnnotationElement(
-    ) {
-        jalview.schemabinding.version2.AnnotationElement[] array = new jalview.schemabinding.version2.AnnotationElement[0];
-        return (jalview.schemabinding.version2.AnnotationElement[]) this._annotationElementList.toArray(array);
-    }
-
-    /**
-     * Method getAnnotationElementCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getAnnotationElementCount(
-    ) {
-        return this._annotationElementList.size();
-    }
-
-    /**
-     * Returns the value of field 'description'.
-     * 
-     * @return the value of field 'Description'.
-     */
-    public java.lang.String getDescription(
-    ) {
-        return this._description;
-    }
-
-    /**
-     * Returns the value of field 'graph'.
-     * 
-     * @return the value of field 'Graph'.
-     */
-    public boolean getGraph(
-    ) {
-        return this._graph;
-    }
-
-    /**
-     * Returns the value of field 'graphColour'.
-     * 
-     * @return the value of field 'GraphColour'.
-     */
-    public int getGraphColour(
-    ) {
-        return this._graphColour;
-    }
-
-    /**
-     * Returns the value of field 'graphGroup'.
-     * 
-     * @return the value of field 'GraphGroup'.
-     */
-    public int getGraphGroup(
-    ) {
-        return this._graphGroup;
-    }
-
-    /**
-     * Returns the value of field 'graphType'.
-     * 
-     * @return the value of field 'GraphType'.
-     */
-    public int getGraphType(
-    ) {
-        return this._graphType;
-    }
-
-    /**
-     * Returns the value of field 'id'.
-     * 
-     * @return the value of field 'Id'.
-     */
-    public java.lang.String getId(
-    ) {
-        return this._id;
-    }
-
-    /**
-     * Returns the value of field 'label'.
-     * 
-     * @return the value of field 'Label'.
-     */
-    public java.lang.String getLabel(
-    ) {
-        return this._label;
-    }
-
-    /**
-     * Returns the value of field 'score'.
-     * 
-     * @return the value of field 'Score'.
-     */
-    public double getScore(
-    ) {
-        return this._score;
-    }
-
-    /**
-     * Returns the value of field 'scoreOnly'.
-     * 
-     * @return the value of field 'ScoreOnly'.
-     */
-    public boolean getScoreOnly(
-    ) {
-        return this._scoreOnly;
-    }
-
-    /**
-     * Returns the value of field 'sequenceRef'.
-     * 
-     * @return the value of field 'SequenceRef'.
-     */
-    public java.lang.String getSequenceRef(
-    ) {
-        return this._sequenceRef;
-    }
-
-    /**
-     * Returns the value of field 'thresholdLine'.
-     * 
-     * @return the value of field 'ThresholdLine'.
-     */
-    public jalview.schemabinding.version2.ThresholdLine getThresholdLine(
-    ) {
-        return this._thresholdLine;
-    }
-
-    /**
-     * Returns the value of field 'visible'.
-     * 
-     * @return the value of field 'Visible'.
-     */
-    public boolean getVisible(
-    ) {
-        return this._visible;
-    }
-
-    /**
-     * Method hasGraph.
-     * 
-     * @return true if at least one Graph has been added
-     */
-    public boolean hasGraph(
-    ) {
-        return this._has_graph;
-    }
-
-    /**
-     * Method hasGraphColour.
-     * 
-     * @return true if at least one GraphColour has been added
-     */
-    public boolean hasGraphColour(
-    ) {
-        return this._has_graphColour;
-    }
-
-    /**
-     * Method hasGraphGroup.
-     * 
-     * @return true if at least one GraphGroup has been added
-     */
-    public boolean hasGraphGroup(
-    ) {
-        return this._has_graphGroup;
-    }
-
-    /**
-     * Method hasGraphType.
-     * 
-     * @return true if at least one GraphType has been added
-     */
-    public boolean hasGraphType(
-    ) {
-        return this._has_graphType;
-    }
-
-    /**
-     * Method hasScore.
-     * 
-     * @return true if at least one Score has been added
-     */
-    public boolean hasScore(
-    ) {
-        return this._has_score;
-    }
-
-    /**
-     * Method hasScoreOnly.
-     * 
-     * @return true if at least one ScoreOnly has been added
-     */
-    public boolean hasScoreOnly(
-    ) {
-        return this._has_scoreOnly;
-    }
-
-    /**
-     * Method hasVisible.
-     * 
-     * @return true if at least one Visible has been added
-     */
-    public boolean hasVisible(
-    ) {
-        return this._has_visible;
-    }
-
-    /**
-     * Returns the value of field 'graph'.
-     * 
-     * @return the value of field 'Graph'.
-     */
-    public boolean isGraph(
-    ) {
-        return this._graph;
-    }
-
-    /**
-     * Returns the value of field 'scoreOnly'.
-     * 
-     * @return the value of field 'ScoreOnly'.
-     */
-    public boolean isScoreOnly(
-    ) {
-        return this._scoreOnly;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * Returns the value of field 'visible'.
-     * 
-     * @return the value of field 'Visible'.
-     */
-    public boolean isVisible(
-    ) {
-        return this._visible;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     */
-    public void removeAllAnnotationElement(
-    ) {
-        this._annotationElementList.clear();
-    }
-
-    /**
-     * Method removeAnnotationElement.
-     * 
-     * @param vAnnotationElement
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeAnnotationElement(
-            final jalview.schemabinding.version2.AnnotationElement vAnnotationElement) {
-        boolean removed = _annotationElementList.remove(vAnnotationElement);
-        return removed;
-    }
-
-    /**
-     * Method removeAnnotationElementAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.AnnotationElement removeAnnotationElementAt(
-            final int index) {
-        java.lang.Object obj = this._annotationElementList.remove(index);
-        return (jalview.schemabinding.version2.AnnotationElement) obj;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vAnnotationElement
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setAnnotationElement(
-            final int index,
-            final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._annotationElementList.size()) {
-            throw new IndexOutOfBoundsException("setAnnotationElement: Index value '" + index + "' not in range [0.." + (this._annotationElementList.size() - 1) + "]");
-        }
-        
-        this._annotationElementList.set(index, vAnnotationElement);
-    }
-
-    /**
-     * 
-     * 
-     * @param vAnnotationElementArray
-     */
-    public void setAnnotationElement(
-            final jalview.schemabinding.version2.AnnotationElement[] vAnnotationElementArray) {
-        //-- copy array
-        _annotationElementList.clear();
-        
-        for (int i = 0; i < vAnnotationElementArray.length; i++) {
-                this._annotationElementList.add(vAnnotationElementArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of field 'description'.
-     * 
-     * @param description the value of field 'description'.
-     */
-    public void setDescription(
-            final java.lang.String description) {
-        this._description = description;
-    }
-
-    /**
-     * Sets the value of field 'graph'.
-     * 
-     * @param graph the value of field 'graph'.
-     */
-    public void setGraph(
-            final boolean graph) {
-        this._graph = graph;
-        this._has_graph = true;
-    }
-
-    /**
-     * Sets the value of field 'graphColour'.
-     * 
-     * @param graphColour the value of field 'graphColour'.
-     */
-    public void setGraphColour(
-            final int graphColour) {
-        this._graphColour = graphColour;
-        this._has_graphColour = true;
-    }
-
-    /**
-     * Sets the value of field 'graphGroup'.
-     * 
-     * @param graphGroup the value of field 'graphGroup'.
-     */
-    public void setGraphGroup(
-            final int graphGroup) {
-        this._graphGroup = graphGroup;
-        this._has_graphGroup = true;
-    }
-
-    /**
-     * Sets the value of field 'graphType'.
-     * 
-     * @param graphType the value of field 'graphType'.
-     */
-    public void setGraphType(
-            final int graphType) {
-        this._graphType = graphType;
-        this._has_graphType = true;
-    }
-
-    /**
-     * Sets the value of field 'id'.
-     * 
-     * @param id the value of field 'id'.
-     */
-    public void setId(
-            final java.lang.String id) {
-        this._id = id;
-    }
-
-    /**
-     * Sets the value of field 'label'.
-     * 
-     * @param label the value of field 'label'.
-     */
-    public void setLabel(
-            final java.lang.String label) {
-        this._label = label;
-    }
-
-    /**
-     * Sets the value of field 'score'.
-     * 
-     * @param score the value of field 'score'.
-     */
-    public void setScore(
-            final double score) {
-        this._score = score;
-        this._has_score = true;
-    }
-
-    /**
-     * Sets the value of field 'scoreOnly'.
-     * 
-     * @param scoreOnly the value of field 'scoreOnly'.
-     */
-    public void setScoreOnly(
-            final boolean scoreOnly) {
-        this._scoreOnly = scoreOnly;
-        this._has_scoreOnly = true;
-    }
-
-    /**
-     * Sets the value of field 'sequenceRef'.
-     * 
-     * @param sequenceRef the value of field 'sequenceRef'.
-     */
-    public void setSequenceRef(
-            final java.lang.String sequenceRef) {
-        this._sequenceRef = sequenceRef;
-    }
-
-    /**
-     * Sets the value of field 'thresholdLine'.
-     * 
-     * @param thresholdLine the value of field 'thresholdLine'.
-     */
-    public void setThresholdLine(
-            final jalview.schemabinding.version2.ThresholdLine thresholdLine) {
-        this._thresholdLine = thresholdLine;
-    }
-
-    /**
-     * Sets the value of field 'visible'.
-     * 
-     * @param visible the value of field 'visible'.
-     */
-    public void setVisible(
-            final boolean visible) {
-        this._visible = visible;
-        this._has_visible = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.Annotation
-     */
-    public static jalview.schemabinding.version2.Annotation unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.Annotation) Unmarshaller.unmarshal(jalview.schemabinding.version2.Annotation.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+public class Annotation implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _graph.
+   */
+  private boolean _graph;
+
+  /**
+   * keeps track of state for field: _graph
+   */
+  private boolean _has_graph;
+
+  /**
+   * Field _graphType.
+   */
+  private int _graphType;
+
+  /**
+   * keeps track of state for field: _graphType
+   */
+  private boolean _has_graphType;
+
+  /**
+   * Field _sequenceRef.
+   */
+  private java.lang.String _sequenceRef;
+
+  /**
+   * Field _graphColour.
+   */
+  private int _graphColour;
+
+  /**
+   * keeps track of state for field: _graphColour
+   */
+  private boolean _has_graphColour;
+
+  /**
+   * Field _graphGroup.
+   */
+  private int _graphGroup;
+
+  /**
+   * keeps track of state for field: _graphGroup
+   */
+  private boolean _has_graphGroup;
+
+  /**
+   * Field _id.
+   */
+  private java.lang.String _id;
+
+  /**
+   * Field _scoreOnly.
+   */
+  private boolean _scoreOnly = false;
+
+  /**
+   * keeps track of state for field: _scoreOnly
+   */
+  private boolean _has_scoreOnly;
+
+  /**
+   * Field _score.
+   */
+  private double _score;
+
+  /**
+   * keeps track of state for field: _score
+   */
+  private boolean _has_score;
+
+  /**
+   * Field _visible.
+   */
+  private boolean _visible;
+
+  /**
+   * keeps track of state for field: _visible
+   */
+  private boolean _has_visible;
+
+  /**
+   * Field _annotationElementList.
+   */
+  private java.util.Vector _annotationElementList;
+
+  /**
+   * Field _label.
+   */
+  private java.lang.String _label;
+
+  /**
+   * Field _description.
+   */
+  private java.lang.String _description;
+
+  /**
+   * Field _thresholdLine.
+   */
+  private jalview.schemabinding.version2.ThresholdLine _thresholdLine;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Annotation()
+  {
+    super();
+    this._annotationElementList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vAnnotationElement
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addAnnotationElement(
+          final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._annotationElementList.addElement(vAnnotationElement);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAnnotationElement
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addAnnotationElement(
+          final int index,
+          final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._annotationElementList.add(index, vAnnotationElement);
+  }
+
+  /**
+   */
+  public void deleteGraph()
+  {
+    this._has_graph = false;
+  }
+
+  /**
+   */
+  public void deleteGraphColour()
+  {
+    this._has_graphColour = false;
+  }
+
+  /**
+   */
+  public void deleteGraphGroup()
+  {
+    this._has_graphGroup = false;
+  }
+
+  /**
+   */
+  public void deleteGraphType()
+  {
+    this._has_graphType = false;
+  }
+
+  /**
+   */
+  public void deleteScore()
+  {
+    this._has_score = false;
+  }
+
+  /**
+   */
+  public void deleteScoreOnly()
+  {
+    this._has_scoreOnly = false;
+  }
+
+  /**
+   */
+  public void deleteVisible()
+  {
+    this._has_visible = false;
+  }
+
+  /**
+   * Method enumerateAnnotationElement.
+   * 
+   * @return an Enumeration over all
+   *         jalview.schemabinding.version2.AnnotationElement elements
+   */
+  public java.util.Enumeration enumerateAnnotationElement()
+  {
+    return this._annotationElementList.elements();
+  }
+
+  /**
+   * Method getAnnotationElement.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.AnnotationElement
+   *         at the given index
+   */
+  public jalview.schemabinding.version2.AnnotationElement getAnnotationElement(
+          final int index) throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._annotationElementList.size())
+    {
+      throw new IndexOutOfBoundsException(
+              "getAnnotationElement: Index value '" + index
+                      + "' not in range [0.."
+                      + (this._annotationElementList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.AnnotationElement) _annotationElementList
+            .get(index);
+  }
+
+  /**
+   * Method getAnnotationElement.Returns the contents of the collection in an
+   * Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.AnnotationElement[] getAnnotationElement()
+  {
+    jalview.schemabinding.version2.AnnotationElement[] array = new jalview.schemabinding.version2.AnnotationElement[0];
+    return (jalview.schemabinding.version2.AnnotationElement[]) this._annotationElementList
+            .toArray(array);
+  }
+
+  /**
+   * Method getAnnotationElementCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getAnnotationElementCount()
+  {
+    return this._annotationElementList.size();
+  }
+
+  /**
+   * Returns the value of field 'description'.
+   * 
+   * @return the value of field 'Description'.
+   */
+  public java.lang.String getDescription()
+  {
+    return this._description;
+  }
+
+  /**
+   * Returns the value of field 'graph'.
+   * 
+   * @return the value of field 'Graph'.
+   */
+  public boolean getGraph()
+  {
+    return this._graph;
+  }
+
+  /**
+   * Returns the value of field 'graphColour'.
+   * 
+   * @return the value of field 'GraphColour'.
+   */
+  public int getGraphColour()
+  {
+    return this._graphColour;
+  }
+
+  /**
+   * Returns the value of field 'graphGroup'.
+   * 
+   * @return the value of field 'GraphGroup'.
+   */
+  public int getGraphGroup()
+  {
+    return this._graphGroup;
+  }
+
+  /**
+   * Returns the value of field 'graphType'.
+   * 
+   * @return the value of field 'GraphType'.
+   */
+  public int getGraphType()
+  {
+    return this._graphType;
+  }
+
+  /**
+   * Returns the value of field 'id'.
+   * 
+   * @return the value of field 'Id'.
+   */
+  public java.lang.String getId()
+  {
+    return this._id;
+  }
+
+  /**
+   * Returns the value of field 'label'.
+   * 
+   * @return the value of field 'Label'.
+   */
+  public java.lang.String getLabel()
+  {
+    return this._label;
+  }
+
+  /**
+   * Returns the value of field 'score'.
+   * 
+   * @return the value of field 'Score'.
+   */
+  public double getScore()
+  {
+    return this._score;
+  }
+
+  /**
+   * Returns the value of field 'scoreOnly'.
+   * 
+   * @return the value of field 'ScoreOnly'.
+   */
+  public boolean getScoreOnly()
+  {
+    return this._scoreOnly;
+  }
+
+  /**
+   * Returns the value of field 'sequenceRef'.
+   * 
+   * @return the value of field 'SequenceRef'.
+   */
+  public java.lang.String getSequenceRef()
+  {
+    return this._sequenceRef;
+  }
+
+  /**
+   * Returns the value of field 'thresholdLine'.
+   * 
+   * @return the value of field 'ThresholdLine'.
+   */
+  public jalview.schemabinding.version2.ThresholdLine getThresholdLine()
+  {
+    return this._thresholdLine;
+  }
+
+  /**
+   * Returns the value of field 'visible'.
+   * 
+   * @return the value of field 'Visible'.
+   */
+  public boolean getVisible()
+  {
+    return this._visible;
+  }
+
+  /**
+   * Method hasGraph.
+   * 
+   * @return true if at least one Graph has been added
+   */
+  public boolean hasGraph()
+  {
+    return this._has_graph;
+  }
+
+  /**
+   * Method hasGraphColour.
+   * 
+   * @return true if at least one GraphColour has been added
+   */
+  public boolean hasGraphColour()
+  {
+    return this._has_graphColour;
+  }
+
+  /**
+   * Method hasGraphGroup.
+   * 
+   * @return true if at least one GraphGroup has been added
+   */
+  public boolean hasGraphGroup()
+  {
+    return this._has_graphGroup;
+  }
+
+  /**
+   * Method hasGraphType.
+   * 
+   * @return true if at least one GraphType has been added
+   */
+  public boolean hasGraphType()
+  {
+    return this._has_graphType;
+  }
+
+  /**
+   * Method hasScore.
+   * 
+   * @return true if at least one Score has been added
+   */
+  public boolean hasScore()
+  {
+    return this._has_score;
+  }
+
+  /**
+   * Method hasScoreOnly.
+   * 
+   * @return true if at least one ScoreOnly has been added
+   */
+  public boolean hasScoreOnly()
+  {
+    return this._has_scoreOnly;
+  }
+
+  /**
+   * Method hasVisible.
+   * 
+   * @return true if at least one Visible has been added
+   */
+  public boolean hasVisible()
+  {
+    return this._has_visible;
+  }
+
+  /**
+   * Returns the value of field 'graph'.
+   * 
+   * @return the value of field 'Graph'.
+   */
+  public boolean isGraph()
+  {
+    return this._graph;
+  }
+
+  /**
+   * Returns the value of field 'scoreOnly'.
+   * 
+   * @return the value of field 'ScoreOnly'.
+   */
+  public boolean isScoreOnly()
+  {
+    return this._scoreOnly;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * Returns the value of field 'visible'.
+   * 
+   * @return the value of field 'Visible'.
+   */
+  public boolean isVisible()
+  {
+    return this._visible;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   */
+  public void removeAllAnnotationElement()
+  {
+    this._annotationElementList.clear();
+  }
+
+  /**
+   * Method removeAnnotationElement.
+   * 
+   * @param vAnnotationElement
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeAnnotationElement(
+          final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
+  {
+    boolean removed = _annotationElementList.remove(vAnnotationElement);
+    return removed;
+  }
+
+  /**
+   * Method removeAnnotationElementAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.AnnotationElement removeAnnotationElementAt(
+          final int index)
+  {
+    java.lang.Object obj = this._annotationElementList.remove(index);
+    return (jalview.schemabinding.version2.AnnotationElement) obj;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAnnotationElement
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setAnnotationElement(
+          final int index,
+          final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._annotationElementList.size())
+    {
+      throw new IndexOutOfBoundsException(
+              "setAnnotationElement: Index value '" + index
+                      + "' not in range [0.."
+                      + (this._annotationElementList.size() - 1) + "]");
+    }
+
+    this._annotationElementList.set(index, vAnnotationElement);
+  }
+
+  /**
+   * 
+   * 
+   * @param vAnnotationElementArray
+   */
+  public void setAnnotationElement(
+          final jalview.schemabinding.version2.AnnotationElement[] vAnnotationElementArray)
+  {
+    // -- copy array
+    _annotationElementList.clear();
+
+    for (int i = 0; i < vAnnotationElementArray.length; i++)
+    {
+      this._annotationElementList.add(vAnnotationElementArray[i]);
+    }
+  }
+
+  /**
+   * Sets the value of field 'description'.
+   * 
+   * @param description
+   *                the value of field 'description'.
+   */
+  public void setDescription(final java.lang.String description)
+  {
+    this._description = description;
+  }
+
+  /**
+   * Sets the value of field 'graph'.
+   * 
+   * @param graph
+   *                the value of field 'graph'.
+   */
+  public void setGraph(final boolean graph)
+  {
+    this._graph = graph;
+    this._has_graph = true;
+  }
+
+  /**
+   * Sets the value of field 'graphColour'.
+   * 
+   * @param graphColour
+   *                the value of field 'graphColour'.
+   */
+  public void setGraphColour(final int graphColour)
+  {
+    this._graphColour = graphColour;
+    this._has_graphColour = true;
+  }
+
+  /**
+   * Sets the value of field 'graphGroup'.
+   * 
+   * @param graphGroup
+   *                the value of field 'graphGroup'.
+   */
+  public void setGraphGroup(final int graphGroup)
+  {
+    this._graphGroup = graphGroup;
+    this._has_graphGroup = true;
+  }
+
+  /**
+   * Sets the value of field 'graphType'.
+   * 
+   * @param graphType
+   *                the value of field 'graphType'.
+   */
+  public void setGraphType(final int graphType)
+  {
+    this._graphType = graphType;
+    this._has_graphType = true;
+  }
+
+  /**
+   * Sets the value of field 'id'.
+   * 
+   * @param id
+   *                the value of field 'id'.
+   */
+  public void setId(final java.lang.String id)
+  {
+    this._id = id;
+  }
+
+  /**
+   * Sets the value of field 'label'.
+   * 
+   * @param label
+   *                the value of field 'label'.
+   */
+  public void setLabel(final java.lang.String label)
+  {
+    this._label = label;
+  }
+
+  /**
+   * Sets the value of field 'score'.
+   * 
+   * @param score
+   *                the value of field 'score'.
+   */
+  public void setScore(final double score)
+  {
+    this._score = score;
+    this._has_score = true;
+  }
+
+  /**
+   * Sets the value of field 'scoreOnly'.
+   * 
+   * @param scoreOnly
+   *                the value of field 'scoreOnly'.
+   */
+  public void setScoreOnly(final boolean scoreOnly)
+  {
+    this._scoreOnly = scoreOnly;
+    this._has_scoreOnly = true;
+  }
+
+  /**
+   * Sets the value of field 'sequenceRef'.
+   * 
+   * @param sequenceRef
+   *                the value of field 'sequenceRef'.
+   */
+  public void setSequenceRef(final java.lang.String sequenceRef)
+  {
+    this._sequenceRef = sequenceRef;
+  }
+
+  /**
+   * Sets the value of field 'thresholdLine'.
+   * 
+   * @param thresholdLine
+   *                the value of field 'thresholdLine'.
+   */
+  public void setThresholdLine(
+          final jalview.schemabinding.version2.ThresholdLine thresholdLine)
+  {
+    this._thresholdLine = thresholdLine;
+  }
+
+  /**
+   * Sets the value of field 'visible'.
+   * 
+   * @param visible
+   *                the value of field 'visible'.
+   */
+  public void setVisible(final boolean visible)
+  {
+    this._visible = visible;
+    this._has_visible = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.Annotation
+   */
+  public static jalview.schemabinding.version2.Annotation unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.Annotation) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.Annotation.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/AnnotationColours.java b/src/jalview/schemabinding/version2/AnnotationColours.java
index 36f9f93..ff6dea7 100755
--- a/src/jalview/schemabinding/version2/AnnotationColours.java
+++ b/src/jalview/schemabinding/version2/AnnotationColours.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,344 +30,364 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class AnnotationColours implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _aboveThreshold.
-     */
-    private int _aboveThreshold;
-
-    /**
-     * keeps track of state for field: _aboveThreshold
-     */
-    private boolean _has_aboveThreshold;
-
-    /**
-     * Field _annotation.
-     */
-    private java.lang.String _annotation;
-
-    /**
-     * Field _minColour.
-     */
-    private int _minColour;
-
-    /**
-     * keeps track of state for field: _minColour
-     */
-    private boolean _has_minColour;
-
-    /**
-     * Field _maxColour.
-     */
-    private int _maxColour;
-
-    /**
-     * keeps track of state for field: _maxColour
-     */
-    private boolean _has_maxColour;
-
-    /**
-     * Field _colourScheme.
-     */
-    private java.lang.String _colourScheme;
-
-    /**
-     * Field _threshold.
-     */
-    private float _threshold;
-
-    /**
-     * keeps track of state for field: _threshold
-     */
-    private boolean _has_threshold;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public AnnotationColours() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     */
-    public void deleteAboveThreshold(
-    ) {
-        this._has_aboveThreshold= false;
-    }
-
-    /**
-     */
-    public void deleteMaxColour(
-    ) {
-        this._has_maxColour= false;
-    }
-
-    /**
-     */
-    public void deleteMinColour(
-    ) {
-        this._has_minColour= false;
-    }
-
-    /**
-     */
-    public void deleteThreshold(
-    ) {
-        this._has_threshold= false;
-    }
-
-    /**
-     * Returns the value of field 'aboveThreshold'.
-     * 
-     * @return the value of field 'AboveThreshold'.
-     */
-    public int getAboveThreshold(
-    ) {
-        return this._aboveThreshold;
-    }
-
-    /**
-     * Returns the value of field 'annotation'.
-     * 
-     * @return the value of field 'Annotation'.
-     */
-    public java.lang.String getAnnotation(
-    ) {
-        return this._annotation;
-    }
-
-    /**
-     * Returns the value of field 'colourScheme'.
-     * 
-     * @return the value of field 'ColourScheme'.
-     */
-    public java.lang.String getColourScheme(
-    ) {
-        return this._colourScheme;
-    }
-
-    /**
-     * Returns the value of field 'maxColour'.
-     * 
-     * @return the value of field 'MaxColour'.
-     */
-    public int getMaxColour(
-    ) {
-        return this._maxColour;
-    }
-
-    /**
-     * Returns the value of field 'minColour'.
-     * 
-     * @return the value of field 'MinColour'.
-     */
-    public int getMinColour(
-    ) {
-        return this._minColour;
-    }
-
-    /**
-     * Returns the value of field 'threshold'.
-     * 
-     * @return the value of field 'Threshold'.
-     */
-    public float getThreshold(
-    ) {
-        return this._threshold;
-    }
-
-    /**
-     * Method hasAboveThreshold.
-     * 
-     * @return true if at least one AboveThreshold has been added
-     */
-    public boolean hasAboveThreshold(
-    ) {
-        return this._has_aboveThreshold;
-    }
-
-    /**
-     * Method hasMaxColour.
-     * 
-     * @return true if at least one MaxColour has been added
-     */
-    public boolean hasMaxColour(
-    ) {
-        return this._has_maxColour;
-    }
-
-    /**
-     * Method hasMinColour.
-     * 
-     * @return true if at least one MinColour has been added
-     */
-    public boolean hasMinColour(
-    ) {
-        return this._has_minColour;
-    }
-
-    /**
-     * Method hasThreshold.
-     * 
-     * @return true if at least one Threshold has been added
-     */
-    public boolean hasThreshold(
-    ) {
-        return this._has_threshold;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'aboveThreshold'.
-     * 
-     * @param aboveThreshold the value of field 'aboveThreshold'.
-     */
-    public void setAboveThreshold(
-            final int aboveThreshold) {
-        this._aboveThreshold = aboveThreshold;
-        this._has_aboveThreshold = true;
-    }
-
-    /**
-     * Sets the value of field 'annotation'.
-     * 
-     * @param annotation the value of field 'annotation'.
-     */
-    public void setAnnotation(
-            final java.lang.String annotation) {
-        this._annotation = annotation;
-    }
-
-    /**
-     * Sets the value of field 'colourScheme'.
-     * 
-     * @param colourScheme the value of field 'colourScheme'.
-     */
-    public void setColourScheme(
-            final java.lang.String colourScheme) {
-        this._colourScheme = colourScheme;
-    }
-
-    /**
-     * Sets the value of field 'maxColour'.
-     * 
-     * @param maxColour the value of field 'maxColour'.
-     */
-    public void setMaxColour(
-            final int maxColour) {
-        this._maxColour = maxColour;
-        this._has_maxColour = true;
-    }
-
-    /**
-     * Sets the value of field 'minColour'.
-     * 
-     * @param minColour the value of field 'minColour'.
-     */
-    public void setMinColour(
-            final int minColour) {
-        this._minColour = minColour;
-        this._has_minColour = true;
-    }
-
-    /**
-     * Sets the value of field 'threshold'.
-     * 
-     * @param threshold the value of field 'threshold'.
-     */
-    public void setThreshold(
-            final float threshold) {
-        this._threshold = threshold;
-        this._has_threshold = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.AnnotationColours
-     */
-    public static jalview.schemabinding.version2.AnnotationColours unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.AnnotationColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.AnnotationColours.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class AnnotationColours implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _aboveThreshold.
+   */
+  private int _aboveThreshold;
+
+  /**
+   * keeps track of state for field: _aboveThreshold
+   */
+  private boolean _has_aboveThreshold;
+
+  /**
+   * Field _annotation.
+   */
+  private java.lang.String _annotation;
+
+  /**
+   * Field _minColour.
+   */
+  private int _minColour;
+
+  /**
+   * keeps track of state for field: _minColour
+   */
+  private boolean _has_minColour;
+
+  /**
+   * Field _maxColour.
+   */
+  private int _maxColour;
+
+  /**
+   * keeps track of state for field: _maxColour
+   */
+  private boolean _has_maxColour;
+
+  /**
+   * Field _colourScheme.
+   */
+  private java.lang.String _colourScheme;
+
+  /**
+   * Field _threshold.
+   */
+  private float _threshold;
+
+  /**
+   * keeps track of state for field: _threshold
+   */
+  private boolean _has_threshold;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public AnnotationColours()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   */
+  public void deleteAboveThreshold()
+  {
+    this._has_aboveThreshold = false;
+  }
+
+  /**
+   */
+  public void deleteMaxColour()
+  {
+    this._has_maxColour = false;
+  }
+
+  /**
+   */
+  public void deleteMinColour()
+  {
+    this._has_minColour = false;
+  }
+
+  /**
+   */
+  public void deleteThreshold()
+  {
+    this._has_threshold = false;
+  }
+
+  /**
+   * Returns the value of field 'aboveThreshold'.
+   * 
+   * @return the value of field 'AboveThreshold'.
+   */
+  public int getAboveThreshold()
+  {
+    return this._aboveThreshold;
+  }
+
+  /**
+   * Returns the value of field 'annotation'.
+   * 
+   * @return the value of field 'Annotation'.
+   */
+  public java.lang.String getAnnotation()
+  {
+    return this._annotation;
+  }
+
+  /**
+   * Returns the value of field 'colourScheme'.
+   * 
+   * @return the value of field 'ColourScheme'.
+   */
+  public java.lang.String getColourScheme()
+  {
+    return this._colourScheme;
+  }
+
+  /**
+   * Returns the value of field 'maxColour'.
+   * 
+   * @return the value of field 'MaxColour'.
+   */
+  public int getMaxColour()
+  {
+    return this._maxColour;
+  }
+
+  /**
+   * Returns the value of field 'minColour'.
+   * 
+   * @return the value of field 'MinColour'.
+   */
+  public int getMinColour()
+  {
+    return this._minColour;
+  }
+
+  /**
+   * Returns the value of field 'threshold'.
+   * 
+   * @return the value of field 'Threshold'.
+   */
+  public float getThreshold()
+  {
+    return this._threshold;
+  }
+
+  /**
+   * Method hasAboveThreshold.
+   * 
+   * @return true if at least one AboveThreshold has been added
+   */
+  public boolean hasAboveThreshold()
+  {
+    return this._has_aboveThreshold;
+  }
+
+  /**
+   * Method hasMaxColour.
+   * 
+   * @return true if at least one MaxColour has been added
+   */
+  public boolean hasMaxColour()
+  {
+    return this._has_maxColour;
+  }
+
+  /**
+   * Method hasMinColour.
+   * 
+   * @return true if at least one MinColour has been added
+   */
+  public boolean hasMinColour()
+  {
+    return this._has_minColour;
+  }
+
+  /**
+   * Method hasThreshold.
+   * 
+   * @return true if at least one Threshold has been added
+   */
+  public boolean hasThreshold()
+  {
+    return this._has_threshold;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'aboveThreshold'.
+   * 
+   * @param aboveThreshold
+   *                the value of field 'aboveThreshold'.
+   */
+  public void setAboveThreshold(final int aboveThreshold)
+  {
+    this._aboveThreshold = aboveThreshold;
+    this._has_aboveThreshold = true;
+  }
+
+  /**
+   * Sets the value of field 'annotation'.
+   * 
+   * @param annotation
+   *                the value of field 'annotation'.
+   */
+  public void setAnnotation(final java.lang.String annotation)
+  {
+    this._annotation = annotation;
+  }
+
+  /**
+   * Sets the value of field 'colourScheme'.
+   * 
+   * @param colourScheme
+   *                the value of field 'colourScheme'.
+   */
+  public void setColourScheme(final java.lang.String colourScheme)
+  {
+    this._colourScheme = colourScheme;
+  }
+
+  /**
+   * Sets the value of field 'maxColour'.
+   * 
+   * @param maxColour
+   *                the value of field 'maxColour'.
+   */
+  public void setMaxColour(final int maxColour)
+  {
+    this._maxColour = maxColour;
+    this._has_maxColour = true;
+  }
+
+  /**
+   * Sets the value of field 'minColour'.
+   * 
+   * @param minColour
+   *                the value of field 'minColour'.
+   */
+  public void setMinColour(final int minColour)
+  {
+    this._minColour = minColour;
+    this._has_minColour = true;
+  }
+
+  /**
+   * Sets the value of field 'threshold'.
+   * 
+   * @param threshold
+   *                the value of field 'threshold'.
+   */
+  public void setThreshold(final float threshold)
+  {
+    this._threshold = threshold;
+    this._has_threshold = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.AnnotationColours
+   */
+  public static jalview.schemabinding.version2.AnnotationColours unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.AnnotationColours) Unmarshaller
+            .unmarshal(
+                    jalview.schemabinding.version2.AnnotationColours.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/AnnotationElement.java b/src/jalview/schemabinding/version2/AnnotationElement.java
index eca3e6a..576b4ad 100755
--- a/src/jalview/schemabinding/version2/AnnotationElement.java
+++ b/src/jalview/schemabinding/version2/AnnotationElement.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,322 +30,342 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class AnnotationElement implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _position.
-     */
-    private int _position;
-
-    /**
-     * keeps track of state for field: _position
-     */
-    private boolean _has_position;
-
-    /**
-     * Field _colour.
-     */
-    private int _colour;
-
-    /**
-     * keeps track of state for field: _colour
-     */
-    private boolean _has_colour;
-
-    /**
-     * Field _displayCharacter.
-     */
-    private java.lang.String _displayCharacter;
-
-    /**
-     * Field _description.
-     */
-    private java.lang.String _description;
-
-    /**
-     * Field _secondaryStructure.
-     */
-    private java.lang.String _secondaryStructure;
-
-    /**
-     * Field _value.
-     */
-    private float _value;
-
-    /**
-     * keeps track of state for field: _value
-     */
-    private boolean _has_value;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public AnnotationElement() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     */
-    public void deleteColour(
-    ) {
-        this._has_colour= false;
-    }
-
-    /**
-     */
-    public void deletePosition(
-    ) {
-        this._has_position= false;
-    }
-
-    /**
-     */
-    public void deleteValue(
-    ) {
-        this._has_value= false;
-    }
-
-    /**
-     * Returns the value of field 'colour'.
-     * 
-     * @return the value of field 'Colour'.
-     */
-    public int getColour(
-    ) {
-        return this._colour;
-    }
-
-    /**
-     * Returns the value of field 'description'.
-     * 
-     * @return the value of field 'Description'.
-     */
-    public java.lang.String getDescription(
-    ) {
-        return this._description;
-    }
-
-    /**
-     * Returns the value of field 'displayCharacter'.
-     * 
-     * @return the value of field 'DisplayCharacter'.
-     */
-    public java.lang.String getDisplayCharacter(
-    ) {
-        return this._displayCharacter;
-    }
-
-    /**
-     * Returns the value of field 'position'.
-     * 
-     * @return the value of field 'Position'.
-     */
-    public int getPosition(
-    ) {
-        return this._position;
-    }
-
-    /**
-     * Returns the value of field 'secondaryStructure'.
-     * 
-     * @return the value of field 'SecondaryStructure'.
-     */
-    public java.lang.String getSecondaryStructure(
-    ) {
-        return this._secondaryStructure;
-    }
-
-    /**
-     * Returns the value of field 'value'.
-     * 
-     * @return the value of field 'Value'.
-     */
-    public float getValue(
-    ) {
-        return this._value;
-    }
-
-    /**
-     * Method hasColour.
-     * 
-     * @return true if at least one Colour has been added
-     */
-    public boolean hasColour(
-    ) {
-        return this._has_colour;
-    }
-
-    /**
-     * Method hasPosition.
-     * 
-     * @return true if at least one Position has been added
-     */
-    public boolean hasPosition(
-    ) {
-        return this._has_position;
-    }
-
-    /**
-     * Method hasValue.
-     * 
-     * @return true if at least one Value has been added
-     */
-    public boolean hasValue(
-    ) {
-        return this._has_value;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'colour'.
-     * 
-     * @param colour the value of field 'colour'.
-     */
-    public void setColour(
-            final int colour) {
-        this._colour = colour;
-        this._has_colour = true;
-    }
-
-    /**
-     * Sets the value of field 'description'.
-     * 
-     * @param description the value of field 'description'.
-     */
-    public void setDescription(
-            final java.lang.String description) {
-        this._description = description;
-    }
-
-    /**
-     * Sets the value of field 'displayCharacter'.
-     * 
-     * @param displayCharacter the value of field 'displayCharacter'
-     */
-    public void setDisplayCharacter(
-            final java.lang.String displayCharacter) {
-        this._displayCharacter = displayCharacter;
-    }
-
-    /**
-     * Sets the value of field 'position'.
-     * 
-     * @param position the value of field 'position'.
-     */
-    public void setPosition(
-            final int position) {
-        this._position = position;
-        this._has_position = true;
-    }
-
-    /**
-     * Sets the value of field 'secondaryStructure'.
-     * 
-     * @param secondaryStructure the value of field
-     * 'secondaryStructure'.
-     */
-    public void setSecondaryStructure(
-            final java.lang.String secondaryStructure) {
-        this._secondaryStructure = secondaryStructure;
-    }
-
-    /**
-     * Sets the value of field 'value'.
-     * 
-     * @param value the value of field 'value'.
-     */
-    public void setValue(
-            final float value) {
-        this._value = value;
-        this._has_value = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.AnnotationElement
-     */
-    public static jalview.schemabinding.version2.AnnotationElement unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.AnnotationElement) Unmarshaller.unmarshal(jalview.schemabinding.version2.AnnotationElement.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class AnnotationElement implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _position.
+   */
+  private int _position;
+
+  /**
+   * keeps track of state for field: _position
+   */
+  private boolean _has_position;
+
+  /**
+   * Field _colour.
+   */
+  private int _colour;
+
+  /**
+   * keeps track of state for field: _colour
+   */
+  private boolean _has_colour;
+
+  /**
+   * Field _displayCharacter.
+   */
+  private java.lang.String _displayCharacter;
+
+  /**
+   * Field _description.
+   */
+  private java.lang.String _description;
+
+  /**
+   * Field _secondaryStructure.
+   */
+  private java.lang.String _secondaryStructure;
+
+  /**
+   * Field _value.
+   */
+  private float _value;
+
+  /**
+   * keeps track of state for field: _value
+   */
+  private boolean _has_value;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public AnnotationElement()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   */
+  public void deleteColour()
+  {
+    this._has_colour = false;
+  }
+
+  /**
+   */
+  public void deletePosition()
+  {
+    this._has_position = false;
+  }
+
+  /**
+   */
+  public void deleteValue()
+  {
+    this._has_value = false;
+  }
+
+  /**
+   * Returns the value of field 'colour'.
+   * 
+   * @return the value of field 'Colour'.
+   */
+  public int getColour()
+  {
+    return this._colour;
+  }
+
+  /**
+   * Returns the value of field 'description'.
+   * 
+   * @return the value of field 'Description'.
+   */
+  public java.lang.String getDescription()
+  {
+    return this._description;
+  }
+
+  /**
+   * Returns the value of field 'displayCharacter'.
+   * 
+   * @return the value of field 'DisplayCharacter'.
+   */
+  public java.lang.String getDisplayCharacter()
+  {
+    return this._displayCharacter;
+  }
+
+  /**
+   * Returns the value of field 'position'.
+   * 
+   * @return the value of field 'Position'.
+   */
+  public int getPosition()
+  {
+    return this._position;
+  }
+
+  /**
+   * Returns the value of field 'secondaryStructure'.
+   * 
+   * @return the value of field 'SecondaryStructure'.
+   */
+  public java.lang.String getSecondaryStructure()
+  {
+    return this._secondaryStructure;
+  }
+
+  /**
+   * Returns the value of field 'value'.
+   * 
+   * @return the value of field 'Value'.
+   */
+  public float getValue()
+  {
+    return this._value;
+  }
+
+  /**
+   * Method hasColour.
+   * 
+   * @return true if at least one Colour has been added
+   */
+  public boolean hasColour()
+  {
+    return this._has_colour;
+  }
+
+  /**
+   * Method hasPosition.
+   * 
+   * @return true if at least one Position has been added
+   */
+  public boolean hasPosition()
+  {
+    return this._has_position;
+  }
+
+  /**
+   * Method hasValue.
+   * 
+   * @return true if at least one Value has been added
+   */
+  public boolean hasValue()
+  {
+    return this._has_value;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'colour'.
+   * 
+   * @param colour
+   *                the value of field 'colour'.
+   */
+  public void setColour(final int colour)
+  {
+    this._colour = colour;
+    this._has_colour = true;
+  }
+
+  /**
+   * Sets the value of field 'description'.
+   * 
+   * @param description
+   *                the value of field 'description'.
+   */
+  public void setDescription(final java.lang.String description)
+  {
+    this._description = description;
+  }
+
+  /**
+   * Sets the value of field 'displayCharacter'.
+   * 
+   * @param displayCharacter
+   *                the value of field 'displayCharacter'
+   */
+  public void setDisplayCharacter(final java.lang.String displayCharacter)
+  {
+    this._displayCharacter = displayCharacter;
+  }
+
+  /**
+   * Sets the value of field 'position'.
+   * 
+   * @param position
+   *                the value of field 'position'.
+   */
+  public void setPosition(final int position)
+  {
+    this._position = position;
+    this._has_position = true;
+  }
+
+  /**
+   * Sets the value of field 'secondaryStructure'.
+   * 
+   * @param secondaryStructure
+   *                the value of field 'secondaryStructure'.
+   */
+  public void setSecondaryStructure(
+          final java.lang.String secondaryStructure)
+  {
+    this._secondaryStructure = secondaryStructure;
+  }
+
+  /**
+   * Sets the value of field 'value'.
+   * 
+   * @param value
+   *                the value of field 'value'.
+   */
+  public void setValue(final float value)
+  {
+    this._value = value;
+    this._has_value = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.AnnotationElement
+   */
+  public static jalview.schemabinding.version2.AnnotationElement unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.AnnotationElement) Unmarshaller
+            .unmarshal(
+                    jalview.schemabinding.version2.AnnotationElement.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/Colour.java b/src/jalview/schemabinding/version2/Colour.java
index 54d64ff..c1c1751 100755
--- a/src/jalview/schemabinding/version2/Colour.java
+++ b/src/jalview/schemabinding/version2/Colour.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,151 +30,166 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Colour implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _name.
-     */
-    private java.lang.String _name;
-
-    /**
-     * Field _RGB.
-     */
-    private java.lang.String _RGB;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Colour() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'name'.
-     * 
-     * @return the value of field 'Name'.
-     */
-    public java.lang.String getName(
-    ) {
-        return this._name;
-    }
-
-    /**
-     * Returns the value of field 'RGB'.
-     * 
-     * @return the value of field 'RGB'.
-     */
-    public java.lang.String getRGB(
-    ) {
-        return this._RGB;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'name'.
-     * 
-     * @param name the value of field 'name'.
-     */
-    public void setName(
-            final java.lang.String name) {
-        this._name = name;
-    }
-
-    /**
-     * Sets the value of field 'RGB'.
-     * 
-     * @param RGB the value of field 'RGB'.
-     */
-    public void setRGB(
-            final java.lang.String RGB) {
-        this._RGB = RGB;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.schemabinding.version2.Colour
-     */
-    public static jalview.schemabinding.version2.Colour unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.Colour) Unmarshaller.unmarshal(jalview.schemabinding.version2.Colour.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class Colour implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _name.
+   */
+  private java.lang.String _name;
+
+  /**
+   * Field _RGB.
+   */
+  private java.lang.String _RGB;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Colour()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Returns the value of field 'name'.
+   * 
+   * @return the value of field 'Name'.
+   */
+  public java.lang.String getName()
+  {
+    return this._name;
+  }
+
+  /**
+   * Returns the value of field 'RGB'.
+   * 
+   * @return the value of field 'RGB'.
+   */
+  public java.lang.String getRGB()
+  {
+    return this._RGB;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'name'.
+   * 
+   * @param name
+   *                the value of field 'name'.
+   */
+  public void setName(final java.lang.String name)
+  {
+    this._name = name;
+  }
+
+  /**
+   * Sets the value of field 'RGB'.
+   * 
+   * @param RGB
+   *                the value of field 'RGB'.
+   */
+  public void setRGB(final java.lang.String RGB)
+  {
+    this._RGB = RGB;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.Colour
+   */
+  public static jalview.schemabinding.version2.Colour unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.Colour) Unmarshaller.unmarshal(
+            jalview.schemabinding.version2.Colour.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/DBRef.java b/src/jalview/schemabinding/version2/DBRef.java
index 4d67250..a232298 100644
--- a/src/jalview/schemabinding/version2/DBRef.java
+++ b/src/jalview/schemabinding/version2/DBRef.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,201 +30,219 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class DBRef implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _source.
-     */
-    private java.lang.String _source;
-
-    /**
-     * Field _version.
-     */
-    private java.lang.String _version;
-
-    /**
-     * Field _accessionId.
-     */
-    private java.lang.String _accessionId;
-
-    /**
-     * Field _mapping.
-     */
-    private jalview.schemabinding.version2.Mapping _mapping;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public DBRef() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'accessionId'.
-     * 
-     * @return the value of field 'AccessionId'.
-     */
-    public java.lang.String getAccessionId(
-    ) {
-        return this._accessionId;
-    }
-
-    /**
-     * Returns the value of field 'mapping'.
-     * 
-     * @return the value of field 'Mapping'.
-     */
-    public jalview.schemabinding.version2.Mapping getMapping(
-    ) {
-        return this._mapping;
-    }
-
-    /**
-     * Returns the value of field 'source'.
-     * 
-     * @return the value of field 'Source'.
-     */
-    public java.lang.String getSource(
-    ) {
-        return this._source;
-    }
-
-    /**
-     * Returns the value of field 'version'.
-     * 
-     * @return the value of field 'Version'.
-     */
-    public java.lang.String getVersion(
-    ) {
-        return this._version;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'accessionId'.
-     * 
-     * @param accessionId the value of field 'accessionId'.
-     */
-    public void setAccessionId(
-            final java.lang.String accessionId) {
-        this._accessionId = accessionId;
-    }
-
-    /**
-     * Sets the value of field 'mapping'.
-     * 
-     * @param mapping the value of field 'mapping'.
-     */
-    public void setMapping(
-            final jalview.schemabinding.version2.Mapping mapping) {
-        this._mapping = mapping;
-    }
-
-    /**
-     * Sets the value of field 'source'.
-     * 
-     * @param source the value of field 'source'.
-     */
-    public void setSource(
-            final java.lang.String source) {
-        this._source = source;
-    }
-
-    /**
-     * Sets the value of field 'version'.
-     * 
-     * @param version the value of field 'version'.
-     */
-    public void setVersion(
-            final java.lang.String version) {
-        this._version = version;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.schemabinding.version2.DBRef
-     */
-    public static jalview.schemabinding.version2.DBRef unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.DBRef) Unmarshaller.unmarshal(jalview.schemabinding.version2.DBRef.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class DBRef implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _source.
+   */
+  private java.lang.String _source;
+
+  /**
+   * Field _version.
+   */
+  private java.lang.String _version;
+
+  /**
+   * Field _accessionId.
+   */
+  private java.lang.String _accessionId;
+
+  /**
+   * Field _mapping.
+   */
+  private jalview.schemabinding.version2.Mapping _mapping;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public DBRef()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Returns the value of field 'accessionId'.
+   * 
+   * @return the value of field 'AccessionId'.
+   */
+  public java.lang.String getAccessionId()
+  {
+    return this._accessionId;
+  }
+
+  /**
+   * Returns the value of field 'mapping'.
+   * 
+   * @return the value of field 'Mapping'.
+   */
+  public jalview.schemabinding.version2.Mapping getMapping()
+  {
+    return this._mapping;
+  }
+
+  /**
+   * Returns the value of field 'source'.
+   * 
+   * @return the value of field 'Source'.
+   */
+  public java.lang.String getSource()
+  {
+    return this._source;
+  }
+
+  /**
+   * Returns the value of field 'version'.
+   * 
+   * @return the value of field 'Version'.
+   */
+  public java.lang.String getVersion()
+  {
+    return this._version;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'accessionId'.
+   * 
+   * @param accessionId
+   *                the value of field 'accessionId'.
+   */
+  public void setAccessionId(final java.lang.String accessionId)
+  {
+    this._accessionId = accessionId;
+  }
+
+  /**
+   * Sets the value of field 'mapping'.
+   * 
+   * @param mapping
+   *                the value of field 'mapping'.
+   */
+  public void setMapping(
+          final jalview.schemabinding.version2.Mapping mapping)
+  {
+    this._mapping = mapping;
+  }
+
+  /**
+   * Sets the value of field 'source'.
+   * 
+   * @param source
+   *                the value of field 'source'.
+   */
+  public void setSource(final java.lang.String source)
+  {
+    this._source = source;
+  }
+
+  /**
+   * Sets the value of field 'version'.
+   * 
+   * @param version
+   *                the value of field 'version'.
+   */
+  public void setVersion(final java.lang.String version)
+  {
+    this._version = version;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.DBRef
+   */
+  public static jalview.schemabinding.version2.DBRef unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.DBRef) Unmarshaller.unmarshal(
+            jalview.schemabinding.version2.DBRef.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/Feature.java b/src/jalview/schemabinding/version2/Feature.java
index 109ec6e..90aba34 100755
--- a/src/jalview/schemabinding/version2/Feature.java
+++ b/src/jalview/schemabinding/version2/Feature.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,501 +30,534 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Feature implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _begin.
-     */
-    private int _begin;
-
-    /**
-     * keeps track of state for field: _begin
-     */
-    private boolean _has_begin;
-
-    /**
-     * Field _end.
-     */
-    private int _end;
-
-    /**
-     * keeps track of state for field: _end
-     */
-    private boolean _has_end;
-
-    /**
-     * Field _type.
-     */
-    private java.lang.String _type;
-
-    /**
-     * Field _description.
-     */
-    private java.lang.String _description;
-
-    /**
-     * Field _status.
-     */
-    private java.lang.String _status;
-
-    /**
-     * Field _featureGroup.
-     */
-    private java.lang.String _featureGroup;
-
-    /**
-     * Field _score.
-     */
-    private float _score;
-
-    /**
-     * keeps track of state for field: _score
-     */
-    private boolean _has_score;
-
-    /**
-     * Field _otherDataList.
-     */
-    private java.util.Vector _otherDataList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Feature() {
-        super();
-        this._otherDataList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vOtherData
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addOtherData(
-            final jalview.schemabinding.version2.OtherData vOtherData)
-    throws java.lang.IndexOutOfBoundsException {
-        this._otherDataList.addElement(vOtherData);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vOtherData
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addOtherData(
-            final int index,
-            final jalview.schemabinding.version2.OtherData vOtherData)
-    throws java.lang.IndexOutOfBoundsException {
-        this._otherDataList.add(index, vOtherData);
-    }
-
-    /**
-     */
-    public void deleteBegin(
-    ) {
-        this._has_begin= false;
-    }
-
-    /**
-     */
-    public void deleteEnd(
-    ) {
-        this._has_end= false;
-    }
-
-    /**
-     */
-    public void deleteScore(
-    ) {
-        this._has_score= false;
-    }
-
-    /**
-     * Method enumerateOtherData.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.OtherData elements
-     */
-    public java.util.Enumeration enumerateOtherData(
-    ) {
-        return this._otherDataList.elements();
-    }
-
-    /**
-     * Returns the value of field 'begin'.
-     * 
-     * @return the value of field 'Begin'.
-     */
-    public int getBegin(
-    ) {
-        return this._begin;
-    }
-
-    /**
-     * Returns the value of field 'description'.
-     * 
-     * @return the value of field 'Description'.
-     */
-    public java.lang.String getDescription(
-    ) {
-        return this._description;
-    }
-
-    /**
-     * Returns the value of field 'end'.
-     * 
-     * @return the value of field 'End'.
-     */
-    public int getEnd(
-    ) {
-        return this._end;
-    }
-
-    /**
-     * Returns the value of field 'featureGroup'.
-     * 
-     * @return the value of field 'FeatureGroup'.
-     */
-    public java.lang.String getFeatureGroup(
-    ) {
-        return this._featureGroup;
-    }
-
-    /**
-     * Method getOtherData.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.OtherData at the given index
-     */
-    public jalview.schemabinding.version2.OtherData getOtherData(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._otherDataList.size()) {
-            throw new IndexOutOfBoundsException("getOtherData: Index value '" + index + "' not in range [0.." + (this._otherDataList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.OtherData) _otherDataList.get(index);
-    }
-
-    /**
-     * Method getOtherData.Returns the contents of the collection
-     * in an Array.  <p>Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we <i>know</i>
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.OtherData[] getOtherData(
-    ) {
-        jalview.schemabinding.version2.OtherData[] array = new jalview.schemabinding.version2.OtherData[0];
-        return (jalview.schemabinding.version2.OtherData[]) this._otherDataList.toArray(array);
-    }
-
-    /**
-     * Method getOtherDataCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getOtherDataCount(
-    ) {
-        return this._otherDataList.size();
-    }
-
-    /**
-     * Returns the value of field 'score'.
-     * 
-     * @return the value of field 'Score'.
-     */
-    public float getScore(
-    ) {
-        return this._score;
-    }
-
-    /**
-     * Returns the value of field 'status'.
-     * 
-     * @return the value of field 'Status'.
-     */
-    public java.lang.String getStatus(
-    ) {
-        return this._status;
-    }
-
-    /**
-     * Returns the value of field 'type'.
-     * 
-     * @return the value of field 'Type'.
-     */
-    public java.lang.String getType(
-    ) {
-        return this._type;
-    }
-
-    /**
-     * Method hasBegin.
-     * 
-     * @return true if at least one Begin has been added
-     */
-    public boolean hasBegin(
-    ) {
-        return this._has_begin;
-    }
-
-    /**
-     * Method hasEnd.
-     * 
-     * @return true if at least one End has been added
-     */
-    public boolean hasEnd(
-    ) {
-        return this._has_end;
-    }
-
-    /**
-     * Method hasScore.
-     * 
-     * @return true if at least one Score has been added
-     */
-    public boolean hasScore(
-    ) {
-        return this._has_score;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     */
-    public void removeAllOtherData(
-    ) {
-        this._otherDataList.clear();
-    }
-
-    /**
-     * Method removeOtherData.
-     * 
-     * @param vOtherData
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeOtherData(
-            final jalview.schemabinding.version2.OtherData vOtherData) {
-        boolean removed = _otherDataList.remove(vOtherData);
-        return removed;
-    }
-
-    /**
-     * Method removeOtherDataAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.OtherData removeOtherDataAt(
-            final int index) {
-        java.lang.Object obj = this._otherDataList.remove(index);
-        return (jalview.schemabinding.version2.OtherData) obj;
-    }
-
-    /**
-     * Sets the value of field 'begin'.
-     * 
-     * @param begin the value of field 'begin'.
-     */
-    public void setBegin(
-            final int begin) {
-        this._begin = begin;
-        this._has_begin = true;
-    }
-
-    /**
-     * Sets the value of field 'description'.
-     * 
-     * @param description the value of field 'description'.
-     */
-    public void setDescription(
-            final java.lang.String description) {
-        this._description = description;
-    }
-
-    /**
-     * Sets the value of field 'end'.
-     * 
-     * @param end the value of field 'end'.
-     */
-    public void setEnd(
-            final int end) {
-        this._end = end;
-        this._has_end = true;
-    }
-
-    /**
-     * Sets the value of field 'featureGroup'.
-     * 
-     * @param featureGroup the value of field 'featureGroup'.
-     */
-    public void setFeatureGroup(
-            final java.lang.String featureGroup) {
-        this._featureGroup = featureGroup;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vOtherData
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setOtherData(
-            final int index,
-            final jalview.schemabinding.version2.OtherData vOtherData)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._otherDataList.size()) {
-            throw new IndexOutOfBoundsException("setOtherData: Index value '" + index + "' not in range [0.." + (this._otherDataList.size() - 1) + "]");
-        }
-        
-        this._otherDataList.set(index, vOtherData);
-    }
-
-    /**
-     * 
-     * 
-     * @param vOtherDataArray
-     */
-    public void setOtherData(
-            final jalview.schemabinding.version2.OtherData[] vOtherDataArray) {
-        //-- copy array
-        _otherDataList.clear();
-        
-        for (int i = 0; i < vOtherDataArray.length; i++) {
-                this._otherDataList.add(vOtherDataArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of field 'score'.
-     * 
-     * @param score the value of field 'score'.
-     */
-    public void setScore(
-            final float score) {
-        this._score = score;
-        this._has_score = true;
-    }
-
-    /**
-     * Sets the value of field 'status'.
-     * 
-     * @param status the value of field 'status'.
-     */
-    public void setStatus(
-            final java.lang.String status) {
-        this._status = status;
-    }
-
-    /**
-     * Sets the value of field 'type'.
-     * 
-     * @param type the value of field 'type'.
-     */
-    public void setType(
-            final java.lang.String type) {
-        this._type = type;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.schemabinding.version2.Featur
-     */
-    public static jalview.schemabinding.version2.Feature unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.Feature) Unmarshaller.unmarshal(jalview.schemabinding.version2.Feature.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+public class Feature implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _begin.
+   */
+  private int _begin;
+
+  /**
+   * keeps track of state for field: _begin
+   */
+  private boolean _has_begin;
+
+  /**
+   * Field _end.
+   */
+  private int _end;
+
+  /**
+   * keeps track of state for field: _end
+   */
+  private boolean _has_end;
+
+  /**
+   * Field _type.
+   */
+  private java.lang.String _type;
+
+  /**
+   * Field _description.
+   */
+  private java.lang.String _description;
+
+  /**
+   * Field _status.
+   */
+  private java.lang.String _status;
+
+  /**
+   * Field _featureGroup.
+   */
+  private java.lang.String _featureGroup;
+
+  /**
+   * Field _score.
+   */
+  private float _score;
+
+  /**
+   * keeps track of state for field: _score
+   */
+  private boolean _has_score;
+
+  /**
+   * Field _otherDataList.
+   */
+  private java.util.Vector _otherDataList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Feature()
+  {
+    super();
+    this._otherDataList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vOtherData
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addOtherData(
+          final jalview.schemabinding.version2.OtherData vOtherData)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._otherDataList.addElement(vOtherData);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vOtherData
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addOtherData(final int index,
+          final jalview.schemabinding.version2.OtherData vOtherData)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._otherDataList.add(index, vOtherData);
+  }
+
+  /**
+   */
+  public void deleteBegin()
+  {
+    this._has_begin = false;
+  }
+
+  /**
+   */
+  public void deleteEnd()
+  {
+    this._has_end = false;
+  }
+
+  /**
+   */
+  public void deleteScore()
+  {
+    this._has_score = false;
+  }
+
+  /**
+   * Method enumerateOtherData.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.OtherData
+   *         elements
+   */
+  public java.util.Enumeration enumerateOtherData()
+  {
+    return this._otherDataList.elements();
+  }
+
+  /**
+   * Returns the value of field 'begin'.
+   * 
+   * @return the value of field 'Begin'.
+   */
+  public int getBegin()
+  {
+    return this._begin;
+  }
+
+  /**
+   * Returns the value of field 'description'.
+   * 
+   * @return the value of field 'Description'.
+   */
+  public java.lang.String getDescription()
+  {
+    return this._description;
+  }
+
+  /**
+   * Returns the value of field 'end'.
+   * 
+   * @return the value of field 'End'.
+   */
+  public int getEnd()
+  {
+    return this._end;
+  }
+
+  /**
+   * Returns the value of field 'featureGroup'.
+   * 
+   * @return the value of field 'FeatureGroup'.
+   */
+  public java.lang.String getFeatureGroup()
+  {
+    return this._featureGroup;
+  }
+
+  /**
+   * Method getOtherData.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.OtherData at the
+   *         given index
+   */
+  public jalview.schemabinding.version2.OtherData getOtherData(
+          final int index) throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._otherDataList.size())
+    {
+      throw new IndexOutOfBoundsException("getOtherData: Index value '"
+              + index + "' not in range [0.."
+              + (this._otherDataList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.OtherData) _otherDataList
+            .get(index);
+  }
+
+  /**
+   * Method getOtherData.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.OtherData[] getOtherData()
+  {
+    jalview.schemabinding.version2.OtherData[] array = new jalview.schemabinding.version2.OtherData[0];
+    return (jalview.schemabinding.version2.OtherData[]) this._otherDataList
+            .toArray(array);
+  }
+
+  /**
+   * Method getOtherDataCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getOtherDataCount()
+  {
+    return this._otherDataList.size();
+  }
+
+  /**
+   * Returns the value of field 'score'.
+   * 
+   * @return the value of field 'Score'.
+   */
+  public float getScore()
+  {
+    return this._score;
+  }
+
+  /**
+   * Returns the value of field 'status'.
+   * 
+   * @return the value of field 'Status'.
+   */
+  public java.lang.String getStatus()
+  {
+    return this._status;
+  }
+
+  /**
+   * Returns the value of field 'type'.
+   * 
+   * @return the value of field 'Type'.
+   */
+  public java.lang.String getType()
+  {
+    return this._type;
+  }
+
+  /**
+   * Method hasBegin.
+   * 
+   * @return true if at least one Begin has been added
+   */
+  public boolean hasBegin()
+  {
+    return this._has_begin;
+  }
+
+  /**
+   * Method hasEnd.
+   * 
+   * @return true if at least one End has been added
+   */
+  public boolean hasEnd()
+  {
+    return this._has_end;
+  }
+
+  /**
+   * Method hasScore.
+   * 
+   * @return true if at least one Score has been added
+   */
+  public boolean hasScore()
+  {
+    return this._has_score;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   */
+  public void removeAllOtherData()
+  {
+    this._otherDataList.clear();
+  }
+
+  /**
+   * Method removeOtherData.
+   * 
+   * @param vOtherData
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeOtherData(
+          final jalview.schemabinding.version2.OtherData vOtherData)
+  {
+    boolean removed = _otherDataList.remove(vOtherData);
+    return removed;
+  }
+
+  /**
+   * Method removeOtherDataAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.OtherData removeOtherDataAt(
+          final int index)
+  {
+    java.lang.Object obj = this._otherDataList.remove(index);
+    return (jalview.schemabinding.version2.OtherData) obj;
+  }
+
+  /**
+   * Sets the value of field 'begin'.
+   * 
+   * @param begin
+   *                the value of field 'begin'.
+   */
+  public void setBegin(final int begin)
+  {
+    this._begin = begin;
+    this._has_begin = true;
+  }
+
+  /**
+   * Sets the value of field 'description'.
+   * 
+   * @param description
+   *                the value of field 'description'.
+   */
+  public void setDescription(final java.lang.String description)
+  {
+    this._description = description;
+  }
+
+  /**
+   * Sets the value of field 'end'.
+   * 
+   * @param end
+   *                the value of field 'end'.
+   */
+  public void setEnd(final int end)
+  {
+    this._end = end;
+    this._has_end = true;
+  }
+
+  /**
+   * Sets the value of field 'featureGroup'.
+   * 
+   * @param featureGroup
+   *                the value of field 'featureGroup'.
+   */
+  public void setFeatureGroup(final java.lang.String featureGroup)
+  {
+    this._featureGroup = featureGroup;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vOtherData
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setOtherData(final int index,
+          final jalview.schemabinding.version2.OtherData vOtherData)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._otherDataList.size())
+    {
+      throw new IndexOutOfBoundsException("setOtherData: Index value '"
+              + index + "' not in range [0.."
+              + (this._otherDataList.size() - 1) + "]");
+    }
+
+    this._otherDataList.set(index, vOtherData);
+  }
+
+  /**
+   * 
+   * 
+   * @param vOtherDataArray
+   */
+  public void setOtherData(
+          final jalview.schemabinding.version2.OtherData[] vOtherDataArray)
+  {
+    // -- copy array
+    _otherDataList.clear();
+
+    for (int i = 0; i < vOtherDataArray.length; i++)
+    {
+      this._otherDataList.add(vOtherDataArray[i]);
+    }
+  }
+
+  /**
+   * Sets the value of field 'score'.
+   * 
+   * @param score
+   *                the value of field 'score'.
+   */
+  public void setScore(final float score)
+  {
+    this._score = score;
+    this._has_score = true;
+  }
+
+  /**
+   * Sets the value of field 'status'.
+   * 
+   * @param status
+   *                the value of field 'status'.
+   */
+  public void setStatus(final java.lang.String status)
+  {
+    this._status = status;
+  }
+
+  /**
+   * Sets the value of field 'type'.
+   * 
+   * @param type
+   *                the value of field 'type'.
+   */
+  public void setType(final java.lang.String type)
+  {
+    this._type = type;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.Featur
+   */
+  public static jalview.schemabinding.version2.Feature unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.Feature) Unmarshaller.unmarshal(
+            jalview.schemabinding.version2.Feature.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/FeatureSettings.java b/src/jalview/schemabinding/version2/FeatureSettings.java
index 5ce4054..819b05d 100755
--- a/src/jalview/schemabinding/version2/FeatureSettings.java
+++ b/src/jalview/schemabinding/version2/FeatureSettings.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,414 +30,448 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class FeatureSettings implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _settingList.
-     */
-    private java.util.Vector _settingList;
-
-    /**
-     * Field _groupList.
-     */
-    private java.util.Vector _groupList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public FeatureSettings() {
-        super();
-        this._settingList = new java.util.Vector();
-        this._groupList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vGroup
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addGroup(
-            final jalview.schemabinding.version2.Group vGroup)
-    throws java.lang.IndexOutOfBoundsException {
-        this._groupList.addElement(vGroup);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vGroup
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addGroup(
-            final int index,
-            final jalview.schemabinding.version2.Group vGroup)
-    throws java.lang.IndexOutOfBoundsException {
-        this._groupList.add(index, vGroup);
-    }
-
-    /**
-     * 
-     * 
-     * @param vSetting
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSetting(
-            final jalview.schemabinding.version2.Setting vSetting)
-    throws java.lang.IndexOutOfBoundsException {
-        this._settingList.addElement(vSetting);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSetting
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSetting(
-            final int index,
-            final jalview.schemabinding.version2.Setting vSetting)
-    throws java.lang.IndexOutOfBoundsException {
-        this._settingList.add(index, vSetting);
-    }
-
-    /**
-     * Method enumerateGroup.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.Group elements
-     */
-    public java.util.Enumeration enumerateGroup(
-    ) {
-        return this._groupList.elements();
-    }
-
-    /**
-     * Method enumerateSetting.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.Setting elements
-     */
-    public java.util.Enumeration enumerateSetting(
-    ) {
-        return this._settingList.elements();
-    }
-
-    /**
-     * Method getGroup.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.Group at the given index
-     */
-    public jalview.schemabinding.version2.Group getGroup(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._groupList.size()) {
-            throw new IndexOutOfBoundsException("getGroup: Index value '" + index + "' not in range [0.." + (this._groupList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.Group) _groupList.get(index);
-    }
-
-    /**
-     * Method getGroup.Returns the contents of the collection in an
-     * Array.  <p>Note:  Just in case the collection contents are
-     * changing in another thread, we pass a 0-length Array of the
-     * correct type into the API call.  This way we <i>know</i>
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.Group[] getGroup(
-    ) {
-        jalview.schemabinding.version2.Group[] array = new jalview.schemabinding.version2.Group[0];
-        return (jalview.schemabinding.version2.Group[]) this._groupList.toArray(array);
+public class FeatureSettings implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _settingList.
+   */
+  private java.util.Vector _settingList;
+
+  /**
+   * Field _groupList.
+   */
+  private java.util.Vector _groupList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public FeatureSettings()
+  {
+    super();
+    this._settingList = new java.util.Vector();
+    this._groupList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vGroup
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addGroup(final jalview.schemabinding.version2.Group vGroup)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._groupList.addElement(vGroup);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vGroup
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addGroup(final int index,
+          final jalview.schemabinding.version2.Group vGroup)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._groupList.add(index, vGroup);
+  }
+
+  /**
+   * 
+   * 
+   * @param vSetting
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addSetting(
+          final jalview.schemabinding.version2.Setting vSetting)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._settingList.addElement(vSetting);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSetting
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addSetting(final int index,
+          final jalview.schemabinding.version2.Setting vSetting)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._settingList.add(index, vSetting);
+  }
+
+  /**
+   * Method enumerateGroup.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.Group
+   *         elements
+   */
+  public java.util.Enumeration enumerateGroup()
+  {
+    return this._groupList.elements();
+  }
+
+  /**
+   * Method enumerateSetting.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.Setting
+   *         elements
+   */
+  public java.util.Enumeration enumerateSetting()
+  {
+    return this._settingList.elements();
+  }
+
+  /**
+   * Method getGroup.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.Group at the given
+   *         index
+   */
+  public jalview.schemabinding.version2.Group getGroup(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._groupList.size())
+    {
+      throw new IndexOutOfBoundsException("getGroup: Index value '" + index
+              + "' not in range [0.." + (this._groupList.size() - 1) + "]");
     }
 
-    /**
-     * Method getGroupCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getGroupCount(
-    ) {
-        return this._groupList.size();
+    return (jalview.schemabinding.version2.Group) _groupList.get(index);
+  }
+
+  /**
+   * Method getGroup.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.Group[] getGroup()
+  {
+    jalview.schemabinding.version2.Group[] array = new jalview.schemabinding.version2.Group[0];
+    return (jalview.schemabinding.version2.Group[]) this._groupList
+            .toArray(array);
+  }
+
+  /**
+   * Method getGroupCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getGroupCount()
+  {
+    return this._groupList.size();
+  }
+
+  /**
+   * Method getSetting.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.Setting at the
+   *         given index
+   */
+  public jalview.schemabinding.version2.Setting getSetting(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._settingList.size())
+    {
+      throw new IndexOutOfBoundsException("getSetting: Index value '"
+              + index + "' not in range [0.."
+              + (this._settingList.size() - 1) + "]");
     }
 
-    /**
-     * Method getSetting.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.Setting at the given index
-     */
-    public jalview.schemabinding.version2.Setting getSetting(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._settingList.size()) {
-            throw new IndexOutOfBoundsException("getSetting: Index value '" + index + "' not in range [0.." + (this._settingList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.Setting) _settingList.get(index);
+    return (jalview.schemabinding.version2.Setting) _settingList.get(index);
+  }
+
+  /**
+   * Method getSetting.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.Setting[] getSetting()
+  {
+    jalview.schemabinding.version2.Setting[] array = new jalview.schemabinding.version2.Setting[0];
+    return (jalview.schemabinding.version2.Setting[]) this._settingList
+            .toArray(array);
+  }
+
+  /**
+   * Method getSettingCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getSettingCount()
+  {
+    return this._settingList.size();
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
-
-    /**
-     * Method getSetting.Returns the contents of the collection in
-     * an Array.  <p>Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we <i>know</i>
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.Setting[] getSetting(
-    ) {
-        jalview.schemabinding.version2.Setting[] array = new jalview.schemabinding.version2.Setting[0];
-        return (jalview.schemabinding.version2.Setting[]) this._settingList.toArray(array);
-    }
-
-    /**
-     * Method getSettingCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getSettingCount(
-    ) {
-        return this._settingList.size();
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     */
-    public void removeAllGroup(
-    ) {
-        this._groupList.clear();
-    }
-
-    /**
-     */
-    public void removeAllSetting(
-    ) {
-        this._settingList.clear();
-    }
-
-    /**
-     * Method removeGroup.
-     * 
-     * @param vGroup
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeGroup(
-            final jalview.schemabinding.version2.Group vGroup) {
-        boolean removed = _groupList.remove(vGroup);
-        return removed;
-    }
-
-    /**
-     * Method removeGroupAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.Group removeGroupAt(
-            final int index) {
-        java.lang.Object obj = this._groupList.remove(index);
-        return (jalview.schemabinding.version2.Group) obj;
-    }
-
-    /**
-     * Method removeSetting.
-     * 
-     * @param vSetting
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeSetting(
-            final jalview.schemabinding.version2.Setting vSetting) {
-        boolean removed = _settingList.remove(vSetting);
-        return removed;
-    }
-
-    /**
-     * Method removeSettingAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.Setting removeSettingAt(
-            final int index) {
-        java.lang.Object obj = this._settingList.remove(index);
-        return (jalview.schemabinding.version2.Setting) obj;
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   */
+  public void removeAllGroup()
+  {
+    this._groupList.clear();
+  }
+
+  /**
+   */
+  public void removeAllSetting()
+  {
+    this._settingList.clear();
+  }
+
+  /**
+   * Method removeGroup.
+   * 
+   * @param vGroup
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeGroup(
+          final jalview.schemabinding.version2.Group vGroup)
+  {
+    boolean removed = _groupList.remove(vGroup);
+    return removed;
+  }
+
+  /**
+   * Method removeGroupAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.Group removeGroupAt(final int index)
+  {
+    java.lang.Object obj = this._groupList.remove(index);
+    return (jalview.schemabinding.version2.Group) obj;
+  }
+
+  /**
+   * Method removeSetting.
+   * 
+   * @param vSetting
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeSetting(
+          final jalview.schemabinding.version2.Setting vSetting)
+  {
+    boolean removed = _settingList.remove(vSetting);
+    return removed;
+  }
+
+  /**
+   * Method removeSettingAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.Setting removeSettingAt(
+          final int index)
+  {
+    java.lang.Object obj = this._settingList.remove(index);
+    return (jalview.schemabinding.version2.Setting) obj;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vGroup
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setGroup(final int index,
+          final jalview.schemabinding.version2.Group vGroup)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._groupList.size())
+    {
+      throw new IndexOutOfBoundsException("setGroup: Index value '" + index
+              + "' not in range [0.." + (this._groupList.size() - 1) + "]");
     }
 
-    /**
-     * 
-     * 
-     * @param index
-     * @param vGroup
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setGroup(
-            final int index,
-            final jalview.schemabinding.version2.Group vGroup)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._groupList.size()) {
-            throw new IndexOutOfBoundsException("setGroup: Index value '" + index + "' not in range [0.." + (this._groupList.size() - 1) + "]");
-        }
-        
-        this._groupList.set(index, vGroup);
+    this._groupList.set(index, vGroup);
+  }
+
+  /**
+   * 
+   * 
+   * @param vGroupArray
+   */
+  public void setGroup(
+          final jalview.schemabinding.version2.Group[] vGroupArray)
+  {
+    // -- copy array
+    _groupList.clear();
+
+    for (int i = 0; i < vGroupArray.length; i++)
+    {
+      this._groupList.add(vGroupArray[i]);
     }
-
-    /**
-     * 
-     * 
-     * @param vGroupArray
-     */
-    public void setGroup(
-            final jalview.schemabinding.version2.Group[] vGroupArray) {
-        //-- copy array
-        _groupList.clear();
-        
-        for (int i = 0; i < vGroupArray.length; i++) {
-                this._groupList.add(vGroupArray[i]);
-        }
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSetting
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setSetting(
-            final int index,
-            final jalview.schemabinding.version2.Setting vSetting)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._settingList.size()) {
-            throw new IndexOutOfBoundsException("setSetting: Index value '" + index + "' not in range [0.." + (this._settingList.size() - 1) + "]");
-        }
-        
-        this._settingList.set(index, vSetting);
-    }
-
-    /**
-     * 
-     * 
-     * @param vSettingArray
-     */
-    public void setSetting(
-            final jalview.schemabinding.version2.Setting[] vSettingArray) {
-        //-- copy array
-        _settingList.clear();
-        
-        for (int i = 0; i < vSettingArray.length; i++) {
-                this._settingList.add(vSettingArray[i]);
-        }
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.FeatureSettings
-     */
-    public static jalview.schemabinding.version2.FeatureSettings unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.FeatureSettings) Unmarshaller.unmarshal(jalview.schemabinding.version2.FeatureSettings.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSetting
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setSetting(final int index,
+          final jalview.schemabinding.version2.Setting vSetting)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._settingList.size())
+    {
+      throw new IndexOutOfBoundsException("setSetting: Index value '"
+              + index + "' not in range [0.."
+              + (this._settingList.size() - 1) + "]");
     }
 
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+    this._settingList.set(index, vSetting);
+  }
+
+  /**
+   * 
+   * 
+   * @param vSettingArray
+   */
+  public void setSetting(
+          final jalview.schemabinding.version2.Setting[] vSettingArray)
+  {
+    // -- copy array
+    _settingList.clear();
+
+    for (int i = 0; i < vSettingArray.length; i++)
+    {
+      this._settingList.add(vSettingArray[i]);
     }
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.FeatureSettings
+   */
+  public static jalview.schemabinding.version2.FeatureSettings unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.FeatureSettings) Unmarshaller
+            .unmarshal(
+                    jalview.schemabinding.version2.FeatureSettings.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/Features.java b/src/jalview/schemabinding/version2/Features.java
index 47b28a3..d577efc 100755
--- a/src/jalview/schemabinding/version2/Features.java
+++ b/src/jalview/schemabinding/version2/Features.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,98 +30,110 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Features extends Feature 
-implements java.io.Serializable
+public class Features extends Feature implements java.io.Serializable
 {
 
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
 
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Features() {
-        super();
-    }
+  public Features()
+  {
+    super();
+  }
 
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
 
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
 
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
 
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.schemabinding.version2.Featur
-     */
-    public static jalview.schemabinding.version2.Feature unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.Feature) Unmarshaller.unmarshal(jalview.schemabinding.version2.Features.class, reader);
-    }
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.Featur
+   */
+  public static jalview.schemabinding.version2.Feature unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.Feature) Unmarshaller.unmarshal(
+            jalview.schemabinding.version2.Features.class, reader);
+  }
 
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/Group.java b/src/jalview/schemabinding/version2/Group.java
index 826667e..bcc26d1 100644
--- a/src/jalview/schemabinding/version2/Group.java
+++ b/src/jalview/schemabinding/version2/Group.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,184 +30,199 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Group implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _name.
-     */
-    private java.lang.String _name;
-
-    /**
-     * Field _display.
-     */
-    private boolean _display;
-
-    /**
-     * keeps track of state for field: _display
-     */
-    private boolean _has_display;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Group() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     */
-    public void deleteDisplay(
-    ) {
-        this._has_display= false;
-    }
-
-    /**
-     * Returns the value of field 'display'.
-     * 
-     * @return the value of field 'Display'.
-     */
-    public boolean getDisplay(
-    ) {
-        return this._display;
-    }
-
-    /**
-     * Returns the value of field 'name'.
-     * 
-     * @return the value of field 'Name'.
-     */
-    public java.lang.String getName(
-    ) {
-        return this._name;
-    }
-
-    /**
-     * Method hasDisplay.
-     * 
-     * @return true if at least one Display has been added
-     */
-    public boolean hasDisplay(
-    ) {
-        return this._has_display;
-    }
-
-    /**
-     * Returns the value of field 'display'.
-     * 
-     * @return the value of field 'Display'.
-     */
-    public boolean isDisplay(
-    ) {
-        return this._display;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'display'.
-     * 
-     * @param display the value of field 'display'.
-     */
-    public void setDisplay(
-            final boolean display) {
-        this._display = display;
-        this._has_display = true;
-    }
-
-    /**
-     * Sets the value of field 'name'.
-     * 
-     * @param name the value of field 'name'.
-     */
-    public void setName(
-            final java.lang.String name) {
-        this._name = name;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.schemabinding.version2.Group
-     */
-    public static jalview.schemabinding.version2.Group unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.Group) Unmarshaller.unmarshal(jalview.schemabinding.version2.Group.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class Group implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _name.
+   */
+  private java.lang.String _name;
+
+  /**
+   * Field _display.
+   */
+  private boolean _display;
+
+  /**
+   * keeps track of state for field: _display
+   */
+  private boolean _has_display;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Group()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   */
+  public void deleteDisplay()
+  {
+    this._has_display = false;
+  }
+
+  /**
+   * Returns the value of field 'display'.
+   * 
+   * @return the value of field 'Display'.
+   */
+  public boolean getDisplay()
+  {
+    return this._display;
+  }
+
+  /**
+   * Returns the value of field 'name'.
+   * 
+   * @return the value of field 'Name'.
+   */
+  public java.lang.String getName()
+  {
+    return this._name;
+  }
+
+  /**
+   * Method hasDisplay.
+   * 
+   * @return true if at least one Display has been added
+   */
+  public boolean hasDisplay()
+  {
+    return this._has_display;
+  }
+
+  /**
+   * Returns the value of field 'display'.
+   * 
+   * @return the value of field 'Display'.
+   */
+  public boolean isDisplay()
+  {
+    return this._display;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'display'.
+   * 
+   * @param display
+   *                the value of field 'display'.
+   */
+  public void setDisplay(final boolean display)
+  {
+    this._display = display;
+    this._has_display = true;
+  }
+
+  /**
+   * Sets the value of field 'name'.
+   * 
+   * @param name
+   *                the value of field 'name'.
+   */
+  public void setName(final java.lang.String name)
+  {
+    this._name = name;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.Group
+   */
+  public static jalview.schemabinding.version2.Group unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.Group) Unmarshaller.unmarshal(
+            jalview.schemabinding.version2.Group.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/HiddenColumns.java b/src/jalview/schemabinding/version2/HiddenColumns.java
index 716bfbc..2e201c9 100644
--- a/src/jalview/schemabinding/version2/HiddenColumns.java
+++ b/src/jalview/schemabinding/version2/HiddenColumns.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,198 +30,213 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class HiddenColumns implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _start.
-     */
-    private int _start;
-
-    /**
-     * keeps track of state for field: _start
-     */
-    private boolean _has_start;
-
-    /**
-     * Field _end.
-     */
-    private int _end;
-
-    /**
-     * keeps track of state for field: _end
-     */
-    private boolean _has_end;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public HiddenColumns() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     */
-    public void deleteEnd(
-    ) {
-        this._has_end= false;
-    }
-
-    /**
-     */
-    public void deleteStart(
-    ) {
-        this._has_start= false;
-    }
-
-    /**
-     * Returns the value of field 'end'.
-     * 
-     * @return the value of field 'End'.
-     */
-    public int getEnd(
-    ) {
-        return this._end;
-    }
-
-    /**
-     * Returns the value of field 'start'.
-     * 
-     * @return the value of field 'Start'.
-     */
-    public int getStart(
-    ) {
-        return this._start;
-    }
-
-    /**
-     * Method hasEnd.
-     * 
-     * @return true if at least one End has been added
-     */
-    public boolean hasEnd(
-    ) {
-        return this._has_end;
-    }
-
-    /**
-     * Method hasStart.
-     * 
-     * @return true if at least one Start has been added
-     */
-    public boolean hasStart(
-    ) {
-        return this._has_start;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'end'.
-     * 
-     * @param end the value of field 'end'.
-     */
-    public void setEnd(
-            final int end) {
-        this._end = end;
-        this._has_end = true;
-    }
-
-    /**
-     * Sets the value of field 'start'.
-     * 
-     * @param start the value of field 'start'.
-     */
-    public void setStart(
-            final int start) {
-        this._start = start;
-        this._has_start = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.HiddenColumns
-     */
-    public static jalview.schemabinding.version2.HiddenColumns unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.HiddenColumns) Unmarshaller.unmarshal(jalview.schemabinding.version2.HiddenColumns.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class HiddenColumns implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _start.
+   */
+  private int _start;
+
+  /**
+   * keeps track of state for field: _start
+   */
+  private boolean _has_start;
+
+  /**
+   * Field _end.
+   */
+  private int _end;
+
+  /**
+   * keeps track of state for field: _end
+   */
+  private boolean _has_end;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public HiddenColumns()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   */
+  public void deleteEnd()
+  {
+    this._has_end = false;
+  }
+
+  /**
+   */
+  public void deleteStart()
+  {
+    this._has_start = false;
+  }
+
+  /**
+   * Returns the value of field 'end'.
+   * 
+   * @return the value of field 'End'.
+   */
+  public int getEnd()
+  {
+    return this._end;
+  }
+
+  /**
+   * Returns the value of field 'start'.
+   * 
+   * @return the value of field 'Start'.
+   */
+  public int getStart()
+  {
+    return this._start;
+  }
+
+  /**
+   * Method hasEnd.
+   * 
+   * @return true if at least one End has been added
+   */
+  public boolean hasEnd()
+  {
+    return this._has_end;
+  }
+
+  /**
+   * Method hasStart.
+   * 
+   * @return true if at least one Start has been added
+   */
+  public boolean hasStart()
+  {
+    return this._has_start;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'end'.
+   * 
+   * @param end
+   *                the value of field 'end'.
+   */
+  public void setEnd(final int end)
+  {
+    this._end = end;
+    this._has_end = true;
+  }
+
+  /**
+   * Sets the value of field 'start'.
+   * 
+   * @param start
+   *                the value of field 'start'.
+   */
+  public void setStart(final int start)
+  {
+    this._start = start;
+    this._has_start = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.HiddenColumns
+   */
+  public static jalview.schemabinding.version2.HiddenColumns unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.HiddenColumns) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.HiddenColumns.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/JGroup.java b/src/jalview/schemabinding/version2/JGroup.java
index ca77ed2..c24533e 100755
--- a/src/jalview/schemabinding/version2/JGroup.java
+++ b/src/jalview/schemabinding/version2/JGroup.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,863 +30,892 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class JGroup implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _start.
-     */
-    private int _start;
-
-    /**
-     * keeps track of state for field: _start
-     */
-    private boolean _has_start;
-
-    /**
-     * Field _end.
-     */
-    private int _end;
-
-    /**
-     * keeps track of state for field: _end
-     */
-    private boolean _has_end;
-
-    /**
-     * Field _name.
-     */
-    private java.lang.String _name;
-
-    /**
-     * Field _colour.
-     */
-    private java.lang.String _colour;
-
-    /**
-     * Field _consThreshold.
-     */
-    private int _consThreshold;
-
-    /**
-     * keeps track of state for field: _consThreshold
-     */
-    private boolean _has_consThreshold;
-
-    /**
-     * Field _pidThreshold.
-     */
-    private int _pidThreshold;
-
-    /**
-     * keeps track of state for field: _pidThreshold
-     */
-    private boolean _has_pidThreshold;
-
-    /**
-     * Field _outlineColour.
-     */
-    private int _outlineColour;
-
-    /**
-     * keeps track of state for field: _outlineColour
-     */
-    private boolean _has_outlineColour;
-
-    /**
-     * Field _displayBoxes.
-     */
-    private boolean _displayBoxes;
-
-    /**
-     * keeps track of state for field: _displayBoxes
-     */
-    private boolean _has_displayBoxes;
-
-    /**
-     * Field _displayText.
-     */
-    private boolean _displayText;
-
-    /**
-     * keeps track of state for field: _displayText
-     */
-    private boolean _has_displayText;
-
-    /**
-     * Field _colourText.
-     */
-    private boolean _colourText;
-
-    /**
-     * keeps track of state for field: _colourText
-     */
-    private boolean _has_colourText;
-
-    /**
-     * Field _textCol1.
-     */
-    private int _textCol1;
-
-    /**
-     * keeps track of state for field: _textCol1
-     */
-    private boolean _has_textCol1;
-
-    /**
-     * Field _textCol2.
-     */
-    private int _textCol2;
-
-    /**
-     * keeps track of state for field: _textCol2
-     */
-    private boolean _has_textCol2;
-
-    /**
-     * Field _textColThreshold.
-     */
-    private int _textColThreshold;
-
-    /**
-     * keeps track of state for field: _textColThreshold
-     */
-    private boolean _has_textColThreshold;
-
-    /**
-     * Field _seqList.
-     */
-    private java.util.Vector _seqList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JGroup() {
-        super();
-        this._seqList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vSeq
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSeq(
-            final java.lang.String vSeq)
-    throws java.lang.IndexOutOfBoundsException {
-        this._seqList.addElement(vSeq);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSeq
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSeq(
-            final int index,
-            final java.lang.String vSeq)
-    throws java.lang.IndexOutOfBoundsException {
-        this._seqList.add(index, vSeq);
-    }
-
-    /**
-     */
-    public void deleteColourText(
-    ) {
-        this._has_colourText= false;
-    }
-
-    /**
-     */
-    public void deleteConsThreshold(
-    ) {
-        this._has_consThreshold= false;
-    }
-
-    /**
-     */
-    public void deleteDisplayBoxes(
-    ) {
-        this._has_displayBoxes= false;
-    }
-
-    /**
-     */
-    public void deleteDisplayText(
-    ) {
-        this._has_displayText= false;
-    }
-
-    /**
-     */
-    public void deleteEnd(
-    ) {
-        this._has_end= false;
-    }
-
-    /**
-     */
-    public void deleteOutlineColour(
-    ) {
-        this._has_outlineColour= false;
-    }
-
-    /**
-     */
-    public void deletePidThreshold(
-    ) {
-        this._has_pidThreshold= false;
-    }
-
-    /**
-     */
-    public void deleteStart(
-    ) {
-        this._has_start= false;
-    }
-
-    /**
-     */
-    public void deleteTextCol1(
-    ) {
-        this._has_textCol1= false;
-    }
-
-    /**
-     */
-    public void deleteTextCol2(
-    ) {
-        this._has_textCol2= false;
-    }
-
-    /**
-     */
-    public void deleteTextColThreshold(
-    ) {
-        this._has_textColThreshold= false;
-    }
-
-    /**
-     * Method enumerateSeq.
-     * 
-     * @return an Enumeration over all java.lang.String elements
-     */
-    public java.util.Enumeration enumerateSeq(
-    ) {
-        return this._seqList.elements();
-    }
-
-    /**
-     * Returns the value of field 'colour'.
-     * 
-     * @return the value of field 'Colour'.
-     */
-    public java.lang.String getColour(
-    ) {
-        return this._colour;
-    }
-
-    /**
-     * Returns the value of field 'colourText'.
-     * 
-     * @return the value of field 'ColourText'.
-     */
-    public boolean getColourText(
-    ) {
-        return this._colourText;
-    }
-
-    /**
-     * Returns the value of field 'consThreshold'.
-     * 
-     * @return the value of field 'ConsThreshold'.
-     */
-    public int getConsThreshold(
-    ) {
-        return this._consThreshold;
-    }
-
-    /**
-     * Returns the value of field 'displayBoxes'.
-     * 
-     * @return the value of field 'DisplayBoxes'.
-     */
-    public boolean getDisplayBoxes(
-    ) {
-        return this._displayBoxes;
-    }
-
-    /**
-     * Returns the value of field 'displayText'.
-     * 
-     * @return the value of field 'DisplayText'.
-     */
-    public boolean getDisplayText(
-    ) {
-        return this._displayText;
-    }
-
-    /**
-     * Returns the value of field 'end'.
-     * 
-     * @return the value of field 'End'.
-     */
-    public int getEnd(
-    ) {
-        return this._end;
-    }
-
-    /**
-     * Returns the value of field 'name'.
-     * 
-     * @return the value of field 'Name'.
-     */
-    public java.lang.String getName(
-    ) {
-        return this._name;
-    }
-
-    /**
-     * Returns the value of field 'outlineColour'.
-     * 
-     * @return the value of field 'OutlineColour'.
-     */
-    public int getOutlineColour(
-    ) {
-        return this._outlineColour;
-    }
-
-    /**
-     * Returns the value of field 'pidThreshold'.
-     * 
-     * @return the value of field 'PidThreshold'.
-     */
-    public int getPidThreshold(
-    ) {
-        return this._pidThreshold;
-    }
-
-    /**
-     * Method getSeq.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the java.lang.String at the given index
-     */
-    public java.lang.String getSeq(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._seqList.size()) {
-            throw new IndexOutOfBoundsException("getSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");
-        }
-        
-        return (java.lang.String) _seqList.get(index);
-    }
-
-    /**
-     * Method getSeq.Returns the contents of the collection in an
-     * Array.  <p>Note:  Just in case the collection contents are
-     * changing in another thread, we pass a 0-length Array of the
-     * correct type into the API call.  This way we <i>know</i>
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public java.lang.String[] getSeq(
-    ) {
-        java.lang.String[] array = new java.lang.String[0];
-        return (java.lang.String[]) this._seqList.toArray(array);
-    }
-
-    /**
-     * Method getSeqCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getSeqCount(
-    ) {
-        return this._seqList.size();
-    }
-
-    /**
-     * Returns the value of field 'start'.
-     * 
-     * @return the value of field 'Start'.
-     */
-    public int getStart(
-    ) {
-        return this._start;
-    }
-
-    /**
-     * Returns the value of field 'textCol1'.
-     * 
-     * @return the value of field 'TextCol1'.
-     */
-    public int getTextCol1(
-    ) {
-        return this._textCol1;
-    }
-
-    /**
-     * Returns the value of field 'textCol2'.
-     * 
-     * @return the value of field 'TextCol2'.
-     */
-    public int getTextCol2(
-    ) {
-        return this._textCol2;
-    }
-
-    /**
-     * Returns the value of field 'textColThreshold'.
-     * 
-     * @return the value of field 'TextColThreshold'.
-     */
-    public int getTextColThreshold(
-    ) {
-        return this._textColThreshold;
-    }
-
-    /**
-     * Method hasColourText.
-     * 
-     * @return true if at least one ColourText has been added
-     */
-    public boolean hasColourText(
-    ) {
-        return this._has_colourText;
-    }
-
-    /**
-     * Method hasConsThreshold.
-     * 
-     * @return true if at least one ConsThreshold has been added
-     */
-    public boolean hasConsThreshold(
-    ) {
-        return this._has_consThreshold;
-    }
-
-    /**
-     * Method hasDisplayBoxes.
-     * 
-     * @return true if at least one DisplayBoxes has been added
-     */
-    public boolean hasDisplayBoxes(
-    ) {
-        return this._has_displayBoxes;
-    }
-
-    /**
-     * Method hasDisplayText.
-     * 
-     * @return true if at least one DisplayText has been added
-     */
-    public boolean hasDisplayText(
-    ) {
-        return this._has_displayText;
-    }
-
-    /**
-     * Method hasEnd.
-     * 
-     * @return true if at least one End has been added
-     */
-    public boolean hasEnd(
-    ) {
-        return this._has_end;
-    }
-
-    /**
-     * Method hasOutlineColour.
-     * 
-     * @return true if at least one OutlineColour has been added
-     */
-    public boolean hasOutlineColour(
-    ) {
-        return this._has_outlineColour;
-    }
-
-    /**
-     * Method hasPidThreshold.
-     * 
-     * @return true if at least one PidThreshold has been added
-     */
-    public boolean hasPidThreshold(
-    ) {
-        return this._has_pidThreshold;
-    }
-
-    /**
-     * Method hasStart.
-     * 
-     * @return true if at least one Start has been added
-     */
-    public boolean hasStart(
-    ) {
-        return this._has_start;
-    }
-
-    /**
-     * Method hasTextCol1.
-     * 
-     * @return true if at least one TextCol1 has been added
-     */
-    public boolean hasTextCol1(
-    ) {
-        return this._has_textCol1;
-    }
-
-    /**
-     * Method hasTextCol2.
-     * 
-     * @return true if at least one TextCol2 has been added
-     */
-    public boolean hasTextCol2(
-    ) {
-        return this._has_textCol2;
-    }
-
-    /**
-     * Method hasTextColThreshold.
-     * 
-     * @return true if at least one TextColThreshold has been added
-     */
-    public boolean hasTextColThreshold(
-    ) {
-        return this._has_textColThreshold;
-    }
-
-    /**
-     * Returns the value of field 'colourText'.
-     * 
-     * @return the value of field 'ColourText'.
-     */
-    public boolean isColourText(
-    ) {
-        return this._colourText;
-    }
-
-    /**
-     * Returns the value of field 'displayBoxes'.
-     * 
-     * @return the value of field 'DisplayBoxes'.
-     */
-    public boolean isDisplayBoxes(
-    ) {
-        return this._displayBoxes;
-    }
-
-    /**
-     * Returns the value of field 'displayText'.
-     * 
-     * @return the value of field 'DisplayText'.
-     */
-    public boolean isDisplayText(
-    ) {
-        return this._displayText;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     */
-    public void removeAllSeq(
-    ) {
-        this._seqList.clear();
-    }
-
-    /**
-     * Method removeSeq.
-     * 
-     * @param vSeq
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeSeq(
-            final java.lang.String vSeq) {
-        boolean removed = _seqList.remove(vSeq);
-        return removed;
-    }
-
-    /**
-     * Method removeSeqAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public java.lang.String removeSeqAt(
-            final int index) {
-        java.lang.Object obj = this._seqList.remove(index);
-        return (java.lang.String) obj;
-    }
-
-    /**
-     * Sets the value of field 'colour'.
-     * 
-     * @param colour the value of field 'colour'.
-     */
-    public void setColour(
-            final java.lang.String colour) {
-        this._colour = colour;
-    }
-
-    /**
-     * Sets the value of field 'colourText'.
-     * 
-     * @param colourText the value of field 'colourText'.
-     */
-    public void setColourText(
-            final boolean colourText) {
-        this._colourText = colourText;
-        this._has_colourText = true;
-    }
-
-    /**
-     * Sets the value of field 'consThreshold'.
-     * 
-     * @param consThreshold the value of field 'consThreshold'.
-     */
-    public void setConsThreshold(
-            final int consThreshold) {
-        this._consThreshold = consThreshold;
-        this._has_consThreshold = true;
-    }
-
-    /**
-     * Sets the value of field 'displayBoxes'.
-     * 
-     * @param displayBoxes the value of field 'displayBoxes'.
-     */
-    public void setDisplayBoxes(
-            final boolean displayBoxes) {
-        this._displayBoxes = displayBoxes;
-        this._has_displayBoxes = true;
-    }
-
-    /**
-     * Sets the value of field 'displayText'.
-     * 
-     * @param displayText the value of field 'displayText'.
-     */
-    public void setDisplayText(
-            final boolean displayText) {
-        this._displayText = displayText;
-        this._has_displayText = true;
-    }
-
-    /**
-     * Sets the value of field 'end'.
-     * 
-     * @param end the value of field 'end'.
-     */
-    public void setEnd(
-            final int end) {
-        this._end = end;
-        this._has_end = true;
-    }
-
-    /**
-     * Sets the value of field 'name'.
-     * 
-     * @param name the value of field 'name'.
-     */
-    public void setName(
-            final java.lang.String name) {
-        this._name = name;
-    }
-
-    /**
-     * Sets the value of field 'outlineColour'.
-     * 
-     * @param outlineColour the value of field 'outlineColour'.
-     */
-    public void setOutlineColour(
-            final int outlineColour) {
-        this._outlineColour = outlineColour;
-        this._has_outlineColour = true;
-    }
-
-    /**
-     * Sets the value of field 'pidThreshold'.
-     * 
-     * @param pidThreshold the value of field 'pidThreshold'.
-     */
-    public void setPidThreshold(
-            final int pidThreshold) {
-        this._pidThreshold = pidThreshold;
-        this._has_pidThreshold = true;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSeq
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setSeq(
-            final int index,
-            final java.lang.String vSeq)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._seqList.size()) {
-            throw new IndexOutOfBoundsException("setSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");
-        }
-        
-        this._seqList.set(index, vSeq);
-    }
-
-    /**
-     * 
-     * 
-     * @param vSeqArray
-     */
-    public void setSeq(
-            final java.lang.String[] vSeqArray) {
-        //-- copy array
-        _seqList.clear();
-        
-        for (int i = 0; i < vSeqArray.length; i++) {
-                this._seqList.add(vSeqArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of field 'start'.
-     * 
-     * @param start the value of field 'start'.
-     */
-    public void setStart(
-            final int start) {
-        this._start = start;
-        this._has_start = true;
-    }
-
-    /**
-     * Sets the value of field 'textCol1'.
-     * 
-     * @param textCol1 the value of field 'textCol1'.
-     */
-    public void setTextCol1(
-            final int textCol1) {
-        this._textCol1 = textCol1;
-        this._has_textCol1 = true;
-    }
-
-    /**
-     * Sets the value of field 'textCol2'.
-     * 
-     * @param textCol2 the value of field 'textCol2'.
-     */
-    public void setTextCol2(
-            final int textCol2) {
-        this._textCol2 = textCol2;
-        this._has_textCol2 = true;
-    }
-
-    /**
-     * Sets the value of field 'textColThreshold'.
-     * 
-     * @param textColThreshold the value of field 'textColThreshold'
-     */
-    public void setTextColThreshold(
-            final int textColThreshold) {
-        this._textColThreshold = textColThreshold;
-        this._has_textColThreshold = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.schemabinding.version2.JGroup
-     */
-    public static jalview.schemabinding.version2.JGroup unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.JGroup) Unmarshaller.unmarshal(jalview.schemabinding.version2.JGroup.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+public class JGroup implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _start.
+   */
+  private int _start;
+
+  /**
+   * keeps track of state for field: _start
+   */
+  private boolean _has_start;
+
+  /**
+   * Field _end.
+   */
+  private int _end;
+
+  /**
+   * keeps track of state for field: _end
+   */
+  private boolean _has_end;
+
+  /**
+   * Field _name.
+   */
+  private java.lang.String _name;
+
+  /**
+   * Field _colour.
+   */
+  private java.lang.String _colour;
+
+  /**
+   * Field _consThreshold.
+   */
+  private int _consThreshold;
+
+  /**
+   * keeps track of state for field: _consThreshold
+   */
+  private boolean _has_consThreshold;
+
+  /**
+   * Field _pidThreshold.
+   */
+  private int _pidThreshold;
+
+  /**
+   * keeps track of state for field: _pidThreshold
+   */
+  private boolean _has_pidThreshold;
+
+  /**
+   * Field _outlineColour.
+   */
+  private int _outlineColour;
+
+  /**
+   * keeps track of state for field: _outlineColour
+   */
+  private boolean _has_outlineColour;
+
+  /**
+   * Field _displayBoxes.
+   */
+  private boolean _displayBoxes;
+
+  /**
+   * keeps track of state for field: _displayBoxes
+   */
+  private boolean _has_displayBoxes;
+
+  /**
+   * Field _displayText.
+   */
+  private boolean _displayText;
+
+  /**
+   * keeps track of state for field: _displayText
+   */
+  private boolean _has_displayText;
+
+  /**
+   * Field _colourText.
+   */
+  private boolean _colourText;
+
+  /**
+   * keeps track of state for field: _colourText
+   */
+  private boolean _has_colourText;
+
+  /**
+   * Field _textCol1.
+   */
+  private int _textCol1;
+
+  /**
+   * keeps track of state for field: _textCol1
+   */
+  private boolean _has_textCol1;
+
+  /**
+   * Field _textCol2.
+   */
+  private int _textCol2;
+
+  /**
+   * keeps track of state for field: _textCol2
+   */
+  private boolean _has_textCol2;
+
+  /**
+   * Field _textColThreshold.
+   */
+  private int _textColThreshold;
+
+  /**
+   * keeps track of state for field: _textColThreshold
+   */
+  private boolean _has_textColThreshold;
+
+  /**
+   * Field _seqList.
+   */
+  private java.util.Vector _seqList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public JGroup()
+  {
+    super();
+    this._seqList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vSeq
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addSeq(final java.lang.String vSeq)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._seqList.addElement(vSeq);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSeq
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addSeq(final int index, final java.lang.String vSeq)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._seqList.add(index, vSeq);
+  }
+
+  /**
+   */
+  public void deleteColourText()
+  {
+    this._has_colourText = false;
+  }
+
+  /**
+   */
+  public void deleteConsThreshold()
+  {
+    this._has_consThreshold = false;
+  }
+
+  /**
+   */
+  public void deleteDisplayBoxes()
+  {
+    this._has_displayBoxes = false;
+  }
+
+  /**
+   */
+  public void deleteDisplayText()
+  {
+    this._has_displayText = false;
+  }
+
+  /**
+   */
+  public void deleteEnd()
+  {
+    this._has_end = false;
+  }
+
+  /**
+   */
+  public void deleteOutlineColour()
+  {
+    this._has_outlineColour = false;
+  }
+
+  /**
+   */
+  public void deletePidThreshold()
+  {
+    this._has_pidThreshold = false;
+  }
+
+  /**
+   */
+  public void deleteStart()
+  {
+    this._has_start = false;
+  }
+
+  /**
+   */
+  public void deleteTextCol1()
+  {
+    this._has_textCol1 = false;
+  }
+
+  /**
+   */
+  public void deleteTextCol2()
+  {
+    this._has_textCol2 = false;
+  }
+
+  /**
+   */
+  public void deleteTextColThreshold()
+  {
+    this._has_textColThreshold = false;
+  }
+
+  /**
+   * Method enumerateSeq.
+   * 
+   * @return an Enumeration over all java.lang.String elements
+   */
+  public java.util.Enumeration enumerateSeq()
+  {
+    return this._seqList.elements();
+  }
+
+  /**
+   * Returns the value of field 'colour'.
+   * 
+   * @return the value of field 'Colour'.
+   */
+  public java.lang.String getColour()
+  {
+    return this._colour;
+  }
+
+  /**
+   * Returns the value of field 'colourText'.
+   * 
+   * @return the value of field 'ColourText'.
+   */
+  public boolean getColourText()
+  {
+    return this._colourText;
+  }
+
+  /**
+   * Returns the value of field 'consThreshold'.
+   * 
+   * @return the value of field 'ConsThreshold'.
+   */
+  public int getConsThreshold()
+  {
+    return this._consThreshold;
+  }
+
+  /**
+   * Returns the value of field 'displayBoxes'.
+   * 
+   * @return the value of field 'DisplayBoxes'.
+   */
+  public boolean getDisplayBoxes()
+  {
+    return this._displayBoxes;
+  }
+
+  /**
+   * Returns the value of field 'displayText'.
+   * 
+   * @return the value of field 'DisplayText'.
+   */
+  public boolean getDisplayText()
+  {
+    return this._displayText;
+  }
+
+  /**
+   * Returns the value of field 'end'.
+   * 
+   * @return the value of field 'End'.
+   */
+  public int getEnd()
+  {
+    return this._end;
+  }
+
+  /**
+   * Returns the value of field 'name'.
+   * 
+   * @return the value of field 'Name'.
+   */
+  public java.lang.String getName()
+  {
+    return this._name;
+  }
+
+  /**
+   * Returns the value of field 'outlineColour'.
+   * 
+   * @return the value of field 'OutlineColour'.
+   */
+  public int getOutlineColour()
+  {
+    return this._outlineColour;
+  }
+
+  /**
+   * Returns the value of field 'pidThreshold'.
+   * 
+   * @return the value of field 'PidThreshold'.
+   */
+  public int getPidThreshold()
+  {
+    return this._pidThreshold;
+  }
+
+  /**
+   * Method getSeq.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the java.lang.String at the given index
+   */
+  public java.lang.String getSeq(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._seqList.size())
+    {
+      throw new IndexOutOfBoundsException("getSeq: Index value '" + index
+              + "' not in range [0.." + (this._seqList.size() - 1) + "]");
+    }
+
+    return (java.lang.String) _seqList.get(index);
+  }
+
+  /**
+   * Method getSeq.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public java.lang.String[] getSeq()
+  {
+    java.lang.String[] array = new java.lang.String[0];
+    return (java.lang.String[]) this._seqList.toArray(array);
+  }
+
+  /**
+   * Method getSeqCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getSeqCount()
+  {
+    return this._seqList.size();
+  }
+
+  /**
+   * Returns the value of field 'start'.
+   * 
+   * @return the value of field 'Start'.
+   */
+  public int getStart()
+  {
+    return this._start;
+  }
+
+  /**
+   * Returns the value of field 'textCol1'.
+   * 
+   * @return the value of field 'TextCol1'.
+   */
+  public int getTextCol1()
+  {
+    return this._textCol1;
+  }
+
+  /**
+   * Returns the value of field 'textCol2'.
+   * 
+   * @return the value of field 'TextCol2'.
+   */
+  public int getTextCol2()
+  {
+    return this._textCol2;
+  }
+
+  /**
+   * Returns the value of field 'textColThreshold'.
+   * 
+   * @return the value of field 'TextColThreshold'.
+   */
+  public int getTextColThreshold()
+  {
+    return this._textColThreshold;
+  }
+
+  /**
+   * Method hasColourText.
+   * 
+   * @return true if at least one ColourText has been added
+   */
+  public boolean hasColourText()
+  {
+    return this._has_colourText;
+  }
+
+  /**
+   * Method hasConsThreshold.
+   * 
+   * @return true if at least one ConsThreshold has been added
+   */
+  public boolean hasConsThreshold()
+  {
+    return this._has_consThreshold;
+  }
+
+  /**
+   * Method hasDisplayBoxes.
+   * 
+   * @return true if at least one DisplayBoxes has been added
+   */
+  public boolean hasDisplayBoxes()
+  {
+    return this._has_displayBoxes;
+  }
+
+  /**
+   * Method hasDisplayText.
+   * 
+   * @return true if at least one DisplayText has been added
+   */
+  public boolean hasDisplayText()
+  {
+    return this._has_displayText;
+  }
+
+  /**
+   * Method hasEnd.
+   * 
+   * @return true if at least one End has been added
+   */
+  public boolean hasEnd()
+  {
+    return this._has_end;
+  }
+
+  /**
+   * Method hasOutlineColour.
+   * 
+   * @return true if at least one OutlineColour has been added
+   */
+  public boolean hasOutlineColour()
+  {
+    return this._has_outlineColour;
+  }
+
+  /**
+   * Method hasPidThreshold.
+   * 
+   * @return true if at least one PidThreshold has been added
+   */
+  public boolean hasPidThreshold()
+  {
+    return this._has_pidThreshold;
+  }
+
+  /**
+   * Method hasStart.
+   * 
+   * @return true if at least one Start has been added
+   */
+  public boolean hasStart()
+  {
+    return this._has_start;
+  }
+
+  /**
+   * Method hasTextCol1.
+   * 
+   * @return true if at least one TextCol1 has been added
+   */
+  public boolean hasTextCol1()
+  {
+    return this._has_textCol1;
+  }
+
+  /**
+   * Method hasTextCol2.
+   * 
+   * @return true if at least one TextCol2 has been added
+   */
+  public boolean hasTextCol2()
+  {
+    return this._has_textCol2;
+  }
+
+  /**
+   * Method hasTextColThreshold.
+   * 
+   * @return true if at least one TextColThreshold has been added
+   */
+  public boolean hasTextColThreshold()
+  {
+    return this._has_textColThreshold;
+  }
+
+  /**
+   * Returns the value of field 'colourText'.
+   * 
+   * @return the value of field 'ColourText'.
+   */
+  public boolean isColourText()
+  {
+    return this._colourText;
+  }
+
+  /**
+   * Returns the value of field 'displayBoxes'.
+   * 
+   * @return the value of field 'DisplayBoxes'.
+   */
+  public boolean isDisplayBoxes()
+  {
+    return this._displayBoxes;
+  }
+
+  /**
+   * Returns the value of field 'displayText'.
+   * 
+   * @return the value of field 'DisplayText'.
+   */
+  public boolean isDisplayText()
+  {
+    return this._displayText;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   */
+  public void removeAllSeq()
+  {
+    this._seqList.clear();
+  }
+
+  /**
+   * Method removeSeq.
+   * 
+   * @param vSeq
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeSeq(final java.lang.String vSeq)
+  {
+    boolean removed = _seqList.remove(vSeq);
+    return removed;
+  }
+
+  /**
+   * Method removeSeqAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public java.lang.String removeSeqAt(final int index)
+  {
+    java.lang.Object obj = this._seqList.remove(index);
+    return (java.lang.String) obj;
+  }
+
+  /**
+   * Sets the value of field 'colour'.
+   * 
+   * @param colour
+   *                the value of field 'colour'.
+   */
+  public void setColour(final java.lang.String colour)
+  {
+    this._colour = colour;
+  }
+
+  /**
+   * Sets the value of field 'colourText'.
+   * 
+   * @param colourText
+   *                the value of field 'colourText'.
+   */
+  public void setColourText(final boolean colourText)
+  {
+    this._colourText = colourText;
+    this._has_colourText = true;
+  }
+
+  /**
+   * Sets the value of field 'consThreshold'.
+   * 
+   * @param consThreshold
+   *                the value of field 'consThreshold'.
+   */
+  public void setConsThreshold(final int consThreshold)
+  {
+    this._consThreshold = consThreshold;
+    this._has_consThreshold = true;
+  }
+
+  /**
+   * Sets the value of field 'displayBoxes'.
+   * 
+   * @param displayBoxes
+   *                the value of field 'displayBoxes'.
+   */
+  public void setDisplayBoxes(final boolean displayBoxes)
+  {
+    this._displayBoxes = displayBoxes;
+    this._has_displayBoxes = true;
+  }
+
+  /**
+   * Sets the value of field 'displayText'.
+   * 
+   * @param displayText
+   *                the value of field 'displayText'.
+   */
+  public void setDisplayText(final boolean displayText)
+  {
+    this._displayText = displayText;
+    this._has_displayText = true;
+  }
+
+  /**
+   * Sets the value of field 'end'.
+   * 
+   * @param end
+   *                the value of field 'end'.
+   */
+  public void setEnd(final int end)
+  {
+    this._end = end;
+    this._has_end = true;
+  }
+
+  /**
+   * Sets the value of field 'name'.
+   * 
+   * @param name
+   *                the value of field 'name'.
+   */
+  public void setName(final java.lang.String name)
+  {
+    this._name = name;
+  }
+
+  /**
+   * Sets the value of field 'outlineColour'.
+   * 
+   * @param outlineColour
+   *                the value of field 'outlineColour'.
+   */
+  public void setOutlineColour(final int outlineColour)
+  {
+    this._outlineColour = outlineColour;
+    this._has_outlineColour = true;
+  }
+
+  /**
+   * Sets the value of field 'pidThreshold'.
+   * 
+   * @param pidThreshold
+   *                the value of field 'pidThreshold'.
+   */
+  public void setPidThreshold(final int pidThreshold)
+  {
+    this._pidThreshold = pidThreshold;
+    this._has_pidThreshold = true;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSeq
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setSeq(final int index, final java.lang.String vSeq)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._seqList.size())
+    {
+      throw new IndexOutOfBoundsException("setSeq: Index value '" + index
+              + "' not in range [0.." + (this._seqList.size() - 1) + "]");
+    }
+
+    this._seqList.set(index, vSeq);
+  }
+
+  /**
+   * 
+   * 
+   * @param vSeqArray
+   */
+  public void setSeq(final java.lang.String[] vSeqArray)
+  {
+    // -- copy array
+    _seqList.clear();
+
+    for (int i = 0; i < vSeqArray.length; i++)
+    {
+      this._seqList.add(vSeqArray[i]);
+    }
+  }
+
+  /**
+   * Sets the value of field 'start'.
+   * 
+   * @param start
+   *                the value of field 'start'.
+   */
+  public void setStart(final int start)
+  {
+    this._start = start;
+    this._has_start = true;
+  }
+
+  /**
+   * Sets the value of field 'textCol1'.
+   * 
+   * @param textCol1
+   *                the value of field 'textCol1'.
+   */
+  public void setTextCol1(final int textCol1)
+  {
+    this._textCol1 = textCol1;
+    this._has_textCol1 = true;
+  }
+
+  /**
+   * Sets the value of field 'textCol2'.
+   * 
+   * @param textCol2
+   *                the value of field 'textCol2'.
+   */
+  public void setTextCol2(final int textCol2)
+  {
+    this._textCol2 = textCol2;
+    this._has_textCol2 = true;
+  }
+
+  /**
+   * Sets the value of field 'textColThreshold'.
+   * 
+   * @param textColThreshold
+   *                the value of field 'textColThreshold'
+   */
+  public void setTextColThreshold(final int textColThreshold)
+  {
+    this._textColThreshold = textColThreshold;
+    this._has_textColThreshold = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.JGroup
+   */
+  public static jalview.schemabinding.version2.JGroup unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.JGroup) Unmarshaller.unmarshal(
+            jalview.schemabinding.version2.JGroup.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/JSeq.java b/src/jalview/schemabinding/version2/JSeq.java
index a5dc2f7..90bee0f 100755
--- a/src/jalview/schemabinding/version2/JSeq.java
+++ b/src/jalview/schemabinding/version2/JSeq.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,796 +30,851 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class JSeq implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _colour.
-     */
-    private int _colour;
-
-    /**
-     * keeps track of state for field: _colour
-     */
-    private boolean _has_colour;
-
-    /**
-     * Field _start.
-     */
-    private int _start;
-
-    /**
-     * keeps track of state for field: _start
-     */
-    private boolean _has_start;
-
-    /**
-     * Field _end.
-     */
-    private int _end;
-
-    /**
-     * keeps track of state for field: _end
-     */
-    private boolean _has_end;
-
-    /**
-     * Field _id.
-     */
-    private java.lang.String _id;
-
-    /**
-     * Field _hidden.
-     */
-    private boolean _hidden;
-
-    /**
-     * keeps track of state for field: _hidden
-     */
-    private boolean _has_hidden;
-
-    /**
-     * Field _featuresList.
-     */
-    private java.util.Vector _featuresList;
-
-    /**
-     * Field _pdbidsList.
-     */
-    private java.util.Vector _pdbidsList;
-
-    /**
-     * Field _hiddenSequencesList.
-     */
-    private java.util.Vector _hiddenSequencesList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JSeq() {
-        super();
-        this._featuresList = new java.util.Vector();
-        this._pdbidsList = new java.util.Vector();
-        this._hiddenSequencesList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vFeatures
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addFeatures(
-            final jalview.schemabinding.version2.Features vFeatures)
-    throws java.lang.IndexOutOfBoundsException {
-        this._featuresList.addElement(vFeatures);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vFeatures
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addFeatures(
-            final int index,
-            final jalview.schemabinding.version2.Features vFeatures)
-    throws java.lang.IndexOutOfBoundsException {
-        this._featuresList.add(index, vFeatures);
-    }
-
-    /**
-     * 
-     * 
-     * @param vHiddenSequences
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addHiddenSequences(
-            final int vHiddenSequences)
-    throws java.lang.IndexOutOfBoundsException {
-        this._hiddenSequencesList.addElement(new java.lang.Integer(vHiddenSequences));
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vHiddenSequences
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addHiddenSequences(
-            final int index,
-            final int vHiddenSequences)
-    throws java.lang.IndexOutOfBoundsException {
-        this._hiddenSequencesList.add(index, new java.lang.Integer(vHiddenSequences));
-    }
-
-    /**
-     * 
-     * 
-     * @param vPdbids
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addPdbids(
-            final jalview.schemabinding.version2.Pdbids vPdbids)
-    throws java.lang.IndexOutOfBoundsException {
-        this._pdbidsList.addElement(vPdbids);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vPdbids
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addPdbids(
-            final int index,
-            final jalview.schemabinding.version2.Pdbids vPdbids)
-    throws java.lang.IndexOutOfBoundsException {
-        this._pdbidsList.add(index, vPdbids);
-    }
-
-    /**
-     */
-    public void deleteColour(
-    ) {
-        this._has_colour= false;
-    }
-
-    /**
-     */
-    public void deleteEnd(
-    ) {
-        this._has_end= false;
-    }
-
-    /**
-     */
-    public void deleteHidden(
-    ) {
-        this._has_hidden= false;
-    }
-
-    /**
-     */
-    public void deleteStart(
-    ) {
-        this._has_start= false;
-    }
-
-    /**
-     * Method enumerateFeatures.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.Features elements
-     */
-    public java.util.Enumeration enumerateFeatures(
-    ) {
-        return this._featuresList.elements();
-    }
-
-    /**
-     * Method enumerateHiddenSequences.
-     * 
-     * @return an Enumeration over all int elements
-     */
-    public java.util.Enumeration enumerateHiddenSequences(
-    ) {
-        return this._hiddenSequencesList.elements();
-    }
-
-    /**
-     * Method enumeratePdbids.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.Pdbids elements
-     */
-    public java.util.Enumeration enumeratePdbids(
-    ) {
-        return this._pdbidsList.elements();
-    }
-
-    /**
-     * Returns the value of field 'colour'.
-     * 
-     * @return the value of field 'Colour'.
-     */
-    public int getColour(
-    ) {
-        return this._colour;
-    }
-
-    /**
-     * Returns the value of field 'end'.
-     * 
-     * @return the value of field 'End'.
-     */
-    public int getEnd(
-    ) {
-        return this._end;
-    }
-
-    /**
-     * Method getFeatures.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.Features at the given index
-     */
-    public jalview.schemabinding.version2.Features getFeatures(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._featuresList.size()) {
-            throw new IndexOutOfBoundsException("getFeatures: Index value '" + index + "' not in range [0.." + (this._featuresList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.Features) _featuresList.get(index);
-    }
-
-    /**
-     * Method getFeatures.Returns the contents of the collection in
-     * an Array.  <p>Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we <i>know</i>
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.Features[] getFeatures(
-    ) {
-        jalview.schemabinding.version2.Features[] array = new jalview.schemabinding.version2.Features[0];
-        return (jalview.schemabinding.version2.Features[]) this._featuresList.toArray(array);
-    }
-
-    /**
-     * Method getFeaturesCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getFeaturesCount(
-    ) {
-        return this._featuresList.size();
-    }
-
-    /**
-     * Returns the value of field 'hidden'.
-     * 
-     * @return the value of field 'Hidden'.
-     */
-    public boolean getHidden(
-    ) {
-        return this._hidden;
-    }
-
-    /**
-     * Method getHiddenSequences.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the int at the given index
-     */
-    public int getHiddenSequences(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._hiddenSequencesList.size()) {
-            throw new IndexOutOfBoundsException("getHiddenSequences: Index value '" + index + "' not in range [0.." + (this._hiddenSequencesList.size() - 1) + "]");
-        }
-        
-        return ((java.lang.Integer) _hiddenSequencesList.get(index)).intValue();
-    }
-
-    /**
-     * Method getHiddenSequences.Returns the contents of the
-     * collection in an Array.  
-     * 
-     * @return this collection as an Array
-     */
-    public int[] getHiddenSequences(
-    ) {
-        int size = this._hiddenSequencesList.size();
-        int[] array = new int[size];
-        java.util.Iterator iter = _hiddenSequencesList.iterator();
-        for (int index = 0; index < size; index++) {
-            array[index] = ((java.lang.Integer) iter.next()).intValue();
-        }
-        return array;
-    }
-
-    /**
-     * Method getHiddenSequencesCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getHiddenSequencesCount(
-    ) {
-        return this._hiddenSequencesList.size();
-    }
-
-    /**
-     * Returns the value of field 'id'.
-     * 
-     * @return the value of field 'Id'.
-     */
-    public java.lang.String getId(
-    ) {
-        return this._id;
-    }
-
-    /**
-     * Method getPdbids.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.Pdbids at the given index
-     */
-    public jalview.schemabinding.version2.Pdbids getPdbids(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._pdbidsList.size()) {
-            throw new IndexOutOfBoundsException("getPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.Pdbids) _pdbidsList.get(index);
-    }
-
-    /**
-     * Method getPdbids.Returns the contents of the collection in
-     * an Array.  <p>Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we <i>know</i>
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.Pdbids[] getPdbids(
-    ) {
-        jalview.schemabinding.version2.Pdbids[] array = new jalview.schemabinding.version2.Pdbids[0];
-        return (jalview.schemabinding.version2.Pdbids[]) this._pdbidsList.toArray(array);
-    }
-
-    /**
-     * Method getPdbidsCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getPdbidsCount(
-    ) {
-        return this._pdbidsList.size();
-    }
-
-    /**
-     * Returns the value of field 'start'.
-     * 
-     * @return the value of field 'Start'.
-     */
-    public int getStart(
-    ) {
-        return this._start;
-    }
-
-    /**
-     * Method hasColour.
-     * 
-     * @return true if at least one Colour has been added
-     */
-    public boolean hasColour(
-    ) {
-        return this._has_colour;
-    }
-
-    /**
-     * Method hasEnd.
-     * 
-     * @return true if at least one End has been added
-     */
-    public boolean hasEnd(
-    ) {
-        return this._has_end;
-    }
-
-    /**
-     * Method hasHidden.
-     * 
-     * @return true if at least one Hidden has been added
-     */
-    public boolean hasHidden(
-    ) {
-        return this._has_hidden;
-    }
-
-    /**
-     * Method hasStart.
-     * 
-     * @return true if at least one Start has been added
-     */
-    public boolean hasStart(
-    ) {
-        return this._has_start;
-    }
-
-    /**
-     * Returns the value of field 'hidden'.
-     * 
-     * @return the value of field 'Hidden'.
-     */
-    public boolean isHidden(
-    ) {
-        return this._hidden;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     */
-    public void removeAllFeatures(
-    ) {
-        this._featuresList.clear();
-    }
-
-    /**
-     */
-    public void removeAllHiddenSequences(
-    ) {
-        this._hiddenSequencesList.clear();
-    }
-
-    /**
-     */
-    public void removeAllPdbids(
-    ) {
-        this._pdbidsList.clear();
-    }
-
-    /**
-     * Method removeFeatures.
-     * 
-     * @param vFeatures
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeFeatures(
-            final jalview.schemabinding.version2.Features vFeatures) {
-        boolean removed = _featuresList.remove(vFeatures);
-        return removed;
-    }
-
-    /**
-     * Method removeFeaturesAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.Features removeFeaturesAt(
-            final int index) {
-        java.lang.Object obj = this._featuresList.remove(index);
-        return (jalview.schemabinding.version2.Features) obj;
-    }
-
-    /**
-     * Method removeHiddenSequences.
-     * 
-     * @param vHiddenSequences
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeHiddenSequences(
-            final int vHiddenSequences) {
-        boolean removed = _hiddenSequencesList.remove(new java.lang.Integer(vHiddenSequences));
-        return removed;
-    }
-
-    /**
-     * Method removeHiddenSequencesAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public int removeHiddenSequencesAt(
-            final int index) {
-        java.lang.Object obj = this._hiddenSequencesList.remove(index);
-        return ((java.lang.Integer) obj).intValue();
-    }
-
-    /**
-     * Method removePdbids.
-     * 
-     * @param vPdbids
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removePdbids(
-            final jalview.schemabinding.version2.Pdbids vPdbids) {
-        boolean removed = _pdbidsList.remove(vPdbids);
-        return removed;
-    }
-
-    /**
-     * Method removePdbidsAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.Pdbids removePdbidsAt(
-            final int index) {
-        java.lang.Object obj = this._pdbidsList.remove(index);
-        return (jalview.schemabinding.version2.Pdbids) obj;
-    }
-
-    /**
-     * Sets the value of field 'colour'.
-     * 
-     * @param colour the value of field 'colour'.
-     */
-    public void setColour(
-            final int colour) {
-        this._colour = colour;
-        this._has_colour = true;
-    }
-
-    /**
-     * Sets the value of field 'end'.
-     * 
-     * @param end the value of field 'end'.
-     */
-    public void setEnd(
-            final int end) {
-        this._end = end;
-        this._has_end = true;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vFeatures
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setFeatures(
-            final int index,
-            final jalview.schemabinding.version2.Features vFeatures)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._featuresList.size()) {
-            throw new IndexOutOfBoundsException("setFeatures: Index value '" + index + "' not in range [0.." + (this._featuresList.size() - 1) + "]");
-        }
-        
-        this._featuresList.set(index, vFeatures);
-    }
-
-    /**
-     * 
-     * 
-     * @param vFeaturesArray
-     */
-    public void setFeatures(
-            final jalview.schemabinding.version2.Features[] vFeaturesArray) {
-        //-- copy array
-        _featuresList.clear();
-        
-        for (int i = 0; i < vFeaturesArray.length; i++) {
-                this._featuresList.add(vFeaturesArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of field 'hidden'.
-     * 
-     * @param hidden the value of field 'hidden'.
-     */
-    public void setHidden(
-            final boolean hidden) {
-        this._hidden = hidden;
-        this._has_hidden = true;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vHiddenSequences
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setHiddenSequences(
-            final int index,
-            final int vHiddenSequences)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._hiddenSequencesList.size()) {
-            throw new IndexOutOfBoundsException("setHiddenSequences: Index value '" + index + "' not in range [0.." + (this._hiddenSequencesList.size() - 1) + "]");
-        }
-        
-        this._hiddenSequencesList.set(index, new java.lang.Integer(vHiddenSequences));
-    }
-
-    /**
-     * 
-     * 
-     * @param vHiddenSequencesArray
-     */
-    public void setHiddenSequences(
-            final int[] vHiddenSequencesArray) {
-        //-- copy array
-        _hiddenSequencesList.clear();
-        
-        for (int i = 0; i < vHiddenSequencesArray.length; i++) {
-                this._hiddenSequencesList.add(new java.lang.Integer(vHiddenSequencesArray[i]));
-        }
-    }
-
-    /**
-     * Sets the value of field 'id'.
-     * 
-     * @param id the value of field 'id'.
-     */
-    public void setId(
-            final java.lang.String id) {
-        this._id = id;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vPdbids
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setPdbids(
-            final int index,
-            final jalview.schemabinding.version2.Pdbids vPdbids)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._pdbidsList.size()) {
-            throw new IndexOutOfBoundsException("setPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]");
-        }
-        
-        this._pdbidsList.set(index, vPdbids);
-    }
-
-    /**
-     * 
-     * 
-     * @param vPdbidsArray
-     */
-    public void setPdbids(
-            final jalview.schemabinding.version2.Pdbids[] vPdbidsArray) {
-        //-- copy array
-        _pdbidsList.clear();
-        
-        for (int i = 0; i < vPdbidsArray.length; i++) {
-                this._pdbidsList.add(vPdbidsArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of field 'start'.
-     * 
-     * @param start the value of field 'start'.
-     */
-    public void setStart(
-            final int start) {
-        this._start = start;
-        this._has_start = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.schemabinding.version2.JSeq
-     */
-    public static jalview.schemabinding.version2.JSeq unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.JSeq) Unmarshaller.unmarshal(jalview.schemabinding.version2.JSeq.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+public class JSeq implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _colour.
+   */
+  private int _colour;
+
+  /**
+   * keeps track of state for field: _colour
+   */
+  private boolean _has_colour;
+
+  /**
+   * Field _start.
+   */
+  private int _start;
+
+  /**
+   * keeps track of state for field: _start
+   */
+  private boolean _has_start;
+
+  /**
+   * Field _end.
+   */
+  private int _end;
+
+  /**
+   * keeps track of state for field: _end
+   */
+  private boolean _has_end;
+
+  /**
+   * Field _id.
+   */
+  private java.lang.String _id;
+
+  /**
+   * Field _hidden.
+   */
+  private boolean _hidden;
+
+  /**
+   * keeps track of state for field: _hidden
+   */
+  private boolean _has_hidden;
+
+  /**
+   * Field _featuresList.
+   */
+  private java.util.Vector _featuresList;
+
+  /**
+   * Field _pdbidsList.
+   */
+  private java.util.Vector _pdbidsList;
+
+  /**
+   * Field _hiddenSequencesList.
+   */
+  private java.util.Vector _hiddenSequencesList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public JSeq()
+  {
+    super();
+    this._featuresList = new java.util.Vector();
+    this._pdbidsList = new java.util.Vector();
+    this._hiddenSequencesList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vFeatures
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addFeatures(
+          final jalview.schemabinding.version2.Features vFeatures)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._featuresList.addElement(vFeatures);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vFeatures
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addFeatures(final int index,
+          final jalview.schemabinding.version2.Features vFeatures)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._featuresList.add(index, vFeatures);
+  }
+
+  /**
+   * 
+   * 
+   * @param vHiddenSequences
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addHiddenSequences(final int vHiddenSequences)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._hiddenSequencesList.addElement(new java.lang.Integer(
+            vHiddenSequences));
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vHiddenSequences
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addHiddenSequences(final int index, final int vHiddenSequences)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._hiddenSequencesList.add(index, new java.lang.Integer(
+            vHiddenSequences));
+  }
+
+  /**
+   * 
+   * 
+   * @param vPdbids
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addPdbids(final jalview.schemabinding.version2.Pdbids vPdbids)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._pdbidsList.addElement(vPdbids);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vPdbids
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addPdbids(final int index,
+          final jalview.schemabinding.version2.Pdbids vPdbids)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._pdbidsList.add(index, vPdbids);
+  }
+
+  /**
+   */
+  public void deleteColour()
+  {
+    this._has_colour = false;
+  }
+
+  /**
+   */
+  public void deleteEnd()
+  {
+    this._has_end = false;
+  }
+
+  /**
+   */
+  public void deleteHidden()
+  {
+    this._has_hidden = false;
+  }
+
+  /**
+   */
+  public void deleteStart()
+  {
+    this._has_start = false;
+  }
+
+  /**
+   * Method enumerateFeatures.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.Features
+   *         elements
+   */
+  public java.util.Enumeration enumerateFeatures()
+  {
+    return this._featuresList.elements();
+  }
+
+  /**
+   * Method enumerateHiddenSequences.
+   * 
+   * @return an Enumeration over all int elements
+   */
+  public java.util.Enumeration enumerateHiddenSequences()
+  {
+    return this._hiddenSequencesList.elements();
+  }
+
+  /**
+   * Method enumeratePdbids.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.Pdbids
+   *         elements
+   */
+  public java.util.Enumeration enumeratePdbids()
+  {
+    return this._pdbidsList.elements();
+  }
+
+  /**
+   * Returns the value of field 'colour'.
+   * 
+   * @return the value of field 'Colour'.
+   */
+  public int getColour()
+  {
+    return this._colour;
+  }
+
+  /**
+   * Returns the value of field 'end'.
+   * 
+   * @return the value of field 'End'.
+   */
+  public int getEnd()
+  {
+    return this._end;
+  }
+
+  /**
+   * Method getFeatures.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.Features at the
+   *         given index
+   */
+  public jalview.schemabinding.version2.Features getFeatures(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._featuresList.size())
+    {
+      throw new IndexOutOfBoundsException("getFeatures: Index value '"
+              + index + "' not in range [0.."
+              + (this._featuresList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.Features) _featuresList
+            .get(index);
+  }
+
+  /**
+   * Method getFeatures.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.Features[] getFeatures()
+  {
+    jalview.schemabinding.version2.Features[] array = new jalview.schemabinding.version2.Features[0];
+    return (jalview.schemabinding.version2.Features[]) this._featuresList
+            .toArray(array);
+  }
+
+  /**
+   * Method getFeaturesCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getFeaturesCount()
+  {
+    return this._featuresList.size();
+  }
+
+  /**
+   * Returns the value of field 'hidden'.
+   * 
+   * @return the value of field 'Hidden'.
+   */
+  public boolean getHidden()
+  {
+    return this._hidden;
+  }
+
+  /**
+   * Method getHiddenSequences.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the int at the given index
+   */
+  public int getHiddenSequences(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._hiddenSequencesList.size())
+    {
+      throw new IndexOutOfBoundsException(
+              "getHiddenSequences: Index value '" + index
+                      + "' not in range [0.."
+                      + (this._hiddenSequencesList.size() - 1) + "]");
+    }
+
+    return ((java.lang.Integer) _hiddenSequencesList.get(index)).intValue();
+  }
+
+  /**
+   * Method getHiddenSequences.Returns the contents of the collection in an
+   * Array.
+   * 
+   * @return this collection as an Array
+   */
+  public int[] getHiddenSequences()
+  {
+    int size = this._hiddenSequencesList.size();
+    int[] array = new int[size];
+    java.util.Iterator iter = _hiddenSequencesList.iterator();
+    for (int index = 0; index < size; index++)
+    {
+      array[index] = ((java.lang.Integer) iter.next()).intValue();
+    }
+    return array;
+  }
+
+  /**
+   * Method getHiddenSequencesCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getHiddenSequencesCount()
+  {
+    return this._hiddenSequencesList.size();
+  }
+
+  /**
+   * Returns the value of field 'id'.
+   * 
+   * @return the value of field 'Id'.
+   */
+  public java.lang.String getId()
+  {
+    return this._id;
+  }
+
+  /**
+   * Method getPdbids.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.Pdbids at the given
+   *         index
+   */
+  public jalview.schemabinding.version2.Pdbids getPdbids(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._pdbidsList.size())
+    {
+      throw new IndexOutOfBoundsException("getPdbids: Index value '"
+              + index + "' not in range [0.."
+              + (this._pdbidsList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.Pdbids) _pdbidsList.get(index);
+  }
+
+  /**
+   * Method getPdbids.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.Pdbids[] getPdbids()
+  {
+    jalview.schemabinding.version2.Pdbids[] array = new jalview.schemabinding.version2.Pdbids[0];
+    return (jalview.schemabinding.version2.Pdbids[]) this._pdbidsList
+            .toArray(array);
+  }
+
+  /**
+   * Method getPdbidsCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getPdbidsCount()
+  {
+    return this._pdbidsList.size();
+  }
+
+  /**
+   * Returns the value of field 'start'.
+   * 
+   * @return the value of field 'Start'.
+   */
+  public int getStart()
+  {
+    return this._start;
+  }
+
+  /**
+   * Method hasColour.
+   * 
+   * @return true if at least one Colour has been added
+   */
+  public boolean hasColour()
+  {
+    return this._has_colour;
+  }
+
+  /**
+   * Method hasEnd.
+   * 
+   * @return true if at least one End has been added
+   */
+  public boolean hasEnd()
+  {
+    return this._has_end;
+  }
+
+  /**
+   * Method hasHidden.
+   * 
+   * @return true if at least one Hidden has been added
+   */
+  public boolean hasHidden()
+  {
+    return this._has_hidden;
+  }
+
+  /**
+   * Method hasStart.
+   * 
+   * @return true if at least one Start has been added
+   */
+  public boolean hasStart()
+  {
+    return this._has_start;
+  }
+
+  /**
+   * Returns the value of field 'hidden'.
+   * 
+   * @return the value of field 'Hidden'.
+   */
+  public boolean isHidden()
+  {
+    return this._hidden;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   */
+  public void removeAllFeatures()
+  {
+    this._featuresList.clear();
+  }
+
+  /**
+   */
+  public void removeAllHiddenSequences()
+  {
+    this._hiddenSequencesList.clear();
+  }
+
+  /**
+   */
+  public void removeAllPdbids()
+  {
+    this._pdbidsList.clear();
+  }
+
+  /**
+   * Method removeFeatures.
+   * 
+   * @param vFeatures
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeFeatures(
+          final jalview.schemabinding.version2.Features vFeatures)
+  {
+    boolean removed = _featuresList.remove(vFeatures);
+    return removed;
+  }
+
+  /**
+   * Method removeFeaturesAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.Features removeFeaturesAt(
+          final int index)
+  {
+    java.lang.Object obj = this._featuresList.remove(index);
+    return (jalview.schemabinding.version2.Features) obj;
+  }
+
+  /**
+   * Method removeHiddenSequences.
+   * 
+   * @param vHiddenSequences
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeHiddenSequences(final int vHiddenSequences)
+  {
+    boolean removed = _hiddenSequencesList.remove(new java.lang.Integer(
+            vHiddenSequences));
+    return removed;
+  }
+
+  /**
+   * Method removeHiddenSequencesAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public int removeHiddenSequencesAt(final int index)
+  {
+    java.lang.Object obj = this._hiddenSequencesList.remove(index);
+    return ((java.lang.Integer) obj).intValue();
+  }
+
+  /**
+   * Method removePdbids.
+   * 
+   * @param vPdbids
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removePdbids(
+          final jalview.schemabinding.version2.Pdbids vPdbids)
+  {
+    boolean removed = _pdbidsList.remove(vPdbids);
+    return removed;
+  }
+
+  /**
+   * Method removePdbidsAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.Pdbids removePdbidsAt(
+          final int index)
+  {
+    java.lang.Object obj = this._pdbidsList.remove(index);
+    return (jalview.schemabinding.version2.Pdbids) obj;
+  }
+
+  /**
+   * Sets the value of field 'colour'.
+   * 
+   * @param colour
+   *                the value of field 'colour'.
+   */
+  public void setColour(final int colour)
+  {
+    this._colour = colour;
+    this._has_colour = true;
+  }
+
+  /**
+   * Sets the value of field 'end'.
+   * 
+   * @param end
+   *                the value of field 'end'.
+   */
+  public void setEnd(final int end)
+  {
+    this._end = end;
+    this._has_end = true;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vFeatures
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setFeatures(final int index,
+          final jalview.schemabinding.version2.Features vFeatures)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._featuresList.size())
+    {
+      throw new IndexOutOfBoundsException("setFeatures: Index value '"
+              + index + "' not in range [0.."
+              + (this._featuresList.size() - 1) + "]");
+    }
+
+    this._featuresList.set(index, vFeatures);
+  }
+
+  /**
+   * 
+   * 
+   * @param vFeaturesArray
+   */
+  public void setFeatures(
+          final jalview.schemabinding.version2.Features[] vFeaturesArray)
+  {
+    // -- copy array
+    _featuresList.clear();
+
+    for (int i = 0; i < vFeaturesArray.length; i++)
+    {
+      this._featuresList.add(vFeaturesArray[i]);
+    }
+  }
+
+  /**
+   * Sets the value of field 'hidden'.
+   * 
+   * @param hidden
+   *                the value of field 'hidden'.
+   */
+  public void setHidden(final boolean hidden)
+  {
+    this._hidden = hidden;
+    this._has_hidden = true;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vHiddenSequences
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setHiddenSequences(final int index, final int vHiddenSequences)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._hiddenSequencesList.size())
+    {
+      throw new IndexOutOfBoundsException(
+              "setHiddenSequences: Index value '" + index
+                      + "' not in range [0.."
+                      + (this._hiddenSequencesList.size() - 1) + "]");
+    }
+
+    this._hiddenSequencesList.set(index, new java.lang.Integer(
+            vHiddenSequences));
+  }
+
+  /**
+   * 
+   * 
+   * @param vHiddenSequencesArray
+   */
+  public void setHiddenSequences(final int[] vHiddenSequencesArray)
+  {
+    // -- copy array
+    _hiddenSequencesList.clear();
+
+    for (int i = 0; i < vHiddenSequencesArray.length; i++)
+    {
+      this._hiddenSequencesList.add(new java.lang.Integer(
+              vHiddenSequencesArray[i]));
+    }
+  }
+
+  /**
+   * Sets the value of field 'id'.
+   * 
+   * @param id
+   *                the value of field 'id'.
+   */
+  public void setId(final java.lang.String id)
+  {
+    this._id = id;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vPdbids
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setPdbids(final int index,
+          final jalview.schemabinding.version2.Pdbids vPdbids)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._pdbidsList.size())
+    {
+      throw new IndexOutOfBoundsException("setPdbids: Index value '"
+              + index + "' not in range [0.."
+              + (this._pdbidsList.size() - 1) + "]");
+    }
+
+    this._pdbidsList.set(index, vPdbids);
+  }
+
+  /**
+   * 
+   * 
+   * @param vPdbidsArray
+   */
+  public void setPdbids(
+          final jalview.schemabinding.version2.Pdbids[] vPdbidsArray)
+  {
+    // -- copy array
+    _pdbidsList.clear();
+
+    for (int i = 0; i < vPdbidsArray.length; i++)
+    {
+      this._pdbidsList.add(vPdbidsArray[i]);
+    }
+  }
+
+  /**
+   * Sets the value of field 'start'.
+   * 
+   * @param start
+   *                the value of field 'start'.
+   */
+  public void setStart(final int start)
+  {
+    this._start = start;
+    this._has_start = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.JSeq
+   */
+  public static jalview.schemabinding.version2.JSeq unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.JSeq) Unmarshaller.unmarshal(
+            jalview.schemabinding.version2.JSeq.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/JalviewModel.java b/src/jalview/schemabinding/version2/JalviewModel.java
index f7e049a..9c7fead 100755
--- a/src/jalview/schemabinding/version2/JalviewModel.java
+++ b/src/jalview/schemabinding/version2/JalviewModel.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,203 +30,221 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class JalviewModel implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _creationDate.
-     */
-    private java.util.Date _creationDate;
-
-    /**
-     * Field _version.
-     */
-    private java.lang.String _version;
-
-    /**
-     * Field _vamsasModel.
-     */
-    private jalview.schemabinding.version2.VamsasModel _vamsasModel;
-
-    /**
-     * Field _jalviewModelSequence.
-     */
-    private jalview.schemabinding.version2.JalviewModelSequence _jalviewModelSequence;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JalviewModel() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'creationDate'.
-     * 
-     * @return the value of field 'CreationDate'.
-     */
-    public java.util.Date getCreationDate(
-    ) {
-        return this._creationDate;
-    }
-
-    /**
-     * Returns the value of field 'jalviewModelSequence'.
-     * 
-     * @return the value of field 'JalviewModelSequence'.
-     */
-    public jalview.schemabinding.version2.JalviewModelSequence getJalviewModelSequence(
-    ) {
-        return this._jalviewModelSequence;
-    }
-
-    /**
-     * Returns the value of field 'vamsasModel'.
-     * 
-     * @return the value of field 'VamsasModel'.
-     */
-    public jalview.schemabinding.version2.VamsasModel getVamsasModel(
-    ) {
-        return this._vamsasModel;
-    }
-
-    /**
-     * Returns the value of field 'version'.
-     * 
-     * @return the value of field 'Version'.
-     */
-    public java.lang.String getVersion(
-    ) {
-        return this._version;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'creationDate'.
-     * 
-     * @param creationDate the value of field 'creationDate'.
-     */
-    public void setCreationDate(
-            final java.util.Date creationDate) {
-        this._creationDate = creationDate;
-    }
-
-    /**
-     * Sets the value of field 'jalviewModelSequence'.
-     * 
-     * @param jalviewModelSequence the value of field
-     * 'jalviewModelSequence'.
-     */
-    public void setJalviewModelSequence(
-            final jalview.schemabinding.version2.JalviewModelSequence jalviewModelSequence) {
-        this._jalviewModelSequence = jalviewModelSequence;
-    }
-
-    /**
-     * Sets the value of field 'vamsasModel'.
-     * 
-     * @param vamsasModel the value of field 'vamsasModel'.
-     */
-    public void setVamsasModel(
-            final jalview.schemabinding.version2.VamsasModel vamsasModel) {
-        this._vamsasModel = vamsasModel;
-    }
-
-    /**
-     * Sets the value of field 'version'.
-     * 
-     * @param version the value of field 'version'.
-     */
-    public void setVersion(
-            final java.lang.String version) {
-        this._version = version;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.JalviewModel
-     */
-    public static jalview.schemabinding.version2.JalviewModel unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.JalviewModel) Unmarshaller.unmarshal(jalview.schemabinding.version2.JalviewModel.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class JalviewModel implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _creationDate.
+   */
+  private java.util.Date _creationDate;
+
+  /**
+   * Field _version.
+   */
+  private java.lang.String _version;
+
+  /**
+   * Field _vamsasModel.
+   */
+  private jalview.schemabinding.version2.VamsasModel _vamsasModel;
+
+  /**
+   * Field _jalviewModelSequence.
+   */
+  private jalview.schemabinding.version2.JalviewModelSequence _jalviewModelSequence;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public JalviewModel()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Returns the value of field 'creationDate'.
+   * 
+   * @return the value of field 'CreationDate'.
+   */
+  public java.util.Date getCreationDate()
+  {
+    return this._creationDate;
+  }
+
+  /**
+   * Returns the value of field 'jalviewModelSequence'.
+   * 
+   * @return the value of field 'JalviewModelSequence'.
+   */
+  public jalview.schemabinding.version2.JalviewModelSequence getJalviewModelSequence()
+  {
+    return this._jalviewModelSequence;
+  }
+
+  /**
+   * Returns the value of field 'vamsasModel'.
+   * 
+   * @return the value of field 'VamsasModel'.
+   */
+  public jalview.schemabinding.version2.VamsasModel getVamsasModel()
+  {
+    return this._vamsasModel;
+  }
+
+  /**
+   * Returns the value of field 'version'.
+   * 
+   * @return the value of field 'Version'.
+   */
+  public java.lang.String getVersion()
+  {
+    return this._version;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'creationDate'.
+   * 
+   * @param creationDate
+   *                the value of field 'creationDate'.
+   */
+  public void setCreationDate(final java.util.Date creationDate)
+  {
+    this._creationDate = creationDate;
+  }
+
+  /**
+   * Sets the value of field 'jalviewModelSequence'.
+   * 
+   * @param jalviewModelSequence
+   *                the value of field 'jalviewModelSequence'.
+   */
+  public void setJalviewModelSequence(
+          final jalview.schemabinding.version2.JalviewModelSequence jalviewModelSequence)
+  {
+    this._jalviewModelSequence = jalviewModelSequence;
+  }
+
+  /**
+   * Sets the value of field 'vamsasModel'.
+   * 
+   * @param vamsasModel
+   *                the value of field 'vamsasModel'.
+   */
+  public void setVamsasModel(
+          final jalview.schemabinding.version2.VamsasModel vamsasModel)
+  {
+    this._vamsasModel = vamsasModel;
+  }
+
+  /**
+   * Sets the value of field 'version'.
+   * 
+   * @param version
+   *                the value of field 'version'.
+   */
+  public void setVersion(final java.lang.String version)
+  {
+    this._version = version;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.JalviewModel
+   */
+  public static jalview.schemabinding.version2.JalviewModel unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.JalviewModel) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.JalviewModel.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/JalviewModelSequence.java b/src/jalview/schemabinding/version2/JalviewModelSequence.java
index cb66b37..8d5cda1 100755
--- a/src/jalview/schemabinding/version2/JalviewModelSequence.java
+++ b/src/jalview/schemabinding/version2/JalviewModelSequence.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,907 +30,972 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class JalviewModelSequence implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _JSeqList.
-     */
-    private java.util.Vector _JSeqList;
-
-    /**
-     * Field _JGroupList.
-     */
-    private java.util.Vector _JGroupList;
-
-    /**
-     * Field _viewportList.
-     */
-    private java.util.Vector _viewportList;
-
-    /**
-     * Field _userColoursList.
-     */
-    private java.util.Vector _userColoursList;
-
-    /**
-     * Field _treeList.
-     */
-    private java.util.Vector _treeList;
-
-    /**
-     * Field _featureSettings.
-     */
-    private jalview.schemabinding.version2.FeatureSettings _featureSettings;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JalviewModelSequence() {
-        super();
-        this._JSeqList = new java.util.Vector();
-        this._JGroupList = new java.util.Vector();
-        this._viewportList = new java.util.Vector();
-        this._userColoursList = new java.util.Vector();
-        this._treeList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vJGroup
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addJGroup(
-            final jalview.schemabinding.version2.JGroup vJGroup)
-    throws java.lang.IndexOutOfBoundsException {
-        this._JGroupList.addElement(vJGroup);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vJGroup
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addJGroup(
-            final int index,
-            final jalview.schemabinding.version2.JGroup vJGroup)
-    throws java.lang.IndexOutOfBoundsException {
-        this._JGroupList.add(index, vJGroup);
-    }
-
-    /**
-     * 
-     * 
-     * @param vJSeq
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addJSeq(
-            final jalview.schemabinding.version2.JSeq vJSeq)
-    throws java.lang.IndexOutOfBoundsException {
-        this._JSeqList.addElement(vJSeq);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vJSeq
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addJSeq(
-            final int index,
-            final jalview.schemabinding.version2.JSeq vJSeq)
-    throws java.lang.IndexOutOfBoundsException {
-        this._JSeqList.add(index, vJSeq);
-    }
-
-    /**
-     * 
-     * 
-     * @param vTree
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addTree(
-            final jalview.schemabinding.version2.Tree vTree)
-    throws java.lang.IndexOutOfBoundsException {
-        this._treeList.addElement(vTree);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vTree
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addTree(
-            final int index,
-            final jalview.schemabinding.version2.Tree vTree)
-    throws java.lang.IndexOutOfBoundsException {
-        this._treeList.add(index, vTree);
-    }
-
-    /**
-     * 
-     * 
-     * @param vUserColours
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addUserColours(
-            final jalview.schemabinding.version2.UserColours vUserColours)
-    throws java.lang.IndexOutOfBoundsException {
-        this._userColoursList.addElement(vUserColours);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vUserColours
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addUserColours(
-            final int index,
-            final jalview.schemabinding.version2.UserColours vUserColours)
-    throws java.lang.IndexOutOfBoundsException {
-        this._userColoursList.add(index, vUserColours);
-    }
-
-    /**
-     * 
-     * 
-     * @param vViewport
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addViewport(
-            final jalview.schemabinding.version2.Viewport vViewport)
-    throws java.lang.IndexOutOfBoundsException {
-        this._viewportList.addElement(vViewport);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vViewport
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addViewport(
-            final int index,
-            final jalview.schemabinding.version2.Viewport vViewport)
-    throws java.lang.IndexOutOfBoundsException {
-        this._viewportList.add(index, vViewport);
-    }
-
-    /**
-     * Method enumerateJGroup.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.JGroup elements
-     */
-    public java.util.Enumeration enumerateJGroup(
-    ) {
-        return this._JGroupList.elements();
-    }
-
-    /**
-     * Method enumerateJSeq.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.JSeq elements
-     */
-    public java.util.Enumeration enumerateJSeq(
-    ) {
-        return this._JSeqList.elements();
-    }
-
-    /**
-     * Method enumerateTree.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.Tree elements
-     */
-    public java.util.Enumeration enumerateTree(
-    ) {
-        return this._treeList.elements();
-    }
-
-    /**
-     * Method enumerateUserColours.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.UserColours elements
-     */
-    public java.util.Enumeration enumerateUserColours(
-    ) {
-        return this._userColoursList.elements();
-    }
-
-    /**
-     * Method enumerateViewport.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.Viewport elements
-     */
-    public java.util.Enumeration enumerateViewport(
-    ) {
-        return this._viewportList.elements();
-    }
-
-    /**
-     * Returns the value of field 'featureSettings'.
-     * 
-     * @return the value of field 'FeatureSettings'.
-     */
-    public jalview.schemabinding.version2.FeatureSettings getFeatureSettings(
-    ) {
-        return this._featureSettings;
-    }
-
-    /**
-     * Method getJGroup.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.JGroup at the given index
-     */
-    public jalview.schemabinding.version2.JGroup getJGroup(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._JGroupList.size()) {
-            throw new IndexOutOfBoundsException("getJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.JGroup) _JGroupList.get(index);
-    }
-
-    /**
-     * Method getJGroup.Returns the contents of the collection in
-     * an Array.  <p>Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we <i>know</i>
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.JGroup[] getJGroup(
-    ) {
-        jalview.schemabinding.version2.JGroup[] array = new jalview.schemabinding.version2.JGroup[0];
-        return (jalview.schemabinding.version2.JGroup[]) this._JGroupList.toArray(array);
-    }
-
-    /**
-     * Method getJGroupCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getJGroupCount(
-    ) {
-        return this._JGroupList.size();
-    }
-
-    /**
-     * Method getJSeq.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the jalview.schemabinding.version2.JSeq
-     * at the given index
-     */
-    public jalview.schemabinding.version2.JSeq getJSeq(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._JSeqList.size()) {
-            throw new IndexOutOfBoundsException("getJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.JSeq) _JSeqList.get(index);
-    }
-
-    /**
-     * Method getJSeq.Returns the contents of the collection in an
-     * Array.  <p>Note:  Just in case the collection contents are
-     * changing in another thread, we pass a 0-length Array of the
-     * correct type into the API call.  This way we <i>know</i>
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.JSeq[] getJSeq(
-    ) {
-        jalview.schemabinding.version2.JSeq[] array = new jalview.schemabinding.version2.JSeq[0];
-        return (jalview.schemabinding.version2.JSeq[]) this._JSeqList.toArray(array);
-    }
-
-    /**
-     * Method getJSeqCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getJSeqCount(
-    ) {
-        return this._JSeqList.size();
-    }
-
-    /**
-     * Method getTree.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the jalview.schemabinding.version2.Tree
-     * at the given index
-     */
-    public jalview.schemabinding.version2.Tree getTree(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._treeList.size()) {
-            throw new IndexOutOfBoundsException("getTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.Tree) _treeList.get(index);
-    }
-
-    /**
-     * Method getTree.Returns the contents of the collection in an
-     * Array.  <p>Note:  Just in case the collection contents are
-     * changing in another thread, we pass a 0-length Array of the
-     * correct type into the API call.  This way we <i>know</i>
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.Tree[] getTree(
-    ) {
-        jalview.schemabinding.version2.Tree[] array = new jalview.schemabinding.version2.Tree[0];
-        return (jalview.schemabinding.version2.Tree[]) this._treeList.toArray(array);
-    }
-
-    /**
-     * Method getTreeCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getTreeCount(
-    ) {
-        return this._treeList.size();
-    }
-
-    /**
-     * Method getUserColours.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.UserColours at the given index
-     */
-    public jalview.schemabinding.version2.UserColours getUserColours(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._userColoursList.size()) {
-            throw new IndexOutOfBoundsException("getUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.UserColours) _userColoursList.get(index);
-    }
-
-    /**
-     * Method getUserColours.Returns the contents of the collection
-     * in an Array.  <p>Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we <i>know</i>
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.UserColours[] getUserColours(
-    ) {
-        jalview.schemabinding.version2.UserColours[] array = new jalview.schemabinding.version2.UserColours[0];
-        return (jalview.schemabinding.version2.UserColours[]) this._userColoursList.toArray(array);
-    }
-
-    /**
-     * Method getUserColoursCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getUserColoursCount(
-    ) {
-        return this._userColoursList.size();
-    }
-
-    /**
-     * Method getViewport.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.Viewport at the given index
-     */
-    public jalview.schemabinding.version2.Viewport getViewport(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._viewportList.size()) {
-            throw new IndexOutOfBoundsException("getViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.Viewport) _viewportList.get(index);
-    }
-
-    /**
-     * Method getViewport.Returns the contents of the collection in
-     * an Array.  <p>Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we <i>know</i>
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.Viewport[] getViewport(
-    ) {
-        jalview.schemabinding.version2.Viewport[] array = new jalview.schemabinding.version2.Viewport[0];
-        return (jalview.schemabinding.version2.Viewport[]) this._viewportList.toArray(array);
-    }
-
-    /**
-     * Method getViewportCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getViewportCount(
-    ) {
-        return this._viewportList.size();
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     */
-    public void removeAllJGroup(
-    ) {
-        this._JGroupList.clear();
-    }
-
-    /**
-     */
-    public void removeAllJSeq(
-    ) {
-        this._JSeqList.clear();
-    }
-
-    /**
-     */
-    public void removeAllTree(
-    ) {
-        this._treeList.clear();
-    }
-
-    /**
-     */
-    public void removeAllUserColours(
-    ) {
-        this._userColoursList.clear();
-    }
-
-    /**
-     */
-    public void removeAllViewport(
-    ) {
-        this._viewportList.clear();
-    }
-
-    /**
-     * Method removeJGroup.
-     * 
-     * @param vJGroup
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeJGroup(
-            final jalview.schemabinding.version2.JGroup vJGroup) {
-        boolean removed = _JGroupList.remove(vJGroup);
-        return removed;
-    }
-
-    /**
-     * Method removeJGroupAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.JGroup removeJGroupAt(
-            final int index) {
-        java.lang.Object obj = this._JGroupList.remove(index);
-        return (jalview.schemabinding.version2.JGroup) obj;
-    }
-
-    /**
-     * Method removeJSeq.
-     * 
-     * @param vJSeq
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeJSeq(
-            final jalview.schemabinding.version2.JSeq vJSeq) {
-        boolean removed = _JSeqList.remove(vJSeq);
-        return removed;
-    }
-
-    /**
-     * Method removeJSeqAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.JSeq removeJSeqAt(
-            final int index) {
-        java.lang.Object obj = this._JSeqList.remove(index);
-        return (jalview.schemabinding.version2.JSeq) obj;
-    }
-
-    /**
-     * Method removeTree.
-     * 
-     * @param vTree
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeTree(
-            final jalview.schemabinding.version2.Tree vTree) {
-        boolean removed = _treeList.remove(vTree);
-        return removed;
-    }
-
-    /**
-     * Method removeTreeAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.Tree removeTreeAt(
-            final int index) {
-        java.lang.Object obj = this._treeList.remove(index);
-        return (jalview.schemabinding.version2.Tree) obj;
-    }
-
-    /**
-     * Method removeUserColours.
-     * 
-     * @param vUserColours
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeUserColours(
-            final jalview.schemabinding.version2.UserColours vUserColours) {
-        boolean removed = _userColoursList.remove(vUserColours);
-        return removed;
-    }
-
-    /**
-     * Method removeUserColoursAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.UserColours removeUserColoursAt(
-            final int index) {
-        java.lang.Object obj = this._userColoursList.remove(index);
-        return (jalview.schemabinding.version2.UserColours) obj;
-    }
-
-    /**
-     * Method removeViewport.
-     * 
-     * @param vViewport
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeViewport(
-            final jalview.schemabinding.version2.Viewport vViewport) {
-        boolean removed = _viewportList.remove(vViewport);
-        return removed;
-    }
-
-    /**
-     * Method removeViewportAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.Viewport removeViewportAt(
-            final int index) {
-        java.lang.Object obj = this._viewportList.remove(index);
-        return (jalview.schemabinding.version2.Viewport) obj;
-    }
-
-    /**
-     * Sets the value of field 'featureSettings'.
-     * 
-     * @param featureSettings the value of field 'featureSettings'.
-     */
-    public void setFeatureSettings(
-            final jalview.schemabinding.version2.FeatureSettings featureSettings) {
-        this._featureSettings = featureSettings;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vJGroup
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setJGroup(
-            final int index,
-            final jalview.schemabinding.version2.JGroup vJGroup)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._JGroupList.size()) {
-            throw new IndexOutOfBoundsException("setJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]");
-        }
-        
-        this._JGroupList.set(index, vJGroup);
-    }
-
-    /**
-     * 
-     * 
-     * @param vJGroupArray
-     */
-    public void setJGroup(
-            final jalview.schemabinding.version2.JGroup[] vJGroupArray) {
-        //-- copy array
-        _JGroupList.clear();
-        
-        for (int i = 0; i < vJGroupArray.length; i++) {
-                this._JGroupList.add(vJGroupArray[i]);
-        }
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vJSeq
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setJSeq(
-            final int index,
-            final jalview.schemabinding.version2.JSeq vJSeq)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._JSeqList.size()) {
-            throw new IndexOutOfBoundsException("setJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
-        }
-        
-        this._JSeqList.set(index, vJSeq);
-    }
-
-    /**
-     * 
-     * 
-     * @param vJSeqArray
-     */
-    public void setJSeq(
-            final jalview.schemabinding.version2.JSeq[] vJSeqArray) {
-        //-- copy array
-        _JSeqList.clear();
-        
-        for (int i = 0; i < vJSeqArray.length; i++) {
-                this._JSeqList.add(vJSeqArray[i]);
-        }
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vTree
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setTree(
-            final int index,
-            final jalview.schemabinding.version2.Tree vTree)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._treeList.size()) {
-            throw new IndexOutOfBoundsException("setTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
-        }
-        
-        this._treeList.set(index, vTree);
-    }
-
-    /**
-     * 
-     * 
-     * @param vTreeArray
-     */
-    public void setTree(
-            final jalview.schemabinding.version2.Tree[] vTreeArray) {
-        //-- copy array
-        _treeList.clear();
-        
-        for (int i = 0; i < vTreeArray.length; i++) {
-                this._treeList.add(vTreeArray[i]);
-        }
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vUserColours
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setUserColours(
-            final int index,
-            final jalview.schemabinding.version2.UserColours vUserColours)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._userColoursList.size()) {
-            throw new IndexOutOfBoundsException("setUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]");
-        }
-        
-        this._userColoursList.set(index, vUserColours);
-    }
-
-    /**
-     * 
-     * 
-     * @param vUserColoursArray
-     */
-    public void setUserColours(
-            final jalview.schemabinding.version2.UserColours[] vUserColoursArray) {
-        //-- copy array
-        _userColoursList.clear();
-        
-        for (int i = 0; i < vUserColoursArray.length; i++) {
-                this._userColoursList.add(vUserColoursArray[i]);
-        }
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vViewport
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setViewport(
-            final int index,
-            final jalview.schemabinding.version2.Viewport vViewport)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._viewportList.size()) {
-            throw new IndexOutOfBoundsException("setViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]");
-        }
-        
-        this._viewportList.set(index, vViewport);
-    }
-
-    /**
-     * 
-     * 
-     * @param vViewportArray
-     */
-    public void setViewport(
-            final jalview.schemabinding.version2.Viewport[] vViewportArray) {
-        //-- copy array
-        _viewportList.clear();
-        
-        for (int i = 0; i < vViewportArray.length; i++) {
-                this._viewportList.add(vViewportArray[i]);
-        }
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.JalviewModelSequence
-     */
-    public static jalview.schemabinding.version2.JalviewModelSequence unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.JalviewModelSequence) Unmarshaller.unmarshal(jalview.schemabinding.version2.JalviewModelSequence.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+public class JalviewModelSequence implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _JSeqList.
+   */
+  private java.util.Vector _JSeqList;
+
+  /**
+   * Field _JGroupList.
+   */
+  private java.util.Vector _JGroupList;
+
+  /**
+   * Field _viewportList.
+   */
+  private java.util.Vector _viewportList;
+
+  /**
+   * Field _userColoursList.
+   */
+  private java.util.Vector _userColoursList;
+
+  /**
+   * Field _treeList.
+   */
+  private java.util.Vector _treeList;
+
+  /**
+   * Field _featureSettings.
+   */
+  private jalview.schemabinding.version2.FeatureSettings _featureSettings;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public JalviewModelSequence()
+  {
+    super();
+    this._JSeqList = new java.util.Vector();
+    this._JGroupList = new java.util.Vector();
+    this._viewportList = new java.util.Vector();
+    this._userColoursList = new java.util.Vector();
+    this._treeList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vJGroup
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addJGroup(final jalview.schemabinding.version2.JGroup vJGroup)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._JGroupList.addElement(vJGroup);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vJGroup
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addJGroup(final int index,
+          final jalview.schemabinding.version2.JGroup vJGroup)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._JGroupList.add(index, vJGroup);
+  }
+
+  /**
+   * 
+   * 
+   * @param vJSeq
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addJSeq(final jalview.schemabinding.version2.JSeq vJSeq)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._JSeqList.addElement(vJSeq);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vJSeq
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addJSeq(final int index,
+          final jalview.schemabinding.version2.JSeq vJSeq)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._JSeqList.add(index, vJSeq);
+  }
+
+  /**
+   * 
+   * 
+   * @param vTree
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addTree(final jalview.schemabinding.version2.Tree vTree)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._treeList.addElement(vTree);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vTree
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addTree(final int index,
+          final jalview.schemabinding.version2.Tree vTree)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._treeList.add(index, vTree);
+  }
+
+  /**
+   * 
+   * 
+   * @param vUserColours
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addUserColours(
+          final jalview.schemabinding.version2.UserColours vUserColours)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._userColoursList.addElement(vUserColours);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vUserColours
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addUserColours(final int index,
+          final jalview.schemabinding.version2.UserColours vUserColours)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._userColoursList.add(index, vUserColours);
+  }
+
+  /**
+   * 
+   * 
+   * @param vViewport
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addViewport(
+          final jalview.schemabinding.version2.Viewport vViewport)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._viewportList.addElement(vViewport);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vViewport
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addViewport(final int index,
+          final jalview.schemabinding.version2.Viewport vViewport)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._viewportList.add(index, vViewport);
+  }
+
+  /**
+   * Method enumerateJGroup.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.JGroup
+   *         elements
+   */
+  public java.util.Enumeration enumerateJGroup()
+  {
+    return this._JGroupList.elements();
+  }
+
+  /**
+   * Method enumerateJSeq.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.JSeq
+   *         elements
+   */
+  public java.util.Enumeration enumerateJSeq()
+  {
+    return this._JSeqList.elements();
+  }
+
+  /**
+   * Method enumerateTree.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.Tree
+   *         elements
+   */
+  public java.util.Enumeration enumerateTree()
+  {
+    return this._treeList.elements();
+  }
+
+  /**
+   * Method enumerateUserColours.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.UserColours
+   *         elements
+   */
+  public java.util.Enumeration enumerateUserColours()
+  {
+    return this._userColoursList.elements();
+  }
+
+  /**
+   * Method enumerateViewport.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.Viewport
+   *         elements
+   */
+  public java.util.Enumeration enumerateViewport()
+  {
+    return this._viewportList.elements();
+  }
+
+  /**
+   * Returns the value of field 'featureSettings'.
+   * 
+   * @return the value of field 'FeatureSettings'.
+   */
+  public jalview.schemabinding.version2.FeatureSettings getFeatureSettings()
+  {
+    return this._featureSettings;
+  }
+
+  /**
+   * Method getJGroup.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.JGroup at the given
+   *         index
+   */
+  public jalview.schemabinding.version2.JGroup getJGroup(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._JGroupList.size())
+    {
+      throw new IndexOutOfBoundsException("getJGroup: Index value '"
+              + index + "' not in range [0.."
+              + (this._JGroupList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.JGroup) _JGroupList.get(index);
+  }
+
+  /**
+   * Method getJGroup.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.JGroup[] getJGroup()
+  {
+    jalview.schemabinding.version2.JGroup[] array = new jalview.schemabinding.version2.JGroup[0];
+    return (jalview.schemabinding.version2.JGroup[]) this._JGroupList
+            .toArray(array);
+  }
+
+  /**
+   * Method getJGroupCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getJGroupCount()
+  {
+    return this._JGroupList.size();
+  }
+
+  /**
+   * Method getJSeq.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.JSeq at the given
+   *         index
+   */
+  public jalview.schemabinding.version2.JSeq getJSeq(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._JSeqList.size())
+    {
+      throw new IndexOutOfBoundsException("getJSeq: Index value '" + index
+              + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.JSeq) _JSeqList.get(index);
+  }
+
+  /**
+   * Method getJSeq.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.JSeq[] getJSeq()
+  {
+    jalview.schemabinding.version2.JSeq[] array = new jalview.schemabinding.version2.JSeq[0];
+    return (jalview.schemabinding.version2.JSeq[]) this._JSeqList
+            .toArray(array);
+  }
+
+  /**
+   * Method getJSeqCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getJSeqCount()
+  {
+    return this._JSeqList.size();
+  }
+
+  /**
+   * Method getTree.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.Tree at the given
+   *         index
+   */
+  public jalview.schemabinding.version2.Tree getTree(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._treeList.size())
+    {
+      throw new IndexOutOfBoundsException("getTree: Index value '" + index
+              + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.Tree) _treeList.get(index);
+  }
+
+  /**
+   * Method getTree.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.Tree[] getTree()
+  {
+    jalview.schemabinding.version2.Tree[] array = new jalview.schemabinding.version2.Tree[0];
+    return (jalview.schemabinding.version2.Tree[]) this._treeList
+            .toArray(array);
+  }
+
+  /**
+   * Method getTreeCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getTreeCount()
+  {
+    return this._treeList.size();
+  }
+
+  /**
+   * Method getUserColours.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.UserColours at the
+   *         given index
+   */
+  public jalview.schemabinding.version2.UserColours getUserColours(
+          final int index) throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._userColoursList.size())
+    {
+      throw new IndexOutOfBoundsException("getUserColours: Index value '"
+              + index + "' not in range [0.."
+              + (this._userColoursList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.UserColours) _userColoursList
+            .get(index);
+  }
+
+  /**
+   * Method getUserColours.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.UserColours[] getUserColours()
+  {
+    jalview.schemabinding.version2.UserColours[] array = new jalview.schemabinding.version2.UserColours[0];
+    return (jalview.schemabinding.version2.UserColours[]) this._userColoursList
+            .toArray(array);
+  }
+
+  /**
+   * Method getUserColoursCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getUserColoursCount()
+  {
+    return this._userColoursList.size();
+  }
+
+  /**
+   * Method getViewport.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.Viewport at the
+   *         given index
+   */
+  public jalview.schemabinding.version2.Viewport getViewport(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._viewportList.size())
+    {
+      throw new IndexOutOfBoundsException("getViewport: Index value '"
+              + index + "' not in range [0.."
+              + (this._viewportList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.Viewport) _viewportList
+            .get(index);
+  }
+
+  /**
+   * Method getViewport.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.Viewport[] getViewport()
+  {
+    jalview.schemabinding.version2.Viewport[] array = new jalview.schemabinding.version2.Viewport[0];
+    return (jalview.schemabinding.version2.Viewport[]) this._viewportList
+            .toArray(array);
+  }
+
+  /**
+   * Method getViewportCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getViewportCount()
+  {
+    return this._viewportList.size();
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   */
+  public void removeAllJGroup()
+  {
+    this._JGroupList.clear();
+  }
+
+  /**
+   */
+  public void removeAllJSeq()
+  {
+    this._JSeqList.clear();
+  }
+
+  /**
+   */
+  public void removeAllTree()
+  {
+    this._treeList.clear();
+  }
+
+  /**
+   */
+  public void removeAllUserColours()
+  {
+    this._userColoursList.clear();
+  }
+
+  /**
+   */
+  public void removeAllViewport()
+  {
+    this._viewportList.clear();
+  }
+
+  /**
+   * Method removeJGroup.
+   * 
+   * @param vJGroup
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeJGroup(
+          final jalview.schemabinding.version2.JGroup vJGroup)
+  {
+    boolean removed = _JGroupList.remove(vJGroup);
+    return removed;
+  }
+
+  /**
+   * Method removeJGroupAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.JGroup removeJGroupAt(
+          final int index)
+  {
+    java.lang.Object obj = this._JGroupList.remove(index);
+    return (jalview.schemabinding.version2.JGroup) obj;
+  }
+
+  /**
+   * Method removeJSeq.
+   * 
+   * @param vJSeq
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeJSeq(final jalview.schemabinding.version2.JSeq vJSeq)
+  {
+    boolean removed = _JSeqList.remove(vJSeq);
+    return removed;
+  }
+
+  /**
+   * Method removeJSeqAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.JSeq removeJSeqAt(final int index)
+  {
+    java.lang.Object obj = this._JSeqList.remove(index);
+    return (jalview.schemabinding.version2.JSeq) obj;
+  }
+
+  /**
+   * Method removeTree.
+   * 
+   * @param vTree
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeTree(final jalview.schemabinding.version2.Tree vTree)
+  {
+    boolean removed = _treeList.remove(vTree);
+    return removed;
+  }
+
+  /**
+   * Method removeTreeAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.Tree removeTreeAt(final int index)
+  {
+    java.lang.Object obj = this._treeList.remove(index);
+    return (jalview.schemabinding.version2.Tree) obj;
+  }
+
+  /**
+   * Method removeUserColours.
+   * 
+   * @param vUserColours
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeUserColours(
+          final jalview.schemabinding.version2.UserColours vUserColours)
+  {
+    boolean removed = _userColoursList.remove(vUserColours);
+    return removed;
+  }
+
+  /**
+   * Method removeUserColoursAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.UserColours removeUserColoursAt(
+          final int index)
+  {
+    java.lang.Object obj = this._userColoursList.remove(index);
+    return (jalview.schemabinding.version2.UserColours) obj;
+  }
+
+  /**
+   * Method removeViewport.
+   * 
+   * @param vViewport
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeViewport(
+          final jalview.schemabinding.version2.Viewport vViewport)
+  {
+    boolean removed = _viewportList.remove(vViewport);
+    return removed;
+  }
+
+  /**
+   * Method removeViewportAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.Viewport removeViewportAt(
+          final int index)
+  {
+    java.lang.Object obj = this._viewportList.remove(index);
+    return (jalview.schemabinding.version2.Viewport) obj;
+  }
+
+  /**
+   * Sets the value of field 'featureSettings'.
+   * 
+   * @param featureSettings
+   *                the value of field 'featureSettings'.
+   */
+  public void setFeatureSettings(
+          final jalview.schemabinding.version2.FeatureSettings featureSettings)
+  {
+    this._featureSettings = featureSettings;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vJGroup
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setJGroup(final int index,
+          final jalview.schemabinding.version2.JGroup vJGroup)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._JGroupList.size())
+    {
+      throw new IndexOutOfBoundsException("setJGroup: Index value '"
+              + index + "' not in range [0.."
+              + (this._JGroupList.size() - 1) + "]");
+    }
+
+    this._JGroupList.set(index, vJGroup);
+  }
+
+  /**
+   * 
+   * 
+   * @param vJGroupArray
+   */
+  public void setJGroup(
+          final jalview.schemabinding.version2.JGroup[] vJGroupArray)
+  {
+    // -- copy array
+    _JGroupList.clear();
+
+    for (int i = 0; i < vJGroupArray.length; i++)
+    {
+      this._JGroupList.add(vJGroupArray[i]);
+    }
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vJSeq
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setJSeq(final int index,
+          final jalview.schemabinding.version2.JSeq vJSeq)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._JSeqList.size())
+    {
+      throw new IndexOutOfBoundsException("setJSeq: Index value '" + index
+              + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
+    }
+
+    this._JSeqList.set(index, vJSeq);
+  }
+
+  /**
+   * 
+   * 
+   * @param vJSeqArray
+   */
+  public void setJSeq(final jalview.schemabinding.version2.JSeq[] vJSeqArray)
+  {
+    // -- copy array
+    _JSeqList.clear();
+
+    for (int i = 0; i < vJSeqArray.length; i++)
+    {
+      this._JSeqList.add(vJSeqArray[i]);
+    }
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vTree
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setTree(final int index,
+          final jalview.schemabinding.version2.Tree vTree)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._treeList.size())
+    {
+      throw new IndexOutOfBoundsException("setTree: Index value '" + index
+              + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+    }
+
+    this._treeList.set(index, vTree);
+  }
+
+  /**
+   * 
+   * 
+   * @param vTreeArray
+   */
+  public void setTree(final jalview.schemabinding.version2.Tree[] vTreeArray)
+  {
+    // -- copy array
+    _treeList.clear();
+
+    for (int i = 0; i < vTreeArray.length; i++)
+    {
+      this._treeList.add(vTreeArray[i]);
+    }
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vUserColours
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setUserColours(final int index,
+          final jalview.schemabinding.version2.UserColours vUserColours)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._userColoursList.size())
+    {
+      throw new IndexOutOfBoundsException("setUserColours: Index value '"
+              + index + "' not in range [0.."
+              + (this._userColoursList.size() - 1) + "]");
+    }
+
+    this._userColoursList.set(index, vUserColours);
+  }
+
+  /**
+   * 
+   * 
+   * @param vUserColoursArray
+   */
+  public void setUserColours(
+          final jalview.schemabinding.version2.UserColours[] vUserColoursArray)
+  {
+    // -- copy array
+    _userColoursList.clear();
+
+    for (int i = 0; i < vUserColoursArray.length; i++)
+    {
+      this._userColoursList.add(vUserColoursArray[i]);
+    }
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vViewport
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setViewport(final int index,
+          final jalview.schemabinding.version2.Viewport vViewport)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._viewportList.size())
+    {
+      throw new IndexOutOfBoundsException("setViewport: Index value '"
+              + index + "' not in range [0.."
+              + (this._viewportList.size() - 1) + "]");
+    }
+
+    this._viewportList.set(index, vViewport);
+  }
+
+  /**
+   * 
+   * 
+   * @param vViewportArray
+   */
+  public void setViewport(
+          final jalview.schemabinding.version2.Viewport[] vViewportArray)
+  {
+    // -- copy array
+    _viewportList.clear();
+
+    for (int i = 0; i < vViewportArray.length; i++)
+    {
+      this._viewportList.add(vViewportArray[i]);
+    }
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.JalviewModelSequence
+   */
+  public static jalview.schemabinding.version2.JalviewModelSequence unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.JalviewModelSequence) Unmarshaller
+            .unmarshal(
+                    jalview.schemabinding.version2.JalviewModelSequence.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/JalviewUserColours.java b/src/jalview/schemabinding/version2/JalviewUserColours.java
index 7c059da..72126e0 100755
--- a/src/jalview/schemabinding/version2/JalviewUserColours.java
+++ b/src/jalview/schemabinding/version2/JalviewUserColours.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,281 +30,301 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class JalviewUserColours implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _schemeName.
-     */
-    private java.lang.String _schemeName;
-
-    /**
-     * Field _colourList.
-     */
-    private java.util.Vector _colourList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JalviewUserColours() {
-        super();
-        this._colourList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vColour
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addColour(
-            final Colour vColour)
-    throws java.lang.IndexOutOfBoundsException {
-        this._colourList.addElement(vColour);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vColour
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addColour(
-            final int index,
-            final Colour vColour)
-    throws java.lang.IndexOutOfBoundsException {
-        this._colourList.add(index, vColour);
-    }
-
-    /**
-     * Method enumerateColour.
-     * 
-     * @return an Enumeration over all Colour elements
-     */
-    public java.util.Enumeration enumerateColour(
-    ) {
-        return this._colourList.elements();
-    }
-
-    /**
-     * Method getColour.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the Colour at the given index
-     */
-    public Colour getColour(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._colourList.size()) {
-            throw new IndexOutOfBoundsException("getColour: Index value '" + index + "' not in range [0.." + (this._colourList.size() - 1) + "]");
-        }
-        
-        return (Colour) _colourList.get(index);
-    }
-
-    /**
-     * Method getColour.Returns the contents of the collection in
-     * an Array.  <p>Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we <i>know</i>
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public Colour[] getColour(
-    ) {
-        Colour[] array = new Colour[0];
-        return (Colour[]) this._colourList.toArray(array);
-    }
-
-    /**
-     * Method getColourCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getColourCount(
-    ) {
-        return this._colourList.size();
-    }
-
-    /**
-     * Returns the value of field 'schemeName'.
-     * 
-     * @return the value of field 'SchemeName'.
-     */
-    public java.lang.String getSchemeName(
-    ) {
-        return this._schemeName;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
+public class JalviewUserColours implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _schemeName.
+   */
+  private java.lang.String _schemeName;
+
+  /**
+   * Field _colourList.
+   */
+  private java.util.Vector _colourList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public JalviewUserColours()
+  {
+    super();
+    this._colourList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vColour
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addColour(final Colour vColour)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._colourList.addElement(vColour);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vColour
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addColour(final int index, final Colour vColour)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._colourList.add(index, vColour);
+  }
+
+  /**
+   * Method enumerateColour.
+   * 
+   * @return an Enumeration over all Colour elements
+   */
+  public java.util.Enumeration enumerateColour()
+  {
+    return this._colourList.elements();
+  }
+
+  /**
+   * Method getColour.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the Colour at the given index
+   */
+  public Colour getColour(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._colourList.size())
+    {
+      throw new IndexOutOfBoundsException("getColour: Index value '"
+              + index + "' not in range [0.."
+              + (this._colourList.size() - 1) + "]");
     }
 
-    /**
-     */
-    public void removeAllColour(
-    ) {
-        this._colourList.clear();
+    return (Colour) _colourList.get(index);
+  }
+
+  /**
+   * Method getColour.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public Colour[] getColour()
+  {
+    Colour[] array = new Colour[0];
+    return (Colour[]) this._colourList.toArray(array);
+  }
+
+  /**
+   * Method getColourCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getColourCount()
+  {
+    return this._colourList.size();
+  }
+
+  /**
+   * Returns the value of field 'schemeName'.
+   * 
+   * @return the value of field 'SchemeName'.
+   */
+  public java.lang.String getSchemeName()
+  {
+    return this._schemeName;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
-
-    /**
-     * Method removeColour.
-     * 
-     * @param vColour
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeColour(
-            final Colour vColour) {
-        boolean removed = _colourList.remove(vColour);
-        return removed;
-    }
-
-    /**
-     * Method removeColourAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public Colour removeColourAt(
-            final int index) {
-        java.lang.Object obj = this._colourList.remove(index);
-        return (Colour) obj;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vColour
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setColour(
-            final int index,
-            final Colour vColour)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._colourList.size()) {
-            throw new IndexOutOfBoundsException("setColour: Index value '" + index + "' not in range [0.." + (this._colourList.size() - 1) + "]");
-        }
-        
-        this._colourList.set(index, vColour);
-    }
-
-    /**
-     * 
-     * 
-     * @param vColourArray
-     */
-    public void setColour(
-            final Colour[] vColourArray) {
-        //-- copy array
-        _colourList.clear();
-        
-        for (int i = 0; i < vColourArray.length; i++) {
-                this._colourList.add(vColourArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of field 'schemeName'.
-     * 
-     * @param schemeName the value of field 'schemeName'.
-     */
-    public void setSchemeName(
-            final java.lang.String schemeName) {
-        this._schemeName = schemeName;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.JalviewUserColours
-     */
-    public static jalview.schemabinding.version2.JalviewUserColours unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.JalviewUserColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.JalviewUserColours.class, reader);
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   */
+  public void removeAllColour()
+  {
+    this._colourList.clear();
+  }
+
+  /**
+   * Method removeColour.
+   * 
+   * @param vColour
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeColour(final Colour vColour)
+  {
+    boolean removed = _colourList.remove(vColour);
+    return removed;
+  }
+
+  /**
+   * Method removeColourAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public Colour removeColourAt(final int index)
+  {
+    java.lang.Object obj = this._colourList.remove(index);
+    return (Colour) obj;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vColour
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setColour(final int index, final Colour vColour)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._colourList.size())
+    {
+      throw new IndexOutOfBoundsException("setColour: Index value '"
+              + index + "' not in range [0.."
+              + (this._colourList.size() - 1) + "]");
     }
 
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+    this._colourList.set(index, vColour);
+  }
+
+  /**
+   * 
+   * 
+   * @param vColourArray
+   */
+  public void setColour(final Colour[] vColourArray)
+  {
+    // -- copy array
+    _colourList.clear();
+
+    for (int i = 0; i < vColourArray.length; i++)
+    {
+      this._colourList.add(vColourArray[i]);
     }
+  }
+
+  /**
+   * Sets the value of field 'schemeName'.
+   * 
+   * @param schemeName
+   *                the value of field 'schemeName'.
+   */
+  public void setSchemeName(final java.lang.String schemeName)
+  {
+    this._schemeName = schemeName;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.JalviewUserColours
+   */
+  public static jalview.schemabinding.version2.JalviewUserColours unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.JalviewUserColours) Unmarshaller
+            .unmarshal(
+                    jalview.schemabinding.version2.JalviewUserColours.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/MapListFrom.java b/src/jalview/schemabinding/version2/MapListFrom.java
index acfe18e..3ecf00f 100644
--- a/src/jalview/schemabinding/version2/MapListFrom.java
+++ b/src/jalview/schemabinding/version2/MapListFrom.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,198 +30,213 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class MapListFrom implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _start.
-     */
-    private int _start;
-
-    /**
-     * keeps track of state for field: _start
-     */
-    private boolean _has_start;
-
-    /**
-     * Field _end.
-     */
-    private int _end;
-
-    /**
-     * keeps track of state for field: _end
-     */
-    private boolean _has_end;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public MapListFrom() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     */
-    public void deleteEnd(
-    ) {
-        this._has_end= false;
-    }
-
-    /**
-     */
-    public void deleteStart(
-    ) {
-        this._has_start= false;
-    }
-
-    /**
-     * Returns the value of field 'end'.
-     * 
-     * @return the value of field 'End'.
-     */
-    public int getEnd(
-    ) {
-        return this._end;
-    }
-
-    /**
-     * Returns the value of field 'start'.
-     * 
-     * @return the value of field 'Start'.
-     */
-    public int getStart(
-    ) {
-        return this._start;
-    }
-
-    /**
-     * Method hasEnd.
-     * 
-     * @return true if at least one End has been added
-     */
-    public boolean hasEnd(
-    ) {
-        return this._has_end;
-    }
-
-    /**
-     * Method hasStart.
-     * 
-     * @return true if at least one Start has been added
-     */
-    public boolean hasStart(
-    ) {
-        return this._has_start;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'end'.
-     * 
-     * @param end the value of field 'end'.
-     */
-    public void setEnd(
-            final int end) {
-        this._end = end;
-        this._has_end = true;
-    }
-
-    /**
-     * Sets the value of field 'start'.
-     * 
-     * @param start the value of field 'start'.
-     */
-    public void setStart(
-            final int start) {
-        this._start = start;
-        this._has_start = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.MapListFrom
-     */
-    public static jalview.schemabinding.version2.MapListFrom unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.MapListFrom) Unmarshaller.unmarshal(jalview.schemabinding.version2.MapListFrom.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class MapListFrom implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _start.
+   */
+  private int _start;
+
+  /**
+   * keeps track of state for field: _start
+   */
+  private boolean _has_start;
+
+  /**
+   * Field _end.
+   */
+  private int _end;
+
+  /**
+   * keeps track of state for field: _end
+   */
+  private boolean _has_end;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public MapListFrom()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   */
+  public void deleteEnd()
+  {
+    this._has_end = false;
+  }
+
+  /**
+   */
+  public void deleteStart()
+  {
+    this._has_start = false;
+  }
+
+  /**
+   * Returns the value of field 'end'.
+   * 
+   * @return the value of field 'End'.
+   */
+  public int getEnd()
+  {
+    return this._end;
+  }
+
+  /**
+   * Returns the value of field 'start'.
+   * 
+   * @return the value of field 'Start'.
+   */
+  public int getStart()
+  {
+    return this._start;
+  }
+
+  /**
+   * Method hasEnd.
+   * 
+   * @return true if at least one End has been added
+   */
+  public boolean hasEnd()
+  {
+    return this._has_end;
+  }
+
+  /**
+   * Method hasStart.
+   * 
+   * @return true if at least one Start has been added
+   */
+  public boolean hasStart()
+  {
+    return this._has_start;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'end'.
+   * 
+   * @param end
+   *                the value of field 'end'.
+   */
+  public void setEnd(final int end)
+  {
+    this._end = end;
+    this._has_end = true;
+  }
+
+  /**
+   * Sets the value of field 'start'.
+   * 
+   * @param start
+   *                the value of field 'start'.
+   */
+  public void setStart(final int start)
+  {
+    this._start = start;
+    this._has_start = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.MapListFrom
+   */
+  public static jalview.schemabinding.version2.MapListFrom unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.MapListFrom) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.MapListFrom.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/MapListTo.java b/src/jalview/schemabinding/version2/MapListTo.java
index 8c3a7e0..0bb9fc6 100644
--- a/src/jalview/schemabinding/version2/MapListTo.java
+++ b/src/jalview/schemabinding/version2/MapListTo.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,198 +30,213 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class MapListTo implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _start.
-     */
-    private int _start;
-
-    /**
-     * keeps track of state for field: _start
-     */
-    private boolean _has_start;
-
-    /**
-     * Field _end.
-     */
-    private int _end;
-
-    /**
-     * keeps track of state for field: _end
-     */
-    private boolean _has_end;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public MapListTo() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     */
-    public void deleteEnd(
-    ) {
-        this._has_end= false;
-    }
-
-    /**
-     */
-    public void deleteStart(
-    ) {
-        this._has_start= false;
-    }
-
-    /**
-     * Returns the value of field 'end'.
-     * 
-     * @return the value of field 'End'.
-     */
-    public int getEnd(
-    ) {
-        return this._end;
-    }
-
-    /**
-     * Returns the value of field 'start'.
-     * 
-     * @return the value of field 'Start'.
-     */
-    public int getStart(
-    ) {
-        return this._start;
-    }
-
-    /**
-     * Method hasEnd.
-     * 
-     * @return true if at least one End has been added
-     */
-    public boolean hasEnd(
-    ) {
-        return this._has_end;
-    }
-
-    /**
-     * Method hasStart.
-     * 
-     * @return true if at least one Start has been added
-     */
-    public boolean hasStart(
-    ) {
-        return this._has_start;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'end'.
-     * 
-     * @param end the value of field 'end'.
-     */
-    public void setEnd(
-            final int end) {
-        this._end = end;
-        this._has_end = true;
-    }
-
-    /**
-     * Sets the value of field 'start'.
-     * 
-     * @param start the value of field 'start'.
-     */
-    public void setStart(
-            final int start) {
-        this._start = start;
-        this._has_start = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.MapListTo
-     */
-    public static jalview.schemabinding.version2.MapListTo unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.MapListTo) Unmarshaller.unmarshal(jalview.schemabinding.version2.MapListTo.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class MapListTo implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _start.
+   */
+  private int _start;
+
+  /**
+   * keeps track of state for field: _start
+   */
+  private boolean _has_start;
+
+  /**
+   * Field _end.
+   */
+  private int _end;
+
+  /**
+   * keeps track of state for field: _end
+   */
+  private boolean _has_end;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public MapListTo()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   */
+  public void deleteEnd()
+  {
+    this._has_end = false;
+  }
+
+  /**
+   */
+  public void deleteStart()
+  {
+    this._has_start = false;
+  }
+
+  /**
+   * Returns the value of field 'end'.
+   * 
+   * @return the value of field 'End'.
+   */
+  public int getEnd()
+  {
+    return this._end;
+  }
+
+  /**
+   * Returns the value of field 'start'.
+   * 
+   * @return the value of field 'Start'.
+   */
+  public int getStart()
+  {
+    return this._start;
+  }
+
+  /**
+   * Method hasEnd.
+   * 
+   * @return true if at least one End has been added
+   */
+  public boolean hasEnd()
+  {
+    return this._has_end;
+  }
+
+  /**
+   * Method hasStart.
+   * 
+   * @return true if at least one Start has been added
+   */
+  public boolean hasStart()
+  {
+    return this._has_start;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'end'.
+   * 
+   * @param end
+   *                the value of field 'end'.
+   */
+  public void setEnd(final int end)
+  {
+    this._end = end;
+    this._has_end = true;
+  }
+
+  /**
+   * Sets the value of field 'start'.
+   * 
+   * @param start
+   *                the value of field 'start'.
+   */
+  public void setStart(final int start)
+  {
+    this._start = start;
+    this._has_start = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.MapListTo
+   */
+  public static jalview.schemabinding.version2.MapListTo unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.MapListTo) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.MapListTo.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/MapListType.java b/src/jalview/schemabinding/version2/MapListType.java
index 21d56e7..efb1bc5 100644
--- a/src/jalview/schemabinding/version2/MapListType.java
+++ b/src/jalview/schemabinding/version2/MapListType.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -17,566 +28,585 @@ import org.exolab.castor.xml.Unmarshaller;
 /**
  * developed after mapRangeType from
  * http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
- *  
- *  This effectively represents a java.util.MapList object
- *  
+ * 
+ * This effectively represents a java.util.MapList object
+ * 
  * 
  * @version $Revision$ $Date$
  */
-public class MapListType implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * number of dictionary symbol widths involved in each
-     *  mapped position on this sequence (for example, 3 for a dna
-     * sequence exon
-     *  region that is being mapped to a protein sequence). This is
-     * optional,
-     *  since the unit can be usually be inferred from the
-     * dictionary type of
-     *  each sequence involved in the mapping. 
-     */
-    private long _mapFromUnit;
-
-    /**
-     * keeps track of state for field: _mapFromUnit
-     */
-    private boolean _has_mapFromUnit;
-
-    /**
-     * number of dictionary symbol widths involved in each
-     *  mapped position on this sequence (for example, 3 for a dna
-     * sequence exon
-     *  region that is being mapped to a protein sequence). This is
-     * optional,
-     *  since the unit can be usually be inferred from the
-     * dictionary type of
-     *  each sequence involved in the mapping. 
-     */
-    private long _mapToUnit;
-
-    /**
-     * keeps track of state for field: _mapToUnit
-     */
-    private boolean _has_mapToUnit;
-
-    /**
-     * a region from start to end inclusive
-     */
-    private java.util.Vector _mapListFromList;
-
-    /**
-     * a region from start to end inclusive
-     */
-    private java.util.Vector _mapListToList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public MapListType() {
-        super();
-        this._mapListFromList = new java.util.Vector();
-        this._mapListToList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vMapListFrom
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addMapListFrom(
-            final jalview.schemabinding.version2.MapListFrom vMapListFrom)
-    throws java.lang.IndexOutOfBoundsException {
-        this._mapListFromList.addElement(vMapListFrom);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vMapListFrom
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addMapListFrom(
-            final int index,
-            final jalview.schemabinding.version2.MapListFrom vMapListFrom)
-    throws java.lang.IndexOutOfBoundsException {
-        this._mapListFromList.add(index, vMapListFrom);
-    }
-
-    /**
-     * 
-     * 
-     * @param vMapListTo
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addMapListTo(
-            final jalview.schemabinding.version2.MapListTo vMapListTo)
-    throws java.lang.IndexOutOfBoundsException {
-        this._mapListToList.addElement(vMapListTo);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vMapListTo
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addMapListTo(
-            final int index,
-            final jalview.schemabinding.version2.MapListTo vMapListTo)
-    throws java.lang.IndexOutOfBoundsException {
-        this._mapListToList.add(index, vMapListTo);
-    }
-
-    /**
-     */
-    public void deleteMapFromUnit(
-    ) {
-        this._has_mapFromUnit= false;
-    }
-
-    /**
-     */
-    public void deleteMapToUnit(
-    ) {
-        this._has_mapToUnit= false;
-    }
-
-    /**
-     * Method enumerateMapListFrom.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.MapListFrom elements
-     */
-    public java.util.Enumeration enumerateMapListFrom(
-    ) {
-        return this._mapListFromList.elements();
-    }
-
-    /**
-     * Method enumerateMapListTo.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.MapListTo elements
-     */
-    public java.util.Enumeration enumerateMapListTo(
-    ) {
-        return this._mapListToList.elements();
-    }
-
-    /**
-     * Returns the value of field 'mapFromUnit'. The field
-     * 'mapFromUnit' has the following description: number of
-     * dictionary symbol widths involved in each
-     *  mapped position on this sequence (for example, 3 for a dna
-     * sequence exon
-     *  region that is being mapped to a protein sequence). This is
-     * optional,
-     *  since the unit can be usually be inferred from the
-     * dictionary type of
-     *  each sequence involved in the mapping. 
-     * 
-     * @return the value of field 'MapFromUnit'.
-     */
-    public long getMapFromUnit(
-    ) {
-        return this._mapFromUnit;
-    }
-
-    /**
-     * Method getMapListFrom.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.MapListFrom at the given index
-     */
-    public jalview.schemabinding.version2.MapListFrom getMapListFrom(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._mapListFromList.size()) {
-            throw new IndexOutOfBoundsException("getMapListFrom: Index value '" + index + "' not in range [0.." + (this._mapListFromList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.MapListFrom) _mapListFromList.get(index);
-    }
-
-    /**
-     * Method getMapListFrom.Returns the contents of the collection
-     * in an Array.  <p>Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we <i>know</i>
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.MapListFrom[] getMapListFrom(
-    ) {
-        jalview.schemabinding.version2.MapListFrom[] array = new jalview.schemabinding.version2.MapListFrom[0];
-        return (jalview.schemabinding.version2.MapListFrom[]) this._mapListFromList.toArray(array);
-    }
-
-    /**
-     * Method getMapListFromCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getMapListFromCount(
-    ) {
-        return this._mapListFromList.size();
-    }
-
-    /**
-     * Method getMapListTo.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.MapListTo at the given index
-     */
-    public jalview.schemabinding.version2.MapListTo getMapListTo(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._mapListToList.size()) {
-            throw new IndexOutOfBoundsException("getMapListTo: Index value '" + index + "' not in range [0.." + (this._mapListToList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.MapListTo) _mapListToList.get(index);
-    }
-
-    /**
-     * Method getMapListTo.Returns the contents of the collection
-     * in an Array.  <p>Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we <i>know</i>
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.MapListTo[] getMapListTo(
-    ) {
-        jalview.schemabinding.version2.MapListTo[] array = new jalview.schemabinding.version2.MapListTo[0];
-        return (jalview.schemabinding.version2.MapListTo[]) this._mapListToList.toArray(array);
-    }
-
-    /**
-     * Method getMapListToCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getMapListToCount(
-    ) {
-        return this._mapListToList.size();
-    }
-
-    /**
-     * Returns the value of field 'mapToUnit'. The field
-     * 'mapToUnit' has the following description: number of
-     * dictionary symbol widths involved in each
-     *  mapped position on this sequence (for example, 3 for a dna
-     * sequence exon
-     *  region that is being mapped to a protein sequence). This is
-     * optional,
-     *  since the unit can be usually be inferred from the
-     * dictionary type of
-     *  each sequence involved in the mapping. 
-     * 
-     * @return the value of field 'MapToUnit'.
-     */
-    public long getMapToUnit(
-    ) {
-        return this._mapToUnit;
-    }
-
-    /**
-     * Method hasMapFromUnit.
-     * 
-     * @return true if at least one MapFromUnit has been added
-     */
-    public boolean hasMapFromUnit(
-    ) {
-        return this._has_mapFromUnit;
-    }
-
-    /**
-     * Method hasMapToUnit.
-     * 
-     * @return true if at least one MapToUnit has been added
-     */
-    public boolean hasMapToUnit(
-    ) {
-        return this._has_mapToUnit;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     */
-    public void removeAllMapListFrom(
-    ) {
-        this._mapListFromList.clear();
-    }
-
-    /**
-     */
-    public void removeAllMapListTo(
-    ) {
-        this._mapListToList.clear();
-    }
-
-    /**
-     * Method removeMapListFrom.
-     * 
-     * @param vMapListFrom
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeMapListFrom(
-            final jalview.schemabinding.version2.MapListFrom vMapListFrom) {
-        boolean removed = _mapListFromList.remove(vMapListFrom);
-        return removed;
-    }
-
-    /**
-     * Method removeMapListFromAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.MapListFrom removeMapListFromAt(
-            final int index) {
-        java.lang.Object obj = this._mapListFromList.remove(index);
-        return (jalview.schemabinding.version2.MapListFrom) obj;
-    }
-
-    /**
-     * Method removeMapListTo.
-     * 
-     * @param vMapListTo
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeMapListTo(
-            final jalview.schemabinding.version2.MapListTo vMapListTo) {
-        boolean removed = _mapListToList.remove(vMapListTo);
-        return removed;
-    }
-
-    /**
-     * Method removeMapListToAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.MapListTo removeMapListToAt(
-            final int index) {
-        java.lang.Object obj = this._mapListToList.remove(index);
-        return (jalview.schemabinding.version2.MapListTo) obj;
-    }
-
-    /**
-     * Sets the value of field 'mapFromUnit'. The field
-     * 'mapFromUnit' has the following description: number of
-     * dictionary symbol widths involved in each
-     *  mapped position on this sequence (for example, 3 for a dna
-     * sequence exon
-     *  region that is being mapped to a protein sequence). This is
-     * optional,
-     *  since the unit can be usually be inferred from the
-     * dictionary type of
-     *  each sequence involved in the mapping. 
-     * 
-     * @param mapFromUnit the value of field 'mapFromUnit'.
-     */
-    public void setMapFromUnit(
-            final long mapFromUnit) {
-        this._mapFromUnit = mapFromUnit;
-        this._has_mapFromUnit = true;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vMapListFrom
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setMapListFrom(
-            final int index,
-            final jalview.schemabinding.version2.MapListFrom vMapListFrom)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._mapListFromList.size()) {
-            throw new IndexOutOfBoundsException("setMapListFrom: Index value '" + index + "' not in range [0.." + (this._mapListFromList.size() - 1) + "]");
-        }
-        
-        this._mapListFromList.set(index, vMapListFrom);
-    }
-
-    /**
-     * 
-     * 
-     * @param vMapListFromArray
-     */
-    public void setMapListFrom(
-            final jalview.schemabinding.version2.MapListFrom[] vMapListFromArray) {
-        //-- copy array
-        _mapListFromList.clear();
-        
-        for (int i = 0; i < vMapListFromArray.length; i++) {
-                this._mapListFromList.add(vMapListFromArray[i]);
-        }
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vMapListTo
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setMapListTo(
-            final int index,
-            final jalview.schemabinding.version2.MapListTo vMapListTo)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._mapListToList.size()) {
-            throw new IndexOutOfBoundsException("setMapListTo: Index value '" + index + "' not in range [0.." + (this._mapListToList.size() - 1) + "]");
-        }
-        
-        this._mapListToList.set(index, vMapListTo);
-    }
-
-    /**
-     * 
-     * 
-     * @param vMapListToArray
-     */
-    public void setMapListTo(
-            final jalview.schemabinding.version2.MapListTo[] vMapListToArray) {
-        //-- copy array
-        _mapListToList.clear();
-        
-        for (int i = 0; i < vMapListToArray.length; i++) {
-                this._mapListToList.add(vMapListToArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of field 'mapToUnit'. The field 'mapToUnit'
-     * has the following description: number of dictionary symbol
-     * widths involved in each
-     *  mapped position on this sequence (for example, 3 for a dna
-     * sequence exon
-     *  region that is being mapped to a protein sequence). This is
-     * optional,
-     *  since the unit can be usually be inferred from the
-     * dictionary type of
-     *  each sequence involved in the mapping. 
-     * 
-     * @param mapToUnit the value of field 'mapToUnit'.
-     */
-    public void setMapToUnit(
-            final long mapToUnit) {
-        this._mapToUnit = mapToUnit;
-        this._has_mapToUnit = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.MapListType
-     */
-    public static jalview.schemabinding.version2.MapListType unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.MapListType) Unmarshaller.unmarshal(jalview.schemabinding.version2.MapListType.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+public class MapListType implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * number of dictionary symbol widths involved in each mapped position on this
+   * sequence (for example, 3 for a dna sequence exon region that is being
+   * mapped to a protein sequence). This is optional, since the unit can be
+   * usually be inferred from the dictionary type of each sequence involved in
+   * the mapping.
+   */
+  private long _mapFromUnit;
+
+  /**
+   * keeps track of state for field: _mapFromUnit
+   */
+  private boolean _has_mapFromUnit;
+
+  /**
+   * number of dictionary symbol widths involved in each mapped position on this
+   * sequence (for example, 3 for a dna sequence exon region that is being
+   * mapped to a protein sequence). This is optional, since the unit can be
+   * usually be inferred from the dictionary type of each sequence involved in
+   * the mapping.
+   */
+  private long _mapToUnit;
+
+  /**
+   * keeps track of state for field: _mapToUnit
+   */
+  private boolean _has_mapToUnit;
+
+  /**
+   * a region from start to end inclusive
+   */
+  private java.util.Vector _mapListFromList;
+
+  /**
+   * a region from start to end inclusive
+   */
+  private java.util.Vector _mapListToList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public MapListType()
+  {
+    super();
+    this._mapListFromList = new java.util.Vector();
+    this._mapListToList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vMapListFrom
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addMapListFrom(
+          final jalview.schemabinding.version2.MapListFrom vMapListFrom)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._mapListFromList.addElement(vMapListFrom);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vMapListFrom
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addMapListFrom(final int index,
+          final jalview.schemabinding.version2.MapListFrom vMapListFrom)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._mapListFromList.add(index, vMapListFrom);
+  }
+
+  /**
+   * 
+   * 
+   * @param vMapListTo
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addMapListTo(
+          final jalview.schemabinding.version2.MapListTo vMapListTo)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._mapListToList.addElement(vMapListTo);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vMapListTo
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addMapListTo(final int index,
+          final jalview.schemabinding.version2.MapListTo vMapListTo)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._mapListToList.add(index, vMapListTo);
+  }
+
+  /**
+   */
+  public void deleteMapFromUnit()
+  {
+    this._has_mapFromUnit = false;
+  }
+
+  /**
+   */
+  public void deleteMapToUnit()
+  {
+    this._has_mapToUnit = false;
+  }
+
+  /**
+   * Method enumerateMapListFrom.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.MapListFrom
+   *         elements
+   */
+  public java.util.Enumeration enumerateMapListFrom()
+  {
+    return this._mapListFromList.elements();
+  }
+
+  /**
+   * Method enumerateMapListTo.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.MapListTo
+   *         elements
+   */
+  public java.util.Enumeration enumerateMapListTo()
+  {
+    return this._mapListToList.elements();
+  }
+
+  /**
+   * Returns the value of field 'mapFromUnit'. The field 'mapFromUnit' has the
+   * following description: number of dictionary symbol widths involved in each
+   * mapped position on this sequence (for example, 3 for a dna sequence exon
+   * region that is being mapped to a protein sequence). This is optional, since
+   * the unit can be usually be inferred from the dictionary type of each
+   * sequence involved in the mapping.
+   * 
+   * @return the value of field 'MapFromUnit'.
+   */
+  public long getMapFromUnit()
+  {
+    return this._mapFromUnit;
+  }
+
+  /**
+   * Method getMapListFrom.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.MapListFrom at the
+   *         given index
+   */
+  public jalview.schemabinding.version2.MapListFrom getMapListFrom(
+          final int index) throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._mapListFromList.size())
+    {
+      throw new IndexOutOfBoundsException("getMapListFrom: Index value '"
+              + index + "' not in range [0.."
+              + (this._mapListFromList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.MapListFrom) _mapListFromList
+            .get(index);
+  }
+
+  /**
+   * Method getMapListFrom.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.MapListFrom[] getMapListFrom()
+  {
+    jalview.schemabinding.version2.MapListFrom[] array = new jalview.schemabinding.version2.MapListFrom[0];
+    return (jalview.schemabinding.version2.MapListFrom[]) this._mapListFromList
+            .toArray(array);
+  }
+
+  /**
+   * Method getMapListFromCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getMapListFromCount()
+  {
+    return this._mapListFromList.size();
+  }
+
+  /**
+   * Method getMapListTo.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.MapListTo at the
+   *         given index
+   */
+  public jalview.schemabinding.version2.MapListTo getMapListTo(
+          final int index) throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._mapListToList.size())
+    {
+      throw new IndexOutOfBoundsException("getMapListTo: Index value '"
+              + index + "' not in range [0.."
+              + (this._mapListToList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.MapListTo) _mapListToList
+            .get(index);
+  }
+
+  /**
+   * Method getMapListTo.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.MapListTo[] getMapListTo()
+  {
+    jalview.schemabinding.version2.MapListTo[] array = new jalview.schemabinding.version2.MapListTo[0];
+    return (jalview.schemabinding.version2.MapListTo[]) this._mapListToList
+            .toArray(array);
+  }
+
+  /**
+   * Method getMapListToCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getMapListToCount()
+  {
+    return this._mapListToList.size();
+  }
+
+  /**
+   * Returns the value of field 'mapToUnit'. The field 'mapToUnit' has the
+   * following description: number of dictionary symbol widths involved in each
+   * mapped position on this sequence (for example, 3 for a dna sequence exon
+   * region that is being mapped to a protein sequence). This is optional, since
+   * the unit can be usually be inferred from the dictionary type of each
+   * sequence involved in the mapping.
+   * 
+   * @return the value of field 'MapToUnit'.
+   */
+  public long getMapToUnit()
+  {
+    return this._mapToUnit;
+  }
+
+  /**
+   * Method hasMapFromUnit.
+   * 
+   * @return true if at least one MapFromUnit has been added
+   */
+  public boolean hasMapFromUnit()
+  {
+    return this._has_mapFromUnit;
+  }
+
+  /**
+   * Method hasMapToUnit.
+   * 
+   * @return true if at least one MapToUnit has been added
+   */
+  public boolean hasMapToUnit()
+  {
+    return this._has_mapToUnit;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   */
+  public void removeAllMapListFrom()
+  {
+    this._mapListFromList.clear();
+  }
+
+  /**
+   */
+  public void removeAllMapListTo()
+  {
+    this._mapListToList.clear();
+  }
+
+  /**
+   * Method removeMapListFrom.
+   * 
+   * @param vMapListFrom
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeMapListFrom(
+          final jalview.schemabinding.version2.MapListFrom vMapListFrom)
+  {
+    boolean removed = _mapListFromList.remove(vMapListFrom);
+    return removed;
+  }
+
+  /**
+   * Method removeMapListFromAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.MapListFrom removeMapListFromAt(
+          final int index)
+  {
+    java.lang.Object obj = this._mapListFromList.remove(index);
+    return (jalview.schemabinding.version2.MapListFrom) obj;
+  }
+
+  /**
+   * Method removeMapListTo.
+   * 
+   * @param vMapListTo
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeMapListTo(
+          final jalview.schemabinding.version2.MapListTo vMapListTo)
+  {
+    boolean removed = _mapListToList.remove(vMapListTo);
+    return removed;
+  }
+
+  /**
+   * Method removeMapListToAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.MapListTo removeMapListToAt(
+          final int index)
+  {
+    java.lang.Object obj = this._mapListToList.remove(index);
+    return (jalview.schemabinding.version2.MapListTo) obj;
+  }
+
+  /**
+   * Sets the value of field 'mapFromUnit'. The field 'mapFromUnit' has the
+   * following description: number of dictionary symbol widths involved in each
+   * mapped position on this sequence (for example, 3 for a dna sequence exon
+   * region that is being mapped to a protein sequence). This is optional, since
+   * the unit can be usually be inferred from the dictionary type of each
+   * sequence involved in the mapping.
+   * 
+   * @param mapFromUnit
+   *                the value of field 'mapFromUnit'.
+   */
+  public void setMapFromUnit(final long mapFromUnit)
+  {
+    this._mapFromUnit = mapFromUnit;
+    this._has_mapFromUnit = true;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vMapListFrom
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setMapListFrom(final int index,
+          final jalview.schemabinding.version2.MapListFrom vMapListFrom)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._mapListFromList.size())
+    {
+      throw new IndexOutOfBoundsException("setMapListFrom: Index value '"
+              + index + "' not in range [0.."
+              + (this._mapListFromList.size() - 1) + "]");
+    }
+
+    this._mapListFromList.set(index, vMapListFrom);
+  }
+
+  /**
+   * 
+   * 
+   * @param vMapListFromArray
+   */
+  public void setMapListFrom(
+          final jalview.schemabinding.version2.MapListFrom[] vMapListFromArray)
+  {
+    // -- copy array
+    _mapListFromList.clear();
+
+    for (int i = 0; i < vMapListFromArray.length; i++)
+    {
+      this._mapListFromList.add(vMapListFromArray[i]);
+    }
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vMapListTo
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setMapListTo(final int index,
+          final jalview.schemabinding.version2.MapListTo vMapListTo)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._mapListToList.size())
+    {
+      throw new IndexOutOfBoundsException("setMapListTo: Index value '"
+              + index + "' not in range [0.."
+              + (this._mapListToList.size() - 1) + "]");
+    }
+
+    this._mapListToList.set(index, vMapListTo);
+  }
+
+  /**
+   * 
+   * 
+   * @param vMapListToArray
+   */
+  public void setMapListTo(
+          final jalview.schemabinding.version2.MapListTo[] vMapListToArray)
+  {
+    // -- copy array
+    _mapListToList.clear();
+
+    for (int i = 0; i < vMapListToArray.length; i++)
+    {
+      this._mapListToList.add(vMapListToArray[i]);
+    }
+  }
+
+  /**
+   * Sets the value of field 'mapToUnit'. The field 'mapToUnit' has the
+   * following description: number of dictionary symbol widths involved in each
+   * mapped position on this sequence (for example, 3 for a dna sequence exon
+   * region that is being mapped to a protein sequence). This is optional, since
+   * the unit can be usually be inferred from the dictionary type of each
+   * sequence involved in the mapping.
+   * 
+   * @param mapToUnit
+   *                the value of field 'mapToUnit'.
+   */
+  public void setMapToUnit(final long mapToUnit)
+  {
+    this._mapToUnit = mapToUnit;
+    this._has_mapToUnit = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.MapListType
+   */
+  public static jalview.schemabinding.version2.MapListType unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.MapListType) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.MapListType.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/Mapping.java b/src/jalview/schemabinding/version2/Mapping.java
index 8dbc12f..fc9edc9 100644
--- a/src/jalview/schemabinding/version2/Mapping.java
+++ b/src/jalview/schemabinding/version2/Mapping.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,147 +30,159 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Mapping extends jalview.schemabinding.version2.MapListType 
-implements java.io.Serializable
+public class Mapping extends jalview.schemabinding.version2.MapListType
+        implements java.io.Serializable
 {
 
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Internal choice value storage
-     */
-    private java.lang.Object _choiceValue;
-
-    /**
-     * Field _mappingChoice.
-     */
-    private jalview.schemabinding.version2.MappingChoice _mappingChoice;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Mapping() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'choiceValue'. The field
-     * 'choiceValue' has the following description: Internal choice
-     * value storage
-     * 
-     * @return the value of field 'ChoiceValue'.
-     */
-    public java.lang.Object getChoiceValue(
-    ) {
-        return this._choiceValue;
-    }
-
-    /**
-     * Returns the value of field 'mappingChoice'.
-     * 
-     * @return the value of field 'MappingChoice'.
-     */
-    public jalview.schemabinding.version2.MappingChoice getMappingChoice(
-    ) {
-        return this._mappingChoice;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'mappingChoice'.
-     * 
-     * @param mappingChoice the value of field 'mappingChoice'.
-     */
-    public void setMappingChoice(
-            final jalview.schemabinding.version2.MappingChoice mappingChoice) {
-        this._mappingChoice = mappingChoice;
-        this._choiceValue = mappingChoice;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.MapListType
-     */
-    public static jalview.schemabinding.version2.MapListType unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.MapListType) Unmarshaller.unmarshal(jalview.schemabinding.version2.Mapping.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Internal choice value storage
+   */
+  private java.lang.Object _choiceValue;
+
+  /**
+   * Field _mappingChoice.
+   */
+  private jalview.schemabinding.version2.MappingChoice _mappingChoice;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Mapping()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Returns the value of field 'choiceValue'. The field 'choiceValue' has the
+   * following description: Internal choice value storage
+   * 
+   * @return the value of field 'ChoiceValue'.
+   */
+  public java.lang.Object getChoiceValue()
+  {
+    return this._choiceValue;
+  }
+
+  /**
+   * Returns the value of field 'mappingChoice'.
+   * 
+   * @return the value of field 'MappingChoice'.
+   */
+  public jalview.schemabinding.version2.MappingChoice getMappingChoice()
+  {
+    return this._mappingChoice;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'mappingChoice'.
+   * 
+   * @param mappingChoice
+   *                the value of field 'mappingChoice'.
+   */
+  public void setMappingChoice(
+          final jalview.schemabinding.version2.MappingChoice mappingChoice)
+  {
+    this._mappingChoice = mappingChoice;
+    this._choiceValue = mappingChoice;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.MapListType
+   */
+  public static jalview.schemabinding.version2.MapListType unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.MapListType) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.Mapping.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/MappingChoice.java b/src/jalview/schemabinding/version2/MappingChoice.java
index 5f1930d..ae49027 100644
--- a/src/jalview/schemabinding/version2/MappingChoice.java
+++ b/src/jalview/schemabinding/version2/MappingChoice.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,152 +30,168 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class MappingChoice implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _sequence.
-     */
-    private jalview.schemabinding.version2.Sequence _sequence;
-
-    /**
-     * Field _dseqFor.
-     */
-    private java.lang.String _dseqFor;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public MappingChoice() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'dseqFor'.
-     * 
-     * @return the value of field 'DseqFor'.
-     */
-    public java.lang.String getDseqFor(
-    ) {
-        return this._dseqFor;
-    }
-
-    /**
-     * Returns the value of field 'sequence'.
-     * 
-     * @return the value of field 'Sequence'.
-     */
-    public jalview.schemabinding.version2.Sequence getSequence(
-    ) {
-        return this._sequence;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'dseqFor'.
-     * 
-     * @param dseqFor the value of field 'dseqFor'.
-     */
-    public void setDseqFor(
-            final java.lang.String dseqFor) {
-        this._dseqFor = dseqFor;
-    }
-
-    /**
-     * Sets the value of field 'sequence'.
-     * 
-     * @param sequence the value of field 'sequence'.
-     */
-    public void setSequence(
-            final jalview.schemabinding.version2.Sequence sequence) {
-        this._sequence = sequence;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.MappingChoice
-     */
-    public static jalview.schemabinding.version2.MappingChoice unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.MappingChoice) Unmarshaller.unmarshal(jalview.schemabinding.version2.MappingChoice.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class MappingChoice implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _sequence.
+   */
+  private jalview.schemabinding.version2.Sequence _sequence;
+
+  /**
+   * Field _dseqFor.
+   */
+  private java.lang.String _dseqFor;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public MappingChoice()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Returns the value of field 'dseqFor'.
+   * 
+   * @return the value of field 'DseqFor'.
+   */
+  public java.lang.String getDseqFor()
+  {
+    return this._dseqFor;
+  }
+
+  /**
+   * Returns the value of field 'sequence'.
+   * 
+   * @return the value of field 'Sequence'.
+   */
+  public jalview.schemabinding.version2.Sequence getSequence()
+  {
+    return this._sequence;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'dseqFor'.
+   * 
+   * @param dseqFor
+   *                the value of field 'dseqFor'.
+   */
+  public void setDseqFor(final java.lang.String dseqFor)
+  {
+    this._dseqFor = dseqFor;
+  }
+
+  /**
+   * Sets the value of field 'sequence'.
+   * 
+   * @param sequence
+   *                the value of field 'sequence'.
+   */
+  public void setSequence(
+          final jalview.schemabinding.version2.Sequence sequence)
+  {
+    this._sequence = sequence;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.MappingChoice
+   */
+  public static jalview.schemabinding.version2.MappingChoice unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.MappingChoice) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.MappingChoice.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/OtherData.java b/src/jalview/schemabinding/version2/OtherData.java
index 94a5566..54b63a8 100644
--- a/src/jalview/schemabinding/version2/OtherData.java
+++ b/src/jalview/schemabinding/version2/OtherData.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,152 +30,167 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class OtherData implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _key.
-     */
-    private java.lang.String _key;
-
-    /**
-     * Field _value.
-     */
-    private java.lang.String _value;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public OtherData() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'key'.
-     * 
-     * @return the value of field 'Key'.
-     */
-    public java.lang.String getKey(
-    ) {
-        return this._key;
-    }
-
-    /**
-     * Returns the value of field 'value'.
-     * 
-     * @return the value of field 'Value'.
-     */
-    public java.lang.String getValue(
-    ) {
-        return this._value;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'key'.
-     * 
-     * @param key the value of field 'key'.
-     */
-    public void setKey(
-            final java.lang.String key) {
-        this._key = key;
-    }
-
-    /**
-     * Sets the value of field 'value'.
-     * 
-     * @param value the value of field 'value'.
-     */
-    public void setValue(
-            final java.lang.String value) {
-        this._value = value;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.OtherData
-     */
-    public static jalview.schemabinding.version2.OtherData unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.OtherData) Unmarshaller.unmarshal(jalview.schemabinding.version2.OtherData.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class OtherData implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _key.
+   */
+  private java.lang.String _key;
+
+  /**
+   * Field _value.
+   */
+  private java.lang.String _value;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public OtherData()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Returns the value of field 'key'.
+   * 
+   * @return the value of field 'Key'.
+   */
+  public java.lang.String getKey()
+  {
+    return this._key;
+  }
+
+  /**
+   * Returns the value of field 'value'.
+   * 
+   * @return the value of field 'Value'.
+   */
+  public java.lang.String getValue()
+  {
+    return this._value;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'key'.
+   * 
+   * @param key
+   *                the value of field 'key'.
+   */
+  public void setKey(final java.lang.String key)
+  {
+    this._key = key;
+  }
+
+  /**
+   * Sets the value of field 'value'.
+   * 
+   * @param value
+   *                the value of field 'value'.
+   */
+  public void setValue(final java.lang.String value)
+  {
+    this._value = value;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.OtherData
+   */
+  public static jalview.schemabinding.version2.OtherData unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.OtherData) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.OtherData.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/Pdbentry.java b/src/jalview/schemabinding/version2/Pdbentry.java
index 6ff1819..1d4fff0 100755
--- a/src/jalview/schemabinding/version2/Pdbentry.java
+++ b/src/jalview/schemabinding/version2/Pdbentry.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,334 +30,361 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Pdbentry implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _id.
-     */
-    private java.lang.String _id;
-
-    /**
-     * Field _type.
-     */
-    private java.lang.String _type;
-
-    /**
-     * Field _file.
-     */
-    private java.lang.String _file;
-
-    /**
-     * Field _items.
-     */
-    private java.util.Vector _items;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Pdbentry() {
-        super();
-        this._items = new java.util.Vector();
+public class Pdbentry implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _id.
+   */
+  private java.lang.String _id;
+
+  /**
+   * Field _type.
+   */
+  private java.lang.String _type;
+
+  /**
+   * Field _file.
+   */
+  private java.lang.String _file;
+
+  /**
+   * Field _items.
+   */
+  private java.util.Vector _items;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Pdbentry()
+  {
+    super();
+    this._items = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vPdbentryItem
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addPdbentryItem(
+          final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._items.addElement(vPdbentryItem);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vPdbentryItem
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addPdbentryItem(final int index,
+          final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._items.add(index, vPdbentryItem);
+  }
+
+  /**
+   * Method enumeratePdbentryItem.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.PdbentryItem
+   *         elements
+   */
+  public java.util.Enumeration enumeratePdbentryItem()
+  {
+    return this._items.elements();
+  }
+
+  /**
+   * Returns the value of field 'file'.
+   * 
+   * @return the value of field 'File'.
+   */
+  public java.lang.String getFile()
+  {
+    return this._file;
+  }
+
+  /**
+   * Returns the value of field 'id'.
+   * 
+   * @return the value of field 'Id'.
+   */
+  public java.lang.String getId()
+  {
+    return this._id;
+  }
+
+  /**
+   * Method getPdbentryItem.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.PdbentryItem at the
+   *         given inde
+   */
+  public jalview.schemabinding.version2.PdbentryItem getPdbentryItem(
+          final int index) throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._items.size())
+    {
+      throw new IndexOutOfBoundsException("getPdbentryItem: Index value '"
+              + index + "' not in range [0.." + (this._items.size() - 1)
+              + "]");
     }
 
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vPdbentryItem
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addPdbentryItem(
-            final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)
-    throws java.lang.IndexOutOfBoundsException {
-        this._items.addElement(vPdbentryItem);
+    return (jalview.schemabinding.version2.PdbentryItem) _items.get(index);
+  }
+
+  /**
+   * Method getPdbentryItem.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.PdbentryItem[] getPdbentryItem()
+  {
+    jalview.schemabinding.version2.PdbentryItem[] array = new jalview.schemabinding.version2.PdbentryItem[0];
+    return (jalview.schemabinding.version2.PdbentryItem[]) this._items
+            .toArray(array);
+  }
+
+  /**
+   * Method getPdbentryItemCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getPdbentryItemCount()
+  {
+    return this._items.size();
+  }
+
+  /**
+   * Returns the value of field 'type'.
+   * 
+   * @return the value of field 'Type'.
+   */
+  public java.lang.String getType()
+  {
+    return this._type;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vPdbentryItem
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addPdbentryItem(
-            final int index,
-            final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)
-    throws java.lang.IndexOutOfBoundsException {
-        this._items.add(index, vPdbentryItem);
-    }
-
-    /**
-     * Method enumeratePdbentryItem.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.PdbentryItem elements
-     */
-    public java.util.Enumeration enumeratePdbentryItem(
-    ) {
-        return this._items.elements();
-    }
-
-    /**
-     * Returns the value of field 'file'.
-     * 
-     * @return the value of field 'File'.
-     */
-    public java.lang.String getFile(
-    ) {
-        return this._file;
-    }
-
-    /**
-     * Returns the value of field 'id'.
-     * 
-     * @return the value of field 'Id'.
-     */
-    public java.lang.String getId(
-    ) {
-        return this._id;
-    }
-
-    /**
-     * Method getPdbentryItem.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.PdbentryItem at the given inde
-     */
-    public jalview.schemabinding.version2.PdbentryItem getPdbentryItem(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._items.size()) {
-            throw new IndexOutOfBoundsException("getPdbentryItem: Index value '" + index + "' not in range [0.." + (this._items.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.PdbentryItem) _items.get(index);
-    }
-
-    /**
-     * Method getPdbentryItem.Returns the contents of the
-     * collection in an Array.  <p>Note:  Just in case the
-     * collection contents are changing in another thread, we pass
-     * a 0-length Array of the correct type into the API call. 
-     * This way we <i>know</i> that the Array returned is of
-     * exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.PdbentryItem[] getPdbentryItem(
-    ) {
-        jalview.schemabinding.version2.PdbentryItem[] array = new jalview.schemabinding.version2.PdbentryItem[0];
-        return (jalview.schemabinding.version2.PdbentryItem[]) this._items.toArray(array);
-    }
-
-    /**
-     * Method getPdbentryItemCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getPdbentryItemCount(
-    ) {
-        return this._items.size();
-    }
-
-    /**
-     * Returns the value of field 'type'.
-     * 
-     * @return the value of field 'Type'.
-     */
-    public java.lang.String getType(
-    ) {
-        return this._type;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     */
-    public void removeAllPdbentryItem(
-    ) {
-        this._items.clear();
-    }
-
-    /**
-     * Method removePdbentryItem.
-     * 
-     * @param vPdbentryItem
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removePdbentryItem(
-            final jalview.schemabinding.version2.PdbentryItem vPdbentryItem) {
-        boolean removed = _items.remove(vPdbentryItem);
-        return removed;
-    }
-
-    /**
-     * Method removePdbentryItemAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.PdbentryItem removePdbentryItemAt(
-            final int index) {
-        java.lang.Object obj = this._items.remove(index);
-        return (jalview.schemabinding.version2.PdbentryItem) obj;
-    }
-
-    /**
-     * Sets the value of field 'file'.
-     * 
-     * @param file the value of field 'file'.
-     */
-    public void setFile(
-            final java.lang.String file) {
-        this._file = file;
-    }
-
-    /**
-     * Sets the value of field 'id'.
-     * 
-     * @param id the value of field 'id'.
-     */
-    public void setId(
-            final java.lang.String id) {
-        this._id = id;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vPdbentryItem
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setPdbentryItem(
-            final int index,
-            final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._items.size()) {
-            throw new IndexOutOfBoundsException("setPdbentryItem: Index value '" + index + "' not in range [0.." + (this._items.size() - 1) + "]");
-        }
-        
-        this._items.set(index, vPdbentryItem);
-    }
-
-    /**
-     * 
-     * 
-     * @param vPdbentryItemArray
-     */
-    public void setPdbentryItem(
-            final jalview.schemabinding.version2.PdbentryItem[] vPdbentryItemArray) {
-        //-- copy array
-        _items.clear();
-        
-        for (int i = 0; i < vPdbentryItemArray.length; i++) {
-                this._items.add(vPdbentryItemArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of field 'type'.
-     * 
-     * @param type the value of field 'type'.
-     */
-    public void setType(
-            final java.lang.String type) {
-        this._type = type;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.Pdbentry
-     */
-    public static jalview.schemabinding.version2.Pdbentry unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.Pdbentry) Unmarshaller.unmarshal(jalview.schemabinding.version2.Pdbentry.class, reader);
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   */
+  public void removeAllPdbentryItem()
+  {
+    this._items.clear();
+  }
+
+  /**
+   * Method removePdbentryItem.
+   * 
+   * @param vPdbentryItem
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removePdbentryItem(
+          final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)
+  {
+    boolean removed = _items.remove(vPdbentryItem);
+    return removed;
+  }
+
+  /**
+   * Method removePdbentryItemAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.PdbentryItem removePdbentryItemAt(
+          final int index)
+  {
+    java.lang.Object obj = this._items.remove(index);
+    return (jalview.schemabinding.version2.PdbentryItem) obj;
+  }
+
+  /**
+   * Sets the value of field 'file'.
+   * 
+   * @param file
+   *                the value of field 'file'.
+   */
+  public void setFile(final java.lang.String file)
+  {
+    this._file = file;
+  }
+
+  /**
+   * Sets the value of field 'id'.
+   * 
+   * @param id
+   *                the value of field 'id'.
+   */
+  public void setId(final java.lang.String id)
+  {
+    this._id = id;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vPdbentryItem
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setPdbentryItem(final int index,
+          final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._items.size())
+    {
+      throw new IndexOutOfBoundsException("setPdbentryItem: Index value '"
+              + index + "' not in range [0.." + (this._items.size() - 1)
+              + "]");
     }
 
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+    this._items.set(index, vPdbentryItem);
+  }
+
+  /**
+   * 
+   * 
+   * @param vPdbentryItemArray
+   */
+  public void setPdbentryItem(
+          final jalview.schemabinding.version2.PdbentryItem[] vPdbentryItemArray)
+  {
+    // -- copy array
+    _items.clear();
+
+    for (int i = 0; i < vPdbentryItemArray.length; i++)
+    {
+      this._items.add(vPdbentryItemArray[i]);
     }
+  }
+
+  /**
+   * Sets the value of field 'type'.
+   * 
+   * @param type
+   *                the value of field 'type'.
+   */
+  public void setType(final java.lang.String type)
+  {
+    this._type = type;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.Pdbentry
+   */
+  public static jalview.schemabinding.version2.Pdbentry unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.Pdbentry) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.Pdbentry.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/PdbentryItem.java b/src/jalview/schemabinding/version2/PdbentryItem.java
index 3dbc99c..94de615 100755
--- a/src/jalview/schemabinding/version2/PdbentryItem.java
+++ b/src/jalview/schemabinding/version2/PdbentryItem.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
 /**
@@ -12,181 +23,193 @@ package jalview.schemabinding.version2;
  * 
  * @version $Revision$ $Date$
  */
-public class PdbentryItem implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _propertyList.
-     */
-    private java.util.Vector _propertyList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public PdbentryItem() {
-        super();
-        this._propertyList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vProperty
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addProperty(
-            final jalview.schemabinding.version2.Property vProperty)
-    throws java.lang.IndexOutOfBoundsException {
-        this._propertyList.addElement(vProperty);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vProperty
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addProperty(
-            final int index,
-            final jalview.schemabinding.version2.Property vProperty)
-    throws java.lang.IndexOutOfBoundsException {
-        this._propertyList.add(index, vProperty);
-    }
-
-    /**
-     * Method enumerateProperty.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.Property elements
-     */
-    public java.util.Enumeration enumerateProperty(
-    ) {
-        return this._propertyList.elements();
-    }
-
-    /**
-     * Method getProperty.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.Property at the given index
-     */
-    public jalview.schemabinding.version2.Property getProperty(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._propertyList.size()) {
-            throw new IndexOutOfBoundsException("getProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.Property) _propertyList.get(index);
-    }
-
-    /**
-     * Method getProperty.Returns the contents of the collection in
-     * an Array.  <p>Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we <i>know</i>
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.Property[] getProperty(
-    ) {
-        jalview.schemabinding.version2.Property[] array = new jalview.schemabinding.version2.Property[0];
-        return (jalview.schemabinding.version2.Property[]) this._propertyList.toArray(array);
-    }
-
-    /**
-     * Method getPropertyCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getPropertyCount(
-    ) {
-        return this._propertyList.size();
-    }
-
-    /**
-     */
-    public void removeAllProperty(
-    ) {
-        this._propertyList.clear();
-    }
-
-    /**
-     * Method removeProperty.
-     * 
-     * @param vProperty
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeProperty(
-            final jalview.schemabinding.version2.Property vProperty) {
-        boolean removed = _propertyList.remove(vProperty);
-        return removed;
-    }
-
-    /**
-     * Method removePropertyAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.Property removePropertyAt(
-            final int index) {
-        java.lang.Object obj = this._propertyList.remove(index);
-        return (jalview.schemabinding.version2.Property) obj;
+public class PdbentryItem implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _propertyList.
+   */
+  private java.util.Vector _propertyList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public PdbentryItem()
+  {
+    super();
+    this._propertyList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vProperty
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addProperty(
+          final jalview.schemabinding.version2.Property vProperty)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._propertyList.addElement(vProperty);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vProperty
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addProperty(final int index,
+          final jalview.schemabinding.version2.Property vProperty)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._propertyList.add(index, vProperty);
+  }
+
+  /**
+   * Method enumerateProperty.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.Property
+   *         elements
+   */
+  public java.util.Enumeration enumerateProperty()
+  {
+    return this._propertyList.elements();
+  }
+
+  /**
+   * Method getProperty.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.Property at the
+   *         given index
+   */
+  public jalview.schemabinding.version2.Property getProperty(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._propertyList.size())
+    {
+      throw new IndexOutOfBoundsException("getProperty: Index value '"
+              + index + "' not in range [0.."
+              + (this._propertyList.size() - 1) + "]");
     }
 
-    /**
-     * 
-     * 
-     * @param index
-     * @param vProperty
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setProperty(
-            final int index,
-            final jalview.schemabinding.version2.Property vProperty)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._propertyList.size()) {
-            throw new IndexOutOfBoundsException("setProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
-        }
-        
-        this._propertyList.set(index, vProperty);
+    return (jalview.schemabinding.version2.Property) _propertyList
+            .get(index);
+  }
+
+  /**
+   * Method getProperty.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.Property[] getProperty()
+  {
+    jalview.schemabinding.version2.Property[] array = new jalview.schemabinding.version2.Property[0];
+    return (jalview.schemabinding.version2.Property[]) this._propertyList
+            .toArray(array);
+  }
+
+  /**
+   * Method getPropertyCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getPropertyCount()
+  {
+    return this._propertyList.size();
+  }
+
+  /**
+   */
+  public void removeAllProperty()
+  {
+    this._propertyList.clear();
+  }
+
+  /**
+   * Method removeProperty.
+   * 
+   * @param vProperty
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeProperty(
+          final jalview.schemabinding.version2.Property vProperty)
+  {
+    boolean removed = _propertyList.remove(vProperty);
+    return removed;
+  }
+
+  /**
+   * Method removePropertyAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.Property removePropertyAt(
+          final int index)
+  {
+    java.lang.Object obj = this._propertyList.remove(index);
+    return (jalview.schemabinding.version2.Property) obj;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vProperty
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setProperty(final int index,
+          final jalview.schemabinding.version2.Property vProperty)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._propertyList.size())
+    {
+      throw new IndexOutOfBoundsException("setProperty: Index value '"
+              + index + "' not in range [0.."
+              + (this._propertyList.size() - 1) + "]");
     }
 
-    /**
-     * 
-     * 
-     * @param vPropertyArray
-     */
-    public void setProperty(
-            final jalview.schemabinding.version2.Property[] vPropertyArray) {
-        //-- copy array
-        _propertyList.clear();
-        
-        for (int i = 0; i < vPropertyArray.length; i++) {
-                this._propertyList.add(vPropertyArray[i]);
-        }
+    this._propertyList.set(index, vProperty);
+  }
+
+  /**
+   * 
+   * 
+   * @param vPropertyArray
+   */
+  public void setProperty(
+          final jalview.schemabinding.version2.Property[] vPropertyArray)
+  {
+    // -- copy array
+    _propertyList.clear();
+
+    for (int i = 0; i < vPropertyArray.length; i++)
+    {
+      this._propertyList.add(vPropertyArray[i]);
     }
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/Pdbids.java b/src/jalview/schemabinding/version2/Pdbids.java
index 04685b9..d0556c0 100755
--- a/src/jalview/schemabinding/version2/Pdbids.java
+++ b/src/jalview/schemabinding/version2/Pdbids.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,262 +30,289 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Pdbids extends jalview.schemabinding.version2.Pdbentry 
-implements java.io.Serializable
+public class Pdbids extends jalview.schemabinding.version2.Pdbentry
+        implements java.io.Serializable
 {
 
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
 
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
+  /**
+   * Field _structureStateList.
+   */
+  private java.util.Vector _structureStateList;
 
-    /**
-     * Field _structureStateList.
-     */
-    private java.util.Vector _structureStateList;
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
 
+  public Pdbids()
+  {
+    super();
+    this._structureStateList = new java.util.Vector();
+  }
 
-      //----------------/
-     //- Constructors -/
-    //----------------/
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    public Pdbids() {
-        super();
-        this._structureStateList = new java.util.Vector();
-    }
+  /**
+   * 
+   * 
+   * @param vStructureState
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addStructureState(
+          final jalview.schemabinding.version2.StructureState vStructureState)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._structureStateList.addElement(vStructureState);
+  }
 
+  /**
+   * 
+   * 
+   * @param index
+   * @param vStructureState
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addStructureState(
+          final int index,
+          final jalview.schemabinding.version2.StructureState vStructureState)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._structureStateList.add(index, vStructureState);
+  }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+  /**
+   * Method enumerateStructureState.
+   * 
+   * @return an Enumeration over all
+   *         jalview.schemabinding.version2.StructureState elements
+   */
+  public java.util.Enumeration enumerateStructureState()
+  {
+    return this._structureStateList.elements();
+  }
 
-    /**
-     * 
-     * 
-     * @param vStructureState
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addStructureState(
-            final jalview.schemabinding.version2.StructureState vStructureState)
-    throws java.lang.IndexOutOfBoundsException {
-        this._structureStateList.addElement(vStructureState);
+  /**
+   * Method getStructureState.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.StructureState at
+   *         the given index
+   */
+  public jalview.schemabinding.version2.StructureState getStructureState(
+          final int index) throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._structureStateList.size())
+    {
+      throw new IndexOutOfBoundsException(
+              "getStructureState: Index value '" + index
+                      + "' not in range [0.."
+                      + (this._structureStateList.size() - 1) + "]");
     }
 
-    /**
-     * 
-     * 
-     * @param index
-     * @param vStructureState
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addStructureState(
-            final int index,
-            final jalview.schemabinding.version2.StructureState vStructureState)
-    throws java.lang.IndexOutOfBoundsException {
-        this._structureStateList.add(index, vStructureState);
-    }
+    return (jalview.schemabinding.version2.StructureState) _structureStateList
+            .get(index);
+  }
 
-    /**
-     * Method enumerateStructureState.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.StructureState elements
-     */
-    public java.util.Enumeration enumerateStructureState(
-    ) {
-        return this._structureStateList.elements();
-    }
+  /**
+   * Method getStructureState.Returns the contents of the collection in an
+   * Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.StructureState[] getStructureState()
+  {
+    jalview.schemabinding.version2.StructureState[] array = new jalview.schemabinding.version2.StructureState[0];
+    return (jalview.schemabinding.version2.StructureState[]) this._structureStateList
+            .toArray(array);
+  }
 
-    /**
-     * Method getStructureState.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.StructureState at the given
-     * index
-     */
-    public jalview.schemabinding.version2.StructureState getStructureState(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._structureStateList.size()) {
-            throw new IndexOutOfBoundsException("getStructureState: Index value '" + index + "' not in range [0.." + (this._structureStateList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.StructureState) _structureStateList.get(index);
-    }
+  /**
+   * Method getStructureStateCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getStructureStateCount()
+  {
+    return this._structureStateList.size();
+  }
 
-    /**
-     * Method getStructureState.Returns the contents of the
-     * collection in an Array.  <p>Note:  Just in case the
-     * collection contents are changing in another thread, we pass
-     * a 0-length Array of the correct type into the API call. 
-     * This way we <i>know</i> that the Array returned is of
-     * exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.StructureState[] getStructureState(
-    ) {
-        jalview.schemabinding.version2.StructureState[] array = new jalview.schemabinding.version2.StructureState[0];
-        return (jalview.schemabinding.version2.StructureState[]) this._structureStateList.toArray(array);
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
 
-    /**
-     * Method getStructureStateCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getStructureStateCount(
-    ) {
-        return this._structureStateList.size();
-    }
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
 
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
 
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
+  /**
+   */
+  public void removeAllStructureState()
+  {
+    this._structureStateList.clear();
+  }
 
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
+  /**
+   * Method removeStructureState.
+   * 
+   * @param vStructureState
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeStructureState(
+          final jalview.schemabinding.version2.StructureState vStructureState)
+  {
+    boolean removed = _structureStateList.remove(vStructureState);
+    return removed;
+  }
 
-    /**
-     */
-    public void removeAllStructureState(
-    ) {
-        this._structureStateList.clear();
-    }
+  /**
+   * Method removeStructureStateAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.StructureState removeStructureStateAt(
+          final int index)
+  {
+    java.lang.Object obj = this._structureStateList.remove(index);
+    return (jalview.schemabinding.version2.StructureState) obj;
+  }
 
-    /**
-     * Method removeStructureState.
-     * 
-     * @param vStructureState
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeStructureState(
-            final jalview.schemabinding.version2.StructureState vStructureState) {
-        boolean removed = _structureStateList.remove(vStructureState);
-        return removed;
+  /**
+   * 
+   * 
+   * @param index
+   * @param vStructureState
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setStructureState(
+          final int index,
+          final jalview.schemabinding.version2.StructureState vStructureState)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._structureStateList.size())
+    {
+      throw new IndexOutOfBoundsException(
+              "setStructureState: Index value '" + index
+                      + "' not in range [0.."
+                      + (this._structureStateList.size() - 1) + "]");
     }
 
-    /**
-     * Method removeStructureStateAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.StructureState removeStructureStateAt(
-            final int index) {
-        java.lang.Object obj = this._structureStateList.remove(index);
-        return (jalview.schemabinding.version2.StructureState) obj;
-    }
+    this._structureStateList.set(index, vStructureState);
+  }
 
-    /**
-     * 
-     * 
-     * @param index
-     * @param vStructureState
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setStructureState(
-            final int index,
-            final jalview.schemabinding.version2.StructureState vStructureState)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._structureStateList.size()) {
-            throw new IndexOutOfBoundsException("setStructureState: Index value '" + index + "' not in range [0.." + (this._structureStateList.size() - 1) + "]");
-        }
-        
-        this._structureStateList.set(index, vStructureState);
-    }
+  /**
+   * 
+   * 
+   * @param vStructureStateArray
+   */
+  public void setStructureState(
+          final jalview.schemabinding.version2.StructureState[] vStructureStateArray)
+  {
+    // -- copy array
+    _structureStateList.clear();
 
-    /**
-     * 
-     * 
-     * @param vStructureStateArray
-     */
-    public void setStructureState(
-            final jalview.schemabinding.version2.StructureState[] vStructureStateArray) {
-        //-- copy array
-        _structureStateList.clear();
-        
-        for (int i = 0; i < vStructureStateArray.length; i++) {
-                this._structureStateList.add(vStructureStateArray[i]);
-        }
+    for (int i = 0; i < vStructureStateArray.length; i++)
+    {
+      this._structureStateList.add(vStructureStateArray[i]);
     }
+  }
 
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.Pdbentry
-     */
-    public static jalview.schemabinding.version2.Pdbentry unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.Pdbentry) Unmarshaller.unmarshal(jalview.schemabinding.version2.Pdbids.class, reader);
-    }
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.Pdbentry
+   */
+  public static jalview.schemabinding.version2.Pdbentry unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.Pdbentry) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.Pdbids.class, reader);
+  }
 
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/Property.java b/src/jalview/schemabinding/version2/Property.java
index bfc4dde..ce54ffd 100755
--- a/src/jalview/schemabinding/version2/Property.java
+++ b/src/jalview/schemabinding/version2/Property.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,152 +30,167 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Property implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _name.
-     */
-    private java.lang.String _name;
-
-    /**
-     * Field _value.
-     */
-    private java.lang.String _value;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Property() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'name'.
-     * 
-     * @return the value of field 'Name'.
-     */
-    public java.lang.String getName(
-    ) {
-        return this._name;
-    }
-
-    /**
-     * Returns the value of field 'value'.
-     * 
-     * @return the value of field 'Value'.
-     */
-    public java.lang.String getValue(
-    ) {
-        return this._value;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'name'.
-     * 
-     * @param name the value of field 'name'.
-     */
-    public void setName(
-            final java.lang.String name) {
-        this._name = name;
-    }
-
-    /**
-     * Sets the value of field 'value'.
-     * 
-     * @param value the value of field 'value'.
-     */
-    public void setValue(
-            final java.lang.String value) {
-        this._value = value;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.Property
-     */
-    public static jalview.schemabinding.version2.Property unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.Property) Unmarshaller.unmarshal(jalview.schemabinding.version2.Property.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class Property implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _name.
+   */
+  private java.lang.String _name;
+
+  /**
+   * Field _value.
+   */
+  private java.lang.String _value;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Property()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Returns the value of field 'name'.
+   * 
+   * @return the value of field 'Name'.
+   */
+  public java.lang.String getName()
+  {
+    return this._name;
+  }
+
+  /**
+   * Returns the value of field 'value'.
+   * 
+   * @return the value of field 'Value'.
+   */
+  public java.lang.String getValue()
+  {
+    return this._value;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'name'.
+   * 
+   * @param name
+   *                the value of field 'name'.
+   */
+  public void setName(final java.lang.String name)
+  {
+    this._name = name;
+  }
+
+  /**
+   * Sets the value of field 'value'.
+   * 
+   * @param value
+   *                the value of field 'value'.
+   */
+  public void setValue(final java.lang.String value)
+  {
+    this._value = value;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.Property
+   */
+  public static jalview.schemabinding.version2.Property unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.Property) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.Property.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/Sequence.java b/src/jalview/schemabinding/version2/Sequence.java
index e606eeb..7360772 100755
--- a/src/jalview/schemabinding/version2/Sequence.java
+++ b/src/jalview/schemabinding/version2/Sequence.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,293 +30,314 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Sequence extends jalview.schemabinding.version2.SequenceType 
-implements java.io.Serializable
+public class Sequence extends jalview.schemabinding.version2.SequenceType
+        implements java.io.Serializable
 {
 
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * dataset sequence id for this sequence. Will be created as
-     * union of sequences.
-     *  
-     */
-    private java.lang.String _dsseqid;
-
-    /**
-     * Field _DBRefList.
-     */
-    private java.util.Vector _DBRefList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Sequence() {
-        super();
-        this._DBRefList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vDBRef
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addDBRef(
-            final jalview.schemabinding.version2.DBRef vDBRef)
-    throws java.lang.IndexOutOfBoundsException {
-        this._DBRefList.addElement(vDBRef);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vDBRef
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addDBRef(
-            final int index,
-            final jalview.schemabinding.version2.DBRef vDBRef)
-    throws java.lang.IndexOutOfBoundsException {
-        this._DBRefList.add(index, vDBRef);
-    }
-
-    /**
-     * Method enumerateDBRef.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.DBRef elements
-     */
-    public java.util.Enumeration enumerateDBRef(
-    ) {
-        return this._DBRefList.elements();
-    }
-
-    /**
-     * Method getDBRef.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.DBRef at the given index
-     */
-    public jalview.schemabinding.version2.DBRef getDBRef(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._DBRefList.size()) {
-            throw new IndexOutOfBoundsException("getDBRef: Index value '" + index + "' not in range [0.." + (this._DBRefList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.DBRef) _DBRefList.get(index);
-    }
-
-    /**
-     * Method getDBRef.Returns the contents of the collection in an
-     * Array.  <p>Note:  Just in case the collection contents are
-     * changing in another thread, we pass a 0-length Array of the
-     * correct type into the API call.  This way we <i>know</i>
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.DBRef[] getDBRef(
-    ) {
-        jalview.schemabinding.version2.DBRef[] array = new jalview.schemabinding.version2.DBRef[0];
-        return (jalview.schemabinding.version2.DBRef[]) this._DBRefList.toArray(array);
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * dataset sequence id for this sequence. Will be created as union of
+   * sequences.
+   * 
+   */
+  private java.lang.String _dsseqid;
+
+  /**
+   * Field _DBRefList.
+   */
+  private java.util.Vector _DBRefList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Sequence()
+  {
+    super();
+    this._DBRefList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vDBRef
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addDBRef(final jalview.schemabinding.version2.DBRef vDBRef)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._DBRefList.addElement(vDBRef);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vDBRef
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addDBRef(final int index,
+          final jalview.schemabinding.version2.DBRef vDBRef)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._DBRefList.add(index, vDBRef);
+  }
+
+  /**
+   * Method enumerateDBRef.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.DBRef
+   *         elements
+   */
+  public java.util.Enumeration enumerateDBRef()
+  {
+    return this._DBRefList.elements();
+  }
+
+  /**
+   * Method getDBRef.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.DBRef at the given
+   *         index
+   */
+  public jalview.schemabinding.version2.DBRef getDBRef(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._DBRefList.size())
+    {
+      throw new IndexOutOfBoundsException("getDBRef: Index value '" + index
+              + "' not in range [0.." + (this._DBRefList.size() - 1) + "]");
     }
 
-    /**
-     * Method getDBRefCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getDBRefCount(
-    ) {
-        return this._DBRefList.size();
+    return (jalview.schemabinding.version2.DBRef) _DBRefList.get(index);
+  }
+
+  /**
+   * Method getDBRef.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.DBRef[] getDBRef()
+  {
+    jalview.schemabinding.version2.DBRef[] array = new jalview.schemabinding.version2.DBRef[0];
+    return (jalview.schemabinding.version2.DBRef[]) this._DBRefList
+            .toArray(array);
+  }
+
+  /**
+   * Method getDBRefCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getDBRefCount()
+  {
+    return this._DBRefList.size();
+  }
+
+  /**
+   * Returns the value of field 'dsseqid'. The field 'dsseqid' has the following
+   * description: dataset sequence id for this sequence. Will be created as
+   * union of sequences.
+   * 
+   * 
+   * @return the value of field 'Dsseqid'.
+   */
+  public java.lang.String getDsseqid()
+  {
+    return this._dsseqid;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
-
-    /**
-     * Returns the value of field 'dsseqid'. The field 'dsseqid'
-     * has the following description: dataset sequence id for this
-     * sequence. Will be created as union of sequences.
-     *  
-     * 
-     * @return the value of field 'Dsseqid'.
-     */
-    public java.lang.String getDsseqid(
-    ) {
-        return this._dsseqid;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     */
-    public void removeAllDBRef(
-    ) {
-        this._DBRefList.clear();
-    }
-
-    /**
-     * Method removeDBRef.
-     * 
-     * @param vDBRef
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeDBRef(
-            final jalview.schemabinding.version2.DBRef vDBRef) {
-        boolean removed = _DBRefList.remove(vDBRef);
-        return removed;
-    }
-
-    /**
-     * Method removeDBRefAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.DBRef removeDBRefAt(
-            final int index) {
-        java.lang.Object obj = this._DBRefList.remove(index);
-        return (jalview.schemabinding.version2.DBRef) obj;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vDBRef
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setDBRef(
-            final int index,
-            final jalview.schemabinding.version2.DBRef vDBRef)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._DBRefList.size()) {
-            throw new IndexOutOfBoundsException("setDBRef: Index value '" + index + "' not in range [0.." + (this._DBRefList.size() - 1) + "]");
-        }
-        
-        this._DBRefList.set(index, vDBRef);
-    }
-
-    /**
-     * 
-     * 
-     * @param vDBRefArray
-     */
-    public void setDBRef(
-            final jalview.schemabinding.version2.DBRef[] vDBRefArray) {
-        //-- copy array
-        _DBRefList.clear();
-        
-        for (int i = 0; i < vDBRefArray.length; i++) {
-                this._DBRefList.add(vDBRefArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of field 'dsseqid'. The field 'dsseqid' has
-     * the following description: dataset sequence id for this
-     * sequence. Will be created as union of sequences.
-     *  
-     * 
-     * @param dsseqid the value of field 'dsseqid'.
-     */
-    public void setDsseqid(
-            final java.lang.String dsseqid) {
-        this._dsseqid = dsseqid;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.SequenceType
-     */
-    public static jalview.schemabinding.version2.SequenceType unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.SequenceType) Unmarshaller.unmarshal(jalview.schemabinding.version2.Sequence.class, reader);
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   */
+  public void removeAllDBRef()
+  {
+    this._DBRefList.clear();
+  }
+
+  /**
+   * Method removeDBRef.
+   * 
+   * @param vDBRef
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeDBRef(
+          final jalview.schemabinding.version2.DBRef vDBRef)
+  {
+    boolean removed = _DBRefList.remove(vDBRef);
+    return removed;
+  }
+
+  /**
+   * Method removeDBRefAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.DBRef removeDBRefAt(final int index)
+  {
+    java.lang.Object obj = this._DBRefList.remove(index);
+    return (jalview.schemabinding.version2.DBRef) obj;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vDBRef
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setDBRef(final int index,
+          final jalview.schemabinding.version2.DBRef vDBRef)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._DBRefList.size())
+    {
+      throw new IndexOutOfBoundsException("setDBRef: Index value '" + index
+              + "' not in range [0.." + (this._DBRefList.size() - 1) + "]");
     }
 
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+    this._DBRefList.set(index, vDBRef);
+  }
+
+  /**
+   * 
+   * 
+   * @param vDBRefArray
+   */
+  public void setDBRef(
+          final jalview.schemabinding.version2.DBRef[] vDBRefArray)
+  {
+    // -- copy array
+    _DBRefList.clear();
+
+    for (int i = 0; i < vDBRefArray.length; i++)
+    {
+      this._DBRefList.add(vDBRefArray[i]);
     }
+  }
+
+  /**
+   * Sets the value of field 'dsseqid'. The field 'dsseqid' has the following
+   * description: dataset sequence id for this sequence. Will be created as
+   * union of sequences.
+   * 
+   * 
+   * @param dsseqid
+   *                the value of field 'dsseqid'.
+   */
+  public void setDsseqid(final java.lang.String dsseqid)
+  {
+    this._dsseqid = dsseqid;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.SequenceType
+   */
+  public static jalview.schemabinding.version2.SequenceType unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.SequenceType) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.Sequence.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/SequenceSet.java b/src/jalview/schemabinding/version2/SequenceSet.java
index 481c37f..3179078 100755
--- a/src/jalview/schemabinding/version2/SequenceSet.java
+++ b/src/jalview/schemabinding/version2/SequenceSet.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,789 +30,858 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class SequenceSet implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _gapChar.
-     */
-    private java.lang.String _gapChar;
-
-    /**
-     * reference to set where jalview will gather the dataset
-     * sequences for all sequences in the set. 
-     *  
-     */
-    private java.lang.String _datasetId;
-
-    /**
-     * Field _sequenceList.
-     */
-    private java.util.Vector _sequenceList;
-
-    /**
-     * Field _annotationList.
-     */
-    private java.util.Vector _annotationList;
-
-    /**
-     * Field _sequenceSetPropertiesList.
-     */
-    private java.util.Vector _sequenceSetPropertiesList;
-
-    /**
-     * Field _alcodonFrameList.
-     */
-    private java.util.Vector _alcodonFrameList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public SequenceSet() {
-        super();
-        this._sequenceList = new java.util.Vector();
-        this._annotationList = new java.util.Vector();
-        this._sequenceSetPropertiesList = new java.util.Vector();
-        this._alcodonFrameList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vAlcodonFrame
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addAlcodonFrame(
-            final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)
-    throws java.lang.IndexOutOfBoundsException {
-        this._alcodonFrameList.addElement(vAlcodonFrame);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vAlcodonFrame
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addAlcodonFrame(
-            final int index,
-            final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)
-    throws java.lang.IndexOutOfBoundsException {
-        this._alcodonFrameList.add(index, vAlcodonFrame);
-    }
-
-    /**
-     * 
-     * 
-     * @param vAnnotation
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addAnnotation(
-            final jalview.schemabinding.version2.Annotation vAnnotation)
-    throws java.lang.IndexOutOfBoundsException {
-        this._annotationList.addElement(vAnnotation);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vAnnotation
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addAnnotation(
-            final int index,
-            final jalview.schemabinding.version2.Annotation vAnnotation)
-    throws java.lang.IndexOutOfBoundsException {
-        this._annotationList.add(index, vAnnotation);
-    }
-
-    /**
-     * 
-     * 
-     * @param vSequence
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSequence(
-            final jalview.schemabinding.version2.Sequence vSequence)
-    throws java.lang.IndexOutOfBoundsException {
-        this._sequenceList.addElement(vSequence);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSequence
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSequence(
-            final int index,
-            final jalview.schemabinding.version2.Sequence vSequence)
-    throws java.lang.IndexOutOfBoundsException {
-        this._sequenceList.add(index, vSequence);
-    }
-
-    /**
-     * 
-     * 
-     * @param vSequenceSetProperties
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSequenceSetProperties(
-            final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
-    throws java.lang.IndexOutOfBoundsException {
-        this._sequenceSetPropertiesList.addElement(vSequenceSetProperties);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSequenceSetProperties
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSequenceSetProperties(
-            final int index,
-            final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
-    throws java.lang.IndexOutOfBoundsException {
-        this._sequenceSetPropertiesList.add(index, vSequenceSetProperties);
-    }
-
-    /**
-     * Method enumerateAlcodonFrame.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.AlcodonFrame elements
-     */
-    public java.util.Enumeration enumerateAlcodonFrame(
-    ) {
-        return this._alcodonFrameList.elements();
-    }
-
-    /**
-     * Method enumerateAnnotation.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.Annotation elements
-     */
-    public java.util.Enumeration enumerateAnnotation(
-    ) {
-        return this._annotationList.elements();
-    }
-
-    /**
-     * Method enumerateSequence.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.Sequence elements
-     */
-    public java.util.Enumeration enumerateSequence(
-    ) {
-        return this._sequenceList.elements();
-    }
-
-    /**
-     * Method enumerateSequenceSetProperties.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.SequenceSetProperties elements
-     */
-    public java.util.Enumeration enumerateSequenceSetProperties(
-    ) {
-        return this._sequenceSetPropertiesList.elements();
-    }
-
-    /**
-     * Method getAlcodonFrame.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.AlcodonFrame at the given inde
-     */
-    public jalview.schemabinding.version2.AlcodonFrame getAlcodonFrame(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._alcodonFrameList.size()) {
-            throw new IndexOutOfBoundsException("getAlcodonFrame: Index value '" + index + "' not in range [0.." + (this._alcodonFrameList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.AlcodonFrame) _alcodonFrameList.get(index);
-    }
-
-    /**
-     * Method getAlcodonFrame.Returns the contents of the
-     * collection in an Array.  <p>Note:  Just in case the
-     * collection contents are changing in another thread, we pass
-     * a 0-length Array of the correct type into the API call. 
-     * This way we <i>know</i> that the Array returned is of
-     * exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.AlcodonFrame[] getAlcodonFrame(
-    ) {
-        jalview.schemabinding.version2.AlcodonFrame[] array = new jalview.schemabinding.version2.AlcodonFrame[0];
-        return (jalview.schemabinding.version2.AlcodonFrame[]) this._alcodonFrameList.toArray(array);
-    }
-
-    /**
-     * Method getAlcodonFrameCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getAlcodonFrameCount(
-    ) {
-        return this._alcodonFrameList.size();
-    }
-
-    /**
-     * Method getAnnotation.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.Annotation at the given index
-     */
-    public jalview.schemabinding.version2.Annotation getAnnotation(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._annotationList.size()) {
-            throw new IndexOutOfBoundsException("getAnnotation: Index value '" + index + "' not in range [0.." + (this._annotationList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.Annotation) _annotationList.get(index);
-    }
-
-    /**
-     * Method getAnnotation.Returns the contents of the collection
-     * in an Array.  <p>Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we <i>know</i>
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.Annotation[] getAnnotation(
-    ) {
-        jalview.schemabinding.version2.Annotation[] array = new jalview.schemabinding.version2.Annotation[0];
-        return (jalview.schemabinding.version2.Annotation[]) this._annotationList.toArray(array);
-    }
-
-    /**
-     * Method getAnnotationCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getAnnotationCount(
-    ) {
-        return this._annotationList.size();
-    }
-
-    /**
-     * Returns the value of field 'datasetId'. The field
-     * 'datasetId' has the following description: reference to set
-     * where jalview will gather the dataset sequences for all
-     * sequences in the set. 
-     *  
-     * 
-     * @return the value of field 'DatasetId'.
-     */
-    public java.lang.String getDatasetId(
-    ) {
-        return this._datasetId;
-    }
-
-    /**
-     * Returns the value of field 'gapChar'.
-     * 
-     * @return the value of field 'GapChar'.
-     */
-    public java.lang.String getGapChar(
-    ) {
-        return this._gapChar;
-    }
-
-    /**
-     * Method getSequence.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.Sequence at the given index
-     */
-    public jalview.schemabinding.version2.Sequence getSequence(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._sequenceList.size()) {
-            throw new IndexOutOfBoundsException("getSequence: Index value '" + index + "' not in range [0.." + (this._sequenceList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.Sequence) _sequenceList.get(index);
-    }
-
-    /**
-     * Method getSequence.Returns the contents of the collection in
-     * an Array.  <p>Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we <i>know</i>
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.Sequence[] getSequence(
-    ) {
-        jalview.schemabinding.version2.Sequence[] array = new jalview.schemabinding.version2.Sequence[0];
-        return (jalview.schemabinding.version2.Sequence[]) this._sequenceList.toArray(array);
-    }
-
-    /**
-     * Method getSequenceCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getSequenceCount(
-    ) {
-        return this._sequenceList.size();
-    }
-
-    /**
-     * Method getSequenceSetProperties.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.SequenceSetProperties at the
-     * given index
-     */
-    public jalview.schemabinding.version2.SequenceSetProperties getSequenceSetProperties(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._sequenceSetPropertiesList.size()) {
-            throw new IndexOutOfBoundsException("getSequenceSetProperties: Index value '" + index + "' not in range [0.." + (this._sequenceSetPropertiesList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.SequenceSetProperties) _sequenceSetPropertiesList.get(index);
-    }
-
-    /**
-     * Method getSequenceSetProperties.Returns the contents of the
-     * collection in an Array.  <p>Note:  Just in case the
-     * collection contents are changing in another thread, we pass
-     * a 0-length Array of the correct type into the API call. 
-     * This way we <i>know</i> that the Array returned is of
-     * exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.SequenceSetProperties[] getSequenceSetProperties(
-    ) {
-        jalview.schemabinding.version2.SequenceSetProperties[] array = new jalview.schemabinding.version2.SequenceSetProperties[0];
-        return (jalview.schemabinding.version2.SequenceSetProperties[]) this._sequenceSetPropertiesList.toArray(array);
-    }
-
-    /**
-     * Method getSequenceSetPropertiesCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getSequenceSetPropertiesCount(
-    ) {
-        return this._sequenceSetPropertiesList.size();
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Method removeAlcodonFrame.
-     * 
-     * @param vAlcodonFrame
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeAlcodonFrame(
-            final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) {
-        boolean removed = _alcodonFrameList.remove(vAlcodonFrame);
-        return removed;
-    }
-
-    /**
-     * Method removeAlcodonFrameAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.AlcodonFrame removeAlcodonFrameAt(
-            final int index) {
-        java.lang.Object obj = this._alcodonFrameList.remove(index);
-        return (jalview.schemabinding.version2.AlcodonFrame) obj;
-    }
-
-    /**
-     */
-    public void removeAllAlcodonFrame(
-    ) {
-        this._alcodonFrameList.clear();
-    }
-
-    /**
-     */
-    public void removeAllAnnotation(
-    ) {
-        this._annotationList.clear();
-    }
-
-    /**
-     */
-    public void removeAllSequence(
-    ) {
-        this._sequenceList.clear();
-    }
-
-    /**
-     */
-    public void removeAllSequenceSetProperties(
-    ) {
-        this._sequenceSetPropertiesList.clear();
-    }
-
-    /**
-     * Method removeAnnotation.
-     * 
-     * @param vAnnotation
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeAnnotation(
-            final jalview.schemabinding.version2.Annotation vAnnotation) {
-        boolean removed = _annotationList.remove(vAnnotation);
-        return removed;
-    }
-
-    /**
-     * Method removeAnnotationAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.Annotation removeAnnotationAt(
-            final int index) {
-        java.lang.Object obj = this._annotationList.remove(index);
-        return (jalview.schemabinding.version2.Annotation) obj;
-    }
-
-    /**
-     * Method removeSequence.
-     * 
-     * @param vSequence
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeSequence(
-            final jalview.schemabinding.version2.Sequence vSequence) {
-        boolean removed = _sequenceList.remove(vSequence);
-        return removed;
-    }
-
-    /**
-     * Method removeSequenceAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.Sequence removeSequenceAt(
-            final int index) {
-        java.lang.Object obj = this._sequenceList.remove(index);
-        return (jalview.schemabinding.version2.Sequence) obj;
-    }
-
-    /**
-     * Method removeSequenceSetProperties.
-     * 
-     * @param vSequenceSetProperties
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeSequenceSetProperties(
-            final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) {
-        boolean removed = _sequenceSetPropertiesList.remove(vSequenceSetProperties);
-        return removed;
-    }
-
-    /**
-     * Method removeSequenceSetPropertiesAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.SequenceSetProperties removeSequenceSetPropertiesAt(
-            final int index) {
-        java.lang.Object obj = this._sequenceSetPropertiesList.remove(index);
-        return (jalview.schemabinding.version2.SequenceSetProperties) obj;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vAlcodonFrame
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setAlcodonFrame(
-            final int index,
-            final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._alcodonFrameList.size()) {
-            throw new IndexOutOfBoundsException("setAlcodonFrame: Index value '" + index + "' not in range [0.." + (this._alcodonFrameList.size() - 1) + "]");
-        }
-        
-        this._alcodonFrameList.set(index, vAlcodonFrame);
-    }
-
-    /**
-     * 
-     * 
-     * @param vAlcodonFrameArray
-     */
-    public void setAlcodonFrame(
-            final jalview.schemabinding.version2.AlcodonFrame[] vAlcodonFrameArray) {
-        //-- copy array
-        _alcodonFrameList.clear();
-        
-        for (int i = 0; i < vAlcodonFrameArray.length; i++) {
-                this._alcodonFrameList.add(vAlcodonFrameArray[i]);
-        }
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vAnnotation
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setAnnotation(
-            final int index,
-            final jalview.schemabinding.version2.Annotation vAnnotation)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._annotationList.size()) {
-            throw new IndexOutOfBoundsException("setAnnotation: Index value '" + index + "' not in range [0.." + (this._annotationList.size() - 1) + "]");
-        }
-        
-        this._annotationList.set(index, vAnnotation);
-    }
-
-    /**
-     * 
-     * 
-     * @param vAnnotationArray
-     */
-    public void setAnnotation(
-            final jalview.schemabinding.version2.Annotation[] vAnnotationArray) {
-        //-- copy array
-        _annotationList.clear();
-        
-        for (int i = 0; i < vAnnotationArray.length; i++) {
-                this._annotationList.add(vAnnotationArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of field 'datasetId'. The field 'datasetId'
-     * has the following description: reference to set where
-     * jalview will gather the dataset sequences for all sequences
-     * in the set. 
-     *  
-     * 
-     * @param datasetId the value of field 'datasetId'.
-     */
-    public void setDatasetId(
-            final java.lang.String datasetId) {
-        this._datasetId = datasetId;
-    }
-
-    /**
-     * Sets the value of field 'gapChar'.
-     * 
-     * @param gapChar the value of field 'gapChar'.
-     */
-    public void setGapChar(
-            final java.lang.String gapChar) {
-        this._gapChar = gapChar;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSequence
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setSequence(
-            final int index,
-            final jalview.schemabinding.version2.Sequence vSequence)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._sequenceList.size()) {
-            throw new IndexOutOfBoundsException("setSequence: Index value '" + index + "' not in range [0.." + (this._sequenceList.size() - 1) + "]");
-        }
-        
-        this._sequenceList.set(index, vSequence);
-    }
-
-    /**
-     * 
-     * 
-     * @param vSequenceArray
-     */
-    public void setSequence(
-            final jalview.schemabinding.version2.Sequence[] vSequenceArray) {
-        //-- copy array
-        _sequenceList.clear();
-        
-        for (int i = 0; i < vSequenceArray.length; i++) {
-                this._sequenceList.add(vSequenceArray[i]);
-        }
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSequenceSetProperties
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setSequenceSetProperties(
-            final int index,
-            final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._sequenceSetPropertiesList.size()) {
-            throw new IndexOutOfBoundsException("setSequenceSetProperties: Index value '" + index + "' not in range [0.." + (this._sequenceSetPropertiesList.size() - 1) + "]");
-        }
-        
-        this._sequenceSetPropertiesList.set(index, vSequenceSetProperties);
-    }
-
-    /**
-     * 
-     * 
-     * @param vSequenceSetPropertiesArray
-     */
-    public void setSequenceSetProperties(
-            final jalview.schemabinding.version2.SequenceSetProperties[] vSequenceSetPropertiesArray) {
-        //-- copy array
-        _sequenceSetPropertiesList.clear();
-        
-        for (int i = 0; i < vSequenceSetPropertiesArray.length; i++) {
-                this._sequenceSetPropertiesList.add(vSequenceSetPropertiesArray[i]);
-        }
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.SequenceSet
-     */
-    public static jalview.schemabinding.version2.SequenceSet unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.SequenceSet) Unmarshaller.unmarshal(jalview.schemabinding.version2.SequenceSet.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+public class SequenceSet implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _gapChar.
+   */
+  private java.lang.String _gapChar;
+
+  /**
+   * reference to set where jalview will gather the dataset sequences for all
+   * sequences in the set.
+   * 
+   */
+  private java.lang.String _datasetId;
+
+  /**
+   * Field _sequenceList.
+   */
+  private java.util.Vector _sequenceList;
+
+  /**
+   * Field _annotationList.
+   */
+  private java.util.Vector _annotationList;
+
+  /**
+   * Field _sequenceSetPropertiesList.
+   */
+  private java.util.Vector _sequenceSetPropertiesList;
+
+  /**
+   * Field _alcodonFrameList.
+   */
+  private java.util.Vector _alcodonFrameList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public SequenceSet()
+  {
+    super();
+    this._sequenceList = new java.util.Vector();
+    this._annotationList = new java.util.Vector();
+    this._sequenceSetPropertiesList = new java.util.Vector();
+    this._alcodonFrameList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vAlcodonFrame
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addAlcodonFrame(
+          final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._alcodonFrameList.addElement(vAlcodonFrame);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAlcodonFrame
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addAlcodonFrame(final int index,
+          final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._alcodonFrameList.add(index, vAlcodonFrame);
+  }
+
+  /**
+   * 
+   * 
+   * @param vAnnotation
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addAnnotation(
+          final jalview.schemabinding.version2.Annotation vAnnotation)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._annotationList.addElement(vAnnotation);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAnnotation
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addAnnotation(final int index,
+          final jalview.schemabinding.version2.Annotation vAnnotation)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._annotationList.add(index, vAnnotation);
+  }
+
+  /**
+   * 
+   * 
+   * @param vSequence
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addSequence(
+          final jalview.schemabinding.version2.Sequence vSequence)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._sequenceList.addElement(vSequence);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSequence
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addSequence(final int index,
+          final jalview.schemabinding.version2.Sequence vSequence)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._sequenceList.add(index, vSequence);
+  }
+
+  /**
+   * 
+   * 
+   * @param vSequenceSetProperties
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addSequenceSetProperties(
+          final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._sequenceSetPropertiesList.addElement(vSequenceSetProperties);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSequenceSetProperties
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addSequenceSetProperties(
+          final int index,
+          final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._sequenceSetPropertiesList.add(index, vSequenceSetProperties);
+  }
+
+  /**
+   * Method enumerateAlcodonFrame.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.AlcodonFrame
+   *         elements
+   */
+  public java.util.Enumeration enumerateAlcodonFrame()
+  {
+    return this._alcodonFrameList.elements();
+  }
+
+  /**
+   * Method enumerateAnnotation.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.Annotation
+   *         elements
+   */
+  public java.util.Enumeration enumerateAnnotation()
+  {
+    return this._annotationList.elements();
+  }
+
+  /**
+   * Method enumerateSequence.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.Sequence
+   *         elements
+   */
+  public java.util.Enumeration enumerateSequence()
+  {
+    return this._sequenceList.elements();
+  }
+
+  /**
+   * Method enumerateSequenceSetProperties.
+   * 
+   * @return an Enumeration over all
+   *         jalview.schemabinding.version2.SequenceSetProperties elements
+   */
+  public java.util.Enumeration enumerateSequenceSetProperties()
+  {
+    return this._sequenceSetPropertiesList.elements();
+  }
+
+  /**
+   * Method getAlcodonFrame.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.AlcodonFrame at the
+   *         given inde
+   */
+  public jalview.schemabinding.version2.AlcodonFrame getAlcodonFrame(
+          final int index) throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._alcodonFrameList.size())
+    {
+      throw new IndexOutOfBoundsException("getAlcodonFrame: Index value '"
+              + index + "' not in range [0.."
+              + (this._alcodonFrameList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.AlcodonFrame) _alcodonFrameList
+            .get(index);
+  }
+
+  /**
+   * Method getAlcodonFrame.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.AlcodonFrame[] getAlcodonFrame()
+  {
+    jalview.schemabinding.version2.AlcodonFrame[] array = new jalview.schemabinding.version2.AlcodonFrame[0];
+    return (jalview.schemabinding.version2.AlcodonFrame[]) this._alcodonFrameList
+            .toArray(array);
+  }
+
+  /**
+   * Method getAlcodonFrameCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getAlcodonFrameCount()
+  {
+    return this._alcodonFrameList.size();
+  }
+
+  /**
+   * Method getAnnotation.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.Annotation at the
+   *         given index
+   */
+  public jalview.schemabinding.version2.Annotation getAnnotation(
+          final int index) throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._annotationList.size())
+    {
+      throw new IndexOutOfBoundsException("getAnnotation: Index value '"
+              + index + "' not in range [0.."
+              + (this._annotationList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.Annotation) _annotationList
+            .get(index);
+  }
+
+  /**
+   * Method getAnnotation.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.Annotation[] getAnnotation()
+  {
+    jalview.schemabinding.version2.Annotation[] array = new jalview.schemabinding.version2.Annotation[0];
+    return (jalview.schemabinding.version2.Annotation[]) this._annotationList
+            .toArray(array);
+  }
+
+  /**
+   * Method getAnnotationCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getAnnotationCount()
+  {
+    return this._annotationList.size();
+  }
+
+  /**
+   * Returns the value of field 'datasetId'. The field 'datasetId' has the
+   * following description: reference to set where jalview will gather the
+   * dataset sequences for all sequences in the set.
+   * 
+   * 
+   * @return the value of field 'DatasetId'.
+   */
+  public java.lang.String getDatasetId()
+  {
+    return this._datasetId;
+  }
+
+  /**
+   * Returns the value of field 'gapChar'.
+   * 
+   * @return the value of field 'GapChar'.
+   */
+  public java.lang.String getGapChar()
+  {
+    return this._gapChar;
+  }
+
+  /**
+   * Method getSequence.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.Sequence at the
+   *         given index
+   */
+  public jalview.schemabinding.version2.Sequence getSequence(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._sequenceList.size())
+    {
+      throw new IndexOutOfBoundsException("getSequence: Index value '"
+              + index + "' not in range [0.."
+              + (this._sequenceList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.Sequence) _sequenceList
+            .get(index);
+  }
+
+  /**
+   * Method getSequence.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.Sequence[] getSequence()
+  {
+    jalview.schemabinding.version2.Sequence[] array = new jalview.schemabinding.version2.Sequence[0];
+    return (jalview.schemabinding.version2.Sequence[]) this._sequenceList
+            .toArray(array);
+  }
+
+  /**
+   * Method getSequenceCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getSequenceCount()
+  {
+    return this._sequenceList.size();
+  }
+
+  /**
+   * Method getSequenceSetProperties.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the
+   *         jalview.schemabinding.version2.SequenceSetProperties at the given
+   *         index
+   */
+  public jalview.schemabinding.version2.SequenceSetProperties getSequenceSetProperties(
+          final int index) throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._sequenceSetPropertiesList.size())
+    {
+      throw new IndexOutOfBoundsException(
+              "getSequenceSetProperties: Index value '" + index
+                      + "' not in range [0.."
+                      + (this._sequenceSetPropertiesList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.SequenceSetProperties) _sequenceSetPropertiesList
+            .get(index);
+  }
+
+  /**
+   * Method getSequenceSetProperties.Returns the contents of the collection in
+   * an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.SequenceSetProperties[] getSequenceSetProperties()
+  {
+    jalview.schemabinding.version2.SequenceSetProperties[] array = new jalview.schemabinding.version2.SequenceSetProperties[0];
+    return (jalview.schemabinding.version2.SequenceSetProperties[]) this._sequenceSetPropertiesList
+            .toArray(array);
+  }
+
+  /**
+   * Method getSequenceSetPropertiesCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getSequenceSetPropertiesCount()
+  {
+    return this._sequenceSetPropertiesList.size();
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Method removeAlcodonFrame.
+   * 
+   * @param vAlcodonFrame
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeAlcodonFrame(
+          final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)
+  {
+    boolean removed = _alcodonFrameList.remove(vAlcodonFrame);
+    return removed;
+  }
+
+  /**
+   * Method removeAlcodonFrameAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.AlcodonFrame removeAlcodonFrameAt(
+          final int index)
+  {
+    java.lang.Object obj = this._alcodonFrameList.remove(index);
+    return (jalview.schemabinding.version2.AlcodonFrame) obj;
+  }
+
+  /**
+   */
+  public void removeAllAlcodonFrame()
+  {
+    this._alcodonFrameList.clear();
+  }
+
+  /**
+   */
+  public void removeAllAnnotation()
+  {
+    this._annotationList.clear();
+  }
+
+  /**
+   */
+  public void removeAllSequence()
+  {
+    this._sequenceList.clear();
+  }
+
+  /**
+   */
+  public void removeAllSequenceSetProperties()
+  {
+    this._sequenceSetPropertiesList.clear();
+  }
+
+  /**
+   * Method removeAnnotation.
+   * 
+   * @param vAnnotation
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeAnnotation(
+          final jalview.schemabinding.version2.Annotation vAnnotation)
+  {
+    boolean removed = _annotationList.remove(vAnnotation);
+    return removed;
+  }
+
+  /**
+   * Method removeAnnotationAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.Annotation removeAnnotationAt(
+          final int index)
+  {
+    java.lang.Object obj = this._annotationList.remove(index);
+    return (jalview.schemabinding.version2.Annotation) obj;
+  }
+
+  /**
+   * Method removeSequence.
+   * 
+   * @param vSequence
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeSequence(
+          final jalview.schemabinding.version2.Sequence vSequence)
+  {
+    boolean removed = _sequenceList.remove(vSequence);
+    return removed;
+  }
+
+  /**
+   * Method removeSequenceAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.Sequence removeSequenceAt(
+          final int index)
+  {
+    java.lang.Object obj = this._sequenceList.remove(index);
+    return (jalview.schemabinding.version2.Sequence) obj;
+  }
+
+  /**
+   * Method removeSequenceSetProperties.
+   * 
+   * @param vSequenceSetProperties
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeSequenceSetProperties(
+          final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
+  {
+    boolean removed = _sequenceSetPropertiesList
+            .remove(vSequenceSetProperties);
+    return removed;
+  }
+
+  /**
+   * Method removeSequenceSetPropertiesAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.SequenceSetProperties removeSequenceSetPropertiesAt(
+          final int index)
+  {
+    java.lang.Object obj = this._sequenceSetPropertiesList.remove(index);
+    return (jalview.schemabinding.version2.SequenceSetProperties) obj;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAlcodonFrame
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setAlcodonFrame(final int index,
+          final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._alcodonFrameList.size())
+    {
+      throw new IndexOutOfBoundsException("setAlcodonFrame: Index value '"
+              + index + "' not in range [0.."
+              + (this._alcodonFrameList.size() - 1) + "]");
+    }
+
+    this._alcodonFrameList.set(index, vAlcodonFrame);
+  }
+
+  /**
+   * 
+   * 
+   * @param vAlcodonFrameArray
+   */
+  public void setAlcodonFrame(
+          final jalview.schemabinding.version2.AlcodonFrame[] vAlcodonFrameArray)
+  {
+    // -- copy array
+    _alcodonFrameList.clear();
+
+    for (int i = 0; i < vAlcodonFrameArray.length; i++)
+    {
+      this._alcodonFrameList.add(vAlcodonFrameArray[i]);
+    }
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAnnotation
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setAnnotation(final int index,
+          final jalview.schemabinding.version2.Annotation vAnnotation)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._annotationList.size())
+    {
+      throw new IndexOutOfBoundsException("setAnnotation: Index value '"
+              + index + "' not in range [0.."
+              + (this._annotationList.size() - 1) + "]");
+    }
+
+    this._annotationList.set(index, vAnnotation);
+  }
+
+  /**
+   * 
+   * 
+   * @param vAnnotationArray
+   */
+  public void setAnnotation(
+          final jalview.schemabinding.version2.Annotation[] vAnnotationArray)
+  {
+    // -- copy array
+    _annotationList.clear();
+
+    for (int i = 0; i < vAnnotationArray.length; i++)
+    {
+      this._annotationList.add(vAnnotationArray[i]);
+    }
+  }
+
+  /**
+   * Sets the value of field 'datasetId'. The field 'datasetId' has the
+   * following description: reference to set where jalview will gather the
+   * dataset sequences for all sequences in the set.
+   * 
+   * 
+   * @param datasetId
+   *                the value of field 'datasetId'.
+   */
+  public void setDatasetId(final java.lang.String datasetId)
+  {
+    this._datasetId = datasetId;
+  }
+
+  /**
+   * Sets the value of field 'gapChar'.
+   * 
+   * @param gapChar
+   *                the value of field 'gapChar'.
+   */
+  public void setGapChar(final java.lang.String gapChar)
+  {
+    this._gapChar = gapChar;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSequence
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setSequence(final int index,
+          final jalview.schemabinding.version2.Sequence vSequence)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._sequenceList.size())
+    {
+      throw new IndexOutOfBoundsException("setSequence: Index value '"
+              + index + "' not in range [0.."
+              + (this._sequenceList.size() - 1) + "]");
+    }
+
+    this._sequenceList.set(index, vSequence);
+  }
+
+  /**
+   * 
+   * 
+   * @param vSequenceArray
+   */
+  public void setSequence(
+          final jalview.schemabinding.version2.Sequence[] vSequenceArray)
+  {
+    // -- copy array
+    _sequenceList.clear();
+
+    for (int i = 0; i < vSequenceArray.length; i++)
+    {
+      this._sequenceList.add(vSequenceArray[i]);
+    }
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSequenceSetProperties
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setSequenceSetProperties(
+          final int index,
+          final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._sequenceSetPropertiesList.size())
+    {
+      throw new IndexOutOfBoundsException(
+              "setSequenceSetProperties: Index value '" + index
+                      + "' not in range [0.."
+                      + (this._sequenceSetPropertiesList.size() - 1) + "]");
+    }
+
+    this._sequenceSetPropertiesList.set(index, vSequenceSetProperties);
+  }
+
+  /**
+   * 
+   * 
+   * @param vSequenceSetPropertiesArray
+   */
+  public void setSequenceSetProperties(
+          final jalview.schemabinding.version2.SequenceSetProperties[] vSequenceSetPropertiesArray)
+  {
+    // -- copy array
+    _sequenceSetPropertiesList.clear();
+
+    for (int i = 0; i < vSequenceSetPropertiesArray.length; i++)
+    {
+      this._sequenceSetPropertiesList.add(vSequenceSetPropertiesArray[i]);
+    }
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.SequenceSet
+   */
+  public static jalview.schemabinding.version2.SequenceSet unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.SequenceSet) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.SequenceSet.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/SequenceSetProperties.java b/src/jalview/schemabinding/version2/SequenceSetProperties.java
index a078c78..c48c247 100644
--- a/src/jalview/schemabinding/version2/SequenceSetProperties.java
+++ b/src/jalview/schemabinding/version2/SequenceSetProperties.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,152 +30,169 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class SequenceSetProperties implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _key.
-     */
-    private java.lang.String _key;
-
-    /**
-     * Field _value.
-     */
-    private java.lang.String _value;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public SequenceSetProperties() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'key'.
-     * 
-     * @return the value of field 'Key'.
-     */
-    public java.lang.String getKey(
-    ) {
-        return this._key;
-    }
-
-    /**
-     * Returns the value of field 'value'.
-     * 
-     * @return the value of field 'Value'.
-     */
-    public java.lang.String getValue(
-    ) {
-        return this._value;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'key'.
-     * 
-     * @param key the value of field 'key'.
-     */
-    public void setKey(
-            final java.lang.String key) {
-        this._key = key;
-    }
-
-    /**
-     * Sets the value of field 'value'.
-     * 
-     * @param value the value of field 'value'.
-     */
-    public void setValue(
-            final java.lang.String value) {
-        this._value = value;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.SequenceSetProperties
-     */
-    public static jalview.schemabinding.version2.SequenceSetProperties unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.SequenceSetProperties) Unmarshaller.unmarshal(jalview.schemabinding.version2.SequenceSetProperties.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class SequenceSetProperties implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _key.
+   */
+  private java.lang.String _key;
+
+  /**
+   * Field _value.
+   */
+  private java.lang.String _value;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public SequenceSetProperties()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Returns the value of field 'key'.
+   * 
+   * @return the value of field 'Key'.
+   */
+  public java.lang.String getKey()
+  {
+    return this._key;
+  }
+
+  /**
+   * Returns the value of field 'value'.
+   * 
+   * @return the value of field 'Value'.
+   */
+  public java.lang.String getValue()
+  {
+    return this._value;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'key'.
+   * 
+   * @param key
+   *                the value of field 'key'.
+   */
+  public void setKey(final java.lang.String key)
+  {
+    this._key = key;
+  }
+
+  /**
+   * Sets the value of field 'value'.
+   * 
+   * @param value
+   *                the value of field 'value'.
+   */
+  public void setValue(final java.lang.String value)
+  {
+    this._value = value;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled
+   *         jalview.schemabinding.version2.SequenceSetProperties
+   */
+  public static jalview.schemabinding.version2.SequenceSetProperties unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.SequenceSetProperties) Unmarshaller
+            .unmarshal(
+                    jalview.schemabinding.version2.SequenceSetProperties.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/SequenceType.java b/src/jalview/schemabinding/version2/SequenceType.java
index 0d07812..7f61b94 100755
--- a/src/jalview/schemabinding/version2/SequenceType.java
+++ b/src/jalview/schemabinding/version2/SequenceType.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,202 +30,219 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class SequenceType implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _id.
-     */
-    private java.lang.String _id;
-
-    /**
-     * Field _description.
-     */
-    private java.lang.String _description;
-
-    /**
-     * Field _sequence.
-     */
-    private java.lang.String _sequence;
-
-    /**
-     * Field _name.
-     */
-    private java.lang.String _name;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public SequenceType() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'description'.
-     * 
-     * @return the value of field 'Description'.
-     */
-    public java.lang.String getDescription(
-    ) {
-        return this._description;
-    }
-
-    /**
-     * Returns the value of field 'id'.
-     * 
-     * @return the value of field 'Id'.
-     */
-    public java.lang.String getId(
-    ) {
-        return this._id;
-    }
-
-    /**
-     * Returns the value of field 'name'.
-     * 
-     * @return the value of field 'Name'.
-     */
-    public java.lang.String getName(
-    ) {
-        return this._name;
-    }
-
-    /**
-     * Returns the value of field 'sequence'.
-     * 
-     * @return the value of field 'Sequence'.
-     */
-    public java.lang.String getSequence(
-    ) {
-        return this._sequence;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'description'.
-     * 
-     * @param description the value of field 'description'.
-     */
-    public void setDescription(
-            final java.lang.String description) {
-        this._description = description;
-    }
-
-    /**
-     * Sets the value of field 'id'.
-     * 
-     * @param id the value of field 'id'.
-     */
-    public void setId(
-            final java.lang.String id) {
-        this._id = id;
-    }
-
-    /**
-     * Sets the value of field 'name'.
-     * 
-     * @param name the value of field 'name'.
-     */
-    public void setName(
-            final java.lang.String name) {
-        this._name = name;
-    }
-
-    /**
-     * Sets the value of field 'sequence'.
-     * 
-     * @param sequence the value of field 'sequence'.
-     */
-    public void setSequence(
-            final java.lang.String sequence) {
-        this._sequence = sequence;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.SequenceType
-     */
-    public static jalview.schemabinding.version2.SequenceType unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.SequenceType) Unmarshaller.unmarshal(jalview.schemabinding.version2.SequenceType.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class SequenceType implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _id.
+   */
+  private java.lang.String _id;
+
+  /**
+   * Field _description.
+   */
+  private java.lang.String _description;
+
+  /**
+   * Field _sequence.
+   */
+  private java.lang.String _sequence;
+
+  /**
+   * Field _name.
+   */
+  private java.lang.String _name;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public SequenceType()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Returns the value of field 'description'.
+   * 
+   * @return the value of field 'Description'.
+   */
+  public java.lang.String getDescription()
+  {
+    return this._description;
+  }
+
+  /**
+   * Returns the value of field 'id'.
+   * 
+   * @return the value of field 'Id'.
+   */
+  public java.lang.String getId()
+  {
+    return this._id;
+  }
+
+  /**
+   * Returns the value of field 'name'.
+   * 
+   * @return the value of field 'Name'.
+   */
+  public java.lang.String getName()
+  {
+    return this._name;
+  }
+
+  /**
+   * Returns the value of field 'sequence'.
+   * 
+   * @return the value of field 'Sequence'.
+   */
+  public java.lang.String getSequence()
+  {
+    return this._sequence;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'description'.
+   * 
+   * @param description
+   *                the value of field 'description'.
+   */
+  public void setDescription(final java.lang.String description)
+  {
+    this._description = description;
+  }
+
+  /**
+   * Sets the value of field 'id'.
+   * 
+   * @param id
+   *                the value of field 'id'.
+   */
+  public void setId(final java.lang.String id)
+  {
+    this._id = id;
+  }
+
+  /**
+   * Sets the value of field 'name'.
+   * 
+   * @param name
+   *                the value of field 'name'.
+   */
+  public void setName(final java.lang.String name)
+  {
+    this._name = name;
+  }
+
+  /**
+   * Sets the value of field 'sequence'.
+   * 
+   * @param sequence
+   *                the value of field 'sequence'.
+   */
+  public void setSequence(final java.lang.String sequence)
+  {
+    this._sequence = sequence;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.SequenceType
+   */
+  public static jalview.schemabinding.version2.SequenceType unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.SequenceType) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.SequenceType.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/Setting.java b/src/jalview/schemabinding/version2/Setting.java
index 5cd78bd..56c3fe6 100755
--- a/src/jalview/schemabinding/version2/Setting.java
+++ b/src/jalview/schemabinding/version2/Setting.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,280 +30,297 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Setting implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _type.
-     */
-    private java.lang.String _type;
-
-    /**
-     * Field _colour.
-     */
-    private int _colour;
-
-    /**
-     * keeps track of state for field: _colour
-     */
-    private boolean _has_colour;
-
-    /**
-     * Field _display.
-     */
-    private boolean _display;
-
-    /**
-     * keeps track of state for field: _display
-     */
-    private boolean _has_display;
-
-    /**
-     * Field _order.
-     */
-    private float _order;
-
-    /**
-     * keeps track of state for field: _order
-     */
-    private boolean _has_order;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Setting() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     */
-    public void deleteColour(
-    ) {
-        this._has_colour= false;
-    }
-
-    /**
-     */
-    public void deleteDisplay(
-    ) {
-        this._has_display= false;
-    }
-
-    /**
-     */
-    public void deleteOrder(
-    ) {
-        this._has_order= false;
-    }
-
-    /**
-     * Returns the value of field 'colour'.
-     * 
-     * @return the value of field 'Colour'.
-     */
-    public int getColour(
-    ) {
-        return this._colour;
-    }
-
-    /**
-     * Returns the value of field 'display'.
-     * 
-     * @return the value of field 'Display'.
-     */
-    public boolean getDisplay(
-    ) {
-        return this._display;
-    }
-
-    /**
-     * Returns the value of field 'order'.
-     * 
-     * @return the value of field 'Order'.
-     */
-    public float getOrder(
-    ) {
-        return this._order;
-    }
-
-    /**
-     * Returns the value of field 'type'.
-     * 
-     * @return the value of field 'Type'.
-     */
-    public java.lang.String getType(
-    ) {
-        return this._type;
-    }
-
-    /**
-     * Method hasColour.
-     * 
-     * @return true if at least one Colour has been added
-     */
-    public boolean hasColour(
-    ) {
-        return this._has_colour;
-    }
-
-    /**
-     * Method hasDisplay.
-     * 
-     * @return true if at least one Display has been added
-     */
-    public boolean hasDisplay(
-    ) {
-        return this._has_display;
-    }
-
-    /**
-     * Method hasOrder.
-     * 
-     * @return true if at least one Order has been added
-     */
-    public boolean hasOrder(
-    ) {
-        return this._has_order;
-    }
-
-    /**
-     * Returns the value of field 'display'.
-     * 
-     * @return the value of field 'Display'.
-     */
-    public boolean isDisplay(
-    ) {
-        return this._display;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'colour'.
-     * 
-     * @param colour the value of field 'colour'.
-     */
-    public void setColour(
-            final int colour) {
-        this._colour = colour;
-        this._has_colour = true;
-    }
-
-    /**
-     * Sets the value of field 'display'.
-     * 
-     * @param display the value of field 'display'.
-     */
-    public void setDisplay(
-            final boolean display) {
-        this._display = display;
-        this._has_display = true;
-    }
-
-    /**
-     * Sets the value of field 'order'.
-     * 
-     * @param order the value of field 'order'.
-     */
-    public void setOrder(
-            final float order) {
-        this._order = order;
-        this._has_order = true;
-    }
-
-    /**
-     * Sets the value of field 'type'.
-     * 
-     * @param type the value of field 'type'.
-     */
-    public void setType(
-            final java.lang.String type) {
-        this._type = type;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.schemabinding.version2.Settin
-     */
-    public static jalview.schemabinding.version2.Setting unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.Setting) Unmarshaller.unmarshal(jalview.schemabinding.version2.Setting.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class Setting implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _type.
+   */
+  private java.lang.String _type;
+
+  /**
+   * Field _colour.
+   */
+  private int _colour;
+
+  /**
+   * keeps track of state for field: _colour
+   */
+  private boolean _has_colour;
+
+  /**
+   * Field _display.
+   */
+  private boolean _display;
+
+  /**
+   * keeps track of state for field: _display
+   */
+  private boolean _has_display;
+
+  /**
+   * Field _order.
+   */
+  private float _order;
+
+  /**
+   * keeps track of state for field: _order
+   */
+  private boolean _has_order;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Setting()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   */
+  public void deleteColour()
+  {
+    this._has_colour = false;
+  }
+
+  /**
+   */
+  public void deleteDisplay()
+  {
+    this._has_display = false;
+  }
+
+  /**
+   */
+  public void deleteOrder()
+  {
+    this._has_order = false;
+  }
+
+  /**
+   * Returns the value of field 'colour'.
+   * 
+   * @return the value of field 'Colour'.
+   */
+  public int getColour()
+  {
+    return this._colour;
+  }
+
+  /**
+   * Returns the value of field 'display'.
+   * 
+   * @return the value of field 'Display'.
+   */
+  public boolean getDisplay()
+  {
+    return this._display;
+  }
+
+  /**
+   * Returns the value of field 'order'.
+   * 
+   * @return the value of field 'Order'.
+   */
+  public float getOrder()
+  {
+    return this._order;
+  }
+
+  /**
+   * Returns the value of field 'type'.
+   * 
+   * @return the value of field 'Type'.
+   */
+  public java.lang.String getType()
+  {
+    return this._type;
+  }
+
+  /**
+   * Method hasColour.
+   * 
+   * @return true if at least one Colour has been added
+   */
+  public boolean hasColour()
+  {
+    return this._has_colour;
+  }
+
+  /**
+   * Method hasDisplay.
+   * 
+   * @return true if at least one Display has been added
+   */
+  public boolean hasDisplay()
+  {
+    return this._has_display;
+  }
+
+  /**
+   * Method hasOrder.
+   * 
+   * @return true if at least one Order has been added
+   */
+  public boolean hasOrder()
+  {
+    return this._has_order;
+  }
+
+  /**
+   * Returns the value of field 'display'.
+   * 
+   * @return the value of field 'Display'.
+   */
+  public boolean isDisplay()
+  {
+    return this._display;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'colour'.
+   * 
+   * @param colour
+   *                the value of field 'colour'.
+   */
+  public void setColour(final int colour)
+  {
+    this._colour = colour;
+    this._has_colour = true;
+  }
+
+  /**
+   * Sets the value of field 'display'.
+   * 
+   * @param display
+   *                the value of field 'display'.
+   */
+  public void setDisplay(final boolean display)
+  {
+    this._display = display;
+    this._has_display = true;
+  }
+
+  /**
+   * Sets the value of field 'order'.
+   * 
+   * @param order
+   *                the value of field 'order'.
+   */
+  public void setOrder(final float order)
+  {
+    this._order = order;
+    this._has_order = true;
+  }
+
+  /**
+   * Sets the value of field 'type'.
+   * 
+   * @param type
+   *                the value of field 'type'.
+   */
+  public void setType(final java.lang.String type)
+  {
+    this._type = type;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.Settin
+   */
+  public static jalview.schemabinding.version2.Setting unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.Setting) Unmarshaller.unmarshal(
+            jalview.schemabinding.version2.Setting.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/StructureState.java b/src/jalview/schemabinding/version2/StructureState.java
index 968a559..373db78 100644
--- a/src/jalview/schemabinding/version2/StructureState.java
+++ b/src/jalview/schemabinding/version2/StructureState.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,380 +30,399 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class StructureState implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * internal content storage
-     */
-    private java.lang.String _content = "";
-
-    /**
-     * Field _visible.
-     */
-    private boolean _visible;
-
-    /**
-     * keeps track of state for field: _visible
-     */
-    private boolean _has_visible;
-
-    /**
-     * Field _xpos.
-     */
-    private int _xpos;
-
-    /**
-     * keeps track of state for field: _xpos
-     */
-    private boolean _has_xpos;
-
-    /**
-     * Field _ypos.
-     */
-    private int _ypos;
-
-    /**
-     * keeps track of state for field: _ypos
-     */
-    private boolean _has_ypos;
-
-    /**
-     * Field _width.
-     */
-    private int _width;
-
-    /**
-     * keeps track of state for field: _width
-     */
-    private boolean _has_width;
-
-    /**
-     * Field _height.
-     */
-    private int _height;
-
-    /**
-     * keeps track of state for field: _height
-     */
-    private boolean _has_height;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public StructureState() {
-        super();
-        setContent("");
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     */
-    public void deleteHeight(
-    ) {
-        this._has_height= false;
-    }
-
-    /**
-     */
-    public void deleteVisible(
-    ) {
-        this._has_visible= false;
-    }
-
-    /**
-     */
-    public void deleteWidth(
-    ) {
-        this._has_width= false;
-    }
-
-    /**
-     */
-    public void deleteXpos(
-    ) {
-        this._has_xpos= false;
-    }
-
-    /**
-     */
-    public void deleteYpos(
-    ) {
-        this._has_ypos= false;
-    }
-
-    /**
-     * Returns the value of field 'content'. The field 'content'
-     * has the following description: internal content storage
-     * 
-     * @return the value of field 'Content'.
-     */
-    public java.lang.String getContent(
-    ) {
-        return this._content;
-    }
-
-    /**
-     * Returns the value of field 'height'.
-     * 
-     * @return the value of field 'Height'.
-     */
-    public int getHeight(
-    ) {
-        return this._height;
-    }
-
-    /**
-     * Returns the value of field 'visible'.
-     * 
-     * @return the value of field 'Visible'.
-     */
-    public boolean getVisible(
-    ) {
-        return this._visible;
-    }
-
-    /**
-     * Returns the value of field 'width'.
-     * 
-     * @return the value of field 'Width'.
-     */
-    public int getWidth(
-    ) {
-        return this._width;
-    }
-
-    /**
-     * Returns the value of field 'xpos'.
-     * 
-     * @return the value of field 'Xpos'.
-     */
-    public int getXpos(
-    ) {
-        return this._xpos;
-    }
-
-    /**
-     * Returns the value of field 'ypos'.
-     * 
-     * @return the value of field 'Ypos'.
-     */
-    public int getYpos(
-    ) {
-        return this._ypos;
-    }
-
-    /**
-     * Method hasHeight.
-     * 
-     * @return true if at least one Height has been added
-     */
-    public boolean hasHeight(
-    ) {
-        return this._has_height;
-    }
-
-    /**
-     * Method hasVisible.
-     * 
-     * @return true if at least one Visible has been added
-     */
-    public boolean hasVisible(
-    ) {
-        return this._has_visible;
-    }
-
-    /**
-     * Method hasWidth.
-     * 
-     * @return true if at least one Width has been added
-     */
-    public boolean hasWidth(
-    ) {
-        return this._has_width;
-    }
-
-    /**
-     * Method hasXpos.
-     * 
-     * @return true if at least one Xpos has been added
-     */
-    public boolean hasXpos(
-    ) {
-        return this._has_xpos;
-    }
-
-    /**
-     * Method hasYpos.
-     * 
-     * @return true if at least one Ypos has been added
-     */
-    public boolean hasYpos(
-    ) {
-        return this._has_ypos;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * Returns the value of field 'visible'.
-     * 
-     * @return the value of field 'Visible'.
-     */
-    public boolean isVisible(
-    ) {
-        return this._visible;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'content'. The field 'content' has
-     * the following description: internal content storage
-     * 
-     * @param content the value of field 'content'.
-     */
-    public void setContent(
-            final java.lang.String content) {
-        this._content = content;
-    }
-
-    /**
-     * Sets the value of field 'height'.
-     * 
-     * @param height the value of field 'height'.
-     */
-    public void setHeight(
-            final int height) {
-        this._height = height;
-        this._has_height = true;
-    }
-
-    /**
-     * Sets the value of field 'visible'.
-     * 
-     * @param visible the value of field 'visible'.
-     */
-    public void setVisible(
-            final boolean visible) {
-        this._visible = visible;
-        this._has_visible = true;
-    }
-
-    /**
-     * Sets the value of field 'width'.
-     * 
-     * @param width the value of field 'width'.
-     */
-    public void setWidth(
-            final int width) {
-        this._width = width;
-        this._has_width = true;
-    }
-
-    /**
-     * Sets the value of field 'xpos'.
-     * 
-     * @param xpos the value of field 'xpos'.
-     */
-    public void setXpos(
-            final int xpos) {
-        this._xpos = xpos;
-        this._has_xpos = true;
-    }
-
-    /**
-     * Sets the value of field 'ypos'.
-     * 
-     * @param ypos the value of field 'ypos'.
-     */
-    public void setYpos(
-            final int ypos) {
-        this._ypos = ypos;
-        this._has_ypos = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.StructureState
-     */
-    public static jalview.schemabinding.version2.StructureState unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.StructureState) Unmarshaller.unmarshal(jalview.schemabinding.version2.StructureState.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class StructureState implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * internal content storage
+   */
+  private java.lang.String _content = "";
+
+  /**
+   * Field _visible.
+   */
+  private boolean _visible;
+
+  /**
+   * keeps track of state for field: _visible
+   */
+  private boolean _has_visible;
+
+  /**
+   * Field _xpos.
+   */
+  private int _xpos;
+
+  /**
+   * keeps track of state for field: _xpos
+   */
+  private boolean _has_xpos;
+
+  /**
+   * Field _ypos.
+   */
+  private int _ypos;
+
+  /**
+   * keeps track of state for field: _ypos
+   */
+  private boolean _has_ypos;
+
+  /**
+   * Field _width.
+   */
+  private int _width;
+
+  /**
+   * keeps track of state for field: _width
+   */
+  private boolean _has_width;
+
+  /**
+   * Field _height.
+   */
+  private int _height;
+
+  /**
+   * keeps track of state for field: _height
+   */
+  private boolean _has_height;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public StructureState()
+  {
+    super();
+    setContent("");
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   */
+  public void deleteHeight()
+  {
+    this._has_height = false;
+  }
+
+  /**
+   */
+  public void deleteVisible()
+  {
+    this._has_visible = false;
+  }
+
+  /**
+   */
+  public void deleteWidth()
+  {
+    this._has_width = false;
+  }
+
+  /**
+   */
+  public void deleteXpos()
+  {
+    this._has_xpos = false;
+  }
+
+  /**
+   */
+  public void deleteYpos()
+  {
+    this._has_ypos = false;
+  }
+
+  /**
+   * Returns the value of field 'content'. The field 'content' has the following
+   * description: internal content storage
+   * 
+   * @return the value of field 'Content'.
+   */
+  public java.lang.String getContent()
+  {
+    return this._content;
+  }
+
+  /**
+   * Returns the value of field 'height'.
+   * 
+   * @return the value of field 'Height'.
+   */
+  public int getHeight()
+  {
+    return this._height;
+  }
+
+  /**
+   * Returns the value of field 'visible'.
+   * 
+   * @return the value of field 'Visible'.
+   */
+  public boolean getVisible()
+  {
+    return this._visible;
+  }
+
+  /**
+   * Returns the value of field 'width'.
+   * 
+   * @return the value of field 'Width'.
+   */
+  public int getWidth()
+  {
+    return this._width;
+  }
+
+  /**
+   * Returns the value of field 'xpos'.
+   * 
+   * @return the value of field 'Xpos'.
+   */
+  public int getXpos()
+  {
+    return this._xpos;
+  }
+
+  /**
+   * Returns the value of field 'ypos'.
+   * 
+   * @return the value of field 'Ypos'.
+   */
+  public int getYpos()
+  {
+    return this._ypos;
+  }
+
+  /**
+   * Method hasHeight.
+   * 
+   * @return true if at least one Height has been added
+   */
+  public boolean hasHeight()
+  {
+    return this._has_height;
+  }
+
+  /**
+   * Method hasVisible.
+   * 
+   * @return true if at least one Visible has been added
+   */
+  public boolean hasVisible()
+  {
+    return this._has_visible;
+  }
+
+  /**
+   * Method hasWidth.
+   * 
+   * @return true if at least one Width has been added
+   */
+  public boolean hasWidth()
+  {
+    return this._has_width;
+  }
+
+  /**
+   * Method hasXpos.
+   * 
+   * @return true if at least one Xpos has been added
+   */
+  public boolean hasXpos()
+  {
+    return this._has_xpos;
+  }
+
+  /**
+   * Method hasYpos.
+   * 
+   * @return true if at least one Ypos has been added
+   */
+  public boolean hasYpos()
+  {
+    return this._has_ypos;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * Returns the value of field 'visible'.
+   * 
+   * @return the value of field 'Visible'.
+   */
+  public boolean isVisible()
+  {
+    return this._visible;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'content'. The field 'content' has the following
+   * description: internal content storage
+   * 
+   * @param content
+   *                the value of field 'content'.
+   */
+  public void setContent(final java.lang.String content)
+  {
+    this._content = content;
+  }
+
+  /**
+   * Sets the value of field 'height'.
+   * 
+   * @param height
+   *                the value of field 'height'.
+   */
+  public void setHeight(final int height)
+  {
+    this._height = height;
+    this._has_height = true;
+  }
+
+  /**
+   * Sets the value of field 'visible'.
+   * 
+   * @param visible
+   *                the value of field 'visible'.
+   */
+  public void setVisible(final boolean visible)
+  {
+    this._visible = visible;
+    this._has_visible = true;
+  }
+
+  /**
+   * Sets the value of field 'width'.
+   * 
+   * @param width
+   *                the value of field 'width'.
+   */
+  public void setWidth(final int width)
+  {
+    this._width = width;
+    this._has_width = true;
+  }
+
+  /**
+   * Sets the value of field 'xpos'.
+   * 
+   * @param xpos
+   *                the value of field 'xpos'.
+   */
+  public void setXpos(final int xpos)
+  {
+    this._xpos = xpos;
+    this._has_xpos = true;
+  }
+
+  /**
+   * Sets the value of field 'ypos'.
+   * 
+   * @param ypos
+   *                the value of field 'ypos'.
+   */
+  public void setYpos(final int ypos)
+  {
+    this._ypos = ypos;
+    this._has_ypos = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.StructureState
+   */
+  public static jalview.schemabinding.version2.StructureState unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.StructureState) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.StructureState.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/ThresholdLine.java b/src/jalview/schemabinding/version2/ThresholdLine.java
index 4e3f124..91bdfc6 100755
--- a/src/jalview/schemabinding/version2/ThresholdLine.java
+++ b/src/jalview/schemabinding/version2/ThresholdLine.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,223 +30,239 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class ThresholdLine implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _label.
-     */
-    private java.lang.String _label;
-
-    /**
-     * Field _value.
-     */
-    private float _value;
-
-    /**
-     * keeps track of state for field: _value
-     */
-    private boolean _has_value;
-
-    /**
-     * Field _colour.
-     */
-    private int _colour;
-
-    /**
-     * keeps track of state for field: _colour
-     */
-    private boolean _has_colour;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public ThresholdLine() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     */
-    public void deleteColour(
-    ) {
-        this._has_colour= false;
-    }
-
-    /**
-     */
-    public void deleteValue(
-    ) {
-        this._has_value= false;
-    }
-
-    /**
-     * Returns the value of field 'colour'.
-     * 
-     * @return the value of field 'Colour'.
-     */
-    public int getColour(
-    ) {
-        return this._colour;
-    }
-
-    /**
-     * Returns the value of field 'label'.
-     * 
-     * @return the value of field 'Label'.
-     */
-    public java.lang.String getLabel(
-    ) {
-        return this._label;
-    }
-
-    /**
-     * Returns the value of field 'value'.
-     * 
-     * @return the value of field 'Value'.
-     */
-    public float getValue(
-    ) {
-        return this._value;
-    }
-
-    /**
-     * Method hasColour.
-     * 
-     * @return true if at least one Colour has been added
-     */
-    public boolean hasColour(
-    ) {
-        return this._has_colour;
-    }
-
-    /**
-     * Method hasValue.
-     * 
-     * @return true if at least one Value has been added
-     */
-    public boolean hasValue(
-    ) {
-        return this._has_value;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'colour'.
-     * 
-     * @param colour the value of field 'colour'.
-     */
-    public void setColour(
-            final int colour) {
-        this._colour = colour;
-        this._has_colour = true;
-    }
-
-    /**
-     * Sets the value of field 'label'.
-     * 
-     * @param label the value of field 'label'.
-     */
-    public void setLabel(
-            final java.lang.String label) {
-        this._label = label;
-    }
-
-    /**
-     * Sets the value of field 'value'.
-     * 
-     * @param value the value of field 'value'.
-     */
-    public void setValue(
-            final float value) {
-        this._value = value;
-        this._has_value = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.ThresholdLine
-     */
-    public static jalview.schemabinding.version2.ThresholdLine unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.ThresholdLine) Unmarshaller.unmarshal(jalview.schemabinding.version2.ThresholdLine.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class ThresholdLine implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _label.
+   */
+  private java.lang.String _label;
+
+  /**
+   * Field _value.
+   */
+  private float _value;
+
+  /**
+   * keeps track of state for field: _value
+   */
+  private boolean _has_value;
+
+  /**
+   * Field _colour.
+   */
+  private int _colour;
+
+  /**
+   * keeps track of state for field: _colour
+   */
+  private boolean _has_colour;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public ThresholdLine()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   */
+  public void deleteColour()
+  {
+    this._has_colour = false;
+  }
+
+  /**
+   */
+  public void deleteValue()
+  {
+    this._has_value = false;
+  }
+
+  /**
+   * Returns the value of field 'colour'.
+   * 
+   * @return the value of field 'Colour'.
+   */
+  public int getColour()
+  {
+    return this._colour;
+  }
+
+  /**
+   * Returns the value of field 'label'.
+   * 
+   * @return the value of field 'Label'.
+   */
+  public java.lang.String getLabel()
+  {
+    return this._label;
+  }
+
+  /**
+   * Returns the value of field 'value'.
+   * 
+   * @return the value of field 'Value'.
+   */
+  public float getValue()
+  {
+    return this._value;
+  }
+
+  /**
+   * Method hasColour.
+   * 
+   * @return true if at least one Colour has been added
+   */
+  public boolean hasColour()
+  {
+    return this._has_colour;
+  }
+
+  /**
+   * Method hasValue.
+   * 
+   * @return true if at least one Value has been added
+   */
+  public boolean hasValue()
+  {
+    return this._has_value;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'colour'.
+   * 
+   * @param colour
+   *                the value of field 'colour'.
+   */
+  public void setColour(final int colour)
+  {
+    this._colour = colour;
+    this._has_colour = true;
+  }
+
+  /**
+   * Sets the value of field 'label'.
+   * 
+   * @param label
+   *                the value of field 'label'.
+   */
+  public void setLabel(final java.lang.String label)
+  {
+    this._label = label;
+  }
+
+  /**
+   * Sets the value of field 'value'.
+   * 
+   * @param value
+   *                the value of field 'value'.
+   */
+  public void setValue(final float value)
+  {
+    this._value = value;
+    this._has_value = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.ThresholdLine
+   */
+  public static jalview.schemabinding.version2.ThresholdLine unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.ThresholdLine) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.ThresholdLine.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/Tree.java b/src/jalview/schemabinding/version2/Tree.java
index 3bbc231..b523c44 100755
--- a/src/jalview/schemabinding/version2/Tree.java
+++ b/src/jalview/schemabinding/version2/Tree.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,802 +30,830 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Tree implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _width.
-     */
-    private int _width;
-
-    /**
-     * keeps track of state for field: _width
-     */
-    private boolean _has_width;
-
-    /**
-     * Field _height.
-     */
-    private int _height;
-
-    /**
-     * keeps track of state for field: _height
-     */
-    private boolean _has_height;
-
-    /**
-     * Field _xpos.
-     */
-    private int _xpos;
-
-    /**
-     * keeps track of state for field: _xpos
-     */
-    private boolean _has_xpos;
-
-    /**
-     * Field _ypos.
-     */
-    private int _ypos;
-
-    /**
-     * keeps track of state for field: _ypos
-     */
-    private boolean _has_ypos;
-
-    /**
-     * Field _fontName.
-     */
-    private java.lang.String _fontName;
-
-    /**
-     * Field _fontSize.
-     */
-    private int _fontSize;
-
-    /**
-     * keeps track of state for field: _fontSize
-     */
-    private boolean _has_fontSize;
-
-    /**
-     * Field _fontStyle.
-     */
-    private int _fontStyle;
-
-    /**
-     * keeps track of state for field: _fontStyle
-     */
-    private boolean _has_fontStyle;
-
-    /**
-     * Field _threshold.
-     */
-    private float _threshold;
-
-    /**
-     * keeps track of state for field: _threshold
-     */
-    private boolean _has_threshold;
-
-    /**
-     * Field _showBootstrap.
-     */
-    private boolean _showBootstrap;
-
-    /**
-     * keeps track of state for field: _showBootstrap
-     */
-    private boolean _has_showBootstrap;
-
-    /**
-     * Field _showDistances.
-     */
-    private boolean _showDistances;
-
-    /**
-     * keeps track of state for field: _showDistances
-     */
-    private boolean _has_showDistances;
-
-    /**
-     * Field _markUnlinked.
-     */
-    private boolean _markUnlinked;
-
-    /**
-     * keeps track of state for field: _markUnlinked
-     */
-    private boolean _has_markUnlinked;
-
-    /**
-     * Field _fitToWindow.
-     */
-    private boolean _fitToWindow;
-
-    /**
-     * keeps track of state for field: _fitToWindow
-     */
-    private boolean _has_fitToWindow;
-
-    /**
-     * Field _currentTree.
-     */
-    private boolean _currentTree;
-
-    /**
-     * keeps track of state for field: _currentTree
-     */
-    private boolean _has_currentTree;
-
-    /**
-     * Field _title.
-     */
-    private java.lang.String _title;
-
-    /**
-     * Field _newick.
-     */
-    private java.lang.String _newick;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Tree() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     */
-    public void deleteCurrentTree(
-    ) {
-        this._has_currentTree= false;
-    }
-
-    /**
-     */
-    public void deleteFitToWindow(
-    ) {
-        this._has_fitToWindow= false;
-    }
-
-    /**
-     */
-    public void deleteFontSize(
-    ) {
-        this._has_fontSize= false;
-    }
-
-    /**
-     */
-    public void deleteFontStyle(
-    ) {
-        this._has_fontStyle= false;
-    }
-
-    /**
-     */
-    public void deleteHeight(
-    ) {
-        this._has_height= false;
-    }
-
-    /**
-     */
-    public void deleteMarkUnlinked(
-    ) {
-        this._has_markUnlinked= false;
-    }
-
-    /**
-     */
-    public void deleteShowBootstrap(
-    ) {
-        this._has_showBootstrap= false;
-    }
-
-    /**
-     */
-    public void deleteShowDistances(
-    ) {
-        this._has_showDistances= false;
-    }
-
-    /**
-     */
-    public void deleteThreshold(
-    ) {
-        this._has_threshold= false;
-    }
-
-    /**
-     */
-    public void deleteWidth(
-    ) {
-        this._has_width= false;
-    }
-
-    /**
-     */
-    public void deleteXpos(
-    ) {
-        this._has_xpos= false;
-    }
-
-    /**
-     */
-    public void deleteYpos(
-    ) {
-        this._has_ypos= false;
-    }
-
-    /**
-     * Returns the value of field 'currentTree'.
-     * 
-     * @return the value of field 'CurrentTree'.
-     */
-    public boolean getCurrentTree(
-    ) {
-        return this._currentTree;
-    }
-
-    /**
-     * Returns the value of field 'fitToWindow'.
-     * 
-     * @return the value of field 'FitToWindow'.
-     */
-    public boolean getFitToWindow(
-    ) {
-        return this._fitToWindow;
-    }
-
-    /**
-     * Returns the value of field 'fontName'.
-     * 
-     * @return the value of field 'FontName'.
-     */
-    public java.lang.String getFontName(
-    ) {
-        return this._fontName;
-    }
-
-    /**
-     * Returns the value of field 'fontSize'.
-     * 
-     * @return the value of field 'FontSize'.
-     */
-    public int getFontSize(
-    ) {
-        return this._fontSize;
-    }
-
-    /**
-     * Returns the value of field 'fontStyle'.
-     * 
-     * @return the value of field 'FontStyle'.
-     */
-    public int getFontStyle(
-    ) {
-        return this._fontStyle;
-    }
-
-    /**
-     * Returns the value of field 'height'.
-     * 
-     * @return the value of field 'Height'.
-     */
-    public int getHeight(
-    ) {
-        return this._height;
-    }
-
-    /**
-     * Returns the value of field 'markUnlinked'.
-     * 
-     * @return the value of field 'MarkUnlinked'.
-     */
-    public boolean getMarkUnlinked(
-    ) {
-        return this._markUnlinked;
-    }
-
-    /**
-     * Returns the value of field 'newick'.
-     * 
-     * @return the value of field 'Newick'.
-     */
-    public java.lang.String getNewick(
-    ) {
-        return this._newick;
-    }
-
-    /**
-     * Returns the value of field 'showBootstrap'.
-     * 
-     * @return the value of field 'ShowBootstrap'.
-     */
-    public boolean getShowBootstrap(
-    ) {
-        return this._showBootstrap;
-    }
-
-    /**
-     * Returns the value of field 'showDistances'.
-     * 
-     * @return the value of field 'ShowDistances'.
-     */
-    public boolean getShowDistances(
-    ) {
-        return this._showDistances;
-    }
-
-    /**
-     * Returns the value of field 'threshold'.
-     * 
-     * @return the value of field 'Threshold'.
-     */
-    public float getThreshold(
-    ) {
-        return this._threshold;
-    }
-
-    /**
-     * Returns the value of field 'title'.
-     * 
-     * @return the value of field 'Title'.
-     */
-    public java.lang.String getTitle(
-    ) {
-        return this._title;
-    }
-
-    /**
-     * Returns the value of field 'width'.
-     * 
-     * @return the value of field 'Width'.
-     */
-    public int getWidth(
-    ) {
-        return this._width;
-    }
-
-    /**
-     * Returns the value of field 'xpos'.
-     * 
-     * @return the value of field 'Xpos'.
-     */
-    public int getXpos(
-    ) {
-        return this._xpos;
-    }
-
-    /**
-     * Returns the value of field 'ypos'.
-     * 
-     * @return the value of field 'Ypos'.
-     */
-    public int getYpos(
-    ) {
-        return this._ypos;
-    }
-
-    /**
-     * Method hasCurrentTree.
-     * 
-     * @return true if at least one CurrentTree has been added
-     */
-    public boolean hasCurrentTree(
-    ) {
-        return this._has_currentTree;
-    }
-
-    /**
-     * Method hasFitToWindow.
-     * 
-     * @return true if at least one FitToWindow has been added
-     */
-    public boolean hasFitToWindow(
-    ) {
-        return this._has_fitToWindow;
-    }
-
-    /**
-     * Method hasFontSize.
-     * 
-     * @return true if at least one FontSize has been added
-     */
-    public boolean hasFontSize(
-    ) {
-        return this._has_fontSize;
-    }
-
-    /**
-     * Method hasFontStyle.
-     * 
-     * @return true if at least one FontStyle has been added
-     */
-    public boolean hasFontStyle(
-    ) {
-        return this._has_fontStyle;
-    }
-
-    /**
-     * Method hasHeight.
-     * 
-     * @return true if at least one Height has been added
-     */
-    public boolean hasHeight(
-    ) {
-        return this._has_height;
-    }
-
-    /**
-     * Method hasMarkUnlinked.
-     * 
-     * @return true if at least one MarkUnlinked has been added
-     */
-    public boolean hasMarkUnlinked(
-    ) {
-        return this._has_markUnlinked;
-    }
-
-    /**
-     * Method hasShowBootstrap.
-     * 
-     * @return true if at least one ShowBootstrap has been added
-     */
-    public boolean hasShowBootstrap(
-    ) {
-        return this._has_showBootstrap;
-    }
-
-    /**
-     * Method hasShowDistances.
-     * 
-     * @return true if at least one ShowDistances has been added
-     */
-    public boolean hasShowDistances(
-    ) {
-        return this._has_showDistances;
-    }
-
-    /**
-     * Method hasThreshold.
-     * 
-     * @return true if at least one Threshold has been added
-     */
-    public boolean hasThreshold(
-    ) {
-        return this._has_threshold;
-    }
-
-    /**
-     * Method hasWidth.
-     * 
-     * @return true if at least one Width has been added
-     */
-    public boolean hasWidth(
-    ) {
-        return this._has_width;
-    }
-
-    /**
-     * Method hasXpos.
-     * 
-     * @return true if at least one Xpos has been added
-     */
-    public boolean hasXpos(
-    ) {
-        return this._has_xpos;
-    }
-
-    /**
-     * Method hasYpos.
-     * 
-     * @return true if at least one Ypos has been added
-     */
-    public boolean hasYpos(
-    ) {
-        return this._has_ypos;
-    }
-
-    /**
-     * Returns the value of field 'currentTree'.
-     * 
-     * @return the value of field 'CurrentTree'.
-     */
-    public boolean isCurrentTree(
-    ) {
-        return this._currentTree;
-    }
-
-    /**
-     * Returns the value of field 'fitToWindow'.
-     * 
-     * @return the value of field 'FitToWindow'.
-     */
-    public boolean isFitToWindow(
-    ) {
-        return this._fitToWindow;
-    }
-
-    /**
-     * Returns the value of field 'markUnlinked'.
-     * 
-     * @return the value of field 'MarkUnlinked'.
-     */
-    public boolean isMarkUnlinked(
-    ) {
-        return this._markUnlinked;
-    }
-
-    /**
-     * Returns the value of field 'showBootstrap'.
-     * 
-     * @return the value of field 'ShowBootstrap'.
-     */
-    public boolean isShowBootstrap(
-    ) {
-        return this._showBootstrap;
-    }
-
-    /**
-     * Returns the value of field 'showDistances'.
-     * 
-     * @return the value of field 'ShowDistances'.
-     */
-    public boolean isShowDistances(
-    ) {
-        return this._showDistances;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'currentTree'.
-     * 
-     * @param currentTree the value of field 'currentTree'.
-     */
-    public void setCurrentTree(
-            final boolean currentTree) {
-        this._currentTree = currentTree;
-        this._has_currentTree = true;
-    }
-
-    /**
-     * Sets the value of field 'fitToWindow'.
-     * 
-     * @param fitToWindow the value of field 'fitToWindow'.
-     */
-    public void setFitToWindow(
-            final boolean fitToWindow) {
-        this._fitToWindow = fitToWindow;
-        this._has_fitToWindow = true;
-    }
-
-    /**
-     * Sets the value of field 'fontName'.
-     * 
-     * @param fontName the value of field 'fontName'.
-     */
-    public void setFontName(
-            final java.lang.String fontName) {
-        this._fontName = fontName;
-    }
-
-    /**
-     * Sets the value of field 'fontSize'.
-     * 
-     * @param fontSize the value of field 'fontSize'.
-     */
-    public void setFontSize(
-            final int fontSize) {
-        this._fontSize = fontSize;
-        this._has_fontSize = true;
-    }
-
-    /**
-     * Sets the value of field 'fontStyle'.
-     * 
-     * @param fontStyle the value of field 'fontStyle'.
-     */
-    public void setFontStyle(
-            final int fontStyle) {
-        this._fontStyle = fontStyle;
-        this._has_fontStyle = true;
-    }
-
-    /**
-     * Sets the value of field 'height'.
-     * 
-     * @param height the value of field 'height'.
-     */
-    public void setHeight(
-            final int height) {
-        this._height = height;
-        this._has_height = true;
-    }
-
-    /**
-     * Sets the value of field 'markUnlinked'.
-     * 
-     * @param markUnlinked the value of field 'markUnlinked'.
-     */
-    public void setMarkUnlinked(
-            final boolean markUnlinked) {
-        this._markUnlinked = markUnlinked;
-        this._has_markUnlinked = true;
-    }
-
-    /**
-     * Sets the value of field 'newick'.
-     * 
-     * @param newick the value of field 'newick'.
-     */
-    public void setNewick(
-            final java.lang.String newick) {
-        this._newick = newick;
-    }
-
-    /**
-     * Sets the value of field 'showBootstrap'.
-     * 
-     * @param showBootstrap the value of field 'showBootstrap'.
-     */
-    public void setShowBootstrap(
-            final boolean showBootstrap) {
-        this._showBootstrap = showBootstrap;
-        this._has_showBootstrap = true;
-    }
-
-    /**
-     * Sets the value of field 'showDistances'.
-     * 
-     * @param showDistances the value of field 'showDistances'.
-     */
-    public void setShowDistances(
-            final boolean showDistances) {
-        this._showDistances = showDistances;
-        this._has_showDistances = true;
-    }
-
-    /**
-     * Sets the value of field 'threshold'.
-     * 
-     * @param threshold the value of field 'threshold'.
-     */
-    public void setThreshold(
-            final float threshold) {
-        this._threshold = threshold;
-        this._has_threshold = true;
-    }
-
-    /**
-     * Sets the value of field 'title'.
-     * 
-     * @param title the value of field 'title'.
-     */
-    public void setTitle(
-            final java.lang.String title) {
-        this._title = title;
-    }
-
-    /**
-     * Sets the value of field 'width'.
-     * 
-     * @param width the value of field 'width'.
-     */
-    public void setWidth(
-            final int width) {
-        this._width = width;
-        this._has_width = true;
-    }
-
-    /**
-     * Sets the value of field 'xpos'.
-     * 
-     * @param xpos the value of field 'xpos'.
-     */
-    public void setXpos(
-            final int xpos) {
-        this._xpos = xpos;
-        this._has_xpos = true;
-    }
-
-    /**
-     * Sets the value of field 'ypos'.
-     * 
-     * @param ypos the value of field 'ypos'.
-     */
-    public void setYpos(
-            final int ypos) {
-        this._ypos = ypos;
-        this._has_ypos = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.schemabinding.version2.Tree
-     */
-    public static jalview.schemabinding.version2.Tree unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.Tree) Unmarshaller.unmarshal(jalview.schemabinding.version2.Tree.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+public class Tree implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _width.
+   */
+  private int _width;
+
+  /**
+   * keeps track of state for field: _width
+   */
+  private boolean _has_width;
+
+  /**
+   * Field _height.
+   */
+  private int _height;
+
+  /**
+   * keeps track of state for field: _height
+   */
+  private boolean _has_height;
+
+  /**
+   * Field _xpos.
+   */
+  private int _xpos;
+
+  /**
+   * keeps track of state for field: _xpos
+   */
+  private boolean _has_xpos;
+
+  /**
+   * Field _ypos.
+   */
+  private int _ypos;
+
+  /**
+   * keeps track of state for field: _ypos
+   */
+  private boolean _has_ypos;
+
+  /**
+   * Field _fontName.
+   */
+  private java.lang.String _fontName;
+
+  /**
+   * Field _fontSize.
+   */
+  private int _fontSize;
+
+  /**
+   * keeps track of state for field: _fontSize
+   */
+  private boolean _has_fontSize;
+
+  /**
+   * Field _fontStyle.
+   */
+  private int _fontStyle;
+
+  /**
+   * keeps track of state for field: _fontStyle
+   */
+  private boolean _has_fontStyle;
+
+  /**
+   * Field _threshold.
+   */
+  private float _threshold;
+
+  /**
+   * keeps track of state for field: _threshold
+   */
+  private boolean _has_threshold;
+
+  /**
+   * Field _showBootstrap.
+   */
+  private boolean _showBootstrap;
+
+  /**
+   * keeps track of state for field: _showBootstrap
+   */
+  private boolean _has_showBootstrap;
+
+  /**
+   * Field _showDistances.
+   */
+  private boolean _showDistances;
+
+  /**
+   * keeps track of state for field: _showDistances
+   */
+  private boolean _has_showDistances;
+
+  /**
+   * Field _markUnlinked.
+   */
+  private boolean _markUnlinked;
+
+  /**
+   * keeps track of state for field: _markUnlinked
+   */
+  private boolean _has_markUnlinked;
+
+  /**
+   * Field _fitToWindow.
+   */
+  private boolean _fitToWindow;
+
+  /**
+   * keeps track of state for field: _fitToWindow
+   */
+  private boolean _has_fitToWindow;
+
+  /**
+   * Field _currentTree.
+   */
+  private boolean _currentTree;
+
+  /**
+   * keeps track of state for field: _currentTree
+   */
+  private boolean _has_currentTree;
+
+  /**
+   * Field _title.
+   */
+  private java.lang.String _title;
+
+  /**
+   * Field _newick.
+   */
+  private java.lang.String _newick;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Tree()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   */
+  public void deleteCurrentTree()
+  {
+    this._has_currentTree = false;
+  }
+
+  /**
+   */
+  public void deleteFitToWindow()
+  {
+    this._has_fitToWindow = false;
+  }
+
+  /**
+   */
+  public void deleteFontSize()
+  {
+    this._has_fontSize = false;
+  }
+
+  /**
+   */
+  public void deleteFontStyle()
+  {
+    this._has_fontStyle = false;
+  }
+
+  /**
+   */
+  public void deleteHeight()
+  {
+    this._has_height = false;
+  }
+
+  /**
+   */
+  public void deleteMarkUnlinked()
+  {
+    this._has_markUnlinked = false;
+  }
+
+  /**
+   */
+  public void deleteShowBootstrap()
+  {
+    this._has_showBootstrap = false;
+  }
+
+  /**
+   */
+  public void deleteShowDistances()
+  {
+    this._has_showDistances = false;
+  }
+
+  /**
+   */
+  public void deleteThreshold()
+  {
+    this._has_threshold = false;
+  }
+
+  /**
+   */
+  public void deleteWidth()
+  {
+    this._has_width = false;
+  }
+
+  /**
+   */
+  public void deleteXpos()
+  {
+    this._has_xpos = false;
+  }
+
+  /**
+   */
+  public void deleteYpos()
+  {
+    this._has_ypos = false;
+  }
+
+  /**
+   * Returns the value of field 'currentTree'.
+   * 
+   * @return the value of field 'CurrentTree'.
+   */
+  public boolean getCurrentTree()
+  {
+    return this._currentTree;
+  }
+
+  /**
+   * Returns the value of field 'fitToWindow'.
+   * 
+   * @return the value of field 'FitToWindow'.
+   */
+  public boolean getFitToWindow()
+  {
+    return this._fitToWindow;
+  }
+
+  /**
+   * Returns the value of field 'fontName'.
+   * 
+   * @return the value of field 'FontName'.
+   */
+  public java.lang.String getFontName()
+  {
+    return this._fontName;
+  }
+
+  /**
+   * Returns the value of field 'fontSize'.
+   * 
+   * @return the value of field 'FontSize'.
+   */
+  public int getFontSize()
+  {
+    return this._fontSize;
+  }
+
+  /**
+   * Returns the value of field 'fontStyle'.
+   * 
+   * @return the value of field 'FontStyle'.
+   */
+  public int getFontStyle()
+  {
+    return this._fontStyle;
+  }
+
+  /**
+   * Returns the value of field 'height'.
+   * 
+   * @return the value of field 'Height'.
+   */
+  public int getHeight()
+  {
+    return this._height;
+  }
+
+  /**
+   * Returns the value of field 'markUnlinked'.
+   * 
+   * @return the value of field 'MarkUnlinked'.
+   */
+  public boolean getMarkUnlinked()
+  {
+    return this._markUnlinked;
+  }
+
+  /**
+   * Returns the value of field 'newick'.
+   * 
+   * @return the value of field 'Newick'.
+   */
+  public java.lang.String getNewick()
+  {
+    return this._newick;
+  }
+
+  /**
+   * Returns the value of field 'showBootstrap'.
+   * 
+   * @return the value of field 'ShowBootstrap'.
+   */
+  public boolean getShowBootstrap()
+  {
+    return this._showBootstrap;
+  }
+
+  /**
+   * Returns the value of field 'showDistances'.
+   * 
+   * @return the value of field 'ShowDistances'.
+   */
+  public boolean getShowDistances()
+  {
+    return this._showDistances;
+  }
+
+  /**
+   * Returns the value of field 'threshold'.
+   * 
+   * @return the value of field 'Threshold'.
+   */
+  public float getThreshold()
+  {
+    return this._threshold;
+  }
+
+  /**
+   * Returns the value of field 'title'.
+   * 
+   * @return the value of field 'Title'.
+   */
+  public java.lang.String getTitle()
+  {
+    return this._title;
+  }
+
+  /**
+   * Returns the value of field 'width'.
+   * 
+   * @return the value of field 'Width'.
+   */
+  public int getWidth()
+  {
+    return this._width;
+  }
+
+  /**
+   * Returns the value of field 'xpos'.
+   * 
+   * @return the value of field 'Xpos'.
+   */
+  public int getXpos()
+  {
+    return this._xpos;
+  }
+
+  /**
+   * Returns the value of field 'ypos'.
+   * 
+   * @return the value of field 'Ypos'.
+   */
+  public int getYpos()
+  {
+    return this._ypos;
+  }
+
+  /**
+   * Method hasCurrentTree.
+   * 
+   * @return true if at least one CurrentTree has been added
+   */
+  public boolean hasCurrentTree()
+  {
+    return this._has_currentTree;
+  }
+
+  /**
+   * Method hasFitToWindow.
+   * 
+   * @return true if at least one FitToWindow has been added
+   */
+  public boolean hasFitToWindow()
+  {
+    return this._has_fitToWindow;
+  }
+
+  /**
+   * Method hasFontSize.
+   * 
+   * @return true if at least one FontSize has been added
+   */
+  public boolean hasFontSize()
+  {
+    return this._has_fontSize;
+  }
+
+  /**
+   * Method hasFontStyle.
+   * 
+   * @return true if at least one FontStyle has been added
+   */
+  public boolean hasFontStyle()
+  {
+    return this._has_fontStyle;
+  }
+
+  /**
+   * Method hasHeight.
+   * 
+   * @return true if at least one Height has been added
+   */
+  public boolean hasHeight()
+  {
+    return this._has_height;
+  }
+
+  /**
+   * Method hasMarkUnlinked.
+   * 
+   * @return true if at least one MarkUnlinked has been added
+   */
+  public boolean hasMarkUnlinked()
+  {
+    return this._has_markUnlinked;
+  }
+
+  /**
+   * Method hasShowBootstrap.
+   * 
+   * @return true if at least one ShowBootstrap has been added
+   */
+  public boolean hasShowBootstrap()
+  {
+    return this._has_showBootstrap;
+  }
+
+  /**
+   * Method hasShowDistances.
+   * 
+   * @return true if at least one ShowDistances has been added
+   */
+  public boolean hasShowDistances()
+  {
+    return this._has_showDistances;
+  }
+
+  /**
+   * Method hasThreshold.
+   * 
+   * @return true if at least one Threshold has been added
+   */
+  public boolean hasThreshold()
+  {
+    return this._has_threshold;
+  }
+
+  /**
+   * Method hasWidth.
+   * 
+   * @return true if at least one Width has been added
+   */
+  public boolean hasWidth()
+  {
+    return this._has_width;
+  }
+
+  /**
+   * Method hasXpos.
+   * 
+   * @return true if at least one Xpos has been added
+   */
+  public boolean hasXpos()
+  {
+    return this._has_xpos;
+  }
+
+  /**
+   * Method hasYpos.
+   * 
+   * @return true if at least one Ypos has been added
+   */
+  public boolean hasYpos()
+  {
+    return this._has_ypos;
+  }
+
+  /**
+   * Returns the value of field 'currentTree'.
+   * 
+   * @return the value of field 'CurrentTree'.
+   */
+  public boolean isCurrentTree()
+  {
+    return this._currentTree;
+  }
+
+  /**
+   * Returns the value of field 'fitToWindow'.
+   * 
+   * @return the value of field 'FitToWindow'.
+   */
+  public boolean isFitToWindow()
+  {
+    return this._fitToWindow;
+  }
+
+  /**
+   * Returns the value of field 'markUnlinked'.
+   * 
+   * @return the value of field 'MarkUnlinked'.
+   */
+  public boolean isMarkUnlinked()
+  {
+    return this._markUnlinked;
+  }
+
+  /**
+   * Returns the value of field 'showBootstrap'.
+   * 
+   * @return the value of field 'ShowBootstrap'.
+   */
+  public boolean isShowBootstrap()
+  {
+    return this._showBootstrap;
+  }
+
+  /**
+   * Returns the value of field 'showDistances'.
+   * 
+   * @return the value of field 'ShowDistances'.
+   */
+  public boolean isShowDistances()
+  {
+    return this._showDistances;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'currentTree'.
+   * 
+   * @param currentTree
+   *                the value of field 'currentTree'.
+   */
+  public void setCurrentTree(final boolean currentTree)
+  {
+    this._currentTree = currentTree;
+    this._has_currentTree = true;
+  }
+
+  /**
+   * Sets the value of field 'fitToWindow'.
+   * 
+   * @param fitToWindow
+   *                the value of field 'fitToWindow'.
+   */
+  public void setFitToWindow(final boolean fitToWindow)
+  {
+    this._fitToWindow = fitToWindow;
+    this._has_fitToWindow = true;
+  }
+
+  /**
+   * Sets the value of field 'fontName'.
+   * 
+   * @param fontName
+   *                the value of field 'fontName'.
+   */
+  public void setFontName(final java.lang.String fontName)
+  {
+    this._fontName = fontName;
+  }
+
+  /**
+   * Sets the value of field 'fontSize'.
+   * 
+   * @param fontSize
+   *                the value of field 'fontSize'.
+   */
+  public void setFontSize(final int fontSize)
+  {
+    this._fontSize = fontSize;
+    this._has_fontSize = true;
+  }
+
+  /**
+   * Sets the value of field 'fontStyle'.
+   * 
+   * @param fontStyle
+   *                the value of field 'fontStyle'.
+   */
+  public void setFontStyle(final int fontStyle)
+  {
+    this._fontStyle = fontStyle;
+    this._has_fontStyle = true;
+  }
+
+  /**
+   * Sets the value of field 'height'.
+   * 
+   * @param height
+   *                the value of field 'height'.
+   */
+  public void setHeight(final int height)
+  {
+    this._height = height;
+    this._has_height = true;
+  }
+
+  /**
+   * Sets the value of field 'markUnlinked'.
+   * 
+   * @param markUnlinked
+   *                the value of field 'markUnlinked'.
+   */
+  public void setMarkUnlinked(final boolean markUnlinked)
+  {
+    this._markUnlinked = markUnlinked;
+    this._has_markUnlinked = true;
+  }
+
+  /**
+   * Sets the value of field 'newick'.
+   * 
+   * @param newick
+   *                the value of field 'newick'.
+   */
+  public void setNewick(final java.lang.String newick)
+  {
+    this._newick = newick;
+  }
+
+  /**
+   * Sets the value of field 'showBootstrap'.
+   * 
+   * @param showBootstrap
+   *                the value of field 'showBootstrap'.
+   */
+  public void setShowBootstrap(final boolean showBootstrap)
+  {
+    this._showBootstrap = showBootstrap;
+    this._has_showBootstrap = true;
+  }
+
+  /**
+   * Sets the value of field 'showDistances'.
+   * 
+   * @param showDistances
+   *                the value of field 'showDistances'.
+   */
+  public void setShowDistances(final boolean showDistances)
+  {
+    this._showDistances = showDistances;
+    this._has_showDistances = true;
+  }
+
+  /**
+   * Sets the value of field 'threshold'.
+   * 
+   * @param threshold
+   *                the value of field 'threshold'.
+   */
+  public void setThreshold(final float threshold)
+  {
+    this._threshold = threshold;
+    this._has_threshold = true;
+  }
+
+  /**
+   * Sets the value of field 'title'.
+   * 
+   * @param title
+   *                the value of field 'title'.
+   */
+  public void setTitle(final java.lang.String title)
+  {
+    this._title = title;
+  }
+
+  /**
+   * Sets the value of field 'width'.
+   * 
+   * @param width
+   *                the value of field 'width'.
+   */
+  public void setWidth(final int width)
+  {
+    this._width = width;
+    this._has_width = true;
+  }
+
+  /**
+   * Sets the value of field 'xpos'.
+   * 
+   * @param xpos
+   *                the value of field 'xpos'.
+   */
+  public void setXpos(final int xpos)
+  {
+    this._xpos = xpos;
+    this._has_xpos = true;
+  }
+
+  /**
+   * Sets the value of field 'ypos'.
+   * 
+   * @param ypos
+   *                the value of field 'ypos'.
+   */
+  public void setYpos(final int ypos)
+  {
+    this._ypos = ypos;
+    this._has_ypos = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.Tree
+   */
+  public static jalview.schemabinding.version2.Tree unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.Tree) Unmarshaller.unmarshal(
+            jalview.schemabinding.version2.Tree.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/UserColourScheme.java b/src/jalview/schemabinding/version2/UserColourScheme.java
index 3cb65e0..6e3b6c9 100755
--- a/src/jalview/schemabinding/version2/UserColourScheme.java
+++ b/src/jalview/schemabinding/version2/UserColourScheme.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,99 +30,113 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class UserColourScheme extends JalviewUserColours 
-implements java.io.Serializable
+public class UserColourScheme extends JalviewUserColours implements
+        java.io.Serializable
 {
 
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
 
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public UserColourScheme() {
-        super();
-    }
+  public UserColourScheme()
+  {
+    super();
+  }
 
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
 
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
 
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
 
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.JalviewUserColours
-     */
-    public static jalview.schemabinding.version2.JalviewUserColours unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.JalviewUserColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.UserColourScheme.class, reader);
-    }
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.JalviewUserColours
+   */
+  public static jalview.schemabinding.version2.JalviewUserColours unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.JalviewUserColours) Unmarshaller
+            .unmarshal(
+                    jalview.schemabinding.version2.UserColourScheme.class,
+                    reader);
+  }
 
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/UserColours.java b/src/jalview/schemabinding/version2/UserColours.java
index 062024f..b52eba7 100755
--- a/src/jalview/schemabinding/version2/UserColours.java
+++ b/src/jalview/schemabinding/version2/UserColours.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,152 +30,168 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class UserColours implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _id.
-     */
-    private java.lang.String _id;
-
-    /**
-     * Field _userColourScheme.
-     */
-    private jalview.schemabinding.version2.UserColourScheme _userColourScheme;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public UserColours() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'id'.
-     * 
-     * @return the value of field 'Id'.
-     */
-    public java.lang.String getId(
-    ) {
-        return this._id;
-    }
-
-    /**
-     * Returns the value of field 'userColourScheme'.
-     * 
-     * @return the value of field 'UserColourScheme'.
-     */
-    public jalview.schemabinding.version2.UserColourScheme getUserColourScheme(
-    ) {
-        return this._userColourScheme;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'id'.
-     * 
-     * @param id the value of field 'id'.
-     */
-    public void setId(
-            final java.lang.String id) {
-        this._id = id;
-    }
-
-    /**
-     * Sets the value of field 'userColourScheme'.
-     * 
-     * @param userColourScheme the value of field 'userColourScheme'
-     */
-    public void setUserColourScheme(
-            final jalview.schemabinding.version2.UserColourScheme userColourScheme) {
-        this._userColourScheme = userColourScheme;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.UserColours
-     */
-    public static jalview.schemabinding.version2.UserColours unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.UserColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.UserColours.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class UserColours implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _id.
+   */
+  private java.lang.String _id;
+
+  /**
+   * Field _userColourScheme.
+   */
+  private jalview.schemabinding.version2.UserColourScheme _userColourScheme;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public UserColours()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Returns the value of field 'id'.
+   * 
+   * @return the value of field 'Id'.
+   */
+  public java.lang.String getId()
+  {
+    return this._id;
+  }
+
+  /**
+   * Returns the value of field 'userColourScheme'.
+   * 
+   * @return the value of field 'UserColourScheme'.
+   */
+  public jalview.schemabinding.version2.UserColourScheme getUserColourScheme()
+  {
+    return this._userColourScheme;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'id'.
+   * 
+   * @param id
+   *                the value of field 'id'.
+   */
+  public void setId(final java.lang.String id)
+  {
+    this._id = id;
+  }
+
+  /**
+   * Sets the value of field 'userColourScheme'.
+   * 
+   * @param userColourScheme
+   *                the value of field 'userColourScheme'
+   */
+  public void setUserColourScheme(
+          final jalview.schemabinding.version2.UserColourScheme userColourScheme)
+  {
+    this._userColourScheme = userColourScheme;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.UserColours
+   */
+  public static jalview.schemabinding.version2.UserColours unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.UserColours) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.UserColours.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/VAMSAS.java b/src/jalview/schemabinding/version2/VAMSAS.java
index ae8e17f..7a7edf5 100755
--- a/src/jalview/schemabinding/version2/VAMSAS.java
+++ b/src/jalview/schemabinding/version2/VAMSAS.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,411 +30,440 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class VAMSAS implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _treeList.
-     */
-    private java.util.Vector _treeList;
-
-    /**
-     * Field _sequenceSetList.
-     */
-    private java.util.Vector _sequenceSetList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public VAMSAS() {
-        super();
-        this._treeList = new java.util.Vector();
-        this._sequenceSetList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vSequenceSet
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSequenceSet(
-            final jalview.schemabinding.version2.SequenceSet vSequenceSet)
-    throws java.lang.IndexOutOfBoundsException {
-        this._sequenceSetList.addElement(vSequenceSet);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSequenceSet
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSequenceSet(
-            final int index,
-            final jalview.schemabinding.version2.SequenceSet vSequenceSet)
-    throws java.lang.IndexOutOfBoundsException {
-        this._sequenceSetList.add(index, vSequenceSet);
-    }
-
-    /**
-     * 
-     * 
-     * @param vTree
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addTree(
-            final java.lang.String vTree)
-    throws java.lang.IndexOutOfBoundsException {
-        this._treeList.addElement(vTree);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vTree
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addTree(
-            final int index,
-            final java.lang.String vTree)
-    throws java.lang.IndexOutOfBoundsException {
-        this._treeList.add(index, vTree);
-    }
-
-    /**
-     * Method enumerateSequenceSet.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.SequenceSet elements
-     */
-    public java.util.Enumeration enumerateSequenceSet(
-    ) {
-        return this._sequenceSetList.elements();
-    }
-
-    /**
-     * Method enumerateTree.
-     * 
-     * @return an Enumeration over all java.lang.String elements
-     */
-    public java.util.Enumeration enumerateTree(
-    ) {
-        return this._treeList.elements();
-    }
-
-    /**
-     * Method getSequenceSet.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.SequenceSet at the given index
-     */
-    public jalview.schemabinding.version2.SequenceSet getSequenceSet(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._sequenceSetList.size()) {
-            throw new IndexOutOfBoundsException("getSequenceSet: Index value '" + index + "' not in range [0.." + (this._sequenceSetList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.SequenceSet) _sequenceSetList.get(index);
-    }
-
-    /**
-     * Method getSequenceSet.Returns the contents of the collection
-     * in an Array.  <p>Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we <i>know</i>
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.SequenceSet[] getSequenceSet(
-    ) {
-        jalview.schemabinding.version2.SequenceSet[] array = new jalview.schemabinding.version2.SequenceSet[0];
-        return (jalview.schemabinding.version2.SequenceSet[]) this._sequenceSetList.toArray(array);
+public class VAMSAS implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _treeList.
+   */
+  private java.util.Vector _treeList;
+
+  /**
+   * Field _sequenceSetList.
+   */
+  private java.util.Vector _sequenceSetList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public VAMSAS()
+  {
+    super();
+    this._treeList = new java.util.Vector();
+    this._sequenceSetList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vSequenceSet
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addSequenceSet(
+          final jalview.schemabinding.version2.SequenceSet vSequenceSet)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._sequenceSetList.addElement(vSequenceSet);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSequenceSet
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addSequenceSet(final int index,
+          final jalview.schemabinding.version2.SequenceSet vSequenceSet)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._sequenceSetList.add(index, vSequenceSet);
+  }
+
+  /**
+   * 
+   * 
+   * @param vTree
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addTree(final java.lang.String vTree)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._treeList.addElement(vTree);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vTree
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addTree(final int index, final java.lang.String vTree)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._treeList.add(index, vTree);
+  }
+
+  /**
+   * Method enumerateSequenceSet.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.SequenceSet
+   *         elements
+   */
+  public java.util.Enumeration enumerateSequenceSet()
+  {
+    return this._sequenceSetList.elements();
+  }
+
+  /**
+   * Method enumerateTree.
+   * 
+   * @return an Enumeration over all java.lang.String elements
+   */
+  public java.util.Enumeration enumerateTree()
+  {
+    return this._treeList.elements();
+  }
+
+  /**
+   * Method getSequenceSet.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.SequenceSet at the
+   *         given index
+   */
+  public jalview.schemabinding.version2.SequenceSet getSequenceSet(
+          final int index) throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._sequenceSetList.size())
+    {
+      throw new IndexOutOfBoundsException("getSequenceSet: Index value '"
+              + index + "' not in range [0.."
+              + (this._sequenceSetList.size() - 1) + "]");
     }
 
-    /**
-     * Method getSequenceSetCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getSequenceSetCount(
-    ) {
-        return this._sequenceSetList.size();
+    return (jalview.schemabinding.version2.SequenceSet) _sequenceSetList
+            .get(index);
+  }
+
+  /**
+   * Method getSequenceSet.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.SequenceSet[] getSequenceSet()
+  {
+    jalview.schemabinding.version2.SequenceSet[] array = new jalview.schemabinding.version2.SequenceSet[0];
+    return (jalview.schemabinding.version2.SequenceSet[]) this._sequenceSetList
+            .toArray(array);
+  }
+
+  /**
+   * Method getSequenceSetCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getSequenceSetCount()
+  {
+    return this._sequenceSetList.size();
+  }
+
+  /**
+   * Method getTree.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the java.lang.String at the given index
+   */
+  public java.lang.String getTree(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._treeList.size())
+    {
+      throw new IndexOutOfBoundsException("getTree: Index value '" + index
+              + "' not in range [0.." + (this._treeList.size() - 1) + "]");
     }
 
-    /**
-     * Method getTree.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the java.lang.String at the given index
-     */
-    public java.lang.String getTree(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._treeList.size()) {
-            throw new IndexOutOfBoundsException("getTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
-        }
-        
-        return (java.lang.String) _treeList.get(index);
+    return (java.lang.String) _treeList.get(index);
+  }
+
+  /**
+   * Method getTree.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public java.lang.String[] getTree()
+  {
+    java.lang.String[] array = new java.lang.String[0];
+    return (java.lang.String[]) this._treeList.toArray(array);
+  }
+
+  /**
+   * Method getTreeCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getTreeCount()
+  {
+    return this._treeList.size();
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
-
-    /**
-     * Method getTree.Returns the contents of the collection in an
-     * Array.  <p>Note:  Just in case the collection contents are
-     * changing in another thread, we pass a 0-length Array of the
-     * correct type into the API call.  This way we <i>know</i>
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public java.lang.String[] getTree(
-    ) {
-        java.lang.String[] array = new java.lang.String[0];
-        return (java.lang.String[]) this._treeList.toArray(array);
-    }
-
-    /**
-     * Method getTreeCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getTreeCount(
-    ) {
-        return this._treeList.size();
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     */
-    public void removeAllSequenceSet(
-    ) {
-        this._sequenceSetList.clear();
-    }
-
-    /**
-     */
-    public void removeAllTree(
-    ) {
-        this._treeList.clear();
-    }
-
-    /**
-     * Method removeSequenceSet.
-     * 
-     * @param vSequenceSet
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeSequenceSet(
-            final jalview.schemabinding.version2.SequenceSet vSequenceSet) {
-        boolean removed = _sequenceSetList.remove(vSequenceSet);
-        return removed;
-    }
-
-    /**
-     * Method removeSequenceSetAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.SequenceSet removeSequenceSetAt(
-            final int index) {
-        java.lang.Object obj = this._sequenceSetList.remove(index);
-        return (jalview.schemabinding.version2.SequenceSet) obj;
-    }
-
-    /**
-     * Method removeTree.
-     * 
-     * @param vTree
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeTree(
-            final java.lang.String vTree) {
-        boolean removed = _treeList.remove(vTree);
-        return removed;
-    }
-
-    /**
-     * Method removeTreeAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public java.lang.String removeTreeAt(
-            final int index) {
-        java.lang.Object obj = this._treeList.remove(index);
-        return (java.lang.String) obj;
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   */
+  public void removeAllSequenceSet()
+  {
+    this._sequenceSetList.clear();
+  }
+
+  /**
+   */
+  public void removeAllTree()
+  {
+    this._treeList.clear();
+  }
+
+  /**
+   * Method removeSequenceSet.
+   * 
+   * @param vSequenceSet
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeSequenceSet(
+          final jalview.schemabinding.version2.SequenceSet vSequenceSet)
+  {
+    boolean removed = _sequenceSetList.remove(vSequenceSet);
+    return removed;
+  }
+
+  /**
+   * Method removeSequenceSetAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.SequenceSet removeSequenceSetAt(
+          final int index)
+  {
+    java.lang.Object obj = this._sequenceSetList.remove(index);
+    return (jalview.schemabinding.version2.SequenceSet) obj;
+  }
+
+  /**
+   * Method removeTree.
+   * 
+   * @param vTree
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeTree(final java.lang.String vTree)
+  {
+    boolean removed = _treeList.remove(vTree);
+    return removed;
+  }
+
+  /**
+   * Method removeTreeAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public java.lang.String removeTreeAt(final int index)
+  {
+    java.lang.Object obj = this._treeList.remove(index);
+    return (java.lang.String) obj;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSequenceSet
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setSequenceSet(final int index,
+          final jalview.schemabinding.version2.SequenceSet vSequenceSet)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._sequenceSetList.size())
+    {
+      throw new IndexOutOfBoundsException("setSequenceSet: Index value '"
+              + index + "' not in range [0.."
+              + (this._sequenceSetList.size() - 1) + "]");
     }
 
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSequenceSet
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setSequenceSet(
-            final int index,
-            final jalview.schemabinding.version2.SequenceSet vSequenceSet)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._sequenceSetList.size()) {
-            throw new IndexOutOfBoundsException("setSequenceSet: Index value '" + index + "' not in range [0.." + (this._sequenceSetList.size() - 1) + "]");
-        }
-        
-        this._sequenceSetList.set(index, vSequenceSet);
+    this._sequenceSetList.set(index, vSequenceSet);
+  }
+
+  /**
+   * 
+   * 
+   * @param vSequenceSetArray
+   */
+  public void setSequenceSet(
+          final jalview.schemabinding.version2.SequenceSet[] vSequenceSetArray)
+  {
+    // -- copy array
+    _sequenceSetList.clear();
+
+    for (int i = 0; i < vSequenceSetArray.length; i++)
+    {
+      this._sequenceSetList.add(vSequenceSetArray[i]);
     }
-
-    /**
-     * 
-     * 
-     * @param vSequenceSetArray
-     */
-    public void setSequenceSet(
-            final jalview.schemabinding.version2.SequenceSet[] vSequenceSetArray) {
-        //-- copy array
-        _sequenceSetList.clear();
-        
-        for (int i = 0; i < vSequenceSetArray.length; i++) {
-                this._sequenceSetList.add(vSequenceSetArray[i]);
-        }
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vTree
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setTree(
-            final int index,
-            final java.lang.String vTree)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._treeList.size()) {
-            throw new IndexOutOfBoundsException("setTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
-        }
-        
-        this._treeList.set(index, vTree);
-    }
-
-    /**
-     * 
-     * 
-     * @param vTreeArray
-     */
-    public void setTree(
-            final java.lang.String[] vTreeArray) {
-        //-- copy array
-        _treeList.clear();
-        
-        for (int i = 0; i < vTreeArray.length; i++) {
-                this._treeList.add(vTreeArray[i]);
-        }
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.schemabinding.version2.VAMSAS
-     */
-    public static jalview.schemabinding.version2.VAMSAS unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.VAMSAS) Unmarshaller.unmarshal(jalview.schemabinding.version2.VAMSAS.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vTree
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setTree(final int index, final java.lang.String vTree)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._treeList.size())
+    {
+      throw new IndexOutOfBoundsException("setTree: Index value '" + index
+              + "' not in range [0.." + (this._treeList.size() - 1) + "]");
     }
 
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+    this._treeList.set(index, vTree);
+  }
+
+  /**
+   * 
+   * 
+   * @param vTreeArray
+   */
+  public void setTree(final java.lang.String[] vTreeArray)
+  {
+    // -- copy array
+    _treeList.clear();
+
+    for (int i = 0; i < vTreeArray.length; i++)
+    {
+      this._treeList.add(vTreeArray[i]);
     }
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.VAMSAS
+   */
+  public static jalview.schemabinding.version2.VAMSAS unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.VAMSAS) Unmarshaller.unmarshal(
+            jalview.schemabinding.version2.VAMSAS.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/VamsasModel.java b/src/jalview/schemabinding/version2/VamsasModel.java
index 26814dc..135cbda 100755
--- a/src/jalview/schemabinding/version2/VamsasModel.java
+++ b/src/jalview/schemabinding/version2/VamsasModel.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,98 +30,110 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class VamsasModel extends VAMSAS 
-implements java.io.Serializable
+public class VamsasModel extends VAMSAS implements java.io.Serializable
 {
 
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
 
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public VamsasModel() {
-        super();
-    }
+  public VamsasModel()
+  {
+    super();
+  }
 
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
 
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
 
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
 
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.schemabinding.version2.VAMSAS
-     */
-    public static jalview.schemabinding.version2.VAMSAS unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.VAMSAS) Unmarshaller.unmarshal(jalview.schemabinding.version2.VamsasModel.class, reader);
-    }
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.VAMSAS
+   */
+  public static jalview.schemabinding.version2.VAMSAS unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.VAMSAS) Unmarshaller.unmarshal(
+            jalview.schemabinding.version2.VamsasModel.class, reader);
+  }
 
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/Viewport.java b/src/jalview/schemabinding/version2/Viewport.java
index aa97a95..1e1c2b2 100755
--- a/src/jalview/schemabinding/version2/Viewport.java
+++ b/src/jalview/schemabinding/version2/Viewport.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,1735 +30,1786 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Viewport implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _conservationSelected.
-     */
-    private boolean _conservationSelected;
-
-    /**
-     * keeps track of state for field: _conservationSelected
-     */
-    private boolean _has_conservationSelected;
-
-    /**
-     * Field _pidSelected.
-     */
-    private boolean _pidSelected;
-
-    /**
-     * keeps track of state for field: _pidSelected
-     */
-    private boolean _has_pidSelected;
-
-    /**
-     * Field _bgColour.
-     */
-    private java.lang.String _bgColour;
-
-    /**
-     * Field _consThreshold.
-     */
-    private int _consThreshold;
-
-    /**
-     * keeps track of state for field: _consThreshold
-     */
-    private boolean _has_consThreshold;
-
-    /**
-     * Field _pidThreshold.
-     */
-    private int _pidThreshold;
-
-    /**
-     * keeps track of state for field: _pidThreshold
-     */
-    private boolean _has_pidThreshold;
-
-    /**
-     * Field _title.
-     */
-    private java.lang.String _title;
-
-    /**
-     * Field _showFullId.
-     */
-    private boolean _showFullId;
-
-    /**
-     * keeps track of state for field: _showFullId
-     */
-    private boolean _has_showFullId;
-
-    /**
-     * Field _rightAlignIds.
-     */
-    private boolean _rightAlignIds;
-
-    /**
-     * keeps track of state for field: _rightAlignIds
-     */
-    private boolean _has_rightAlignIds;
-
-    /**
-     * Field _showText.
-     */
-    private boolean _showText;
-
-    /**
-     * keeps track of state for field: _showText
-     */
-    private boolean _has_showText;
-
-    /**
-     * Field _showColourText.
-     */
-    private boolean _showColourText;
-
-    /**
-     * keeps track of state for field: _showColourText
-     */
-    private boolean _has_showColourText;
-
-    /**
-     * Field _showBoxes.
-     */
-    private boolean _showBoxes;
-
-    /**
-     * keeps track of state for field: _showBoxes
-     */
-    private boolean _has_showBoxes;
-
-    /**
-     * Field _wrapAlignment.
-     */
-    private boolean _wrapAlignment;
-
-    /**
-     * keeps track of state for field: _wrapAlignment
-     */
-    private boolean _has_wrapAlignment;
-
-    /**
-     * Field _renderGaps.
-     */
-    private boolean _renderGaps;
-
-    /**
-     * keeps track of state for field: _renderGaps
-     */
-    private boolean _has_renderGaps;
-
-    /**
-     * Field _showSequenceFeatures.
-     */
-    private boolean _showSequenceFeatures;
-
-    /**
-     * keeps track of state for field: _showSequenceFeatures
-     */
-    private boolean _has_showSequenceFeatures;
-
-    /**
-     * Field _showAnnotation.
-     */
-    private boolean _showAnnotation;
-
-    /**
-     * keeps track of state for field: _showAnnotation
-     */
-    private boolean _has_showAnnotation;
-
-    /**
-     * Field _xpos.
-     */
-    private int _xpos;
-
-    /**
-     * keeps track of state for field: _xpos
-     */
-    private boolean _has_xpos;
-
-    /**
-     * Field _ypos.
-     */
-    private int _ypos;
-
-    /**
-     * keeps track of state for field: _ypos
-     */
-    private boolean _has_ypos;
-
-    /**
-     * Field _width.
-     */
-    private int _width;
-
-    /**
-     * keeps track of state for field: _width
-     */
-    private boolean _has_width;
-
-    /**
-     * Field _height.
-     */
-    private int _height;
-
-    /**
-     * keeps track of state for field: _height
-     */
-    private boolean _has_height;
-
-    /**
-     * Field _startRes.
-     */
-    private int _startRes;
-
-    /**
-     * keeps track of state for field: _startRes
-     */
-    private boolean _has_startRes;
-
-    /**
-     * Field _startSeq.
-     */
-    private int _startSeq;
-
-    /**
-     * keeps track of state for field: _startSeq
-     */
-    private boolean _has_startSeq;
-
-    /**
-     * Field _fontName.
-     */
-    private java.lang.String _fontName;
-
-    /**
-     * Field _fontSize.
-     */
-    private int _fontSize;
-
-    /**
-     * keeps track of state for field: _fontSize
-     */
-    private boolean _has_fontSize;
-
-    /**
-     * Field _fontStyle.
-     */
-    private int _fontStyle;
-
-    /**
-     * keeps track of state for field: _fontStyle
-     */
-    private boolean _has_fontStyle;
-
-    /**
-     * Field _viewName.
-     */
-    private java.lang.String _viewName;
-
-    /**
-     * Field _sequenceSetId.
-     */
-    private java.lang.String _sequenceSetId;
-
-    /**
-     * Field _gatheredViews.
-     */
-    private boolean _gatheredViews;
-
-    /**
-     * keeps track of state for field: _gatheredViews
-     */
-    private boolean _has_gatheredViews;
-
-    /**
-     * Field _textCol1.
-     */
-    private int _textCol1;
-
-    /**
-     * keeps track of state for field: _textCol1
-     */
-    private boolean _has_textCol1;
-
-    /**
-     * Field _textCol2.
-     */
-    private int _textCol2;
-
-    /**
-     * keeps track of state for field: _textCol2
-     */
-    private boolean _has_textCol2;
-
-    /**
-     * Field _textColThreshold.
-     */
-    private int _textColThreshold;
-
-    /**
-     * keeps track of state for field: _textColThreshold
-     */
-    private boolean _has_textColThreshold;
-
-    /**
-     * Field _annotationColours.
-     */
-    private jalview.schemabinding.version2.AnnotationColours _annotationColours;
-
-    /**
-     * Field _hiddenColumnsList.
-     */
-    private java.util.Vector _hiddenColumnsList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Viewport() {
-        super();
-        this._hiddenColumnsList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vHiddenColumns
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addHiddenColumns(
-            final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
-    throws java.lang.IndexOutOfBoundsException {
-        this._hiddenColumnsList.addElement(vHiddenColumns);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vHiddenColumns
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addHiddenColumns(
-            final int index,
-            final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
-    throws java.lang.IndexOutOfBoundsException {
-        this._hiddenColumnsList.add(index, vHiddenColumns);
-    }
-
-    /**
-     */
-    public void deleteConsThreshold(
-    ) {
-        this._has_consThreshold= false;
-    }
-
-    /**
-     */
-    public void deleteConservationSelected(
-    ) {
-        this._has_conservationSelected= false;
-    }
-
-    /**
-     */
-    public void deleteFontSize(
-    ) {
-        this._has_fontSize= false;
-    }
-
-    /**
-     */
-    public void deleteFontStyle(
-    ) {
-        this._has_fontStyle= false;
-    }
-
-    /**
-     */
-    public void deleteGatheredViews(
-    ) {
-        this._has_gatheredViews= false;
-    }
-
-    /**
-     */
-    public void deleteHeight(
-    ) {
-        this._has_height= false;
-    }
-
-    /**
-     */
-    public void deletePidSelected(
-    ) {
-        this._has_pidSelected= false;
-    }
-
-    /**
-     */
-    public void deletePidThreshold(
-    ) {
-        this._has_pidThreshold= false;
-    }
-
-    /**
-     */
-    public void deleteRenderGaps(
-    ) {
-        this._has_renderGaps= false;
-    }
-
-    /**
-     */
-    public void deleteRightAlignIds(
-    ) {
-        this._has_rightAlignIds= false;
-    }
-
-    /**
-     */
-    public void deleteShowAnnotation(
-    ) {
-        this._has_showAnnotation= false;
-    }
-
-    /**
-     */
-    public void deleteShowBoxes(
-    ) {
-        this._has_showBoxes= false;
-    }
-
-    /**
-     */
-    public void deleteShowColourText(
-    ) {
-        this._has_showColourText= false;
-    }
-
-    /**
-     */
-    public void deleteShowFullId(
-    ) {
-        this._has_showFullId= false;
-    }
-
-    /**
-     */
-    public void deleteShowSequenceFeatures(
-    ) {
-        this._has_showSequenceFeatures= false;
-    }
-
-    /**
-     */
-    public void deleteShowText(
-    ) {
-        this._has_showText= false;
-    }
-
-    /**
-     */
-    public void deleteStartRes(
-    ) {
-        this._has_startRes= false;
-    }
-
-    /**
-     */
-    public void deleteStartSeq(
-    ) {
-        this._has_startSeq= false;
-    }
-
-    /**
-     */
-    public void deleteTextCol1(
-    ) {
-        this._has_textCol1= false;
-    }
-
-    /**
-     */
-    public void deleteTextCol2(
-    ) {
-        this._has_textCol2= false;
-    }
-
-    /**
-     */
-    public void deleteTextColThreshold(
-    ) {
-        this._has_textColThreshold= false;
-    }
-
-    /**
-     */
-    public void deleteWidth(
-    ) {
-        this._has_width= false;
-    }
-
-    /**
-     */
-    public void deleteWrapAlignment(
-    ) {
-        this._has_wrapAlignment= false;
-    }
-
-    /**
-     */
-    public void deleteXpos(
-    ) {
-        this._has_xpos= false;
-    }
-
-    /**
-     */
-    public void deleteYpos(
-    ) {
-        this._has_ypos= false;
-    }
-
-    /**
-     * Method enumerateHiddenColumns.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.HiddenColumns elements
-     */
-    public java.util.Enumeration enumerateHiddenColumns(
-    ) {
-        return this._hiddenColumnsList.elements();
-    }
-
-    /**
-     * Returns the value of field 'annotationColours'.
-     * 
-     * @return the value of field 'AnnotationColours'.
-     */
-    public jalview.schemabinding.version2.AnnotationColours getAnnotationColours(
-    ) {
-        return this._annotationColours;
-    }
-
-    /**
-     * Returns the value of field 'bgColour'.
-     * 
-     * @return the value of field 'BgColour'.
-     */
-    public java.lang.String getBgColour(
-    ) {
-        return this._bgColour;
-    }
-
-    /**
-     * Returns the value of field 'consThreshold'.
-     * 
-     * @return the value of field 'ConsThreshold'.
-     */
-    public int getConsThreshold(
-    ) {
-        return this._consThreshold;
-    }
-
-    /**
-     * Returns the value of field 'conservationSelected'.
-     * 
-     * @return the value of field 'ConservationSelected'.
-     */
-    public boolean getConservationSelected(
-    ) {
-        return this._conservationSelected;
-    }
-
-    /**
-     * Returns the value of field 'fontName'.
-     * 
-     * @return the value of field 'FontName'.
-     */
-    public java.lang.String getFontName(
-    ) {
-        return this._fontName;
-    }
-
-    /**
-     * Returns the value of field 'fontSize'.
-     * 
-     * @return the value of field 'FontSize'.
-     */
-    public int getFontSize(
-    ) {
-        return this._fontSize;
-    }
-
-    /**
-     * Returns the value of field 'fontStyle'.
-     * 
-     * @return the value of field 'FontStyle'.
-     */
-    public int getFontStyle(
-    ) {
-        return this._fontStyle;
-    }
-
-    /**
-     * Returns the value of field 'gatheredViews'.
-     * 
-     * @return the value of field 'GatheredViews'.
-     */
-    public boolean getGatheredViews(
-    ) {
-        return this._gatheredViews;
-    }
-
-    /**
-     * Returns the value of field 'height'.
-     * 
-     * @return the value of field 'Height'.
-     */
-    public int getHeight(
-    ) {
-        return this._height;
-    }
-
-    /**
-     * Method getHiddenColumns.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.HiddenColumns at the given
-     * index
-     */
-    public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._hiddenColumnsList.size()) {
-            throw new IndexOutOfBoundsException("getHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.get(index);
-    }
-
-    /**
-     * Method getHiddenColumns.Returns the contents of the
-     * collection in an Array.  <p>Note:  Just in case the
-     * collection contents are changing in another thread, we pass
-     * a 0-length Array of the correct type into the API call. 
-     * This way we <i>know</i> that the Array returned is of
-     * exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns(
-    ) {
-        jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0];
-        return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList.toArray(array);
-    }
-
-    /**
-     * Method getHiddenColumnsCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getHiddenColumnsCount(
-    ) {
-        return this._hiddenColumnsList.size();
-    }
-
-    /**
-     * Returns the value of field 'pidSelected'.
-     * 
-     * @return the value of field 'PidSelected'.
-     */
-    public boolean getPidSelected(
-    ) {
-        return this._pidSelected;
-    }
-
-    /**
-     * Returns the value of field 'pidThreshold'.
-     * 
-     * @return the value of field 'PidThreshold'.
-     */
-    public int getPidThreshold(
-    ) {
-        return this._pidThreshold;
-    }
-
-    /**
-     * Returns the value of field 'renderGaps'.
-     * 
-     * @return the value of field 'RenderGaps'.
-     */
-    public boolean getRenderGaps(
-    ) {
-        return this._renderGaps;
-    }
-
-    /**
-     * Returns the value of field 'rightAlignIds'.
-     * 
-     * @return the value of field 'RightAlignIds'.
-     */
-    public boolean getRightAlignIds(
-    ) {
-        return this._rightAlignIds;
-    }
-
-    /**
-     * Returns the value of field 'sequenceSetId'.
-     * 
-     * @return the value of field 'SequenceSetId'.
-     */
-    public java.lang.String getSequenceSetId(
-    ) {
-        return this._sequenceSetId;
-    }
-
-    /**
-     * Returns the value of field 'showAnnotation'.
-     * 
-     * @return the value of field 'ShowAnnotation'.
-     */
-    public boolean getShowAnnotation(
-    ) {
-        return this._showAnnotation;
-    }
-
-    /**
-     * Returns the value of field 'showBoxes'.
-     * 
-     * @return the value of field 'ShowBoxes'.
-     */
-    public boolean getShowBoxes(
-    ) {
-        return this._showBoxes;
-    }
-
-    /**
-     * Returns the value of field 'showColourText'.
-     * 
-     * @return the value of field 'ShowColourText'.
-     */
-    public boolean getShowColourText(
-    ) {
-        return this._showColourText;
-    }
-
-    /**
-     * Returns the value of field 'showFullId'.
-     * 
-     * @return the value of field 'ShowFullId'.
-     */
-    public boolean getShowFullId(
-    ) {
-        return this._showFullId;
-    }
-
-    /**
-     * Returns the value of field 'showSequenceFeatures'.
-     * 
-     * @return the value of field 'ShowSequenceFeatures'.
-     */
-    public boolean getShowSequenceFeatures(
-    ) {
-        return this._showSequenceFeatures;
-    }
-
-    /**
-     * Returns the value of field 'showText'.
-     * 
-     * @return the value of field 'ShowText'.
-     */
-    public boolean getShowText(
-    ) {
-        return this._showText;
-    }
-
-    /**
-     * Returns the value of field 'startRes'.
-     * 
-     * @return the value of field 'StartRes'.
-     */
-    public int getStartRes(
-    ) {
-        return this._startRes;
-    }
-
-    /**
-     * Returns the value of field 'startSeq'.
-     * 
-     * @return the value of field 'StartSeq'.
-     */
-    public int getStartSeq(
-    ) {
-        return this._startSeq;
-    }
-
-    /**
-     * Returns the value of field 'textCol1'.
-     * 
-     * @return the value of field 'TextCol1'.
-     */
-    public int getTextCol1(
-    ) {
-        return this._textCol1;
-    }
-
-    /**
-     * Returns the value of field 'textCol2'.
-     * 
-     * @return the value of field 'TextCol2'.
-     */
-    public int getTextCol2(
-    ) {
-        return this._textCol2;
-    }
-
-    /**
-     * Returns the value of field 'textColThreshold'.
-     * 
-     * @return the value of field 'TextColThreshold'.
-     */
-    public int getTextColThreshold(
-    ) {
-        return this._textColThreshold;
-    }
-
-    /**
-     * Returns the value of field 'title'.
-     * 
-     * @return the value of field 'Title'.
-     */
-    public java.lang.String getTitle(
-    ) {
-        return this._title;
-    }
-
-    /**
-     * Returns the value of field 'viewName'.
-     * 
-     * @return the value of field 'ViewName'.
-     */
-    public java.lang.String getViewName(
-    ) {
-        return this._viewName;
-    }
-
-    /**
-     * Returns the value of field 'width'.
-     * 
-     * @return the value of field 'Width'.
-     */
-    public int getWidth(
-    ) {
-        return this._width;
-    }
-
-    /**
-     * Returns the value of field 'wrapAlignment'.
-     * 
-     * @return the value of field 'WrapAlignment'.
-     */
-    public boolean getWrapAlignment(
-    ) {
-        return this._wrapAlignment;
-    }
-
-    /**
-     * Returns the value of field 'xpos'.
-     * 
-     * @return the value of field 'Xpos'.
-     */
-    public int getXpos(
-    ) {
-        return this._xpos;
-    }
-
-    /**
-     * Returns the value of field 'ypos'.
-     * 
-     * @return the value of field 'Ypos'.
-     */
-    public int getYpos(
-    ) {
-        return this._ypos;
-    }
-
-    /**
-     * Method hasConsThreshold.
-     * 
-     * @return true if at least one ConsThreshold has been added
-     */
-    public boolean hasConsThreshold(
-    ) {
-        return this._has_consThreshold;
-    }
-
-    /**
-     * Method hasConservationSelected.
-     * 
-     * @return true if at least one ConservationSelected has been
-     * added
-     */
-    public boolean hasConservationSelected(
-    ) {
-        return this._has_conservationSelected;
-    }
-
-    /**
-     * Method hasFontSize.
-     * 
-     * @return true if at least one FontSize has been added
-     */
-    public boolean hasFontSize(
-    ) {
-        return this._has_fontSize;
-    }
-
-    /**
-     * Method hasFontStyle.
-     * 
-     * @return true if at least one FontStyle has been added
-     */
-    public boolean hasFontStyle(
-    ) {
-        return this._has_fontStyle;
-    }
-
-    /**
-     * Method hasGatheredViews.
-     * 
-     * @return true if at least one GatheredViews has been added
-     */
-    public boolean hasGatheredViews(
-    ) {
-        return this._has_gatheredViews;
-    }
-
-    /**
-     * Method hasHeight.
-     * 
-     * @return true if at least one Height has been added
-     */
-    public boolean hasHeight(
-    ) {
-        return this._has_height;
-    }
-
-    /**
-     * Method hasPidSelected.
-     * 
-     * @return true if at least one PidSelected has been added
-     */
-    public boolean hasPidSelected(
-    ) {
-        return this._has_pidSelected;
-    }
-
-    /**
-     * Method hasPidThreshold.
-     * 
-     * @return true if at least one PidThreshold has been added
-     */
-    public boolean hasPidThreshold(
-    ) {
-        return this._has_pidThreshold;
-    }
-
-    /**
-     * Method hasRenderGaps.
-     * 
-     * @return true if at least one RenderGaps has been added
-     */
-    public boolean hasRenderGaps(
-    ) {
-        return this._has_renderGaps;
-    }
-
-    /**
-     * Method hasRightAlignIds.
-     * 
-     * @return true if at least one RightAlignIds has been added
-     */
-    public boolean hasRightAlignIds(
-    ) {
-        return this._has_rightAlignIds;
-    }
-
-    /**
-     * Method hasShowAnnotation.
-     * 
-     * @return true if at least one ShowAnnotation has been added
-     */
-    public boolean hasShowAnnotation(
-    ) {
-        return this._has_showAnnotation;
-    }
-
-    /**
-     * Method hasShowBoxes.
-     * 
-     * @return true if at least one ShowBoxes has been added
-     */
-    public boolean hasShowBoxes(
-    ) {
-        return this._has_showBoxes;
-    }
-
-    /**
-     * Method hasShowColourText.
-     * 
-     * @return true if at least one ShowColourText has been added
-     */
-    public boolean hasShowColourText(
-    ) {
-        return this._has_showColourText;
-    }
-
-    /**
-     * Method hasShowFullId.
-     * 
-     * @return true if at least one ShowFullId has been added
-     */
-    public boolean hasShowFullId(
-    ) {
-        return this._has_showFullId;
-    }
-
-    /**
-     * Method hasShowSequenceFeatures.
-     * 
-     * @return true if at least one ShowSequenceFeatures has been
-     * added
-     */
-    public boolean hasShowSequenceFeatures(
-    ) {
-        return this._has_showSequenceFeatures;
-    }
-
-    /**
-     * Method hasShowText.
-     * 
-     * @return true if at least one ShowText has been added
-     */
-    public boolean hasShowText(
-    ) {
-        return this._has_showText;
-    }
-
-    /**
-     * Method hasStartRes.
-     * 
-     * @return true if at least one StartRes has been added
-     */
-    public boolean hasStartRes(
-    ) {
-        return this._has_startRes;
-    }
-
-    /**
-     * Method hasStartSeq.
-     * 
-     * @return true if at least one StartSeq has been added
-     */
-    public boolean hasStartSeq(
-    ) {
-        return this._has_startSeq;
-    }
-
-    /**
-     * Method hasTextCol1.
-     * 
-     * @return true if at least one TextCol1 has been added
-     */
-    public boolean hasTextCol1(
-    ) {
-        return this._has_textCol1;
-    }
-
-    /**
-     * Method hasTextCol2.
-     * 
-     * @return true if at least one TextCol2 has been added
-     */
-    public boolean hasTextCol2(
-    ) {
-        return this._has_textCol2;
-    }
-
-    /**
-     * Method hasTextColThreshold.
-     * 
-     * @return true if at least one TextColThreshold has been added
-     */
-    public boolean hasTextColThreshold(
-    ) {
-        return this._has_textColThreshold;
-    }
-
-    /**
-     * Method hasWidth.
-     * 
-     * @return true if at least one Width has been added
-     */
-    public boolean hasWidth(
-    ) {
-        return this._has_width;
-    }
-
-    /**
-     * Method hasWrapAlignment.
-     * 
-     * @return true if at least one WrapAlignment has been added
-     */
-    public boolean hasWrapAlignment(
-    ) {
-        return this._has_wrapAlignment;
-    }
-
-    /**
-     * Method hasXpos.
-     * 
-     * @return true if at least one Xpos has been added
-     */
-    public boolean hasXpos(
-    ) {
-        return this._has_xpos;
-    }
-
-    /**
-     * Method hasYpos.
-     * 
-     * @return true if at least one Ypos has been added
-     */
-    public boolean hasYpos(
-    ) {
-        return this._has_ypos;
-    }
-
-    /**
-     * Returns the value of field 'conservationSelected'.
-     * 
-     * @return the value of field 'ConservationSelected'.
-     */
-    public boolean isConservationSelected(
-    ) {
-        return this._conservationSelected;
-    }
-
-    /**
-     * Returns the value of field 'gatheredViews'.
-     * 
-     * @return the value of field 'GatheredViews'.
-     */
-    public boolean isGatheredViews(
-    ) {
-        return this._gatheredViews;
-    }
-
-    /**
-     * Returns the value of field 'pidSelected'.
-     * 
-     * @return the value of field 'PidSelected'.
-     */
-    public boolean isPidSelected(
-    ) {
-        return this._pidSelected;
-    }
-
-    /**
-     * Returns the value of field 'renderGaps'.
-     * 
-     * @return the value of field 'RenderGaps'.
-     */
-    public boolean isRenderGaps(
-    ) {
-        return this._renderGaps;
-    }
-
-    /**
-     * Returns the value of field 'rightAlignIds'.
-     * 
-     * @return the value of field 'RightAlignIds'.
-     */
-    public boolean isRightAlignIds(
-    ) {
-        return this._rightAlignIds;
-    }
-
-    /**
-     * Returns the value of field 'showAnnotation'.
-     * 
-     * @return the value of field 'ShowAnnotation'.
-     */
-    public boolean isShowAnnotation(
-    ) {
-        return this._showAnnotation;
-    }
-
-    /**
-     * Returns the value of field 'showBoxes'.
-     * 
-     * @return the value of field 'ShowBoxes'.
-     */
-    public boolean isShowBoxes(
-    ) {
-        return this._showBoxes;
-    }
-
-    /**
-     * Returns the value of field 'showColourText'.
-     * 
-     * @return the value of field 'ShowColourText'.
-     */
-    public boolean isShowColourText(
-    ) {
-        return this._showColourText;
-    }
-
-    /**
-     * Returns the value of field 'showFullId'.
-     * 
-     * @return the value of field 'ShowFullId'.
-     */
-    public boolean isShowFullId(
-    ) {
-        return this._showFullId;
-    }
-
-    /**
-     * Returns the value of field 'showSequenceFeatures'.
-     * 
-     * @return the value of field 'ShowSequenceFeatures'.
-     */
-    public boolean isShowSequenceFeatures(
-    ) {
-        return this._showSequenceFeatures;
-    }
-
-    /**
-     * Returns the value of field 'showText'.
-     * 
-     * @return the value of field 'ShowText'.
-     */
-    public boolean isShowText(
-    ) {
-        return this._showText;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * Returns the value of field 'wrapAlignment'.
-     * 
-     * @return the value of field 'WrapAlignment'.
-     */
-    public boolean isWrapAlignment(
-    ) {
-        return this._wrapAlignment;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     */
-    public void removeAllHiddenColumns(
-    ) {
-        this._hiddenColumnsList.clear();
-    }
-
-    /**
-     * Method removeHiddenColumns.
-     * 
-     * @param vHiddenColumns
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeHiddenColumns(
-            final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) {
-        boolean removed = _hiddenColumnsList.remove(vHiddenColumns);
-        return removed;
-    }
-
-    /**
-     * Method removeHiddenColumnsAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt(
-            final int index) {
-        java.lang.Object obj = this._hiddenColumnsList.remove(index);
-        return (jalview.schemabinding.version2.HiddenColumns) obj;
-    }
-
-    /**
-     * Sets the value of field 'annotationColours'.
-     * 
-     * @param annotationColours the value of field
-     * 'annotationColours'.
-     */
-    public void setAnnotationColours(
-            final jalview.schemabinding.version2.AnnotationColours annotationColours) {
-        this._annotationColours = annotationColours;
-    }
-
-    /**
-     * Sets the value of field 'bgColour'.
-     * 
-     * @param bgColour the value of field 'bgColour'.
-     */
-    public void setBgColour(
-            final java.lang.String bgColour) {
-        this._bgColour = bgColour;
-    }
-
-    /**
-     * Sets the value of field 'consThreshold'.
-     * 
-     * @param consThreshold the value of field 'consThreshold'.
-     */
-    public void setConsThreshold(
-            final int consThreshold) {
-        this._consThreshold = consThreshold;
-        this._has_consThreshold = true;
-    }
-
-    /**
-     * Sets the value of field 'conservationSelected'.
-     * 
-     * @param conservationSelected the value of field
-     * 'conservationSelected'.
-     */
-    public void setConservationSelected(
-            final boolean conservationSelected) {
-        this._conservationSelected = conservationSelected;
-        this._has_conservationSelected = true;
-    }
-
-    /**
-     * Sets the value of field 'fontName'.
-     * 
-     * @param fontName the value of field 'fontName'.
-     */
-    public void setFontName(
-            final java.lang.String fontName) {
-        this._fontName = fontName;
-    }
-
-    /**
-     * Sets the value of field 'fontSize'.
-     * 
-     * @param fontSize the value of field 'fontSize'.
-     */
-    public void setFontSize(
-            final int fontSize) {
-        this._fontSize = fontSize;
-        this._has_fontSize = true;
-    }
-
-    /**
-     * Sets the value of field 'fontStyle'.
-     * 
-     * @param fontStyle the value of field 'fontStyle'.
-     */
-    public void setFontStyle(
-            final int fontStyle) {
-        this._fontStyle = fontStyle;
-        this._has_fontStyle = true;
-    }
-
-    /**
-     * Sets the value of field 'gatheredViews'.
-     * 
-     * @param gatheredViews the value of field 'gatheredViews'.
-     */
-    public void setGatheredViews(
-            final boolean gatheredViews) {
-        this._gatheredViews = gatheredViews;
-        this._has_gatheredViews = true;
-    }
-
-    /**
-     * Sets the value of field 'height'.
-     * 
-     * @param height the value of field 'height'.
-     */
-    public void setHeight(
-            final int height) {
-        this._height = height;
-        this._has_height = true;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vHiddenColumns
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setHiddenColumns(
-            final int index,
-            final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._hiddenColumnsList.size()) {
-            throw new IndexOutOfBoundsException("setHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]");
-        }
-        
-        this._hiddenColumnsList.set(index, vHiddenColumns);
-    }
-
-    /**
-     * 
-     * 
-     * @param vHiddenColumnsArray
-     */
-    public void setHiddenColumns(
-            final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray) {
-        //-- copy array
-        _hiddenColumnsList.clear();
-        
-        for (int i = 0; i < vHiddenColumnsArray.length; i++) {
-                this._hiddenColumnsList.add(vHiddenColumnsArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of field 'pidSelected'.
-     * 
-     * @param pidSelected the value of field 'pidSelected'.
-     */
-    public void setPidSelected(
-            final boolean pidSelected) {
-        this._pidSelected = pidSelected;
-        this._has_pidSelected = true;
-    }
-
-    /**
-     * Sets the value of field 'pidThreshold'.
-     * 
-     * @param pidThreshold the value of field 'pidThreshold'.
-     */
-    public void setPidThreshold(
-            final int pidThreshold) {
-        this._pidThreshold = pidThreshold;
-        this._has_pidThreshold = true;
-    }
-
-    /**
-     * Sets the value of field 'renderGaps'.
-     * 
-     * @param renderGaps the value of field 'renderGaps'.
-     */
-    public void setRenderGaps(
-            final boolean renderGaps) {
-        this._renderGaps = renderGaps;
-        this._has_renderGaps = true;
-    }
-
-    /**
-     * Sets the value of field 'rightAlignIds'.
-     * 
-     * @param rightAlignIds the value of field 'rightAlignIds'.
-     */
-    public void setRightAlignIds(
-            final boolean rightAlignIds) {
-        this._rightAlignIds = rightAlignIds;
-        this._has_rightAlignIds = true;
-    }
-
-    /**
-     * Sets the value of field 'sequenceSetId'.
-     * 
-     * @param sequenceSetId the value of field 'sequenceSetId'.
-     */
-    public void setSequenceSetId(
-            final java.lang.String sequenceSetId) {
-        this._sequenceSetId = sequenceSetId;
-    }
-
-    /**
-     * Sets the value of field 'showAnnotation'.
-     * 
-     * @param showAnnotation the value of field 'showAnnotation'.
-     */
-    public void setShowAnnotation(
-            final boolean showAnnotation) {
-        this._showAnnotation = showAnnotation;
-        this._has_showAnnotation = true;
-    }
-
-    /**
-     * Sets the value of field 'showBoxes'.
-     * 
-     * @param showBoxes the value of field 'showBoxes'.
-     */
-    public void setShowBoxes(
-            final boolean showBoxes) {
-        this._showBoxes = showBoxes;
-        this._has_showBoxes = true;
-    }
-
-    /**
-     * Sets the value of field 'showColourText'.
-     * 
-     * @param showColourText the value of field 'showColourText'.
-     */
-    public void setShowColourText(
-            final boolean showColourText) {
-        this._showColourText = showColourText;
-        this._has_showColourText = true;
-    }
-
-    /**
-     * Sets the value of field 'showFullId'.
-     * 
-     * @param showFullId the value of field 'showFullId'.
-     */
-    public void setShowFullId(
-            final boolean showFullId) {
-        this._showFullId = showFullId;
-        this._has_showFullId = true;
-    }
-
-    /**
-     * Sets the value of field 'showSequenceFeatures'.
-     * 
-     * @param showSequenceFeatures the value of field
-     * 'showSequenceFeatures'.
-     */
-    public void setShowSequenceFeatures(
-            final boolean showSequenceFeatures) {
-        this._showSequenceFeatures = showSequenceFeatures;
-        this._has_showSequenceFeatures = true;
-    }
-
-    /**
-     * Sets the value of field 'showText'.
-     * 
-     * @param showText the value of field 'showText'.
-     */
-    public void setShowText(
-            final boolean showText) {
-        this._showText = showText;
-        this._has_showText = true;
-    }
-
-    /**
-     * Sets the value of field 'startRes'.
-     * 
-     * @param startRes the value of field 'startRes'.
-     */
-    public void setStartRes(
-            final int startRes) {
-        this._startRes = startRes;
-        this._has_startRes = true;
-    }
-
-    /**
-     * Sets the value of field 'startSeq'.
-     * 
-     * @param startSeq the value of field 'startSeq'.
-     */
-    public void setStartSeq(
-            final int startSeq) {
-        this._startSeq = startSeq;
-        this._has_startSeq = true;
-    }
-
-    /**
-     * Sets the value of field 'textCol1'.
-     * 
-     * @param textCol1 the value of field 'textCol1'.
-     */
-    public void setTextCol1(
-            final int textCol1) {
-        this._textCol1 = textCol1;
-        this._has_textCol1 = true;
-    }
-
-    /**
-     * Sets the value of field 'textCol2'.
-     * 
-     * @param textCol2 the value of field 'textCol2'.
-     */
-    public void setTextCol2(
-            final int textCol2) {
-        this._textCol2 = textCol2;
-        this._has_textCol2 = true;
-    }
-
-    /**
-     * Sets the value of field 'textColThreshold'.
-     * 
-     * @param textColThreshold the value of field 'textColThreshold'
-     */
-    public void setTextColThreshold(
-            final int textColThreshold) {
-        this._textColThreshold = textColThreshold;
-        this._has_textColThreshold = true;
-    }
-
-    /**
-     * Sets the value of field 'title'.
-     * 
-     * @param title the value of field 'title'.
-     */
-    public void setTitle(
-            final java.lang.String title) {
-        this._title = title;
-    }
-
-    /**
-     * Sets the value of field 'viewName'.
-     * 
-     * @param viewName the value of field 'viewName'.
-     */
-    public void setViewName(
-            final java.lang.String viewName) {
-        this._viewName = viewName;
-    }
-
-    /**
-     * Sets the value of field 'width'.
-     * 
-     * @param width the value of field 'width'.
-     */
-    public void setWidth(
-            final int width) {
-        this._width = width;
-        this._has_width = true;
-    }
-
-    /**
-     * Sets the value of field 'wrapAlignment'.
-     * 
-     * @param wrapAlignment the value of field 'wrapAlignment'.
-     */
-    public void setWrapAlignment(
-            final boolean wrapAlignment) {
-        this._wrapAlignment = wrapAlignment;
-        this._has_wrapAlignment = true;
-    }
-
-    /**
-     * Sets the value of field 'xpos'.
-     * 
-     * @param xpos the value of field 'xpos'.
-     */
-    public void setXpos(
-            final int xpos) {
-        this._xpos = xpos;
-        this._has_xpos = true;
-    }
-
-    /**
-     * Sets the value of field 'ypos'.
-     * 
-     * @param ypos the value of field 'ypos'.
-     */
-    public void setYpos(
-            final int ypos) {
-        this._ypos = ypos;
-        this._has_ypos = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.Viewport
-     */
-    public static jalview.schemabinding.version2.Viewport unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.Viewport) Unmarshaller.unmarshal(jalview.schemabinding.version2.Viewport.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+public class Viewport implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _conservationSelected.
+   */
+  private boolean _conservationSelected;
+
+  /**
+   * keeps track of state for field: _conservationSelected
+   */
+  private boolean _has_conservationSelected;
+
+  /**
+   * Field _pidSelected.
+   */
+  private boolean _pidSelected;
+
+  /**
+   * keeps track of state for field: _pidSelected
+   */
+  private boolean _has_pidSelected;
+
+  /**
+   * Field _bgColour.
+   */
+  private java.lang.String _bgColour;
+
+  /**
+   * Field _consThreshold.
+   */
+  private int _consThreshold;
+
+  /**
+   * keeps track of state for field: _consThreshold
+   */
+  private boolean _has_consThreshold;
+
+  /**
+   * Field _pidThreshold.
+   */
+  private int _pidThreshold;
+
+  /**
+   * keeps track of state for field: _pidThreshold
+   */
+  private boolean _has_pidThreshold;
+
+  /**
+   * Field _title.
+   */
+  private java.lang.String _title;
+
+  /**
+   * Field _showFullId.
+   */
+  private boolean _showFullId;
+
+  /**
+   * keeps track of state for field: _showFullId
+   */
+  private boolean _has_showFullId;
+
+  /**
+   * Field _rightAlignIds.
+   */
+  private boolean _rightAlignIds;
+
+  /**
+   * keeps track of state for field: _rightAlignIds
+   */
+  private boolean _has_rightAlignIds;
+
+  /**
+   * Field _showText.
+   */
+  private boolean _showText;
+
+  /**
+   * keeps track of state for field: _showText
+   */
+  private boolean _has_showText;
+
+  /**
+   * Field _showColourText.
+   */
+  private boolean _showColourText;
+
+  /**
+   * keeps track of state for field: _showColourText
+   */
+  private boolean _has_showColourText;
+
+  /**
+   * Field _showBoxes.
+   */
+  private boolean _showBoxes;
+
+  /**
+   * keeps track of state for field: _showBoxes
+   */
+  private boolean _has_showBoxes;
+
+  /**
+   * Field _wrapAlignment.
+   */
+  private boolean _wrapAlignment;
+
+  /**
+   * keeps track of state for field: _wrapAlignment
+   */
+  private boolean _has_wrapAlignment;
+
+  /**
+   * Field _renderGaps.
+   */
+  private boolean _renderGaps;
+
+  /**
+   * keeps track of state for field: _renderGaps
+   */
+  private boolean _has_renderGaps;
+
+  /**
+   * Field _showSequenceFeatures.
+   */
+  private boolean _showSequenceFeatures;
+
+  /**
+   * keeps track of state for field: _showSequenceFeatures
+   */
+  private boolean _has_showSequenceFeatures;
+
+  /**
+   * Field _showAnnotation.
+   */
+  private boolean _showAnnotation;
+
+  /**
+   * keeps track of state for field: _showAnnotation
+   */
+  private boolean _has_showAnnotation;
+
+  /**
+   * Field _xpos.
+   */
+  private int _xpos;
+
+  /**
+   * keeps track of state for field: _xpos
+   */
+  private boolean _has_xpos;
+
+  /**
+   * Field _ypos.
+   */
+  private int _ypos;
+
+  /**
+   * keeps track of state for field: _ypos
+   */
+  private boolean _has_ypos;
+
+  /**
+   * Field _width.
+   */
+  private int _width;
+
+  /**
+   * keeps track of state for field: _width
+   */
+  private boolean _has_width;
+
+  /**
+   * Field _height.
+   */
+  private int _height;
+
+  /**
+   * keeps track of state for field: _height
+   */
+  private boolean _has_height;
+
+  /**
+   * Field _startRes.
+   */
+  private int _startRes;
+
+  /**
+   * keeps track of state for field: _startRes
+   */
+  private boolean _has_startRes;
+
+  /**
+   * Field _startSeq.
+   */
+  private int _startSeq;
+
+  /**
+   * keeps track of state for field: _startSeq
+   */
+  private boolean _has_startSeq;
+
+  /**
+   * Field _fontName.
+   */
+  private java.lang.String _fontName;
+
+  /**
+   * Field _fontSize.
+   */
+  private int _fontSize;
+
+  /**
+   * keeps track of state for field: _fontSize
+   */
+  private boolean _has_fontSize;
+
+  /**
+   * Field _fontStyle.
+   */
+  private int _fontStyle;
+
+  /**
+   * keeps track of state for field: _fontStyle
+   */
+  private boolean _has_fontStyle;
+
+  /**
+   * Field _viewName.
+   */
+  private java.lang.String _viewName;
+
+  /**
+   * Field _sequenceSetId.
+   */
+  private java.lang.String _sequenceSetId;
+
+  /**
+   * Field _gatheredViews.
+   */
+  private boolean _gatheredViews;
+
+  /**
+   * keeps track of state for field: _gatheredViews
+   */
+  private boolean _has_gatheredViews;
+
+  /**
+   * Field _textCol1.
+   */
+  private int _textCol1;
+
+  /**
+   * keeps track of state for field: _textCol1
+   */
+  private boolean _has_textCol1;
+
+  /**
+   * Field _textCol2.
+   */
+  private int _textCol2;
+
+  /**
+   * keeps track of state for field: _textCol2
+   */
+  private boolean _has_textCol2;
+
+  /**
+   * Field _textColThreshold.
+   */
+  private int _textColThreshold;
+
+  /**
+   * keeps track of state for field: _textColThreshold
+   */
+  private boolean _has_textColThreshold;
+
+  /**
+   * Field _annotationColours.
+   */
+  private jalview.schemabinding.version2.AnnotationColours _annotationColours;
+
+  /**
+   * Field _hiddenColumnsList.
+   */
+  private java.util.Vector _hiddenColumnsList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Viewport()
+  {
+    super();
+    this._hiddenColumnsList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vHiddenColumns
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addHiddenColumns(
+          final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._hiddenColumnsList.addElement(vHiddenColumns);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vHiddenColumns
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addHiddenColumns(final int index,
+          final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._hiddenColumnsList.add(index, vHiddenColumns);
+  }
+
+  /**
+   */
+  public void deleteConsThreshold()
+  {
+    this._has_consThreshold = false;
+  }
+
+  /**
+   */
+  public void deleteConservationSelected()
+  {
+    this._has_conservationSelected = false;
+  }
+
+  /**
+   */
+  public void deleteFontSize()
+  {
+    this._has_fontSize = false;
+  }
+
+  /**
+   */
+  public void deleteFontStyle()
+  {
+    this._has_fontStyle = false;
+  }
+
+  /**
+   */
+  public void deleteGatheredViews()
+  {
+    this._has_gatheredViews = false;
+  }
+
+  /**
+   */
+  public void deleteHeight()
+  {
+    this._has_height = false;
+  }
+
+  /**
+   */
+  public void deletePidSelected()
+  {
+    this._has_pidSelected = false;
+  }
+
+  /**
+   */
+  public void deletePidThreshold()
+  {
+    this._has_pidThreshold = false;
+  }
+
+  /**
+   */
+  public void deleteRenderGaps()
+  {
+    this._has_renderGaps = false;
+  }
+
+  /**
+   */
+  public void deleteRightAlignIds()
+  {
+    this._has_rightAlignIds = false;
+  }
+
+  /**
+   */
+  public void deleteShowAnnotation()
+  {
+    this._has_showAnnotation = false;
+  }
+
+  /**
+   */
+  public void deleteShowBoxes()
+  {
+    this._has_showBoxes = false;
+  }
+
+  /**
+   */
+  public void deleteShowColourText()
+  {
+    this._has_showColourText = false;
+  }
+
+  /**
+   */
+  public void deleteShowFullId()
+  {
+    this._has_showFullId = false;
+  }
+
+  /**
+   */
+  public void deleteShowSequenceFeatures()
+  {
+    this._has_showSequenceFeatures = false;
+  }
+
+  /**
+   */
+  public void deleteShowText()
+  {
+    this._has_showText = false;
+  }
+
+  /**
+   */
+  public void deleteStartRes()
+  {
+    this._has_startRes = false;
+  }
+
+  /**
+   */
+  public void deleteStartSeq()
+  {
+    this._has_startSeq = false;
+  }
+
+  /**
+   */
+  public void deleteTextCol1()
+  {
+    this._has_textCol1 = false;
+  }
+
+  /**
+   */
+  public void deleteTextCol2()
+  {
+    this._has_textCol2 = false;
+  }
+
+  /**
+   */
+  public void deleteTextColThreshold()
+  {
+    this._has_textColThreshold = false;
+  }
+
+  /**
+   */
+  public void deleteWidth()
+  {
+    this._has_width = false;
+  }
+
+  /**
+   */
+  public void deleteWrapAlignment()
+  {
+    this._has_wrapAlignment = false;
+  }
+
+  /**
+   */
+  public void deleteXpos()
+  {
+    this._has_xpos = false;
+  }
+
+  /**
+   */
+  public void deleteYpos()
+  {
+    this._has_ypos = false;
+  }
+
+  /**
+   * Method enumerateHiddenColumns.
+   * 
+   * @return an Enumeration over all
+   *         jalview.schemabinding.version2.HiddenColumns elements
+   */
+  public java.util.Enumeration enumerateHiddenColumns()
+  {
+    return this._hiddenColumnsList.elements();
+  }
+
+  /**
+   * Returns the value of field 'annotationColours'.
+   * 
+   * @return the value of field 'AnnotationColours'.
+   */
+  public jalview.schemabinding.version2.AnnotationColours getAnnotationColours()
+  {
+    return this._annotationColours;
+  }
+
+  /**
+   * Returns the value of field 'bgColour'.
+   * 
+   * @return the value of field 'BgColour'.
+   */
+  public java.lang.String getBgColour()
+  {
+    return this._bgColour;
+  }
+
+  /**
+   * Returns the value of field 'consThreshold'.
+   * 
+   * @return the value of field 'ConsThreshold'.
+   */
+  public int getConsThreshold()
+  {
+    return this._consThreshold;
+  }
+
+  /**
+   * Returns the value of field 'conservationSelected'.
+   * 
+   * @return the value of field 'ConservationSelected'.
+   */
+  public boolean getConservationSelected()
+  {
+    return this._conservationSelected;
+  }
+
+  /**
+   * Returns the value of field 'fontName'.
+   * 
+   * @return the value of field 'FontName'.
+   */
+  public java.lang.String getFontName()
+  {
+    return this._fontName;
+  }
+
+  /**
+   * Returns the value of field 'fontSize'.
+   * 
+   * @return the value of field 'FontSize'.
+   */
+  public int getFontSize()
+  {
+    return this._fontSize;
+  }
+
+  /**
+   * Returns the value of field 'fontStyle'.
+   * 
+   * @return the value of field 'FontStyle'.
+   */
+  public int getFontStyle()
+  {
+    return this._fontStyle;
+  }
+
+  /**
+   * Returns the value of field 'gatheredViews'.
+   * 
+   * @return the value of field 'GatheredViews'.
+   */
+  public boolean getGatheredViews()
+  {
+    return this._gatheredViews;
+  }
+
+  /**
+   * Returns the value of field 'height'.
+   * 
+   * @return the value of field 'Height'.
+   */
+  public int getHeight()
+  {
+    return this._height;
+  }
+
+  /**
+   * Method getHiddenColumns.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.HiddenColumns at
+   *         the given index
+   */
+  public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(
+          final int index) throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._hiddenColumnsList.size())
+    {
+      throw new IndexOutOfBoundsException("getHiddenColumns: Index value '"
+              + index + "' not in range [0.."
+              + (this._hiddenColumnsList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList
+            .get(index);
+  }
+
+  /**
+   * Method getHiddenColumns.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns()
+  {
+    jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0];
+    return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList
+            .toArray(array);
+  }
+
+  /**
+   * Method getHiddenColumnsCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getHiddenColumnsCount()
+  {
+    return this._hiddenColumnsList.size();
+  }
+
+  /**
+   * Returns the value of field 'pidSelected'.
+   * 
+   * @return the value of field 'PidSelected'.
+   */
+  public boolean getPidSelected()
+  {
+    return this._pidSelected;
+  }
+
+  /**
+   * Returns the value of field 'pidThreshold'.
+   * 
+   * @return the value of field 'PidThreshold'.
+   */
+  public int getPidThreshold()
+  {
+    return this._pidThreshold;
+  }
+
+  /**
+   * Returns the value of field 'renderGaps'.
+   * 
+   * @return the value of field 'RenderGaps'.
+   */
+  public boolean getRenderGaps()
+  {
+    return this._renderGaps;
+  }
+
+  /**
+   * Returns the value of field 'rightAlignIds'.
+   * 
+   * @return the value of field 'RightAlignIds'.
+   */
+  public boolean getRightAlignIds()
+  {
+    return this._rightAlignIds;
+  }
+
+  /**
+   * Returns the value of field 'sequenceSetId'.
+   * 
+   * @return the value of field 'SequenceSetId'.
+   */
+  public java.lang.String getSequenceSetId()
+  {
+    return this._sequenceSetId;
+  }
+
+  /**
+   * Returns the value of field 'showAnnotation'.
+   * 
+   * @return the value of field 'ShowAnnotation'.
+   */
+  public boolean getShowAnnotation()
+  {
+    return this._showAnnotation;
+  }
+
+  /**
+   * Returns the value of field 'showBoxes'.
+   * 
+   * @return the value of field 'ShowBoxes'.
+   */
+  public boolean getShowBoxes()
+  {
+    return this._showBoxes;
+  }
+
+  /**
+   * Returns the value of field 'showColourText'.
+   * 
+   * @return the value of field 'ShowColourText'.
+   */
+  public boolean getShowColourText()
+  {
+    return this._showColourText;
+  }
+
+  /**
+   * Returns the value of field 'showFullId'.
+   * 
+   * @return the value of field 'ShowFullId'.
+   */
+  public boolean getShowFullId()
+  {
+    return this._showFullId;
+  }
+
+  /**
+   * Returns the value of field 'showSequenceFeatures'.
+   * 
+   * @return the value of field 'ShowSequenceFeatures'.
+   */
+  public boolean getShowSequenceFeatures()
+  {
+    return this._showSequenceFeatures;
+  }
+
+  /**
+   * Returns the value of field 'showText'.
+   * 
+   * @return the value of field 'ShowText'.
+   */
+  public boolean getShowText()
+  {
+    return this._showText;
+  }
+
+  /**
+   * Returns the value of field 'startRes'.
+   * 
+   * @return the value of field 'StartRes'.
+   */
+  public int getStartRes()
+  {
+    return this._startRes;
+  }
+
+  /**
+   * Returns the value of field 'startSeq'.
+   * 
+   * @return the value of field 'StartSeq'.
+   */
+  public int getStartSeq()
+  {
+    return this._startSeq;
+  }
+
+  /**
+   * Returns the value of field 'textCol1'.
+   * 
+   * @return the value of field 'TextCol1'.
+   */
+  public int getTextCol1()
+  {
+    return this._textCol1;
+  }
+
+  /**
+   * Returns the value of field 'textCol2'.
+   * 
+   * @return the value of field 'TextCol2'.
+   */
+  public int getTextCol2()
+  {
+    return this._textCol2;
+  }
+
+  /**
+   * Returns the value of field 'textColThreshold'.
+   * 
+   * @return the value of field 'TextColThreshold'.
+   */
+  public int getTextColThreshold()
+  {
+    return this._textColThreshold;
+  }
+
+  /**
+   * Returns the value of field 'title'.
+   * 
+   * @return the value of field 'Title'.
+   */
+  public java.lang.String getTitle()
+  {
+    return this._title;
+  }
+
+  /**
+   * Returns the value of field 'viewName'.
+   * 
+   * @return the value of field 'ViewName'.
+   */
+  public java.lang.String getViewName()
+  {
+    return this._viewName;
+  }
+
+  /**
+   * Returns the value of field 'width'.
+   * 
+   * @return the value of field 'Width'.
+   */
+  public int getWidth()
+  {
+    return this._width;
+  }
+
+  /**
+   * Returns the value of field 'wrapAlignment'.
+   * 
+   * @return the value of field 'WrapAlignment'.
+   */
+  public boolean getWrapAlignment()
+  {
+    return this._wrapAlignment;
+  }
+
+  /**
+   * Returns the value of field 'xpos'.
+   * 
+   * @return the value of field 'Xpos'.
+   */
+  public int getXpos()
+  {
+    return this._xpos;
+  }
+
+  /**
+   * Returns the value of field 'ypos'.
+   * 
+   * @return the value of field 'Ypos'.
+   */
+  public int getYpos()
+  {
+    return this._ypos;
+  }
+
+  /**
+   * Method hasConsThreshold.
+   * 
+   * @return true if at least one ConsThreshold has been added
+   */
+  public boolean hasConsThreshold()
+  {
+    return this._has_consThreshold;
+  }
+
+  /**
+   * Method hasConservationSelected.
+   * 
+   * @return true if at least one ConservationSelected has been added
+   */
+  public boolean hasConservationSelected()
+  {
+    return this._has_conservationSelected;
+  }
+
+  /**
+   * Method hasFontSize.
+   * 
+   * @return true if at least one FontSize has been added
+   */
+  public boolean hasFontSize()
+  {
+    return this._has_fontSize;
+  }
+
+  /**
+   * Method hasFontStyle.
+   * 
+   * @return true if at least one FontStyle has been added
+   */
+  public boolean hasFontStyle()
+  {
+    return this._has_fontStyle;
+  }
+
+  /**
+   * Method hasGatheredViews.
+   * 
+   * @return true if at least one GatheredViews has been added
+   */
+  public boolean hasGatheredViews()
+  {
+    return this._has_gatheredViews;
+  }
+
+  /**
+   * Method hasHeight.
+   * 
+   * @return true if at least one Height has been added
+   */
+  public boolean hasHeight()
+  {
+    return this._has_height;
+  }
+
+  /**
+   * Method hasPidSelected.
+   * 
+   * @return true if at least one PidSelected has been added
+   */
+  public boolean hasPidSelected()
+  {
+    return this._has_pidSelected;
+  }
+
+  /**
+   * Method hasPidThreshold.
+   * 
+   * @return true if at least one PidThreshold has been added
+   */
+  public boolean hasPidThreshold()
+  {
+    return this._has_pidThreshold;
+  }
+
+  /**
+   * Method hasRenderGaps.
+   * 
+   * @return true if at least one RenderGaps has been added
+   */
+  public boolean hasRenderGaps()
+  {
+    return this._has_renderGaps;
+  }
+
+  /**
+   * Method hasRightAlignIds.
+   * 
+   * @return true if at least one RightAlignIds has been added
+   */
+  public boolean hasRightAlignIds()
+  {
+    return this._has_rightAlignIds;
+  }
+
+  /**
+   * Method hasShowAnnotation.
+   * 
+   * @return true if at least one ShowAnnotation has been added
+   */
+  public boolean hasShowAnnotation()
+  {
+    return this._has_showAnnotation;
+  }
+
+  /**
+   * Method hasShowBoxes.
+   * 
+   * @return true if at least one ShowBoxes has been added
+   */
+  public boolean hasShowBoxes()
+  {
+    return this._has_showBoxes;
+  }
+
+  /**
+   * Method hasShowColourText.
+   * 
+   * @return true if at least one ShowColourText has been added
+   */
+  public boolean hasShowColourText()
+  {
+    return this._has_showColourText;
+  }
+
+  /**
+   * Method hasShowFullId.
+   * 
+   * @return true if at least one ShowFullId has been added
+   */
+  public boolean hasShowFullId()
+  {
+    return this._has_showFullId;
+  }
+
+  /**
+   * Method hasShowSequenceFeatures.
+   * 
+   * @return true if at least one ShowSequenceFeatures has been added
+   */
+  public boolean hasShowSequenceFeatures()
+  {
+    return this._has_showSequenceFeatures;
+  }
+
+  /**
+   * Method hasShowText.
+   * 
+   * @return true if at least one ShowText has been added
+   */
+  public boolean hasShowText()
+  {
+    return this._has_showText;
+  }
+
+  /**
+   * Method hasStartRes.
+   * 
+   * @return true if at least one StartRes has been added
+   */
+  public boolean hasStartRes()
+  {
+    return this._has_startRes;
+  }
+
+  /**
+   * Method hasStartSeq.
+   * 
+   * @return true if at least one StartSeq has been added
+   */
+  public boolean hasStartSeq()
+  {
+    return this._has_startSeq;
+  }
+
+  /**
+   * Method hasTextCol1.
+   * 
+   * @return true if at least one TextCol1 has been added
+   */
+  public boolean hasTextCol1()
+  {
+    return this._has_textCol1;
+  }
+
+  /**
+   * Method hasTextCol2.
+   * 
+   * @return true if at least one TextCol2 has been added
+   */
+  public boolean hasTextCol2()
+  {
+    return this._has_textCol2;
+  }
+
+  /**
+   * Method hasTextColThreshold.
+   * 
+   * @return true if at least one TextColThreshold has been added
+   */
+  public boolean hasTextColThreshold()
+  {
+    return this._has_textColThreshold;
+  }
+
+  /**
+   * Method hasWidth.
+   * 
+   * @return true if at least one Width has been added
+   */
+  public boolean hasWidth()
+  {
+    return this._has_width;
+  }
+
+  /**
+   * Method hasWrapAlignment.
+   * 
+   * @return true if at least one WrapAlignment has been added
+   */
+  public boolean hasWrapAlignment()
+  {
+    return this._has_wrapAlignment;
+  }
+
+  /**
+   * Method hasXpos.
+   * 
+   * @return true if at least one Xpos has been added
+   */
+  public boolean hasXpos()
+  {
+    return this._has_xpos;
+  }
+
+  /**
+   * Method hasYpos.
+   * 
+   * @return true if at least one Ypos has been added
+   */
+  public boolean hasYpos()
+  {
+    return this._has_ypos;
+  }
+
+  /**
+   * Returns the value of field 'conservationSelected'.
+   * 
+   * @return the value of field 'ConservationSelected'.
+   */
+  public boolean isConservationSelected()
+  {
+    return this._conservationSelected;
+  }
+
+  /**
+   * Returns the value of field 'gatheredViews'.
+   * 
+   * @return the value of field 'GatheredViews'.
+   */
+  public boolean isGatheredViews()
+  {
+    return this._gatheredViews;
+  }
+
+  /**
+   * Returns the value of field 'pidSelected'.
+   * 
+   * @return the value of field 'PidSelected'.
+   */
+  public boolean isPidSelected()
+  {
+    return this._pidSelected;
+  }
+
+  /**
+   * Returns the value of field 'renderGaps'.
+   * 
+   * @return the value of field 'RenderGaps'.
+   */
+  public boolean isRenderGaps()
+  {
+    return this._renderGaps;
+  }
+
+  /**
+   * Returns the value of field 'rightAlignIds'.
+   * 
+   * @return the value of field 'RightAlignIds'.
+   */
+  public boolean isRightAlignIds()
+  {
+    return this._rightAlignIds;
+  }
+
+  /**
+   * Returns the value of field 'showAnnotation'.
+   * 
+   * @return the value of field 'ShowAnnotation'.
+   */
+  public boolean isShowAnnotation()
+  {
+    return this._showAnnotation;
+  }
+
+  /**
+   * Returns the value of field 'showBoxes'.
+   * 
+   * @return the value of field 'ShowBoxes'.
+   */
+  public boolean isShowBoxes()
+  {
+    return this._showBoxes;
+  }
+
+  /**
+   * Returns the value of field 'showColourText'.
+   * 
+   * @return the value of field 'ShowColourText'.
+   */
+  public boolean isShowColourText()
+  {
+    return this._showColourText;
+  }
+
+  /**
+   * Returns the value of field 'showFullId'.
+   * 
+   * @return the value of field 'ShowFullId'.
+   */
+  public boolean isShowFullId()
+  {
+    return this._showFullId;
+  }
+
+  /**
+   * Returns the value of field 'showSequenceFeatures'.
+   * 
+   * @return the value of field 'ShowSequenceFeatures'.
+   */
+  public boolean isShowSequenceFeatures()
+  {
+    return this._showSequenceFeatures;
+  }
+
+  /**
+   * Returns the value of field 'showText'.
+   * 
+   * @return the value of field 'ShowText'.
+   */
+  public boolean isShowText()
+  {
+    return this._showText;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * Returns the value of field 'wrapAlignment'.
+   * 
+   * @return the value of field 'WrapAlignment'.
+   */
+  public boolean isWrapAlignment()
+  {
+    return this._wrapAlignment;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *                 if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   */
+  public void removeAllHiddenColumns()
+  {
+    this._hiddenColumnsList.clear();
+  }
+
+  /**
+   * Method removeHiddenColumns.
+   * 
+   * @param vHiddenColumns
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeHiddenColumns(
+          final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
+  {
+    boolean removed = _hiddenColumnsList.remove(vHiddenColumns);
+    return removed;
+  }
+
+  /**
+   * Method removeHiddenColumnsAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt(
+          final int index)
+  {
+    java.lang.Object obj = this._hiddenColumnsList.remove(index);
+    return (jalview.schemabinding.version2.HiddenColumns) obj;
+  }
+
+  /**
+   * Sets the value of field 'annotationColours'.
+   * 
+   * @param annotationColours
+   *                the value of field 'annotationColours'.
+   */
+  public void setAnnotationColours(
+          final jalview.schemabinding.version2.AnnotationColours annotationColours)
+  {
+    this._annotationColours = annotationColours;
+  }
+
+  /**
+   * Sets the value of field 'bgColour'.
+   * 
+   * @param bgColour
+   *                the value of field 'bgColour'.
+   */
+  public void setBgColour(final java.lang.String bgColour)
+  {
+    this._bgColour = bgColour;
+  }
+
+  /**
+   * Sets the value of field 'consThreshold'.
+   * 
+   * @param consThreshold
+   *                the value of field 'consThreshold'.
+   */
+  public void setConsThreshold(final int consThreshold)
+  {
+    this._consThreshold = consThreshold;
+    this._has_consThreshold = true;
+  }
+
+  /**
+   * Sets the value of field 'conservationSelected'.
+   * 
+   * @param conservationSelected
+   *                the value of field 'conservationSelected'.
+   */
+  public void setConservationSelected(final boolean conservationSelected)
+  {
+    this._conservationSelected = conservationSelected;
+    this._has_conservationSelected = true;
+  }
+
+  /**
+   * Sets the value of field 'fontName'.
+   * 
+   * @param fontName
+   *                the value of field 'fontName'.
+   */
+  public void setFontName(final java.lang.String fontName)
+  {
+    this._fontName = fontName;
+  }
+
+  /**
+   * Sets the value of field 'fontSize'.
+   * 
+   * @param fontSize
+   *                the value of field 'fontSize'.
+   */
+  public void setFontSize(final int fontSize)
+  {
+    this._fontSize = fontSize;
+    this._has_fontSize = true;
+  }
+
+  /**
+   * Sets the value of field 'fontStyle'.
+   * 
+   * @param fontStyle
+   *                the value of field 'fontStyle'.
+   */
+  public void setFontStyle(final int fontStyle)
+  {
+    this._fontStyle = fontStyle;
+    this._has_fontStyle = true;
+  }
+
+  /**
+   * Sets the value of field 'gatheredViews'.
+   * 
+   * @param gatheredViews
+   *                the value of field 'gatheredViews'.
+   */
+  public void setGatheredViews(final boolean gatheredViews)
+  {
+    this._gatheredViews = gatheredViews;
+    this._has_gatheredViews = true;
+  }
+
+  /**
+   * Sets the value of field 'height'.
+   * 
+   * @param height
+   *                the value of field 'height'.
+   */
+  public void setHeight(final int height)
+  {
+    this._height = height;
+    this._has_height = true;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vHiddenColumns
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setHiddenColumns(final int index,
+          final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._hiddenColumnsList.size())
+    {
+      throw new IndexOutOfBoundsException("setHiddenColumns: Index value '"
+              + index + "' not in range [0.."
+              + (this._hiddenColumnsList.size() - 1) + "]");
+    }
+
+    this._hiddenColumnsList.set(index, vHiddenColumns);
+  }
+
+  /**
+   * 
+   * 
+   * @param vHiddenColumnsArray
+   */
+  public void setHiddenColumns(
+          final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray)
+  {
+    // -- copy array
+    _hiddenColumnsList.clear();
+
+    for (int i = 0; i < vHiddenColumnsArray.length; i++)
+    {
+      this._hiddenColumnsList.add(vHiddenColumnsArray[i]);
+    }
+  }
+
+  /**
+   * Sets the value of field 'pidSelected'.
+   * 
+   * @param pidSelected
+   *                the value of field 'pidSelected'.
+   */
+  public void setPidSelected(final boolean pidSelected)
+  {
+    this._pidSelected = pidSelected;
+    this._has_pidSelected = true;
+  }
+
+  /**
+   * Sets the value of field 'pidThreshold'.
+   * 
+   * @param pidThreshold
+   *                the value of field 'pidThreshold'.
+   */
+  public void setPidThreshold(final int pidThreshold)
+  {
+    this._pidThreshold = pidThreshold;
+    this._has_pidThreshold = true;
+  }
+
+  /**
+   * Sets the value of field 'renderGaps'.
+   * 
+   * @param renderGaps
+   *                the value of field 'renderGaps'.
+   */
+  public void setRenderGaps(final boolean renderGaps)
+  {
+    this._renderGaps = renderGaps;
+    this._has_renderGaps = true;
+  }
+
+  /**
+   * Sets the value of field 'rightAlignIds'.
+   * 
+   * @param rightAlignIds
+   *                the value of field 'rightAlignIds'.
+   */
+  public void setRightAlignIds(final boolean rightAlignIds)
+  {
+    this._rightAlignIds = rightAlignIds;
+    this._has_rightAlignIds = true;
+  }
+
+  /**
+   * Sets the value of field 'sequenceSetId'.
+   * 
+   * @param sequenceSetId
+   *                the value of field 'sequenceSetId'.
+   */
+  public void setSequenceSetId(final java.lang.String sequenceSetId)
+  {
+    this._sequenceSetId = sequenceSetId;
+  }
+
+  /**
+   * Sets the value of field 'showAnnotation'.
+   * 
+   * @param showAnnotation
+   *                the value of field 'showAnnotation'.
+   */
+  public void setShowAnnotation(final boolean showAnnotation)
+  {
+    this._showAnnotation = showAnnotation;
+    this._has_showAnnotation = true;
+  }
+
+  /**
+   * Sets the value of field 'showBoxes'.
+   * 
+   * @param showBoxes
+   *                the value of field 'showBoxes'.
+   */
+  public void setShowBoxes(final boolean showBoxes)
+  {
+    this._showBoxes = showBoxes;
+    this._has_showBoxes = true;
+  }
+
+  /**
+   * Sets the value of field 'showColourText'.
+   * 
+   * @param showColourText
+   *                the value of field 'showColourText'.
+   */
+  public void setShowColourText(final boolean showColourText)
+  {
+    this._showColourText = showColourText;
+    this._has_showColourText = true;
+  }
+
+  /**
+   * Sets the value of field 'showFullId'.
+   * 
+   * @param showFullId
+   *                the value of field 'showFullId'.
+   */
+  public void setShowFullId(final boolean showFullId)
+  {
+    this._showFullId = showFullId;
+    this._has_showFullId = true;
+  }
+
+  /**
+   * Sets the value of field 'showSequenceFeatures'.
+   * 
+   * @param showSequenceFeatures
+   *                the value of field 'showSequenceFeatures'.
+   */
+  public void setShowSequenceFeatures(final boolean showSequenceFeatures)
+  {
+    this._showSequenceFeatures = showSequenceFeatures;
+    this._has_showSequenceFeatures = true;
+  }
+
+  /**
+   * Sets the value of field 'showText'.
+   * 
+   * @param showText
+   *                the value of field 'showText'.
+   */
+  public void setShowText(final boolean showText)
+  {
+    this._showText = showText;
+    this._has_showText = true;
+  }
+
+  /**
+   * Sets the value of field 'startRes'.
+   * 
+   * @param startRes
+   *                the value of field 'startRes'.
+   */
+  public void setStartRes(final int startRes)
+  {
+    this._startRes = startRes;
+    this._has_startRes = true;
+  }
+
+  /**
+   * Sets the value of field 'startSeq'.
+   * 
+   * @param startSeq
+   *                the value of field 'startSeq'.
+   */
+  public void setStartSeq(final int startSeq)
+  {
+    this._startSeq = startSeq;
+    this._has_startSeq = true;
+  }
+
+  /**
+   * Sets the value of field 'textCol1'.
+   * 
+   * @param textCol1
+   *                the value of field 'textCol1'.
+   */
+  public void setTextCol1(final int textCol1)
+  {
+    this._textCol1 = textCol1;
+    this._has_textCol1 = true;
+  }
+
+  /**
+   * Sets the value of field 'textCol2'.
+   * 
+   * @param textCol2
+   *                the value of field 'textCol2'.
+   */
+  public void setTextCol2(final int textCol2)
+  {
+    this._textCol2 = textCol2;
+    this._has_textCol2 = true;
+  }
+
+  /**
+   * Sets the value of field 'textColThreshold'.
+   * 
+   * @param textColThreshold
+   *                the value of field 'textColThreshold'
+   */
+  public void setTextColThreshold(final int textColThreshold)
+  {
+    this._textColThreshold = textColThreshold;
+    this._has_textColThreshold = true;
+  }
+
+  /**
+   * Sets the value of field 'title'.
+   * 
+   * @param title
+   *                the value of field 'title'.
+   */
+  public void setTitle(final java.lang.String title)
+  {
+    this._title = title;
+  }
+
+  /**
+   * Sets the value of field 'viewName'.
+   * 
+   * @param viewName
+   *                the value of field 'viewName'.
+   */
+  public void setViewName(final java.lang.String viewName)
+  {
+    this._viewName = viewName;
+  }
+
+  /**
+   * Sets the value of field 'width'.
+   * 
+   * @param width
+   *                the value of field 'width'.
+   */
+  public void setWidth(final int width)
+  {
+    this._width = width;
+    this._has_width = true;
+  }
+
+  /**
+   * Sets the value of field 'wrapAlignment'.
+   * 
+   * @param wrapAlignment
+   *                the value of field 'wrapAlignment'.
+   */
+  public void setWrapAlignment(final boolean wrapAlignment)
+  {
+    this._wrapAlignment = wrapAlignment;
+    this._has_wrapAlignment = true;
+  }
+
+  /**
+   * Sets the value of field 'xpos'.
+   * 
+   * @param xpos
+   *                the value of field 'xpos'.
+   */
+  public void setXpos(final int xpos)
+  {
+    this._xpos = xpos;
+    this._has_xpos = true;
+  }
+
+  /**
+   * Sets the value of field 'ypos'.
+   * 
+   * @param ypos
+   *                the value of field 'ypos'.
+   */
+  public void setYpos(final int ypos)
+  {
+    this._ypos = ypos;
+    this._has_ypos = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *                 if object is null or if any SAXException is thrown during
+   *                 marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   * @return the unmarshaled jalview.schemabinding.version2.Viewport
+   */
+  public static jalview.schemabinding.version2.Viewport unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.Viewport) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.Viewport.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *                 if this object is an invalid instance according to the
+   *                 schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java
index fbc56a3..fe62433 100644
--- a/src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.AlcodMap;
 
@@ -18,217 +29,230 @@ import jalview.schemabinding.version2.AlcodMap;
  * 
  * @version $Revision$ $Date$
  */
-public class AlcodMapDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public AlcodMapDescriptor() {
-        super();
-        _nsURI = "www.vamsas.ac.uk/jalview/version2";
-        _xmlName = "alcodMap";
-        _elementDefinition = true;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _dnasq
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dnasq", "dnasq", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                AlcodMap target = (AlcodMap) object;
-                return target.getDnasq();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    AlcodMap target = (AlcodMap) object;
-                    target.setDnasq( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _dnasq
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-        //-- _mapping
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Mapping.class, "_mapping", "Mapping", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                AlcodMap target = (AlcodMap) object;
-                return target.getMapping();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    AlcodMap target = (AlcodMap) object;
-                    target.setMapping( (jalview.schemabinding.version2.Mapping) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.Mapping();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _mapping
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-        }
-        desc.setValidator(fieldValidator);
-    }
+public class AlcodMapDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public AlcodMapDescriptor()
+  {
+    super();
+    _nsURI = "www.vamsas.ac.uk/jalview/version2";
+    _xmlName = "alcodMap";
+    _elementDefinition = true;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
 
+    // -- _dnasq
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_dnasq", "dnasq",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        AlcodMap target = (AlcodMap) object;
+        return target.getDnasq();
+      }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          AlcodMap target = (AlcodMap) object;
+          target.setDnasq((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _dnasq
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.AlcodMap.class;
-    }
+    // -- _mapping
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.Mapping.class, "_mapping",
+            "Mapping", org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        AlcodMap target = (AlcodMap) object;
+        return target.getMapping();
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          AlcodMap target = (AlcodMap) object;
+          target.setMapping((jalview.schemabinding.version2.Mapping) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.Mapping();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
+    // -- validation code for: _mapping
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.AlcodMap.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java
index cd87309..49bfe1d 100644
--- a/src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.Alcodon;
 
@@ -18,263 +29,296 @@ import jalview.schemabinding.version2.Alcodon;
  * 
  * @version $Revision$ $Date$
  */
-public class AlcodonDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+public class AlcodonDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
 
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
 
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
 
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
 
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
 
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
 
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
 
+  public AlcodonDescriptor()
+  {
+    super();
+    _nsURI = "www.vamsas.ac.uk/jalview/version2";
+    _xmlName = "alcodon";
+    _elementDefinition = true;
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
 
-      //----------------/
-     //- Constructors -/
-    //----------------/
+    // -- _pos1
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Long.TYPE, "_pos1", "pos1",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Alcodon target = (Alcodon) object;
+        if (!target.hasPos1())
+        {
+          return null;
+        }
+        return new java.lang.Long(target.getPos1());
+      }
 
-    public AlcodonDescriptor() {
-        super();
-        _nsURI = "www.vamsas.ac.uk/jalview/version2";
-        _xmlName = "alcodon";
-        _elementDefinition = true;
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _pos1
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_pos1", "pos1", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Alcodon target = (Alcodon) object;
-                if (!target.hasPos1()) { return null; }
-                return new java.lang.Long(target.getPos1());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Alcodon target = (Alcodon) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deletePos1();
-                        return;
-                    }
-                    target.setPos1( ((java.lang.Long) value).longValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _pos1
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.LongValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.LongValidator();
-            fieldValidator.setValidator(typeValidator);
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Alcodon target = (Alcodon) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deletePos1();
+            return;
+          }
+          target.setPos1(((java.lang.Long) value).longValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _pos2
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_pos2", "pos2", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Alcodon target = (Alcodon) object;
-                if (!target.hasPos2()) { return null; }
-                return new java.lang.Long(target.getPos2());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Alcodon target = (Alcodon) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deletePos2();
-                        return;
-                    }
-                    target.setPos2( ((java.lang.Long) value).longValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _pos2
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.LongValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.LongValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _pos1
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.LongValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.LongValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _pos2
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Long.TYPE, "_pos2", "pos2",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Alcodon target = (Alcodon) object;
+        if (!target.hasPos2())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _pos3
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_pos3", "pos3", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Alcodon target = (Alcodon) object;
-                if (!target.hasPos3()) { return null; }
-                return new java.lang.Long(target.getPos3());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Alcodon target = (Alcodon) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deletePos3();
-                        return;
-                    }
-                    target.setPos3( ((java.lang.Long) value).longValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _pos3
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.LongValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.LongValidator();
-            fieldValidator.setValidator(typeValidator);
+        return new java.lang.Long(target.getPos2());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Alcodon target = (Alcodon) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deletePos2();
+            return;
+          }
+          target.setPos2(((java.lang.Long) value).longValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-    }
+      }
 
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+    // -- validation code for: _pos2
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.LongValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.LongValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _pos3
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Long.TYPE, "_pos3", "pos3",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Alcodon target = (Alcodon) object;
+        if (!target.hasPos3())
+        {
+          return null;
+        }
+        return new java.lang.Long(target.getPos3());
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Alcodon target = (Alcodon) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deletePos3();
+            return;
+          }
+          target.setPos3(((java.lang.Long) value).longValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _pos3
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.LongValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.LongValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.Alcodon.class;
-    }
+  }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Alcodon.class;
+  }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java
index 5341376..8901c8f 100644
--- a/src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.AlcodonFrame;
 
@@ -18,227 +29,251 @@ import jalview.schemabinding.version2.AlcodonFrame;
  * 
  * @version $Revision$ $Date$
  */
-public class AlcodonFrameDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public AlcodonFrameDescriptor() {
-        super();
-        _nsURI = "www.vamsas.ac.uk/jalview/version2";
-        _xmlName = "AlcodonFrame";
-        _elementDefinition = true;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- initialize element descriptors
-        
-        //-- _alcodonList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Alcodon.class, "_alcodonList", "alcodon", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                AlcodonFrame target = (AlcodonFrame) object;
-                return target.getAlcodon();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    AlcodonFrame target = (AlcodonFrame) object;
-                    target.addAlcodon( (jalview.schemabinding.version2.Alcodon) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    AlcodonFrame target = (AlcodonFrame) object;
-                    target.removeAllAlcodon();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.Alcodon();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _alcodonList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+public class AlcodonFrameDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public AlcodonFrameDescriptor()
+  {
+    super();
+    _nsURI = "www.vamsas.ac.uk/jalview/version2";
+    _xmlName = "AlcodonFrame";
+    _elementDefinition = true;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- initialize element descriptors
+
+    // -- _alcodonList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.Alcodon.class, "_alcodonList",
+            "alcodon", org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        AlcodonFrame target = (AlcodonFrame) object;
+        return target.getAlcodon();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          AlcodonFrame target = (AlcodonFrame) object;
+          target.addAlcodon((jalview.schemabinding.version2.Alcodon) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _alcodMapList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AlcodMap.class, "_alcodMapList", "alcodMap", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                AlcodonFrame target = (AlcodonFrame) object;
-                return target.getAlcodMap();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    AlcodonFrame target = (AlcodonFrame) object;
-                    target.addAlcodMap( (jalview.schemabinding.version2.AlcodMap) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    AlcodonFrame target = (AlcodonFrame) object;
-                    target.removeAllAlcodMap();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.AlcodMap();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _alcodMapList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          AlcodonFrame target = (AlcodonFrame) object;
+          target.removeAllAlcodon();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.Alcodon();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _alcodonList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+    // -- _alcodMapList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.AlcodMap.class, "_alcodMapList",
+            "alcodMap", org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        AlcodonFrame target = (AlcodonFrame) object;
+        return target.getAlcodMap();
+      }
 
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          AlcodonFrame target = (AlcodonFrame) object;
+          target
+                  .addAlcodMap((jalview.schemabinding.version2.AlcodMap) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          AlcodonFrame target = (AlcodonFrame) object;
+          target.removeAllAlcodMap();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
-        return null;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.AlcodMap();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _alcodMapList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.AlcodonFrame.class;
-    }
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.AlcodonFrame.class;
+  }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java
index 3d32ff6..4e606ed 100644
--- a/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.AnnotationColours;
 
@@ -18,386 +29,447 @@ import jalview.schemabinding.version2.AnnotationColours;
  * 
  * @version $Revision$ $Date$
  */
-public class AnnotationColoursDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public AnnotationColoursDescriptor() {
-        super();
-        _nsURI = "www.jalview.org";
-        _xmlName = "AnnotationColours";
-        _elementDefinition = true;
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _aboveThreshold
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_aboveThreshold", "aboveThreshold", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                AnnotationColours target = (AnnotationColours) object;
-                if (!target.hasAboveThreshold()) { return null; }
-                return new java.lang.Integer(target.getAboveThreshold());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    AnnotationColours target = (AnnotationColours) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteAboveThreshold();
-                        return;
-                    }
-                    target.setAboveThreshold( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _aboveThreshold
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _annotation
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_annotation", "annotation", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                AnnotationColours target = (AnnotationColours) object;
-                return target.getAnnotation();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    AnnotationColours target = (AnnotationColours) object;
-                    target.setAnnotation( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _annotation
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+public class AnnotationColoursDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public AnnotationColoursDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org";
+    _xmlName = "AnnotationColours";
+    _elementDefinition = true;
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _aboveThreshold
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_aboveThreshold", "aboveThreshold",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        AnnotationColours target = (AnnotationColours) object;
+        if (!target.hasAboveThreshold())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _minColour
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_minColour", "minColour", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                AnnotationColours target = (AnnotationColours) object;
-                if (!target.hasMinColour()) { return null; }
-                return new java.lang.Integer(target.getMinColour());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    AnnotationColours target = (AnnotationColours) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteMinColour();
-                        return;
-                    }
-                    target.setMinColour( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _minColour
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return new java.lang.Integer(target.getAboveThreshold());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          AnnotationColours target = (AnnotationColours) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteAboveThreshold();
+            return;
+          }
+          target.setAboveThreshold(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _maxColour
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_maxColour", "maxColour", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                AnnotationColours target = (AnnotationColours) object;
-                if (!target.hasMaxColour()) { return null; }
-                return new java.lang.Integer(target.getMaxColour());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    AnnotationColours target = (AnnotationColours) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteMaxColour();
-                        return;
-                    }
-                    target.setMaxColour( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _maxColour
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _aboveThreshold
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _annotation
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_annotation", "annotation",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        AnnotationColours target = (AnnotationColours) object;
+        return target.getAnnotation();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          AnnotationColours target = (AnnotationColours) object;
+          target.setAnnotation((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _colourScheme
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_colourScheme", "colourScheme", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                AnnotationColours target = (AnnotationColours) object;
-                return target.getColourScheme();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    AnnotationColours target = (AnnotationColours) object;
-                    target.setColourScheme( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _colourScheme
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _annotation
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _minColour
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_minColour", "minColour",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        AnnotationColours target = (AnnotationColours) object;
+        if (!target.hasMinColour())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _threshold
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                AnnotationColours target = (AnnotationColours) object;
-                if (!target.hasThreshold()) { return null; }
-                return new java.lang.Float(target.getThreshold());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    AnnotationColours target = (AnnotationColours) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteThreshold();
-                        return;
-                    }
-                    target.setThreshold( ((java.lang.Float) value).floatValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _threshold
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.FloatValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive((float) -3.4028235E38);
-            typeValidator.setMaxInclusive((float) 3.4028235E38);
+        return new java.lang.Integer(target.getMinColour());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          AnnotationColours target = (AnnotationColours) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteMinColour();
+            return;
+          }
+          target.setMinColour(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-    }
+      }
 
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+    // -- validation code for: _minColour
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _maxColour
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_maxColour", "maxColour",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        AnnotationColours target = (AnnotationColours) object;
+        if (!target.hasMaxColour())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getMaxColour());
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          AnnotationColours target = (AnnotationColours) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteMaxColour();
+            return;
+          }
+          target.setMaxColour(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _maxColour
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- _colourScheme
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_colourScheme", "colourScheme",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        AnnotationColours target = (AnnotationColours) object;
+        return target.getColourScheme();
+      }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.AnnotationColours.class;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          AnnotationColours target = (AnnotationColours) object;
+          target.setColourScheme((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
+    // -- validation code for: _colourScheme
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _threshold
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Float.TYPE, "_threshold", "threshold",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        AnnotationColours target = (AnnotationColours) object;
+        if (!target.hasThreshold())
+        {
+          return null;
+        }
+        return new java.lang.Float(target.getThreshold());
+      }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          AnnotationColours target = (AnnotationColours) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteThreshold();
+            return;
+          }
+          target.setThreshold(((java.lang.Float) value).floatValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+    // -- validation code for: _threshold
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.FloatValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive((float) -3.4028235E38);
+      typeValidator.setMaxInclusive((float) 3.4028235E38);
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
+
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.AnnotationColours.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java
index 44576ee..d69c267 100644
--- a/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.Annotation;
 
@@ -18,665 +29,808 @@ import jalview.schemabinding.version2.Annotation;
  * 
  * @version $Revision$ $Date$
  */
-public class AnnotationDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public AnnotationDescriptor() {
-        super();
-        _nsURI = "www.vamsas.ac.uk/jalview/version2";
-        _xmlName = "Annotation";
-        _elementDefinition = true;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _graph
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_graph", "graph", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Annotation target = (Annotation) object;
-                if (!target.hasGraph()) { return null; }
-                return (target.getGraph() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Annotation target = (Annotation) object;
-                    // ignore null values for non optional primitives
-                    if (value == null) { return; }
-                    
-                    target.setGraph( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _graph
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _graphType
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_graphType", "graphType", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Annotation target = (Annotation) object;
-                if (!target.hasGraphType()) { return null; }
-                return new java.lang.Integer(target.getGraphType());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Annotation target = (Annotation) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteGraphType();
-                        return;
-                    }
-                    target.setGraphType( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _graphType
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+public class AnnotationDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public AnnotationDescriptor()
+  {
+    super();
+    _nsURI = "www.vamsas.ac.uk/jalview/version2";
+    _xmlName = "Annotation";
+    _elementDefinition = true;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _graph
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_graph", "graph",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Annotation target = (Annotation) object;
+        if (!target.hasGraph())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _sequenceRef
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequenceRef", "sequenceRef", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Annotation target = (Annotation) object;
-                return target.getSequenceRef();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Annotation target = (Annotation) object;
-                    target.setSequenceRef( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _sequenceRef
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+        return (target.getGraph() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Annotation target = (Annotation) object;
+          // ignore null values for non optional primitives
+          if (value == null)
+          {
+            return;
+          }
+
+          target.setGraph(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _graphColour
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_graphColour", "graphColour", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Annotation target = (Annotation) object;
-                if (!target.hasGraphColour()) { return null; }
-                return new java.lang.Integer(target.getGraphColour());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Annotation target = (Annotation) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteGraphColour();
-                        return;
-                    }
-                    target.setGraphColour( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _graphColour
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _graph
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _graphType
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_graphType", "graphType",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Annotation target = (Annotation) object;
+        if (!target.hasGraphType())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _graphGroup
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_graphGroup", "graphGroup", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Annotation target = (Annotation) object;
-                if (!target.hasGraphGroup()) { return null; }
-                return new java.lang.Integer(target.getGraphGroup());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Annotation target = (Annotation) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteGraphGroup();
-                        return;
-                    }
-                    target.setGraphGroup( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _graphGroup
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return new java.lang.Integer(target.getGraphType());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Annotation target = (Annotation) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteGraphType();
+            return;
+          }
+          target.setGraphType(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _id
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Annotation target = (Annotation) object;
-                return target.getId();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Annotation target = (Annotation) object;
-                    target.setId( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _id
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _graphType
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _sequenceRef
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_sequenceRef", "sequenceRef",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Annotation target = (Annotation) object;
+        return target.getSequenceRef();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Annotation target = (Annotation) object;
+          target.setSequenceRef((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _scoreOnly
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_scoreOnly", "scoreOnly", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Annotation target = (Annotation) object;
-                if (!target.hasScoreOnly()) { return null; }
-                return (target.getScoreOnly() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Annotation target = (Annotation) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteScoreOnly();
-                        return;
-                    }
-                    target.setScoreOnly( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _scoreOnly
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _sequenceRef
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _graphColour
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_graphColour", "graphColour",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Annotation target = (Annotation) object;
+        if (!target.hasGraphColour())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _score
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Double.TYPE, "_score", "score", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Annotation target = (Annotation) object;
-                if (!target.hasScore()) { return null; }
-                return new java.lang.Double(target.getScore());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Annotation target = (Annotation) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteScore();
-                        return;
-                    }
-                    target.setScore( ((java.lang.Double) value).doubleValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _score
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.DoubleValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.DoubleValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-1.7976931348623157E308);
-            typeValidator.setMaxInclusive(1.7976931348623157E308);
+        return new java.lang.Integer(target.getGraphColour());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Annotation target = (Annotation) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteGraphColour();
+            return;
+          }
+          target.setGraphColour(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _visible
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_visible", "visible", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Annotation target = (Annotation) object;
-                if (!target.hasVisible()) { return null; }
-                return (target.getVisible() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Annotation target = (Annotation) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteVisible();
-                        return;
-                    }
-                    target.setVisible( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _visible
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _graphColour
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _graphGroup
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_graphGroup", "graphGroup",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Annotation target = (Annotation) object;
+        if (!target.hasGraphGroup())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-        //-- _annotationElementList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AnnotationElement.class, "_annotationElementList", "annotationElement", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Annotation target = (Annotation) object;
-                return target.getAnnotationElement();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Annotation target = (Annotation) object;
-                    target.addAnnotationElement( (jalview.schemabinding.version2.AnnotationElement) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    Annotation target = (Annotation) object;
-                    target.removeAllAnnotationElement();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.AnnotationElement();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _annotationElementList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+        return new java.lang.Integer(target.getGraphGroup());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Annotation target = (Annotation) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteGraphGroup();
+            return;
+          }
+          target.setGraphGroup(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _label
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_label", "label", org.exolab.castor.xml.NodeType.Element);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Annotation target = (Annotation) object;
-                return target.getLabel();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Annotation target = (Annotation) object;
-                    target.setLabel( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _label
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _graphGroup
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _id
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_id", "id",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Annotation target = (Annotation) object;
+        return target.getId();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Annotation target = (Annotation) object;
+          target.setId((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _description
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Annotation target = (Annotation) object;
-                return target.getDescription();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Annotation target = (Annotation) object;
-                    target.setDescription( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _description
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _id
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _scoreOnly
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_scoreOnly", "scoreOnly",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Annotation target = (Annotation) object;
+        if (!target.hasScoreOnly())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _thresholdLine
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.ThresholdLine.class, "_thresholdLine", "thresholdLine", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Annotation target = (Annotation) object;
-                return target.getThresholdLine();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Annotation target = (Annotation) object;
-                    target.setThresholdLine( (jalview.schemabinding.version2.ThresholdLine) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.ThresholdLine();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _thresholdLine
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
+        return (target.getScoreOnly() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Annotation target = (Annotation) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteScoreOnly();
+            return;
+          }
+          target.setScoreOnly(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-    }
+      }
 
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+    // -- validation code for: _scoreOnly
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _score
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Double.TYPE, "_score", "score",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Annotation target = (Annotation) object;
+        if (!target.hasScore())
+        {
+          return null;
+        }
+        return new java.lang.Double(target.getScore());
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Annotation target = (Annotation) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteScore();
+            return;
+          }
+          target.setScore(((java.lang.Double) value).doubleValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _score
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.DoubleValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.DoubleValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-1.7976931348623157E308);
+      typeValidator.setMaxInclusive(1.7976931348623157E308);
     }
+    desc.setValidator(fieldValidator);
+    // -- _visible
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_visible", "visible",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Annotation target = (Annotation) object;
+        if (!target.hasVisible())
+        {
+          return null;
+        }
+        return (target.getVisible() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.Annotation.class;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Annotation target = (Annotation) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteVisible();
+            return;
+          }
+          target.setVisible(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
+    // -- validation code for: _visible
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
+
+    // -- _annotationElementList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.AnnotationElement.class,
+            "_annotationElementList", "annotationElement",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Annotation target = (Annotation) object;
+        return target.getAnnotationElement();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Annotation target = (Annotation) object;
+          target
+                  .addAnnotationElement((jalview.schemabinding.version2.AnnotationElement) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          Annotation target = (Annotation) object;
+          target.removeAllAnnotationElement();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.AnnotationElement();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _annotationElementList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+    // -- _label
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_label", "label",
+            org.exolab.castor.xml.NodeType.Element);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Annotation target = (Annotation) object;
+        return target.getLabel();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Annotation target = (Annotation) object;
+          target.setLabel((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _label
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _description
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_description", "description",
+            org.exolab.castor.xml.NodeType.Element);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Annotation target = (Annotation) object;
+        return target.getDescription();
+      }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Annotation target = (Annotation) object;
+          target.setDescription((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _description
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _thresholdLine
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.ThresholdLine.class,
+            "_thresholdLine", "thresholdLine",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Annotation target = (Annotation) object;
+        return target.getThresholdLine();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Annotation target = (Annotation) object;
+          target
+                  .setThresholdLine((jalview.schemabinding.version2.ThresholdLine) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.ThresholdLine();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _thresholdLine
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Annotation.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java
index 61221a1..71b365a 100644
--- a/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.AnnotationElement;
 
@@ -18,388 +29,447 @@ import jalview.schemabinding.version2.AnnotationElement;
  * 
  * @version $Revision$ $Date$
  */
-public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public AnnotationElementDescriptor() {
-        super();
-        _nsURI = "www.vamsas.ac.uk/jalview/version2";
-        _xmlName = "annotationElement";
-        _elementDefinition = true;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _position
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_position", "position", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                AnnotationElement target = (AnnotationElement) object;
-                if (!target.hasPosition()) { return null; }
-                return new java.lang.Integer(target.getPosition());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    AnnotationElement target = (AnnotationElement) object;
-                    // ignore null values for non optional primitives
-                    if (value == null) { return; }
-                    
-                    target.setPosition( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _position
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _colour
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                AnnotationElement target = (AnnotationElement) object;
-                if (!target.hasColour()) { return null; }
-                return new java.lang.Integer(target.getColour());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    AnnotationElement target = (AnnotationElement) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteColour();
-                        return;
-                    }
-                    target.setColour( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _colour
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
-        }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-        //-- _displayCharacter
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_displayCharacter", "displayCharacter", org.exolab.castor.xml.NodeType.Element);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                AnnotationElement target = (AnnotationElement) object;
-                return target.getDisplayCharacter();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    AnnotationElement target = (AnnotationElement) object;
-                    target.setDisplayCharacter( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _displayCharacter
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+public class AnnotationElementDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public AnnotationElementDescriptor()
+  {
+    super();
+    _nsURI = "www.vamsas.ac.uk/jalview/version2";
+    _xmlName = "annotationElement";
+    _elementDefinition = true;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _position
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_position", "position",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        AnnotationElement target = (AnnotationElement) object;
+        if (!target.hasPosition())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _description
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                AnnotationElement target = (AnnotationElement) object;
-                return target.getDescription();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    AnnotationElement target = (AnnotationElement) object;
-                    target.setDescription( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _description
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+        return new java.lang.Integer(target.getPosition());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          AnnotationElement target = (AnnotationElement) object;
+          // ignore null values for non optional primitives
+          if (value == null)
+          {
+            return;
+          }
+
+          target.setPosition(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _secondaryStructure
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_secondaryStructure", "secondaryStructure", org.exolab.castor.xml.NodeType.Element);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                AnnotationElement target = (AnnotationElement) object;
-                return target.getSecondaryStructure();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    AnnotationElement target = (AnnotationElement) object;
-                    target.setSecondaryStructure( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _secondaryStructure
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-            typeValidator.setLength(1);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _position
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _colour
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_colour", "colour",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        AnnotationElement target = (AnnotationElement) object;
+        if (!target.hasColour())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _value
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_value", "value", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                AnnotationElement target = (AnnotationElement) object;
-                if (!target.hasValue()) { return null; }
-                return new java.lang.Float(target.getValue());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    AnnotationElement target = (AnnotationElement) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteValue();
-                        return;
-                    }
-                    target.setValue( ((java.lang.Float) value).floatValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _value
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.FloatValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive((float) -3.4028235E38);
-            typeValidator.setMaxInclusive((float) 3.4028235E38);
+        return new java.lang.Integer(target.getColour());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          AnnotationElement target = (AnnotationElement) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteColour();
+            return;
+          }
+          target.setColour(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _colour
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
 
+    // -- _displayCharacter
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_displayCharacter",
+            "displayCharacter", org.exolab.castor.xml.NodeType.Element);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        AnnotationElement target = (AnnotationElement) object;
+        return target.getDisplayCharacter();
+      }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          AnnotationElement target = (AnnotationElement) object;
+          target.setDisplayCharacter((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _displayCharacter
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _description
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_description", "description",
+            org.exolab.castor.xml.NodeType.Element);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        AnnotationElement target = (AnnotationElement) object;
+        return target.getDescription();
+      }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.AnnotationElement.class;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          AnnotationElement target = (AnnotationElement) object;
+          target.setDescription((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
+    // -- validation code for: _description
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _secondaryStructure
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_secondaryStructure",
+            "secondaryStructure", org.exolab.castor.xml.NodeType.Element);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        AnnotationElement target = (AnnotationElement) object;
+        return target.getSecondaryStructure();
+      }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          AnnotationElement target = (AnnotationElement) object;
+          target.setSecondaryStructure((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
+    // -- validation code for: _secondaryStructure
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+      typeValidator.setLength(1);
     }
+    desc.setValidator(fieldValidator);
+    // -- _value
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Float.TYPE, "_value", "value",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        AnnotationElement target = (AnnotationElement) object;
+        if (!target.hasValue())
+        {
+          return null;
+        }
+        return new java.lang.Float(target.getValue());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          AnnotationElement target = (AnnotationElement) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteValue();
+            return;
+          }
+          target.setValue(((java.lang.Float) value).floatValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+    // -- validation code for: _value
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.FloatValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive((float) -3.4028235E38);
+      typeValidator.setMaxInclusive((float) 3.4028235E38);
     }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.AnnotationElement.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java b/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java
index bdd9739..d7d4d19 100644
--- a/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.Colour;
 
@@ -18,215 +29,228 @@ import jalview.schemabinding.version2.Colour;
  * 
  * @version $Revision$ $Date$
  */
-public class ColourDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public ColourDescriptor() {
-        super();
-        _xmlName = "colour";
-        _elementDefinition = true;
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _name
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "Name", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Colour target = (Colour) object;
-                return target.getName();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Colour target = (Colour) object;
-                    target.setName( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _name
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _RGB
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_RGB", "RGB", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Colour target = (Colour) object;
-                return target.getRGB();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Colour target = (Colour) object;
-                    target.setRGB( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _RGB
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-    }
+public class ColourDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
 
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public ColourDescriptor()
+  {
+    super();
+    _xmlName = "colour";
+    _elementDefinition = true;
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _name
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_name", "Name",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Colour target = (Colour) object;
+        return target.getName();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Colour target = (Colour) object;
+          target.setName((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _name
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _RGB
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_RGB", "RGB",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Colour target = (Colour) object;
+        return target.getRGB();
+      }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.Colour.class;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Colour target = (Colour) object;
+          target.setRGB((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
+    // -- validation code for: _RGB
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+  }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Colour.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java b/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java
index 1a55978..d23f637 100644
--- a/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.DBRef;
 
@@ -18,287 +29,316 @@ import jalview.schemabinding.version2.DBRef;
  * 
  * @version $Revision$ $Date$
  */
-public class DBRefDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public DBRefDescriptor() {
-        super();
-        _nsURI = "www.vamsas.ac.uk/jalview/version2";
-        _xmlName = "DBRef";
-        _elementDefinition = true;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _source
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_source", "source", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                DBRef target = (DBRef) object;
-                return target.getSource();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    DBRef target = (DBRef) object;
-                    target.setSource( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _source
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _version
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "version", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                DBRef target = (DBRef) object;
-                return target.getVersion();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    DBRef target = (DBRef) object;
-                    target.setVersion( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _version
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _accessionId
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_accessionId", "accessionId", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                DBRef target = (DBRef) object;
-                return target.getAccessionId();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    DBRef target = (DBRef) object;
-                    target.setAccessionId( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _accessionId
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-        //-- _mapping
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Mapping.class, "_mapping", "Mapping", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                DBRef target = (DBRef) object;
-                return target.getMapping();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    DBRef target = (DBRef) object;
-                    target.setMapping( (jalview.schemabinding.version2.Mapping) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.Mapping();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _mapping
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-        }
-        desc.setValidator(fieldValidator);
-    }
+public class DBRefDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
 
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public DBRefDescriptor()
+  {
+    super();
+    _nsURI = "www.vamsas.ac.uk/jalview/version2";
+    _xmlName = "DBRef";
+    _elementDefinition = true;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _source
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_source", "source",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        DBRef target = (DBRef) object;
+        return target.getSource();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          DBRef target = (DBRef) object;
+          target.setSource((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _source
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _version
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_version", "version",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        DBRef target = (DBRef) object;
+        return target.getVersion();
+      }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.DBRef.class;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          DBRef target = (DBRef) object;
+          target.setVersion((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
+    // -- validation code for: _version
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _accessionId
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_accessionId", "accessionId",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        DBRef target = (DBRef) object;
+        return target.getAccessionId();
+      }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          DBRef target = (DBRef) object;
+          target.setAccessionId((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _accessionId
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
+
+    // -- _mapping
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.Mapping.class, "_mapping",
+            "Mapping", org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        DBRef target = (DBRef) object;
+        return target.getMapping();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          DBRef target = (DBRef) object;
+          target.setMapping((jalview.schemabinding.version2.Mapping) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.Mapping();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _mapping
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.DBRef.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java b/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java
index 92c919e..6e2c377 100644
--- a/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.Feature;
 
@@ -18,464 +29,548 @@ import jalview.schemabinding.version2.Feature;
  * 
  * @version $Revision$ $Date$
  */
-public class FeatureDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public FeatureDescriptor() {
-        super();
-        _nsURI = "www.jalview.org";
-        _xmlName = "feature";
-        _elementDefinition = false;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _begin
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_begin", "begin", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Feature target = (Feature) object;
-                if (!target.hasBegin()) { return null; }
-                return new java.lang.Integer(target.getBegin());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Feature target = (Feature) object;
-                    // ignore null values for non optional primitives
-                    if (value == null) { return; }
-                    
-                    target.setBegin( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _begin
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _end
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Feature target = (Feature) object;
-                if (!target.hasEnd()) { return null; }
-                return new java.lang.Integer(target.getEnd());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Feature target = (Feature) object;
-                    // ignore null values for non optional primitives
-                    if (value == null) { return; }
-                    
-                    target.setEnd( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _end
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _type
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Feature target = (Feature) object;
-                return target.getType();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Feature target = (Feature) object;
-                    target.setType( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _type
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _description
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Feature target = (Feature) object;
-                return target.getDescription();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Feature target = (Feature) object;
-                    target.setDescription( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _description
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _status
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_status", "status", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Feature target = (Feature) object;
-                return target.getStatus();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Feature target = (Feature) object;
-                    target.setStatus( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _status
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _featureGroup
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_featureGroup", "featureGroup", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Feature target = (Feature) object;
-                return target.getFeatureGroup();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Feature target = (Feature) object;
-                    target.setFeatureGroup( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _featureGroup
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _score
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_score", "score", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Feature target = (Feature) object;
-                if (!target.hasScore()) { return null; }
-                return new java.lang.Float(target.getScore());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Feature target = (Feature) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteScore();
-                        return;
-                    }
-                    target.setScore( ((java.lang.Float) value).floatValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _score
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.FloatValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive((float) -3.4028235E38);
-            typeValidator.setMaxInclusive((float) 3.4028235E38);
+public class FeatureDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public FeatureDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org";
+    _xmlName = "feature";
+    _elementDefinition = false;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _begin
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_begin", "begin",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Feature target = (Feature) object;
+        if (!target.hasBegin())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-        //-- _otherDataList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.OtherData.class, "_otherDataList", "otherData", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Feature target = (Feature) object;
-                return target.getOtherData();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Feature target = (Feature) object;
-                    target.addOtherData( (jalview.schemabinding.version2.OtherData) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    Feature target = (Feature) object;
-                    target.removeAllOtherData();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.OtherData();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _otherDataList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+        return new java.lang.Integer(target.getBegin());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Feature target = (Feature) object;
+          // ignore null values for non optional primitives
+          if (value == null)
+          {
+            return;
+          }
+
+          target.setBegin(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _begin
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- _end
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_end", "end",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Feature target = (Feature) object;
+        if (!target.hasEnd())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getEnd());
+      }
 
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Feature target = (Feature) object;
+          // ignore null values for non optional primitives
+          if (value == null)
+          {
+            return;
+          }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+          target.setEnd(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _end
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- _type
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_type", "type",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Feature target = (Feature) object;
+        return target.getType();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Feature target = (Feature) object;
+          target.setType((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.Feature.class;
+    // -- validation code for: _type
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _description
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_description", "description",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Feature target = (Feature) object;
+        return target.getDescription();
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Feature target = (Feature) object;
+          target.setDescription((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _description
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _status
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_status", "status",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Feature target = (Feature) object;
+        return target.getStatus();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Feature target = (Feature) object;
+          target.setStatus((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
+    // -- validation code for: _status
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _featureGroup
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_featureGroup", "featureGroup",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Feature target = (Feature) object;
+        return target.getFeatureGroup();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Feature target = (Feature) object;
+          target.setFeatureGroup((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
+    // -- validation code for: _featureGroup
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _score
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Float.TYPE, "_score", "score",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Feature target = (Feature) object;
+        if (!target.hasScore())
+        {
+          return null;
+        }
+        return new java.lang.Float(target.getScore());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Feature target = (Feature) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteScore();
+            return;
+          }
+          target.setScore(((java.lang.Float) value).floatValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
+    // -- validation code for: _score
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.FloatValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive((float) -3.4028235E38);
+      typeValidator.setMaxInclusive((float) 3.4028235E38);
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+    // -- _otherDataList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.OtherData.class,
+            "_otherDataList", "otherData",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Feature target = (Feature) object;
+        return target.getOtherData();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Feature target = (Feature) object;
+          target
+                  .addOtherData((jalview.schemabinding.version2.OtherData) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          Feature target = (Feature) object;
+          target.removeAllOtherData();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.OtherData();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _otherDataList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Feature.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java b/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java
index 930aac9..367aeda 100644
--- a/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.FeatureSettings;
 
@@ -18,227 +29,250 @@ import jalview.schemabinding.version2.FeatureSettings;
  * 
  * @version $Revision$ $Date$
  */
-public class FeatureSettingsDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public FeatureSettingsDescriptor() {
-        super();
-        _nsURI = "www.jalview.org";
-        _xmlName = "FeatureSettings";
-        _elementDefinition = true;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- initialize element descriptors
-        
-        //-- _settingList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Setting.class, "_settingList", "setting", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                FeatureSettings target = (FeatureSettings) object;
-                return target.getSetting();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    FeatureSettings target = (FeatureSettings) object;
-                    target.addSetting( (jalview.schemabinding.version2.Setting) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    FeatureSettings target = (FeatureSettings) object;
-                    target.removeAllSetting();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.Setting();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _settingList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+public class FeatureSettingsDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public FeatureSettingsDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org";
+    _xmlName = "FeatureSettings";
+    _elementDefinition = true;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- initialize element descriptors
+
+    // -- _settingList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.Setting.class, "_settingList",
+            "setting", org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        FeatureSettings target = (FeatureSettings) object;
+        return target.getSetting();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          FeatureSettings target = (FeatureSettings) object;
+          target.addSetting((jalview.schemabinding.version2.Setting) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _groupList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Group.class, "_groupList", "group", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                FeatureSettings target = (FeatureSettings) object;
-                return target.getGroup();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    FeatureSettings target = (FeatureSettings) object;
-                    target.addGroup( (jalview.schemabinding.version2.Group) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    FeatureSettings target = (FeatureSettings) object;
-                    target.removeAllGroup();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.Group();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _groupList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          FeatureSettings target = (FeatureSettings) object;
+          target.removeAllSetting();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.Setting();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _settingList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+    // -- _groupList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.Group.class, "_groupList",
+            "group", org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        FeatureSettings target = (FeatureSettings) object;
+        return target.getGroup();
+      }
 
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          FeatureSettings target = (FeatureSettings) object;
+          target.addGroup((jalview.schemabinding.version2.Group) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          FeatureSettings target = (FeatureSettings) object;
+          target.removeAllGroup();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
-        return null;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.Group();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _groupList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.FeatureSettings.class;
-    }
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.FeatureSettings.class;
+  }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java b/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java
index 380d46e..ab9951d 100644
--- a/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.Features;
 
@@ -18,134 +29,131 @@ import jalview.schemabinding.version2.Features;
  * 
  * @version $Revision$ $Date$
  */
-public class FeaturesDescriptor extends jalview.schemabinding.version2.descriptors.FeatureDescriptor {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public FeaturesDescriptor() {
-        super();
-        setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.FeatureDescriptor());
-        _nsURI = "www.jalview.org";
-        _xmlName = "features";
-        _elementDefinition = true;
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
-        return null;
-    }
-
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
-    }
-
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.Features.class;
-    }
-
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
-
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
-
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
-
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
-
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+public class FeaturesDescriptor extends
+        jalview.schemabinding.version2.descriptors.FeatureDescriptor
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public FeaturesDescriptor()
+  {
+    super();
+    setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.FeatureDescriptor());
+    _nsURI = "www.jalview.org";
+    _xmlName = "features";
+    _elementDefinition = true;
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Features.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java b/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java
index 417dbbb..a33663e 100644
--- a/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.Group;
 
@@ -18,220 +29,240 @@ import jalview.schemabinding.version2.Group;
  * 
  * @version $Revision$ $Date$
  */
-public class GroupDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public GroupDescriptor() {
-        super();
-        _nsURI = "www.jalview.org";
-        _xmlName = "group";
-        _elementDefinition = true;
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _name
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Group target = (Group) object;
-                return target.getName();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Group target = (Group) object;
-                    target.setName( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _name
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _display
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_display", "display", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Group target = (Group) object;
-                if (!target.hasDisplay()) { return null; }
-                return (target.getDisplay() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Group target = (Group) object;
-                    // ignore null values for non optional primitives
-                    if (value == null) { return; }
-                    
-                    target.setDisplay( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _display
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+public class GroupDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public GroupDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org";
+    _xmlName = "group";
+    _elementDefinition = true;
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _name
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_name", "name",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Group target = (Group) object;
+        return target.getName();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Group target = (Group) object;
+          target.setName((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _name
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _display
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_display", "display",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Group target = (Group) object;
+        if (!target.hasDisplay())
+        {
+          return null;
+        }
+        return (target.getDisplay() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
 
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Group target = (Group) object;
+          // ignore null values for non optional primitives
+          if (value == null)
+          {
+            return;
+          }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+          target.setDisplay(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _display
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.Group.class;
-    }
+  }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Group.class;
+  }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java b/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java
index f307ee4..9182852 100644
--- a/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.HiddenColumns;
 
@@ -18,226 +29,247 @@ import jalview.schemabinding.version2.HiddenColumns;
  * 
  * @version $Revision$ $Date$
  */
-public class HiddenColumnsDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public HiddenColumnsDescriptor() {
-        super();
-        _nsURI = "www.jalview.org";
-        _xmlName = "hiddenColumns";
-        _elementDefinition = true;
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _start
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                HiddenColumns target = (HiddenColumns) object;
-                if (!target.hasStart()) { return null; }
-                return new java.lang.Integer(target.getStart());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    HiddenColumns target = (HiddenColumns) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteStart();
-                        return;
-                    }
-                    target.setStart( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _start
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+public class HiddenColumnsDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public HiddenColumnsDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org";
+    _xmlName = "hiddenColumns";
+    _elementDefinition = true;
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _start
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_start", "start",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        HiddenColumns target = (HiddenColumns) object;
+        if (!target.hasStart())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _end
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                HiddenColumns target = (HiddenColumns) object;
-                if (!target.hasEnd()) { return null; }
-                return new java.lang.Integer(target.getEnd());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    HiddenColumns target = (HiddenColumns) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteEnd();
-                        return;
-                    }
-                    target.setEnd( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _end
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return new java.lang.Integer(target.getStart());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          HiddenColumns target = (HiddenColumns) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteStart();
+            return;
+          }
+          target.setStart(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-    }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
+    // -- validation code for: _start
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _end
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_end", "end",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        HiddenColumns target = (HiddenColumns) object;
+        if (!target.hasEnd())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getEnd());
+      }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          HiddenColumns target = (HiddenColumns) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteEnd();
+            return;
+          }
+          target.setEnd(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _end
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.HiddenColumns.class;
-    }
+  }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.HiddenColumns.class;
+  }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java
index 21b3b67..8ff6830 100644
--- a/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.JGroup;
 
@@ -18,732 +29,897 @@ import jalview.schemabinding.version2.JGroup;
  * 
  * @version $Revision$ $Date$
  */
-public class JGroupDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JGroupDescriptor() {
-        super();
-        _nsURI = "www.jalview.org";
-        _xmlName = "JGroup";
-        _elementDefinition = true;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _start
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JGroup target = (JGroup) object;
-                if (!target.hasStart()) { return null; }
-                return new java.lang.Integer(target.getStart());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JGroup target = (JGroup) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteStart();
-                        return;
-                    }
-                    target.setStart( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _start
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+public class JGroupDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public JGroupDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org";
+    _xmlName = "JGroup";
+    _elementDefinition = true;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _start
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_start", "start",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JGroup target = (JGroup) object;
+        if (!target.hasStart())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _end
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JGroup target = (JGroup) object;
-                if (!target.hasEnd()) { return null; }
-                return new java.lang.Integer(target.getEnd());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JGroup target = (JGroup) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteEnd();
-                        return;
-                    }
-                    target.setEnd( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _end
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return new java.lang.Integer(target.getStart());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JGroup target = (JGroup) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteStart();
+            return;
+          }
+          target.setStart(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _name
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JGroup target = (JGroup) object;
-                return target.getName();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JGroup target = (JGroup) object;
-                    target.setName( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _name
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _start
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _end
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_end", "end",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JGroup target = (JGroup) object;
+        if (!target.hasEnd())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _colour
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JGroup target = (JGroup) object;
-                return target.getColour();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JGroup target = (JGroup) object;
-                    target.setColour( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _colour
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+        return new java.lang.Integer(target.getEnd());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JGroup target = (JGroup) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteEnd();
+            return;
+          }
+          target.setEnd(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _consThreshold
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_consThreshold", "consThreshold", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JGroup target = (JGroup) object;
-                if (!target.hasConsThreshold()) { return null; }
-                return new java.lang.Integer(target.getConsThreshold());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JGroup target = (JGroup) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteConsThreshold();
-                        return;
-                    }
-                    target.setConsThreshold( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _consThreshold
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _end
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _name
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_name", "name",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JGroup target = (JGroup) object;
+        return target.getName();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JGroup target = (JGroup) object;
+          target.setName((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _pidThreshold
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_pidThreshold", "pidThreshold", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JGroup target = (JGroup) object;
-                if (!target.hasPidThreshold()) { return null; }
-                return new java.lang.Integer(target.getPidThreshold());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JGroup target = (JGroup) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deletePidThreshold();
-                        return;
-                    }
-                    target.setPidThreshold( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _pidThreshold
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _name
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _colour
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_colour", "colour",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JGroup target = (JGroup) object;
+        return target.getColour();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JGroup target = (JGroup) object;
+          target.setColour((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _outlineColour
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_outlineColour", "outlineColour", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JGroup target = (JGroup) object;
-                if (!target.hasOutlineColour()) { return null; }
-                return new java.lang.Integer(target.getOutlineColour());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JGroup target = (JGroup) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteOutlineColour();
-                        return;
-                    }
-                    target.setOutlineColour( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _outlineColour
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _colour
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _consThreshold
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_consThreshold", "consThreshold",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JGroup target = (JGroup) object;
+        if (!target.hasConsThreshold())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _displayBoxes
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_displayBoxes", "displayBoxes", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JGroup target = (JGroup) object;
-                if (!target.hasDisplayBoxes()) { return null; }
-                return (target.getDisplayBoxes() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JGroup target = (JGroup) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteDisplayBoxes();
-                        return;
-                    }
-                    target.setDisplayBoxes( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _displayBoxes
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+        return new java.lang.Integer(target.getConsThreshold());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JGroup target = (JGroup) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteConsThreshold();
+            return;
+          }
+          target.setConsThreshold(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _displayText
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_displayText", "displayText", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JGroup target = (JGroup) object;
-                if (!target.hasDisplayText()) { return null; }
-                return (target.getDisplayText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JGroup target = (JGroup) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteDisplayText();
-                        return;
-                    }
-                    target.setDisplayText( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _displayText
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _consThreshold
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _pidThreshold
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_pidThreshold", "pidThreshold",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JGroup target = (JGroup) object;
+        if (!target.hasPidThreshold())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _colourText
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_colourText", "colourText", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JGroup target = (JGroup) object;
-                if (!target.hasColourText()) { return null; }
-                return (target.getColourText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JGroup target = (JGroup) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteColourText();
-                        return;
-                    }
-                    target.setColourText( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _colourText
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+        return new java.lang.Integer(target.getPidThreshold());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JGroup target = (JGroup) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deletePidThreshold();
+            return;
+          }
+          target.setPidThreshold(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _textCol1
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol1", "textCol1", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JGroup target = (JGroup) object;
-                if (!target.hasTextCol1()) { return null; }
-                return new java.lang.Integer(target.getTextCol1());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JGroup target = (JGroup) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteTextCol1();
-                        return;
-                    }
-                    target.setTextCol1( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _textCol1
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _pidThreshold
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _outlineColour
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_outlineColour", "outlineColour",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JGroup target = (JGroup) object;
+        if (!target.hasOutlineColour())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _textCol2
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol2", "textCol2", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JGroup target = (JGroup) object;
-                if (!target.hasTextCol2()) { return null; }
-                return new java.lang.Integer(target.getTextCol2());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JGroup target = (JGroup) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteTextCol2();
-                        return;
-                    }
-                    target.setTextCol2( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _textCol2
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return new java.lang.Integer(target.getOutlineColour());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JGroup target = (JGroup) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteOutlineColour();
+            return;
+          }
+          target.setOutlineColour(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _textColThreshold
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textColThreshold", "textColThreshold", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JGroup target = (JGroup) object;
-                if (!target.hasTextColThreshold()) { return null; }
-                return new java.lang.Integer(target.getTextColThreshold());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JGroup target = (JGroup) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteTextColThreshold();
-                        return;
-                    }
-                    target.setTextColThreshold( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _textColThreshold
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _outlineColour
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _displayBoxes
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_displayBoxes", "displayBoxes",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JGroup target = (JGroup) object;
+        if (!target.hasDisplayBoxes())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-        //-- _seqList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_seqList", "seq", org.exolab.castor.xml.NodeType.Element);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JGroup target = (JGroup) object;
-                return target.getSeq();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JGroup target = (JGroup) object;
-                    target.addSeq( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    JGroup target = (JGroup) object;
-                    target.removeAllSeq();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setRequired(true);
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _seqList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+        return (target.getDisplayBoxes() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JGroup target = (JGroup) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteDisplayBoxes();
+            return;
+          }
+          target
+                  .setDisplayBoxes(((java.lang.Boolean) value)
+                          .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-    }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
+    // -- validation code for: _displayBoxes
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _displayText
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_displayText", "displayText",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JGroup target = (JGroup) object;
+        if (!target.hasDisplayText())
+        {
+          return null;
+        }
+        return (target.getDisplayText() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JGroup target = (JGroup) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteDisplayText();
+            return;
+          }
+          target.setDisplayText(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _displayText
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    desc.setValidator(fieldValidator);
+    // -- _colourText
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_colourText", "colourText",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JGroup target = (JGroup) object;
+        if (!target.hasColourText())
+        {
+          return null;
+        }
+        return (target.getColourText() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.JGroup.class;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JGroup target = (JGroup) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteColourText();
+            return;
+          }
+          target.setColourText(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
+    // -- validation code for: _colourText
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    desc.setValidator(fieldValidator);
+    // -- _textCol1
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_textCol1", "textCol1",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JGroup target = (JGroup) object;
+        if (!target.hasTextCol1())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getTextCol1());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JGroup target = (JGroup) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteTextCol1();
+            return;
+          }
+          target.setTextCol1(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _textCol1
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- _textCol2
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_textCol2", "textCol2",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JGroup target = (JGroup) object;
+        if (!target.hasTextCol2())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getTextCol2());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JGroup target = (JGroup) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteTextCol2();
+            return;
+          }
+          target.setTextCol2(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _textCol2
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- _textColThreshold
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_textColThreshold",
+            "textColThreshold", org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JGroup target = (JGroup) object;
+        if (!target.hasTextColThreshold())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getTextColThreshold());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JGroup target = (JGroup) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteTextColThreshold();
+            return;
+          }
+          target
+                  .setTextColThreshold(((java.lang.Integer) value)
+                          .intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
+    // -- validation code for: _textColThreshold
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
+
+    // -- _seqList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_seqList", "seq",
+            org.exolab.castor.xml.NodeType.Element);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JGroup target = (JGroup) object;
+        return target.getSeq();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JGroup target = (JGroup) object;
+          target.addSeq((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          JGroup target = (JGroup) object;
+          target.removeAllSeq();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setRequired(true);
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _seqList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.JGroup.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java
index 427702d..c46f426 100644
--- a/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.JSeq;
 
@@ -18,486 +29,587 @@ import jalview.schemabinding.version2.JSeq;
  * 
  * @version $Revision$ $Date$
  */
-public class JSeqDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JSeqDescriptor() {
-        super();
-        _nsURI = "www.jalview.org";
-        _xmlName = "JSeq";
-        _elementDefinition = true;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _colour
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JSeq target = (JSeq) object;
-                if (!target.hasColour()) { return null; }
-                return new java.lang.Integer(target.getColour());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JSeq target = (JSeq) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteColour();
-                        return;
-                    }
-                    target.setColour( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _colour
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _start
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JSeq target = (JSeq) object;
-                if (!target.hasStart()) { return null; }
-                return new java.lang.Integer(target.getStart());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JSeq target = (JSeq) object;
-                    // ignore null values for non optional primitives
-                    if (value == null) { return; }
-                    
-                    target.setStart( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _start
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _end
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JSeq target = (JSeq) object;
-                if (!target.hasEnd()) { return null; }
-                return new java.lang.Integer(target.getEnd());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JSeq target = (JSeq) object;
-                    // ignore null values for non optional primitives
-                    if (value == null) { return; }
-                    
-                    target.setEnd( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _end
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _id
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JSeq target = (JSeq) object;
-                return target.getId();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JSeq target = (JSeq) object;
-                    target.setId( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _id
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _hidden
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_hidden", "hidden", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JSeq target = (JSeq) object;
-                if (!target.hasHidden()) { return null; }
-                return (target.getHidden() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JSeq target = (JSeq) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteHidden();
-                        return;
-                    }
-                    target.setHidden( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _hidden
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+public class JSeqDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public JSeqDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org";
+    _xmlName = "JSeq";
+    _elementDefinition = true;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _colour
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_colour", "colour",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JSeq target = (JSeq) object;
+        if (!target.hasColour())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-        //-- _featuresList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Features.class, "_featuresList", "features", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JSeq target = (JSeq) object;
-                return target.getFeatures();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JSeq target = (JSeq) object;
-                    target.addFeatures( (jalview.schemabinding.version2.Features) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    JSeq target = (JSeq) object;
-                    target.removeAllFeatures();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.Features();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _featuresList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+        return new java.lang.Integer(target.getColour());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JSeq target = (JSeq) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteColour();
+            return;
+          }
+          target.setColour(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _pdbidsList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Pdbids.class, "_pdbidsList", "pdbids", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JSeq target = (JSeq) object;
-                return target.getPdbids();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JSeq target = (JSeq) object;
-                    target.addPdbids( (jalview.schemabinding.version2.Pdbids) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    JSeq target = (JSeq) object;
-                    target.removeAllPdbids();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.Pdbids();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _pdbidsList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _colour
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _start
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_start", "start",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JSeq target = (JSeq) object;
+        if (!target.hasStart())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _hiddenSequencesList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_hiddenSequencesList", "hiddenSequences", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JSeq target = (JSeq) object;
-                return target.getHiddenSequences();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JSeq target = (JSeq) object;
-                    // ignore null values for non optional primitives
-                    if (value == null) { return; }
-                    
-                    target.addHiddenSequences( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    JSeq target = (JSeq) object;
-                    target.removeAllHiddenSequences();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _hiddenSequencesList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return new java.lang.Integer(target.getStart());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JSeq target = (JSeq) object;
+          // ignore null values for non optional primitives
+          if (value == null)
+          {
+            return;
+          }
+
+          target.setStart(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _start
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- _end
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_end", "end",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JSeq target = (JSeq) object;
+        if (!target.hasEnd())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getEnd());
+      }
 
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JSeq target = (JSeq) object;
+          // ignore null values for non optional primitives
+          if (value == null)
+          {
+            return;
+          }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+          target.setEnd(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _end
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- _id
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_id", "id",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JSeq target = (JSeq) object;
+        return target.getId();
+      }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.JSeq.class;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JSeq target = (JSeq) object;
+          target.setId((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
+    // -- validation code for: _id
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _hidden
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_hidden", "hidden",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JSeq target = (JSeq) object;
+        if (!target.hasHidden())
+        {
+          return null;
+        }
+        return (target.getHidden() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JSeq target = (JSeq) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteHidden();
+            return;
+          }
+          target.setHidden(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _hidden
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
+
+    // -- _featuresList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.Features.class, "_featuresList",
+            "features", org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JSeq target = (JSeq) object;
+        return target.getFeatures();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JSeq target = (JSeq) object;
+          target
+                  .addFeatures((jalview.schemabinding.version2.Features) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          JSeq target = (JSeq) object;
+          target.removeAllFeatures();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.Features();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _featuresList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+    // -- _pdbidsList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.Pdbids.class, "_pdbidsList",
+            "pdbids", org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JSeq target = (JSeq) object;
+        return target.getPdbids();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JSeq target = (JSeq) object;
+          target.addPdbids((jalview.schemabinding.version2.Pdbids) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          JSeq target = (JSeq) object;
+          target.removeAllPdbids();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.Pdbids();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
+    // -- validation code for: _pdbidsList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+    // -- _hiddenSequencesList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_hiddenSequencesList",
+            "hiddenSequences", org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JSeq target = (JSeq) object;
+        return target.getHiddenSequences();
+      }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JSeq target = (JSeq) object;
+          // ignore null values for non optional primitives
+          if (value == null)
+          {
+            return;
+          }
+
+          target.addHiddenSequences(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          JSeq target = (JSeq) object;
+          target.removeAllHiddenSequences();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _hiddenSequencesList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.JSeq.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java
index 9aad95c..2d17aee 100644
--- a/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.JalviewModel;
 
@@ -18,295 +29,329 @@ import jalview.schemabinding.version2.JalviewModel;
  * 
  * @version $Revision$ $Date$
  */
-public class JalviewModelDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JalviewModelDescriptor() {
-        super();
-        _nsURI = "www.jalview.org";
-        _xmlName = "JalviewModel";
-        _elementDefinition = false;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- initialize element descriptors
-        
-        //-- _creationDate
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.util.Date.class, "_creationDate", "creationDate", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JalviewModel target = (JalviewModel) object;
-                return target.getCreationDate();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JalviewModel target = (JalviewModel) object;
-                    target.setCreationDate( (java.util.Date) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new java.util.Date();
-            }
-        };
-        handler = new org.exolab.castor.xml.handlers.DateFieldHandler(handler);
-        desc.setImmutable(true);
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _creationDate
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.DateTimeValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.DateTimeValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _version
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "version", org.exolab.castor.xml.NodeType.Element);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JalviewModel target = (JalviewModel) object;
-                return target.getVersion();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JalviewModel target = (JalviewModel) object;
-                    target.setVersion( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _version
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _vamsasModel
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.VamsasModel.class, "_vamsasModel", "vamsasModel", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JalviewModel target = (JalviewModel) object;
-                return target.getVamsasModel();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JalviewModel target = (JalviewModel) object;
-                    target.setVamsasModel( (jalview.schemabinding.version2.VamsasModel) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.VamsasModel();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _vamsasModel
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-        }
-        desc.setValidator(fieldValidator);
-        //-- _jalviewModelSequence
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.JalviewModelSequence.class, "_jalviewModelSequence", "-error-if-this-is-used-", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JalviewModel target = (JalviewModel) object;
-                return target.getJalviewModelSequence();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JalviewModel target = (JalviewModel) object;
-                    target.setJalviewModelSequence( (jalview.schemabinding.version2.JalviewModelSequence) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.JalviewModelSequence();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setContainer(true);
-        desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.JalviewModelSequenceDescriptor());
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _jalviewModelSequence
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
+public class JalviewModelDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public JalviewModelDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org";
+    _xmlName = "JalviewModel";
+    _elementDefinition = false;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- initialize element descriptors
+
+    // -- _creationDate
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.util.Date.class, "_creationDate", "creationDate",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JalviewModel target = (JalviewModel) object;
+        return target.getCreationDate();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JalviewModel target = (JalviewModel) object;
+          target.setCreationDate((java.util.Date) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-    }
+      }
 
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new java.util.Date();
+      }
+    };
+    handler = new org.exolab.castor.xml.handlers.DateFieldHandler(handler);
+    desc.setImmutable(true);
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+    // -- validation code for: _creationDate
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.DateTimeValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.DateTimeValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _version
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_version", "version",
+            org.exolab.castor.xml.NodeType.Element);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JalviewModel target = (JalviewModel) object;
+        return target.getVersion();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JalviewModel target = (JalviewModel) object;
+          target.setVersion((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _version
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _vamsasModel
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.VamsasModel.class,
+            "_vamsasModel", "vamsasModel",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JalviewModel target = (JalviewModel) object;
+        return target.getVamsasModel();
+      }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.JalviewModel.class;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JalviewModel target = (JalviewModel) object;
+          target
+                  .setVamsasModel((jalview.schemabinding.version2.VamsasModel) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.VamsasModel();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
+    // -- validation code for: _vamsasModel
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+    // -- _jalviewModelSequence
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.JalviewModelSequence.class,
+            "_jalviewModelSequence", "-error-if-this-is-used-",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JalviewModel target = (JalviewModel) object;
+        return target.getJalviewModelSequence();
+      }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JalviewModel target = (JalviewModel) object;
+          target
+                  .setJalviewModelSequence((jalview.schemabinding.version2.JalviewModelSequence) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.JalviewModelSequence();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setContainer(true);
+    desc
+            .setClassDescriptor(new jalview.schemabinding.version2.descriptors.JalviewModelSequenceDescriptor());
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+    // -- validation code for: _jalviewModelSequence
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.JalviewModel.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java
index d6fd0ba..8c87fa2 100644
--- a/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.JalviewModelSequence;
 
@@ -18,387 +29,462 @@ import jalview.schemabinding.version2.JalviewModelSequence;
  * 
  * @version $Revision$ $Date$
  */
-public class JalviewModelSequenceDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JalviewModelSequenceDescriptor() {
-        super();
-        _nsURI = "www.jalview.org";
-        _elementDefinition = false;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- initialize element descriptors
-        
-        //-- _JSeqList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.JSeq.class, "_JSeqList", "JSeq", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JalviewModelSequence target = (JalviewModelSequence) object;
-                return target.getJSeq();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JalviewModelSequence target = (JalviewModelSequence) object;
-                    target.addJSeq( (jalview.schemabinding.version2.JSeq) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    JalviewModelSequence target = (JalviewModelSequence) object;
-                    target.removeAllJSeq();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.JSeq();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setRequired(true);
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _JSeqList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
+public class JalviewModelSequenceDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public JalviewModelSequenceDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org";
+    _elementDefinition = false;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- initialize element descriptors
+
+    // -- _JSeqList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.JSeq.class, "_JSeqList", "JSeq",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JalviewModelSequence target = (JalviewModelSequence) object;
+        return target.getJSeq();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JalviewModelSequence target = (JalviewModelSequence) object;
+          target.addJSeq((jalview.schemabinding.version2.JSeq) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _JGroupList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.JGroup.class, "_JGroupList", "JGroup", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JalviewModelSequence target = (JalviewModelSequence) object;
-                return target.getJGroup();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JalviewModelSequence target = (JalviewModelSequence) object;
-                    target.addJGroup( (jalview.schemabinding.version2.JGroup) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    JalviewModelSequence target = (JalviewModelSequence) object;
-                    target.removeAllJGroup();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.JGroup();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _JGroupList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          JalviewModelSequence target = (JalviewModelSequence) object;
+          target.removeAllJSeq();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _viewportList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Viewport.class, "_viewportList", "Viewport", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JalviewModelSequence target = (JalviewModelSequence) object;
-                return target.getViewport();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JalviewModelSequence target = (JalviewModelSequence) object;
-                    target.addViewport( (jalview.schemabinding.version2.Viewport) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    JalviewModelSequence target = (JalviewModelSequence) object;
-                    target.removeAllViewport();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.Viewport();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setRequired(true);
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _viewportList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.JSeq();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setRequired(true);
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _JSeqList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+    }
+    desc.setValidator(fieldValidator);
+    // -- _JGroupList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.JGroup.class, "_JGroupList",
+            "JGroup", org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JalviewModelSequence target = (JalviewModelSequence) object;
+        return target.getJGroup();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JalviewModelSequence target = (JalviewModelSequence) object;
+          target.addJGroup((jalview.schemabinding.version2.JGroup) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _userColoursList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.UserColours.class, "_userColoursList", "UserColours", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JalviewModelSequence target = (JalviewModelSequence) object;
-                return target.getUserColours();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JalviewModelSequence target = (JalviewModelSequence) object;
-                    target.addUserColours( (jalview.schemabinding.version2.UserColours) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    JalviewModelSequence target = (JalviewModelSequence) object;
-                    target.removeAllUserColours();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.UserColours();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _userColoursList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          JalviewModelSequence target = (JalviewModelSequence) object;
+          target.removeAllJGroup();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _treeList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Tree.class, "_treeList", "tree", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JalviewModelSequence target = (JalviewModelSequence) object;
-                return target.getTree();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JalviewModelSequence target = (JalviewModelSequence) object;
-                    target.addTree( (jalview.schemabinding.version2.Tree) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    JalviewModelSequence target = (JalviewModelSequence) object;
-                    target.removeAllTree();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.Tree();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _treeList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.JGroup();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _JGroupList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
+    }
+    desc.setValidator(fieldValidator);
+    // -- _viewportList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.Viewport.class, "_viewportList",
+            "Viewport", org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JalviewModelSequence target = (JalviewModelSequence) object;
+        return target.getViewport();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JalviewModelSequence target = (JalviewModelSequence) object;
+          target
+                  .addViewport((jalview.schemabinding.version2.Viewport) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _featureSettings
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.FeatureSettings.class, "_featureSettings", "FeatureSettings", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JalviewModelSequence target = (JalviewModelSequence) object;
-                return target.getFeatureSettings();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JalviewModelSequence target = (JalviewModelSequence) object;
-                    target.setFeatureSettings( (jalview.schemabinding.version2.FeatureSettings) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.FeatureSettings();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _featureSettings
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          JalviewModelSequence target = (JalviewModelSequence) object;
+          target.removeAllViewport();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.Viewport();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setRequired(true);
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _viewportList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+    // -- _userColoursList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.UserColours.class,
+            "_userColoursList", "UserColours",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JalviewModelSequence target = (JalviewModelSequence) object;
+        return target.getUserColours();
+      }
 
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JalviewModelSequence target = (JalviewModelSequence) object;
+          target
+                  .addUserColours((jalview.schemabinding.version2.UserColours) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          JalviewModelSequence target = (JalviewModelSequence) object;
+          target.removeAllUserColours();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
-        return null;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.UserColours();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _userColoursList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+    // -- _treeList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.Tree.class, "_treeList", "tree",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JalviewModelSequence target = (JalviewModelSequence) object;
+        return target.getTree();
+      }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.JalviewModelSequence.class;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JalviewModelSequence target = (JalviewModelSequence) object;
+          target.addTree((jalview.schemabinding.version2.Tree) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          JalviewModelSequence target = (JalviewModelSequence) object;
+          target.removeAllTree();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.Tree();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
+    // -- validation code for: _treeList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+    // -- _featureSettings
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.FeatureSettings.class,
+            "_featureSettings", "FeatureSettings",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JalviewModelSequence target = (JalviewModelSequence) object;
+        return target.getFeatureSettings();
+      }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JalviewModelSequence target = (JalviewModelSequence) object;
+          target
+                  .setFeatureSettings((jalview.schemabinding.version2.FeatureSettings) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.FeatureSettings();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+    // -- validation code for: _featureSettings
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.JalviewModelSequence.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java
index dd155dd..9891a28 100644
--- a/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.Colour;
 import jalview.schemabinding.version2.JalviewUserColours;
@@ -19,222 +30,240 @@ import jalview.schemabinding.version2.JalviewUserColours;
  * 
  * @version $Revision$ $Date$
  */
-public class JalviewUserColoursDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JalviewUserColoursDescriptor() {
-        super();
-        _nsURI = "www.jalview.org/colours";
-        _xmlName = "JalviewUserColours";
-        _elementDefinition = false;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _schemeName
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_schemeName", "schemeName", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JalviewUserColours target = (JalviewUserColours) object;
-                return target.getSchemeName();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JalviewUserColours target = (JalviewUserColours) object;
-                    target.setSchemeName( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _schemeName
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-        //-- _colourList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(Colour.class, "_colourList", "colour", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JalviewUserColours target = (JalviewUserColours) object;
-                return target.getColour();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JalviewUserColours target = (JalviewUserColours) object;
-                    target.addColour( (Colour) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    JalviewUserColours target = (JalviewUserColours) object;
-                    target.removeAllColour();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new Colour();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _colourList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-        }
-        desc.setValidator(fieldValidator);
-    }
+public class JalviewUserColoursDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
 
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public JalviewUserColoursDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org/colours";
+    _xmlName = "JalviewUserColours";
+    _elementDefinition = false;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _schemeName
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_schemeName", "schemeName",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JalviewUserColours target = (JalviewUserColours) object;
+        return target.getSchemeName();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JalviewUserColours target = (JalviewUserColours) object;
+          target.setSchemeName((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _schemeName
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.JalviewUserColours.class;
-    }
+    // -- _colourList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            Colour.class, "_colourList", "colour",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JalviewUserColours target = (JalviewUserColours) object;
+        return target.getColour();
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JalviewUserColours target = (JalviewUserColours) object;
+          target.addColour((Colour) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          JalviewUserColours target = (JalviewUserColours) object;
+          target.removeAllColour();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new Colour();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
+    // -- validation code for: _colourList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.JalviewUserColours.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java
index f39b18f..78c44ab 100644
--- a/src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.MapListFrom;
 
@@ -18,226 +29,251 @@ import jalview.schemabinding.version2.MapListFrom;
  * 
  * @version $Revision$ $Date$
  */
-public class MapListFromDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public MapListFromDescriptor() {
-        super();
-        _nsURI = "www.vamsas.ac.uk/jalview/version2";
-        _xmlName = "mapListFrom";
-        _elementDefinition = true;
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _start
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                MapListFrom target = (MapListFrom) object;
-                if (!target.hasStart()) { return null; }
-                return new java.lang.Integer(target.getStart());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    MapListFrom target = (MapListFrom) object;
-                    // ignore null values for non optional primitives
-                    if (value == null) { return; }
-                    
-                    target.setStart( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _start
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+public class MapListFromDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public MapListFromDescriptor()
+  {
+    super();
+    _nsURI = "www.vamsas.ac.uk/jalview/version2";
+    _xmlName = "mapListFrom";
+    _elementDefinition = true;
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _start
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_start", "start",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        MapListFrom target = (MapListFrom) object;
+        if (!target.hasStart())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _end
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                MapListFrom target = (MapListFrom) object;
-                if (!target.hasEnd()) { return null; }
-                return new java.lang.Integer(target.getEnd());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    MapListFrom target = (MapListFrom) object;
-                    // ignore null values for non optional primitives
-                    if (value == null) { return; }
-                    
-                    target.setEnd( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _end
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return new java.lang.Integer(target.getStart());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          MapListFrom target = (MapListFrom) object;
+          // ignore null values for non optional primitives
+          if (value == null)
+          {
+            return;
+          }
+
+          target.setStart(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _start
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- _end
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_end", "end",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        MapListFrom target = (MapListFrom) object;
+        if (!target.hasEnd())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getEnd());
+      }
 
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          MapListFrom target = (MapListFrom) object;
+          // ignore null values for non optional primitives
+          if (value == null)
+          {
+            return;
+          }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+          target.setEnd(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _end
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.MapListFrom.class;
-    }
+  }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.MapListFrom.class;
+  }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java
index 4de1738..fb92e6f 100644
--- a/src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.MapListTo;
 
@@ -18,226 +29,251 @@ import jalview.schemabinding.version2.MapListTo;
  * 
  * @version $Revision$ $Date$
  */
-public class MapListToDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public MapListToDescriptor() {
-        super();
-        _nsURI = "www.vamsas.ac.uk/jalview/version2";
-        _xmlName = "mapListTo";
-        _elementDefinition = true;
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _start
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                MapListTo target = (MapListTo) object;
-                if (!target.hasStart()) { return null; }
-                return new java.lang.Integer(target.getStart());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    MapListTo target = (MapListTo) object;
-                    // ignore null values for non optional primitives
-                    if (value == null) { return; }
-                    
-                    target.setStart( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _start
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+public class MapListToDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public MapListToDescriptor()
+  {
+    super();
+    _nsURI = "www.vamsas.ac.uk/jalview/version2";
+    _xmlName = "mapListTo";
+    _elementDefinition = true;
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _start
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_start", "start",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        MapListTo target = (MapListTo) object;
+        if (!target.hasStart())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _end
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                MapListTo target = (MapListTo) object;
-                if (!target.hasEnd()) { return null; }
-                return new java.lang.Integer(target.getEnd());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    MapListTo target = (MapListTo) object;
-                    // ignore null values for non optional primitives
-                    if (value == null) { return; }
-                    
-                    target.setEnd( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _end
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return new java.lang.Integer(target.getStart());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          MapListTo target = (MapListTo) object;
+          // ignore null values for non optional primitives
+          if (value == null)
+          {
+            return;
+          }
+
+          target.setStart(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _start
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- _end
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_end", "end",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        MapListTo target = (MapListTo) object;
+        if (!target.hasEnd())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getEnd());
+      }
 
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          MapListTo target = (MapListTo) object;
+          // ignore null values for non optional primitives
+          if (value == null)
+          {
+            return;
+          }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+          target.setEnd(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _end
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.MapListTo.class;
-    }
+  }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.MapListTo.class;
+  }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java
index 7dc7bc5..0f8d0e9 100644
--- a/src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.MapListType;
 
@@ -18,311 +29,366 @@ import jalview.schemabinding.version2.MapListType;
  * 
  * @version $Revision$ $Date$
  */
-public class MapListTypeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public MapListTypeDescriptor() {
-        super();
-        _nsURI = "www.vamsas.ac.uk/jalview/version2";
-        _xmlName = "mapListType";
-        _elementDefinition = false;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _mapFromUnit
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_mapFromUnit", "mapFromUnit", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                MapListType target = (MapListType) object;
-                if (!target.hasMapFromUnit()) { return null; }
-                return new java.lang.Long(target.getMapFromUnit());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    MapListType target = (MapListType) object;
-                    // ignore null values for non optional primitives
-                    if (value == null) { return; }
-                    
-                    target.setMapFromUnit( ((java.lang.Long) value).longValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _mapFromUnit
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.LongValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.LongValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(1L);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _mapToUnit
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_mapToUnit", "mapToUnit", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                MapListType target = (MapListType) object;
-                if (!target.hasMapToUnit()) { return null; }
-                return new java.lang.Long(target.getMapToUnit());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    MapListType target = (MapListType) object;
-                    // ignore null values for non optional primitives
-                    if (value == null) { return; }
-                    
-                    target.setMapToUnit( ((java.lang.Long) value).longValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _mapToUnit
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.LongValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.LongValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(1L);
-        }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-        //-- _mapListFromList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.MapListFrom.class, "_mapListFromList", "mapListFrom", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                MapListType target = (MapListType) object;
-                return target.getMapListFrom();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    MapListType target = (MapListType) object;
-                    target.addMapListFrom( (jalview.schemabinding.version2.MapListFrom) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    MapListType target = (MapListType) object;
-                    target.removeAllMapListFrom();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.MapListFrom();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _mapListFromList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+public class MapListTypeDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public MapListTypeDescriptor()
+  {
+    super();
+    _nsURI = "www.vamsas.ac.uk/jalview/version2";
+    _xmlName = "mapListType";
+    _elementDefinition = false;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _mapFromUnit
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Long.TYPE, "_mapFromUnit", "mapFromUnit",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        MapListType target = (MapListType) object;
+        if (!target.hasMapFromUnit())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _mapListToList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.MapListTo.class, "_mapListToList", "mapListTo", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                MapListType target = (MapListType) object;
-                return target.getMapListTo();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    MapListType target = (MapListType) object;
-                    target.addMapListTo( (jalview.schemabinding.version2.MapListTo) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    MapListType target = (MapListType) object;
-                    target.removeAllMapListTo();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.MapListTo();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _mapListToList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+        return new java.lang.Long(target.getMapFromUnit());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          MapListType target = (MapListType) object;
+          // ignore null values for non optional primitives
+          if (value == null)
+          {
+            return;
+          }
+
+          target.setMapFromUnit(((java.lang.Long) value).longValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _mapFromUnit
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.LongValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.LongValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(1L);
     }
+    desc.setValidator(fieldValidator);
+    // -- _mapToUnit
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Long.TYPE, "_mapToUnit", "mapToUnit",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        MapListType target = (MapListType) object;
+        if (!target.hasMapToUnit())
+        {
+          return null;
+        }
+        return new java.lang.Long(target.getMapToUnit());
+      }
 
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          MapListType target = (MapListType) object;
+          // ignore null values for non optional primitives
+          if (value == null)
+          {
+            return;
+          }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+          target.setMapToUnit(((java.lang.Long) value).longValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _mapToUnit
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.LongValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.LongValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(1L);
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.MapListType.class;
-    }
+    // -- _mapListFromList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.MapListFrom.class,
+            "_mapListFromList", "mapListFrom",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        MapListType target = (MapListType) object;
+        return target.getMapListFrom();
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          MapListType target = (MapListType) object;
+          target
+                  .addMapListFrom((jalview.schemabinding.version2.MapListFrom) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          MapListType target = (MapListType) object;
+          target.removeAllMapListFrom();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.MapListFrom();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
+    // -- validation code for: _mapListFromList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+    // -- _mapListToList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.MapListTo.class,
+            "_mapListToList", "mapListTo",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        MapListType target = (MapListType) object;
+        return target.getMapListTo();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          MapListType target = (MapListType) object;
+          target
+                  .addMapListTo((jalview.schemabinding.version2.MapListTo) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          MapListType target = (MapListType) object;
+          target.removeAllMapListTo();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.MapListTo();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _mapListToList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.MapListType.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java
index 63543d7..6f69b87 100644
--- a/src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.MappingChoice;
 
@@ -18,213 +29,227 @@ import jalview.schemabinding.version2.MappingChoice;
  * 
  * @version $Revision$ $Date$
  */
-public class MappingChoiceDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public MappingChoiceDescriptor() {
-        super();
-        _nsURI = "www.vamsas.ac.uk/jalview/version2";
-        _elementDefinition = false;
-        
-        //-- set grouping compositor
-        setCompositorAsChoice();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- initialize element descriptors
-        
-        //-- _sequence
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Sequence.class, "_sequence", "Sequence", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                MappingChoice target = (MappingChoice) object;
-                return target.getSequence();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    MappingChoice target = (MappingChoice) object;
-                    target.setSequence( (jalview.schemabinding.version2.Sequence) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.Sequence();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _sequence
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-        }
-        desc.setValidator(fieldValidator);
-        //-- _dseqFor
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dseqFor", "dseqFor", org.exolab.castor.xml.NodeType.Element);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                MappingChoice target = (MappingChoice) object;
-                return target.getDseqFor();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    MappingChoice target = (MappingChoice) object;
-                    target.setDseqFor( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _dseqFor
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+public class MappingChoiceDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public MappingChoiceDescriptor()
+  {
+    super();
+    _nsURI = "www.vamsas.ac.uk/jalview/version2";
+    _elementDefinition = false;
+
+    // -- set grouping compositor
+    setCompositorAsChoice();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- initialize element descriptors
+
+    // -- _sequence
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.Sequence.class, "_sequence",
+            "Sequence", org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        MappingChoice target = (MappingChoice) object;
+        return target.getSequence();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          MappingChoice target = (MappingChoice) object;
+          target
+                  .setSequence((jalview.schemabinding.version2.Sequence) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.Sequence();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _sequence
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+    // -- _dseqFor
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_dseqFor", "dseqFor",
+            org.exolab.castor.xml.NodeType.Element);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        MappingChoice target = (MappingChoice) object;
+        return target.getDseqFor();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          MappingChoice target = (MappingChoice) object;
+          target.setDseqFor((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _dseqFor
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
-
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
-    }
-
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.MappingChoice.class;
-    }
-
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
-
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
-
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
-
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
-
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.MappingChoice.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java
index 95e1a87..0f30a75 100644
--- a/src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.Mapping;
 
@@ -18,179 +29,187 @@ import jalview.schemabinding.version2.Mapping;
  * 
  * @version $Revision$ $Date$
  */
-public class MappingDescriptor extends jalview.schemabinding.version2.descriptors.MapListTypeDescriptor {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public MappingDescriptor() {
-        super();
-        setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.MapListTypeDescriptor());
-        _nsURI = "www.vamsas.ac.uk/jalview/version2";
-        _xmlName = "Mapping";
-        _elementDefinition = true;
-        
-        //-- set grouping compositor
-        setCompositorAsChoice();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- initialize element descriptors
-        
-        //-- _mappingChoice
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.MappingChoice.class, "_mappingChoice", "-error-if-this-is-used-", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Mapping target = (Mapping) object;
-                return target.getMappingChoice();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Mapping target = (Mapping) object;
-                    target.setMappingChoice( (jalview.schemabinding.version2.MappingChoice) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.MappingChoice();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setContainer(true);
-        desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.MappingChoiceDescriptor());
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _mappingChoice
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
+public class MappingDescriptor extends
+        jalview.schemabinding.version2.descriptors.MapListTypeDescriptor
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public MappingDescriptor()
+  {
+    super();
+    setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.MapListTypeDescriptor());
+    _nsURI = "www.vamsas.ac.uk/jalview/version2";
+    _xmlName = "Mapping";
+    _elementDefinition = true;
+
+    // -- set grouping compositor
+    setCompositorAsChoice();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- initialize element descriptors
+
+    // -- _mappingChoice
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.MappingChoice.class,
+            "_mappingChoice", "-error-if-this-is-used-",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Mapping target = (Mapping) object;
+        return target.getMappingChoice();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Mapping target = (Mapping) object;
+          target
+                  .setMappingChoice((jalview.schemabinding.version2.MappingChoice) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
-        return null;
-    }
-
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
-    }
-
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.Mapping.class;
-    }
-
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
-
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
-
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
-
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
-
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.MappingChoice();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setContainer(true);
+    desc
+            .setClassDescriptor(new jalview.schemabinding.version2.descriptors.MappingChoiceDescriptor());
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _mappingChoice
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Mapping.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java b/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java
index 46f6682..ad04be7 100644
--- a/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.OtherData;
 
@@ -18,218 +29,231 @@ import jalview.schemabinding.version2.OtherData;
  * 
  * @version $Revision$ $Date$
  */
-public class OtherDataDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public OtherDataDescriptor() {
-        super();
-        _nsURI = "www.jalview.org";
-        _xmlName = "otherData";
-        _elementDefinition = true;
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _key
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_key", "key", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                OtherData target = (OtherData) object;
-                return target.getKey();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    OtherData target = (OtherData) object;
-                    target.setKey( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _key
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _value
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_value", "value", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                OtherData target = (OtherData) object;
-                return target.getValue();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    OtherData target = (OtherData) object;
-                    target.setValue( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _value
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-    }
+public class OtherDataDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
 
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public OtherDataDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org";
+    _xmlName = "otherData";
+    _elementDefinition = true;
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _key
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_key", "key",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        OtherData target = (OtherData) object;
+        return target.getKey();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          OtherData target = (OtherData) object;
+          target.setKey((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _key
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _value
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_value", "value",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        OtherData target = (OtherData) object;
+        return target.getValue();
+      }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.OtherData.class;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          OtherData target = (OtherData) object;
+          target.setValue((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
+    // -- validation code for: _value
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+  }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.OtherData.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java
index dbf0c3a..df41b22 100644
--- a/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.Pdbentry;
 
@@ -18,295 +29,331 @@ import jalview.schemabinding.version2.Pdbentry;
  * 
  * @version $Revision$ $Date$
  */
-public class PdbentryDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public PdbentryDescriptor() {
-        super();
-        _xmlName = "pdbentry";
-        _elementDefinition = false;
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _id
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Pdbentry target = (Pdbentry) object;
-                return target.getId();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Pdbentry target = (Pdbentry) object;
-                    target.setId( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _id
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _type
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Pdbentry target = (Pdbentry) object;
-                return target.getType();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Pdbentry target = (Pdbentry) object;
-                    target.setType( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _type
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _file
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_file", "file", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Pdbentry target = (Pdbentry) object;
-                return target.getFile();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Pdbentry target = (Pdbentry) object;
-                    target.setFile( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _file
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-        //-- _items
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.PdbentryItem.class, "_items", (java.lang.String) null, org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Pdbentry target = (Pdbentry) object;
-                return target.getPdbentryItem();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Pdbentry target = (Pdbentry) object;
-                    target.addPdbentryItem( (jalview.schemabinding.version2.PdbentryItem) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    Pdbentry target = (Pdbentry) object;
-                    target.removeAllPdbentryItem();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.PdbentryItem();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setContainer(true);
-        desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.PdbentryItemDescriptor());
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _items
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
-        }
-        desc.setValidator(fieldValidator);
-    }
+public class PdbentryDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
 
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public PdbentryDescriptor()
+  {
+    super();
+    _xmlName = "pdbentry";
+    _elementDefinition = false;
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _id
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_id", "id",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Pdbentry target = (Pdbentry) object;
+        return target.getId();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Pdbentry target = (Pdbentry) object;
+          target.setId((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _id
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _type
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_type", "type",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Pdbentry target = (Pdbentry) object;
+        return target.getType();
+      }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.Pdbentry.class;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Pdbentry target = (Pdbentry) object;
+          target.setType((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
+    // -- validation code for: _type
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _file
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_file", "file",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Pdbentry target = (Pdbentry) object;
+        return target.getFile();
+      }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Pdbentry target = (Pdbentry) object;
+          target.setFile((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
+    // -- validation code for: _file
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
+
+    // -- _items
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.PdbentryItem.class, "_items",
+            (java.lang.String) null, org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Pdbentry target = (Pdbentry) object;
+        return target.getPdbentryItem();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Pdbentry target = (Pdbentry) object;
+          target
+                  .addPdbentryItem((jalview.schemabinding.version2.PdbentryItem) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          Pdbentry target = (Pdbentry) object;
+          target.removeAllPdbentryItem();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.PdbentryItem();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setContainer(true);
+    desc
+            .setClassDescriptor(new jalview.schemabinding.version2.descriptors.PdbentryItemDescriptor());
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _items
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Pdbentry.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java
index 693ad61..e13879d 100644
--- a/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.PdbentryItem;
 
@@ -18,185 +29,196 @@ import jalview.schemabinding.version2.PdbentryItem;
  * 
  * @version $Revision$ $Date$
  */
-public class PdbentryItemDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public PdbentryItemDescriptor() {
-        super();
-        _nsURI = "www.jalview.org";
-        _xmlName = "pdbentry";
-        _elementDefinition = false;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- initialize element descriptors
-        
-        //-- _propertyList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Property.class, "_propertyList", "property", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                PdbentryItem target = (PdbentryItem) object;
-                return target.getProperty();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    PdbentryItem target = (PdbentryItem) object;
-                    target.addProperty( (jalview.schemabinding.version2.Property) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    PdbentryItem target = (PdbentryItem) object;
-                    target.removeAllProperty();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.Property();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _propertyList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+public class PdbentryItemDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public PdbentryItemDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org";
+    _xmlName = "pdbentry";
+    _elementDefinition = false;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- initialize element descriptors
+
+    // -- _propertyList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.Property.class, "_propertyList",
+            "property", org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        PdbentryItem target = (PdbentryItem) object;
+        return target.getProperty();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          PdbentryItem target = (PdbentryItem) object;
+          target
+                  .addProperty((jalview.schemabinding.version2.Property) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
-        return null;
-    }
-
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
-    }
-
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.PdbentryItem.class;
-    }
-
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
-
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
-
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
-
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
-
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          PdbentryItem target = (PdbentryItem) object;
+          target.removeAllProperty();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.Property();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _propertyList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.PdbentryItem.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java
index 2547f1d..620de04 100644
--- a/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.Pdbids;
 
@@ -18,186 +29,198 @@ import jalview.schemabinding.version2.Pdbids;
  * 
  * @version $Revision$ $Date$
  */
-public class PdbidsDescriptor extends jalview.schemabinding.version2.descriptors.PdbentryDescriptor {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public PdbidsDescriptor() {
-        super();
-        setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.PdbentryDescriptor());
-        _nsURI = "www.jalview.org";
-        _xmlName = "pdbids";
-        _elementDefinition = true;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- initialize element descriptors
-        
-        //-- _structureStateList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.StructureState.class, "_structureStateList", "structureState", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Pdbids target = (Pdbids) object;
-                return target.getStructureState();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Pdbids target = (Pdbids) object;
-                    target.addStructureState( (jalview.schemabinding.version2.StructureState) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    Pdbids target = (Pdbids) object;
-                    target.removeAllStructureState();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.StructureState();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _structureStateList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+public class PdbidsDescriptor extends
+        jalview.schemabinding.version2.descriptors.PdbentryDescriptor
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public PdbidsDescriptor()
+  {
+    super();
+    setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.PdbentryDescriptor());
+    _nsURI = "www.jalview.org";
+    _xmlName = "pdbids";
+    _elementDefinition = true;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- initialize element descriptors
+
+    // -- _structureStateList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.StructureState.class,
+            "_structureStateList", "structureState",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Pdbids target = (Pdbids) object;
+        return target.getStructureState();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Pdbids target = (Pdbids) object;
+          target
+                  .addStructureState((jalview.schemabinding.version2.StructureState) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
-        return null;
-    }
-
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
-    }
-
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.Pdbids.class;
-    }
-
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
-
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
-
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
-
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
-
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          Pdbids target = (Pdbids) object;
+          target.removeAllStructureState();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.StructureState();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _structureStateList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Pdbids.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java
index 15f2e37..84eaa2f 100644
--- a/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.Property;
 
@@ -18,218 +29,231 @@ import jalview.schemabinding.version2.Property;
  * 
  * @version $Revision$ $Date$
  */
-public class PropertyDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public PropertyDescriptor() {
-        super();
-        _nsURI = "www.jalview.org";
-        _xmlName = "property";
-        _elementDefinition = true;
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _name
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Property target = (Property) object;
-                return target.getName();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Property target = (Property) object;
-                    target.setName( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _name
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _value
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_value", "value", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Property target = (Property) object;
-                return target.getValue();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Property target = (Property) object;
-                    target.setValue( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _value
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-    }
+public class PropertyDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
 
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public PropertyDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org";
+    _xmlName = "property";
+    _elementDefinition = true;
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _name
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_name", "name",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Property target = (Property) object;
+        return target.getName();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Property target = (Property) object;
+          target.setName((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _name
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _value
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_value", "value",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Property target = (Property) object;
+        return target.getValue();
+      }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.Property.class;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Property target = (Property) object;
+          target.setValue((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
+    // -- validation code for: _value
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+  }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Property.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java
index 4dfd168..ed55820 100644
--- a/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.Sequence;
 
@@ -18,223 +29,241 @@ import jalview.schemabinding.version2.Sequence;
  * 
  * @version $Revision$ $Date$
  */
-public class SequenceDescriptor extends jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public SequenceDescriptor() {
-        super();
-        setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor());
-        _nsURI = "www.vamsas.ac.uk/jalview/version2";
-        _xmlName = "Sequence";
-        _elementDefinition = true;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _dsseqid
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dsseqid", "dsseqid", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Sequence target = (Sequence) object;
-                return target.getDsseqid();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Sequence target = (Sequence) object;
-                    target.setDsseqid( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _dsseqid
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-        //-- _DBRefList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.DBRef.class, "_DBRefList", "DBRef", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Sequence target = (Sequence) object;
-                return target.getDBRef();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Sequence target = (Sequence) object;
-                    target.addDBRef( (jalview.schemabinding.version2.DBRef) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    Sequence target = (Sequence) object;
-                    target.removeAllDBRef();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.DBRef();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _DBRefList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
-        }
-        desc.setValidator(fieldValidator);
-    }
+public class SequenceDescriptor extends
+        jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
 
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public SequenceDescriptor()
+  {
+    super();
+    setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor());
+    _nsURI = "www.vamsas.ac.uk/jalview/version2";
+    _xmlName = "Sequence";
+    _elementDefinition = true;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _dsseqid
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_dsseqid", "dsseqid",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Sequence target = (Sequence) object;
+        return target.getDsseqid();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Sequence target = (Sequence) object;
+          target.setDsseqid((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _dsseqid
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.Sequence.class;
-    }
+    // -- _DBRefList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.DBRef.class, "_DBRefList",
+            "DBRef", org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Sequence target = (Sequence) object;
+        return target.getDBRef();
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Sequence target = (Sequence) object;
+          target.addDBRef((jalview.schemabinding.version2.DBRef) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          Sequence target = (Sequence) object;
+          target.removeAllDBRef();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.DBRef();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
+    // -- validation code for: _DBRefList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Sequence.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java
index aa0c798..e265961 100644
--- a/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.SequenceSet;
 
@@ -18,387 +29,459 @@ import jalview.schemabinding.version2.SequenceSet;
  * 
  * @version $Revision$ $Date$
  */
-public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public SequenceSetDescriptor() {
-        super();
-        _nsURI = "www.vamsas.ac.uk/jalview/version2";
-        _xmlName = "SequenceSet";
-        _elementDefinition = true;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _gapChar
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_gapChar", "gapChar", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                SequenceSet target = (SequenceSet) object;
-                return target.getGapChar();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    SequenceSet target = (SequenceSet) object;
-                    target.setGapChar( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _gapChar
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+public class SequenceSetDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public SequenceSetDescriptor()
+  {
+    super();
+    _nsURI = "www.vamsas.ac.uk/jalview/version2";
+    _xmlName = "SequenceSet";
+    _elementDefinition = true;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _gapChar
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_gapChar", "gapChar",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        SequenceSet target = (SequenceSet) object;
+        return target.getGapChar();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          SequenceSet target = (SequenceSet) object;
+          target.setGapChar((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _datasetId
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_datasetId", "datasetId", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                SequenceSet target = (SequenceSet) object;
-                return target.getDatasetId();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    SequenceSet target = (SequenceSet) object;
-                    target.setDatasetId( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _datasetId
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _gapChar
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _datasetId
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_datasetId", "datasetId",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        SequenceSet target = (SequenceSet) object;
+        return target.getDatasetId();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          SequenceSet target = (SequenceSet) object;
+          target.setDatasetId((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-        //-- _sequenceList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Sequence.class, "_sequenceList", "Sequence", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                SequenceSet target = (SequenceSet) object;
-                return target.getSequence();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    SequenceSet target = (SequenceSet) object;
-                    target.addSequence( (jalview.schemabinding.version2.Sequence) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    SequenceSet target = (SequenceSet) object;
-                    target.removeAllSequence();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.Sequence();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _sequenceList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _datasetId
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
+
+    // -- _sequenceList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.Sequence.class, "_sequenceList",
+            "Sequence", org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        SequenceSet target = (SequenceSet) object;
+        return target.getSequence();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          SequenceSet target = (SequenceSet) object;
+          target
+                  .addSequence((jalview.schemabinding.version2.Sequence) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _annotationList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Annotation.class, "_annotationList", "Annotation", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                SequenceSet target = (SequenceSet) object;
-                return target.getAnnotation();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    SequenceSet target = (SequenceSet) object;
-                    target.addAnnotation( (jalview.schemabinding.version2.Annotation) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    SequenceSet target = (SequenceSet) object;
-                    target.removeAllAnnotation();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.Annotation();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _annotationList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          SequenceSet target = (SequenceSet) object;
+          target.removeAllSequence();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _sequenceSetPropertiesList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.SequenceSetProperties.class, "_sequenceSetPropertiesList", "sequenceSetProperties", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                SequenceSet target = (SequenceSet) object;
-                return target.getSequenceSetProperties();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    SequenceSet target = (SequenceSet) object;
-                    target.addSequenceSetProperties( (jalview.schemabinding.version2.SequenceSetProperties) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    SequenceSet target = (SequenceSet) object;
-                    target.removeAllSequenceSetProperties();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.SequenceSetProperties();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _sequenceSetPropertiesList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.Sequence();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _sequenceList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
+    }
+    desc.setValidator(fieldValidator);
+    // -- _annotationList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.Annotation.class,
+            "_annotationList", "Annotation",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        SequenceSet target = (SequenceSet) object;
+        return target.getAnnotation();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          SequenceSet target = (SequenceSet) object;
+          target
+                  .addAnnotation((jalview.schemabinding.version2.Annotation) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _alcodonFrameList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AlcodonFrame.class, "_alcodonFrameList", "AlcodonFrame", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                SequenceSet target = (SequenceSet) object;
-                return target.getAlcodonFrame();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    SequenceSet target = (SequenceSet) object;
-                    target.addAlcodonFrame( (jalview.schemabinding.version2.AlcodonFrame) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    SequenceSet target = (SequenceSet) object;
-                    target.removeAllAlcodonFrame();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.AlcodonFrame();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _alcodonFrameList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          SequenceSet target = (SequenceSet) object;
+          target.removeAllAnnotation();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.Annotation();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _annotationList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+    // -- _sequenceSetPropertiesList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.SequenceSetProperties.class,
+            "_sequenceSetPropertiesList", "sequenceSetProperties",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        SequenceSet target = (SequenceSet) object;
+        return target.getSequenceSetProperties();
+      }
 
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          SequenceSet target = (SequenceSet) object;
+          target
+                  .addSequenceSetProperties((jalview.schemabinding.version2.SequenceSetProperties) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          SequenceSet target = (SequenceSet) object;
+          target.removeAllSequenceSetProperties();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
-        return null;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.SequenceSetProperties();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _sequenceSetPropertiesList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+    // -- _alcodonFrameList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.AlcodonFrame.class,
+            "_alcodonFrameList", "AlcodonFrame",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        SequenceSet target = (SequenceSet) object;
+        return target.getAlcodonFrame();
+      }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.SequenceSet.class;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          SequenceSet target = (SequenceSet) object;
+          target
+                  .addAlcodonFrame((jalview.schemabinding.version2.AlcodonFrame) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          SequenceSet target = (SequenceSet) object;
+          target.removeAllAlcodonFrame();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.AlcodonFrame();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
+    // -- validation code for: _alcodonFrameList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.SequenceSet.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java
index 9c3c578..79ce7eb 100644
--- a/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.SequenceSetProperties;
 
@@ -18,214 +29,227 @@ import jalview.schemabinding.version2.SequenceSetProperties;
  * 
  * @version $Revision$ $Date$
  */
-public class SequenceSetPropertiesDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public SequenceSetPropertiesDescriptor() {
-        super();
-        _nsURI = "www.vamsas.ac.uk/jalview/version2";
-        _xmlName = "sequenceSetProperties";
-        _elementDefinition = true;
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _key
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_key", "key", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                SequenceSetProperties target = (SequenceSetProperties) object;
-                return target.getKey();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    SequenceSetProperties target = (SequenceSetProperties) object;
-                    target.setKey( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _key
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _value
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_value", "value", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                SequenceSetProperties target = (SequenceSetProperties) object;
-                return target.getValue();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    SequenceSetProperties target = (SequenceSetProperties) object;
-                    target.setValue( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _value
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+public class SequenceSetPropertiesDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public SequenceSetPropertiesDescriptor()
+  {
+    super();
+    _nsURI = "www.vamsas.ac.uk/jalview/version2";
+    _xmlName = "sequenceSetProperties";
+    _elementDefinition = true;
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _key
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_key", "key",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        SequenceSetProperties target = (SequenceSetProperties) object;
+        return target.getKey();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          SequenceSetProperties target = (SequenceSetProperties) object;
+          target.setKey((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-    }
+      }
 
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _key
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _value
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_value", "value",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        SequenceSetProperties target = (SequenceSetProperties) object;
+        return target.getValue();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          SequenceSetProperties target = (SequenceSetProperties) object;
+          target.setValue((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
-    }
-
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.SequenceSetProperties.class;
-    }
-
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
-
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
-
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
-
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
-
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _value
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
+
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.SequenceSetProperties.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java
index fa73621..653903f 100644
--- a/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.SequenceType;
 
@@ -18,293 +29,322 @@ import jalview.schemabinding.version2.SequenceType;
  * 
  * @version $Revision$ $Date$
  */
-public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public SequenceTypeDescriptor() {
-        super();
-        _nsURI = "www.vamsas.ac.uk/jalview/version2";
-        _xmlName = "SequenceType";
-        _elementDefinition = false;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _id
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                SequenceType target = (SequenceType) object;
-                return target.getId();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    SequenceType target = (SequenceType) object;
-                    target.setId( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _id
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _description
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                SequenceType target = (SequenceType) object;
-                return target.getDescription();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    SequenceType target = (SequenceType) object;
-                    target.setDescription( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _description
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-        //-- _sequence
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequence", "sequence", org.exolab.castor.xml.NodeType.Element);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                SequenceType target = (SequenceType) object;
-                return target.getSequence();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    SequenceType target = (SequenceType) object;
-                    target.setSequence( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _sequence
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+public class SequenceTypeDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public SequenceTypeDescriptor()
+  {
+    super();
+    _nsURI = "www.vamsas.ac.uk/jalview/version2";
+    _xmlName = "SequenceType";
+    _elementDefinition = false;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _id
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_id", "id",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        SequenceType target = (SequenceType) object;
+        return target.getId();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          SequenceType target = (SequenceType) object;
+          target.setId((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _name
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Element);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                SequenceType target = (SequenceType) object;
-                return target.getName();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    SequenceType target = (SequenceType) object;
-                    target.setName( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _name
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _id
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _description
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_description", "description",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        SequenceType target = (SequenceType) object;
+        return target.getDescription();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          SequenceType target = (SequenceType) object;
+          target.setDescription((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _description
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
 
+    // -- _sequence
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_sequence", "sequence",
+            org.exolab.castor.xml.NodeType.Element);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        SequenceType target = (SequenceType) object;
+        return target.getSequence();
+      }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          SequenceType target = (SequenceType) object;
+          target.setSequence((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _sequence
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _name
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_name", "name",
+            org.exolab.castor.xml.NodeType.Element);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        SequenceType target = (SequenceType) object;
+        return target.getName();
+      }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.SequenceType.class;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          SequenceType target = (SequenceType) object;
+          target.setName((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
+    // -- validation code for: _name
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+  }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.SequenceType.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java
index 23783bb..122205d 100644
--- a/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.Setting;
 
@@ -18,306 +29,352 @@ import jalview.schemabinding.version2.Setting;
  * 
  * @version $Revision$ $Date$
  */
-public class SettingDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public SettingDescriptor() {
-        super();
-        _nsURI = "www.jalview.org";
-        _xmlName = "setting";
-        _elementDefinition = true;
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _type
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Setting target = (Setting) object;
-                return target.getType();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Setting target = (Setting) object;
-                    target.setType( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _type
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _colour
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Setting target = (Setting) object;
-                if (!target.hasColour()) { return null; }
-                return new java.lang.Integer(target.getColour());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Setting target = (Setting) object;
-                    // ignore null values for non optional primitives
-                    if (value == null) { return; }
-                    
-                    target.setColour( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _colour
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+public class SettingDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public SettingDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org";
+    _xmlName = "setting";
+    _elementDefinition = true;
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _type
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_type", "type",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Setting target = (Setting) object;
+        return target.getType();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Setting target = (Setting) object;
+          target.setType((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _display
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_display", "display", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Setting target = (Setting) object;
-                if (!target.hasDisplay()) { return null; }
-                return (target.getDisplay() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Setting target = (Setting) object;
-                    // ignore null values for non optional primitives
-                    if (value == null) { return; }
-                    
-                    target.setDisplay( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _display
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _type
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _colour
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_colour", "colour",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Setting target = (Setting) object;
+        if (!target.hasColour())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _order
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_order", "order", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Setting target = (Setting) object;
-                if (!target.hasOrder()) { return null; }
-                return new java.lang.Float(target.getOrder());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Setting target = (Setting) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteOrder();
-                        return;
-                    }
-                    target.setOrder( ((java.lang.Float) value).floatValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _order
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.FloatValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive((float) -3.4028235E38);
-            typeValidator.setMaxInclusive((float) 3.4028235E38);
+        return new java.lang.Integer(target.getColour());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Setting target = (Setting) object;
+          // ignore null values for non optional primitives
+          if (value == null)
+          {
+            return;
+          }
+
+          target.setColour(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _colour
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- _display
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_display", "display",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Setting target = (Setting) object;
+        if (!target.hasDisplay())
+        {
+          return null;
+        }
+        return (target.getDisplay() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
 
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Setting target = (Setting) object;
+          // ignore null values for non optional primitives
+          if (value == null)
+          {
+            return;
+          }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+          target.setDisplay(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _display
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    desc.setValidator(fieldValidator);
+    // -- _order
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Float.TYPE, "_order", "order",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Setting target = (Setting) object;
+        if (!target.hasOrder())
+        {
+          return null;
+        }
+        return new java.lang.Float(target.getOrder());
+      }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.Setting.class;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Setting target = (Setting) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteOrder();
+            return;
+          }
+          target.setOrder(((java.lang.Float) value).floatValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
+    // -- validation code for: _order
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.FloatValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive((float) -3.4028235E38);
+      typeValidator.setMaxInclusive((float) 3.4028235E38);
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+  }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Setting.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java b/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java
index 8584429..a5cfd08 100644
--- a/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.StructureState;
 
@@ -18,389 +29,455 @@ import jalview.schemabinding.version2.StructureState;
  * 
  * @version $Revision$ $Date$
  */
-public class StructureStateDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public StructureStateDescriptor() {
-        super();
-        _nsURI = "www.jalview.org";
-        _xmlName = "structureState";
-        _elementDefinition = true;
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- _content
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_content", "PCDATA", org.exolab.castor.xml.NodeType.Text);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                StructureState target = (StructureState) object;
-                return target.getContent();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    StructureState target = (StructureState) object;
-                    target.setContent( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _content
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- initialize attribute descriptors
-        
-        //-- _visible
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_visible", "visible", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                StructureState target = (StructureState) object;
-                if (!target.hasVisible()) { return null; }
-                return (target.getVisible() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    StructureState target = (StructureState) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteVisible();
-                        return;
-                    }
-                    target.setVisible( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _visible
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+public class StructureStateDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public StructureStateDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org";
+    _xmlName = "structureState";
+    _elementDefinition = true;
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- _content
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_content", "PCDATA",
+            org.exolab.castor.xml.NodeType.Text);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        StructureState target = (StructureState) object;
+        return target.getContent();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          StructureState target = (StructureState) object;
+          target.setContent((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _xpos
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                StructureState target = (StructureState) object;
-                if (!target.hasXpos()) { return null; }
-                return new java.lang.Integer(target.getXpos());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    StructureState target = (StructureState) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteXpos();
-                        return;
-                    }
-                    target.setXpos( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _xpos
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _content
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- initialize attribute descriptors
+
+    // -- _visible
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_visible", "visible",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        StructureState target = (StructureState) object;
+        if (!target.hasVisible())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _ypos
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                StructureState target = (StructureState) object;
-                if (!target.hasYpos()) { return null; }
-                return new java.lang.Integer(target.getYpos());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    StructureState target = (StructureState) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteYpos();
-                        return;
-                    }
-                    target.setYpos( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _ypos
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return (target.getVisible() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          StructureState target = (StructureState) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteVisible();
+            return;
+          }
+          target.setVisible(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _width
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_width", "width", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                StructureState target = (StructureState) object;
-                if (!target.hasWidth()) { return null; }
-                return new java.lang.Integer(target.getWidth());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    StructureState target = (StructureState) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteWidth();
-                        return;
-                    }
-                    target.setWidth( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _width
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _visible
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _xpos
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_xpos", "xpos",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        StructureState target = (StructureState) object;
+        if (!target.hasXpos())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _height
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_height", "height", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                StructureState target = (StructureState) object;
-                if (!target.hasHeight()) { return null; }
-                return new java.lang.Integer(target.getHeight());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    StructureState target = (StructureState) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteHeight();
-                        return;
-                    }
-                    target.setHeight( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _height
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return new java.lang.Integer(target.getXpos());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          StructureState target = (StructureState) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteXpos();
+            return;
+          }
+          target.setXpos(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-    }
+      }
 
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+    // -- validation code for: _xpos
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _ypos
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_ypos", "ypos",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        StructureState target = (StructureState) object;
+        if (!target.hasYpos())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getYpos());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          StructureState target = (StructureState) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteYpos();
+            return;
+          }
+          target.setYpos(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _ypos
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- _width
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_width", "width",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        StructureState target = (StructureState) object;
+        if (!target.hasWidth())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getWidth());
+      }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.StructureState.class;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          StructureState target = (StructureState) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteWidth();
+            return;
+          }
+          target.setWidth(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
+    // -- validation code for: _width
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- _height
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_height", "height",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        StructureState target = (StructureState) object;
+        if (!target.hasHeight())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getHeight());
+      }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          StructureState target = (StructureState) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteHeight();
+            return;
+          }
+          target.setHeight(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+    // -- validation code for: _height
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
+
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.StructureState.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java b/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java
index 951e7ca..34e9f46 100644
--- a/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.ThresholdLine;
 
@@ -18,263 +29,292 @@ import jalview.schemabinding.version2.ThresholdLine;
  * 
  * @version $Revision$ $Date$
  */
-public class ThresholdLineDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+public class ThresholdLineDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
 
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
 
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
 
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
 
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
 
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
 
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
 
+  public ThresholdLineDescriptor()
+  {
+    super();
+    _nsURI = "www.vamsas.ac.uk/jalview/version2";
+    _xmlName = "thresholdLine";
+    _elementDefinition = true;
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
 
-      //----------------/
-     //- Constructors -/
-    //----------------/
+    // -- _label
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_label", "label",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        ThresholdLine target = (ThresholdLine) object;
+        return target.getLabel();
+      }
 
-    public ThresholdLineDescriptor() {
-        super();
-        _nsURI = "www.vamsas.ac.uk/jalview/version2";
-        _xmlName = "thresholdLine";
-        _elementDefinition = true;
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _label
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_label", "label", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                ThresholdLine target = (ThresholdLine) object;
-                return target.getLabel();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    ThresholdLine target = (ThresholdLine) object;
-                    target.setLabel( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _label
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          ThresholdLine target = (ThresholdLine) object;
+          target.setLabel((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _value
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_value", "value", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                ThresholdLine target = (ThresholdLine) object;
-                if (!target.hasValue()) { return null; }
-                return new java.lang.Float(target.getValue());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    ThresholdLine target = (ThresholdLine) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteValue();
-                        return;
-                    }
-                    target.setValue( ((java.lang.Float) value).floatValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _value
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.FloatValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive((float) -3.4028235E38);
-            typeValidator.setMaxInclusive((float) 3.4028235E38);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _label
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _value
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Float.TYPE, "_value", "value",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        ThresholdLine target = (ThresholdLine) object;
+        if (!target.hasValue())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _colour
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                ThresholdLine target = (ThresholdLine) object;
-                if (!target.hasColour()) { return null; }
-                return new java.lang.Integer(target.getColour());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    ThresholdLine target = (ThresholdLine) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteColour();
-                        return;
-                    }
-                    target.setColour( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _colour
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return new java.lang.Float(target.getValue());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          ThresholdLine target = (ThresholdLine) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteValue();
+            return;
+          }
+          target.setValue(((java.lang.Float) value).floatValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-    }
+      }
 
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _value
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.FloatValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive((float) -3.4028235E38);
+      typeValidator.setMaxInclusive((float) 3.4028235E38);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _colour
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_colour", "colour",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        ThresholdLine target = (ThresholdLine) object;
+        if (!target.hasColour())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getColour());
+      }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          ThresholdLine target = (ThresholdLine) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteColour();
+            return;
+          }
+          target.setColour(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _colour
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.ThresholdLine.class;
-    }
+  }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.ThresholdLine.class;
+  }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java
index 9d508a4..5a983e7 100644
--- a/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.Tree;
 
@@ -18,762 +29,936 @@ import jalview.schemabinding.version2.Tree;
  * 
  * @version $Revision$ $Date$
  */
-public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public TreeDescriptor() {
-        super();
-        _nsURI = "www.jalview.org";
-        _xmlName = "tree";
-        _elementDefinition = true;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _width
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_width", "width", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                if (!target.hasWidth()) { return null; }
-                return new java.lang.Integer(target.getWidth());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteWidth();
-                        return;
-                    }
-                    target.setWidth( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _width
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+public class TreeDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public TreeDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org";
+    _xmlName = "tree";
+    _elementDefinition = true;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _width
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_width", "width",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        if (!target.hasWidth())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _height
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_height", "height", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                if (!target.hasHeight()) { return null; }
-                return new java.lang.Integer(target.getHeight());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteHeight();
-                        return;
-                    }
-                    target.setHeight( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _height
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return new java.lang.Integer(target.getWidth());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteWidth();
+            return;
+          }
+          target.setWidth(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _xpos
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                if (!target.hasXpos()) { return null; }
-                return new java.lang.Integer(target.getXpos());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteXpos();
-                        return;
-                    }
-                    target.setXpos( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _xpos
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _width
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _height
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_height", "height",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        if (!target.hasHeight())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _ypos
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                if (!target.hasYpos()) { return null; }
-                return new java.lang.Integer(target.getYpos());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteYpos();
-                        return;
-                    }
-                    target.setYpos( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _ypos
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return new java.lang.Integer(target.getHeight());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteHeight();
+            return;
+          }
+          target.setHeight(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _fontName
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_fontName", "fontName", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                return target.getFontName();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    target.setFontName( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _fontName
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _height
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _xpos
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_xpos", "xpos",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        if (!target.hasXpos())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _fontSize
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontSize", "fontSize", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                if (!target.hasFontSize()) { return null; }
-                return new java.lang.Integer(target.getFontSize());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteFontSize();
-                        return;
-                    }
-                    target.setFontSize( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _fontSize
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return new java.lang.Integer(target.getXpos());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteXpos();
+            return;
+          }
+          target.setXpos(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _fontStyle
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontStyle", "fontStyle", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                if (!target.hasFontStyle()) { return null; }
-                return new java.lang.Integer(target.getFontStyle());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteFontStyle();
-                        return;
-                    }
-                    target.setFontStyle( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _fontStyle
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _xpos
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _ypos
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_ypos", "ypos",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        if (!target.hasYpos())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _threshold
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                if (!target.hasThreshold()) { return null; }
-                return new java.lang.Float(target.getThreshold());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteThreshold();
-                        return;
-                    }
-                    target.setThreshold( ((java.lang.Float) value).floatValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _threshold
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.FloatValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive((float) -3.4028235E38);
-            typeValidator.setMaxInclusive((float) 3.4028235E38);
+        return new java.lang.Integer(target.getYpos());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteYpos();
+            return;
+          }
+          target.setYpos(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _showBootstrap
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showBootstrap", "showBootstrap", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                if (!target.hasShowBootstrap()) { return null; }
-                return (target.getShowBootstrap() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteShowBootstrap();
-                        return;
-                    }
-                    target.setShowBootstrap( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _showBootstrap
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _ypos
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _fontName
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_fontName", "fontName",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        return target.getFontName();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          target.setFontName((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _showDistances
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showDistances", "showDistances", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                if (!target.hasShowDistances()) { return null; }
-                return (target.getShowDistances() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteShowDistances();
-                        return;
-                    }
-                    target.setShowDistances( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _showDistances
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _fontName
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _fontSize
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_fontSize", "fontSize",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        if (!target.hasFontSize())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _markUnlinked
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_markUnlinked", "markUnlinked", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                if (!target.hasMarkUnlinked()) { return null; }
-                return (target.getMarkUnlinked() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteMarkUnlinked();
-                        return;
-                    }
-                    target.setMarkUnlinked( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _markUnlinked
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+        return new java.lang.Integer(target.getFontSize());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteFontSize();
+            return;
+          }
+          target.setFontSize(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _fitToWindow
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_fitToWindow", "fitToWindow", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                if (!target.hasFitToWindow()) { return null; }
-                return (target.getFitToWindow() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteFitToWindow();
-                        return;
-                    }
-                    target.setFitToWindow( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _fitToWindow
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _fontSize
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _fontStyle
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_fontStyle", "fontStyle",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        if (!target.hasFontStyle())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _currentTree
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_currentTree", "currentTree", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                if (!target.hasCurrentTree()) { return null; }
-                return (target.getCurrentTree() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteCurrentTree();
-                        return;
-                    }
-                    target.setCurrentTree( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _currentTree
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+        return new java.lang.Integer(target.getFontStyle());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteFontStyle();
+            return;
+          }
+          target.setFontStyle(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-        //-- _title
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", org.exolab.castor.xml.NodeType.Element);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                return target.getTitle();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    target.setTitle( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _title
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _fontStyle
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _threshold
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Float.TYPE, "_threshold", "threshold",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        if (!target.hasThreshold())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _newick
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_newick", "newick", org.exolab.castor.xml.NodeType.Element);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                return target.getNewick();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    target.setNewick( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _newick
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+        return new java.lang.Float(target.getThreshold());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteThreshold();
+            return;
+          }
+          target.setThreshold(((java.lang.Float) value).floatValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-    }
+      }
 
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _threshold
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.FloatValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive((float) -3.4028235E38);
+      typeValidator.setMaxInclusive((float) 3.4028235E38);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _showBootstrap
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_showBootstrap", "showBootstrap",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        if (!target.hasShowBootstrap())
+        {
+          return null;
+        }
+        return (target.getShowBootstrap() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteShowBootstrap();
+            return;
+          }
+          target.setShowBootstrap(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _showBootstrap
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    desc.setValidator(fieldValidator);
+    // -- _showDistances
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_showDistances", "showDistances",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        if (!target.hasShowDistances())
+        {
+          return null;
+        }
+        return (target.getShowDistances() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteShowDistances();
+            return;
+          }
+          target.setShowDistances(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.Tree.class;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _showDistances
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    desc.setValidator(fieldValidator);
+    // -- _markUnlinked
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_markUnlinked", "markUnlinked",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        if (!target.hasMarkUnlinked())
+        {
+          return null;
+        }
+        return (target.getMarkUnlinked() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteMarkUnlinked();
+            return;
+          }
+          target
+                  .setMarkUnlinked(((java.lang.Boolean) value)
+                          .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
+    // -- validation code for: _markUnlinked
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    desc.setValidator(fieldValidator);
+    // -- _fitToWindow
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_fitToWindow", "fitToWindow",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        if (!target.hasFitToWindow())
+        {
+          return null;
+        }
+        return (target.getFitToWindow() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteFitToWindow();
+            return;
+          }
+          target.setFitToWindow(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
+    // -- validation code for: _fitToWindow
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    desc.setValidator(fieldValidator);
+    // -- _currentTree
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_currentTree", "currentTree",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        if (!target.hasCurrentTree())
+        {
+          return null;
+        }
+        return (target.getCurrentTree() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteCurrentTree();
+            return;
+          }
+          target.setCurrentTree(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _currentTree
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
+
+    // -- _title
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_title", "title",
+            org.exolab.castor.xml.NodeType.Element);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        return target.getTitle();
+      }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          target.setTitle((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _title
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _newick
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_newick", "newick",
+            org.exolab.castor.xml.NodeType.Element);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        return target.getNewick();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          target.setNewick((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _newick
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Tree.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java
index be7012a..57d24c3 100644
--- a/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.UserColourScheme;
 
@@ -18,134 +29,132 @@ import jalview.schemabinding.version2.UserColourScheme;
  * 
  * @version $Revision$ $Date$
  */
-public class UserColourSchemeDescriptor extends jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public UserColourSchemeDescriptor() {
-        super();
-        setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor());
-        _nsURI = "www.jalview.org";
-        _xmlName = "UserColourScheme";
-        _elementDefinition = true;
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
-        return null;
-    }
-
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
-    }
-
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.UserColourScheme.class;
-    }
-
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
-
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
-
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
-
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
-
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+public class UserColourSchemeDescriptor
+        extends
+        jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public UserColourSchemeDescriptor()
+  {
+    super();
+    setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor());
+    _nsURI = "www.jalview.org";
+    _xmlName = "UserColourScheme";
+    _elementDefinition = true;
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.UserColourScheme.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java b/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java
index bda1c5e..053d0c7 100644
--- a/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.UserColours;
 
@@ -18,215 +29,230 @@ import jalview.schemabinding.version2.UserColours;
  * 
  * @version $Revision$ $Date$
  */
-public class UserColoursDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public UserColoursDescriptor() {
-        super();
-        _nsURI = "www.jalview.org";
-        _xmlName = "UserColours";
-        _elementDefinition = true;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _id
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                UserColours target = (UserColours) object;
-                return target.getId();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    UserColours target = (UserColours) object;
-                    target.setId( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _id
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-        //-- _userColourScheme
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.UserColourScheme.class, "_userColourScheme", "UserColourScheme", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                UserColours target = (UserColours) object;
-                return target.getUserColourScheme();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    UserColours target = (UserColours) object;
-                    target.setUserColourScheme( (jalview.schemabinding.version2.UserColourScheme) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.UserColourScheme();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _userColourScheme
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-        }
-        desc.setValidator(fieldValidator);
-    }
+public class UserColoursDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public UserColoursDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org";
+    _xmlName = "UserColours";
+    _elementDefinition = true;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
 
+    // -- _id
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_id", "id",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        UserColours target = (UserColours) object;
+        return target.getId();
+      }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          UserColours target = (UserColours) object;
+          target.setId((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _id
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.UserColours.class;
-    }
+    // -- _userColourScheme
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.UserColourScheme.class,
+            "_userColourScheme", "UserColourScheme",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        UserColours target = (UserColours) object;
+        return target.getUserColourScheme();
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          UserColours target = (UserColours) object;
+          target
+                  .setUserColourScheme((jalview.schemabinding.version2.UserColourScheme) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.UserColourScheme();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
+    // -- validation code for: _userColourScheme
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.UserColours.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java b/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java
index 375f435..6935c49 100644
--- a/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.VAMSAS;
 
@@ -18,232 +29,257 @@ import jalview.schemabinding.version2.VAMSAS;
  * 
  * @version $Revision$ $Date$
  */
-public class VAMSASDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public VAMSASDescriptor() {
-        super();
-        _nsURI = "www.vamsas.ac.uk/jalview/version2";
-        _xmlName = "VAMSAS";
-        _elementDefinition = false;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- initialize element descriptors
-        
-        //-- _treeList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_treeList", "Tree", org.exolab.castor.xml.NodeType.Element);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                VAMSAS target = (VAMSAS) object;
-                return target.getTree();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    VAMSAS target = (VAMSAS) object;
-                    target.addTree( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    VAMSAS target = (VAMSAS) object;
-                    target.removeAllTree();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _treeList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+public class VAMSASDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public VAMSASDescriptor()
+  {
+    super();
+    _nsURI = "www.vamsas.ac.uk/jalview/version2";
+    _xmlName = "VAMSAS";
+    _elementDefinition = false;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- initialize element descriptors
+
+    // -- _treeList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_treeList", "Tree",
+            org.exolab.castor.xml.NodeType.Element);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        VAMSAS target = (VAMSAS) object;
+        return target.getTree();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          VAMSAS target = (VAMSAS) object;
+          target.addTree((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _sequenceSetList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.SequenceSet.class, "_sequenceSetList", "SequenceSet", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                VAMSAS target = (VAMSAS) object;
-                return target.getSequenceSet();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    VAMSAS target = (VAMSAS) object;
-                    target.addSequenceSet( (jalview.schemabinding.version2.SequenceSet) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    VAMSAS target = (VAMSAS) object;
-                    target.removeAllSequenceSet();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.SequenceSet();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _sequenceSetList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          VAMSAS target = (VAMSAS) object;
+          target.removeAllTree();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _treeList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _sequenceSetList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.SequenceSet.class,
+            "_sequenceSetList", "SequenceSet",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        VAMSAS target = (VAMSAS) object;
+        return target.getSequenceSet();
+      }
 
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          VAMSAS target = (VAMSAS) object;
+          target
+                  .addSequenceSet((jalview.schemabinding.version2.SequenceSet) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          VAMSAS target = (VAMSAS) object;
+          target.removeAllSequenceSet();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
-        return null;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.SequenceSet();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _sequenceSetList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.VAMSAS.class;
-    }
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.VAMSAS.class;
+  }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java b/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java
index bc14cfd..26502d0 100644
--- a/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.VamsasModel;
 
@@ -18,134 +29,131 @@ import jalview.schemabinding.version2.VamsasModel;
  * 
  * @version $Revision$ $Date$
  */
-public class VamsasModelDescriptor extends jalview.schemabinding.version2.descriptors.VAMSASDescriptor {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public VamsasModelDescriptor() {
-        super();
-        setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.VAMSASDescriptor());
-        _nsURI = "www.jalview.org";
-        _xmlName = "vamsasModel";
-        _elementDefinition = true;
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
-        return null;
-    }
-
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
-    }
-
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.VamsasModel.class;
-    }
-
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
-
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
-
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
-
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
-
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+public class VamsasModelDescriptor extends
+        jalview.schemabinding.version2.descriptors.VAMSASDescriptor
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public VamsasModelDescriptor()
+  {
+    super();
+    setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.VAMSASDescriptor());
+    _nsURI = "www.jalview.org";
+    _xmlName = "vamsasModel";
+    _elementDefinition = true;
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.VamsasModel.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java b/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java
index 4faa6c1..93fa6f1 100644
--- a/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java
@@ -1,15 +1,26 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import jalview.schemabinding.version2.Viewport;
 
@@ -18,1454 +29,1839 @@ import jalview.schemabinding.version2.Viewport;
  * 
  * @version $Revision$ $Date$
  */
-public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public ViewportDescriptor() {
-        super();
-        _nsURI = "www.jalview.org";
-        _xmlName = "Viewport";
-        _elementDefinition = true;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _conservationSelected
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_conservationSelected", "conservationSelected", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasConservationSelected()) { return null; }
-                return (target.getConservationSelected() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteConservationSelected();
-                        return;
-                    }
-                    target.setConservationSelected( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _conservationSelected
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+public class ViewportDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public ViewportDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org";
+    _xmlName = "Viewport";
+    _elementDefinition = true;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _conservationSelected
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_conservationSelected",
+            "conservationSelected",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasConservationSelected())
+        {
+          return null;
+        }
+        return (target.getConservationSelected() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteConservationSelected();
+            return;
+          }
+          target.setConservationSelected(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _conservationSelected
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _pidSelected
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_pidSelected", "pidSelected",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasPidSelected())
+        {
+          return null;
+        }
+        return (target.getPidSelected() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deletePidSelected();
+            return;
+          }
+          target.setPidSelected(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _pidSelected
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _bgColour
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_bgColour", "bgColour",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        return target.getBgColour();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          target.setBgColour((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _bgColour
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _consThreshold
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_consThreshold", "consThreshold",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasConsThreshold())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getConsThreshold());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteConsThreshold();
+            return;
+          }
+          target.setConsThreshold(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _consThreshold
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _pidThreshold
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_pidThreshold", "pidThreshold",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasPidThreshold())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getPidThreshold());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deletePidThreshold();
+            return;
+          }
+          target.setPidThreshold(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _pidThreshold
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _title
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_title", "title",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        return target.getTitle();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          target.setTitle((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _pidSelected
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_pidSelected", "pidSelected", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasPidSelected()) { return null; }
-                return (target.getPidSelected() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deletePidSelected();
-                        return;
-                    }
-                    target.setPidSelected( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _pidSelected
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _title
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _showFullId
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_showFullId", "showFullId",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasShowFullId())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _bgColour
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_bgColour", "bgColour", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                return target.getBgColour();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    target.setBgColour( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _bgColour
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+        return (target.getShowFullId() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteShowFullId();
+            return;
+          }
+          target.setShowFullId(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _consThreshold
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_consThreshold", "consThreshold", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasConsThreshold()) { return null; }
-                return new java.lang.Integer(target.getConsThreshold());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteConsThreshold();
-                        return;
-                    }
-                    target.setConsThreshold( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _consThreshold
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _showFullId
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _rightAlignIds
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_rightAlignIds", "rightAlignIds",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasRightAlignIds())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _pidThreshold
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_pidThreshold", "pidThreshold", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasPidThreshold()) { return null; }
-                return new java.lang.Integer(target.getPidThreshold());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deletePidThreshold();
-                        return;
-                    }
-                    target.setPidThreshold( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _pidThreshold
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return (target.getRightAlignIds() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteRightAlignIds();
+            return;
+          }
+          target.setRightAlignIds(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _title
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                return target.getTitle();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    target.setTitle( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _title
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _rightAlignIds
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _showText
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_showText", "showText",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasShowText())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _showFullId
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showFullId", "showFullId", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasShowFullId()) { return null; }
-                return (target.getShowFullId() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteShowFullId();
-                        return;
-                    }
-                    target.setShowFullId( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _showFullId
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+        return (target.getShowText() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteShowText();
+            return;
+          }
+          target.setShowText(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _rightAlignIds
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_rightAlignIds", "rightAlignIds", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasRightAlignIds()) { return null; }
-                return (target.getRightAlignIds() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteRightAlignIds();
-                        return;
-                    }
-                    target.setRightAlignIds( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _rightAlignIds
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _showText
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _showColourText
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_showColourText", "showColourText",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasShowColourText())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _showText
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showText", "showText", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasShowText()) { return null; }
-                return (target.getShowText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteShowText();
-                        return;
-                    }
-                    target.setShowText( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _showText
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+        return (target.getShowColourText() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteShowColourText();
+            return;
+          }
+          target.setShowColourText(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _showColourText
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showColourText", "showColourText", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasShowColourText()) { return null; }
-                return (target.getShowColourText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteShowColourText();
-                        return;
-                    }
-                    target.setShowColourText( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _showColourText
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _showColourText
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _showBoxes
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_showBoxes", "showBoxes",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasShowBoxes())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _showBoxes
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showBoxes", "showBoxes", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasShowBoxes()) { return null; }
-                return (target.getShowBoxes() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteShowBoxes();
-                        return;
-                    }
-                    target.setShowBoxes( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _showBoxes
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+        return (target.getShowBoxes() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteShowBoxes();
+            return;
+          }
+          target.setShowBoxes(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _wrapAlignment
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_wrapAlignment", "wrapAlignment", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasWrapAlignment()) { return null; }
-                return (target.getWrapAlignment() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteWrapAlignment();
-                        return;
-                    }
-                    target.setWrapAlignment( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _wrapAlignment
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _showBoxes
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _wrapAlignment
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_wrapAlignment", "wrapAlignment",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasWrapAlignment())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _renderGaps
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_renderGaps", "renderGaps", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasRenderGaps()) { return null; }
-                return (target.getRenderGaps() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteRenderGaps();
-                        return;
-                    }
-                    target.setRenderGaps( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _renderGaps
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+        return (target.getWrapAlignment() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteWrapAlignment();
+            return;
+          }
+          target.setWrapAlignment(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _showSequenceFeatures
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showSequenceFeatures", "showSequenceFeatures", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasShowSequenceFeatures()) { return null; }
-                return (target.getShowSequenceFeatures() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteShowSequenceFeatures();
-                        return;
-                    }
-                    target.setShowSequenceFeatures( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _showSequenceFeatures
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _wrapAlignment
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _renderGaps
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_renderGaps", "renderGaps",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasRenderGaps())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _showAnnotation
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showAnnotation", "showAnnotation", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasShowAnnotation()) { return null; }
-                return (target.getShowAnnotation() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteShowAnnotation();
-                        return;
-                    }
-                    target.setShowAnnotation( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _showAnnotation
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+        return (target.getRenderGaps() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteRenderGaps();
+            return;
+          }
+          target.setRenderGaps(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _xpos
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasXpos()) { return null; }
-                return new java.lang.Integer(target.getXpos());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteXpos();
-                        return;
-                    }
-                    target.setXpos( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _xpos
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _renderGaps
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _showSequenceFeatures
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_showSequenceFeatures",
+            "showSequenceFeatures",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasShowSequenceFeatures())
+        {
+          return null;
+        }
+        return (target.getShowSequenceFeatures() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteShowSequenceFeatures();
+            return;
+          }
+          target.setShowSequenceFeatures(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _showSequenceFeatures
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _showAnnotation
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_showAnnotation", "showAnnotation",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasShowAnnotation())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _ypos
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasYpos()) { return null; }
-                return new java.lang.Integer(target.getYpos());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteYpos();
-                        return;
-                    }
-                    target.setYpos( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _ypos
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return (target.getShowAnnotation() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteShowAnnotation();
+            return;
+          }
+          target.setShowAnnotation(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _width
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_width", "width", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasWidth()) { return null; }
-                return new java.lang.Integer(target.getWidth());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteWidth();
-                        return;
-                    }
-                    target.setWidth( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _width
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _showAnnotation
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _xpos
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_xpos", "xpos",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasXpos())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _height
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_height", "height", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasHeight()) { return null; }
-                return new java.lang.Integer(target.getHeight());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteHeight();
-                        return;
-                    }
-                    target.setHeight( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _height
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return new java.lang.Integer(target.getXpos());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteXpos();
+            return;
+          }
+          target.setXpos(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _startRes
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_startRes", "startRes", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasStartRes()) { return null; }
-                return new java.lang.Integer(target.getStartRes());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteStartRes();
-                        return;
-                    }
-                    target.setStartRes( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _startRes
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _xpos
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _ypos
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_ypos", "ypos",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasYpos())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _startSeq
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_startSeq", "startSeq", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasStartSeq()) { return null; }
-                return new java.lang.Integer(target.getStartSeq());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteStartSeq();
-                        return;
-                    }
-                    target.setStartSeq( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _startSeq
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return new java.lang.Integer(target.getYpos());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteYpos();
+            return;
+          }
+          target.setYpos(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _fontName
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_fontName", "fontName", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                return target.getFontName();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    target.setFontName( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _fontName
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _ypos
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _width
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_width", "width",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasWidth())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _fontSize
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontSize", "fontSize", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasFontSize()) { return null; }
-                return new java.lang.Integer(target.getFontSize());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteFontSize();
-                        return;
-                    }
-                    target.setFontSize( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _fontSize
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return new java.lang.Integer(target.getWidth());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteWidth();
+            return;
+          }
+          target.setWidth(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _fontStyle
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontStyle", "fontStyle", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasFontStyle()) { return null; }
-                return new java.lang.Integer(target.getFontStyle());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteFontStyle();
-                        return;
-                    }
-                    target.setFontStyle( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _fontStyle
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _width
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _height
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_height", "height",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasHeight())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _viewName
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_viewName", "viewName", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                return target.getViewName();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    target.setViewName( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _viewName
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+        return new java.lang.Integer(target.getHeight());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteHeight();
+            return;
+          }
+          target.setHeight(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _sequenceSetId
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequenceSetId", "sequenceSetId", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                return target.getSequenceSetId();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    target.setSequenceSetId( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _sequenceSetId
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _height
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _startRes
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_startRes", "startRes",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasStartRes())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _gatheredViews
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_gatheredViews", "gatheredViews", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasGatheredViews()) { return null; }
-                return (target.getGatheredViews() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteGatheredViews();
-                        return;
-                    }
-                    target.setGatheredViews( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _gatheredViews
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+        return new java.lang.Integer(target.getStartRes());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteStartRes();
+            return;
+          }
+          target.setStartRes(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _textCol1
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol1", "textCol1", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasTextCol1()) { return null; }
-                return new java.lang.Integer(target.getTextCol1());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteTextCol1();
-                        return;
-                    }
-                    target.setTextCol1( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _textCol1
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _startRes
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _startSeq
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_startSeq", "startSeq",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasStartSeq())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _textCol2
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol2", "textCol2", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasTextCol2()) { return null; }
-                return new java.lang.Integer(target.getTextCol2());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteTextCol2();
-                        return;
-                    }
-                    target.setTextCol2( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _textCol2
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return new java.lang.Integer(target.getStartSeq());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteStartSeq();
+            return;
+          }
+          target.setStartSeq(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _textColThreshold
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textColThreshold", "textColThreshold", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasTextColThreshold()) { return null; }
-                return new java.lang.Integer(target.getTextColThreshold());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteTextColThreshold();
-                        return;
-                    }
-                    target.setTextColThreshold( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _textColThreshold
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _startSeq
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _fontName
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_fontName", "fontName",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        return target.getFontName();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          target.setFontName((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-        //-- _annotationColours
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AnnotationColours.class, "_annotationColours", "AnnotationColours", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                return target.getAnnotationColours();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    target.setAnnotationColours( (jalview.schemabinding.version2.AnnotationColours) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.AnnotationColours();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _annotationColours
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _fontName
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _fontSize
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_fontSize", "fontSize",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasFontSize())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _hiddenColumnsList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.HiddenColumns.class, "_hiddenColumnsList", "hiddenColumns", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                return target.getHiddenColumns();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    target.addHiddenColumns( (jalview.schemabinding.version2.HiddenColumns) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    Viewport target = (Viewport) object;
-                    target.removeAllHiddenColumns();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.HiddenColumns();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _hiddenColumnsList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+        return new java.lang.Integer(target.getFontSize());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteFontSize();
+            return;
+          }
+          target.setFontSize(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _fontSize
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- _fontStyle
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_fontStyle", "fontStyle",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasFontStyle())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getFontStyle());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteFontStyle();
+            return;
+          }
+          target.setFontStyle(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _fontStyle
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _viewName
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_viewName", "viewName",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        return target.getViewName();
+      }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          target.setViewName((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _viewName
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _sequenceSetId
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_sequenceSetId", "sequenceSetId",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        return target.getSequenceSetId();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          target.setSequenceSetId((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _sequenceSetId
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _gatheredViews
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_gatheredViews", "gatheredViews",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasGatheredViews())
+        {
+          return null;
+        }
+        return (target.getGatheredViews() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteGatheredViews();
+            return;
+          }
+          target.setGatheredViews(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.Viewport.class;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _gatheredViews
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    desc.setValidator(fieldValidator);
+    // -- _textCol1
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_textCol1", "textCol1",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasTextCol1())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getTextCol1());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteTextCol1();
+            return;
+          }
+          target.setTextCol1(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
+    // -- validation code for: _textCol1
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- _textCol2
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_textCol2", "textCol2",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasTextCol2())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getTextCol2());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteTextCol2();
+            return;
+          }
+          target.setTextCol2(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
+    // -- validation code for: _textCol2
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- _textColThreshold
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_textColThreshold",
+            "textColThreshold", org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasTextColThreshold())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getTextColThreshold());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteTextColThreshold();
+            return;
+          }
+          target
+                  .setTextColThreshold(((java.lang.Integer) value)
+                          .intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _textColThreshold
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
+
+    // -- _annotationColours
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.AnnotationColours.class,
+            "_annotationColours", "AnnotationColours",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        return target.getAnnotationColours();
+      }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          target
+                  .setAnnotationColours((jalview.schemabinding.version2.AnnotationColours) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.AnnotationColours();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _annotationColours
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+    // -- _hiddenColumnsList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.HiddenColumns.class,
+            "_hiddenColumnsList", "hiddenColumns",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        return target.getHiddenColumns();
+      }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          target
+                  .addHiddenColumns((jalview.schemabinding.version2.HiddenColumns) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          target.removeAllHiddenColumns();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.HiddenColumns();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _hiddenColumnsList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Viewport.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 6a7a3cf..57cd1fa 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -1,230 +1,227 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.schemes;
-
-import java.awt.*;
-
-import jalview.datamodel.*;
-
-public class AnnotationColourGradient
-    extends ResidueColourScheme
-{
-  public static int NO_THRESHOLD = -1;
-  public static int BELOW_THRESHOLD = 0;
-  public static int ABOVE_THRESHOLD = 1;
-
-  public AlignmentAnnotation annotation;
-  int aboveAnnotationThreshold = -1;
-  public boolean thresholdIsMinMax = false;
-
-  GraphLine annotationThreshold;
-
-  float r1, g1, b1, rr, gg, bb, dr, dg, db;
-
-  ColourSchemeI colourScheme;
-
-  public boolean predefinedColours = false;
-
-  /**
-   * Creates a new AnnotationColourGradient object.
-   */
-  public AnnotationColourGradient(AlignmentAnnotation annotation,
-                                  ColourSchemeI originalColour,
-                                  int aboveThreshold)
-  {
-    if (originalColour instanceof AnnotationColourGradient)
-    {
-      colourScheme = ( (AnnotationColourGradient) originalColour).colourScheme;
-    }
-    else
-    {
-      colourScheme = originalColour;
-    }
-
-    this.annotation = annotation;
-
-    aboveAnnotationThreshold = aboveThreshold;
-
-    if (aboveThreshold != NO_THRESHOLD && annotation.threshold != null)
-    {
-      annotationThreshold = annotation.threshold;
-    }
-  }
-
-  /**
-   * Creates a new AnnotationColourGradient object.
-   */
-  public AnnotationColourGradient(AlignmentAnnotation annotation,
-                                  Color minColour, Color maxColour,
-                                  int aboveThreshold)
-  {
-    this.annotation = annotation;
-
-    aboveAnnotationThreshold = aboveThreshold;
-
-    if (aboveThreshold != NO_THRESHOLD && annotation.threshold != null)
-    {
-      annotationThreshold = annotation.threshold;
-    }
-
-    r1 = minColour.getRed();
-    g1 = minColour.getGreen();
-    b1 = minColour.getBlue();
-
-    rr = maxColour.getRed() - r1;
-    gg = maxColour.getGreen() - g1;
-    bb = maxColour.getBlue() - b1;
-  }
-
-  public String getAnnotation()
-  {
-    return annotation.label;
-  }
-
-  public int getAboveThreshold()
-  {
-    return aboveAnnotationThreshold;
-  }
-
-  public float getAnnotationThreshold()
-  {
-    if (annotationThreshold == null)
-    {
-      return 0;
-    }
-    else
-    {
-      return annotationThreshold.value;
-    }
-  }
-
-  public ColourSchemeI getBaseColour()
-  {
-    return colourScheme;
-  }
-
-  public Color getMinColour()
-  {
-    return new Color( (int) r1, (int) g1, (int) b1);
-  }
-
-  public Color getMaxColour()
-  {
-    return new Color( (int) (r1 + rr), (int) (g1 + gg), (int) (b1 + bb));
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param n DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Color findColour(char c)
-  {
-    return Color.red;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param n DOCUMENT ME!
-   * @param j DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Color findColour(char c, int j)
-  {
-    Color currentColour = Color.white;
-
-    if ( (threshold == 0) || aboveThreshold(c, j))
-    {
-      if (j < annotation.annotations.length
-          && annotation.annotations[j] != null
-          && !jalview.util.Comparison.isGap(c))
-      {
-
-       if (predefinedColours)
-        {
-          if(annotation.annotations[j].colour != null)
-              return annotation.annotations[j].colour;
-          else
-            return currentColour;
-        }
-
-        if (aboveAnnotationThreshold == NO_THRESHOLD
-            ||
-            (annotationThreshold != null && aboveAnnotationThreshold == ABOVE_THRESHOLD &&
-             annotation.annotations[j].value >= annotationThreshold.value)
-            ||
-            (annotationThreshold != null && aboveAnnotationThreshold == BELOW_THRESHOLD &&
-             annotation.annotations[j].value <= annotationThreshold.value))
-        {
-
-          float range=1f;
-          if (thresholdIsMinMax
-              && annotation.threshold != null
-              && aboveAnnotationThreshold == ABOVE_THRESHOLD
-              && annotation.annotations[j].value>annotation.threshold.value)
-          {
-            range =
-                (annotation.annotations[j].value - annotation.threshold.value) /
-                (annotation.graphMax - annotation.threshold.value);
-          }
-          else if (thresholdIsMinMax
-                   && annotation.threshold != null
-                   && aboveAnnotationThreshold == BELOW_THRESHOLD
-              &&  annotation.annotations[j].value > annotation.graphMin)
-          {
-            range =
-                ( annotation.annotations[j].value - annotation.graphMin ) /
-                (annotation.threshold.value - annotation.graphMin );
-          }
-          else
-          {
-            range = (annotation.annotations[j].value -
-                     annotation.graphMin) /
-                (annotation.graphMax - annotation.graphMin);
-          }
-
-
-          if (colourScheme != null)
-          {
-            currentColour = colourScheme.findColour(c, j);
-          }
-          else if (range != 0)
-          {
-            dr = rr * range   + r1;
-            dg = gg * range   + g1;
-            db = bb * range   + b1;
-
-            currentColour = new Color( (int) dr, (int) dg, (int) db);
-          }
-        }
-      }
-    }
-
-    if (conservationColouring)
-    {
-      currentColour = applyConservation(currentColour, j);
-    }
-
-    return currentColour;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.schemes;
+
+import java.awt.*;
+
+import jalview.datamodel.*;
+
+public class AnnotationColourGradient extends ResidueColourScheme
+{
+  public static int NO_THRESHOLD = -1;
+
+  public static int BELOW_THRESHOLD = 0;
+
+  public static int ABOVE_THRESHOLD = 1;
+
+  public AlignmentAnnotation annotation;
+
+  int aboveAnnotationThreshold = -1;
+
+  public boolean thresholdIsMinMax = false;
+
+  GraphLine annotationThreshold;
+
+  float r1, g1, b1, rr, gg, bb, dr, dg, db;
+
+  ColourSchemeI colourScheme;
+
+  public boolean predefinedColours = false;
+
+  /**
+   * Creates a new AnnotationColourGradient object.
+   */
+  public AnnotationColourGradient(AlignmentAnnotation annotation,
+          ColourSchemeI originalColour, int aboveThreshold)
+  {
+    if (originalColour instanceof AnnotationColourGradient)
+    {
+      colourScheme = ((AnnotationColourGradient) originalColour).colourScheme;
+    }
+    else
+    {
+      colourScheme = originalColour;
+    }
+
+    this.annotation = annotation;
+
+    aboveAnnotationThreshold = aboveThreshold;
+
+    if (aboveThreshold != NO_THRESHOLD && annotation.threshold != null)
+    {
+      annotationThreshold = annotation.threshold;
+    }
+  }
+
+  /**
+   * Creates a new AnnotationColourGradient object.
+   */
+  public AnnotationColourGradient(AlignmentAnnotation annotation,
+          Color minColour, Color maxColour, int aboveThreshold)
+  {
+    this.annotation = annotation;
+
+    aboveAnnotationThreshold = aboveThreshold;
+
+    if (aboveThreshold != NO_THRESHOLD && annotation.threshold != null)
+    {
+      annotationThreshold = annotation.threshold;
+    }
+
+    r1 = minColour.getRed();
+    g1 = minColour.getGreen();
+    b1 = minColour.getBlue();
+
+    rr = maxColour.getRed() - r1;
+    gg = maxColour.getGreen() - g1;
+    bb = maxColour.getBlue() - b1;
+  }
+
+  public String getAnnotation()
+  {
+    return annotation.label;
+  }
+
+  public int getAboveThreshold()
+  {
+    return aboveAnnotationThreshold;
+  }
+
+  public float getAnnotationThreshold()
+  {
+    if (annotationThreshold == null)
+    {
+      return 0;
+    }
+    else
+    {
+      return annotationThreshold.value;
+    }
+  }
+
+  public ColourSchemeI getBaseColour()
+  {
+    return colourScheme;
+  }
+
+  public Color getMinColour()
+  {
+    return new Color((int) r1, (int) g1, (int) b1);
+  }
+
+  public Color getMaxColour()
+  {
+    return new Color((int) (r1 + rr), (int) (g1 + gg), (int) (b1 + bb));
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param n
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public Color findColour(char c)
+  {
+    return Color.red;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param n
+   *                DOCUMENT ME!
+   * @param j
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public Color findColour(char c, int j)
+  {
+    Color currentColour = Color.white;
+
+    if ((threshold == 0) || aboveThreshold(c, j))
+    {
+      if (j < annotation.annotations.length
+              && annotation.annotations[j] != null
+              && !jalview.util.Comparison.isGap(c))
+      {
+
+        if (predefinedColours)
+        {
+          if (annotation.annotations[j].colour != null)
+            return annotation.annotations[j].colour;
+          else
+            return currentColour;
+        }
+
+        if (aboveAnnotationThreshold == NO_THRESHOLD
+                || (annotationThreshold != null
+                        && aboveAnnotationThreshold == ABOVE_THRESHOLD && annotation.annotations[j].value >= annotationThreshold.value)
+                || (annotationThreshold != null
+                        && aboveAnnotationThreshold == BELOW_THRESHOLD && annotation.annotations[j].value <= annotationThreshold.value))
+        {
+
+          float range = 1f;
+          if (thresholdIsMinMax
+                  && annotation.threshold != null
+                  && aboveAnnotationThreshold == ABOVE_THRESHOLD
+                  && annotation.annotations[j].value > annotation.threshold.value)
+          {
+            range = (annotation.annotations[j].value - annotation.threshold.value)
+                    / (annotation.graphMax - annotation.threshold.value);
+          }
+          else if (thresholdIsMinMax && annotation.threshold != null
+                  && aboveAnnotationThreshold == BELOW_THRESHOLD
+                  && annotation.annotations[j].value > annotation.graphMin)
+          {
+            range = (annotation.annotations[j].value - annotation.graphMin)
+                    / (annotation.threshold.value - annotation.graphMin);
+          }
+          else
+          {
+            range = (annotation.annotations[j].value - annotation.graphMin)
+                    / (annotation.graphMax - annotation.graphMin);
+          }
+
+          if (colourScheme != null)
+          {
+            currentColour = colourScheme.findColour(c, j);
+          }
+          else if (range != 0)
+          {
+            dr = rr * range + r1;
+            dg = gg * range + g1;
+            db = bb * range + b1;
+
+            currentColour = new Color((int) dr, (int) dg, (int) db);
+          }
+        }
+      }
+    }
+
+    if (conservationColouring)
+    {
+      currentColour = applyConservation(currentColour, j);
+    }
+
+    return currentColour;
+  }
+}
diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 0db55c0..57b1664 100755
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -1,94 +1,89 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.schemes;
-
-import java.awt.*;
-
-import jalview.analysis.*;
-
-public class Blosum62ColourScheme
-    extends ResidueColourScheme
-{
-  public Blosum62ColourScheme()
-  {
-    super();
-  }
-
-  public Color findColour(char res, int j)
-  {
-    if ('a' <= res && res <= 'z')
-    {
-      // TO UPPERCASE !!!
-      res -= ('a' - 'A');
-    }
-
-    if (consensus == null ||
-        j >= consensus.length ||
-        consensus[j] == null ||
-        (threshold != 0 && !aboveThreshold(res, j)))
-    {
-      return Color.white;
-    }
-
-    Color currentColour;
-
-    if (!jalview.util.Comparison.isGap(res))
-    {
-      String max = (String) consensus[j].get(AAFrequency.MAXRESIDUE);
-
-      if (max.indexOf(res) > -1)
-      {
-        currentColour = new Color(154, 154, 255);
-      }
-      else
-      {
-        int c = 0;
-        int max_aa = 0;
-        int n = max.length();
-
-        do
-        {
-          c += ResidueProperties.getBLOSUM62(
-              max.charAt(max_aa), res);
-        }
-        while (++max_aa < n);
-
-        if (c > 0)
-        {
-          currentColour = new Color(204, 204, 255);
-        }
-        else
-        {
-          currentColour = Color.white;
-        }
-      }
-
-      if (conservationColouring)
-      {
-        currentColour = applyConservation(currentColour, j);
-      }
-    }
-    else
-    {
-      return Color.white;
-    }
-
-    return currentColour;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.schemes;
+
+import java.awt.*;
+
+import jalview.analysis.*;
+
+public class Blosum62ColourScheme extends ResidueColourScheme
+{
+  public Blosum62ColourScheme()
+  {
+    super();
+  }
+
+  public Color findColour(char res, int j)
+  {
+    if ('a' <= res && res <= 'z')
+    {
+      // TO UPPERCASE !!!
+      res -= ('a' - 'A');
+    }
+
+    if (consensus == null || j >= consensus.length || consensus[j] == null
+            || (threshold != 0 && !aboveThreshold(res, j)))
+    {
+      return Color.white;
+    }
+
+    Color currentColour;
+
+    if (!jalview.util.Comparison.isGap(res))
+    {
+      String max = (String) consensus[j].get(AAFrequency.MAXRESIDUE);
+
+      if (max.indexOf(res) > -1)
+      {
+        currentColour = new Color(154, 154, 255);
+      }
+      else
+      {
+        int c = 0;
+        int max_aa = 0;
+        int n = max.length();
+
+        do
+        {
+          c += ResidueProperties.getBLOSUM62(max.charAt(max_aa), res);
+        } while (++max_aa < n);
+
+        if (c > 0)
+        {
+          currentColour = new Color(204, 204, 255);
+        }
+        else
+        {
+          currentColour = Color.white;
+        }
+      }
+
+      if (conservationColouring)
+      {
+        currentColour = applyConservation(currentColour, j);
+      }
+    }
+    else
+    {
+      return Color.white;
+    }
+
+    return currentColour;
+  }
+}
diff --git a/src/jalview/schemes/BuriedColourScheme.java b/src/jalview/schemes/BuriedColourScheme.java
index c973035..476e9f7 100755
--- a/src/jalview/schemes/BuriedColourScheme.java
+++ b/src/jalview/schemes/BuriedColourScheme.java
@@ -1,52 +1,52 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.schemes;
-
-import java.awt.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class BuriedColourScheme
-    extends ScoreColourScheme
-{
-  /**
-   * Creates a new BuriedColourScheme object.
-   */
-  public BuriedColourScheme()
-  {
-    super(ResidueProperties.buried, ResidueProperties.buriedmin,
-          ResidueProperties.buriedmax);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param c DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Color makeColour(float c)
-  {
-    return new Color(0, (float) (1.0 - c), c);
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.schemes;
+
+import java.awt.*;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class BuriedColourScheme extends ScoreColourScheme
+{
+  /**
+   * Creates a new BuriedColourScheme object.
+   */
+  public BuriedColourScheme()
+  {
+    super(ResidueProperties.buried, ResidueProperties.buriedmin,
+            ResidueProperties.buriedmax);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param c
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public Color makeColour(float c)
+  {
+    return new Color(0, (float) (1.0 - c), c);
+  }
+}
diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index bc2f9ea..5f9f8f0 100755
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -24,28 +24,38 @@ import java.awt.*;
 
 import jalview.datamodel.*;
 
-public class ClustalxColourScheme
-    extends ResidueColourScheme // implements IParameterizable
+public class ClustalxColourScheme extends ResidueColourScheme // implements
+                                                              // IParameterizable
 {
   public static Hashtable colhash = new Hashtable();
+
   Hashtable[] cons;
+
   int[][] cons2;
+
   ConsensusColour[] colours;
+
   ConsensusColour[] ResidueColour;
+
   int size;
+
   Consensus[] conses = new Consensus[32];
+
   Vector colourTable = new Vector();
-  private boolean includeGaps=true;
-  
+
+  private boolean includeGaps = true;
+
   {
-    colhash.put("RED", new Color( (float) 0.9, (float) 0.2, (float) 0.1));
-    colhash.put("BLUE", new Color( (float) 0.5, (float) 0.7, (float) 0.9));
-    colhash.put("GREEN", new Color( (float) 0.1, (float) 0.8, (float) 0.1));
-    colhash.put("ORANGE", new Color( (float) 0.9, (float) 0.6, (float) 0.3));
-    colhash.put("CYAN", new Color( (float) 0.1, (float) 0.7, (float) 0.7));
-    colhash.put("PINK", new Color( (float) 0.9, (float) 0.5, (float) 0.5));
-    colhash.put("MAGENTA", new Color( (float) 0.8, (float) 0.3, (float) 0.8));
-    colhash.put("YELLOW", new Color( (float) 0.8, (float) 0.8, (float) 0.0));
+    colhash.put("RED", new Color((float) 0.9, (float) 0.2, (float) 0.1));
+    colhash.put("BLUE", new Color((float) 0.5, (float) 0.7, (float) 0.9));
+    colhash.put("GREEN", new Color((float) 0.1, (float) 0.8, (float) 0.1));
+    colhash.put("ORANGE", new Color((float) 0.9, (float) 0.6, (float) 0.3));
+    colhash.put("CYAN", new Color((float) 0.1, (float) 0.7, (float) 0.7));
+    colhash.put("PINK", new Color((float) 0.9, (float) 0.5, (float) 0.5));
+    colhash
+            .put("MAGENTA",
+                    new Color((float) 0.8, (float) 0.3, (float) 0.8));
+    colhash.put("YELLOW", new Color((float) 0.8, (float) 0.8, (float) 0.0));
   }
 
   public ClustalxColourScheme(Vector seqs, int maxWidth)
@@ -56,7 +66,9 @@ public class ClustalxColourScheme
   public void resetClustalX(Vector seqs, int maxWidth)
   {
     cons2 = new int[maxWidth][24];
-    includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to get the current setting of the includeGaps param.
+    includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to
+                                    // get the current setting of the
+                                    // includeGaps param.
     int start = 0;
 
     // Initialize the array
@@ -75,13 +87,13 @@ public class ClustalxColourScheme
 
     while (j < seqs.size())
     {
-      seq = ( (SequenceI) seqs.elementAt(j)).getSequence();
+      seq = ((SequenceI) seqs.elementAt(j)).getSequence();
 
       int end_j = seq.length - 1;
 
       for (i = start; i <= end_j; i++)
       {
-        if ( (seq.length - 1) < i)
+        if ((seq.length - 1) < i)
         {
           res = 23;
         }
@@ -95,7 +107,7 @@ public class ClustalxColourScheme
 
       j++;
     }
-    
+
     this.size = seqs.size();
     makeColours();
   }
@@ -140,82 +152,82 @@ public class ClustalxColourScheme
     colours = new ConsensusColour[11];
 
     Consensus[] tmp8 = new Consensus[1];
-    tmp8[0] = conses[30]; //G
-    colours[7] = new ConsensusColour( (Color) colhash.get("ORANGE"), tmp8);
+    tmp8[0] = conses[30]; // G
+    colours[7] = new ConsensusColour((Color) colhash.get("ORANGE"), tmp8);
 
     Consensus[] tmp9 = new Consensus[1];
-    tmp9[0] = conses[31]; //P
-    colours[8] = new ConsensusColour( (Color) colhash.get("YELLOW"), tmp9);
+    tmp9[0] = conses[31]; // P
+    colours[8] = new ConsensusColour((Color) colhash.get("YELLOW"), tmp9);
 
     Consensus[] tmp10 = new Consensus[1];
-    tmp10[0] = conses[27]; //C
-    colours[9] = new ConsensusColour( (Color) colhash.get("PINK"), tmp8);
+    tmp10[0] = conses[27]; // C
+    colours[9] = new ConsensusColour((Color) colhash.get("PINK"), tmp8);
 
     Consensus[] tmp1 = new Consensus[14];
-    tmp1[0] = conses[0]; //%
-    tmp1[1] = conses[1]; //#
-    tmp1[2] = conses[26]; //A
-    tmp1[3] = conses[27]; //C
-    tmp1[4] = conses[11]; //F
-    tmp1[5] = conses[13]; //H
-    tmp1[6] = conses[14]; //I
-    tmp1[7] = conses[15]; //L
-    tmp1[8] = conses[16]; //M
-    tmp1[9] = conses[23]; //V
-    tmp1[10] = conses[24]; //W
-    tmp1[11] = conses[25]; //Y
-    tmp1[12] = conses[18]; //P
-    tmp1[13] = conses[19]; //p
-    colours[0] = new ConsensusColour( (Color) colhash.get("BLUE"), tmp1);
-
-    colours[10] = new ConsensusColour( (Color) colhash.get("CYAN"), tmp1);
+    tmp1[0] = conses[0]; // %
+    tmp1[1] = conses[1]; // #
+    tmp1[2] = conses[26]; // A
+    tmp1[3] = conses[27]; // C
+    tmp1[4] = conses[11]; // F
+    tmp1[5] = conses[13]; // H
+    tmp1[6] = conses[14]; // I
+    tmp1[7] = conses[15]; // L
+    tmp1[8] = conses[16]; // M
+    tmp1[9] = conses[23]; // V
+    tmp1[10] = conses[24]; // W
+    tmp1[11] = conses[25]; // Y
+    tmp1[12] = conses[18]; // P
+    tmp1[13] = conses[19]; // p
+    colours[0] = new ConsensusColour((Color) colhash.get("BLUE"), tmp1);
+
+    colours[10] = new ConsensusColour((Color) colhash.get("CYAN"), tmp1);
 
     Consensus[] tmp2 = new Consensus[5];
-    tmp2[0] = conses[8]; //t
-    tmp2[1] = conses[21]; //S
-    tmp2[2] = conses[22]; //T
-    tmp2[3] = conses[0]; //%
-    tmp2[4] = conses[1]; //#
-    colours[1] = new ConsensusColour( (Color) colhash.get("GREEN"), tmp2);
+    tmp2[0] = conses[8]; // t
+    tmp2[1] = conses[21]; // S
+    tmp2[2] = conses[22]; // T
+    tmp2[3] = conses[0]; // %
+    tmp2[4] = conses[1]; // #
+    colours[1] = new ConsensusColour((Color) colhash.get("GREEN"), tmp2);
 
     Consensus[] tmp3 = new Consensus[3];
 
-    tmp3[0] = conses[17]; //N
-    tmp3[1] = conses[29]; //D
-    tmp3[2] = conses[5]; //n
-    colours[2] = new ConsensusColour( (Color) colhash.get("GREEN"), tmp3);
+    tmp3[0] = conses[17]; // N
+    tmp3[1] = conses[29]; // D
+    tmp3[2] = conses[5]; // n
+    colours[2] = new ConsensusColour((Color) colhash.get("GREEN"), tmp3);
 
     Consensus[] tmp4 = new Consensus[6];
     tmp4[0] = conses[6]; // q = QE
-    tmp4[1] = conses[19]; //Q
-    tmp4[2] = conses[22]; //E
-    tmp4[3] = conses[3]; //+
-    tmp4[4] = conses[28]; //K
-    tmp4[5] = conses[20]; //R
-    colours[3] = new ConsensusColour( (Color) colhash.get("GREEN"), tmp4);
+    tmp4[1] = conses[19]; // Q
+    tmp4[2] = conses[22]; // E
+    tmp4[3] = conses[3]; // +
+    tmp4[4] = conses[28]; // K
+    tmp4[5] = conses[20]; // R
+    colours[3] = new ConsensusColour((Color) colhash.get("GREEN"), tmp4);
 
     Consensus[] tmp5 = new Consensus[4];
-    tmp5[0] = conses[3]; //+
-    tmp5[1] = conses[28]; //K
-    tmp5[2] = conses[20]; //R
-    tmp5[3] = conses[19]; //Q
-    colours[4] = new ConsensusColour( (Color) colhash.get("RED"), tmp5);
+    tmp5[0] = conses[3]; // +
+    tmp5[1] = conses[28]; // K
+    tmp5[2] = conses[20]; // R
+    tmp5[3] = conses[19]; // Q
+    colours[4] = new ConsensusColour((Color) colhash.get("RED"), tmp5);
 
     Consensus[] tmp6 = new Consensus[5];
-    tmp6[0] = conses[3]; //-
-    tmp6[1] = conses[29]; //D
-    tmp6[2] = conses[10]; //E
-    tmp6[3] = conses[6]; //q
-    tmp6[4] = conses[19]; //Q
-    colours[5] = new ConsensusColour( (Color) colhash.get("MAGENTA"), tmp6);
+    tmp6[0] = conses[3]; // -
+    tmp6[1] = conses[29]; // D
+    tmp6[2] = conses[10]; // E
+    tmp6[3] = conses[6]; // q
+    tmp6[4] = conses[19]; // Q
+    colours[5] = new ConsensusColour((Color) colhash.get("MAGENTA"), tmp6);
 
     Consensus[] tmp7 = new Consensus[5];
-    tmp7[0] = conses[3]; //-
-    tmp7[1] = conses[29]; //D
-    tmp7[2] = conses[10]; //E
-    tmp7[3] = conses[17]; //N
-    tmp7[4] = conses[2]; //DE
-    colours[6] = new ConsensusColour( (Color) colhash.get("MAGENTA"), tmp7);
+    tmp7[0] = conses[3]; // -
+    tmp7[1] = conses[29]; // D
+    tmp7[2] = conses[10]; // E
+    tmp7[3] = conses[17]; // N
+    tmp7[4] = conses[2]; // DE
+    colours[6] = new ConsensusColour((Color) colhash.get("MAGENTA"), tmp7);
 
     // Now attach the ConsensusColours to the residue letters
     ResidueColour = new ConsensusColour[20];
@@ -250,7 +262,8 @@ public class ClustalxColourScheme
   {
     Color currentColour;
 
-    if (cons2.length <= j || (includeGaps && threshold != 0 && !aboveThreshold(c, j)))
+    if (cons2.length <= j
+            || (includeGaps && threshold != 0 && !aboveThreshold(c, j)))
     {
       return Color.white;
     }
@@ -266,7 +279,8 @@ public class ClustalxColourScheme
 
     for (int k = 0; k < ResidueColour[i].conses.length; k++)
     {
-      if (ResidueColour[i].conses[k].isConserved(cons2, j, size, includeGaps))
+      if (ResidueColour[i].conses[k].isConserved(cons2, j, size,
+              includeGaps))
       {
         currentColour = ResidueColour[i].c;
       }
@@ -297,7 +311,8 @@ public class ClustalxColourScheme
   }
 
   /**
-   * @param includeGaps the includeGaps to set
+   * @param includeGaps
+   *                the includeGaps to set
    */
   protected void setIncludeGaps(boolean includeGaps)
   {
@@ -308,13 +323,14 @@ public class ClustalxColourScheme
 class ConsensusColour
 {
   Consensus[] conses;
+
   Color c;
 
   public ConsensusColour(Color c, Consensus[] conses)
   {
     this.conses = conses;
 
-    //    this.list = list;
+    // this.list = list;
     this.c = c;
   }
 }
diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index 96699c6..8deb556 100755
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -1,43 +1,43 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.schemes;
-
-import java.awt.*;
-
-public interface ColourSchemeI
-{
-  public Color findColour(char c);
-
-  public Color findColour(char c, int j);
-
-  public void setConsensus(java.util.Hashtable[] h);
-
-  public void setConservation(jalview.analysis.Conservation c);
-
-  public boolean conservationApplied();
-
-  public void setConservationInc(int i);
-
-  public int getConservationInc();
-
-  public int getThreshold();
-
-  public void setThreshold(int ct, boolean ignoreGaps);
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.schemes;
+
+import java.awt.*;
+
+public interface ColourSchemeI
+{
+  public Color findColour(char c);
+
+  public Color findColour(char c, int j);
+
+  public void setConsensus(java.util.Hashtable[] h);
+
+  public void setConservation(jalview.analysis.Conservation c);
+
+  public boolean conservationApplied();
+
+  public void setConservationInc(int i);
+
+  public int getConservationInc();
+
+  public int getThreshold();
+
+  public void setThreshold(int ct, boolean ignoreGaps);
+
+}
diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 2f81d13..162ba46 100755
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -69,9 +69,9 @@ public class ColourSchemeProperty
 
   /** No Colourscheme Index */
   public static final int NONE = 12;
+
   /** Undefined Colourscheme Index */
   public static final int UNDEFINED = 13;
-  
 
   /**
    * DOCUMENT ME!
diff --git a/src/jalview/schemes/Consensus.java b/src/jalview/schemes/Consensus.java
index 5cd7b52..c60b0b6 100755
--- a/src/jalview/schemes/Consensus.java
+++ b/src/jalview/schemes/Consensus.java
@@ -1,37 +1,39 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
 package jalview.schemes;
 
-////////////////////////////////////////////
+// //////////////////////////////////////////
 // This does nothing at all at the moment!!!!!!!!!!
 // AW 15th Dec 2004
-/////////////////////////////////////////
+// ///////////////////////////////////////
 public class Consensus
 {
   int[] mask;
+
   double threshold;
+
   String maskstr;
 
   public Consensus(String mask, double threshold)
   {
     // this.id = id;
-    //    this.mask = mask;
+    // this.mask = mask;
     this.maskstr = mask;
     setMask(mask);
     this.threshold = threshold;
@@ -41,8 +43,8 @@ public class Consensus
   {
     this.mask = setNums(s);
 
-    //   for (int i=0; i < mask.length; i++) {
-    //  System.out.println(mask[i] + " " + ResidueProperties.aa[mask[i]]);
+    // for (int i=0; i < mask.length; i++) {
+    // System.out.println(mask[i] + " " + ResidueProperties.aa[mask[i]]);
     // }
   }
 
@@ -54,21 +56,23 @@ public class Consensus
     return isConserved(cons2, col, size, true);
   }
 
-  public boolean isConserved(int[][] cons2, int col, int size, boolean includeGaps)
+  public boolean isConserved(int[][] cons2, int col, int size,
+          boolean includeGaps)
   {
     int tot = 0;
     if (!includeGaps)
     {
-      size -= cons2[col][cons2[col].length-1]; 
+      size -= cons2[col][cons2[col].length - 1];
     }
     for (int i = 0; i < mask.length; i++)
     {
       tot += cons2[col][mask[i]];
     }
 
-    if ( (double) tot > ( (threshold * size) / 100))
+    if ((double) tot > ((threshold * size) / 100))
     {
-        // System.out.println("True conserved "+tot+" from "+threshold+" out of "+size+" : "+maskstr);
+      // System.out.println("True conserved "+tot+" from "+threshold+" out of
+      // "+size+" : "+maskstr);
       return true;
     }
 
diff --git a/src/jalview/schemes/HelixColourScheme.java b/src/jalview/schemes/HelixColourScheme.java
index 7894965..4ab0431 100755
--- a/src/jalview/schemes/HelixColourScheme.java
+++ b/src/jalview/schemes/HelixColourScheme.java
@@ -1,36 +1,35 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.schemes;
-
-import java.awt.*;
-
-public class HelixColourScheme
-    extends ScoreColourScheme
-{
-  public HelixColourScheme()
-  {
-    super(ResidueProperties.helix, ResidueProperties.helixmin,
-          ResidueProperties.helixmax);
-  }
-
-  public Color makeColour(float c)
-  {
-    return new Color(c, (float) 1.0 - c, c);
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.schemes;
+
+import java.awt.*;
+
+public class HelixColourScheme extends ScoreColourScheme
+{
+  public HelixColourScheme()
+  {
+    super(ResidueProperties.helix, ResidueProperties.helixmin,
+            ResidueProperties.helixmax);
+  }
+
+  public Color makeColour(float c)
+  {
+    return new Color(c, (float) 1.0 - c, c);
+  }
+}
diff --git a/src/jalview/schemes/HydrophobicColourScheme.java b/src/jalview/schemes/HydrophobicColourScheme.java
index 9af174d..b934714 100755
--- a/src/jalview/schemes/HydrophobicColourScheme.java
+++ b/src/jalview/schemes/HydrophobicColourScheme.java
@@ -1,52 +1,52 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.schemes;
-
-import java.awt.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class HydrophobicColourScheme
-    extends ScoreColourScheme
-{
-  /**
-   * Creates a new HydrophobicColourScheme object.
-   */
-  public HydrophobicColourScheme()
-  {
-    super(ResidueProperties.hyd, ResidueProperties.hydmin,
-          ResidueProperties.hydmax);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param c DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Color makeColour(float c)
-  {
-    return new Color(c, (float) 0.0, (float) 1.0 - c);
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.schemes;
+
+import java.awt.*;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class HydrophobicColourScheme extends ScoreColourScheme
+{
+  /**
+   * Creates a new HydrophobicColourScheme object.
+   */
+  public HydrophobicColourScheme()
+  {
+    super(ResidueProperties.hyd, ResidueProperties.hydmin,
+            ResidueProperties.hydmax);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param c
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public Color makeColour(float c)
+  {
+    return new Color(c, (float) 0.0, (float) 1.0 - c);
+  }
+}
diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index 4e14202..39a0d6c 100755
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -1,87 +1,88 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.schemes;
-
-import java.awt.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class NucleotideColourScheme
-    extends ResidueColourScheme
-{
-  /**
-   * Creates a new NucleotideColourScheme object.
-   */
-  public NucleotideColourScheme()
-  {
-    super(ResidueProperties.nucleotide, 0);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param n DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Color findColour(char c)
-  {
-    // System.out.println("called"); log.debug
-    return colors[ResidueProperties.nucleotideIndex[c]];
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param n DOCUMENT ME!
-   * @param j DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Color findColour(char c, int j)
-  {
-    Color currentColour;
-    if ( (threshold == 0) || aboveThreshold(c, j))
-    {
-      try
-      {
-        currentColour = colors[ResidueProperties.nucleotideIndex[c]];
-      }
-      catch (Exception ex)
-      {
-        return Color.white;
-      }
-    }
-    else
-    {
-      return Color.white;
-    }
-
-    if (conservationColouring)
-    {
-      currentColour = applyConservation(currentColour, j);
-    }
-
-    return currentColour;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.schemes;
+
+import java.awt.*;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class NucleotideColourScheme extends ResidueColourScheme
+{
+  /**
+   * Creates a new NucleotideColourScheme object.
+   */
+  public NucleotideColourScheme()
+  {
+    super(ResidueProperties.nucleotide, 0);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param n
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public Color findColour(char c)
+  {
+    // System.out.println("called"); log.debug
+    return colors[ResidueProperties.nucleotideIndex[c]];
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param n
+   *                DOCUMENT ME!
+   * @param j
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public Color findColour(char c, int j)
+  {
+    Color currentColour;
+    if ((threshold == 0) || aboveThreshold(c, j))
+    {
+      try
+      {
+        currentColour = colors[ResidueProperties.nucleotideIndex[c]];
+      } catch (Exception ex)
+      {
+        return Color.white;
+      }
+    }
+    else
+    {
+      return Color.white;
+    }
+
+    if (conservationColouring)
+    {
+      currentColour = applyConservation(currentColour, j);
+    }
+
+    return currentColour;
+  }
+}
diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index e1dbf46..18fc6e4 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -1,94 +1,93 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.schemes;
-
-import java.awt.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-
-public class PIDColourScheme
-    extends ResidueColourScheme
-{
-  public Color[] pidColours;
-  public float[] thresholds;
-  SequenceGroup group;
-
-  public PIDColourScheme()
-  {
-    this.pidColours = ResidueProperties.pidColours;
-    this.thresholds = ResidueProperties.pidThresholds;
-  }
-
-  public Color findColour(char c, int j)
-  {
-    if ('a' <= c && c <= 'z')
-    {
-      c -= ('a' - 'A');
-    }
-
-    if (consensus == null
-        || j >= consensus.length
-        || consensus[j] == null)
-    {
-      return Color.white;
-    }
-
-    if ( (threshold != 0) && !aboveThreshold(c, j))
-    {
-      return Color.white;
-    }
-
-    Color currentColour = Color.white;
-
-    double sc = 0;
-
-    if (consensus.length <= j)
-    {
-      return Color.white;
-    }
-
-    if ( (Integer.parseInt(consensus[j].get(AAFrequency.MAXCOUNT).toString()) !=
-          -1) &&
-        consensus[j].contains(String.valueOf(c)))
-    {
-      sc = ( (Float) consensus[j].get(ignoreGaps)).floatValue();
-
-      if (!jalview.util.Comparison.isGap(c))
-      {
-        for (int i = 0; i < thresholds.length; i++)
-        {
-          if (sc > thresholds[i])
-          {
-            currentColour = pidColours[i];
-
-            break;
-          }
-        }
-      }
-    }
-
-    if (conservationColouring)
-    {
-      currentColour = applyConservation(currentColour, j);
-    }
-
-    return currentColour;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.schemes;
+
+import java.awt.*;
+
+import jalview.analysis.*;
+import jalview.datamodel.*;
+
+public class PIDColourScheme extends ResidueColourScheme
+{
+  public Color[] pidColours;
+
+  public float[] thresholds;
+
+  SequenceGroup group;
+
+  public PIDColourScheme()
+  {
+    this.pidColours = ResidueProperties.pidColours;
+    this.thresholds = ResidueProperties.pidThresholds;
+  }
+
+  public Color findColour(char c, int j)
+  {
+    if ('a' <= c && c <= 'z')
+    {
+      c -= ('a' - 'A');
+    }
+
+    if (consensus == null || j >= consensus.length || consensus[j] == null)
+    {
+      return Color.white;
+    }
+
+    if ((threshold != 0) && !aboveThreshold(c, j))
+    {
+      return Color.white;
+    }
+
+    Color currentColour = Color.white;
+
+    double sc = 0;
+
+    if (consensus.length <= j)
+    {
+      return Color.white;
+    }
+
+    if ((Integer
+            .parseInt(consensus[j].get(AAFrequency.MAXCOUNT).toString()) != -1)
+            && consensus[j].contains(String.valueOf(c)))
+    {
+      sc = ((Float) consensus[j].get(ignoreGaps)).floatValue();
+
+      if (!jalview.util.Comparison.isGap(c))
+      {
+        for (int i = 0; i < thresholds.length; i++)
+        {
+          if (sc > thresholds[i])
+          {
+            currentColour = pidColours[i];
+
+            break;
+          }
+        }
+      }
+    }
+
+    if (conservationColouring)
+    {
+      currentColour = applyConservation(currentColour, j);
+    }
+
+    return currentColour;
+  }
+}
diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index f43aa02..4990791 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -1,271 +1,281 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.schemes;
-
-import java.util.*;
-
-import java.awt.*;
-
-import jalview.analysis.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class ResidueColourScheme
-    implements ColourSchemeI
-{
-
-  boolean conservationColouring = false;
-
-  Color[] colors;
-  int threshold = 0;
-
-  /* Set when threshold colouring to either pid_gaps or pid_nogaps*/
-  protected String ignoreGaps = AAFrequency.PID_GAPS;
-
-  /** Consenus as a hashtable array */
-  Hashtable[] consensus;
-
-  /** Conservation string as a char array */
-  char[] conservation;
-  int conservationLength=0;
-
-  /** DOCUMENT ME!! */
-  int inc = 30;
-
-  /**
-   * Creates a new ResidueColourScheme object.
-   *
-   * @param colors DOCUMENT ME!
-   * @param threshold DOCUMENT ME!
-   */
-  public ResidueColourScheme(Color[] colours, int threshold)
-  {
-    this.colors = colours;
-    this.threshold = threshold;
-  }
-
-  /**
-   * Creates a new ResidueColourScheme object.
-   */
-  public ResidueColourScheme()
-  {
-  }
-
-  /**
-   * Find a colour without an index in a sequence
-   */
-  public Color findColour(char c)
-  {
-    return colors[ResidueProperties.aaIndex[c]];
-  }
-
-  public Color findColour(char c, int j)
-  {
-    Color currentColour;
-
-    if ( (threshold == 0) || aboveThreshold(c, j))
-    {
-      currentColour = colors[ResidueProperties.aaIndex[c]];
-    }
-    else
-    {
-      currentColour = Color.white;
-    }
-
-    if (conservationColouring)
-    {
-      currentColour = applyConservation(currentColour, j);
-    }
-
-    return currentColour;
-  }
-
-  /**
-   * Get the percentage threshold for this colour scheme
-   *
-   * @return Returns the percentage threshold
-   */
-  public int getThreshold()
-  {
-    return threshold;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param ct DOCUMENT ME!
-   */
-  public void setThreshold(int ct, boolean ignoreGaps)
-  {
-    threshold = ct;
-    if (ignoreGaps)
-    {
-      this.ignoreGaps = AAFrequency.PID_NOGAPS;
-    }
-    else
-    {
-      this.ignoreGaps = AAFrequency.PID_GAPS;
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param s DOCUMENT ME!
-   * @param j DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public boolean aboveThreshold(char c, int j)
-  {
-    if ('a' <= c && c <= 'z')
-    {
-      // TO UPPERCASE !!!
-      //Faster than toUpperCase
-      c -= ('a' - 'A');
-    }
-
-    if (consensus == null || consensus.length<j || consensus[j] == null)
-    {
-      return false;
-    }
-
-    if ( ( ( (Integer) consensus[j].get(AAFrequency.MAXCOUNT)).intValue() != -1) &&
-        consensus[j].contains(String.valueOf(c)))
-    {
-      if ( ( (Float) consensus[j].get(ignoreGaps)).floatValue() >= threshold)
-      {
-        return true;
-      }
-    }
-
-    return false;
-  }
-
-  public boolean conservationApplied()
-  {
-    return conservationColouring;
-  }
-
-  public void setConservationInc(int i)
-  {
-    inc = i;
-  }
-
-  public int getConservationInc()
-  {
-    return inc;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param consensus DOCUMENT ME!
-   */
-  public void setConsensus(Hashtable[] consensus)
-  {
-    if (consensus == null)
-    {
-      return;
-    }
-
-    this.consensus = consensus;
-  }
-
-  public void setConservation(Conservation cons)
-  {
-    if (cons == null)
-    {
-      conservationColouring = false;
-      conservation = null;
-    }
-    else
-    {
-      conservationColouring = true;
-      int i, iSize = cons.getConsSequence().getLength();
-      conservation = new char[iSize];
-      for (i = 0; i < iSize; i++)
-      {
-        conservation[i] = cons.getConsSequence().getCharAt(i);
-      }
-      conservationLength = conservation.length;
-    }
-
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param s DOCUMENT ME!
-   * @param i DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-
-  Color applyConservation(Color currentColour, int i)
-  {
-
-    if ((conservationLength>i) && (conservation[i] != '*') && (conservation[i] != '+'))
-    {
-      if ( jalview.util.Comparison.isGap(conservation[i]))
-      {
-        currentColour = Color.white;
-      }
-      else
-      {
-        float t = 11 - (conservation[i] - '0');
-        if (t == 0)
-        {
-          return Color.white;
-        }
-
-        int red = currentColour.getRed();
-        int green = currentColour.getGreen();
-        int blue = currentColour.getBlue();
-
-        int dr = 255 - red;
-        int dg = 255 - green;
-        int db = 255 - blue;
-
-        dr *= t / 10f;
-        dg *= t / 10f;
-        db *= t / 10f;
-
-        red += (inc / 20f) * dr;
-        green += (inc / 20f) * dg;
-        blue += (inc / 20f) * db;
-
-        if (red > 255 || green > 255 || blue > 255)
-        {
-          currentColour = Color.white;
-        }
-        else
-        {
-          currentColour = new Color(red, green, blue);
-        }
-      }
-    }
-    return currentColour;
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.schemes;
+
+import java.util.*;
+
+import java.awt.*;
+
+import jalview.analysis.*;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class ResidueColourScheme implements ColourSchemeI
+{
+
+  boolean conservationColouring = false;
+
+  Color[] colors;
+
+  int threshold = 0;
+
+  /* Set when threshold colouring to either pid_gaps or pid_nogaps */
+  protected String ignoreGaps = AAFrequency.PID_GAPS;
+
+  /** Consenus as a hashtable array */
+  Hashtable[] consensus;
+
+  /** Conservation string as a char array */
+  char[] conservation;
+
+  int conservationLength = 0;
+
+  /** DOCUMENT ME!! */
+  int inc = 30;
+
+  /**
+   * Creates a new ResidueColourScheme object.
+   * 
+   * @param colors
+   *                DOCUMENT ME!
+   * @param threshold
+   *                DOCUMENT ME!
+   */
+  public ResidueColourScheme(Color[] colours, int threshold)
+  {
+    this.colors = colours;
+    this.threshold = threshold;
+  }
+
+  /**
+   * Creates a new ResidueColourScheme object.
+   */
+  public ResidueColourScheme()
+  {
+  }
+
+  /**
+   * Find a colour without an index in a sequence
+   */
+  public Color findColour(char c)
+  {
+    return colors[ResidueProperties.aaIndex[c]];
+  }
+
+  public Color findColour(char c, int j)
+  {
+    Color currentColour;
+
+    if ((threshold == 0) || aboveThreshold(c, j))
+    {
+      currentColour = colors[ResidueProperties.aaIndex[c]];
+    }
+    else
+    {
+      currentColour = Color.white;
+    }
+
+    if (conservationColouring)
+    {
+      currentColour = applyConservation(currentColour, j);
+    }
+
+    return currentColour;
+  }
+
+  /**
+   * Get the percentage threshold for this colour scheme
+   * 
+   * @return Returns the percentage threshold
+   */
+  public int getThreshold()
+  {
+    return threshold;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param ct
+   *                DOCUMENT ME!
+   */
+  public void setThreshold(int ct, boolean ignoreGaps)
+  {
+    threshold = ct;
+    if (ignoreGaps)
+    {
+      this.ignoreGaps = AAFrequency.PID_NOGAPS;
+    }
+    else
+    {
+      this.ignoreGaps = AAFrequency.PID_GAPS;
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param s
+   *                DOCUMENT ME!
+   * @param j
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public boolean aboveThreshold(char c, int j)
+  {
+    if ('a' <= c && c <= 'z')
+    {
+      // TO UPPERCASE !!!
+      // Faster than toUpperCase
+      c -= ('a' - 'A');
+    }
+
+    if (consensus == null || consensus.length < j || consensus[j] == null)
+    {
+      return false;
+    }
+
+    if ((((Integer) consensus[j].get(AAFrequency.MAXCOUNT)).intValue() != -1)
+            && consensus[j].contains(String.valueOf(c)))
+    {
+      if (((Float) consensus[j].get(ignoreGaps)).floatValue() >= threshold)
+      {
+        return true;
+      }
+    }
+
+    return false;
+  }
+
+  public boolean conservationApplied()
+  {
+    return conservationColouring;
+  }
+
+  public void setConservationInc(int i)
+  {
+    inc = i;
+  }
+
+  public int getConservationInc()
+  {
+    return inc;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param consensus
+   *                DOCUMENT ME!
+   */
+  public void setConsensus(Hashtable[] consensus)
+  {
+    if (consensus == null)
+    {
+      return;
+    }
+
+    this.consensus = consensus;
+  }
+
+  public void setConservation(Conservation cons)
+  {
+    if (cons == null)
+    {
+      conservationColouring = false;
+      conservation = null;
+    }
+    else
+    {
+      conservationColouring = true;
+      int i, iSize = cons.getConsSequence().getLength();
+      conservation = new char[iSize];
+      for (i = 0; i < iSize; i++)
+      {
+        conservation[i] = cons.getConsSequence().getCharAt(i);
+      }
+      conservationLength = conservation.length;
+    }
+
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param s
+   *                DOCUMENT ME!
+   * @param i
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+
+  Color applyConservation(Color currentColour, int i)
+  {
+
+    if ((conservationLength > i) && (conservation[i] != '*')
+            && (conservation[i] != '+'))
+    {
+      if (jalview.util.Comparison.isGap(conservation[i]))
+      {
+        currentColour = Color.white;
+      }
+      else
+      {
+        float t = 11 - (conservation[i] - '0');
+        if (t == 0)
+        {
+          return Color.white;
+        }
+
+        int red = currentColour.getRed();
+        int green = currentColour.getGreen();
+        int blue = currentColour.getBlue();
+
+        int dr = 255 - red;
+        int dg = 255 - green;
+        int db = 255 - blue;
+
+        dr *= t / 10f;
+        dg *= t / 10f;
+        db *= t / 10f;
+
+        red += (inc / 20f) * dr;
+        green += (inc / 20f) * dg;
+        blue += (inc / 20f) * db;
+
+        if (red > 255 || green > 255 || blue > 255)
+        {
+          currentColour = Color.white;
+        }
+        else
+        {
+          currentColour = new Color(red, green, blue);
+        }
+      }
+    }
+    return currentColour;
+  }
+
+}
diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 98868d2..77938dd 100755
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -25,11 +25,16 @@ import java.awt.*;
 public class ResidueProperties
 {
   public static Hashtable scoreMatrices = new Hashtable();
-  //Stores residue codes/names and colours and other things
+
+  // Stores residue codes/names and colours and other things
   public static final int[] aaIndex; // aaHash version 2.1.1 and below
+
   public static final int[] nucleotideIndex;
+
   public static final Hashtable aa3Hash = new Hashtable();
+
   public static final Hashtable aa2Triplet = new Hashtable();
+
   public static final Hashtable nucleotideName = new Hashtable();
 
   static
@@ -87,7 +92,8 @@ public class ResidueProperties
     aaIndex['b'] = 20;
     aaIndex['z'] = 21;
     aaIndex['x'] = 22;
-    aaIndex['u'] = 22; // TODO: selenocystine triplet and codons needed. also extend subt. matrices
+    aaIndex['u'] = 22; // TODO: selenocystine triplet and codons needed. also
+                        // extend subt. matrices
   }
 
   static
@@ -146,9 +152,9 @@ public class ResidueProperties
     aa3Hash.put("ALA", new Integer(0));
     aa3Hash.put("ARG", new Integer(1));
     aa3Hash.put("ASN", new Integer(2));
-    aa3Hash.put("ASP", new Integer(3)); //D
+    aa3Hash.put("ASP", new Integer(3)); // D
     aa3Hash.put("CYS", new Integer(4));
-    aa3Hash.put("GLN", new Integer(5)); //Q
+    aa3Hash.put("GLN", new Integer(5)); // Q
     aa3Hash.put("GLU", new Integer(6)); // E
     aa3Hash.put("GLY", new Integer(7));
     aa3Hash.put("HIS", new Integer(8));
@@ -219,11 +225,11 @@ public class ResidueProperties
   }
 
   public static final String[] aa =
-      {
-      "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F",
-      "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "_", "*", ".", " "
-  };
+  { "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F",
+      "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "_", "*", ".", " " };
+
   public static final Color midBlue = new Color(100, 100, 255);
+
   public static final Vector scaleColours = new Vector();
 
   static
@@ -241,27 +247,26 @@ public class ResidueProperties
   }
 
   public static final Color[] taylor =
-      {
-      new Color(204, 255, 0), // A  Greenish-yellowy-yellow
-      new Color(0, 0, 255), // R  Blueish-bluey-blue
-      new Color(204, 0, 255), // N  Blueish-reddy-blue
-      new Color(255, 0, 0), // D  Reddish-reddy-red
-      new Color(255, 255, 0), // C  Yellowish-yellowy-yellow
-      new Color(255, 0, 204), // Q  Reddish-bluey-red
-      new Color(255, 0, 102), // E  Blueish-reddy-red
-      new Color(255, 153, 0), // G  Yellowy-reddy-yellow
-      new Color(0, 102, 255), // H  Greenish-bluey-blue
-      new Color(102, 255, 0), // I  Greenish-yellowy-green
-      new Color(51, 255, 0), // L  Yellowish-greeny-green
-      new Color(102, 0, 255), // K  Reddish-bluey-blue
-      new Color(0, 255, 0), // M  Greenish-greeny-green
-      new Color(0, 255, 102), // F  Blueish-greeny-green
-      new Color(255, 204, 0), // P  Reddish-yellowy-yellow
-      new Color(255, 51, 0), // S  Yellowish-reddy-red
-      new Color(255, 102, 0), // T  Reddish-yellowy-red
-      new Color(0, 204, 255), // W  Blueish-greeny-green
-      new Color(0, 255, 204), // Y  Greenish-bluey-green
-      new Color(153, 255, 0), // V  Yellowish-greeny-yellow
+  { new Color(204, 255, 0), // A Greenish-yellowy-yellow
+      new Color(0, 0, 255), // R Blueish-bluey-blue
+      new Color(204, 0, 255), // N Blueish-reddy-blue
+      new Color(255, 0, 0), // D Reddish-reddy-red
+      new Color(255, 255, 0), // C Yellowish-yellowy-yellow
+      new Color(255, 0, 204), // Q Reddish-bluey-red
+      new Color(255, 0, 102), // E Blueish-reddy-red
+      new Color(255, 153, 0), // G Yellowy-reddy-yellow
+      new Color(0, 102, 255), // H Greenish-bluey-blue
+      new Color(102, 255, 0), // I Greenish-yellowy-green
+      new Color(51, 255, 0), // L Yellowish-greeny-green
+      new Color(102, 0, 255), // K Reddish-bluey-blue
+      new Color(0, 255, 0), // M Greenish-greeny-green
+      new Color(0, 255, 102), // F Blueish-greeny-green
+      new Color(255, 204, 0), // P Reddish-yellowy-yellow
+      new Color(255, 51, 0), // S Yellowish-reddy-red
+      new Color(255, 102, 0), // T Reddish-yellowy-red
+      new Color(0, 204, 255), // W Blueish-greeny-green
+      new Color(0, 255, 204), // Y Greenish-bluey-green
+      new Color(153, 255, 0), // V Yellowish-greeny-yellow
       Color.white, // B
       Color.white, // Z
       Color.white, // X
@@ -269,18 +274,18 @@ public class ResidueProperties
       Color.white, // *
       Color.white // .
   };
+
   public static final Color[] nucleotide =
-      {
-      new Color(100, 247, 63), // A
+  { new Color(100, 247, 63), // A
       new Color(255, 179, 64), // C
       new Color(235, 65, 60), // G
       new Color(60, 136, 238), // T
       new Color(60, 136, 238) // U
   };
+
   // Zappo
   public static final Color[] zappo =
-      {
-      Color.pink, // A
+  { Color.pink, // A
       midBlue, // R
       Color.green, // N
       Color.red, // D
@@ -311,272 +316,181 @@ public class ResidueProperties
 
   // Dunno where I got these numbers from
   public static final double[] hyd2 =
-      {
-      0.62, //A
-      0.29, //R
-      -0.90, //N
-      -0.74, //D
-      1.19, //C
-      0.48, //Q
-      -0.40, //E
-      1.38, //G
-      -1.50, //H
-      1.06, //I
-      0.64, //L
-      -0.78, //K
-      0.12, //M
-      -0.85, //F
-      -2.53, //P
-      -0.18, //S
-      -0.05, //T
-      1.08, //W
-      0.81, //Y
-      0.0, //V
-      0.26, //B
-      0.0, //Z
-      0.0 //X
+  { 0.62, // A
+      0.29, // R
+      -0.90, // N
+      -0.74, // D
+      1.19, // C
+      0.48, // Q
+      -0.40, // E
+      1.38, // G
+      -1.50, // H
+      1.06, // I
+      0.64, // L
+      -0.78, // K
+      0.12, // M
+      -0.85, // F
+      -2.53, // P
+      -0.18, // S
+      -0.05, // T
+      1.08, // W
+      0.81, // Y
+      0.0, // V
+      0.26, // B
+      0.0, // Z
+      0.0 // X
   };
+
   public static final double[] helix =
-      {
-      1.42, 0.98, 0.67, 1.01, 0.70, 1.11, 1.51, 0.57, 1.00, 1.08, 1.21, 1.16,
-      1.45, 1.13, 0.57, 0.77, 0.83, 1.08, 0.69, 1.06, 0.84, 1.31, 1.00, 0.0
-  };
+  { 1.42, 0.98, 0.67, 1.01, 0.70, 1.11, 1.51, 0.57, 1.00, 1.08, 1.21, 1.16,
+      1.45, 1.13, 0.57, 0.77, 0.83, 1.08, 0.69, 1.06, 0.84, 1.31, 1.00, 0.0 };
+
   public static final double helixmin = 0.57;
+
   public static final double helixmax = 1.51;
+
   public static final double[] strand =
-      {
-      0.83, 0.93, 0.89, 0.54, 1.19, 1.10, 0.37, 0.75, 0.87, 1.60, 1.30, 0.74,
-      1.05, 1.38, 0.55, 0.75, 1.19, 1.37, 1.47, 1.70, 0.72, 0.74, 1.0, 0.0
-  };
+  { 0.83, 0.93, 0.89, 0.54, 1.19, 1.10, 0.37, 0.75, 0.87, 1.60, 1.30, 0.74,
+      1.05, 1.38, 0.55, 0.75, 1.19, 1.37, 1.47, 1.70, 0.72, 0.74, 1.0, 0.0 };
+
   public static final double strandmin = 0.37;
+
   public static final double strandmax = 1.7;
+
   public static final double[] turn =
-      {
-      0.66, 0.95, 1.56, 1.46, 1.19, 0.98, 0.74, 1.56, 0.95, 0.47, 0.59, 1.01,
-      0.60, 0.60, 1.52, 1.43, 0.96, 0.96, 1.14, 0.50, 1.51, 0.86, 1.00, 0, 0
-  };
+  { 0.66, 0.95, 1.56, 1.46, 1.19, 0.98, 0.74, 1.56, 0.95, 0.47, 0.59, 1.01,
+      0.60, 0.60, 1.52, 1.43, 0.96, 0.96, 1.14, 0.50, 1.51, 0.86, 1.00, 0,
+      0 };
+
   public static final double turnmin = 0.47;
+
   public static final double turnmax = 1.56;
+
   public static final double[] buried =
-      {
-      1.7, 0.1, 0.4, 0.4, 4.6, 0.3, 0.3, 1.8, 0.8, 3.1, 2.4, 0.05, 1.9, 2.2,
-      0.6, 0.8, 0.7, 1.6, 0.5, 2.9, 0.4, 0.3, 1.358, 0.00
-  };
+  { 1.7, 0.1, 0.4, 0.4, 4.6, 0.3, 0.3, 1.8, 0.8, 3.1, 2.4, 0.05, 1.9, 2.2,
+      0.6, 0.8, 0.7, 1.6, 0.5, 2.9, 0.4, 0.3, 1.358, 0.00 };
+
   public static final double buriedmin = 0.05;
+
   public static final double buriedmax = 4.6;
 
   // This is hydropathy index
   // Kyte, J., and Doolittle, R.F., J. Mol. Biol.
   // 1157, 105-132, 1982
   public static final double[] hyd =
-      {
-      1.8, -4.5, -3.5, -3.5, 2.5, -3.5, -3.5, -0.4, -3.2, 4.5, 3.8, -3.9, 1.9,
-      2.8, -1.6, -0.8, -0.7, -0.9, -1.3, 4.2, -3.5, -3.5, -0.49, 0.0
-  };
+  { 1.8, -4.5, -3.5, -3.5, 2.5, -3.5, -3.5, -0.4, -3.2, 4.5, 3.8, -3.9,
+      1.9, 2.8, -1.6, -0.8, -0.7, -0.9, -1.3, 4.2, -3.5, -3.5, -0.49, 0.0 };
+
   public static final double hydmax = 4.5;
+
   public static final double hydmin = -3.9;
 
-  //public static final double hydmax = 1.38;
-  //public static final double hydmin = -2.53;
+  // public static final double hydmax = 1.38;
+  // public static final double hydmin = -2.53;
   private static final int[][] BLOSUM62 =
-      {
-      {
-      4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3,
-      -2, 0, -2, -1, 0, -4
-  },
-      {
-      -1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3, -2,
-      -3, -1, 0, -1, -4
-  },
-      {
-      -2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2, -3,
-      3, 0, -1, -4
-  },
-      {
-      -2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4,
-      -3, -3, 4, 1, -1, -4
-  },
-      {
-      0, 3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2,
-      -2, -1, -3, -3, -2, -4
-  },
-      {
-      -1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1,
-      -2, 0, 3, -1, -4
-  },
-      {
-      -1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2,
-      -2, 1, 4, -1, -4
-  },
-      {
-      0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2,
-      -3, -3, -1, -2, -1, -4
-  },
-      {
-      -2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2, 2,
-      -3, 0, 0, -1, -4
-  },
-      {
-      -1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3,
-      -1, 3, -3, -3, -1, -4
-  },
-      {
-      -1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2,
-      -1, 1, -4, -3, -1, -4
-  },
-      {
-      -1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3, -2,
-      -2, 0, 1, -1, -4
-  },
-      {
-      -1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1,
-      -1, 1, -3, -1, -1, -4
-  },
-      {
-      -2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1, 3,
-      -1, -3, -3, -1, -4
-  },
-      {
-      -1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1,
-      -4, -3, -2, -2, -1, -2, -4
-  },
-      {
-      1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2,
-      -2, 0, 0, 0, -4
-  },
-      {
-      0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2,
-      -2, 0, -1, -1, 0, -4
-  },
-      {
-      -3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2,
-      11, 2, -3, -4, -3, -2, -4
-  },
-      {
-      -2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2,
-      7, -1, -3, -2, -1, -4
-  },
-      {
-      0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3,
-      -1, 4, -3, -2, -1, -4
-  },
-      {
-      -2, -1, 3, 4, -3, 0, 1, -1, 0, -3, -4, 0, -3, -3, -2, 0, -1, -4, -3,
-      -3, 4, 1, -1, -4
-  },
-      {
-      -1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3, 1, -1, -3, -1, 0, -1, -3, -2,
-      -2, 1, 4, -1, -4
-  },
-      {
-      0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, 0, -2,
-      -1, -1, -1, -1, -1, -4
-  },
-      {
-      -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4,
-      -4, -4, -4, -4, -4, -4, 1
-  },
-  };
+  {
+      { 4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3,
+          -2, 0, -2, -1, 0, -4 },
+      { -1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3,
+          -2, -3, -1, 0, -1, -4 },
+      { -2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2,
+          -3, 3, 0, -1, -4 },
+      { -2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4,
+          -3, -3, 4, 1, -1, -4 },
+      { 0, 3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1,
+          -2, -2, -1, -3, -3, -2, -4 },
+      { -1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1,
+          -2, 0, 3, -1, -4 },
+      { -1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2,
+          -2, 1, 4, -1, -4 },
+      { 0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2,
+          -3, -3, -1, -2, -1, -4 },
+      { -2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2,
+          2, -3, 0, 0, -1, -4 },
+      { -1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3,
+          -1, 3, -3, -3, -1, -4 },
+      { -1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2,
+          -1, 1, -4, -3, -1, -4 },
+      { -1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3,
+          -2, -2, 0, 1, -1, -4 },
+      { -1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1,
+          -1, 1, -3, -1, -1, -4 },
+      { -2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1,
+          3, -1, -3, -3, -1, -4 },
+      { -1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1,
+          -4, -3, -2, -2, -1, -2, -4 },
+      { 1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2,
+          -2, 0, 0, 0, -4 },
+      { 0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2,
+          -2, 0, -1, -1, 0, -4 },
+      { -3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2,
+          11, 2, -3, -4, -3, -2, -4 },
+      { -2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2,
+          2, 7, -1, -3, -2, -1, -4 },
+      { 0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3,
+          -1, 4, -3, -2, -1, -4 },
+      { -2, -1, 3, 4, -3, 0, 1, -1, 0, -3, -4, 0, -3, -3, -2, 0, -1, -4,
+          -3, -3, 4, 1, -1, -4 },
+      { -1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3, 1, -1, -3, -1, 0, -1, -3, -2,
+          -2, 1, 4, -1, -4 },
+      { 0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, 0,
+          -2, -1, -1, -1, -1, -1, -4 },
+      { -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4,
+          -4, -4, -4, -4, -4, -4, 1 }, };
+
   static final int[][] PAM250 =
-      {
-      {
-      2, -2, 0, 0, -2, 0, 0, 1, -1, -1, -2, -1, -1, -3, 1, 1, 1, -6, -3, 0,
-      0, 0, 0, -8
-  },
-      {
-      -2, 6, 0, -1, -4, 1, -1, -3, 2, -2, -3, 3, 0, -4, 0, 0, -1, 2, -4,
-      -2, -1, 0, -1, -8
-  },
-      {
-      0, 0, 2, 2, -4, 1, 1, 0, 2, -2, -3, 1, -2, -3, 0, 1, 0, -4, -2, -2,
-      2, 1, 0, -8
-  },
-      {
-      0, -1, 2, 4, -5, 2, 3, 1, 1, -2, -4, 0, -3, -6, -1, 0, 0, -7, -4, -2,
-      3, 3, -1, -8
-  },
-      {
-      -2, -4, -4, -5, 12, -5, -5, -3, -3, -2, -6, -5, -5, -4, -3, 0, -2,
-      -8, 0, -2, -4, -5, -3, -8
-  },
-      {
-      0, 1, 1, 2, -5, 4, 2, -1, 3, -2, -2, 1, -1, -5, 0, -1, -1, -5, -4,
-      -2, 1, 3, -1, -8
-  },
-      {
-      0, -1, 1, 3, -5, 2, 4, 0, 1, -2, -3, 0, -2, -5, -1, 0, 0, -7, -4, -2,
-      3, 3, -1, -8
-  },
-      {
-      1, -3, 0, 1, -3, -1, 0, 5, -2, -3, -4, -2, -3, -5, 0, 1, 0, -7, -5,
-      -1, 0, 0, -1, -8
-  },
-      {
-      -1, 2, 2, 1, -3, 3, 1, -2, 6, -2, -2, 0, -2, -2, 0, -1, -1, -3, 0,
-      -2, 1, 2, -1, -8
-  },
-      {
-      -1, -2, -2, -2, -2, -2, -2, -3, -2, 5, 2, -2, 2, 1, -2, -1, 0, -5,
-      -1, 4, -2, -2, -1, -8
-  },
-      {
-      -2, -3, -3, -4, -6, -2, -3, -4, -2, 2, 6, -3, 4, 2, -3, -3, -2, -2,
-      -1, 2, -3, -3, -1, -8
-  },
-      {
-      -1, 3, 1, 0, -5, 1, 0, -2, 0, -2, -3, 5, 0, -5, -1, 0, 0, -3, -4, -2,
-      1, 0, -1, -8
-  },
-      {
-      -1, 0, -2, -3, -5, -1, -2, -3, -2, 2, 4, 0, 6, 0, -2, -2, -1, -4, -2,
-      2, -2, -2, -1, -8
-  },
-      {
-      -3, -4, -3, -6, -4, -5, -5, -5, -2, 1, 2, -5, 0, 9, -5, -3, -3, 0, 7,
-      -1, -4, -5, -2, -8
-  },
-      {
-      1, 0, 0, -1, -3, 0, -1, 0, 0, -2, -3, -1, -2, -5, 6, 1, 0, -6, -5,
-      -1, -1, 0, -1, -8
-  },
-      {
-      1, 0, 1, 0, 0, -1, 0, 1, -1, -1, -3, 0, -2, -3, 1, 2, 1, -2, -3, -1,
-      0, 0, 0, -8
-  },
-      {
-      1, -1, 0, 0, -2, -1, 0, 0, -1, 0, -2, 0, -1, -3, 0, 1, 3, -5, -3, 0,
-      0, -1, 0, -8
-  },
-      {
-      -6, 2, -4, -7, -8, -5, -7, -7, -3, -5, -2, -3, -4, 0, -6, -2, -5, 17,
-      0, -6, -5, -6, -4, -8
-  },
-      {
-      -3, -4, -2, -4, 0, -4, -4, -5, 0, -1, -1, -4, -2, 7, -5, -3, -3, 0,
-      10, -2, -3, -4, -2, -8
-  },
-      {
-      0, -2, -2, -2, -2, -2, -2, -1, -2, 4, 2, -2, 2, -1, -1, -1, 0, -6,
-      -2, 4, -2, -2, -1, -8
-  },
-      {
-      0, -1, 2, 3, -4, 1, 3, 0, 1, -2, -3, 1, -2, -4, -1, 0, 0, -5, -3, -2,
-      3, 2, -1, -8
-  },
-      {
-      0, 0, 1, 3, -5, 3, 3, 0, 2, -2, -3, 0, -2, -5, 0, 0, -1, -6, -4, -2,
-      2, 3, -1, -8
-  },
-      {
-      0, -1, 0, -1, -3, -1, -1, -1, -1, -1, -1, -1, -1, -2, -1, 0, 0, -4,
-      -2, -1, -1, -1, -1, -8
-  },
-      {
-      -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8,
-      -8, -8, -8, -8, -8, -8, 1
-  },
-  };
-  public static final Hashtable ssHash = new Hashtable(); // stores the number value of the aa
+  {
+      { 2, -2, 0, 0, -2, 0, 0, 1, -1, -1, -2, -1, -1, -3, 1, 1, 1, -6, -3,
+          0, 0, 0, 0, -8 },
+      { -2, 6, 0, -1, -4, 1, -1, -3, 2, -2, -3, 3, 0, -4, 0, 0, -1, 2, -4,
+          -2, -1, 0, -1, -8 },
+      { 0, 0, 2, 2, -4, 1, 1, 0, 2, -2, -3, 1, -2, -3, 0, 1, 0, -4, -2, -2,
+          2, 1, 0, -8 },
+      { 0, -1, 2, 4, -5, 2, 3, 1, 1, -2, -4, 0, -3, -6, -1, 0, 0, -7, -4,
+          -2, 3, 3, -1, -8 },
+      { -2, -4, -4, -5, 12, -5, -5, -3, -3, -2, -6, -5, -5, -4, -3, 0, -2,
+          -8, 0, -2, -4, -5, -3, -8 },
+      { 0, 1, 1, 2, -5, 4, 2, -1, 3, -2, -2, 1, -1, -5, 0, -1, -1, -5, -4,
+          -2, 1, 3, -1, -8 },
+      { 0, -1, 1, 3, -5, 2, 4, 0, 1, -2, -3, 0, -2, -5, -1, 0, 0, -7, -4,
+          -2, 3, 3, -1, -8 },
+      { 1, -3, 0, 1, -3, -1, 0, 5, -2, -3, -4, -2, -3, -5, 0, 1, 0, -7, -5,
+          -1, 0, 0, -1, -8 },
+      { -1, 2, 2, 1, -3, 3, 1, -2, 6, -2, -2, 0, -2, -2, 0, -1, -1, -3, 0,
+          -2, 1, 2, -1, -8 },
+      { -1, -2, -2, -2, -2, -2, -2, -3, -2, 5, 2, -2, 2, 1, -2, -1, 0, -5,
+          -1, 4, -2, -2, -1, -8 },
+      { -2, -3, -3, -4, -6, -2, -3, -4, -2, 2, 6, -3, 4, 2, -3, -3, -2, -2,
+          -1, 2, -3, -3, -1, -8 },
+      { -1, 3, 1, 0, -5, 1, 0, -2, 0, -2, -3, 5, 0, -5, -1, 0, 0, -3, -4,
+          -2, 1, 0, -1, -8 },
+      { -1, 0, -2, -3, -5, -1, -2, -3, -2, 2, 4, 0, 6, 0, -2, -2, -1, -4,
+          -2, 2, -2, -2, -1, -8 },
+      { -3, -4, -3, -6, -4, -5, -5, -5, -2, 1, 2, -5, 0, 9, -5, -3, -3, 0,
+          7, -1, -4, -5, -2, -8 },
+      { 1, 0, 0, -1, -3, 0, -1, 0, 0, -2, -3, -1, -2, -5, 6, 1, 0, -6, -5,
+          -1, -1, 0, -1, -8 },
+      { 1, 0, 1, 0, 0, -1, 0, 1, -1, -1, -3, 0, -2, -3, 1, 2, 1, -2, -3,
+          -1, 0, 0, 0, -8 },
+      { 1, -1, 0, 0, -2, -1, 0, 0, -1, 0, -2, 0, -1, -3, 0, 1, 3, -5, -3,
+          0, 0, -1, 0, -8 },
+      { -6, 2, -4, -7, -8, -5, -7, -7, -3, -5, -2, -3, -4, 0, -6, -2, -5,
+          17, 0, -6, -5, -6, -4, -8 },
+      { -3, -4, -2, -4, 0, -4, -4, -5, 0, -1, -1, -4, -2, 7, -5, -3, -3, 0,
+          10, -2, -3, -4, -2, -8 },
+      { 0, -2, -2, -2, -2, -2, -2, -1, -2, 4, 2, -2, 2, -1, -1, -1, 0, -6,
+          -2, 4, -2, -2, -1, -8 },
+      { 0, -1, 2, 3, -4, 1, 3, 0, 1, -2, -3, 1, -2, -4, -1, 0, 0, -5, -3,
+          -2, 3, 2, -1, -8 },
+      { 0, 0, 1, 3, -5, 3, 3, 0, 2, -2, -3, 0, -2, -5, 0, 0, -1, -6, -4,
+          -2, 2, 3, -1, -8 },
+      { 0, -1, 0, -1, -3, -1, -1, -1, -1, -1, -1, -1, -1, -2, -1, 0, 0, -4,
+          -2, -1, -1, -1, -1, -8 },
+      { -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8,
+          -8, -8, -8, -8, -8, -8, 1 }, };
+
+  public static final Hashtable ssHash = new Hashtable(); // stores the number
+                                                          // value of the aa
 
   static
   {
@@ -592,17 +506,12 @@ public class ResidueProperties
   }
 
   static final int[][] DNA =
-      {
-      {
-      5, -4, -4, -4, 1}, // C
-      {
-      -4, 5, -4, -4, 1}, // T
-      {
-      -4, -4, 5, -4, 1}, // A
-      {
-      -4, -4, -4, 5, 1}, // G
-      {
-      1, 1, 1, 1, 1}, // -
+  {
+  { 5, -4, -4, -4, 1 }, // C
+      { -4, 5, -4, -4, 1 }, // T
+      { -4, -4, 5, -4, 1 }, // A
+      { -4, -4, -4, 5, 1 }, // G
+      { 1, 1, 1, 1, 1 }, // -
   };
   /**
    * register matrices in list
@@ -615,35 +524,55 @@ public class ResidueProperties
   }
 
   public static final Color[] pidColours =
-      {
-      midBlue, new Color(153, 153, 255),
-      //    Color.lightGray,
-      new Color(204, 204, 255),
-  };
+  { midBlue, new Color(153, 153, 255),
+  // Color.lightGray,
+      new Color(204, 204, 255), };
+
   public static final float[] pidThresholds =
-      {
-      80, 60, 40, };
+  { 80, 60, 40, };
+
   public static Hashtable codonHash = new Hashtable();
+
   public static Vector Lys = new Vector();
+
   public static Vector Asn = new Vector();
+
   public static Vector Gln = new Vector();
+
   public static Vector His = new Vector();
+
   public static Vector Glu = new Vector();
+
   public static Vector Asp = new Vector();
+
   public static Vector Tyr = new Vector();
+
   public static Vector Thr = new Vector();
+
   public static Vector Pro = new Vector();
+
   public static Vector Ala = new Vector();
+
   public static Vector Ser = new Vector();
+
   public static Vector Arg = new Vector();
+
   public static Vector Gly = new Vector();
+
   public static Vector Trp = new Vector();
+
   public static Vector Cys = new Vector();
+
   public static Vector Ile = new Vector();
+
   public static Vector Met = new Vector();
+
   public static Vector Leu = new Vector();
+
   public static Vector Val = new Vector();
+
   public static Vector Phe = new Vector();
+
   public static Vector STOP = new Vector();
 
   static
@@ -843,17 +772,27 @@ public class ResidueProperties
     Phe.addElement("TTT");
   }
 
-  //Stores residue codes/names and colours and other things
+  // Stores residue codes/names and colours and other things
   public static Hashtable propHash = new Hashtable();
+
   public static Hashtable hydrophobic = new Hashtable();
+
   public static Hashtable polar = new Hashtable();
+
   public static Hashtable small = new Hashtable();
+
   public static Hashtable positive = new Hashtable();
+
   public static Hashtable negative = new Hashtable();
+
   public static Hashtable charged = new Hashtable();
+
   public static Hashtable aromatic = new Hashtable();
+
   public static Hashtable aliphatic = new Hashtable();
+
   public static Hashtable tiny = new Hashtable();
+
   public static Hashtable proline = new Hashtable();
 
   static
@@ -1181,10 +1120,9 @@ public class ResidueProperties
       int b = aaIndex[c2];
 
       pog = ResidueProperties.BLOSUM62[a][b];
-    }
-    catch (Exception e)
+    } catch (Exception e)
     {
-      //System.out.println("Unknown residue in " + A1 + " " + A2);
+      // System.out.println("Unknown residue in " + A1 + " " + A2);
     }
 
     return pog;
@@ -1230,6 +1168,7 @@ public class ResidueProperties
 
   /**
    * get a ScoreMatrix based on its string name
+   * 
    * @param pwtype
    * @return matrix in scoreMatrices with key pwtype or null
    */
@@ -1254,7 +1193,8 @@ public class ResidueProperties
   }
 
   public static Hashtable toDssp3State;
-  static {
+  static
+  {
     toDssp3State = new Hashtable();
     toDssp3State.put("H", "H");
     toDssp3State.put("E", "E");
@@ -1266,35 +1206,40 @@ public class ResidueProperties
     toDssp3State.put("I", "H");
     toDssp3State.put("X", " ");
   }
+
   /**
    * translate from other dssp secondary structure alphabets to 3-state
+   * 
    * @param ssstring
    * @return ssstring as a three-state secondary structure assignment.
    */
   public static String getDssp3state(String ssstring)
   {
-    if (ssstring==null)
+    if (ssstring == null)
     {
       return null;
     }
     StringBuffer ss = new StringBuffer();
-    for (int i=0; i<ssstring.length(); i++)
+    for (int i = 0; i < ssstring.length(); i++)
     {
-      String ssc = ssstring.substring(i, i+1);
+      String ssc = ssstring.substring(i, i + 1);
       if (toDssp3State.containsKey(ssc))
       {
         ss.append((String) toDssp3State.get(ssc));
-      } else {
+      }
+      else
+      {
         ss.append(" ");
       }
     }
     return ss.toString();
   }
+
   // main method generates perl representation of residue property hash
-  /// cut here
+  // / cut here
   public static void main(String[] args)
   {
-    Hashtable aa = new Hashtable(); 
+    Hashtable aa = new Hashtable();
     System.out.println("my %aa = {");
     // invert property hashes
     Enumeration prop = propHash.keys();
@@ -1307,13 +1252,13 @@ public class ResidueProperties
       {
         String rname = (String) res.nextElement();
         Vector aprops = (Vector) aa.get(rname);
-        if (aprops==null)
+        if (aprops == null)
         {
           aprops = new Vector();
           aa.put(rname, aprops);
         }
         Integer hasprop = (Integer) phash.get(rname);
-        if (hasprop.intValue()==1)
+        if (hasprop.intValue() == 1)
         {
           aprops.addElement(pname);
         }
@@ -1323,18 +1268,18 @@ public class ResidueProperties
     while (res.hasMoreElements())
     {
       String rname = (String) res.nextElement();
-      
-      System.out.print("'"+rname+"' => [");
+
+      System.out.print("'" + rname + "' => [");
       Enumeration props = ((Vector) aa.get(rname)).elements();
       while (props.hasMoreElements())
       {
-        System.out.print("'"+(String)props.nextElement()+"'");
+        System.out.print("'" + (String) props.nextElement() + "'");
         if (props.hasMoreElements())
         {
           System.out.println(", ");
         }
       }
-      System.out.println("]"+(res.hasMoreElements() ? "," : ""));
+      System.out.println("]" + (res.hasMoreElements() ? "," : ""));
     }
     System.out.println("};");
   }
diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index 134ed4c..743df65 100755
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -1,121 +1,126 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.schemes;
-
-import java.awt.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class ScoreColourScheme
-    extends ResidueColourScheme
-{
-  /** DOCUMENT ME!! */
-  public double min;
-
-  /** DOCUMENT ME!! */
-  public double max;
-
-  /** DOCUMENT ME!! */
-  public double[] scores;
-
-  /**
-   * Creates a new ScoreColourScheme object.
-   *
-   * @param scores DOCUMENT ME!
-   * @param min DOCUMENT ME!
-   * @param max DOCUMENT ME!
-   */
-  public ScoreColourScheme(double[] scores, double min, double max)
-  {
-    super();
-
-    this.scores = scores;
-    this.min = min;
-    this.max = max;
-
-    // Make colours in constructor
-    // Why wasn't this done earlier?
-    int i, iSize = scores.length;
-    colors = new Color[scores.length];
-    for (i = 0; i < iSize; i++)
-    {
-      float red = (float) (scores[i] - (float) min) / (float) (max - min);
-
-      if (red > 1.0f)
-      {
-        red = 1.0f;
-      }
-
-      if (red < 0.0f)
-      {
-        red = 0.0f;
-      }
-      colors[i] = makeColour(red);
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param s DOCUMENT ME!
-   * @param j DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Color findColour(char c, int j)
-  {
-    if (threshold > 0)
-    {
-      if (!aboveThreshold(c, j))
-      {
-        return Color.white;
-      }
-    }
-
-    if (jalview.util.Comparison.isGap(c))
-    {
-      return Color.white;
-    }
-
-    Color currentColour = colors[ResidueProperties.aaIndex[c]];
-
-    if (conservationColouring)
-    {
-      currentColour = applyConservation(currentColour, j);
-    }
-
-    return currentColour;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param c DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Color makeColour(float c)
-  {
-    return new Color(c, (float) 0.0, (float) 1.0 - c);
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.schemes;
+
+import java.awt.*;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class ScoreColourScheme extends ResidueColourScheme
+{
+  /** DOCUMENT ME!! */
+  public double min;
+
+  /** DOCUMENT ME!! */
+  public double max;
+
+  /** DOCUMENT ME!! */
+  public double[] scores;
+
+  /**
+   * Creates a new ScoreColourScheme object.
+   * 
+   * @param scores
+   *                DOCUMENT ME!
+   * @param min
+   *                DOCUMENT ME!
+   * @param max
+   *                DOCUMENT ME!
+   */
+  public ScoreColourScheme(double[] scores, double min, double max)
+  {
+    super();
+
+    this.scores = scores;
+    this.min = min;
+    this.max = max;
+
+    // Make colours in constructor
+    // Why wasn't this done earlier?
+    int i, iSize = scores.length;
+    colors = new Color[scores.length];
+    for (i = 0; i < iSize; i++)
+    {
+      float red = (float) (scores[i] - (float) min) / (float) (max - min);
+
+      if (red > 1.0f)
+      {
+        red = 1.0f;
+      }
+
+      if (red < 0.0f)
+      {
+        red = 0.0f;
+      }
+      colors[i] = makeColour(red);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param s
+   *                DOCUMENT ME!
+   * @param j
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public Color findColour(char c, int j)
+  {
+    if (threshold > 0)
+    {
+      if (!aboveThreshold(c, j))
+      {
+        return Color.white;
+      }
+    }
+
+    if (jalview.util.Comparison.isGap(c))
+    {
+      return Color.white;
+    }
+
+    Color currentColour = colors[ResidueProperties.aaIndex[c]];
+
+    if (conservationColouring)
+    {
+      currentColour = applyConservation(currentColour, j);
+    }
+
+    return currentColour;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param c
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public Color makeColour(float c)
+  {
+    return new Color(c, (float) 0.0, (float) 1.0 - c);
+  }
+}
diff --git a/src/jalview/schemes/ScoreMatrix.java b/src/jalview/schemes/ScoreMatrix.java
index 69a0922..a5a5ed3 100644
--- a/src/jalview/schemes/ScoreMatrix.java
+++ b/src/jalview/schemes/ScoreMatrix.java
@@ -1,16 +1,37 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.schemes;
 
 public class ScoreMatrix
 {
   String name;
+
   /**
    * reference to integer score matrix
    */
   int[][] matrix;
+
   /**
    * 0 for Protein Score matrix. 1 for dna score matrix
    */
   int type;
+
   ScoreMatrix(String name, int[][] matrix, int type)
   {
     this.matrix = matrix;
@@ -33,7 +54,7 @@ public class ScoreMatrix
   }
 
   /**
-   *
+   * 
    * @param A1
    * @param A2
    * @return score for substituting first char in A1 with first char in A2
@@ -49,16 +70,15 @@ public class ScoreMatrix
 
     try
     {
-      int a = (type == 0) ? ResidueProperties.aaIndex[c] :
-          ResidueProperties.nucleotideIndex[c];
-      int b = (type == 0) ? ResidueProperties.aaIndex[d] :
-          ResidueProperties.nucleotideIndex[d];
+      int a = (type == 0) ? ResidueProperties.aaIndex[c]
+              : ResidueProperties.nucleotideIndex[c];
+      int b = (type == 0) ? ResidueProperties.aaIndex[d]
+              : ResidueProperties.nucleotideIndex[d];
 
       pog = matrix[a][b];
-    }
-    catch (Exception e)
+    } catch (Exception e)
     {
-      //System.out.println("Unknown residue in " + A1 + " " + A2);
+      // System.out.println("Unknown residue in " + A1 + " " + A2);
     }
 
     return pog;
diff --git a/src/jalview/schemes/StrandColourScheme.java b/src/jalview/schemes/StrandColourScheme.java
index ec57d50..8c69fcc 100755
--- a/src/jalview/schemes/StrandColourScheme.java
+++ b/src/jalview/schemes/StrandColourScheme.java
@@ -1,52 +1,52 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.schemes;
-
-import java.awt.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class StrandColourScheme
-    extends ScoreColourScheme
-{
-  /**
-   * Creates a new StrandColourScheme object.
-   */
-  public StrandColourScheme()
-  {
-    super(ResidueProperties.strand, ResidueProperties.strandmin,
-          ResidueProperties.strandmax);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param c DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Color makeColour(float c)
-  {
-    return new Color(c, c, (float) 1.0 - c);
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.schemes;
+
+import java.awt.*;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class StrandColourScheme extends ScoreColourScheme
+{
+  /**
+   * Creates a new StrandColourScheme object.
+   */
+  public StrandColourScheme()
+  {
+    super(ResidueProperties.strand, ResidueProperties.strandmin,
+            ResidueProperties.strandmax);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param c
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public Color makeColour(float c)
+  {
+    return new Color(c, c, (float) 1.0 - c);
+  }
+}
diff --git a/src/jalview/schemes/TaylorColourScheme.java b/src/jalview/schemes/TaylorColourScheme.java
index 3a5c4da..590191b 100755
--- a/src/jalview/schemes/TaylorColourScheme.java
+++ b/src/jalview/schemes/TaylorColourScheme.java
@@ -1,28 +1,27 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.schemes;
-
-public class TaylorColourScheme
-    extends ResidueColourScheme
-{
-  public TaylorColourScheme()
-  {
-    super(ResidueProperties.taylor, 0);
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.schemes;
+
+public class TaylorColourScheme extends ResidueColourScheme
+{
+  public TaylorColourScheme()
+  {
+    super(ResidueProperties.taylor, 0);
+  }
+}
diff --git a/src/jalview/schemes/TurnColourScheme.java b/src/jalview/schemes/TurnColourScheme.java
index 2bd779b..e461586 100755
--- a/src/jalview/schemes/TurnColourScheme.java
+++ b/src/jalview/schemes/TurnColourScheme.java
@@ -1,52 +1,52 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.schemes;
-
-import java.awt.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class TurnColourScheme
-    extends ScoreColourScheme
-{
-  /**
-   * Creates a new TurnColourScheme object.
-   */
-  public TurnColourScheme()
-  {
-    super(ResidueProperties.turn, ResidueProperties.turnmin,
-          ResidueProperties.turnmax);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param c DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Color makeColour(float c)
-  {
-    return new Color(c, 1 - c, 1 - c);
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.schemes;
+
+import java.awt.*;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class TurnColourScheme extends ScoreColourScheme
+{
+  /**
+   * Creates a new TurnColourScheme object.
+   */
+  public TurnColourScheme()
+  {
+    super(ResidueProperties.turn, ResidueProperties.turnmin,
+            ResidueProperties.turnmax);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param c
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public Color makeColour(float c)
+  {
+    return new Color(c, 1 - c, 1 - c);
+  }
+}
diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index ab9ad2f..e42fd29 100755
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -22,15 +22,15 @@ import java.util.*;
 
 import java.awt.*;
 
-public class UserColourScheme
-    extends ResidueColourScheme
+public class UserColourScheme extends ResidueColourScheme
 {
   Color[] lowerCaseColours;
 
   protected String schemeName;
 
   public UserColourScheme()
-  {}
+  {
+  }
 
   public UserColourScheme(Color[] newColors)
   {
@@ -84,9 +84,9 @@ public class UserColourScheme
     {
       int value = Integer.parseInt(colour, 16);
       col = new Color(value);
+    } catch (NumberFormatException ex)
+    {
     }
-    catch (NumberFormatException ex)
-    {}
 
     if (col == null)
     {
@@ -97,15 +97,15 @@ public class UserColourScheme
     {
       try
       {
-        java.util.StringTokenizer st = new java.util.StringTokenizer(colour,
-            ",");
+        java.util.StringTokenizer st = new java.util.StringTokenizer(
+                colour, ",");
         int r = Integer.parseInt(st.nextToken());
         int g = Integer.parseInt(st.nextToken());
         int b = Integer.parseInt(st.nextToken());
         col = new Color(r, g, b);
+      } catch (Exception ex)
+      {
       }
-      catch (Exception ex)
-      {}
     }
 
     return col;
@@ -194,11 +194,10 @@ public class UserColourScheme
           }
         }
       }
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
-      System.out.println("Error parsing userDefinedColours:\n"
-                         + token + "\n" + ex);
+      System.out.println("Error parsing userDefinedColours:\n" + token
+              + "\n" + ex);
     }
 
   }
@@ -208,7 +207,7 @@ public class UserColourScheme
     Color currentColour;
     int index = ResidueProperties.aaIndex[c];
 
-    if ( (threshold == 0) || aboveThreshold(c, j))
+    if ((threshold == 0) || aboveThreshold(c, j))
     {
       if (lowerCaseColours != null && 'a' <= c && c <= 'z')
       {
diff --git a/src/jalview/schemes/ZappoColourScheme.java b/src/jalview/schemes/ZappoColourScheme.java
index f674a51..27f1f33 100755
--- a/src/jalview/schemes/ZappoColourScheme.java
+++ b/src/jalview/schemes/ZappoColourScheme.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -20,12 +20,11 @@ package jalview.schemes;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class ZappoColourScheme
-    extends ResidueColourScheme
+public class ZappoColourScheme extends ResidueColourScheme
 {
   /**
    * Creates a new ZappoColourScheme object.
diff --git a/src/jalview/structure/SequenceListener.java b/src/jalview/structure/SequenceListener.java
index 5370e12..7021f95 100644
--- a/src/jalview/structure/SequenceListener.java
+++ b/src/jalview/structure/SequenceListener.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
diff --git a/src/jalview/structure/StructureListener.java b/src/jalview/structure/StructureListener.java
index 5436eae..0f7bf30 100644
--- a/src/jalview/structure/StructureListener.java
+++ b/src/jalview/structure/StructureListener.java
@@ -1,32 +1,34 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.structure;
-
-public interface StructureListener
-{
-  public String getPdbFile();
-
-  public void mouseOverStructure(int atomIndex, String strInfo);
-
-  public void highlightAtom(int atomIndex, int pdbResNum, String chain, String pdbId);
-
-  public void updateColours(Object source);
-
-  public java.awt.Color getColour(int atomIndex, int pdbResNum, String chain, String pdbId);
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.structure;
+
+public interface StructureListener
+{
+  public String getPdbFile();
+
+  public void mouseOverStructure(int atomIndex, String strInfo);
+
+  public void highlightAtom(int atomIndex, int pdbResNum, String chain,
+          String pdbId);
+
+  public void updateColours(Object source);
+
+  public java.awt.Color getColour(int atomIndex, int pdbResNum,
+          String chain, String pdbId);
+}
diff --git a/src/jalview/structure/StructureMapping.java b/src/jalview/structure/StructureMapping.java
index 06e6bc3..b119e73 100644
--- a/src/jalview/structure/StructureMapping.java
+++ b/src/jalview/structure/StructureMapping.java
@@ -1,100 +1,99 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.structure;
-
-import jalview.datamodel.*;
-
-public class StructureMapping
-{
-  String mappingDetails;
-  SequenceI sequence;
-  String pdbfile;
-  String pdbid;
-  String pdbchain;
-
-  //Mapping index 0 is resNum, index 1 is atomNo
-  int[][] mapping;
-
-  public StructureMapping(SequenceI seq,
-                          String pdbfile,
-                          String pdbid,
-                          String chain,
-                          int[][] mapping,
-                          String mappingDetails)
-  {
-    sequence = seq;
-    this.pdbfile = pdbfile;
-    this.pdbid = pdbid;
-    this.pdbchain = chain;
-    this.mapping = mapping;
-    this.mappingDetails = mappingDetails;
-  }
-
-  public SequenceI getSequence()
-  {
-    return sequence;
-  }
-
-  public String getChain()
-  {
-    return pdbchain;
-  }
-
-  public String getPdbId()
-  {
-    return pdbid;
-  }
-
-  public int getAtomNum(int seqpos)
-  {
-    if (mapping.length > seqpos)
-    {
-      return mapping[seqpos][1];
-    }
-    else
-    {
-      return 0;
-    }
-  }
-
-  public int getPDBResNum(int seqpos)
-  {
-    if (mapping.length > seqpos)
-    {
-      return mapping[seqpos][0];
-    }
-    else
-    {
-      return 0;
-    }
-  }
-
-  public int getSeqPos(int pdbResNum)
-  {
-    for (int i = 0; i < mapping.length; i++)
-    {
-      if (mapping[i][0] == pdbResNum)
-      {
-        return i;
-      }
-    }
-    return -1;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.structure;
+
+import jalview.datamodel.*;
+
+public class StructureMapping
+{
+  String mappingDetails;
+
+  SequenceI sequence;
+
+  String pdbfile;
+
+  String pdbid;
+
+  String pdbchain;
+
+  // Mapping index 0 is resNum, index 1 is atomNo
+  int[][] mapping;
+
+  public StructureMapping(SequenceI seq, String pdbfile, String pdbid,
+          String chain, int[][] mapping, String mappingDetails)
+  {
+    sequence = seq;
+    this.pdbfile = pdbfile;
+    this.pdbid = pdbid;
+    this.pdbchain = chain;
+    this.mapping = mapping;
+    this.mappingDetails = mappingDetails;
+  }
+
+  public SequenceI getSequence()
+  {
+    return sequence;
+  }
+
+  public String getChain()
+  {
+    return pdbchain;
+  }
+
+  public String getPdbId()
+  {
+    return pdbid;
+  }
+
+  public int getAtomNum(int seqpos)
+  {
+    if (mapping.length > seqpos)
+    {
+      return mapping[seqpos][1];
+    }
+    else
+    {
+      return 0;
+    }
+  }
+
+  public int getPDBResNum(int seqpos)
+  {
+    if (mapping.length > seqpos)
+    {
+      return mapping[seqpos][0];
+    }
+    else
+    {
+      return 0;
+    }
+  }
+
+  public int getSeqPos(int pdbResNum)
+  {
+    for (int i = 0; i < mapping.length; i++)
+    {
+      if (mapping[i][0] == pdbResNum)
+      {
+        return i;
+      }
+    }
+    return -1;
+  }
+}
diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index e12e3ab..2f3a312 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -278,9 +278,9 @@ public class StructureSelectionManager
             indexpos = mappings[j].getSeqPos(pdbResNum);
             results.addResult(mappings[j].sequence, indexpos, indexpos);
             // construct highlighted sequence list
-            if (seqmappings!=null)
+            if (seqmappings != null)
             {
-              
+
               Enumeration e = seqmappings.elements();
               while (e.hasMoreElements())
 
diff --git a/src/jalview/structure/VamsasListener.java b/src/jalview/structure/VamsasListener.java
index 1bf3931..962c928 100644
--- a/src/jalview/structure/VamsasListener.java
+++ b/src/jalview/structure/VamsasListener.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.structure;
 
 import jalview.datamodel.SequenceI;
diff --git a/src/jalview/util/BrowserLauncher.java b/src/jalview/util/BrowserLauncher.java
index 2b8a4bd..f3c8cfd 100755
--- a/src/jalview/util/BrowserLauncher.java
+++ b/src/jalview/util/BrowserLauncher.java
@@ -1,931 +1,890 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.util;
-
-import java.io.*;
-import java.lang.reflect.*;
-
-/**
- * BrowserLauncher is a class that provides one static method, openURL, which opens the default
- * web browser for the current user of the system to the given URL.  It may support other
- * protocols depending on the system -- mailto, ftp, etc. -- but that has not been rigorously
- * tested and is not guaranteed to work.
- * <p>
- * Yes, this is platform-specific code, and yes, it may rely on classes on certain platforms
- * that are not part of the standard JDK.  What we're trying to do, though, is to take something
- * that's frequently desirable but inherently platform-specific -- opening a default browser --
- * and allow programmers (you, for example) to do so without worrying about dropping into native
- * code or doing anything else similarly evil.
- * <p>
- * Anyway, this code is completely in Java and will run on all JDK 1.1-compliant systems without
- * modification or a need for additional libraries.  All classes that are required on certain
- * platforms to allow this to run are dynamically loaded at runtime via reflection and, if not
- * found, will not cause this to do anything other than returning an error when opening the
- * browser.
- * <p>
- * There are certain system requirements for this class, as it's running through Runtime.exec(),
- * which is Java's way of making a native system call.  Currently, this requires that a Macintosh
- * have a Finder which supports the GURL event, which is true for Mac OS 8.0 and 8.1 systems that
- * have the Internet Scripting AppleScript dictionary installed in the Scripting Additions folder
- * in the Extensions folder (which is installed by default as far as I know under Mac OS 8.0 and
- * 8.1), and for all Mac OS 8.5 and later systems.  On Windows, it only runs under Win32 systems
- * (Windows 95, 98, and NT 4.0, as well as later versions of all).  On other systems, this drops
- * back from the inherently platform-sensitive concept of a default browser and simply attempts
- * to launch Netscape via a shell command.
- * <p>
- * This code is Copyright 1999-2001 by Eric Albert (ejalbert\@cs.stanford.edu) and may be
- * redistributed or modified in any form without restrictions as long as the portion of this
- * comment from this paragraph through the end of the comment is not removed.  The author
- * requests that he be notified of any application, applet, or other binary that makes use of
- * this code, but that's more out of curiosity than anything and is not required.  This software
- * includes no warranty.  The author is not repsonsible for any loss of data or functionality
- * or any adverse or unexpected effects of using this software.
- * <p>
- * Credits:
- * <br>Steven Spencer, JavaWorld magazine (<a href="http://www.javaworld.com/javaworld/javatips/jw-javatip66.html">Java Tip 66</a>)
- * <br>Thanks also to Ron B. Yeh, Eric Shapiro, Ben Engber, Paul Teitlebaum, Andrea Cantatore,
- * Larry Barowski, Trevor Bedzek, Frank Miedrich, and Ron Rabakukk
- *
- * @author Eric Albert (<a href="mailto:ejalbert@cs.stanford.edu">ejalbert@cs.stanford.edu</a>)
- * @version 1.4b1 (Released June 20, 2001)
- */
-public class BrowserLauncher
-{
-  /**
-   * The Java virtual machine that we are running on.  Actually, in most cases we only care
-   * about the operating system, but some operating systems require us to switch on the VM. */
-  private static int jvm;
-
-  /** The browser for the system */
-  private static Object browser;
-
-  /**
-   * Caches whether any classes, methods, and fields that are not part of the JDK and need to
-   * be dynamically loaded at runtime loaded successfully.
-   * <p>
-   * Note that if this is <code>false</code>, <code>openURL()</code> will always return an
-   * IOException.
-   */
-  private static boolean loadedWithoutErrors;
-
-  /** The com.apple.mrj.MRJFileUtils class */
-  private static Class mrjFileUtilsClass;
-
-  /** The com.apple.mrj.MRJOSType class */
-  private static Class mrjOSTypeClass;
-
-  /** The com.apple.MacOS.AEDesc class */
-  private static Class aeDescClass;
-
-  /** The &lt;init&gt;(int) method of com.apple.MacOS.AETarget */
-  private static Constructor aeTargetConstructor;
-
-  /** The &lt;init&gt;(int, int, int) method of com.apple.MacOS.AppleEvent */
-  private static Constructor appleEventConstructor;
-
-  /** The &lt;init&gt;(String) method of com.apple.MacOS.AEDesc */
-  private static Constructor aeDescConstructor;
-
-  /** The findFolder method of com.apple.mrj.MRJFileUtils */
-  private static Method findFolder;
-
-  /** The getFileCreator method of com.apple.mrj.MRJFileUtils */
-  private static Method getFileCreator;
-
-  /** The getFileType method of com.apple.mrj.MRJFileUtils */
-  private static Method getFileType;
-
-  /** The openURL method of com.apple.mrj.MRJFileUtils */
-  private static Method openURL;
-
-  /** The makeOSType method of com.apple.MacOS.OSUtils */
-  private static Method makeOSType;
-
-  /** The putParameter method of com.apple.MacOS.AppleEvent */
-  private static Method putParameter;
-
-  /** The sendNoReply method of com.apple.MacOS.AppleEvent */
-  private static Method sendNoReply;
-
-  /** Actually an MRJOSType pointing to the System Folder on a Macintosh */
-  private static Object kSystemFolderType;
-
-  /** The keyDirectObject AppleEvent parameter type */
-  private static Integer keyDirectObject;
-
-  /** The kAutoGenerateReturnID AppleEvent code */
-  private static Integer kAutoGenerateReturnID;
-
-  /** The kAnyTransactionID AppleEvent code */
-  private static Integer kAnyTransactionID;
-
-  /** The linkage object required for JDirect 3 on Mac OS X. */
-  private static Object linkage;
-
-  /** The framework to reference on Mac OS X */
-  private static final String JDirect_MacOSX = "/System/Library/Frameworks/Carbon.framework/Frameworks/HIToolbox.framework/HIToolbox";
-
-  /** JVM constant for MRJ 2.0 */
-  private static final int MRJ_2_0 = 0;
-
-  /** JVM constant for MRJ 2.1 or later */
-  private static final int MRJ_2_1 = 1;
-
-  /** JVM constant for Java on Mac OS X 10.0 (MRJ 3.0) */
-  private static final int MRJ_3_0 = 3;
-
-  /** JVM constant for MRJ 3.1 */
-  private static final int MRJ_3_1 = 4;
-
-  /** JVM constant for any Windows NT JVM */
-  private static final int WINDOWS_NT = 5;
-
-  /** JVM constant for any Windows 9x JVM */
-  private static final int WINDOWS_9x = 6;
-
-  /** JVM constant for any other platform */
-  private static final int OTHER = -1;
-
-  /**
-   * The file type of the Finder on a Macintosh.  Hardcoding "Finder" would keep non-U.S. English
-   * systems from working properly.
-   */
-  private static final String FINDER_TYPE = "FNDR";
-
-  /**
-   * The creator code of the Finder on a Macintosh, which is needed to send AppleEvents to the
-   * application.
-   */
-  private static final String FINDER_CREATOR = "MACS";
-
-  /** The name for the AppleEvent type corresponding to a GetURL event. */
-  private static final String GURL_EVENT = "GURL";
-
-  /**
-   * The first parameter that needs to be passed into Runtime.exec() to open the default web
-   * browser on Windows.
-   */
-  private static final String FIRST_WINDOWS_PARAMETER = "/c";
-
-  /** The second parameter for Runtime.exec() on Windows. */
-  private static final String SECOND_WINDOWS_PARAMETER = "start";
-
-  /**
-   * The third parameter for Runtime.exec() on Windows.  This is a "title"
-   * parameter that the command line expects.  Setting this parameter allows
-   * URLs containing spaces to work.
-   */
-  private static final String THIRD_WINDOWS_PARAMETER = "\"\"";
-
-  /**
-   * The shell parameters for Netscape that opens a given URL in an already-open copy of Netscape
-   * on many command-line systems.
-   */
-  private static final String NETSCAPE_REMOTE_PARAMETER = "-remote";
-  private static final String NETSCAPE_OPEN_PARAMETER_START = "openURL(";
-  private static final String NETSCAPE_OPEN_NEW_WINDOW = ", new-window";
-  private static final String NETSCAPE_OPEN_PARAMETER_END = ")";
-
-  /**
-   * The message from any exception thrown throughout the initialization process.
-   */
-  private static String errorMessage;
-
-  /**
-   * An initialization block that determines the operating system and loads the necessary
-   * runtime data.
-   */
-  static
-  {
-    loadedWithoutErrors = true;
-
-    String osName = System.getProperty("os.name");
-
-    if (osName.startsWith("Mac OS"))
-    {
-      String mrjVersion = System.getProperty("mrj.version");
-      String majorMRJVersion = mrjVersion.substring(0, 3);
-
-      try
-      {
-        double version = Double.valueOf(majorMRJVersion).doubleValue();
-
-        if (version == 2)
-        {
-          jvm = MRJ_2_0;
-        }
-        else if ( (version >= 2.1) && (version < 3))
-        {
-          // Assume that all 2.x versions of MRJ work the same.  MRJ 2.1 actually
-          // works via Runtime.exec() and 2.2 supports that but has an openURL() method
-          // as well that we currently ignore.
-          jvm = MRJ_2_1;
-        }
-        else if (version == 3.0)
-        {
-          jvm = MRJ_3_0;
-        }
-        else if (version >= 3.1)
-        {
-          // Assume that all 3.1 and later versions of MRJ work the same.
-          jvm = MRJ_3_1;
-        }
-        else
-        {
-          loadedWithoutErrors = false;
-          errorMessage = "Unsupported MRJ version: " + version;
-        }
-      }
-      catch (NumberFormatException nfe)
-      {
-        loadedWithoutErrors = false;
-        errorMessage = "Invalid MRJ version: " + mrjVersion;
-      }
-    }
-    else if (osName.startsWith("Windows"))
-    {
-      if (osName.indexOf("9") != -1)
-      {
-        jvm = WINDOWS_9x;
-      }
-      else
-      {
-        jvm = WINDOWS_NT;
-      }
-    }
-    else
-    {
-      jvm = OTHER;
-    }
-
-    if (loadedWithoutErrors)
-    { // if we haven't hit any errors yet
-      loadedWithoutErrors = loadClasses();
-    }
-  }
-
-  /**
-   * This class should be never be instantiated; this just ensures so.
-   */
-  private BrowserLauncher()
-  {
-  }
-
-  /**
-   * Called by a static initializer to load any classes, fields, and methods required at runtime
-   * to locate the user's web browser.
-   * @return <code>true</code> if all intialization succeeded
-   *                        <code>false</code> if any portion of the initialization failed
-   */
-  private static boolean loadClasses()
-  {
-    switch (jvm)
-    {
-      case MRJ_2_0:
-
-        try
-        {
-          Class aeTargetClass = Class.forName("com.apple.MacOS.AETarget");
-          Class osUtilsClass = Class.forName("com.apple.MacOS.OSUtils");
-          Class appleEventClass = Class.forName(
-              "com.apple.MacOS.AppleEvent");
-          Class aeClass = Class.forName("com.apple.MacOS.ae");
-          aeDescClass = Class.forName("com.apple.MacOS.AEDesc");
-
-          aeTargetConstructor = aeTargetClass.getDeclaredConstructor(new Class[]
-              {
-              int.class
-          });
-          appleEventConstructor = appleEventClass.getDeclaredConstructor(new
-              Class[]
-              {
-              int.class, int.class, aeTargetClass, int.class,
-              int.class
-          });
-          aeDescConstructor = aeDescClass.getDeclaredConstructor(new Class[]
-              {
-              String.class
-          });
-
-          makeOSType = osUtilsClass.getDeclaredMethod("makeOSType",
-              new Class[]
-              {String.class});
-          putParameter = appleEventClass.getDeclaredMethod("putParameter",
-              new Class[]
-              {int.class, aeDescClass});
-          sendNoReply = appleEventClass.getDeclaredMethod("sendNoReply",
-              new Class[]
-              {});
-
-          Field keyDirectObjectField = aeClass.getDeclaredField(
-              "keyDirectObject");
-          keyDirectObject = (Integer) keyDirectObjectField.get(null);
-
-          Field autoGenerateReturnIDField = appleEventClass.getDeclaredField(
-              "kAutoGenerateReturnID");
-          kAutoGenerateReturnID = (Integer) autoGenerateReturnIDField.get(null);
-
-          Field anyTransactionIDField = appleEventClass.getDeclaredField(
-              "kAnyTransactionID");
-          kAnyTransactionID = (Integer) anyTransactionIDField.get(null);
-        }
-        catch (ClassNotFoundException cnfe)
-        {
-          errorMessage = cnfe.getMessage();
-
-          return false;
-        }
-        catch (NoSuchMethodException nsme)
-        {
-          errorMessage = nsme.getMessage();
-
-          return false;
-        }
-        catch (NoSuchFieldException nsfe)
-        {
-          errorMessage = nsfe.getMessage();
-
-          return false;
-        }
-        catch (IllegalAccessException iae)
-        {
-          errorMessage = iae.getMessage();
-
-          return false;
-        }
-
-        break
-            ;
-
-      case MRJ_2_1:
-
-        try
-        {
-          mrjFileUtilsClass = Class.forName("com.apple.mrj.MRJFileUtils");
-          mrjOSTypeClass = Class.forName("com.apple.mrj.MRJOSType");
-
-          Field systemFolderField = mrjFileUtilsClass.getDeclaredField(
-              "kSystemFolderType");
-          kSystemFolderType = systemFolderField.get(null);
-          findFolder = mrjFileUtilsClass.getDeclaredMethod("findFolder",
-              new Class[]
-              {mrjOSTypeClass});
-          getFileCreator = mrjFileUtilsClass.getDeclaredMethod("getFileCreator",
-              new Class[]
-              {File.class});
-          getFileType = mrjFileUtilsClass.getDeclaredMethod("getFileType",
-              new Class[]
-              {File.class});
-        }
-        catch (ClassNotFoundException cnfe)
-        {
-          errorMessage = cnfe.getMessage();
-
-          return false;
-        }
-        catch (NoSuchFieldException nsfe)
-        {
-          errorMessage = nsfe.getMessage();
-
-          return false;
-        }
-        catch (NoSuchMethodException nsme)
-        {
-          errorMessage = nsme.getMessage();
-
-          return false;
-        }
-        catch (SecurityException se)
-        {
-          errorMessage = se.getMessage();
-
-          return false;
-        }
-        catch (IllegalAccessException iae)
-        {
-          errorMessage = iae.getMessage();
-
-          return false;
-        }
-
-        break
-            ;
-
-      case MRJ_3_0:
-
-        try
-        {
-          Class linker = Class.forName("com.apple.mrj.jdirect.Linker");
-          Constructor constructor = linker.getConstructor(new Class[]
-              {
-              Class.class
-          });
-          linkage = constructor.newInstance(new Object[]
-                                            {
-                                            BrowserLauncher.class
-          });
-        }
-        catch (ClassNotFoundException cnfe)
-        {
-          errorMessage = cnfe.getMessage();
-
-          return false;
-        }
-        catch (NoSuchMethodException nsme)
-        {
-          errorMessage = nsme.getMessage();
-
-          return false;
-        }
-        catch (InvocationTargetException ite)
-        {
-          errorMessage = ite.getMessage();
-
-          return false;
-        }
-        catch (InstantiationException ie)
-        {
-          errorMessage = ie.getMessage();
-
-          return false;
-        }
-        catch (IllegalAccessException iae)
-        {
-          errorMessage = iae.getMessage();
-
-          return false;
-        }
-
-        break
-            ;
-
-      case MRJ_3_1:
-
-        try
-        {
-          mrjFileUtilsClass = Class.forName("com.apple.mrj.MRJFileUtils");
-          openURL = mrjFileUtilsClass.getDeclaredMethod("openURL",
-              new Class[]
-              {String.class});
-        }
-        catch (ClassNotFoundException cnfe)
-        {
-          errorMessage = cnfe.getMessage();
-
-          return false;
-        }
-        catch (NoSuchMethodException nsme)
-        {
-          errorMessage = nsme.getMessage();
-
-          return false;
-        }
-
-        break
-            ;
-
-      default:
-        break;
-    }
-
-    return true;
-  }
-
-  /**
-   * Attempts to locate the default web browser on the local system.    s results so it
-   * only locates the browser once for each use of this class per JVM instance.
-   * @return The browser for the system.  Note that this may not be what you would consider
-   *                        to be a standard web browser; instead, it's the application that gets called to
-   *                        open the default web browser.  In some cases, this will be a non-String object
-   *                        that provides the means of calling the default browser.
-   */
-  private static Object locateBrowser()
-  {
-    if (browser != null)
-    {
-      return browser;
-    }
-
-    switch (jvm)
-    {
-      case MRJ_2_0:
-
-        try
-        {
-          Integer finderCreatorCode = (Integer) makeOSType.invoke(null,
-              new Object[]
-              {FINDER_CREATOR});
-          Object aeTarget = aeTargetConstructor.newInstance(new Object[]
-              {
-              finderCreatorCode
-          });
-          Integer gurlType = (Integer) makeOSType.invoke(null,
-              new Object[]
-              {GURL_EVENT});
-          Object appleEvent = appleEventConstructor.newInstance(new Object[]
-              {
-              gurlType, gurlType, aeTarget, kAutoGenerateReturnID,
-              kAnyTransactionID
-          });
-
-          // Don't set browser = appleEvent because then the next time we call
-          // locateBrowser(), we'll get the same AppleEvent, to which we'll already have
-          // added the relevant parameter. Instead, regenerate the AppleEvent every time.
-          // There's probably a way to do this better; if any has any ideas, please let
-          // me know.
-          return appleEvent;
-        }
-        catch (IllegalAccessException iae)
-        {
-          browser = null;
-          errorMessage = iae.getMessage();
-
-          return browser;
-        }
-        catch (InstantiationException ie)
-        {
-          browser = null;
-          errorMessage = ie.getMessage();
-
-          return browser;
-        }
-        catch (InvocationTargetException ite)
-        {
-          browser = null;
-          errorMessage = ite.getMessage();
-
-          return browser;
-        }
-
-        case MRJ_2_1:
-
-          File systemFolder;
-
-          try
-          {
-            systemFolder = (File) findFolder.invoke(null,
-                new Object[]
-                {kSystemFolderType});
-          }
-          catch (IllegalArgumentException iare)
-          {
-            browser = null;
-            errorMessage = iare.getMessage();
-
-            return browser;
-          }
-          catch (IllegalAccessException iae)
-          {
-            browser = null;
-            errorMessage = iae.getMessage();
-
-            return browser;
-          }
-          catch (InvocationTargetException ite)
-          {
-            browser = null;
-            errorMessage = ite.getTargetException().getClass() + ": " +
-                ite.getTargetException().getMessage();
-
-            return browser;
-          }
-
-          String[] systemFolderFiles = systemFolder.list();
-
-          // Avoid a FilenameFilter because that can't be stopped mid-list
-          for (int i = 0; i < systemFolderFiles.length; i++)
-          {
-            try
-            {
-              File file = new File(systemFolder, systemFolderFiles[i]);
-
-              if (!file.isFile())
-              {
-                continue;
-              }
-
-              // We're looking for a file with a creator code of 'MACS' and
-              // a type of 'FNDR'.  Only requiring the type results in non-Finder
-              // applications being picked up on certain Mac OS 9 systems,
-              // especially German ones, and sending a GURL event to those
-              // applications results in a logout under Multiple Users.
-              Object fileType = getFileType.invoke(null,
-                  new Object[]
-                  {file});
-
-              if (FINDER_TYPE.equals(fileType.toString()))
-              {
-                Object fileCreator = getFileCreator.invoke(null,
-                    new Object[]
-                    {file});
-
-                if (FINDER_CREATOR.equals(fileCreator.toString()))
-                {
-                  browser = file.toString(); // Actually the Finder, but that's OK
-
-                  return browser;
-                }
-              }
-            }
-            catch (IllegalArgumentException iare)
-            {
-              errorMessage = iare.getMessage();
-
-              return null;
-            }
-            catch (IllegalAccessException iae)
-            {
-              browser = null;
-              errorMessage = iae.getMessage();
-
-              return browser;
-            }
-            catch (InvocationTargetException ite)
-            {
-              browser = null;
-              errorMessage = ite.getTargetException().getClass() + ": " +
-                  ite.getTargetException().getMessage();
-
-              return browser;
-            }
-          }
-
-          browser = null;
-
-          break;
-
-      case MRJ_3_0:
-      case MRJ_3_1:
-        browser = ""; // Return something non-null
-
-        break;
-
-      case WINDOWS_NT:
-        browser = "cmd.exe";
-
-        break;
-
-      case WINDOWS_9x:
-        browser = "command.com";
-
-        break;
-
-      case OTHER:
-      default:
-        browser = jalview.bin.Cache.getDefault("DEFAULT_BROWSER", "firefox");
-
-        break;
-    }
-
-    return browser;
-  }
-
-  /**
-   * used to ensure that browser is up-to-date after a configuration
-   * change (Unix DEFAULT_BROWSER property change).
-   */
-  public static void resetBrowser()
-  {
-    browser = null;
-  }
-
-  /**
-   * Attempts to open the default web browser to the given URL.
-   * @param url The URL to open
-   * @throws IOException If the web browser could not be located or does not run
-   */
-  public static void openURL(String url)
-      throws IOException
-  {
-    if (!loadedWithoutErrors)
-    {
-      throw new IOException("Exception in finding browser: " +
-                            errorMessage);
-    }
-
-    Object browser = locateBrowser();
-
-    if (browser == null)
-    {
-      throw new IOException("Unable to locate browser: " + errorMessage);
-    }
-
-    switch (jvm)
-    {
-      case MRJ_2_0:
-
-        Object aeDesc = null;
-
-        try
-        {
-          aeDesc = aeDescConstructor.newInstance(new Object[]
-                                                 {url});
-          putParameter.invoke(browser,
-                              new Object[]
-                              {keyDirectObject, aeDesc});
-          sendNoReply.invoke(browser, new Object[]
-                             {});
-        }
-        catch (InvocationTargetException ite)
-        {
-          throw new IOException(
-              "InvocationTargetException while creating AEDesc: " +
-              ite.getMessage());
-        }
-        catch (IllegalAccessException iae)
-        {
-          throw new IOException(
-              "IllegalAccessException while building AppleEvent: " +
-              iae.getMessage());
-        }
-        catch (InstantiationException ie)
-        {
-          throw new IOException(
-              "InstantiationException while creating AEDesc: " +
-              ie.getMessage());
-        }
-        finally
-        {
-          aeDesc = null; // Encourage it to get disposed if it was created
-          browser = null; // Ditto
-        }
-
-        break;
-
-      case MRJ_2_1:
-        Runtime.getRuntime().exec(new String[]
-                                  { (String) browser, url});
-
-        break;
-
-      case MRJ_3_0:
-
-        int[] instance = new int[1];
-        int result = ICStart(instance, 0);
-
-        if (result == 0)
-        {
-          int[] selectionStart = new int[]
-              {
-              0};
-          byte[] urlBytes = url.getBytes();
-          int[] selectionEnd = new int[]
-              {
-              urlBytes.length};
-          result = ICLaunchURL(instance[0], new byte[]
-                               {0}, urlBytes,
-                               urlBytes.length, selectionStart, selectionEnd);
-
-          if (result == 0)
-          {
-            // Ignore the return value; the URL was launched successfully
-            // regardless of what happens here.
-            ICStop(instance);
-          }
-          else
-          {
-            throw new IOException("Unable to launch URL: " + result);
-          }
-        }
-        else
-        {
-          throw new IOException(
-              "Unable to create an Internet Config instance: " + result);
-        }
-
-        break;
-
-      case MRJ_3_1:
-
-        try
-        {
-          openURL.invoke(null, new Object[]
-                         {url});
-        }
-        catch (InvocationTargetException ite)
-        {
-          throw new IOException(
-              "InvocationTargetException while calling openURL: " +
-              ite.getMessage());
-        }
-        catch (IllegalAccessException iae)
-        {
-          throw new IOException(
-              "IllegalAccessException while calling openURL: " +
-              iae.getMessage());
-        }
-
-        break
-            ;
-
-      case WINDOWS_NT:
-      case WINDOWS_9x:
-
-        // Add quotes around the URL to allow ampersands and other special
-        // characters to work.
-        Process process = Runtime.getRuntime().exec(new String[]
-            {
-            (String) browser, FIRST_WINDOWS_PARAMETER,
-            SECOND_WINDOWS_PARAMETER, THIRD_WINDOWS_PARAMETER,
-            '"' + url + '"'
-        });
-
-        // This avoids a memory leak on some versions of Java on Windows.
-        // That's hinted at in <http://developer.java.sun.com/developer/qow/archive/68/>.
-        try
-        {
-          process.waitFor();
-          process.exitValue();
-        }
-        catch (InterruptedException ie)
-        {
-          throw new IOException(
-              "InterruptedException while launching browser: " +
-              ie.getMessage());
-        }
-
-        break
-            ;
-
-      case OTHER:
-
-        // Assume that we're on Unix and that Netscape (actually Firefox) is installed
-        // First, attempt to open the URL in a currently running session of Netscape
-        // JBPNote log debug
-
-        /* System.out.println("Executing : "+browser+" "+
-         NETSCAPE_REMOTE_PARAMETER+" "+
-         NETSCAPE_OPEN_PARAMETER_START +
-         url +
-         NETSCAPE_OPEN_NEW_WINDOW +
-         NETSCAPE_OPEN_PARAMETER_END);
-         */
-        process = Runtime.getRuntime().exec(new String[]
-                                            {
-                                            (String) browser,
-                                            NETSCAPE_REMOTE_PARAMETER,
-
-                                            NETSCAPE_OPEN_PARAMETER_START + url +
-                                            NETSCAPE_OPEN_NEW_WINDOW +
-                                            NETSCAPE_OPEN_PARAMETER_END
-        });
-
-        try
-        {
-          int exitCode = process.waitFor();
-
-          if (exitCode != 0)
-          { // if Netscape was not open
-            Runtime.getRuntime().exec(new String[]
-                                      { (String) browser, url});
-          }
-        }
-        catch (InterruptedException ie)
-        {
-          throw new IOException(
-              "InterruptedException while launching browser: " +
-              ie.getMessage());
-        }
-
-        break
-            ;
-
-      default:
-
-        // This should never occur, but if it does, we'll try the simplest thing possible
-        Runtime.getRuntime().exec(new String[]
-                                  { (String) browser, url});
-
-        break;
-    }
-  }
-
-  /**
-   * Methods required for Mac OS X.  The presence of native methods does not cause
-   * any problems on other platforms.
-   */
-  private native static int ICStart(int[] instance, int signature);
-
-  private native static int ICStop(int[] instance);
-
-  private native static int ICLaunchURL(int instance, byte[] hint,
-                                        byte[] data, int len,
-                                        int[] selectionStart,
-                                        int[] selectionEnd);
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.util;
+
+import java.io.*;
+import java.lang.reflect.*;
+
+/**
+ * BrowserLauncher is a class that provides one static method, openURL, which
+ * opens the default web browser for the current user of the system to the given
+ * URL. It may support other protocols depending on the system -- mailto, ftp,
+ * etc. -- but that has not been rigorously tested and is not guaranteed to
+ * work.
+ * <p>
+ * Yes, this is platform-specific code, and yes, it may rely on classes on
+ * certain platforms that are not part of the standard JDK. What we're trying to
+ * do, though, is to take something that's frequently desirable but inherently
+ * platform-specific -- opening a default browser -- and allow programmers (you,
+ * for example) to do so without worrying about dropping into native code or
+ * doing anything else similarly evil.
+ * <p>
+ * Anyway, this code is completely in Java and will run on all JDK 1.1-compliant
+ * systems without modification or a need for additional libraries. All classes
+ * that are required on certain platforms to allow this to run are dynamically
+ * loaded at runtime via reflection and, if not found, will not cause this to do
+ * anything other than returning an error when opening the browser.
+ * <p>
+ * There are certain system requirements for this class, as it's running through
+ * Runtime.exec(), which is Java's way of making a native system call.
+ * Currently, this requires that a Macintosh have a Finder which supports the
+ * GURL event, which is true for Mac OS 8.0 and 8.1 systems that have the
+ * Internet Scripting AppleScript dictionary installed in the Scripting
+ * Additions folder in the Extensions folder (which is installed by default as
+ * far as I know under Mac OS 8.0 and 8.1), and for all Mac OS 8.5 and later
+ * systems. On Windows, it only runs under Win32 systems (Windows 95, 98, and NT
+ * 4.0, as well as later versions of all). On other systems, this drops back
+ * from the inherently platform-sensitive concept of a default browser and
+ * simply attempts to launch Netscape via a shell command.
+ * <p>
+ * This code is Copyright 1999-2001 by Eric Albert (ejalbert\@cs.stanford.edu)
+ * and may be redistributed or modified in any form without restrictions as long
+ * as the portion of this comment from this paragraph through the end of the
+ * comment is not removed. The author requests that he be notified of any
+ * application, applet, or other binary that makes use of this code, but that's
+ * more out of curiosity than anything and is not required. This software
+ * includes no warranty. The author is not repsonsible for any loss of data or
+ * functionality or any adverse or unexpected effects of using this software.
+ * <p>
+ * Credits: <br>
+ * Steven Spencer, JavaWorld magazine (<a
+ * href="http://www.javaworld.com/javaworld/javatips/jw-javatip66.html">Java Tip
+ * 66</a>) <br>
+ * Thanks also to Ron B. Yeh, Eric Shapiro, Ben Engber, Paul Teitlebaum, Andrea
+ * Cantatore, Larry Barowski, Trevor Bedzek, Frank Miedrich, and Ron Rabakukk
+ * 
+ * @author Eric Albert (<a
+ *         href="mailto:ejalbert@cs.stanford.edu">ejalbert@cs.stanford.edu</a>)
+ * @version 1.4b1 (Released June 20, 2001)
+ */
+public class BrowserLauncher
+{
+  /**
+   * The Java virtual machine that we are running on. Actually, in most cases we
+   * only care about the operating system, but some operating systems require us
+   * to switch on the VM.
+   */
+  private static int jvm;
+
+  /** The browser for the system */
+  private static Object browser;
+
+  /**
+   * Caches whether any classes, methods, and fields that are not part of the
+   * JDK and need to be dynamically loaded at runtime loaded successfully.
+   * <p>
+   * Note that if this is <code>false</code>, <code>openURL()</code> will
+   * always return an IOException.
+   */
+  private static boolean loadedWithoutErrors;
+
+  /** The com.apple.mrj.MRJFileUtils class */
+  private static Class mrjFileUtilsClass;
+
+  /** The com.apple.mrj.MRJOSType class */
+  private static Class mrjOSTypeClass;
+
+  /** The com.apple.MacOS.AEDesc class */
+  private static Class aeDescClass;
+
+  /** The &lt;init&gt;(int) method of com.apple.MacOS.AETarget */
+  private static Constructor aeTargetConstructor;
+
+  /** The &lt;init&gt;(int, int, int) method of com.apple.MacOS.AppleEvent */
+  private static Constructor appleEventConstructor;
+
+  /** The &lt;init&gt;(String) method of com.apple.MacOS.AEDesc */
+  private static Constructor aeDescConstructor;
+
+  /** The findFolder method of com.apple.mrj.MRJFileUtils */
+  private static Method findFolder;
+
+  /** The getFileCreator method of com.apple.mrj.MRJFileUtils */
+  private static Method getFileCreator;
+
+  /** The getFileType method of com.apple.mrj.MRJFileUtils */
+  private static Method getFileType;
+
+  /** The openURL method of com.apple.mrj.MRJFileUtils */
+  private static Method openURL;
+
+  /** The makeOSType method of com.apple.MacOS.OSUtils */
+  private static Method makeOSType;
+
+  /** The putParameter method of com.apple.MacOS.AppleEvent */
+  private static Method putParameter;
+
+  /** The sendNoReply method of com.apple.MacOS.AppleEvent */
+  private static Method sendNoReply;
+
+  /** Actually an MRJOSType pointing to the System Folder on a Macintosh */
+  private static Object kSystemFolderType;
+
+  /** The keyDirectObject AppleEvent parameter type */
+  private static Integer keyDirectObject;
+
+  /** The kAutoGenerateReturnID AppleEvent code */
+  private static Integer kAutoGenerateReturnID;
+
+  /** The kAnyTransactionID AppleEvent code */
+  private static Integer kAnyTransactionID;
+
+  /** The linkage object required for JDirect 3 on Mac OS X. */
+  private static Object linkage;
+
+  /** The framework to reference on Mac OS X */
+  private static final String JDirect_MacOSX = "/System/Library/Frameworks/Carbon.framework/Frameworks/HIToolbox.framework/HIToolbox";
+
+  /** JVM constant for MRJ 2.0 */
+  private static final int MRJ_2_0 = 0;
+
+  /** JVM constant for MRJ 2.1 or later */
+  private static final int MRJ_2_1 = 1;
+
+  /** JVM constant for Java on Mac OS X 10.0 (MRJ 3.0) */
+  private static final int MRJ_3_0 = 3;
+
+  /** JVM constant for MRJ 3.1 */
+  private static final int MRJ_3_1 = 4;
+
+  /** JVM constant for any Windows NT JVM */
+  private static final int WINDOWS_NT = 5;
+
+  /** JVM constant for any Windows 9x JVM */
+  private static final int WINDOWS_9x = 6;
+
+  /** JVM constant for any other platform */
+  private static final int OTHER = -1;
+
+  /**
+   * The file type of the Finder on a Macintosh. Hardcoding "Finder" would keep
+   * non-U.S. English systems from working properly.
+   */
+  private static final String FINDER_TYPE = "FNDR";
+
+  /**
+   * The creator code of the Finder on a Macintosh, which is needed to send
+   * AppleEvents to the application.
+   */
+  private static final String FINDER_CREATOR = "MACS";
+
+  /** The name for the AppleEvent type corresponding to a GetURL event. */
+  private static final String GURL_EVENT = "GURL";
+
+  /**
+   * The first parameter that needs to be passed into Runtime.exec() to open the
+   * default web browser on Windows.
+   */
+  private static final String FIRST_WINDOWS_PARAMETER = "/c";
+
+  /** The second parameter for Runtime.exec() on Windows. */
+  private static final String SECOND_WINDOWS_PARAMETER = "start";
+
+  /**
+   * The third parameter for Runtime.exec() on Windows. This is a "title"
+   * parameter that the command line expects. Setting this parameter allows URLs
+   * containing spaces to work.
+   */
+  private static final String THIRD_WINDOWS_PARAMETER = "\"\"";
+
+  /**
+   * The shell parameters for Netscape that opens a given URL in an already-open
+   * copy of Netscape on many command-line systems.
+   */
+  private static final String NETSCAPE_REMOTE_PARAMETER = "-remote";
+
+  private static final String NETSCAPE_OPEN_PARAMETER_START = "openURL(";
+
+  private static final String NETSCAPE_OPEN_NEW_WINDOW = ", new-window";
+
+  private static final String NETSCAPE_OPEN_PARAMETER_END = ")";
+
+  /**
+   * The message from any exception thrown throughout the initialization
+   * process.
+   */
+  private static String errorMessage;
+
+  /**
+   * An initialization block that determines the operating system and loads the
+   * necessary runtime data.
+   */
+  static
+  {
+    loadedWithoutErrors = true;
+
+    String osName = System.getProperty("os.name");
+
+    if (osName.startsWith("Mac OS"))
+    {
+      String mrjVersion = System.getProperty("mrj.version");
+      String majorMRJVersion = mrjVersion.substring(0, 3);
+
+      try
+      {
+        double version = Double.valueOf(majorMRJVersion).doubleValue();
+
+        if (version == 2)
+        {
+          jvm = MRJ_2_0;
+        }
+        else if ((version >= 2.1) && (version < 3))
+        {
+          // Assume that all 2.x versions of MRJ work the same. MRJ 2.1 actually
+          // works via Runtime.exec() and 2.2 supports that but has an openURL()
+          // method
+          // as well that we currently ignore.
+          jvm = MRJ_2_1;
+        }
+        else if (version == 3.0)
+        {
+          jvm = MRJ_3_0;
+        }
+        else if (version >= 3.1)
+        {
+          // Assume that all 3.1 and later versions of MRJ work the same.
+          jvm = MRJ_3_1;
+        }
+        else
+        {
+          loadedWithoutErrors = false;
+          errorMessage = "Unsupported MRJ version: " + version;
+        }
+      } catch (NumberFormatException nfe)
+      {
+        loadedWithoutErrors = false;
+        errorMessage = "Invalid MRJ version: " + mrjVersion;
+      }
+    }
+    else if (osName.startsWith("Windows"))
+    {
+      if (osName.indexOf("9") != -1)
+      {
+        jvm = WINDOWS_9x;
+      }
+      else
+      {
+        jvm = WINDOWS_NT;
+      }
+    }
+    else
+    {
+      jvm = OTHER;
+    }
+
+    if (loadedWithoutErrors)
+    { // if we haven't hit any errors yet
+      loadedWithoutErrors = loadClasses();
+    }
+  }
+
+  /**
+   * This class should be never be instantiated; this just ensures so.
+   */
+  private BrowserLauncher()
+  {
+  }
+
+  /**
+   * Called by a static initializer to load any classes, fields, and methods
+   * required at runtime to locate the user's web browser.
+   * 
+   * @return <code>true</code> if all intialization succeeded
+   *         <code>false</code> if any portion of the initialization failed
+   */
+  private static boolean loadClasses()
+  {
+    switch (jvm)
+    {
+    case MRJ_2_0:
+
+      try
+      {
+        Class aeTargetClass = Class.forName("com.apple.MacOS.AETarget");
+        Class osUtilsClass = Class.forName("com.apple.MacOS.OSUtils");
+        Class appleEventClass = Class.forName("com.apple.MacOS.AppleEvent");
+        Class aeClass = Class.forName("com.apple.MacOS.ae");
+        aeDescClass = Class.forName("com.apple.MacOS.AEDesc");
+
+        aeTargetConstructor = aeTargetClass
+                .getDeclaredConstructor(new Class[]
+                { int.class });
+        appleEventConstructor = appleEventClass
+                .getDeclaredConstructor(new Class[]
+                { int.class, int.class, aeTargetClass, int.class, int.class });
+        aeDescConstructor = aeDescClass.getDeclaredConstructor(new Class[]
+        { String.class });
+
+        makeOSType = osUtilsClass.getDeclaredMethod("makeOSType",
+                new Class[]
+                { String.class });
+        putParameter = appleEventClass.getDeclaredMethod("putParameter",
+                new Class[]
+                { int.class, aeDescClass });
+        sendNoReply = appleEventClass.getDeclaredMethod("sendNoReply",
+                new Class[]
+                {});
+
+        Field keyDirectObjectField = aeClass
+                .getDeclaredField("keyDirectObject");
+        keyDirectObject = (Integer) keyDirectObjectField.get(null);
+
+        Field autoGenerateReturnIDField = appleEventClass
+                .getDeclaredField("kAutoGenerateReturnID");
+        kAutoGenerateReturnID = (Integer) autoGenerateReturnIDField
+                .get(null);
+
+        Field anyTransactionIDField = appleEventClass
+                .getDeclaredField("kAnyTransactionID");
+        kAnyTransactionID = (Integer) anyTransactionIDField.get(null);
+      } catch (ClassNotFoundException cnfe)
+      {
+        errorMessage = cnfe.getMessage();
+
+        return false;
+      } catch (NoSuchMethodException nsme)
+      {
+        errorMessage = nsme.getMessage();
+
+        return false;
+      } catch (NoSuchFieldException nsfe)
+      {
+        errorMessage = nsfe.getMessage();
+
+        return false;
+      } catch (IllegalAccessException iae)
+      {
+        errorMessage = iae.getMessage();
+
+        return false;
+      }
+
+      break;
+
+    case MRJ_2_1:
+
+      try
+      {
+        mrjFileUtilsClass = Class.forName("com.apple.mrj.MRJFileUtils");
+        mrjOSTypeClass = Class.forName("com.apple.mrj.MRJOSType");
+
+        Field systemFolderField = mrjFileUtilsClass
+                .getDeclaredField("kSystemFolderType");
+        kSystemFolderType = systemFolderField.get(null);
+        findFolder = mrjFileUtilsClass.getDeclaredMethod("findFolder",
+                new Class[]
+                { mrjOSTypeClass });
+        getFileCreator = mrjFileUtilsClass.getDeclaredMethod(
+                "getFileCreator", new Class[]
+                { File.class });
+        getFileType = mrjFileUtilsClass.getDeclaredMethod("getFileType",
+                new Class[]
+                { File.class });
+      } catch (ClassNotFoundException cnfe)
+      {
+        errorMessage = cnfe.getMessage();
+
+        return false;
+      } catch (NoSuchFieldException nsfe)
+      {
+        errorMessage = nsfe.getMessage();
+
+        return false;
+      } catch (NoSuchMethodException nsme)
+      {
+        errorMessage = nsme.getMessage();
+
+        return false;
+      } catch (SecurityException se)
+      {
+        errorMessage = se.getMessage();
+
+        return false;
+      } catch (IllegalAccessException iae)
+      {
+        errorMessage = iae.getMessage();
+
+        return false;
+      }
+
+      break;
+
+    case MRJ_3_0:
+
+      try
+      {
+        Class linker = Class.forName("com.apple.mrj.jdirect.Linker");
+        Constructor constructor = linker.getConstructor(new Class[]
+        { Class.class });
+        linkage = constructor.newInstance(new Object[]
+        { BrowserLauncher.class });
+      } catch (ClassNotFoundException cnfe)
+      {
+        errorMessage = cnfe.getMessage();
+
+        return false;
+      } catch (NoSuchMethodException nsme)
+      {
+        errorMessage = nsme.getMessage();
+
+        return false;
+      } catch (InvocationTargetException ite)
+      {
+        errorMessage = ite.getMessage();
+
+        return false;
+      } catch (InstantiationException ie)
+      {
+        errorMessage = ie.getMessage();
+
+        return false;
+      } catch (IllegalAccessException iae)
+      {
+        errorMessage = iae.getMessage();
+
+        return false;
+      }
+
+      break;
+
+    case MRJ_3_1:
+
+      try
+      {
+        mrjFileUtilsClass = Class.forName("com.apple.mrj.MRJFileUtils");
+        openURL = mrjFileUtilsClass.getDeclaredMethod("openURL",
+                new Class[]
+                { String.class });
+      } catch (ClassNotFoundException cnfe)
+      {
+        errorMessage = cnfe.getMessage();
+
+        return false;
+      } catch (NoSuchMethodException nsme)
+      {
+        errorMessage = nsme.getMessage();
+
+        return false;
+      }
+
+      break;
+
+    default:
+      break;
+    }
+
+    return true;
+  }
+
+  /**
+   * Attempts to locate the default web browser on the local system. s results
+   * so it only locates the browser once for each use of this class per JVM
+   * instance.
+   * 
+   * @return The browser for the system. Note that this may not be what you
+   *         would consider to be a standard web browser; instead, it's the
+   *         application that gets called to open the default web browser. In
+   *         some cases, this will be a non-String object that provides the
+   *         means of calling the default browser.
+   */
+  private static Object locateBrowser()
+  {
+    if (browser != null)
+    {
+      return browser;
+    }
+
+    switch (jvm)
+    {
+    case MRJ_2_0:
+
+      try
+      {
+        Integer finderCreatorCode = (Integer) makeOSType.invoke(null,
+                new Object[]
+                { FINDER_CREATOR });
+        Object aeTarget = aeTargetConstructor.newInstance(new Object[]
+        { finderCreatorCode });
+        Integer gurlType = (Integer) makeOSType.invoke(null, new Object[]
+        { GURL_EVENT });
+        Object appleEvent = appleEventConstructor.newInstance(new Object[]
+        { gurlType, gurlType, aeTarget, kAutoGenerateReturnID,
+            kAnyTransactionID });
+
+        // Don't set browser = appleEvent because then the next time we call
+        // locateBrowser(), we'll get the same AppleEvent, to which we'll
+        // already have
+        // added the relevant parameter. Instead, regenerate the AppleEvent
+        // every time.
+        // There's probably a way to do this better; if any has any ideas,
+        // please let
+        // me know.
+        return appleEvent;
+      } catch (IllegalAccessException iae)
+      {
+        browser = null;
+        errorMessage = iae.getMessage();
+
+        return browser;
+      } catch (InstantiationException ie)
+      {
+        browser = null;
+        errorMessage = ie.getMessage();
+
+        return browser;
+      } catch (InvocationTargetException ite)
+      {
+        browser = null;
+        errorMessage = ite.getMessage();
+
+        return browser;
+      }
+
+    case MRJ_2_1:
+
+      File systemFolder;
+
+      try
+      {
+        systemFolder = (File) findFolder.invoke(null, new Object[]
+        { kSystemFolderType });
+      } catch (IllegalArgumentException iare)
+      {
+        browser = null;
+        errorMessage = iare.getMessage();
+
+        return browser;
+      } catch (IllegalAccessException iae)
+      {
+        browser = null;
+        errorMessage = iae.getMessage();
+
+        return browser;
+      } catch (InvocationTargetException ite)
+      {
+        browser = null;
+        errorMessage = ite.getTargetException().getClass() + ": "
+                + ite.getTargetException().getMessage();
+
+        return browser;
+      }
+
+      String[] systemFolderFiles = systemFolder.list();
+
+      // Avoid a FilenameFilter because that can't be stopped mid-list
+      for (int i = 0; i < systemFolderFiles.length; i++)
+      {
+        try
+        {
+          File file = new File(systemFolder, systemFolderFiles[i]);
+
+          if (!file.isFile())
+          {
+            continue;
+          }
+
+          // We're looking for a file with a creator code of 'MACS' and
+          // a type of 'FNDR'. Only requiring the type results in non-Finder
+          // applications being picked up on certain Mac OS 9 systems,
+          // especially German ones, and sending a GURL event to those
+          // applications results in a logout under Multiple Users.
+          Object fileType = getFileType.invoke(null, new Object[]
+          { file });
+
+          if (FINDER_TYPE.equals(fileType.toString()))
+          {
+            Object fileCreator = getFileCreator.invoke(null, new Object[]
+            { file });
+
+            if (FINDER_CREATOR.equals(fileCreator.toString()))
+            {
+              browser = file.toString(); // Actually the Finder, but that's OK
+
+              return browser;
+            }
+          }
+        } catch (IllegalArgumentException iare)
+        {
+          errorMessage = iare.getMessage();
+
+          return null;
+        } catch (IllegalAccessException iae)
+        {
+          browser = null;
+          errorMessage = iae.getMessage();
+
+          return browser;
+        } catch (InvocationTargetException ite)
+        {
+          browser = null;
+          errorMessage = ite.getTargetException().getClass() + ": "
+                  + ite.getTargetException().getMessage();
+
+          return browser;
+        }
+      }
+
+      browser = null;
+
+      break;
+
+    case MRJ_3_0:
+    case MRJ_3_1:
+      browser = ""; // Return something non-null
+
+      break;
+
+    case WINDOWS_NT:
+      browser = "cmd.exe";
+
+      break;
+
+    case WINDOWS_9x:
+      browser = "command.com";
+
+      break;
+
+    case OTHER:
+    default:
+      browser = jalview.bin.Cache.getDefault("DEFAULT_BROWSER", "firefox");
+
+      break;
+    }
+
+    return browser;
+  }
+
+  /**
+   * used to ensure that browser is up-to-date after a configuration change
+   * (Unix DEFAULT_BROWSER property change).
+   */
+  public static void resetBrowser()
+  {
+    browser = null;
+  }
+
+  /**
+   * Attempts to open the default web browser to the given URL.
+   * 
+   * @param url
+   *                The URL to open
+   * @throws IOException
+   *                 If the web browser could not be located or does not run
+   */
+  public static void openURL(String url) throws IOException
+  {
+    if (!loadedWithoutErrors)
+    {
+      throw new IOException("Exception in finding browser: " + errorMessage);
+    }
+
+    Object browser = locateBrowser();
+
+    if (browser == null)
+    {
+      throw new IOException("Unable to locate browser: " + errorMessage);
+    }
+
+    switch (jvm)
+    {
+    case MRJ_2_0:
+
+      Object aeDesc = null;
+
+      try
+      {
+        aeDesc = aeDescConstructor.newInstance(new Object[]
+        { url });
+        putParameter.invoke(browser, new Object[]
+        { keyDirectObject, aeDesc });
+        sendNoReply.invoke(browser, new Object[]
+        {});
+      } catch (InvocationTargetException ite)
+      {
+        throw new IOException(
+                "InvocationTargetException while creating AEDesc: "
+                        + ite.getMessage());
+      } catch (IllegalAccessException iae)
+      {
+        throw new IOException(
+                "IllegalAccessException while building AppleEvent: "
+                        + iae.getMessage());
+      } catch (InstantiationException ie)
+      {
+        throw new IOException(
+                "InstantiationException while creating AEDesc: "
+                        + ie.getMessage());
+      } finally
+      {
+        aeDesc = null; // Encourage it to get disposed if it was created
+        browser = null; // Ditto
+      }
+
+      break;
+
+    case MRJ_2_1:
+      Runtime.getRuntime().exec(new String[]
+      { (String) browser, url });
+
+      break;
+
+    case MRJ_3_0:
+
+      int[] instance = new int[1];
+      int result = ICStart(instance, 0);
+
+      if (result == 0)
+      {
+        int[] selectionStart = new int[]
+        { 0 };
+        byte[] urlBytes = url.getBytes();
+        int[] selectionEnd = new int[]
+        { urlBytes.length };
+        result = ICLaunchURL(instance[0], new byte[]
+        { 0 }, urlBytes, urlBytes.length, selectionStart, selectionEnd);
+
+        if (result == 0)
+        {
+          // Ignore the return value; the URL was launched successfully
+          // regardless of what happens here.
+          ICStop(instance);
+        }
+        else
+        {
+          throw new IOException("Unable to launch URL: " + result);
+        }
+      }
+      else
+      {
+        throw new IOException(
+                "Unable to create an Internet Config instance: " + result);
+      }
+
+      break;
+
+    case MRJ_3_1:
+
+      try
+      {
+        openURL.invoke(null, new Object[]
+        { url });
+      } catch (InvocationTargetException ite)
+      {
+        throw new IOException(
+                "InvocationTargetException while calling openURL: "
+                        + ite.getMessage());
+      } catch (IllegalAccessException iae)
+      {
+        throw new IOException(
+                "IllegalAccessException while calling openURL: "
+                        + iae.getMessage());
+      }
+
+      break;
+
+    case WINDOWS_NT:
+    case WINDOWS_9x:
+
+      // Add quotes around the URL to allow ampersands and other special
+      // characters to work.
+      Process process = Runtime.getRuntime().exec(
+              new String[]
+              { (String) browser, FIRST_WINDOWS_PARAMETER,
+                  SECOND_WINDOWS_PARAMETER, THIRD_WINDOWS_PARAMETER,
+                  '"' + url + '"' });
+
+      // This avoids a memory leak on some versions of Java on Windows.
+      // That's hinted at in
+      // <http://developer.java.sun.com/developer/qow/archive/68/>.
+      try
+      {
+        process.waitFor();
+        process.exitValue();
+      } catch (InterruptedException ie)
+      {
+        throw new IOException(
+                "InterruptedException while launching browser: "
+                        + ie.getMessage());
+      }
+
+      break;
+
+    case OTHER:
+
+      // Assume that we're on Unix and that Netscape (actually Firefox) is
+      // installed
+      // First, attempt to open the URL in a currently running session of
+      // Netscape
+      // JBPNote log debug
+
+      /*
+       * System.out.println("Executing : "+browser+" "+
+       * NETSCAPE_REMOTE_PARAMETER+" "+ NETSCAPE_OPEN_PARAMETER_START + url +
+       * NETSCAPE_OPEN_NEW_WINDOW + NETSCAPE_OPEN_PARAMETER_END);
+       */
+      process = Runtime.getRuntime().exec(
+              new String[]
+              {
+                  (String) browser,
+                  NETSCAPE_REMOTE_PARAMETER,
+
+                  NETSCAPE_OPEN_PARAMETER_START + url
+                          + NETSCAPE_OPEN_NEW_WINDOW
+                          + NETSCAPE_OPEN_PARAMETER_END });
+
+      try
+      {
+        int exitCode = process.waitFor();
+
+        if (exitCode != 0)
+        { // if Netscape was not open
+          Runtime.getRuntime().exec(new String[]
+          { (String) browser, url });
+        }
+      } catch (InterruptedException ie)
+      {
+        throw new IOException(
+                "InterruptedException while launching browser: "
+                        + ie.getMessage());
+      }
+
+      break;
+
+    default:
+
+      // This should never occur, but if it does, we'll try the simplest thing
+      // possible
+      Runtime.getRuntime().exec(new String[]
+      { (String) browser, url });
+
+      break;
+    }
+  }
+
+  /**
+   * Methods required for Mac OS X. The presence of native methods does not
+   * cause any problems on other platforms.
+   */
+  private native static int ICStart(int[] instance, int signature);
+
+  private native static int ICStop(int[] instance);
+
+  private native static int ICLaunchURL(int instance, byte[] hint,
+          byte[] data, int len, int[] selectionStart, int[] selectionEnd);
+}
diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index 67a668a..9cb2430 100755
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -1,226 +1,236 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.util;
-
-import jalview.datamodel.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class Comparison
-{
-  /** DOCUMENT ME!! */
-  public static final String GapChars = " .-";
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param ii DOCUMENT ME!
-   * @param jj DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public static final float compare(SequenceI ii, SequenceI jj)
-  {
-    return Comparison.compare(ii, jj, 0, ii.getLength() - 1);
-  }
-
-  /**
-   * this was supposed to be an ungapped pid calculation
-   * @param ii SequenceI
-   * @param jj SequenceI
-   * @param start int
-   * @param end int
-   * @return float
-   */
-  public static float compare(SequenceI ii, SequenceI jj, int start, int end)
-  {
-    String si = ii.getSequenceAsString();
-    String sj = jj.getSequenceAsString();
-
-    int ilen = si.length() - 1;
-    int jlen = sj.length() - 1;
-
-    while (jalview.util.Comparison.isGap(si.charAt(start + ilen)))
-    {
-      ilen--;
-    }
-
-    while (jalview.util.Comparison.isGap(sj.charAt(start + jlen)))
-    {
-      jlen--;
-    }
-
-    int count = 0;
-    int match = 0;
-    float pid = -1;
-
-    if (ilen > jlen)
-    {
-      for (int j = 0; j < jlen; j++)
-      {
-        if (si.substring(start + j, start + j + 1).equals(sj.substring(start +
-            j, start + j + 1)))
-        {
-          match++;
-        }
-
-        count++;
-      }
-
-      pid = (float) match / (float) ilen * 100;
-    }
-    else
-    {
-      for (int j = 0; j < jlen; j++)
-      {
-        if (si.substring(start + j, start + j + 1).equals(sj.substring(start +
-            j, start + j + 1)))
-        {
-          match++;
-        }
-
-        count++;
-      }
-
-      pid = (float) match / (float) jlen * 100;
-    }
-
-    return pid;
-  }
-
-  /**
-   * this is a gapped PID calculation
-   *
-   * @param s1 SequenceI
-   * @param s2 SequenceI
-   * @return float
-   */
-  public final static float PID(String seq1, String seq2)
-  {
-    return PID(seq1, seq2, 0, seq1.length());
-  }
-
-  static final int caseShift = 'a' - 'A';
-
-  // Another pid with region specification
-  public final static float PID(String seq1, String seq2, int start, int end)
-  {
-
-    int s1len = seq1.length();
-    int s2len = seq2.length();
-
-    int len = Math.min(s1len, s2len);
-
-    if (end < len)
-    {
-      len = end;
-    }
-
-    if (len < start)
-    {
-      start = len - 1; // we just use a single residue for the difference
-    }
-
-    int bad = 0;
-    char chr1;
-    char chr2;
-
-    for (int i = start; i < len; i++)
-    {
-      chr1 = seq1.charAt(i);
-
-      chr2 = seq2.charAt(i);
-
-      if ('a' <= chr1 && chr1 <= 'z')
-      {
-        // TO UPPERCASE !!!
-        //Faster than toUpperCase
-        chr1 -= caseShift;
-      }
-      if ('a' <= chr2 && chr2 <= 'z')
-      {
-        // TO UPPERCASE !!!
-        //Faster than toUpperCase
-        chr2 -= caseShift;
-      }
-
-      if (chr1 != chr2 && !isGap(chr1) && !isGap(chr2))
-      {
-        bad++;
-      }
-    }
-
-    return ( (float) 100 * (len - bad)) / len;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param c DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public static final boolean isGap(char c)
-  {
-    return (c == '-' || c == '.' || c == ' ') ? true : false;
-  }
-
-  public static final boolean isNucleotide(SequenceI[] seqs)
-  {
-    int i = 0, iSize = seqs.length, j, jSize;
-    float nt = 0, aa = 0;
-    char c;
-    while (i < iSize)
-    {
-      jSize = seqs[i].getLength();
-      for (j = 0; j < jSize; j++)
-      {
-        c = seqs[i].getCharAt(j);
-        if ('a' <= c && c <= 'z')
-        {
-          c -= ('a' - 'A');
-        }
-
-        if (c == 'A' || c == 'G' || c == 'C' || c == 'T' || c == 'U')
-        {
-          nt++;
-        }
-        else if (!jalview.util.Comparison.isGap(seqs[i].getCharAt(j)))
-        {
-          aa++;
-        }
-      }
-      i++;
-    }
-
-    if ( (nt / (nt + aa)) > 0.85f)
-    {
-      return true;
-    }
-    else
-    {
-      return false;
-    }
-
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.util;
+
+import jalview.datamodel.*;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class Comparison
+{
+  /** DOCUMENT ME!! */
+  public static final String GapChars = " .-";
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param ii
+   *                DOCUMENT ME!
+   * @param jj
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public static final float compare(SequenceI ii, SequenceI jj)
+  {
+    return Comparison.compare(ii, jj, 0, ii.getLength() - 1);
+  }
+
+  /**
+   * this was supposed to be an ungapped pid calculation
+   * 
+   * @param ii
+   *                SequenceI
+   * @param jj
+   *                SequenceI
+   * @param start
+   *                int
+   * @param end
+   *                int
+   * @return float
+   */
+  public static float compare(SequenceI ii, SequenceI jj, int start, int end)
+  {
+    String si = ii.getSequenceAsString();
+    String sj = jj.getSequenceAsString();
+
+    int ilen = si.length() - 1;
+    int jlen = sj.length() - 1;
+
+    while (jalview.util.Comparison.isGap(si.charAt(start + ilen)))
+    {
+      ilen--;
+    }
+
+    while (jalview.util.Comparison.isGap(sj.charAt(start + jlen)))
+    {
+      jlen--;
+    }
+
+    int count = 0;
+    int match = 0;
+    float pid = -1;
+
+    if (ilen > jlen)
+    {
+      for (int j = 0; j < jlen; j++)
+      {
+        if (si.substring(start + j, start + j + 1).equals(
+                sj.substring(start + j, start + j + 1)))
+        {
+          match++;
+        }
+
+        count++;
+      }
+
+      pid = (float) match / (float) ilen * 100;
+    }
+    else
+    {
+      for (int j = 0; j < jlen; j++)
+      {
+        if (si.substring(start + j, start + j + 1).equals(
+                sj.substring(start + j, start + j + 1)))
+        {
+          match++;
+        }
+
+        count++;
+      }
+
+      pid = (float) match / (float) jlen * 100;
+    }
+
+    return pid;
+  }
+
+  /**
+   * this is a gapped PID calculation
+   * 
+   * @param s1
+   *                SequenceI
+   * @param s2
+   *                SequenceI
+   * @return float
+   */
+  public final static float PID(String seq1, String seq2)
+  {
+    return PID(seq1, seq2, 0, seq1.length());
+  }
+
+  static final int caseShift = 'a' - 'A';
+
+  // Another pid with region specification
+  public final static float PID(String seq1, String seq2, int start, int end)
+  {
+
+    int s1len = seq1.length();
+    int s2len = seq2.length();
+
+    int len = Math.min(s1len, s2len);
+
+    if (end < len)
+    {
+      len = end;
+    }
+
+    if (len < start)
+    {
+      start = len - 1; // we just use a single residue for the difference
+    }
+
+    int bad = 0;
+    char chr1;
+    char chr2;
+
+    for (int i = start; i < len; i++)
+    {
+      chr1 = seq1.charAt(i);
+
+      chr2 = seq2.charAt(i);
+
+      if ('a' <= chr1 && chr1 <= 'z')
+      {
+        // TO UPPERCASE !!!
+        // Faster than toUpperCase
+        chr1 -= caseShift;
+      }
+      if ('a' <= chr2 && chr2 <= 'z')
+      {
+        // TO UPPERCASE !!!
+        // Faster than toUpperCase
+        chr2 -= caseShift;
+      }
+
+      if (chr1 != chr2 && !isGap(chr1) && !isGap(chr2))
+      {
+        bad++;
+      }
+    }
+
+    return ((float) 100 * (len - bad)) / len;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param c
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public static final boolean isGap(char c)
+  {
+    return (c == '-' || c == '.' || c == ' ') ? true : false;
+  }
+
+  public static final boolean isNucleotide(SequenceI[] seqs)
+  {
+    int i = 0, iSize = seqs.length, j, jSize;
+    float nt = 0, aa = 0;
+    char c;
+    while (i < iSize)
+    {
+      jSize = seqs[i].getLength();
+      for (j = 0; j < jSize; j++)
+      {
+        c = seqs[i].getCharAt(j);
+        if ('a' <= c && c <= 'z')
+        {
+          c -= ('a' - 'A');
+        }
+
+        if (c == 'A' || c == 'G' || c == 'C' || c == 'T' || c == 'U')
+        {
+          nt++;
+        }
+        else if (!jalview.util.Comparison.isGap(seqs[i].getCharAt(j)))
+        {
+          aa++;
+        }
+      }
+      i++;
+    }
+
+    if ((nt / (nt + aa)) > 0.85f)
+    {
+      return true;
+    }
+    else
+    {
+      return false;
+    }
+
+  }
+}
diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java
index 7592748..9704170 100755
--- a/src/jalview/util/DBRefUtils.java
+++ b/src/jalview/util/DBRefUtils.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -28,12 +28,15 @@ public class DBRefUtils
    * Utilities for handling DBRef objects and their collections.
    */
   /**
-   *
-   * @param dbrefs Vector of DBRef objects to search
-   * @param sources String[] array of source DBRef IDs to retrieve
+   * 
+   * @param dbrefs
+   *                Vector of DBRef objects to search
+   * @param sources
+   *                String[] array of source DBRef IDs to retrieve
    * @return Vector
    */
-  public static DBRefEntry[] selectRefs(DBRefEntry[] dbrefs, String[] sources)
+  public static DBRefEntry[] selectRefs(DBRefEntry[] dbrefs,
+          String[] sources)
   {
     if (dbrefs == null)
     {
@@ -68,93 +71,113 @@ public class DBRefUtils
       return reply;
     }
     res = null;
-    // there are probable  memory leaks in the hashtable!
+    // there are probable memory leaks in the hashtable!
     return null;
   }
 
   /**
    * isDasCoordinateSystem
-   *
-   * @param string String
-   * @param dBRefEntry DBRefEntry
-   * @return boolean true if Source DBRefEntry is compatible with DAS CoordinateSystem name
+   * 
+   * @param string
+   *                String
+   * @param dBRefEntry
+   *                DBRefEntry
+   * @return boolean true if Source DBRefEntry is compatible with DAS
+   *         CoordinateSystem name
    */
   public static Hashtable DasCoordinateSystemsLookup = null;
+
   public static boolean isDasCoordinateSystem(String string,
-                                              DBRefEntry dBRefEntry)
+          DBRefEntry dBRefEntry)
   {
     if (DasCoordinateSystemsLookup == null)
-    { 
+    {
       // TODO: Make a DasCoordinateSystemsLookup properties resource
       // Initialise
       DasCoordinateSystemsLookup = new Hashtable();
       DasCoordinateSystemsLookup.put("pdbresnum",
-                                     jalview.datamodel.DBRefSource.PDB);
+              jalview.datamodel.DBRefSource.PDB);
       DasCoordinateSystemsLookup.put("uniprot",
-                                     jalview.datamodel.DBRefSource.UNIPROT);
+              jalview.datamodel.DBRefSource.UNIPROT);
       DasCoordinateSystemsLookup.put("EMBL",
               jalview.datamodel.DBRefSource.EMBL);
-      //DasCoordinateSystemsLookup.put("EMBL",
-      //        jalview.datamodel.DBRefSource.EMBLCDS);
+      // DasCoordinateSystemsLookup.put("EMBL",
+      // jalview.datamodel.DBRefSource.EMBLCDS);
     }
 
-    String coordsys = (String) DasCoordinateSystemsLookup.get(string.
-        toLowerCase());
+    String coordsys = (String) DasCoordinateSystemsLookup.get(string
+            .toLowerCase());
     if (coordsys != null)
     {
       return coordsys.equals(dBRefEntry.getSource());
     }
     return false;
   }
-  public static Hashtable CanonicalSourceNameLookup=null;
+
+  public static Hashtable CanonicalSourceNameLookup = null;
+
   /**
-   * look up source in an internal list of database reference sources
-   * and return the canonical jalview name for the source, or the original
-   * string if it has no canonical form.
+   * look up source in an internal list of database reference sources and return
+   * the canonical jalview name for the source, or the original string if it has
+   * no canonical form.
+   * 
    * @param source
-   * @return canonical jalview source (one of jalview.datamodel.DBRefSource.*) or original source
+   * @return canonical jalview source (one of jalview.datamodel.DBRefSource.*)
+   *         or original source
    */
   public static String getCanonicalName(String source)
   {
-    if (CanonicalSourceNameLookup==null) {
+    if (CanonicalSourceNameLookup == null)
+    {
       CanonicalSourceNameLookup = new Hashtable();
-      CanonicalSourceNameLookup.put("uniprotkb/swiss-prot", jalview.datamodel.DBRefSource.UNIPROT);
-      CanonicalSourceNameLookup.put("uniprotkb/trembl", jalview.datamodel.DBRefSource.UNIPROT);
-      CanonicalSourceNameLookup.put("pdb", jalview.datamodel.DBRefSource.PDB);
+      CanonicalSourceNameLookup.put("uniprotkb/swiss-prot",
+              jalview.datamodel.DBRefSource.UNIPROT);
+      CanonicalSourceNameLookup.put("uniprotkb/trembl",
+              jalview.datamodel.DBRefSource.UNIPROT);
+      CanonicalSourceNameLookup.put("pdb",
+              jalview.datamodel.DBRefSource.PDB);
     }
-    String canonical = (String) CanonicalSourceNameLookup.get(source.
-        toLowerCase());
-    if (canonical==null)
+    String canonical = (String) CanonicalSourceNameLookup.get(source
+            .toLowerCase());
+    if (canonical == null)
     {
       return source;
     }
     return canonical;
   }
+
   /**
-   * find RefEntry corresponding to a particular pattern
-   * the equals method of each entry is used, from String attributes right down to Mapping attributes.
-   * @param ref Set of references to search
-   * @param entry pattern to collect - null any entry for wildcard match
+   * find RefEntry corresponding to a particular pattern the equals method of
+   * each entry is used, from String attributes right down to Mapping
+   * attributes.
+   * 
+   * @param ref
+   *                Set of references to search
+   * @param entry
+   *                pattern to collect - null any entry for wildcard match
    * @return
    */
   public static DBRefEntry[] searchRefs(DBRefEntry[] ref, DBRefEntry entry)
   {
-    return searchRefs(ref, entry, matchDbAndIdAndEitherMapOrEquivalentMapList);
+    return searchRefs(ref, entry,
+            matchDbAndIdAndEitherMapOrEquivalentMapList);
   }
-  public static DBRefEntry[] searchRefs(DBRefEntry[] ref, DBRefEntry entry, DbRefComp comparator)
+
+  public static DBRefEntry[] searchRefs(DBRefEntry[] ref, DBRefEntry entry,
+          DbRefComp comparator)
   {
-    if (ref==null || entry==null)
+    if (ref == null || entry == null)
       return null;
     Vector rfs = new Vector();
-    for (int i=0; i<ref.length;i++)
+    for (int i = 0; i < ref.length; i++)
     {
       if (comparator.matches(entry, ref[i]))
       {
-              rfs.addElement(ref[i]);
+        rfs.addElement(ref[i]);
       }
     }
     // TODO Auto-generated method stub
-    if (rfs.size()>0)
+    if (rfs.size() > 0)
     {
       DBRefEntry[] rf = new DBRefEntry[rfs.size()];
       rfs.copyInto(rf);
@@ -162,233 +185,264 @@ public class DBRefUtils
     }
     return null;
   }
-  public interface DbRefComp {
+
+  public interface DbRefComp
+  {
     public boolean matches(DBRefEntry refa, DBRefEntry refb);
   }
+
   /**
    * match on all non-null fields in refa
    */
   public static DbRefComp matchNonNullonA = new DbRefComp()
+  {
+    public boolean matches(DBRefEntry refa, DBRefEntry refb)
     {
-          public boolean matches(DBRefEntry refa, DBRefEntry refb)
+      if (refa.getSource() == null
+              || refb.getSource().equals(refa.getSource()))
+      {
+        if (refa.getVersion() == null
+                || refb.getVersion().equals(refa.getVersion()))
+        {
+          if (refa.getAccessionId() == null
+                  || refb.getAccessionId().equals(refa.getAccessionId()))
           {
-            if (refa.getSource()==null || refb.getSource().equals(refa.getSource()))
+            if (refa.getMap() == null
+                    || (refb.getMap() != null && refb.getMap().equals(
+                            refa.getMap())))
             {
-              if (refa.getVersion()==null || refb.getVersion().equals(refa.getVersion()))
-              {
-                if (refa.getAccessionId()==null || refb.getAccessionId().equals(refa.getAccessionId()))
-                {
-                  if (refa.getMap()==null || (refb.getMap()!=null && refb.getMap().equals(refa.getMap())))
-                  {
-                    return true; 
-                  }
-                }
-              }
+              return true;
             }
-            return false;
           }
-    };
-    /**
-     * either field is null or field matches for all of source, version, accession id and map.
-     */
-    public static DbRefComp matchEitherNonNull = new DbRefComp()
+        }
+      }
+      return false;
+    }
+  };
+
+  /**
+   * either field is null or field matches for all of source, version, accession
+   * id and map.
+   */
+  public static DbRefComp matchEitherNonNull = new DbRefComp()
+  {
+    public boolean matches(DBRefEntry refa, DBRefEntry refb)
     {
-          public boolean matches(DBRefEntry refa, DBRefEntry refb)
+      if ((refa.getSource() == null || refb.getSource() == null)
+              || refb.getSource().equals(refa.getSource()))
+      {
+        if ((refa.getVersion() == null || refb.getVersion() == null)
+                || refb.getVersion().equals(refa.getVersion()))
+        {
+          if ((refa.getAccessionId() == null || refb.getAccessionId() == null)
+                  || refb.getAccessionId().equals(refa.getAccessionId()))
           {
-            if ((refa.getSource()==null || refb.getSource()==null) 
-                    || refb.getSource().equals(refa.getSource()))
+            if ((refa.getMap() == null || refb.getMap() == null)
+                    || (refb.getMap() != null && refb.getMap().equals(
+                            refa.getMap())))
             {
-              if ((refa.getVersion()==null || refb.getVersion()==null) 
-                      || refb.getVersion().equals(refa.getVersion()))
-              {
-                if ((refa.getAccessionId()==null || refb.getAccessionId()==null) 
-                        || refb.getAccessionId().equals(refa.getAccessionId()))
-                {
-                  if ((refa.getMap()==null || refb.getMap()==null) 
-                          || (refb.getMap()!=null && refb.getMap().equals(refa.getMap())))
-                  {
-                    return true; 
-                  }
-                }
-              }
+              return true;
             }
-            return false;
           }
-    };
-    /**
-     * accession ID and DB must be identical. Version is ignored. Map is either not defined or is a match (or is compatible?)
-     */
-    public static DbRefComp matchDbAndIdAndEitherMap = new DbRefComp()
+        }
+      }
+      return false;
+    }
+  };
+
+  /**
+   * accession ID and DB must be identical. Version is ignored. Map is either
+   * not defined or is a match (or is compatible?)
+   */
+  public static DbRefComp matchDbAndIdAndEitherMap = new DbRefComp()
+  {
+    public boolean matches(DBRefEntry refa, DBRefEntry refb)
     {
-          public boolean matches(DBRefEntry refa, DBRefEntry refb)
+      if (refa.getSource() != null && refb.getSource() != null
+              && refb.getSource().equals(refa.getSource()))
+      {
+        // We dont care about version
+        // if ((refa.getVersion()==null || refb.getVersion()==null)
+        // || refb.getVersion().equals(refa.getVersion()))
+        // {
+        if (refa.getAccessionId() != null && refb.getAccessionId() != null
+                || refb.getAccessionId().equals(refa.getAccessionId()))
+        {
+          if ((refa.getMap() == null || refb.getMap() == null)
+                  || (refa.getMap() != null && refb.getMap() != null && refb
+                          .getMap().equals(refa.getMap())))
           {
-            if (refa.getSource()!=null && refb.getSource()!=null 
-                    && refb.getSource().equals(refa.getSource()))
-            {
-              // We dont care about version
-              //if ((refa.getVersion()==null || refb.getVersion()==null) 
-              //        || refb.getVersion().equals(refa.getVersion()))
-              //{
-              if (refa.getAccessionId()!=null && refb.getAccessionId()!=null 
-                      || refb.getAccessionId().equals(refa.getAccessionId()))
-                {
-                  if ((refa.getMap()==null || refb.getMap()==null) 
-                          || (refa.getMap()!=null && refb.getMap()!=null && refb.getMap().equals(refa.getMap())))
-                  {
-                    return true; 
-                  }
-                }
-              }
-            return false;
+            return true;
           }
-    };
-    /**
-     * accession ID and DB must be identical. Version is ignored. 
-     * No map on either or map but no maplist on either or maplist of map on a is the complement of maplist of map on b.
-     */
-    public static DbRefComp matchDbAndIdAndComplementaryMapList = new DbRefComp()
+        }
+      }
+      return false;
+    }
+  };
+
+  /**
+   * accession ID and DB must be identical. Version is ignored. No map on either
+   * or map but no maplist on either or maplist of map on a is the complement of
+   * maplist of map on b.
+   */
+  public static DbRefComp matchDbAndIdAndComplementaryMapList = new DbRefComp()
+  {
+    public boolean matches(DBRefEntry refa, DBRefEntry refb)
     {
-          public boolean matches(DBRefEntry refa, DBRefEntry refb)
-          {
-            if (refa.getSource()!=null && refb.getSource()!=null 
-                    && refb.getSource().equals(refa.getSource()))
+      if (refa.getSource() != null && refb.getSource() != null
+              && refb.getSource().equals(refa.getSource()))
+      {
+        // We dont care about version
+        // if ((refa.getVersion()==null || refb.getVersion()==null)
+        // || refb.getVersion().equals(refa.getVersion()))
+        // {
+        if (refa.getAccessionId() != null && refb.getAccessionId() != null
+                || refb.getAccessionId().equals(refa.getAccessionId()))
+        {
+          if ((refa.getMap() == null && refb.getMap() == null)
+                  || (refa.getMap() != null && refb.getMap() != null))
+            if ((refb.getMap().getMap() == null && refa.getMap().getMap() == null)
+                    || (refb.getMap().getMap() != null
+                            && refa.getMap().getMap() != null && refb
+                            .getMap().getMap().getInverse().equals(
+                                    refa.getMap().getMap())))
             {
-              // We dont care about version
-              //if ((refa.getVersion()==null || refb.getVersion()==null) 
-              //        || refb.getVersion().equals(refa.getVersion()))
-              //{
-              if (refa.getAccessionId()!=null && refb.getAccessionId()!=null 
-                      || refb.getAccessionId().equals(refa.getAccessionId()))
-                {
-                  if ((refa.getMap()==null && refb.getMap()==null) 
-                          || (refa.getMap()!=null && refb.getMap()!=null))
-                    if ((refb.getMap().getMap()==null && refa.getMap().getMap()==null)
-                            || (refb.getMap().getMap()!=null && refa.getMap().getMap()!=null
-                            && refb.getMap().getMap().getInverse().equals(refa.getMap().getMap())))
-                  {
-                    return true; 
-                  }
-                }
-              }
-            return false;
-          }
-    };
-    /**
-     * accession ID and DB must be identical. Version is ignored. 
-     * No map on both or or map but no maplist on either or maplist of map on a is equivalent to the maplist of map on b.
-     */
-    public static DbRefComp matchDbAndIdAndEquivalentMapList = new DbRefComp()
+              return true;
+            }
+        }
+      }
+      return false;
+    }
+  };
+
+  /**
+   * accession ID and DB must be identical. Version is ignored. No map on both
+   * or or map but no maplist on either or maplist of map on a is equivalent to
+   * the maplist of map on b.
+   */
+  public static DbRefComp matchDbAndIdAndEquivalentMapList = new DbRefComp()
+  {
+    public boolean matches(DBRefEntry refa, DBRefEntry refb)
     {
-          public boolean matches(DBRefEntry refa, DBRefEntry refb)
+      if (refa.getSource() != null && refb.getSource() != null
+              && refb.getSource().equals(refa.getSource()))
+      {
+        // We dont care about version
+        // if ((refa.getVersion()==null || refb.getVersion()==null)
+        // || refb.getVersion().equals(refa.getVersion()))
+        // {
+        if (refa.getAccessionId() != null && refb.getAccessionId() != null
+                || refb.getAccessionId().equals(refa.getAccessionId()))
+        {
+          if (refa.getMap() == null && refb.getMap() == null)
           {
-            if (refa.getSource()!=null && refb.getSource()!=null 
-                    && refb.getSource().equals(refa.getSource()))
-            {
-              // We dont care about version
-              //if ((refa.getVersion()==null || refb.getVersion()==null) 
-              //        || refb.getVersion().equals(refa.getVersion()))
-              //{
-              if (refa.getAccessionId()!=null && refb.getAccessionId()!=null 
-                      || refb.getAccessionId().equals(refa.getAccessionId()))
-                {
-                  if (refa.getMap()==null && refb.getMap()==null)
-                  {
-                    return true;
-                  }
-                  if (refa.getMap()!=null && refb.getMap()!=null
-                          && ((refb.getMap().getMap()==null && refa.getMap().getMap()==null)
-                            || (refb.getMap().getMap()!=null && refa.getMap().getMap()!=null
-                            && refb.getMap().getMap().equals(refa.getMap().getMap()))))
-                  {
-                    return true; 
-                  }
-                }
-              }
-            return false;
+            return true;
+          }
+          if (refa.getMap() != null
+                  && refb.getMap() != null
+                  && ((refb.getMap().getMap() == null && refa.getMap()
+                          .getMap() == null) || (refb.getMap().getMap() != null
+                          && refa.getMap().getMap() != null && refb
+                          .getMap().getMap().equals(refa.getMap().getMap()))))
+          {
+            return true;
           }
-    };
-    /**
-     * accession ID and DB must be identical. Version is ignored. 
-     * No map on either or map but no maplist on either or maplist of map on a is equivalent to the maplist of map on b.
-     */
-    public static DbRefComp matchDbAndIdAndEitherMapOrEquivalentMapList = new DbRefComp()
+        }
+      }
+      return false;
+    }
+  };
+
+  /**
+   * accession ID and DB must be identical. Version is ignored. No map on either
+   * or map but no maplist on either or maplist of map on a is equivalent to the
+   * maplist of map on b.
+   */
+  public static DbRefComp matchDbAndIdAndEitherMapOrEquivalentMapList = new DbRefComp()
+  {
+    public boolean matches(DBRefEntry refa, DBRefEntry refb)
     {
-          public boolean matches(DBRefEntry refa, DBRefEntry refb)
+      if (refa.getSource() != null && refb.getSource() != null
+              && refb.getSource().equals(refa.getSource()))
+      {
+        // We dont care about version
+        // if ((refa.getVersion()==null || refb.getVersion()==null)
+        // || refb.getVersion().equals(refa.getVersion()))
+        // {
+        if (refa.getAccessionId() != null && refb.getAccessionId() != null
+                && refb.getAccessionId().equals(refa.getAccessionId()))
+        {
+          if (refa.getMap() == null || refb.getMap() == null)
           {
-            if (refa.getSource()!=null && refb.getSource()!=null 
-                    && refb.getSource().equals(refa.getSource()))
-            {
-              // We dont care about version
-              //if ((refa.getVersion()==null || refb.getVersion()==null) 
-              //        || refb.getVersion().equals(refa.getVersion()))
-              //{
-              if (refa.getAccessionId()!=null && refb.getAccessionId()!=null 
-                      && refb.getAccessionId().equals(refa.getAccessionId()))
-                {
-                  if (refa.getMap()==null || refb.getMap()==null)
-                  {
-                    return true;
-                  }
-                  if ((refa.getMap()!=null && refb.getMap()!=null)
-                          && (refb.getMap().getMap()==null && refa.getMap().getMap()==null)
-                            || (refb.getMap().getMap()!=null && refa.getMap().getMap()!=null
-                            && refb.getMap().getMap().equals(refa.getMap().getMap())))
-                  {
-                    return true; 
-                  }
-                }
-              }
-            return false;
+            return true;
           }
-    };
-    /**
-     * used by file parsers to generate DBRefs from annotation within file (eg stockholm)
-     * @param dbname
-     * @param version
-     * @param acn
-     * @param seq where to anotate with reference
-     * @return parsed version of entry that was added to seq (if any)
-     */
-    public static DBRefEntry parseToDbRef(SequenceI seq, String dbname, String version,
-            String acn)
+          if ((refa.getMap() != null && refb.getMap() != null)
+                  && (refb.getMap().getMap() == null && refa.getMap()
+                          .getMap() == null)
+                  || (refb.getMap().getMap() != null
+                          && refa.getMap().getMap() != null && refb
+                          .getMap().getMap().equals(refa.getMap().getMap())))
+          {
+            return true;
+          }
+        }
+      }
+      return false;
+    }
+  };
+
+  /**
+   * used by file parsers to generate DBRefs from annotation within file (eg
+   * stockholm)
+   * 
+   * @param dbname
+   * @param version
+   * @param acn
+   * @param seq
+   *                where to anotate with reference
+   * @return parsed version of entry that was added to seq (if any)
+   */
+  public static DBRefEntry parseToDbRef(SequenceI seq, String dbname,
+          String version, String acn)
+  {
+    DBRefEntry ref = null;
+    if (dbname != null)
     {
-      DBRefEntry ref = null;
-      if (dbname!=null)
+      String locsrc = jalview.util.DBRefUtils.getCanonicalName(dbname);
+      if (locsrc.equals(jalview.datamodel.DBRefSource.PDB))
       {
-        String locsrc = jalview.util.DBRefUtils
-        .getCanonicalName(dbname);
-        if (locsrc.equals(jalview.datamodel.DBRefSource.PDB))
+        // check for chaincode and mapping
+        // PFAM style stockhom PDB citation
+        com.stevesoft.pat.Regex r = new com.stevesoft.pat.Regex(
+                "([0-9][0-9A-Za-z]{3})\\s*(.?)\\s*;([0-9]+)-([0-9]+)");
+        if (r.search(acn.trim()))
         {
-          // check for chaincode and mapping
-          // PFAM style stockhom PDB citation
-          com.stevesoft.pat.Regex r = new com.stevesoft.pat.Regex("([0-9][0-9A-Za-z]{3})\\s*(.?)\\s*;([0-9]+)-([0-9]+)");
-          if (r.search(acn.trim()))
+          String pdbid = r.stringMatched(1);
+          String chaincode = r.stringMatched(2);
+          String mapstart = r.stringMatched(3);
+          String mapend = r.stringMatched(4);
+          if (chaincode.equals(" "))
           {
-            String pdbid = r.stringMatched(1);
-            String chaincode = r.stringMatched(2);
-            String mapstart = r.stringMatched(3);
-            String mapend = r.stringMatched(4);
-            if (chaincode.equals(" "))
-            {
-              chaincode = "_";
-            }
-            // construct pdb ref.
-            ref = new DBRefEntry(locsrc, version, pdbid+chaincode);
-            PDBEntry pdbr = new PDBEntry();
-            pdbr.setId(pdbid);
-            seq.addPDBId(pdbr);
+            chaincode = "_";
           }
-        } else {
-          // default:
-          ref = new DBRefEntry(locsrc, version, acn);
+          // construct pdb ref.
+          ref = new DBRefEntry(locsrc, version, pdbid + chaincode);
+          PDBEntry pdbr = new PDBEntry();
+          pdbr.setId(pdbid);
+          seq.addPDBId(pdbr);
         }
       }
-      if (ref!=null)
+      else
       {
-        seq.addDBRef(ref);
+        // default:
+        ref = new DBRefEntry(locsrc, version, acn);
       }
-      return ref;
     }
-        
-          
+    if (ref != null)
+    {
+      seq.addDBRef(ref);
+    }
+    return ref;
+  }
+
 }
diff --git a/src/jalview/util/Format.java b/src/jalview/util/Format.java
index 7c9b585..46abdb9 100755
--- a/src/jalview/util/Format.java
+++ b/src/jalview/util/Format.java
@@ -1,867 +1,942 @@
-/*
- * Cay S. Horstmann & Gary Cornell, Core Java
- * Published By Sun Microsystems Press/Prentice-Hall
- * Copyright (C) 1997 Sun Microsystems Inc.
- * All Rights Reserved.
- *
- * Permission to use, copy, modify, and distribute this
- * software and its documentation for NON-COMMERCIAL purposes
- * and without fee is hereby granted provided that this
- * copyright notice appears in all copies.
- *
- * THE AUTHORS AND PUBLISHER MAKE NO REPRESENTATIONS OR
- * WARRANTIES ABOUT THE SUITABILITY OF THE SOFTWARE, EITHER
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE
- * IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
- * PARTICULAR PURPOSE, OR NON-INFRINGEMENT. THE AUTHORS
- * AND PUBLISHER SHALL NOT BE LIABLE FOR ANY DAMAGES SUFFERED
- * BY LICENSEE AS A RESULT OF USING, MODIFYING OR DISTRIBUTING
- * THIS SOFTWARE OR ITS DERIVATIVES.
- */
-
-/**
- * A class for formatting numbers that follows printf conventions.
- * Also implements C-like atoi and atof functions
- * @version 1.03 25 Oct 1997
- * @author Cay Horstmann
- */
-package jalview.util;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class Format
-{
-  private int width;
-  private int precision;
-  private String pre;
-  private String post;
-  private boolean leading_zeroes;
-  private boolean show_plus;
-  private boolean alternate;
-  private boolean show_space;
-  private boolean left_align;
-  private char fmt; // one of cdeEfgGiosxXos
-
-  /**
-   * Creates a new Format object.
-   *
-   * @param s DOCUMENT ME!
-   */
-  public Format(String s)
-  {
-    width = 0;
-    precision = -1;
-    pre = "";
-    post = "";
-    leading_zeroes = false;
-    show_plus = false;
-    alternate = false;
-    show_space = false;
-    left_align = false;
-    fmt = ' ';
-
-    int length = s.length();
-    int parse_state = 0;
-
-    // 0 = prefix, 1 = flags, 2 = width, 3 = precision,
-    // 4 = format, 5 = end
-    int i = 0;
-
-    while (parse_state == 0)
-    {
-      if (i >= length)
-      {
-        parse_state = 5;
-      }
-      else if (s.charAt(i) == '%')
-      {
-        if (i < (length - 1))
-        {
-          if (s.charAt(i + 1) == '%')
-          {
-            pre = pre + '%';
-            i++;
-          }
-          else
-          {
-            parse_state = 1;
-          }
-        }
-        else
-        {
-          throw new java.lang.IllegalArgumentException();
-        }
-      }
-      else
-      {
-        pre = pre + s.charAt(i);
-      }
-
-      i++;
-    }
-
-    while (parse_state == 1)
-    {
-      if (i >= length)
-      {
-        parse_state = 5;
-      }
-      else if (s.charAt(i) == ' ')
-      {
-        show_space = true;
-      }
-      else if (s.charAt(i) == '-')
-      {
-        left_align = true;
-      }
-      else if (s.charAt(i) == '+')
-      {
-        show_plus = true;
-      }
-      else if (s.charAt(i) == '0')
-      {
-        leading_zeroes = true;
-      }
-      else if (s.charAt(i) == '#')
-      {
-        alternate = true;
-      }
-      else
-      {
-        parse_state = 2;
-        i--;
-      }
-
-      i++;
-    }
-
-    while (parse_state == 2)
-    {
-      if (i >= length)
-      {
-        parse_state = 5;
-      }
-      else if ( ('0' <= s.charAt(i)) && (s.charAt(i) <= '9'))
-      {
-        width = ( (width * 10) + s.charAt(i)) - '0';
-        i++;
-      }
-      else if (s.charAt(i) == '.')
-      {
-        parse_state = 3;
-        precision = 0;
-        i++;
-      }
-      else
-      {
-        parse_state = 4;
-      }
-    }
-
-    while (parse_state == 3)
-    {
-      if (i >= length)
-      {
-        parse_state = 5;
-      }
-      else if ( ('0' <= s.charAt(i)) && (s.charAt(i) <= '9'))
-      {
-        precision = ( (precision * 10) + s.charAt(i)) - '0';
-        i++;
-      }
-      else
-      {
-        parse_state = 4;
-      }
-    }
-
-    if (parse_state == 4)
-    {
-      if (i >= length)
-      {
-        parse_state = 5;
-      }
-      else
-      {
-        fmt = s.charAt(i);
-      }
-
-      i++;
-    }
-
-    if (i < length)
-    {
-      post = s.substring(i, length);
-    }
-  }
-
-  /**
-   * Formats the number following printf conventions.
-   * Main limitation: Can only handle one format parameter at a time
-   * Use multiple Format objects to format more than one number
-   * @param s the format string following printf conventions
-   * The string has a prefix, a format code and a suffix. The prefix and suffix
-   * become part of the formatted output. The format code directs the
-   * formatting of the (single) parameter to be formatted. The code has the
-   * following structure
-   * <ul>
-   * <li> a % (required)
-   * <li> a modifier (optional)
-   * <dl>
-   * <dt> + <dd> forces display of + for positive numbers
-   * <dt> 0 <dd> show leading zeroes
-   * <dt> - <dd> align left in the field
-   * <dt> space <dd> prepend a space in front of positive numbers
-   * <dt> # <dd> use "alternate" format. Add 0 or 0x for octal or hexadecimal numbers. Don't suppress trailing zeroes in general floating point format.
-   * </dl>
-   * <li> an integer denoting field width (optional)
-   * <li> a period followed by an integer denoting precision (optional)
-   * <li> a format descriptor (required)
-   * <dl>
-   * <dt>f <dd> floating point number in fixed format
-   * <dt>e, E <dd> floating point number in exponential notation (scientific format). The E format results in an uppercase E for the exponent (1.14130E+003), the e format in a lowercase e.
-   * <dt>g, G <dd> floating point number in general format (fixed format for small numbers, exponential format for large numbers). Trailing zeroes are suppressed. The G format results in an uppercase E for the exponent (if any), the g format in a lowercase e.
-   * <dt>d, i <dd> integer in decimal
-   * <dt>x <dd> integer in hexadecimal
-   * <dt>o <dd> integer in octal
-   * <dt>s <dd> string
-   * <dt>c <dd> character
-   * </dl>
-   * </ul>
-   * @exception IllegalArgumentException if bad format
-   *
-   */
-  public static String getHexString(java.awt.Color color)
-  {
-    String r;
-    String g;
-    String b;
-    r = Integer.toHexString(color.getRed());
-
-    if (r.length() < 2)
-    {
-      r = "0" + r;
-    }
-
-    g = Integer.toHexString(color.getGreen());
-
-    if (g.length() < 2)
-    {
-      g = "0" + g;
-    }
-
-    b = Integer.toHexString(color.getBlue());
-
-    if (b.length() < 2)
-    {
-      b = "0" + b;
-    }
-
-    return r + g + b;
-  }
-
-  /**
-   * prints a formatted number following printf conventions
-   * @param s a PrintStream
-   * @param fmt the format string
-   * @param x the double to print
-   */
-  public static void print(java.io.PrintStream s, String fmt, double x)
-  {
-    s.print(new Format(fmt).form(x));
-  }
-
-  /**
-   * prints a formatted number following printf conventions
-   * @param s a PrintStream
-   * @param fmt the format string
-   * @param x the long to print
-   */
-  public static void print(java.io.PrintStream s, String fmt, long x)
-  {
-    s.print(new Format(fmt).form(x));
-  }
-
-  /**
-   * prints a formatted number following printf conventions
-   * @param s a PrintStream
-   * @param fmt the format string
-   * @param x the character to
-   */
-  public static void print(java.io.PrintStream s, String fmt, char x)
-  {
-    s.print(new Format(fmt).form(x));
-  }
-
-  /**
-   * prints a formatted number following printf conventions
-   * @param s a PrintStream, fmt the format string
-   * @param x a string that represents the digits to print
-   */
-  public static void print(java.io.PrintStream s, String fmt, String x)
-  {
-    s.print(new Format(fmt).form(x));
-  }
-
-  /**
-   * Converts a string of digits (decimal, octal or hex) to an integer
-   * @param s a string
-   * @return the numeric value of the prefix of s representing a base 10 integer
-   */
-  public static int atoi(String s)
-  {
-    return (int) atol(s);
-  }
-
-  /**
-   * Converts a string of digits (decimal, octal or hex) to a long integer
-   * @param s a string
-   * @return the numeric value of the prefix of s representing a base 10 integer
-   */
-  public static long atol(String s)
-  {
-    int i = 0;
-
-    while ( (i < s.length()) && Character.isWhitespace(s.charAt(i)))
-    {
-      i++;
-    }
-
-    if ( (i < s.length()) && (s.charAt(i) == '0'))
-    {
-      if ( ( (i + 1) < s.length()) &&
-          ( (s.charAt(i + 1) == 'x') || (s.charAt(i + 1) == 'X')))
-      {
-        return parseLong(s.substring(i + 2), 16);
-      }
-      else
-      {
-        return parseLong(s, 8);
-      }
-    }
-    else
-    {
-      return parseLong(s, 10);
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param s DOCUMENT ME!
-   * @param base DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  private static long parseLong(String s, int base)
-  {
-    int i = 0;
-    int sign = 1;
-    long r = 0;
-
-    while ( (i < s.length()) && Character.isWhitespace(s.charAt(i)))
-    {
-      i++;
-    }
-
-    if ( (i < s.length()) && (s.charAt(i) == '-'))
-    {
-      sign = -1;
-      i++;
-    }
-    else if ( (i < s.length()) && (s.charAt(i) == '+'))
-    {
-      i++;
-    }
-
-    while (i < s.length())
-    {
-      char ch = s.charAt(i);
-
-      if ( ('0' <= ch) && (ch < ('0' + base)))
-      {
-        r = ( (r * base) + ch) - '0';
-      }
-      else if ( ('A' <= ch) && (ch < ( ('A' + base) - 10)))
-      {
-        r = ( (r * base) + ch) - 'A' + 10;
-      }
-      else if ( ('a' <= ch) && (ch < ( ('a' + base) - 10)))
-      {
-        r = ( (r * base) + ch) - 'a' + 10;
-      }
-      else
-      {
-        return r * sign;
-      }
-
-      i++;
-    }
-
-    return r * sign;
-  }
-
-  /**
-   * Converts a string of digits to an double
-   * @param s a string
-   */
-  public static double atof(String s)
-  {
-    int i = 0;
-    int sign = 1;
-    double r = 0; // integer part
-    //double f = 0; // fractional part
-    double p = 1; // exponent of fractional part
-    int state = 0; // 0 = int part, 1 = frac part
-
-    while ( (i < s.length()) && Character.isWhitespace(s.charAt(i)))
-    {
-      i++;
-    }
-
-    if ( (i < s.length()) && (s.charAt(i) == '-'))
-    {
-      sign = -1;
-      i++;
-    }
-    else if ( (i < s.length()) && (s.charAt(i) == '+'))
-    {
-      i++;
-    }
-
-    while (i < s.length())
-    {
-      char ch = s.charAt(i);
-
-      if ( ('0' <= ch) && (ch <= '9'))
-      {
-        if (state == 0)
-        {
-          r = ( (r * 10) + ch) - '0';
-        }
-        else if (state == 1)
-        {
-          p = p / 10;
-          r = r + (p * (ch - '0'));
-        }
-      }
-      else if (ch == '.')
-      {
-        if (state == 0)
-        {
-          state = 1;
-        }
-        else
-        {
-          return sign * r;
-        }
-      }
-      else if ( (ch == 'e') || (ch == 'E'))
-      {
-        long e = (int) parseLong(s.substring(i + 1), 10);
-
-        return sign * r * Math.pow(10, e);
-      }
-      else
-      {
-        return sign * r;
-      }
-
-      i++;
-    }
-
-    return sign * r;
-  }
-
-  /**
-   * Formats a double into a string (like sprintf in C)
-   * @param x the number to format
-   * @return the formatted string
-   * @exception IllegalArgumentException if bad argument
-   */
-  public String form(double x)
-  {
-    String r;
-
-    if (precision < 0)
-    {
-      precision = 6;
-    }
-
-    int s = 1;
-
-    if (x < 0)
-    {
-      x = -x;
-      s = -1;
-    }
-
-    if (fmt == 'f')
-    {
-      r = fixed_format(x);
-    }
-    else if ( (fmt == 'e') || (fmt == 'E') || (fmt == 'g') || (fmt == 'G'))
-    {
-      r = exp_format(x);
-    }
-    else
-    {
-      throw new java.lang.IllegalArgumentException();
-    }
-
-    return pad(sign(s, r));
-  }
-
-  /**
-   * Formats a long integer into a string (like sprintf in C)
-   * @param x the number to format
-   * @return the formatted string
-   */
-  public String form(long x)
-  {
-    String r;
-    int s = 0;
-
-    if ( (fmt == 'd') || (fmt == 'i'))
-    {
-      if (x < 0)
-      {
-        r = ("" + x).substring(1);
-        s = -1;
-      }
-      else
-      {
-        r = "" + x;
-        s = 1;
-      }
-    }
-    else if (fmt == 'o')
-    {
-      r = convert(x, 3, 7, "01234567");
-    }
-    else if (fmt == 'x')
-    {
-      r = convert(x, 4, 15, "0123456789abcdef");
-    }
-    else if (fmt == 'X')
-    {
-      r = convert(x, 4, 15, "0123456789ABCDEF");
-    }
-    else
-    {
-      throw new java.lang.IllegalArgumentException();
-    }
-
-    return pad(sign(s, r));
-  }
-
-  /**
-   * Formats a character into a string (like sprintf in C)
-   * @param x the value to format
-   * @return the formatted string
-   */
-  public String form(char c)
-  {
-    if (fmt != 'c')
-    {
-      throw new java.lang.IllegalArgumentException();
-    }
-
-    String r = "" + c;
-
-    return pad(r);
-  }
-
-  /**
-   * Formats a string into a larger string (like sprintf in C)
-   * @param x the value to format
-   * @return the formatted string
-   */
-  public String form(String s)
-  {
-    if (fmt != 's')
-    {
-      throw new java.lang.IllegalArgumentException();
-    }
-
-    if (precision >= 0)
-    {
-      s = s.substring(0, precision);
-    }
-
-    return pad(s);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param c DOCUMENT ME!
-   * @param n DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  private static String repeat(char c, int n)
-  {
-    if (n <= 0)
-    {
-      return "";
-    }
-
-    StringBuffer s = new StringBuffer(n);
-
-    for (int i = 0; i < n; i++)
-    {
-      s.append(c);
-    }
-
-    return s.toString();
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param x DOCUMENT ME!
-   * @param n DOCUMENT ME!
-   * @param m DOCUMENT ME!
-   * @param d DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  private static String convert(long x, int n, int m, String d)
-  {
-    if (x == 0)
-    {
-      return "0";
-    }
-
-    String r = "";
-
-    while (x != 0)
-    {
-      r = d.charAt( (int) (x & m)) + r;
-      x = x >>> n;
-    }
-
-    return r;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param r DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  private String pad(String r)
-  {
-    String p = repeat(' ', width - r.length());
-
-    if (left_align)
-    {
-      return pre + r + p + post;
-    }
-    else
-    {
-      return pre + p + r + post;
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param s DOCUMENT ME!
-   * @param r DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  private String sign(int s, String r)
-  {
-    String p = "";
-
-    if (s < 0)
-    {
-      p = "-";
-    }
-    else if (s > 0)
-    {
-      if (show_plus)
-      {
-        p = "+";
-      }
-      else if (show_space)
-      {
-        p = " ";
-      }
-    }
-    else
-    {
-      if ( (fmt == 'o') && alternate && (r.length() > 0) &&
-          (r.charAt(0) != '0'))
-      {
-        p = "0";
-      }
-      else if ( (fmt == 'x') && alternate)
-      {
-        p = "0x";
-      }
-      else if ( (fmt == 'X') && alternate)
-      {
-        p = "0X";
-      }
-    }
-
-    int w = 0;
-
-    if (leading_zeroes)
-    {
-      w = width;
-    }
-    else if ( ( (fmt == 'd') || (fmt == 'i') || (fmt == 'x') || (fmt == 'X') ||
-               (fmt == 'o')) && (precision > 0))
-    {
-      w = precision;
-    }
-
-    return p + repeat('0', w - p.length() - r.length()) + r;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param d DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  private String fixed_format(double d)
-  {
-    boolean removeTrailing = ( (fmt == 'G') || (fmt == 'g')) && !alternate;
-
-    // remove trailing zeroes and decimal point
-    if (d > 0x7FFFFFFFFFFFFFFFL)
-    {
-      return exp_format(d);
-    }
-
-    if (precision == 0)
-    {
-      return (long) (d + 0.5) + (removeTrailing ? "" : ".");
-    }
-
-    long whole = (long) d;
-    double fr = d - whole; // fractional part
-
-    if ( (fr >= 1) || (fr < 0))
-    {
-      return exp_format(d);
-    }
-
-    double factor = 1;
-    String leading_zeroes = "";
-
-    for (int i = 1; (i <= precision) && (factor <= 0x7FFFFFFFFFFFFFFFL);
-         i++)
-    {
-      factor *= 10;
-      leading_zeroes = leading_zeroes + "0";
-    }
-
-    long l = (long) ( (factor * fr) + 0.5);
-
-    if (l >= factor)
-    {
-      l = 0;
-      whole++;
-    }
-
-    // CSH 10-25-97
-    String z = leading_zeroes + l;
-    z = "." + z.substring(z.length() - precision, z.length());
-
-    if (removeTrailing)
-    {
-      int t = z.length() - 1;
-
-      while ( (t >= 0) && (z.charAt(t) == '0'))
-      {
-        t--;
-      }
-
-      if ( (t >= 0) && (z.charAt(t) == '.'))
-      {
-        t--;
-      }
-
-      z = z.substring(0, t + 1);
-    }
-
-    return whole + z;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param d DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  private String exp_format(double d)
-  {
-    String f = "";
-    int e = 0;
-    double dd = d;
-    double factor = 1;
-
-    if (d != 0)
-    {
-      while (dd > 10)
-      {
-        e++;
-        factor /= 10;
-        dd = dd / 10;
-      }
-
-      while (dd < 1)
-      {
-        e--;
-        factor *= 10;
-        dd = dd * 10;
-      }
-    }
-
-    if ( ( (fmt == 'g') || (fmt == 'G')) && (e >= -4) && (e < precision))
-    {
-      return fixed_format(d);
-    }
-
-    d = d * factor;
-    f = f + fixed_format(d);
-
-    if ( (fmt == 'e') || (fmt == 'g'))
-    {
-      f = f + "e";
-    }
-    else
-    {
-      f = f + "E";
-    }
-
-    String p = "000";
-
-    if (e >= 0)
-    {
-      f = f + "+";
-      p = p + e;
-    }
-    else
-    {
-      f = f + "-";
-      p = p + ( -e);
-    }
-
-    return f + p.substring(p.length() - 3, p.length());
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+/**
+ * A class for formatting numbers that follows printf conventions.
+ * Also implements C-like atoi and atof functions
+ * @version 1.03 25 Oct 1997
+ * @author Cay Horstmann
+ */
+package jalview.util;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class Format
+{
+  private int width;
+
+  private int precision;
+
+  private String pre;
+
+  private String post;
+
+  private boolean leading_zeroes;
+
+  private boolean show_plus;
+
+  private boolean alternate;
+
+  private boolean show_space;
+
+  private boolean left_align;
+
+  private char fmt; // one of cdeEfgGiosxXos
+
+  /**
+   * Creates a new Format object.
+   * 
+   * @param s
+   *                DOCUMENT ME!
+   */
+  public Format(String s)
+  {
+    width = 0;
+    precision = -1;
+    pre = "";
+    post = "";
+    leading_zeroes = false;
+    show_plus = false;
+    alternate = false;
+    show_space = false;
+    left_align = false;
+    fmt = ' ';
+
+    int length = s.length();
+    int parse_state = 0;
+
+    // 0 = prefix, 1 = flags, 2 = width, 3 = precision,
+    // 4 = format, 5 = end
+    int i = 0;
+
+    while (parse_state == 0)
+    {
+      if (i >= length)
+      {
+        parse_state = 5;
+      }
+      else if (s.charAt(i) == '%')
+      {
+        if (i < (length - 1))
+        {
+          if (s.charAt(i + 1) == '%')
+          {
+            pre = pre + '%';
+            i++;
+          }
+          else
+          {
+            parse_state = 1;
+          }
+        }
+        else
+        {
+          throw new java.lang.IllegalArgumentException();
+        }
+      }
+      else
+      {
+        pre = pre + s.charAt(i);
+      }
+
+      i++;
+    }
+
+    while (parse_state == 1)
+    {
+      if (i >= length)
+      {
+        parse_state = 5;
+      }
+      else if (s.charAt(i) == ' ')
+      {
+        show_space = true;
+      }
+      else if (s.charAt(i) == '-')
+      {
+        left_align = true;
+      }
+      else if (s.charAt(i) == '+')
+      {
+        show_plus = true;
+      }
+      else if (s.charAt(i) == '0')
+      {
+        leading_zeroes = true;
+      }
+      else if (s.charAt(i) == '#')
+      {
+        alternate = true;
+      }
+      else
+      {
+        parse_state = 2;
+        i--;
+      }
+
+      i++;
+    }
+
+    while (parse_state == 2)
+    {
+      if (i >= length)
+      {
+        parse_state = 5;
+      }
+      else if (('0' <= s.charAt(i)) && (s.charAt(i) <= '9'))
+      {
+        width = ((width * 10) + s.charAt(i)) - '0';
+        i++;
+      }
+      else if (s.charAt(i) == '.')
+      {
+        parse_state = 3;
+        precision = 0;
+        i++;
+      }
+      else
+      {
+        parse_state = 4;
+      }
+    }
+
+    while (parse_state == 3)
+    {
+      if (i >= length)
+      {
+        parse_state = 5;
+      }
+      else if (('0' <= s.charAt(i)) && (s.charAt(i) <= '9'))
+      {
+        precision = ((precision * 10) + s.charAt(i)) - '0';
+        i++;
+      }
+      else
+      {
+        parse_state = 4;
+      }
+    }
+
+    if (parse_state == 4)
+    {
+      if (i >= length)
+      {
+        parse_state = 5;
+      }
+      else
+      {
+        fmt = s.charAt(i);
+      }
+
+      i++;
+    }
+
+    if (i < length)
+    {
+      post = s.substring(i, length);
+    }
+  }
+
+  /**
+   * Formats the number following printf conventions. Main limitation: Can only
+   * handle one format parameter at a time Use multiple Format objects to format
+   * more than one number
+   * 
+   * @param s
+   *                the format string following printf conventions The string
+   *                has a prefix, a format code and a suffix. The prefix and
+   *                suffix become part of the formatted output. The format code
+   *                directs the formatting of the (single) parameter to be
+   *                formatted. The code has the following structure
+   *                <ul>
+   *                <li> a % (required)
+   *                <li> a modifier (optional)
+   *                <dl>
+   *                <dt> +
+   *                <dd> forces display of + for positive numbers
+   *                <dt> 0
+   *                <dd> show leading zeroes
+   *                <dt> -
+   *                <dd> align left in the field
+   *                <dt> space
+   *                <dd> prepend a space in front of positive numbers
+   *                <dt> #
+   *                <dd> use "alternate" format. Add 0 or 0x for octal or
+   *                hexadecimal numbers. Don't suppress trailing zeroes in
+   *                general floating point format.
+   *                </dl>
+   *                <li> an integer denoting field width (optional)
+   *                <li> a period followed by an integer denoting precision
+   *                (optional)
+   *                <li> a format descriptor (required)
+   *                <dl>
+   *                <dt>f
+   *                <dd> floating point number in fixed format
+   *                <dt>e, E
+   *                <dd> floating point number in exponential notation
+   *                (scientific format). The E format results in an uppercase E
+   *                for the exponent (1.14130E+003), the e format in a lowercase
+   *                e.
+   *                <dt>g, G
+   *                <dd> floating point number in general format (fixed format
+   *                for small numbers, exponential format for large numbers).
+   *                Trailing zeroes are suppressed. The G format results in an
+   *                uppercase E for the exponent (if any), the g format in a
+   *                lowercase e.
+   *                <dt>d, i
+   *                <dd> integer in decimal
+   *                <dt>x
+   *                <dd> integer in hexadecimal
+   *                <dt>o
+   *                <dd> integer in octal
+   *                <dt>s
+   *                <dd> string
+   *                <dt>c
+   *                <dd> character
+   *                </dl>
+   *                </ul>
+   * @exception IllegalArgumentException
+   *                    if bad format
+   * 
+   */
+  public static String getHexString(java.awt.Color color)
+  {
+    String r;
+    String g;
+    String b;
+    r = Integer.toHexString(color.getRed());
+
+    if (r.length() < 2)
+    {
+      r = "0" + r;
+    }
+
+    g = Integer.toHexString(color.getGreen());
+
+    if (g.length() < 2)
+    {
+      g = "0" + g;
+    }
+
+    b = Integer.toHexString(color.getBlue());
+
+    if (b.length() < 2)
+    {
+      b = "0" + b;
+    }
+
+    return r + g + b;
+  }
+
+  /**
+   * prints a formatted number following printf conventions
+   * 
+   * @param s
+   *                a PrintStream
+   * @param fmt
+   *                the format string
+   * @param x
+   *                the double to print
+   */
+  public static void print(java.io.PrintStream s, String fmt, double x)
+  {
+    s.print(new Format(fmt).form(x));
+  }
+
+  /**
+   * prints a formatted number following printf conventions
+   * 
+   * @param s
+   *                a PrintStream
+   * @param fmt
+   *                the format string
+   * @param x
+   *                the long to print
+   */
+  public static void print(java.io.PrintStream s, String fmt, long x)
+  {
+    s.print(new Format(fmt).form(x));
+  }
+
+  /**
+   * prints a formatted number following printf conventions
+   * 
+   * @param s
+   *                a PrintStream
+   * @param fmt
+   *                the format string
+   * @param x
+   *                the character to
+   */
+  public static void print(java.io.PrintStream s, String fmt, char x)
+  {
+    s.print(new Format(fmt).form(x));
+  }
+
+  /**
+   * prints a formatted number following printf conventions
+   * 
+   * @param s
+   *                a PrintStream, fmt the format string
+   * @param x
+   *                a string that represents the digits to print
+   */
+  public static void print(java.io.PrintStream s, String fmt, String x)
+  {
+    s.print(new Format(fmt).form(x));
+  }
+
+  /**
+   * Converts a string of digits (decimal, octal or hex) to an integer
+   * 
+   * @param s
+   *                a string
+   * @return the numeric value of the prefix of s representing a base 10 integer
+   */
+  public static int atoi(String s)
+  {
+    return (int) atol(s);
+  }
+
+  /**
+   * Converts a string of digits (decimal, octal or hex) to a long integer
+   * 
+   * @param s
+   *                a string
+   * @return the numeric value of the prefix of s representing a base 10 integer
+   */
+  public static long atol(String s)
+  {
+    int i = 0;
+
+    while ((i < s.length()) && Character.isWhitespace(s.charAt(i)))
+    {
+      i++;
+    }
+
+    if ((i < s.length()) && (s.charAt(i) == '0'))
+    {
+      if (((i + 1) < s.length())
+              && ((s.charAt(i + 1) == 'x') || (s.charAt(i + 1) == 'X')))
+      {
+        return parseLong(s.substring(i + 2), 16);
+      }
+      else
+      {
+        return parseLong(s, 8);
+      }
+    }
+    else
+    {
+      return parseLong(s, 10);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param s
+   *                DOCUMENT ME!
+   * @param base
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  private static long parseLong(String s, int base)
+  {
+    int i = 0;
+    int sign = 1;
+    long r = 0;
+
+    while ((i < s.length()) && Character.isWhitespace(s.charAt(i)))
+    {
+      i++;
+    }
+
+    if ((i < s.length()) && (s.charAt(i) == '-'))
+    {
+      sign = -1;
+      i++;
+    }
+    else if ((i < s.length()) && (s.charAt(i) == '+'))
+    {
+      i++;
+    }
+
+    while (i < s.length())
+    {
+      char ch = s.charAt(i);
+
+      if (('0' <= ch) && (ch < ('0' + base)))
+      {
+        r = ((r * base) + ch) - '0';
+      }
+      else if (('A' <= ch) && (ch < (('A' + base) - 10)))
+      {
+        r = ((r * base) + ch) - 'A' + 10;
+      }
+      else if (('a' <= ch) && (ch < (('a' + base) - 10)))
+      {
+        r = ((r * base) + ch) - 'a' + 10;
+      }
+      else
+      {
+        return r * sign;
+      }
+
+      i++;
+    }
+
+    return r * sign;
+  }
+
+  /**
+   * Converts a string of digits to an double
+   * 
+   * @param s
+   *                a string
+   */
+  public static double atof(String s)
+  {
+    int i = 0;
+    int sign = 1;
+    double r = 0; // integer part
+    // double f = 0; // fractional part
+    double p = 1; // exponent of fractional part
+    int state = 0; // 0 = int part, 1 = frac part
+
+    while ((i < s.length()) && Character.isWhitespace(s.charAt(i)))
+    {
+      i++;
+    }
+
+    if ((i < s.length()) && (s.charAt(i) == '-'))
+    {
+      sign = -1;
+      i++;
+    }
+    else if ((i < s.length()) && (s.charAt(i) == '+'))
+    {
+      i++;
+    }
+
+    while (i < s.length())
+    {
+      char ch = s.charAt(i);
+
+      if (('0' <= ch) && (ch <= '9'))
+      {
+        if (state == 0)
+        {
+          r = ((r * 10) + ch) - '0';
+        }
+        else if (state == 1)
+        {
+          p = p / 10;
+          r = r + (p * (ch - '0'));
+        }
+      }
+      else if (ch == '.')
+      {
+        if (state == 0)
+        {
+          state = 1;
+        }
+        else
+        {
+          return sign * r;
+        }
+      }
+      else if ((ch == 'e') || (ch == 'E'))
+      {
+        long e = (int) parseLong(s.substring(i + 1), 10);
+
+        return sign * r * Math.pow(10, e);
+      }
+      else
+      {
+        return sign * r;
+      }
+
+      i++;
+    }
+
+    return sign * r;
+  }
+
+  /**
+   * Formats a double into a string (like sprintf in C)
+   * 
+   * @param x
+   *                the number to format
+   * @return the formatted string
+   * @exception IllegalArgumentException
+   *                    if bad argument
+   */
+  public String form(double x)
+  {
+    String r;
+
+    if (precision < 0)
+    {
+      precision = 6;
+    }
+
+    int s = 1;
+
+    if (x < 0)
+    {
+      x = -x;
+      s = -1;
+    }
+
+    if (fmt == 'f')
+    {
+      r = fixed_format(x);
+    }
+    else if ((fmt == 'e') || (fmt == 'E') || (fmt == 'g') || (fmt == 'G'))
+    {
+      r = exp_format(x);
+    }
+    else
+    {
+      throw new java.lang.IllegalArgumentException();
+    }
+
+    return pad(sign(s, r));
+  }
+
+  /**
+   * Formats a long integer into a string (like sprintf in C)
+   * 
+   * @param x
+   *                the number to format
+   * @return the formatted string
+   */
+  public String form(long x)
+  {
+    String r;
+    int s = 0;
+
+    if ((fmt == 'd') || (fmt == 'i'))
+    {
+      if (x < 0)
+      {
+        r = ("" + x).substring(1);
+        s = -1;
+      }
+      else
+      {
+        r = "" + x;
+        s = 1;
+      }
+    }
+    else if (fmt == 'o')
+    {
+      r = convert(x, 3, 7, "01234567");
+    }
+    else if (fmt == 'x')
+    {
+      r = convert(x, 4, 15, "0123456789abcdef");
+    }
+    else if (fmt == 'X')
+    {
+      r = convert(x, 4, 15, "0123456789ABCDEF");
+    }
+    else
+    {
+      throw new java.lang.IllegalArgumentException();
+    }
+
+    return pad(sign(s, r));
+  }
+
+  /**
+   * Formats a character into a string (like sprintf in C)
+   * 
+   * @param x
+   *                the value to format
+   * @return the formatted string
+   */
+  public String form(char c)
+  {
+    if (fmt != 'c')
+    {
+      throw new java.lang.IllegalArgumentException();
+    }
+
+    String r = "" + c;
+
+    return pad(r);
+  }
+
+  /**
+   * Formats a string into a larger string (like sprintf in C)
+   * 
+   * @param x
+   *                the value to format
+   * @return the formatted string
+   */
+  public String form(String s)
+  {
+    if (fmt != 's')
+    {
+      throw new java.lang.IllegalArgumentException();
+    }
+
+    if (precision >= 0)
+    {
+      s = s.substring(0, precision);
+    }
+
+    return pad(s);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param c
+   *                DOCUMENT ME!
+   * @param n
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  private static String repeat(char c, int n)
+  {
+    if (n <= 0)
+    {
+      return "";
+    }
+
+    StringBuffer s = new StringBuffer(n);
+
+    for (int i = 0; i < n; i++)
+    {
+      s.append(c);
+    }
+
+    return s.toString();
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param x
+   *                DOCUMENT ME!
+   * @param n
+   *                DOCUMENT ME!
+   * @param m
+   *                DOCUMENT ME!
+   * @param d
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  private static String convert(long x, int n, int m, String d)
+  {
+    if (x == 0)
+    {
+      return "0";
+    }
+
+    String r = "";
+
+    while (x != 0)
+    {
+      r = d.charAt((int) (x & m)) + r;
+      x = x >>> n;
+    }
+
+    return r;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param r
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  private String pad(String r)
+  {
+    String p = repeat(' ', width - r.length());
+
+    if (left_align)
+    {
+      return pre + r + p + post;
+    }
+    else
+    {
+      return pre + p + r + post;
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param s
+   *                DOCUMENT ME!
+   * @param r
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  private String sign(int s, String r)
+  {
+    String p = "";
+
+    if (s < 0)
+    {
+      p = "-";
+    }
+    else if (s > 0)
+    {
+      if (show_plus)
+      {
+        p = "+";
+      }
+      else if (show_space)
+      {
+        p = " ";
+      }
+    }
+    else
+    {
+      if ((fmt == 'o') && alternate && (r.length() > 0)
+              && (r.charAt(0) != '0'))
+      {
+        p = "0";
+      }
+      else if ((fmt == 'x') && alternate)
+      {
+        p = "0x";
+      }
+      else if ((fmt == 'X') && alternate)
+      {
+        p = "0X";
+      }
+    }
+
+    int w = 0;
+
+    if (leading_zeroes)
+    {
+      w = width;
+    }
+    else if (((fmt == 'd') || (fmt == 'i') || (fmt == 'x') || (fmt == 'X') || (fmt == 'o'))
+            && (precision > 0))
+    {
+      w = precision;
+    }
+
+    return p + repeat('0', w - p.length() - r.length()) + r;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param d
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  private String fixed_format(double d)
+  {
+    boolean removeTrailing = ((fmt == 'G') || (fmt == 'g')) && !alternate;
+
+    // remove trailing zeroes and decimal point
+    if (d > 0x7FFFFFFFFFFFFFFFL)
+    {
+      return exp_format(d);
+    }
+
+    if (precision == 0)
+    {
+      return (long) (d + 0.5) + (removeTrailing ? "" : ".");
+    }
+
+    long whole = (long) d;
+    double fr = d - whole; // fractional part
+
+    if ((fr >= 1) || (fr < 0))
+    {
+      return exp_format(d);
+    }
+
+    double factor = 1;
+    String leading_zeroes = "";
+
+    for (int i = 1; (i <= precision) && (factor <= 0x7FFFFFFFFFFFFFFFL); i++)
+    {
+      factor *= 10;
+      leading_zeroes = leading_zeroes + "0";
+    }
+
+    long l = (long) ((factor * fr) + 0.5);
+
+    if (l >= factor)
+    {
+      l = 0;
+      whole++;
+    }
+
+    // CSH 10-25-97
+    String z = leading_zeroes + l;
+    z = "." + z.substring(z.length() - precision, z.length());
+
+    if (removeTrailing)
+    {
+      int t = z.length() - 1;
+
+      while ((t >= 0) && (z.charAt(t) == '0'))
+      {
+        t--;
+      }
+
+      if ((t >= 0) && (z.charAt(t) == '.'))
+      {
+        t--;
+      }
+
+      z = z.substring(0, t + 1);
+    }
+
+    return whole + z;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param d
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  private String exp_format(double d)
+  {
+    String f = "";
+    int e = 0;
+    double dd = d;
+    double factor = 1;
+
+    if (d != 0)
+    {
+      while (dd > 10)
+      {
+        e++;
+        factor /= 10;
+        dd = dd / 10;
+      }
+
+      while (dd < 1)
+      {
+        e--;
+        factor *= 10;
+        dd = dd * 10;
+      }
+    }
+
+    if (((fmt == 'g') || (fmt == 'G')) && (e >= -4) && (e < precision))
+    {
+      return fixed_format(d);
+    }
+
+    d = d * factor;
+    f = f + fixed_format(d);
+
+    if ((fmt == 'e') || (fmt == 'g'))
+    {
+      f = f + "e";
+    }
+    else
+    {
+      f = f + "E";
+    }
+
+    String p = "000";
+
+    if (e >= 0)
+    {
+      f = f + "+";
+      p = p + e;
+    }
+    else
+    {
+      f = f + "-";
+      p = p + (-e);
+    }
+
+    return f + p.substring(p.length() - 3, p.length());
+  }
+}
diff --git a/src/jalview/util/ImageMaker.java b/src/jalview/util/ImageMaker.java
index 632c2ad..511212a 100755
--- a/src/jalview/util/ImageMaker.java
+++ b/src/jalview/util/ImageMaker.java
@@ -1,190 +1,186 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.util;
-
-import java.io.*;
-import javax.imageio.*;
-
-import java.awt.*;
-import java.awt.image.*;
-
-import org.jibble.epsgraphics.*;
-import jalview.gui.*;
-import jalview.io.*;
-
-public class ImageMaker
-{
-  public static final int EPS = 0;
-  public static final int PNG = 1;
-  int type = -1;
-
-  EpsGraphics2D pg;
-  Graphics graphics;
-  FileOutputStream out;
-  BufferedImage bi;
-
-  public ImageMaker(Component parent, int type, String title,
-                    int width, int height, File file, String EPStitle)
-  {
-    this.type = type;
-
-    if (file == null)
-    {
-      JalviewFileChooser chooser;
-      chooser = type == EPS ? getEPSChooser() : getPNGChooser();
-
-      chooser.setFileView(new jalview.io.JalviewFileView());
-      chooser.setDialogTitle(title);
-      chooser.setToolTipText("Save");
-
-      int value = chooser.showSaveDialog(parent);
-
-      if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
-      {
-        jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-                                      chooser.getSelectedFile().getParent());
-
-        file = chooser.getSelectedFile();
-      }
-    }
-
-    if (file != null)
-    {
-      try
-      {
-        out = new FileOutputStream(file);
-
-        if (type == EPS)
-        {
-          setupEPS(width, height, EPStitle);
-        }
-        else
-        {
-          setupPNG(width, height);
-        }
-      }
-      catch (Exception ex)
-      {
-        System.out.println("Error creating " + (type == EPS ? "EPS" : "PNG") +
-                           " file.");
-      }
-    }
-  }
-
-  public Graphics getGraphics()
-  {
-    return graphics;
-  }
-
-  void setupPNG(int width, int height)
-  {
-    bi = new BufferedImage(width, height,
-                           BufferedImage.TYPE_INT_RGB);
-    graphics = bi.getGraphics();
-    Graphics2D ig2 = (Graphics2D) graphics;
-    ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-                         RenderingHints.VALUE_ANTIALIAS_ON);
-  }
-
-  public void writeImage()
-  {
-    try
-    {
-      switch (type)
-      {
-        case EPS:
-          pg.flush();
-          pg.close();
-          break;
-        case PNG:
-          ImageIO.write(bi, "png", out);
-          out.close();
-          break;
-      }
-    }
-    catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
-  }
-
-  void setupEPS(int width, int height, String title)
-  {
-    boolean accurateText = true;
-
-    String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
-        "Prompt each time");
-
-    // If we need to prompt, and if the GUI is visible then
-    // Prompt for EPS rendering style
-    if (renderStyle.equalsIgnoreCase("Prompt each time")
-        && !
-        (System.getProperty("java.awt.headless") != null
-         && System.getProperty("java.awt.headless").equals("true")))
-    {
-      EPSOptions eps = new EPSOptions();
-      renderStyle = eps.getValue();
-
-      if (renderStyle == null || eps.cancelled)
-      {
-        return;
-      }
-    }
-
-    if (renderStyle.equalsIgnoreCase("text"))
-    {
-      accurateText = false;
-    }
-
-    try
-    {
-      pg = new EpsGraphics2D(title, out, 0, 0, width,
-                             height);
-      Graphics2D ig2 = (Graphics2D) pg;
-      ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-                           RenderingHints.VALUE_ANTIALIAS_ON);
-
-      pg.setAccurateTextMode(accurateText);
-
-      graphics = pg;
-    }
-    catch (Exception ex)
-    {}
-  }
-
-  JalviewFileChooser getPNGChooser()
-  {
-    return new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
-        "LAST_DIRECTORY"), new String[]
-                                             {"png"},
-                                             new String[]
-                                             {"Portable network graphics"},
-                                             "Portable network graphics");
-  }
-
-  JalviewFileChooser getEPSChooser()
-  {
-    return new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
-        "LAST_DIRECTORY"), new String[]
-                                             {"eps"},
-                                             new String[]
-                                             {"Encapsulated Postscript"},
-                                             "Encapsulated Postscript");
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.util;
+
+import java.io.*;
+import javax.imageio.*;
+
+import java.awt.*;
+import java.awt.image.*;
+
+import org.jibble.epsgraphics.*;
+import jalview.gui.*;
+import jalview.io.*;
+
+public class ImageMaker
+{
+  public static final int EPS = 0;
+
+  public static final int PNG = 1;
+
+  int type = -1;
+
+  EpsGraphics2D pg;
+
+  Graphics graphics;
+
+  FileOutputStream out;
+
+  BufferedImage bi;
+
+  public ImageMaker(Component parent, int type, String title, int width,
+          int height, File file, String EPStitle)
+  {
+    this.type = type;
+
+    if (file == null)
+    {
+      JalviewFileChooser chooser;
+      chooser = type == EPS ? getEPSChooser() : getPNGChooser();
+
+      chooser.setFileView(new jalview.io.JalviewFileView());
+      chooser.setDialogTitle(title);
+      chooser.setToolTipText("Save");
+
+      int value = chooser.showSaveDialog(parent);
+
+      if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
+      {
+        jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+                .getSelectedFile().getParent());
+
+        file = chooser.getSelectedFile();
+      }
+    }
+
+    if (file != null)
+    {
+      try
+      {
+        out = new FileOutputStream(file);
+
+        if (type == EPS)
+        {
+          setupEPS(width, height, EPStitle);
+        }
+        else
+        {
+          setupPNG(width, height);
+        }
+      } catch (Exception ex)
+      {
+        System.out.println("Error creating "
+                + (type == EPS ? "EPS" : "PNG") + " file.");
+      }
+    }
+  }
+
+  public Graphics getGraphics()
+  {
+    return graphics;
+  }
+
+  void setupPNG(int width, int height)
+  {
+    bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
+    graphics = bi.getGraphics();
+    Graphics2D ig2 = (Graphics2D) graphics;
+    ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+            RenderingHints.VALUE_ANTIALIAS_ON);
+  }
+
+  public void writeImage()
+  {
+    try
+    {
+      switch (type)
+      {
+      case EPS:
+        pg.flush();
+        pg.close();
+        break;
+      case PNG:
+        ImageIO.write(bi, "png", out);
+        out.close();
+        break;
+      }
+    } catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
+
+  void setupEPS(int width, int height, String title)
+  {
+    boolean accurateText = true;
+
+    String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
+            "Prompt each time");
+
+    // If we need to prompt, and if the GUI is visible then
+    // Prompt for EPS rendering style
+    if (renderStyle.equalsIgnoreCase("Prompt each time")
+            && !(System.getProperty("java.awt.headless") != null && System
+                    .getProperty("java.awt.headless").equals("true")))
+    {
+      EPSOptions eps = new EPSOptions();
+      renderStyle = eps.getValue();
+
+      if (renderStyle == null || eps.cancelled)
+      {
+        return;
+      }
+    }
+
+    if (renderStyle.equalsIgnoreCase("text"))
+    {
+      accurateText = false;
+    }
+
+    try
+    {
+      pg = new EpsGraphics2D(title, out, 0, 0, width, height);
+      Graphics2D ig2 = (Graphics2D) pg;
+      ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+              RenderingHints.VALUE_ANTIALIAS_ON);
+
+      pg.setAccurateTextMode(accurateText);
+
+      graphics = pg;
+    } catch (Exception ex)
+    {
+    }
+  }
+
+  JalviewFileChooser getPNGChooser()
+  {
+    return new jalview.io.JalviewFileChooser(jalview.bin.Cache
+            .getProperty("LAST_DIRECTORY"), new String[]
+    { "png" }, new String[]
+    { "Portable network graphics" }, "Portable network graphics");
+  }
+
+  JalviewFileChooser getEPSChooser()
+  {
+    return new jalview.io.JalviewFileChooser(jalview.bin.Cache
+            .getProperty("LAST_DIRECTORY"), new String[]
+    { "eps" }, new String[]
+    { "Encapsulated Postscript" }, "Encapsulated Postscript");
+  }
+}
diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index 90dfc8c..6405f98 100644
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -494,7 +494,7 @@ public class MapList
     // inefficient implementation
     int fromStart[] = shiftTo(start);
     int fromEnd[] = shiftTo(end); // needs to be inclusive of end of symbol
-                                  // position
+    // position
     if (fromStart == null || fromEnd == null)
       return null;
     int iv[] = getIntervals(fromShifts, fromStart, fromEnd, fromRatio);
@@ -539,15 +539,15 @@ public class MapList
     startpos = fromStart[0]; // first position in fromStart
     endpos = fromEnd[0]; // last position in fromEnd
     int endindx = (fromRatio2 - 1); // additional positions to get to last
-                                    // position from endpos
+    // position from endpos
     int intv = 0, intvSize = fromShifts2.size();
     int iv[], i = 0, fs = -1, fe_s = -1, fe = -1; // containing intervals
     // search intervals to locate ones containing startpos and count endindx
     // positions on from endpos
-    while (intv < intvSize && ( fs == -1 || fe == -1))
+    while (intv < intvSize && (fs == -1 || fe == -1))
     {
       iv = (int[]) fromShifts2.elementAt(intv++);
-      if (fe_s>-1)
+      if (fe_s > -1)
       {
         endpos = iv[0]; // start counting from beginning of interval
         endindx--; // inclusive of endpos
@@ -569,11 +569,12 @@ public class MapList
             if (endpos + endindx <= iv[1])
             {
               fe = i;
-              endpos = endpos + endindx; // end of end token is within this interval
+              endpos = endpos + endindx; // end of end token is within this
+                                          // interval
             }
             else
             {
-              endindx -= iv[1] - endpos;  // skip all this interval too
+              endindx -= iv[1] - endpos; // skip all this interval too
             }
           }
         }
@@ -595,11 +596,12 @@ public class MapList
             if (endpos - endindx >= iv[1])
             {
               fe = i;
-              endpos = endpos - endindx; // end of end token is within this interval
+              endpos = endpos - endindx; // end of end token is within this
+                                          // interval
             }
             else
             {
-              endindx -= endpos-iv[1]; // skip all this interval too
+              endindx -= endpos - iv[1]; // skip all this interval too
             }
           }
         }
@@ -922,10 +924,13 @@ public class MapList
     // test internal consistency
     int to[] = new int[51];
     MapList.testMap(ml, 1, 60);
-    MapList mldna = new MapList(new int[] { 2,2,6,8,12,16}, new int[] { 1,3},3,1);
-    int[] frm = mldna.locateInFrom(1,1);
-    testLocateFrom(mldna, 1,1,new int[] { 2,2,6,7});
-    MapList.testMap(mldna, 1,3);
+    MapList mldna = new MapList(new int[]
+    { 2, 2, 6, 8, 12, 16 }, new int[]
+    { 1, 3 }, 3, 1);
+    int[] frm = mldna.locateInFrom(1, 1);
+    testLocateFrom(mldna, 1, 1, new int[]
+    { 2, 2, 6, 7 });
+    MapList.testMap(mldna, 1, 3);
     /*
      * for (int from=1; from<=51; from++) { int[] too=ml.shiftTo(from); int[]
      * toofrom=ml.shiftFrom(too[0]);
@@ -933,17 +938,19 @@ public class MapList
      * "+too[1]+"\t+-+\tShiftTo("+too[0]+")=="+toofrom[0]+" % "+toofrom[1]); }
      */
     System.out.print("Success?\n"); // if we get here - something must be
-                                    // working!
+    // working!
   }
 
   private static void testLocateFrom(MapList mldna, int i, int j, int[] ks)
   {
     int[] frm = mldna.locateInFrom(i, j);
-    if (frm==ks || java.util.Arrays.equals(frm,ks))
+    if (frm == ks || java.util.Arrays.equals(frm, ks))
     {
-      System.out.println("Success test locate from "+i+" to "+j);
-    } else {
-      System.err.println("Failed test locate from "+i+" to "+j);
+      System.out.println("Success test locate from " + i + " to " + j);
+    }
+    else
+    {
+      System.err.println("Failed test locate from " + i + " to " + j);
       for (int c = 0; c < frm.length; c++)
       {
         System.err.print(frm[c] + ((c % 2 == 0) ? "," : ";"));
diff --git a/src/jalview/util/Platform.java b/src/jalview/util/Platform.java
index 71ad6f7..e225857 100644
--- a/src/jalview/util/Platform.java
+++ b/src/jalview/util/Platform.java
@@ -1,19 +1,39 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.util;
 
 /**
  * System platform information used by Applet and Application
+ * 
  * @author Jim Procter
  */
 public class Platform
 {
   /**
    * sorry folks - Macs really are different
+   * 
    * @return true if we do things in a special way.
    */
   public boolean isAMac()
   {
-    return java.lang.System.getProperty("os.name").indexOf("Mac")>-1;
-    
+    return java.lang.System.getProperty("os.name").indexOf("Mac") > -1;
+
   }
 
 }
diff --git a/src/jalview/util/QuickSort.java b/src/jalview/util/QuickSort.java
index 017921f..8f7e116 100755
--- a/src/jalview/util/QuickSort.java
+++ b/src/jalview/util/QuickSort.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -24,7 +24,7 @@ public class QuickSort
   {
     sort(arr, 0, arr.length - 1, s);
   }
-  
+
   public static void sort(double[] arr, Object[] s)
   {
     sort(arr, 0, arr.length - 1, s);
@@ -58,6 +58,7 @@ public class QuickSort
       sort(arr, q + 1, r, s);
     }
   }
+
   public static void sort(double[] arr, int p, int r, Object[] s)
   {
     int q;
@@ -81,14 +82,12 @@ public class QuickSort
       do
       {
         j = j - 1;
-      }
-      while (arr[j] > x);
+      } while (arr[j] > x);
 
       do
       {
         i = i + 1;
-      }
-      while (arr[i] < x);
+      } while (arr[i] < x);
 
       if (i < j)
       {
@@ -118,14 +117,12 @@ public class QuickSort
       do
       {
         j = j - 1;
-      }
-      while (arr[j] > x);
+      } while (arr[j] > x);
 
       do
       {
         i = i + 1;
-      }
-      while (arr[i] < x);
+      } while (arr[i] < x);
 
       if (i < j)
       {
@@ -155,14 +152,12 @@ public class QuickSort
       do
       {
         j = j - 1;
-      }
-      while (arr[j].compareTo(x) < 0);
+      } while (arr[j].compareTo(x) < 0);
 
       do
       {
         i = i + 1;
-      }
-      while (arr[i].compareTo(x) > 0);
+      } while (arr[i].compareTo(x) > 0);
 
       if (i < j)
       {
diff --git a/src/jalview/util/ShiftList.java b/src/jalview/util/ShiftList.java
index 8885e2c..be416dc 100644
--- a/src/jalview/util/ShiftList.java
+++ b/src/jalview/util/ShiftList.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -21,14 +21,14 @@ package jalview.util;
 import java.util.*;
 
 /**
- * ShiftList
- * Simple way of mapping a linear series to a new linear range with new points introduced.
- * Use at your own risk!
- * Now growing to be used for interval ranges (position, offset) storing deletions/insertions
+ * ShiftList Simple way of mapping a linear series to a new linear range with
+ * new points introduced. Use at your own risk! Now growing to be used for
+ * interval ranges (position, offset) storing deletions/insertions
  */
 public class ShiftList
 {
   public Vector shifts;
+
   public ShiftList()
   {
     shifts = new Vector();
@@ -36,22 +36,25 @@ public class ShiftList
 
   /**
    * addShift
-   * @param pos start position for shift (in original reference frame)
-   * @param shift length of shift
+   * 
+   * @param pos
+   *                start position for shift (in original reference frame)
+   * @param shift
+   *                length of shift
    */
   public void addShift(int pos, int shift)
   {
     int sidx = 0;
     int[] rshift = null;
-    while (sidx < shifts.size() &&
-           (rshift = (int[]) shifts.elementAt(sidx))[0] < pos)
+    while (sidx < shifts.size()
+            && (rshift = (int[]) shifts.elementAt(sidx))[0] < pos)
     {
       sidx++;
     }
     if (sidx == shifts.size())
     {
       shifts.insertElementAt(new int[]
-                             {pos, shift}, sidx);
+      { pos, shift }, sidx);
     }
     else
     {
@@ -61,8 +64,9 @@ public class ShiftList
 
   /**
    * shift
-   *
-   * @param pos int
+   * 
+   * @param pos
+   *                int
    * @return int shifted position
    */
   public int shift(int pos)
@@ -75,8 +79,7 @@ public class ShiftList
     int sidx = 0;
     int rshift[];
     while (sidx < shifts.size()
-           &&
-           (rshift = ( (int[]) shifts.elementAt(sidx++)))[0] <= pos)
+            && (rshift = ((int[]) shifts.elementAt(sidx++)))[0] <= pos)
     {
       shifted += rshift[1];
     }
@@ -93,6 +96,7 @@ public class ShiftList
 
   /**
    * invert the shifts
+   * 
    * @return ShiftList with inverse shift operations
    */
   public ShiftList getInverse()
@@ -106,7 +110,7 @@ public class ShiftList
         if (sh != null)
         {
           inverse.shifts.addElement(new int[]
-                                    {sh[0], -sh[1]});
+          { sh[0], -sh[1] });
         }
       }
     }
@@ -114,8 +118,9 @@ public class ShiftList
   }
 
   /**
-   * parse a 1d map of position 1<i<n to L<pos[i]<N
-   * such as that returned from SequenceI.gapMap()
+   * parse a 1d map of position 1<i<n to L<pos[i]<N such as that returned
+   * from SequenceI.gapMap()
+   * 
    * @param gapMap
    * @return shifts from map index to mapped position
    */
diff --git a/src/jalview/util/TableSorter.java b/src/jalview/util/TableSorter.java
index 469bd7f..a6ead15 100755
--- a/src/jalview/util/TableSorter.java
+++ b/src/jalview/util/TableSorter.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -28,50 +28,39 @@ import javax.swing.event.*;
 import javax.swing.table.*;
 
 /**
- * TableSorter is a decorator for TableModels; adding sorting
- * functionality to a supplied TableModel. TableSorter does
- * not store or copy the data in its TableModel; instead it maintains
- * a map from the row indexes of the view to the row indexes of the
- * model. As requests are made of the sorter (like getValueAt(row, col))
- * they are passed to the underlying model after the row numbers
- * have been translated via the internal mapping array. This way,
- * the TableSorter appears to hold another copy of the table
- * with the rows in a different order.
- * <p/>
- * TableSorter registers itself as a listener to the underlying model,
- * just as the JTable itself would. Events recieved from the model
- * are examined, sometimes manipulated (typically widened), and then
- * passed on to the TableSorter's listeners (typically the JTable).
- * If a change to the model has invalidated the order of TableSorter's
- * rows, a note of this is made and the sorter will resort the
- * rows the next time a value is requested.
- * <p/>
- * When the tableHeader property is set, either by using the
- * setTableHeader() method or the two argument constructor, the
- * table header may be used as a complete UI for TableSorter.
- * The default renderer of the tableHeader is decorated with a renderer
- * that indicates the sorting status of each column. In addition,
- * a mouse listener is installed with the following behavior:
+ * TableSorter is a decorator for TableModels; adding sorting functionality to a
+ * supplied TableModel. TableSorter does not store or copy the data in its
+ * TableModel; instead it maintains a map from the row indexes of the view to
+ * the row indexes of the model. As requests are made of the sorter (like
+ * getValueAt(row, col)) they are passed to the underlying model after the row
+ * numbers have been translated via the internal mapping array. This way, the
+ * TableSorter appears to hold another copy of the table with the rows in a
+ * different order. <p/> TableSorter registers itself as a listener to the
+ * underlying model, just as the JTable itself would. Events recieved from the
+ * model are examined, sometimes manipulated (typically widened), and then
+ * passed on to the TableSorter's listeners (typically the JTable). If a change
+ * to the model has invalidated the order of TableSorter's rows, a note of this
+ * is made and the sorter will resort the rows the next time a value is
+ * requested. <p/> When the tableHeader property is set, either by using the
+ * setTableHeader() method or the two argument constructor, the table header may
+ * be used as a complete UI for TableSorter. The default renderer of the
+ * tableHeader is decorated with a renderer that indicates the sorting status of
+ * each column. In addition, a mouse listener is installed with the following
+ * behavior:
  * <ul>
- * <li>
- * Mouse-click: Clears the sorting status of all other columns
- * and advances the sorting status of that column through three
- * values: {NOT_SORTED, ASCENDING, DESCENDING} (then back to
- * NOT_SORTED again).
- * <li>
- * SHIFT-mouse-click: Clears the sorting status of all other columns
- * and cycles the sorting status of the column through the same
- * three values, in the opposite order: {NOT_SORTED, DESCENDING, ASCENDING}.
- * <li>
- * CONTROL-mouse-click and CONTROL-SHIFT-mouse-click: as above except
- * that the changes to the column do not cancel the statuses of columns
- * that are already sorting - giving a way to initiate a compound
- * sort.
+ * <li> Mouse-click: Clears the sorting status of all other columns and advances
+ * the sorting status of that column through three values: {NOT_SORTED,
+ * ASCENDING, DESCENDING} (then back to NOT_SORTED again).
+ * <li> SHIFT-mouse-click: Clears the sorting status of all other columns and
+ * cycles the sorting status of the column through the same three values, in the
+ * opposite order: {NOT_SORTED, DESCENDING, ASCENDING}.
+ * <li> CONTROL-mouse-click and CONTROL-SHIFT-mouse-click: as above except that
+ * the changes to the column do not cancel the statuses of columns that are
+ * already sorting - giving a way to initiate a compound sort.
  * </ul>
- * <p/>
- * This is a long overdue rewrite of a class of the same name that
- * first appeared in the swing table demos in 1997.
- *
+ * <p/> This is a long overdue rewrite of a class of the same name that first
+ * appeared in the swing table demos in 1997.
+ * 
  * @author Philip Milne
  * @author Brendon McLean
  * @author Dan van Enckevort
@@ -79,24 +68,26 @@ import javax.swing.table.*;
  * @version 2.0 02/27/04
  */
 
-public class TableSorter
-    extends AbstractTableModel
+public class TableSorter extends AbstractTableModel
 {
   protected TableModel tableModel;
 
   public static final int DESCENDING = -1;
+
   public static final int NOT_SORTED = 0;
+
   public static final int ASCENDING = 1;
 
-  private static Directive EMPTY_DIRECTIVE = new Directive( -1, NOT_SORTED);
+  private static Directive EMPTY_DIRECTIVE = new Directive(-1, NOT_SORTED);
 
   public static final Comparator COMPARABLE_COMAPRATOR = new Comparator()
   {
     public int compare(Object o1, Object o2)
     {
-      return ( (Comparable) o1).compareTo(o2);
+      return ((Comparable) o1).compareTo(o2);
     }
   };
+
   public static final Comparator LEXICAL_COMPARATOR = new Comparator()
   {
     public int compare(Object o1, Object o2)
@@ -106,12 +97,17 @@ public class TableSorter
   };
 
   private Row[] viewToModel;
+
   private int[] modelToView;
 
   private JTableHeader tableHeader;
+
   private MouseListener mouseListener;
+
   private TableModelListener tableModelListener;
+
   private Map columnComparators = new HashMap();
+
   private List sortingColumns = new ArrayList();
 
   public TableSorter()
@@ -171,20 +167,20 @@ public class TableSorter
     if (this.tableHeader != null)
     {
       this.tableHeader.removeMouseListener(mouseListener);
-      TableCellRenderer defaultRenderer = this.tableHeader.getDefaultRenderer();
+      TableCellRenderer defaultRenderer = this.tableHeader
+              .getDefaultRenderer();
       if (defaultRenderer instanceof SortableHeaderRenderer)
       {
-        this.tableHeader.setDefaultRenderer( ( (SortableHeaderRenderer)
-                                              defaultRenderer).
-                                            tableCellRenderer);
+        this.tableHeader
+                .setDefaultRenderer(((SortableHeaderRenderer) defaultRenderer).tableCellRenderer);
       }
     }
     this.tableHeader = tableHeader;
     if (this.tableHeader != null)
     {
       this.tableHeader.addMouseListener(mouseListener);
-      this.tableHeader.setDefaultRenderer(
-          new SortableHeaderRenderer(this.tableHeader.getDefaultRenderer()));
+      this.tableHeader.setDefaultRenderer(new SortableHeaderRenderer(
+              this.tableHeader.getDefaultRenderer()));
     }
   }
 
@@ -243,7 +239,7 @@ public class TableSorter
       return null;
     }
     return new Arrow(directive.direction == DESCENDING, size,
-                     sortingColumns.indexOf(directive));
+            sortingColumns.indexOf(directive));
   }
 
   private void cancelSorting()
@@ -356,8 +352,7 @@ public class TableSorter
 
   // Helper classes
 
-  private class Row
-      implements Comparable
+  private class Row implements Comparable
   {
     private int modelIndex;
 
@@ -369,9 +364,9 @@ public class TableSorter
     public int compareTo(Object o)
     {
       int row1 = modelIndex;
-      int row2 = ( (Row) o).modelIndex;
+      int row2 = ((Row) o).modelIndex;
 
-      for (Iterator it = sortingColumns.iterator(); it.hasNext(); )
+      for (Iterator it = sortingColumns.iterator(); it.hasNext();)
       {
         Directive directive = (Directive) it.next();
         int column = directive.column;
@@ -398,15 +393,15 @@ public class TableSorter
         }
         if (comparison != 0)
         {
-          return directive.direction == DESCENDING ? -comparison : comparison;
+          return directive.direction == DESCENDING ? -comparison
+                  : comparison;
         }
       }
       return 0;
     }
   }
 
-  private class TableModelHandler
-      implements TableModelListener
+  private class TableModelHandler implements TableModelListener
   {
     public void tableChanged(TableModelEvent e)
     {
@@ -431,12 +426,16 @@ public class TableSorter
       // We can map a cell event through to the view without widening
       // when the following conditions apply:
       //
-      // a) all the changes are on one row (e.getFirstRow() == e.getLastRow()) and,
-      // b) all the changes are in one column (column != TableModelEvent.ALL_COLUMNS) and,
-      // c) we are not sorting on that column (getSortingStatus(column) == NOT_SORTED) and,
+      // a) all the changes are on one row (e.getFirstRow() == e.getLastRow())
+      // and,
+      // b) all the changes are in one column (column !=
+      // TableModelEvent.ALL_COLUMNS) and,
+      // c) we are not sorting on that column (getSortingStatus(column) ==
+      // NOT_SORTED) and,
       // d) a reverse lookup will not trigger a sort (modelToView != null)
       //
-      // Note: INSERT and DELETE events fail this test as they have column == ALL_COLUMNS.
+      // Note: INSERT and DELETE events fail this test as they have column ==
+      // ALL_COLUMNS.
       //
       // The last check, for (modelToView != null) is to see if modelToView
       // is already allocated. If we don't do this check; sorting can become
@@ -448,26 +447,25 @@ public class TableSorter
       // clause avoids this problem.
       int column = e.getColumn();
       if (e.getFirstRow() == e.getLastRow()
-          && column != TableModelEvent.ALL_COLUMNS
-          && getSortingStatus(column) == NOT_SORTED
-          && modelToView != null)
+              && column != TableModelEvent.ALL_COLUMNS
+              && getSortingStatus(column) == NOT_SORTED
+              && modelToView != null)
       {
         int viewIndex = getModelToView()[e.getFirstRow()];
-        fireTableChanged(new TableModelEvent(TableSorter.this,
-                                             viewIndex, viewIndex,
-                                             column, e.getType()));
+        fireTableChanged(new TableModelEvent(TableSorter.this, viewIndex,
+                viewIndex, column, e.getType()));
         return;
       }
 
-      // Something has happened to the data that may have invalidated the row order.
+      // Something has happened to the data that may have invalidated the row
+      // order.
       clearSortingState();
       fireTableDataChanged();
       return;
     }
   }
 
-  private class MouseHandler
-      extends MouseAdapter
+  private class MouseHandler extends MouseAdapter
   {
     public void mouseClicked(MouseEvent e)
     {
@@ -482,8 +480,10 @@ public class TableSorter
         {
           cancelSorting();
         }
-        // Cycle the sorting states through {NOT_SORTED, ASCENDING, DESCENDING} or
-        // {NOT_SORTED, DESCENDING, ASCENDING} depending on whether shift is pressed.
+        // Cycle the sorting states through {NOT_SORTED, ASCENDING, DESCENDING}
+        // or
+        // {NOT_SORTED, DESCENDING, ASCENDING} depending on whether shift is
+        // pressed.
         status = status + (e.isShiftDown() ? -1 : 1);
         status = (status + 4) % 3 - 1; // signed mod, returning {-1, 0, 1}
         setSortingStatus(column, status);
@@ -491,11 +491,12 @@ public class TableSorter
     }
   }
 
-  private static class Arrow
-      implements Icon
+  private static class Arrow implements Icon
   {
     private boolean descending;
+
     private int size;
+
     private int priority;
 
     public Arrow(boolean descending, int size, int priority)
@@ -539,7 +540,7 @@ public class TableSorter
       g.drawLine(dx, 0, 0, 0);
 
       g.setColor(color);
-      g.translate( -x, -y);
+      g.translate(-x, -y);
     }
 
     public int getIconWidth()
@@ -553,8 +554,7 @@ public class TableSorter
     }
   }
 
-  private class SortableHeaderRenderer
-      implements TableCellRenderer
+  private class SortableHeaderRenderer implements TableCellRenderer
   {
     private TableCellRenderer tableCellRenderer;
 
@@ -564,20 +564,19 @@ public class TableSorter
     }
 
     public Component getTableCellRendererComponent(JTable table,
-        Object value,
-        boolean isSelected,
-        boolean hasFocus,
-        int row,
-        int column)
+            Object value, boolean isSelected, boolean hasFocus, int row,
+            int column)
     {
       Component c = tableCellRenderer.getTableCellRendererComponent(table,
-          value, isSelected, hasFocus, row, column);
+              value, isSelected, hasFocus, row, column);
       if (c instanceof JLabel)
       {
         JLabel l = (JLabel) c;
         l.setHorizontalTextPosition(JLabel.LEFT);
         int modelColumn = table.convertColumnIndexToModel(column);
-        l.setIcon(getHeaderRendererIcon(modelColumn, l.getFont().getSize()));
+        l
+                .setIcon(getHeaderRendererIcon(modelColumn, l.getFont()
+                        .getSize()));
       }
       return c;
     }
@@ -586,6 +585,7 @@ public class TableSorter
   private static class Directive
   {
     private int column;
+
     private int direction;
 
     public Directive(int column, int direction)
diff --git a/src/jalview/util/UrlLink.java b/src/jalview/util/UrlLink.java
index 21dee38..c2df608 100644
--- a/src/jalview/util/UrlLink.java
+++ b/src/jalview/util/UrlLink.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.util;
 
 import java.util.Vector;
@@ -99,7 +117,7 @@ public class UrlLink
       label = link.substring(0, sep = link.lastIndexOf("|"));
       url_prefix = link.substring(sep + 1);
       regexReplace = null; // implies we trim any prefix if necessary //
-                            // regexReplace=".*\\|?(.*)";
+      // regexReplace=".*\\|?(.*)";
       url_suffix = null;
     }
   }
diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index 82b411a..76e73e4 100644
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -31,9 +31,8 @@ import jalview.ws.dbsources.Uniprot;
 import jalview.ws.ebi.EBIFetchClient;
 
 /**
- * Implements a runnable for validating a sequence 
- * against external databases and then propagating 
- * references and features onto the sequence(s)
+ * Implements a runnable for validating a sequence against external databases
+ * and then propagating references and features onto the sequence(s)
  * 
  * @author $author$
  * @version $Revision$
@@ -83,7 +82,7 @@ public class DBRefFetcher implements Runnable
     }
     this.dataset = ds;
     // TODO Jalview 2.5 lots of this code should be in the gui package!
-    sfetcher = jalview.gui.SequenceFetcher.getSequenceFetcherSingleton(af); 
+    sfetcher = jalview.gui.SequenceFetcher.getSequenceFetcherSingleton(af);
     // select appropriate databases based on alignFrame context.
     if (af.getViewport().getAlignment().isNucleotide())
     {
@@ -194,8 +193,10 @@ public class DBRefFetcher implements Runnable
       {
         maxqlen = ((Integer) dbsource.getDbSourceProperties().get(
                 DBRefSource.MULTIACC)).intValue();
-      } else {
-        maxqlen=1;
+      }
+      else
+      {
+        maxqlen = 1;
       }
       // iterate through db for each remaining un-verified sequence
       SequenceI[] currSeqs = new SequenceI[sdataset.size()];
@@ -237,6 +238,10 @@ public class DBRefFetcher implements Runnable
           } catch (Exception ex)
           {
             ex.printStackTrace();
+          } catch (OutOfMemoryError err)
+          {
+            new OOMWarning("retrieving database references ("
+                    + queryString.toString() + ")", err);
           }
           if (retrieved != null)
           {
@@ -351,14 +356,15 @@ public class DBRefFetcher implements Runnable
           }
         }
       }
-      if (sequenceMatches.size()==0)
+      if (sequenceMatches.size() == 0)
       {
-        // failed to match directly on accessionId==query so just compare all sequences to entry
+        // failed to match directly on accessionId==query so just compare all
+        // sequences to entry
         Enumeration e = seqRefs.keys();
         while (e.hasMoreElements())
         {
           Vector sqs = (Vector) seqRefs.get(e.nextElement());
-          if (sqs!=null && sqs.size()>0)
+          if (sqs != null && sqs.size() > 0)
           {
             Enumeration sqe = sqs.elements();
             while (sqe.hasMoreElements())
@@ -388,9 +394,12 @@ public class DBRefFetcher implements Runnable
       for (int m = 0; m < sequenceMatches.size(); m++)
       {
         sequence = (SequenceI) sequenceMatches.elementAt(m);
-        // only update start and end positions and shift features if there are no existing references
-        // TODO: test for legacy where uniprot or EMBL refs exist but no mappings are made (but content matches retrieved set)
-        boolean updateRefFrame = sequence.getDBRef()==null || sequence.getDBRef().length==0;
+        // only update start and end positions and shift features if there are
+        // no existing references
+        // TODO: test for legacy where uniprot or EMBL refs exist but no
+        // mappings are made (but content matches retrieved set)
+        boolean updateRefFrame = sequence.getDBRef() == null
+                || sequence.getDBRef().length == 0;
         // verify sequence against the entry sequence
 
         String nonGapped = AlignSeq.extractGaps("-. ",
@@ -410,20 +419,23 @@ public class DBRefFetcher implements Runnable
                     + " SEQUENCE NOT %100 MATCH \n");
             continue;
           }
-          
+
           sbuffer.append(sequence.getName() + " HAS " + absStart
-                + " PREFIXED RESIDUES COMPARED TO " + dbSource+"\n");
+                  + " PREFIXED RESIDUES COMPARED TO " + dbSource + "\n");
           //
-          //      + " - ANY SEQUENCE FEATURES"
-          //        + " HAVE BEEN ADJUSTED ACCORDINGLY \n");
+          // + " - ANY SEQUENCE FEATURES"
+          // + " HAVE BEEN ADJUSTED ACCORDINGLY \n");
           // absStart = 0;
           // create valid mapping between matching region of local sequence and
           // the mapped sequence
           mp = new Mapping(null, new int[]
-          { sequence.getStart()+absStart, sequence.getStart()+absStart+entrySeq.length()-1 }, new int[]
-          { entry.getStart(),
-              entry.getStart() + entrySeq.length() - 1 }, 1, 1);
-          updateRefFrame=false; // mapping is based on current start/end so don't modify start and end
+          { sequence.getStart() + absStart,
+              sequence.getStart() + absStart + entrySeq.length() - 1 },
+                  new int[]
+                  { entry.getStart(),
+                      entry.getStart() + entrySeq.length() - 1 }, 1, 1);
+          updateRefFrame = false; // mapping is based on current start/end so
+          // don't modify start and end
         }
         else
         {
@@ -443,7 +455,8 @@ public class DBRefFetcher implements Runnable
             SequenceFeature[] sf = sequence.getSequenceFeatures();
             int start = sequence.getStart();
             int end = sequence.getEnd();
-            int startShift = 1-absStart-start; // how much the features are to be shifted by
+            int startShift = 1 - absStart - start; // how much the features are
+            // to be shifted by
             for (int sfi = 0; sfi < sf.length; sfi++)
             {
               if (sf[sfi].getBegin() >= start && sf[sfi].getEnd() <= end)
diff --git a/src/jalview/ws/DasSequenceFeatureFetcher.java b/src/jalview/ws/DasSequenceFeatureFetcher.java
index e3f7478..f252b67 100644
--- a/src/jalview/ws/DasSequenceFeatureFetcher.java
+++ b/src/jalview/ws/DasSequenceFeatureFetcher.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -34,7 +34,7 @@ import jalview.gui.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
@@ -51,43 +51,51 @@ public class DasSequenceFeatureFetcher
   Vector selectedSources;
 
   boolean cancelled = false;
+
   private void debug(String mesg)
   {
     debug(mesg, null);
   }
+
   private void debug(String mesg, Exception e)
   {
-    if (Cache.log!=null)
+    if (Cache.log != null)
     {
       Cache.log.debug(mesg, e);
-    } else {
+    }
+    else
+    {
       System.err.println(mesg);
-      if (e!=null)
-      { 
-        e.printStackTrace(); 
+      if (e != null)
+      {
+        e.printStackTrace();
       }
     }
   }
+
   long startTime;
 
   /**
-   * Creates a new SequenceFeatureFetcher object.
-   * Uses default
-   *
-   * @param align DOCUMENT ME!
-   * @param ap DOCUMENT ME!
+   * Creates a new SequenceFeatureFetcher object. Uses default
+   * 
+   * @param align
+   *                DOCUMENT ME!
+   * @param ap
+   *                DOCUMENT ME!
    */
   public DasSequenceFeatureFetcher(SequenceI[] sequences,
           FeatureSettings fsettings, Vector selectedSources)
   {
     this(sequences, fsettings, selectedSources, true, true);
   }
+
   public DasSequenceFeatureFetcher(SequenceI[] sequences,
-          FeatureSettings fsettings, Vector selectedSources, boolean checkDbrefs, boolean promptFetchDbrefs)
+          FeatureSettings fsettings, Vector selectedSources,
+          boolean checkDbrefs, boolean promptFetchDbrefs)
   {
     this.selectedSources = selectedSources;
     this.sequences = sequences;
-    if (fsettings!=null)
+    if (fsettings != null)
     {
       this.fsettings = fsettings;
       this.af = fsettings.af;
@@ -100,7 +108,8 @@ public class DasSequenceFeatureFetcher
       DasCoordinateSystem[] coords = source.getCoordinateSystem();
       for (int c = 0; c < coords.length; c++)
       {
-        // TODO: match UniProt coord system canonically (?) - does UniProt==uniprot==UNIPROT ? 
+        // TODO: match UniProt coord system canonically (?) - does
+        // UniProt==uniprot==UNIPROT ?
         if (coords[c].getName().indexOf("UniProt") > -1)
         {
           uniprotCount++;
@@ -133,13 +142,15 @@ public class DasSequenceFeatureFetcher
       int reply = JOptionPane.YES_OPTION;
       if (promptFetchDbrefs)
       {
-        reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
-             "Do you want Jalview to find\n"
-                      + "Uniprot Accession ids for given sequence names?",
-              "Find Uniprot Accession Ids", JOptionPane.YES_NO_OPTION,
-              JOptionPane.QUESTION_MESSAGE);
+        reply = JOptionPane
+                .showInternalConfirmDialog(
+                        Desktop.desktop,
+                        "Do you want Jalview to find\n"
+                                + "Uniprot Accession ids for given sequence names?",
+                        "Find Uniprot Accession Ids",
+                        JOptionPane.YES_NO_OPTION,
+                        JOptionPane.QUESTION_MESSAGE);
       }
-              
 
       if (reply == JOptionPane.YES_OPTION)
       {
@@ -168,13 +179,14 @@ public class DasSequenceFeatureFetcher
   }
 
   /**
-   * Spawns a number of dasobert Fetcher threads to add features to sequences in the dataset
+   * Spawns a number of dasobert Fetcher threads to add features to sequences in
+   * the dataset
    */
   void startFetching()
   {
     cancelled = false;
     startTime = System.currentTimeMillis();
-    if (af!=null)
+    if (af != null)
     {
       af.setProgressBar("Fetching DAS Sequence Features", startTime);
     }
@@ -211,7 +223,7 @@ public class DasSequenceFeatureFetcher
     }
 
     sourcesRemaining = selectedSources.size();
-    //Now sending requests one at a time to each server
+    // Now sending requests one at a time to each server
     for (int sourceIndex = 0; sourceIndex < selectedSources.size()
             && !cancelled; sourceIndex++)
     {
@@ -225,18 +237,20 @@ public class DasSequenceFeatureFetcher
   private void setGuiNoDassourceActive()
   {
 
-    if (af!=null)
+    if (af != null)
     {
       af.setProgressBar("No DAS Sources Active", startTime);
     }
-    if (getFeatSettings()!=null)
+    if (getFeatSettings() != null)
     {
       fsettings.noDasSourceActive();
-     }
+    }
   }
 
   /**
-   * Update our fsettings dialog reference if we didn't have one when we were first initialised.
+   * Update our fsettings dialog reference if we didn't have one when we were
+   * first initialised.
+   * 
    * @return fsettings
    */
   private FeatureSettings getFeatSettings()
@@ -253,7 +267,7 @@ public class DasSequenceFeatureFetcher
 
   public void cancel()
   {
-    if (af!=null)
+    if (af != null)
     {
       af.setProgressBar("DAS Feature Fetching Cancelled", startTime);
     }
@@ -307,7 +321,7 @@ public class DasSequenceFeatureFetcher
 
   void featuresAdded(SequenceI seq)
   {
-    if (af==null)
+    if (af == null)
     {
       // no gui to update with features.
       return;
@@ -335,11 +349,13 @@ public class DasSequenceFeatureFetcher
     DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
             seq.getDBRef(), new String[]
             {
-            //  jalview.datamodel.DBRefSource.PDB,
+            // jalview.datamodel.DBRefSource.PDB,
             jalview.datamodel.DBRefSource.UNIPROT,
-            //  jalview.datamodel.DBRefSource.EMBL - not tested on any EMBL coord sys sources
+            // jalview.datamodel.DBRefSource.EMBL - not tested on any EMBL coord
+            // sys sources
             });
-    // TODO: minimal list of DAS queries to make by querying with untyped ID if distinct from any typed IDs
+    // TODO: minimal list of DAS queries to make by querying with untyped ID if
+    // distinct from any typed IDs
 
     boolean dasCoordSysFound = false;
 
@@ -358,8 +374,9 @@ public class DasSequenceFeatureFetcher
           {
             debug("Launched fetcher for coordinate system "
                     + cs[0].getName());
-            //  Will have to pass any mapping information to the fetcher
-            //- the start/end for the DBRefEntry may not be the same as the sequence's start/end
+            // Will have to pass any mapping information to the fetcher
+            // - the start/end for the DBRefEntry may not be the same as the
+            // sequence's start/end
 
             System.out.println(seq.getName() + " "
                     + (seq.getDatasetSequence() == null) + " "
@@ -381,13 +398,14 @@ public class DasSequenceFeatureFetcher
       if (seq.getName().indexOf("|") > -1)
       {
         id = seq.getName().substring(seq.getName().lastIndexOf("|") + 1);
-        if (id.trim().length()<4)
+        if (id.trim().length() < 4)
         {
-          // hack - we regard a significant ID as being at least 4 non-whitespace characters
+          // hack - we regard a significant ID as being at least 4
+          // non-whitespace characters
           id = seq.getName().substring(0, seq.getName().lastIndexOf("|"));
-          if (id.indexOf("|")>-1)
+          if (id.indexOf("|") > -1)
           {
-            id = id.substring(id.lastIndexOf("|")+1);
+            id = id.substring(id.lastIndexOf("|") + 1);
           }
         }
       }
@@ -406,8 +424,10 @@ public class DasSequenceFeatureFetcher
   }
 
   /**
-   * fetch and add das features to a sequence using the given source URL and compatible DbRef id.
-   * new features are mapped using the DbRef mapping to the local coordinate system.
+   * fetch and add das features to a sequence using the given source URL and
+   * compatible DbRef id. new features are mapped using the DbRef mapping to the
+   * local coordinate system.
+   * 
    * @param seq
    * @param SourceUrl
    * @param dbref
@@ -416,8 +436,8 @@ public class DasSequenceFeatureFetcher
           final DasSource dasSource, final DBRefEntry dbref)
   {
 
-    //////////////
-    /// fetch DAS features
+    // ////////////
+    // / fetch DAS features
     final Das1Source source = new Das1Source();
     source.setUrl(dasSource.getUrl());
     source.setNickname(dasSource.getNickname());
@@ -427,11 +447,10 @@ public class DasSequenceFeatureFetcher
       responseComplete(dasSource, seq); // reduce thread count anyhow
       return;
     }
-    debug("new Das Feature Fetcher for " + dbref.getSource()
-            + ":" + dbref.getAccessionId() + " querying "
-            + dasSource.getUrl());
+    debug("new Das Feature Fetcher for " + dbref.getSource() + ":"
+            + dbref.getAccessionId() + " querying " + dasSource.getUrl());
     FeatureThread fetcher = new FeatureThread(dbref.getAccessionId()
-    //  +  ":" + start + "," + end,
+    // + ":" + start + "," + end,
             , source);
 
     fetcher.addFeatureListener(new FeatureListener()
@@ -451,8 +470,8 @@ public class DasSequenceFeatureFetcher
 
         Map[] features = e.getFeatures();
         // add features to sequence
-        debug("das source " + ds.getUrl() + " returned "
-                + features.length + " features");
+        debug("das source " + ds.getUrl() + " returned " + features.length
+                + " features");
 
         if (features.length > 0)
         {
@@ -463,8 +482,7 @@ public class DasSequenceFeatureFetcher
             if (dbref.getMap() != null && f.getBegin() > 0
                     && f.getEnd() > 0)
             {
-              debug("mapping from " + f.getBegin() + " - "
-                      + f.getEnd());
+              debug("mapping from " + f.getBegin() + " - " + f.getEnd());
               SequenceFeature vf[] = null;
 
               try
@@ -486,8 +504,8 @@ public class DasSequenceFeatureFetcher
               {
                 for (int v = 0; v < vf.length; v++)
                 {
-                  debug("mapping to " + v + ": "
-                          + vf[v].getBegin() + " - " + vf[v].getEnd());
+                  debug("mapping to " + v + ": " + vf[v].getBegin() + " - "
+                          + vf[v].getEnd());
                   seq.addSequenceFeature(vf[v]);
                 }
               }
@@ -502,8 +520,8 @@ public class DasSequenceFeatureFetcher
         }
         else
         {
-          //  System.out.println("No features found for " + seq.getName()
-          //                     + " from: " + e.getDasSource().getNickname());
+          // System.out.println("No features found for " + seq.getName()
+          // + " from: " + e.getDasSource().getNickname());
         }
         responseComplete(dasSource, seq);
 
@@ -518,13 +536,13 @@ public class DasSequenceFeatureFetcher
   protected void createFeatureFetcher(final SequenceI seq,
           final DasSource dasSource, String id)
   {
-    //////////////
-    /// fetch DAS features
+    // ////////////
+    // / fetch DAS features
     final Das1Source source = new Das1Source();
     source.setUrl(dasSource.getUrl());
     source.setNickname(dasSource.getNickname());
-    
-    if (id!=null)
+
+    if (id != null)
     {
       id = id.trim();
     }
@@ -533,7 +551,7 @@ public class DasSequenceFeatureFetcher
       debug("new Das Feature Fetcher for " + id + " querying "
               + dasSource.getUrl());
       FeatureThread fetcher = new FeatureThread(id
-      //  +  ":" + start + "," + end,
+      // + ":" + start + "," + end,
               , source);
 
       fetcher.addFeatureListener(new FeatureListener()
@@ -570,8 +588,8 @@ public class DasSequenceFeatureFetcher
           }
           else
           {
-            //  System.out.println("No features found for " + seq.getName()
-            //                     + " from: " + e.getDasSource().getNickname());
+            // System.out.println("No features found for " + seq.getName()
+            // + " from: " + e.getDasSource().getNickname());
           }
           responseComplete(dasSource, seq);
 
@@ -581,16 +599,18 @@ public class DasSequenceFeatureFetcher
       );
 
       fetcher.start();
-    } else {
+    }
+    else
+    {
       // invalid fetch - indicate it is finished.
-      debug("Skipping empty ID for querying "
-              + dasSource.getUrl());
+      debug("Skipping empty ID for querying " + dasSource.getUrl());
       responseComplete(dasSource, seq);
     }
   }
 
   /**
    * creates a jalview sequence feature from a das feature document
+   * 
    * @param dasfeature
    * @return sequence feature object created using dasfeature information
    */
@@ -603,14 +623,10 @@ public class DasSequenceFeatureFetcher
     try
     {
       /**
-       * Different qNames for a DAS Feature - are string keys to the HashMaps in features
-       * "METHOD") ||
-                  qName.equals("TYPE") ||
-                  qName.equals("START") ||
-                  qName.equals("END") ||
-                  qName.equals("NOTE") ||
-                  qName.equals("LINK") ||
-                  qName.equals("SCORE")
+       * Different qNames for a DAS Feature - are string keys to the HashMaps in
+       * features "METHOD") || qName.equals("TYPE") || qName.equals("START") ||
+       * qName.equals("END") || qName.equals("NOTE") || qName.equals("LINK") ||
+       * qName.equals("SCORE")
        */
       String desc = new String();
       if (dasfeature.containsKey("NOTE"))
@@ -659,9 +675,12 @@ public class DasSequenceFeatureFetcher
       return null;
     }
   }
+
   /**
-   * query the default DAS Source Registry for sources.
-   * Uses value of jalview property DAS_REGISTRY_URL and the DasSourceBrowser.DEFAULT_REGISTRY if that doesn't exist. 
+   * query the default DAS Source Registry for sources. Uses value of jalview
+   * property DAS_REGISTRY_URL and the DasSourceBrowser.DEFAULT_REGISTRY if that
+   * doesn't exist.
+   * 
    * @return list of sources
    */
   public static DasSource[] getDASSources()
@@ -671,10 +690,12 @@ public class DasSequenceFeatureFetcher
             DasSourceBrowser.DEFAULT_REGISTRY);
     return getDASSources(registryURL);
   }
+
   /**
    * query the given URL for DasSources.
+   * 
    * @param registryURL
-   * return sources from registryURL
+   *                return sources from registryURL
    */
   public static DasSource[] getDASSources(String registryURL)
   {
diff --git a/src/jalview/ws/Discoverer.java b/src/jalview/ws/Discoverer.java
index 61b8ba1..7e822aa 100755
--- a/src/jalview/ws/Discoverer.java
+++ b/src/jalview/ws/Discoverer.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -19,14 +19,22 @@
 package jalview.ws;
 
 /**
- * <p>Title: </p>
- *
- * <p>Description: </p>
- *
- * <p>Copyright: Copyright (c) 2004</p>
- *
- * <p>Company: Dundee University</p>
- *
+ * <p>
+ * Title:
+ * </p>
+ * 
+ * <p>
+ * Description:
+ * </p>
+ * 
+ * <p>
+ * Copyright: Copyright (c) 2004
+ * </p>
+ * 
+ * <p>
+ * Company: Dundee University
+ * </p>
+ * 
  * @author not attributable
  * @version 1.0
  */
@@ -36,50 +44,56 @@ import javax.swing.*;
 
 import ext.vamsas.*;
 
-public class Discoverer
-    extends Thread implements Runnable
+public class Discoverer extends Thread implements Runnable
 {
   ext.vamsas.IRegistry registry; // the root registry service.
-  private java.beans.PropertyChangeSupport changeSupport = new java.beans.
-      PropertyChangeSupport(this);
+
+  private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
+          this);
 
   /**
    * change listeners are notified of "services" property changes
-   *
-   * @param listener to be added that consumes new services Hashtable object.
+   * 
+   * @param listener
+   *                to be added that consumes new services Hashtable object.
    */
   public void addPropertyChangeListener(
-      java.beans.PropertyChangeListener listener)
+          java.beans.PropertyChangeListener listener)
   {
     changeSupport.addPropertyChangeListener(listener);
   }
 
   /**
-   *
-   *
-   * @param listener to be removed
+   * 
+   * 
+   * @param listener
+   *                to be removed
    */
   public void removePropertyChangeListener(
-      java.beans.PropertyChangeListener listener)
+          java.beans.PropertyChangeListener listener)
   {
     changeSupport.removePropertyChangeListener(listener);
   }
 
   /**
    * Property change listener firing routine
-   *
-   * @param prop services
-   * @param oldvalue old services hash
-   * @param newvalue new services hash
+   * 
+   * @param prop
+   *                services
+   * @param oldvalue
+   *                old services hash
+   * @param newvalue
+   *                new services hash
    */
-  public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
+  public void firePropertyChange(String prop, Object oldvalue,
+          Object newvalue)
   {
     changeSupport.firePropertyChange(prop, oldvalue, newvalue);
   }
 
   /**
    * Initializes the server field with a valid service implementation.
-   *
+   * 
    * @return true if service was located.
    */
   private IRegistry locateWebService(java.net.URL WsURL)
@@ -89,13 +103,14 @@ public class Discoverer
     try
     {
       server = loc.getRegistryService(WsURL);
-      ( (RegistryServiceSoapBindingStub) server).setTimeout(60000); // One minute timeout
-    }
-    catch (Exception ex)
+      ((RegistryServiceSoapBindingStub) server).setTimeout(60000); // One
+                                                                    // minute
+                                                                    // timeout
+    } catch (Exception ex)
     {
-      jalview.bin.Cache.log.error(
-          "Serious!  Service location failed\nfor URL :" + WsURL +
-          "\n", ex);
+      jalview.bin.Cache.log
+              .error("Serious!  Service location failed\nfor URL :" + WsURL
+                      + "\n", ex);
 
       return null;
     }
@@ -106,16 +121,24 @@ public class Discoverer
   }
 
   static private java.net.URL RootServiceURL = null;
+
   static public Vector ServiceURLList = null;
+
   static private boolean reallyDiscoverServices = true;
 
-  public static java.util.Hashtable services = null; // vectors of services stored by abstractServiceType string
+  public static java.util.Hashtable services = null; // vectors of services
+                                                      // stored by
+                                                      // abstractServiceType
+                                                      // string
+
   public static java.util.Vector serviceList = null; // flat list of services
+
   static private Vector getDiscoveryURLS()
   {
     Vector urls = new Vector();
-    String RootServiceURLs = jalview.bin.Cache.getDefault("DISCOVERY_URLS",
-        "http://www.compbio.dundee.ac.uk/JalviewWS/services/ServiceRegistry");
+    String RootServiceURLs = jalview.bin.Cache
+            .getDefault("DISCOVERY_URLS",
+                    "http://www.compbio.dundee.ac.uk/JalviewWS/services/ServiceRegistry");
 
     try
     {
@@ -132,26 +155,26 @@ public class Discoverer
           }
           else
           {
-            jalview.bin.Cache.log.info(
-                "Ignoring duplicate url in DISCOVERY_URLS list");
+            jalview.bin.Cache.log
+                    .info("Ignoring duplicate url in DISCOVERY_URLS list");
           }
-        }
-        catch (Exception ex)
+        } catch (Exception ex)
         {
-          jalview.bin.Cache.log.warn(
-              "Problem whilst trying to make a URL from '" +
-              ( (url != null) ? url : "<null>") + "'");
-          jalview.bin.Cache.log.warn(
-              "This was probably due to a malformed comma separated list"
-              + " in the DISCOVERY_URLS entry of $(HOME)/.jalview_properties)");
+          jalview.bin.Cache.log
+                  .warn("Problem whilst trying to make a URL from '"
+                          + ((url != null) ? url : "<null>") + "'");
+          jalview.bin.Cache.log
+                  .warn("This was probably due to a malformed comma separated list"
+                          + " in the DISCOVERY_URLS entry of $(HOME)/.jalview_properties)");
           jalview.bin.Cache.log.debug("Exception was ", ex);
         }
       }
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
-      jalview.bin.Cache.log.warn(
-          "Error parsing comma separated list of urls in DISCOVERY_URLS.", ex);
+      jalview.bin.Cache.log
+              .warn(
+                      "Error parsing comma separated list of urls in DISCOVERY_URLS.",
+                      ex);
     }
     if (urls.size() > 0)
     {
@@ -165,10 +188,12 @@ public class Discoverer
    */
   static public void doDiscovery()
   {
-    jalview.bin.Cache.log.debug("(Re)-Initialising the discovery URL list.");
+    jalview.bin.Cache.log
+            .debug("(Re)-Initialising the discovery URL list.");
     try
     {
-      reallyDiscoverServices = jalview.bin.Cache.getDefault("DISCOVERY_START", false);
+      reallyDiscoverServices = jalview.bin.Cache.getDefault(
+              "DISCOVERY_START", false);
       if (reallyDiscoverServices)
       {
         ServiceURLList = getDiscoveryURLS();
@@ -179,47 +204,44 @@ public class Discoverer
         services = new Hashtable();
         // Muscle, Clustal and JPred.
         ServiceHandle[] defServices =
-            {
+        {
             new ServiceHandle(
-                "MsaWS",
-                "Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment " +
-                "with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.",
-                "http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS",
-                "Muscle Multiple Protein Sequence Alignment"
-            ),
+                    "MsaWS",
+                    "Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment "
+                            + "with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.",
+                    "http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS",
+                    "Muscle Multiple Protein Sequence Alignment"),
             new ServiceHandle(
-                "MsaWS",
-                "Katoh, K., K. Kuma, K., Toh, H.,  and Miyata, T. (2005) " +
-                "\"MAFFT version 5: improvement in accuracy of multiple sequence alignment.\"" +
-                " Nucleic Acids Research, 33 511-518",
-                "http://www.compbio.dundee.ac.uk/JalviewWS/services/MafftWS",
-                "MAFFT Multiple Sequence Alignment"),
+                    "MsaWS",
+                    "Katoh, K., K. Kuma, K., Toh, H.,  and Miyata, T. (2005) "
+                            + "\"MAFFT version 5: improvement in accuracy of multiple sequence alignment.\""
+                            + " Nucleic Acids Research, 33 511-518",
+                    "http://www.compbio.dundee.ac.uk/JalviewWS/services/MafftWS",
+                    "MAFFT Multiple Sequence Alignment"),
             new ServiceHandle(
-                "MsaWS",
-                "Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple" +
-                " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice." +
-                " Nucleic Acids Research, 22 4673-4680",
-                "http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS",
-                "ClustalW Multiple Sequence Alignment"),
+                    "MsaWS",
+                    "Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple"
+                            + " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."
+                            + " Nucleic Acids Research, 22 4673-4680",
+                    "http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS",
+                    "ClustalW Multiple Sequence Alignment"),
             new ServiceHandle(
-                "SecStrPred",
-                "Cole C., Barber J. D., Barton G.J (2008) "
-                +"The Jpred 3 secondary structure prediction server " 
-                +"Nucleic Acids Research, 36 W197-W201",
-                "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred",
-                "JNet Secondary Structure Prediction"
-            )};
+                    "SecStrPred",
+                    "Cole C., Barber J. D., Barton G.J (2008) "
+                            + "The Jpred 3 secondary structure prediction server "
+                            + "Nucleic Acids Research, 36 W197-W201",
+                    "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred",
+                    "JNet Secondary Structure Prediction") };
         services = new Hashtable();
         serviceList = new Vector();
         buildServiceLists(defServices, serviceList, services);
       }
 
-    }
-    catch (Exception e)
+    } catch (Exception e)
     {
-      System.err.println(
-          "jalview.rootRegistry is not a proper url!\nWas set to " +
-          RootServiceURL + "\n" + e);
+      System.err
+              .println("jalview.rootRegistry is not a proper url!\nWas set to "
+                      + RootServiceURL + "\n" + e);
     }
 
   }
@@ -234,33 +256,32 @@ public class Discoverer
     {
       jalview.bin.Cache.log.debug("Discovering services using " + location);
       shs = locateWebService(location).getServices();
-    }
-    catch (org.apache.axis.AxisFault f)
+    } catch (org.apache.axis.AxisFault f)
     {
       // JBPNote - should do this a better way!
       if (f.getFaultReason().indexOf("(407)") > -1)
       {
         if (jalview.gui.Desktop.desktop != null)
         {
-          JOptionPane.showMessageDialog(jalview.gui.Desktop.desktop, "Please set up your proxy settings in the 'Connections' tab of the Preferences window",
-                                        "Proxy Authorization Failed",
-                                        JOptionPane.WARNING_MESSAGE);
+          JOptionPane
+                  .showMessageDialog(
+                          jalview.gui.Desktop.desktop,
+                          "Please set up your proxy settings in the 'Connections' tab of the Preferences window",
+                          "Proxy Authorization Failed",
+                          JOptionPane.WARNING_MESSAGE);
         }
       }
       else
       {
-        jalview.bin.Cache.log.warn("No Discovery service at " +
-                                   location);
+        jalview.bin.Cache.log.warn("No Discovery service at " + location);
         jalview.bin.Cache.log.debug("Axis Fault", f);
       }
-    }
-    catch (Exception e)
+    } catch (Exception e)
     {
-      jalview.bin.Cache.log.warn("No Discovery service at " +
-                                 location);
+      jalview.bin.Cache.log.warn("No Discovery service at " + location);
       jalview.bin.Cache.log.debug("Discovery Service General Exception", e);
     }
-    if ( (shs != null) && shs.getServices().length > 0)
+    if ((shs != null) && shs.getServices().length > 0)
     {
       return shs.getServices();
     }
@@ -270,23 +291,26 @@ public class Discoverer
   /**
    * Adds a list of services to the service catalog and categorised catalog
    * returns true if ServiceURLList was modified with a new DiscoveryService URL
-   * @param sh ServiceHandle[]
-   * @param cat Vector
-   * @param sscat Hashtable
+   * 
+   * @param sh
+   *                ServiceHandle[]
+   * @param cat
+   *                Vector
+   * @param sscat
+   *                Hashtable
    * @return boolean
    */
   static private boolean buildServiceLists(ServiceHandle[] sh, Vector cat,
-                                           Hashtable sscat)
+          Hashtable sscat)
   {
     boolean seenNewDiscovery = false;
     for (int i = 0, j = sh.length; i < j; i++)
     {
       if (!cat.contains(sh[i]))
       {
-        jalview.bin.Cache.log.debug("A " + sh[i].getAbstractName() +
-                                    " service called " +
-                                    sh[i].getName() + " exists at " +
-                                    sh[i].getEndpointURL() + "\n");
+        jalview.bin.Cache.log.debug("A " + sh[i].getAbstractName()
+                + " service called " + sh[i].getName() + " exists at "
+                + sh[i].getEndpointURL() + "\n");
         if (!sscat.containsKey(sh[i].getAbstractName()))
         {
           sscat.put(sh[i].getAbstractName(), cat = new Vector());
@@ -306,17 +330,17 @@ public class Discoverer
               disc_serv = new java.net.URL(sh[i].getEndpointURL());
               if (!ServiceURLList.contains(disc_serv))
               {
-                jalview.bin.Cache.log.debug(
-                    "Adding new discovery service at " + disc_serv);
+                jalview.bin.Cache.log
+                        .debug("Adding new discovery service at "
+                                + disc_serv);
                 ServiceURLList.add(disc_serv);
                 seenNewDiscovery = true;
               }
-            }
-            catch (Exception e)
+            } catch (Exception e)
             {
               jalview.bin.Cache.log.debug(
-                  "Ignoring bad discovery service URL " + sh[i].getEndpointURL(),
-                  e);
+                      "Ignoring bad discovery service URL "
+                              + sh[i].getEndpointURL(), e);
             }
           }
         }
@@ -333,32 +357,33 @@ public class Discoverer
     int s_url = 0;
     if (ServiceURLList == null)
     {
-      jalview.bin.Cache.log.debug(
-          "No service endpoints to use for service discovery.");
+      jalview.bin.Cache.log
+              .debug("No service endpoints to use for service discovery.");
       return;
     }
     while (s_url < ServiceURLList.size())
     {
-      if ( (sh = getServices( (java.net.URL) ServiceURLList.get(s_url))) != null)
+      if ((sh = getServices((java.net.URL) ServiceURLList.get(s_url))) != null)
       {
 
         buildServiceLists(sh, cat, sscat);
       }
       else
       {
-        jalview.bin.Cache.log.warn(
-            "No services at "
-            + ( (java.net.URL) ServiceURLList.get(s_url))
-            + " - check DISCOVERY_URLS property in .jalview_properties");
+        jalview.bin.Cache.log
+                .warn("No services at "
+                        + ((java.net.URL) ServiceURLList.get(s_url))
+                        + " - check DISCOVERY_URLS property in .jalview_properties");
       }
       s_url++;
     }
     // TODO: decide on correct semantics for services list - PropertyChange
     // provides a way of passing the new object around
     // so no need to access original discovery thread.
-    // Curent decision is to change properties then notify listeners with old and new values.
+    // Curent decision is to change properties then notify listeners with old
+    // and new values.
     Hashtable oldServices = services;
-    //Vector oldServicelist = serviceList;
+    // Vector oldServicelist = serviceList;
     services = sscat;
     serviceList = cat;
     firePropertyChange("services", oldServices, services);
@@ -380,41 +405,50 @@ public class Discoverer
     };
     discoverThread.start();
   }
+
   /**
    * binding service abstract name to handler class
    */
   private static Hashtable serviceClientBindings;
+
   public static WSClient getServiceClient(ServiceHandle sh)
   {
-    if (serviceClientBindings==null)
+    if (serviceClientBindings == null)
     {
       // get a list from Config or create below
       serviceClientBindings = new Hashtable();
-      serviceClientBindings.put("MsaWS",new MsaWSClient());
-      serviceClientBindings.put("SecStrPred",new JPredClient());
-      serviceClientBindings.put("SeqSearch",new SeqSearchWSClient());
+      serviceClientBindings.put("MsaWS", new MsaWSClient());
+      serviceClientBindings.put("SecStrPred", new JPredClient());
+      serviceClientBindings.put("SeqSearch", new SeqSearchWSClient());
     }
-    WSClient instance = (WSClient) serviceClientBindings.get(sh.getAbstractName());
-    if (instance==null)
+    WSClient instance = (WSClient) serviceClientBindings.get(sh
+            .getAbstractName());
+    if (instance == null)
     {
-      System.err.println("WARNING - POSSIBLE IMPLEMENTATION ERROR - cannot find WSClient implementation for "+sh.getAbstractName());
-    } else
+      System.err
+              .println("WARNING - POSSIBLE IMPLEMENTATION ERROR - cannot find WSClient implementation for "
+                      + sh.getAbstractName());
+    }
+    else
     {
       instance.serviceHandle = sh;
     }
     return instance;
   }
   /**
-   * notes on discovery service
-   * 1. need to allow multiple discovery source urls.
-   * 2. user interface to add/control list of urls in preferences
-   * notes on wsclient discovery
-   * 1. need a classpath property with list of additional plugin directories
-   * 2. optional config to cite specific bindings between class name and Abstract service name.
-   * 3. precedence for automatic discovery by using getAbstractName for WSClient - user added plugins override default plugins ?
-   * notes on wsclient gui
-   * code for gui attachment now moved to wsclient implementation. Needs more abstraction but approach seems to work.
-   * is it possible to 'generalise' the data retrieval calls further ? current methods are very specific (gatherForMSA or gatherForSeqOrMsaSecStrPred), new methods for conservation (group or alignment), treecalc (aligned profile), seqannot (sequences selected from dataset, annotation back to dataset).
-   *  
+   * notes on discovery service 1. need to allow multiple discovery source urls.
+   * 2. user interface to add/control list of urls in preferences notes on
+   * wsclient discovery 1. need a classpath property with list of additional
+   * plugin directories 2. optional config to cite specific bindings between
+   * class name and Abstract service name. 3. precedence for automatic discovery
+   * by using getAbstractName for WSClient - user added plugins override default
+   * plugins ? notes on wsclient gui code for gui attachment now moved to
+   * wsclient implementation. Needs more abstraction but approach seems to work.
+   * is it possible to 'generalise' the data retrieval calls further ? current
+   * methods are very specific (gatherForMSA or gatherForSeqOrMsaSecStrPred),
+   * new methods for conservation (group or alignment), treecalc (aligned
+   * profile), seqannot (sequences selected from dataset, annotation back to
+   * dataset).
+   * 
    */
 }
diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index e14816c..3add58d 100755
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -30,20 +30,25 @@ import jalview.bin.*;
 import jalview.datamodel.*;
 import jalview.gui.*;
 
-public class JPredClient
-    extends WSClient
+public class JPredClient extends WSClient
 {
   /**
    * crate a new GUI JPred Job
-   * @param sh ServiceHandle
-   * @param title String
-   * @param msa boolean - true - submit alignment as a sequence profile
-   * @param alview AlignmentView
-   * @param viewonly TODO
+   * 
+   * @param sh
+   *                ServiceHandle
+   * @param title
+   *                String
+   * @param msa
+   *                boolean - true - submit alignment as a sequence profile
+   * @param alview
+   *                AlignmentView
+   * @param viewonly
+   *                TODO
    */
-  public JPredClient(ext.vamsas.ServiceHandle sh, String title, boolean msa,
-                     AlignmentView alview, AlignFrame parentFrame,
-                     boolean viewonly)
+  public JPredClient(ext.vamsas.ServiceHandle sh, String title,
+          boolean msa, AlignmentView alview, AlignFrame parentFrame,
+          boolean viewonly)
   {
     super();
     wsInfo = setWebService(sh);
@@ -52,19 +57,27 @@ public class JPredClient
   }
 
   /**
-   * startJPredClient
-   * TODO: refine submission to cope with local prediction of visible regions or multiple single sequence jobs
-   * TODO: sequence representative support - could submit alignment of representatives as msa.
-   * TODO:  msa hidden region prediction - submit each chunk for prediction. concatenate results of each.
-   * TODO:  single seq prediction - submit each contig of each sequence for prediction (but must cope with flanking regions and short seqs)
-   * @param title String
-   * @param msa boolean
-   * @param alview AlignmentView
-   * @param viewonly if true then the prediction will be made just on the concatenated visible regions
+   * startJPredClient TODO: refine submission to cope with local prediction of
+   * visible regions or multiple single sequence jobs TODO: sequence
+   * representative support - could submit alignment of representatives as msa.
+   * TODO: msa hidden region prediction - submit each chunk for prediction.
+   * concatenate results of each. TODO: single seq prediction - submit each
+   * contig of each sequence for prediction (but must cope with flanking regions
+   * and short seqs)
+   * 
+   * @param title
+   *                String
+   * @param msa
+   *                boolean
+   * @param alview
+   *                AlignmentView
+   * @param viewonly
+   *                if true then the prediction will be made just on the
+   *                concatenated visible regions
    */
   private void startJPredClient(String title, boolean msa,
-                                jalview.datamodel.AlignmentView alview,
-                                AlignFrame parentFrame, boolean viewonly)
+          jalview.datamodel.AlignmentView alview, AlignFrame parentFrame,
+          boolean viewonly)
   {
     AlignmentView input = alview;
     if (wsInfo == null)
@@ -92,7 +105,8 @@ public class JPredClient
       int i = 0;
       if (viscontigs != null)
       {
-        // Construct the delMap - mapping from the positions within the input to Jnet to the contigs in the original sequence
+        // Construct the delMap - mapping from the positions within the input to
+        // Jnet to the contigs in the original sequence
 
         delMap = new int[seq.getEnd() - seq.getStart() + 1];
         int gapMap[] = seq.gapMap();
@@ -103,7 +117,8 @@ public class JPredClient
           {
             spos++;
           }
-          while (spos < gapMap.length && gapMap[spos] <= viscontigs[contig + 1])
+          while (spos < gapMap.length
+                  && gapMap[spos] <= viscontigs[contig + 1])
           {
             delMap[i++] = spos++;
           }
@@ -116,9 +131,9 @@ public class JPredClient
     if (msa && msf.length > 1)
     {
 
-      String altitle = getPredictionName(WebServiceName)+" on " + (viewonly ? "visible " : "") +
-          seq.getName() +
-          " using alignment from " + title;
+      String altitle = getPredictionName(WebServiceName) + " on "
+              + (viewonly ? "visible " : "") + seq.getName()
+              + " using alignment from " + title;
 
       SequenceI aln[] = new SequenceI[msf.length];
       for (int i = 0, j = msf.length; i < j; i++)
@@ -126,7 +141,8 @@ public class JPredClient
         aln[i] = msf[i].getSeq('-');
       }
 
-      Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, true);
+      Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln,
+              true);
       if (viewonly)
       {
         // Remove hidden regions from sequence objects.
@@ -137,16 +153,13 @@ public class JPredClient
         }
         seq.setSequence(seqs[0]);
       }
-      wsInfo.setProgressText("Job details for " + (viewonly ? "visible " : "") +
-                             "MSA based prediction (" +
-                             title + ") on sequence :\n>" + seq.getName() +
-                             "\n" +
-                             AlignSeq.extractGaps("-. ",
-                                                  seq.getSequenceAsString()) +
-                             "\n");
+      wsInfo.setProgressText("Job details for "
+              + (viewonly ? "visible " : "") + "MSA based prediction ("
+              + title + ") on sequence :\n>" + seq.getName() + "\n"
+              + AlignSeq.extractGaps("-. ", seq.getSequenceAsString())
+              + "\n");
       JPredThread jthread = new JPredThread(wsInfo, altitle, server,
-                                            SequenceInfo, aln, delMap, alview,
-                                            parentFrame, WsURL);
+              SequenceInfo, aln, delMap, alview, parentFrame, WsURL);
       wsInfo.setthisService(jthread);
       jthread.start();
     }
@@ -154,31 +167,29 @@ public class JPredClient
     {
       if (!msa && msf.length > 1)
       {
-        throw new Error("Implementation Error! Multiple single sequence prediction jobs are not yet supported.");
+        throw new Error(
+                "Implementation Error! Multiple single sequence prediction jobs are not yet supported.");
       }
-      
-      String altitle = getPredictionName(WebServiceName)+" for " + (viewonly ? "visible " : "") +
-          "sequence " + seq.getName() +
-          " from " +
-          title;
+
+      String altitle = getPredictionName(WebServiceName) + " for "
+              + (viewonly ? "visible " : "") + "sequence " + seq.getName()
+              + " from " + title;
       String seqname = seq.getName();
-      Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(
-          seq);
+      Hashtable SequenceInfo = jalview.analysis.SeqsetUtils
+              .SeqCharacterHash(seq);
       if (viewonly)
       {
         // Remove hidden regions from input sequence
         String seqs[] = alview.getSequenceStrings('-');
         seq.setSequence(seqs[0]);
       }
-      wsInfo.setProgressText("Job details for prediction on " +
-                             (viewonly ? "visible " : "") + "sequence :\n>" +
-                             seqname + "\n" +
-                             AlignSeq.extractGaps("-. ",
-                                                  seq.getSequenceAsString()) +
-                             "\n");
+      wsInfo.setProgressText("Job details for prediction on "
+              + (viewonly ? "visible " : "") + "sequence :\n>" + seqname
+              + "\n"
+              + AlignSeq.extractGaps("-. ", seq.getSequenceAsString())
+              + "\n");
       JPredThread jthread = new JPredThread(wsInfo, altitle, server, WsURL,
-                                            SequenceInfo, seq, delMap, alview,
-                                            parentFrame);
+              SequenceInfo, seq, delMap, alview, parentFrame);
       wsInfo.setthisService(jthread);
       jthread.start();
     }
@@ -186,24 +197,27 @@ public class JPredClient
 
   private String getPredictionName(String webServiceName)
   {
-    if (webServiceName.toLowerCase().indexOf("secondary structure prediction")>-1)
+    if (webServiceName.toLowerCase().indexOf(
+            "secondary structure prediction") > -1)
     {
       return webServiceName;
-    } else {
-      return webServiceName+"secondary structure prediction";
+    }
+    else
+    {
+      return webServiceName + "secondary structure prediction";
     }
   }
 
-  public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI seq,
-                     AlignFrame parentFrame)
+  public JPredClient(ext.vamsas.ServiceHandle sh, String title,
+          SequenceI seq, AlignFrame parentFrame)
   {
     super();
     wsInfo = setWebService(sh);
     startJPredClient(title, seq, parentFrame);
   }
 
-  public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI[] msa,
-                     AlignFrame parentFrame)
+  public JPredClient(ext.vamsas.ServiceHandle sh, String title,
+          SequenceI[] msa, AlignFrame parentFrame)
   {
     wsInfo = setWebService(sh);
     startJPredClient(title, msa, parentFrame);
@@ -227,7 +241,7 @@ public class JPredClient
   }
 
   private void startJPredClient(String title, SequenceI[] msf,
-                                AlignFrame parentFrame)
+          AlignFrame parentFrame)
   {
     if (wsInfo == null)
     {
@@ -236,20 +250,26 @@ public class JPredClient
 
     SequenceI seq = msf[0];
 
-    String altitle = "JNet prediction on " + seq.getName() +
-        " using alignment from " + title;
-
-    wsInfo.setProgressText("Job details for MSA based prediction (" +
-                           title + ") on sequence :\n>" + seq.getName() + "\n" +
-                           AlignSeq.extractGaps("-. ", seq.getSequenceAsString()) +
-                           "\n");
+    String altitle = "JNet prediction on " + seq.getName()
+            + " using alignment from " + title;
+
+    wsInfo
+            .setProgressText("Job details for MSA based prediction ("
+                    + title
+                    + ") on sequence :\n>"
+                    + seq.getName()
+                    + "\n"
+                    + AlignSeq
+                            .extractGaps("-. ", seq.getSequenceAsString())
+                    + "\n");
     SequenceI aln[] = new SequenceI[msf.length];
     for (int i = 0, j = msf.length; i < j; i++)
     {
       aln[i] = new jalview.datamodel.Sequence(msf[i]);
     }
 
-    Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, true);
+    Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln,
+            true);
 
     Jpred server = locateWebService();
     if (server == null)
@@ -257,27 +277,31 @@ public class JPredClient
       return;
     }
 
-    JPredThread jthread = new JPredThread(wsInfo, altitle, server, SequenceInfo,
-                                          aln, null, null, parentFrame, WsURL);
+    JPredThread jthread = new JPredThread(wsInfo, altitle, server,
+            SequenceInfo, aln, null, null, parentFrame, WsURL);
     wsInfo.setthisService(jthread);
     jthread.start();
   }
 
   public void startJPredClient(String title, SequenceI seq,
-                               AlignFrame parentFrame)
+          AlignFrame parentFrame)
   {
     if (wsInfo == null)
     {
       wsInfo = setWebService();
     }
-    wsInfo.setProgressText("Job details for prediction on sequence :\n>" +
-                           seq.getName() + "\n" +
-                           AlignSeq.extractGaps("-. ", seq.getSequenceAsString()) +
-                           "\n");
-    String altitle = "JNet prediction for sequence " + seq.getName() + " from " +
-        title;
-
-    Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);
+    wsInfo
+            .setProgressText("Job details for prediction on sequence :\n>"
+                    + seq.getName()
+                    + "\n"
+                    + AlignSeq
+                            .extractGaps("-. ", seq.getSequenceAsString())
+                    + "\n");
+    String altitle = "JNet prediction for sequence " + seq.getName()
+            + " from " + title;
+
+    Hashtable SequenceInfo = jalview.analysis.SeqsetUtils
+            .SeqCharacterHash(seq);
 
     Jpred server = locateWebService();
     if (server == null)
@@ -286,8 +310,7 @@ public class JPredClient
     }
 
     JPredThread jthread = new JPredThread(wsInfo, altitle, server, WsURL,
-                                          SequenceInfo, seq, null, null,
-                                          parentFrame);
+            SequenceInfo, seq, null, null, parentFrame);
     wsInfo.setthisService(jthread);
     jthread.start();
   }
@@ -296,14 +319,13 @@ public class JPredClient
   {
     WebServiceName = "JNetWS";
     WebServiceJobTitle = "JNet secondary structure prediction";
-    WebServiceReference =
-        "\"Cuff J. A and Barton G.J (2000) Application of " +
-        "multiple sequence alignment profiles to improve protein secondary structure prediction, " +
-        "Proteins 40:502-511\".";
+    WebServiceReference = "\"Cuff J. A and Barton G.J (2000) Application of "
+            + "multiple sequence alignment profiles to improve protein secondary structure prediction, "
+            + "Proteins 40:502-511\".";
     WsURL = "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred";
 
     WebserviceInfo wsInfo = new WebserviceInfo(WebServiceJobTitle,
-                                               WebServiceReference);
+            WebServiceReference);
 
     return wsInfo;
   }
@@ -314,23 +336,22 @@ public class JPredClient
     ext.vamsas.Jpred server = null;
     try
     {
-      server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set from properties
-      ( (JpredSoapBindingStub) server).setTimeout(60000); // one minute stub
-      //((JpredSoapBindingStub)this.server)._setProperty(org.apache.axis.encoding.C, Boolean.TRUE);
+      server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set
+                                                      // from properties
+      ((JpredSoapBindingStub) server).setTimeout(60000); // one minute stub
+      // ((JpredSoapBindingStub)this.server)._setProperty(org.apache.axis.encoding.C,
+      // Boolean.TRUE);
 
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       JOptionPane.showMessageDialog(Desktop.desktop,
-                                    "The Secondary Structure Prediction Service named " +
-                                    WebServiceName + " at " + WsURL +
-                                    " couldn't be located.",
-                                    "Internal Jalview Error",
-                                    JOptionPane.WARNING_MESSAGE);
-      wsInfo.setProgressText("Serious! " + WebServiceName +
-                             " Service location failed\nfor URL :" + WsURL +
-                             "\n" +
-                             ex.getMessage());
+              "The Secondary Structure Prediction Service named "
+                      + WebServiceName + " at " + WsURL
+                      + " couldn't be located.", "Internal Jalview Error",
+              JOptionPane.WARNING_MESSAGE);
+      wsInfo.setProgressText("Serious! " + WebServiceName
+              + " Service location failed\nfor URL :" + WsURL + "\n"
+              + ex.getMessage());
       wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
 
     }
@@ -338,7 +359,8 @@ public class JPredClient
     return server;
   }
 
-  public void attachWSMenuEntry(JMenu wsmenu, final ServiceHandle sh, final AlignFrame af)
+  public void attachWSMenuEntry(JMenu wsmenu, final ServiceHandle sh,
+          final AlignFrame af)
   {
     final JMenuItem method = new JMenuItem(sh.getName());
     method.setToolTipText(sh.getEndpointURL());
@@ -350,15 +372,16 @@ public class JPredClient
         if (msa.getSequences().length == 1)
         {
           // Single Sequence prediction
-          new jalview.ws.JPredClient(sh, af.getTitle(), false, msa, af, true);
+          new jalview.ws.JPredClient(sh, af.getTitle(), false, msa, af,
+                  true);
         }
         else
         {
           if (msa.getSequences().length > 1)
           {
             // Sequence profile based prediction
-            new jalview.ws.JPredClient(sh,
-                af.getTitle(), true, msa, af, true);
+            new jalview.ws.JPredClient(sh, af.getTitle(), true, msa, af,
+                    true);
           }
         }
       }
diff --git a/src/jalview/ws/JPredThread.java b/src/jalview/ws/JPredThread.java
index 106bb53..68360d6 100644
--- a/src/jalview/ws/JPredThread.java
+++ b/src/jalview/ws/JPredThread.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.ws;
 
 import java.util.*;
@@ -11,28 +29,37 @@ import jalview.io.*;
 import jalview.util.*;
 import vamsas.objects.simple.JpredResult;
 
-class JPredThread
-    extends WSThread implements WSClientI
+class JPredThread extends WSThread implements WSClientI
 {
-  // TODO: put mapping between JPredJob input and input data here - JNetAnnotation adding is done after result parsing.
-  class JPredJob
-      extends WSThread.WSJob
+  // TODO: put mapping between JPredJob input and input data here -
+  // JNetAnnotation adding is done after result parsing.
+  class JPredJob extends WSThread.WSJob
   {
-    // TODO: make JPredJob deal only with what was sent to and received from a JNet service
-    int[] predMap = null; // mapping from sequence(i) to the original sequence(predMap[i]) being predicted on
+    // TODO: make JPredJob deal only with what was sent to and received from a
+    // JNet service
+    int[] predMap = null; // mapping from sequence(i) to the original
+                          // sequence(predMap[i]) being predicted on
+
     vamsas.objects.simple.Sequence sequence;
+
     vamsas.objects.simple.Msfalignment msa;
+
     java.util.Hashtable SequenceInfo = null;
-    int msaIndex = 0; // the position of the original sequence in the array of Sequences in the input object that this job holds a prediction for
+
+    int msaIndex = 0; // the position of the original sequence in the array of
+                      // Sequences in the input object that this job holds a
+                      // prediction for
+
     /**
-     *
-     * @return true if getResultSet will return a valid alignment and prediction result.
+     * 
+     * @return true if getResultSet will return a valid alignment and prediction
+     *         result.
      */
     public boolean hasResults()
     {
       if (subjobComplete && result != null && result.isFinished()
-          && ( (JpredResult) result).getPredfile() != null &&
-          ( (JpredResult) result).getAligfile() != null)
+              && ((JpredResult) result).getPredfile() != null
+              && ((JpredResult) result).getAligfile() != null)
       {
         return true;
       }
@@ -49,12 +76,13 @@ class JPredThread
     }
 
     /**
-     *
-     * @return null or Object[] { annotated alignment for this prediction, ColumnSelection for this prediction} or null if no results available.
+     * 
+     * @return null or Object[] { annotated alignment for this prediction,
+     *         ColumnSelection for this prediction} or null if no results
+     *         available.
      * @throws Exception
      */
-    public Object[] getResultSet()
-        throws Exception
+    public Object[] getResultSet() throws Exception
     {
       if (result == null || !result.isFinished())
       {
@@ -64,31 +92,31 @@ class JPredThread
       ColumnSelection alcsel = null;
       int FirstSeq = -1; // the position of the query sequence in Alignment al
 
-      JpredResult result = (JpredResult)this.result;
+      JpredResult result = (JpredResult) this.result;
 
       jalview.bin.Cache.log.debug("Parsing output from JNet job.");
-      // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", "File");
-      jalview.io.JPredFile prediction = new jalview.io.JPredFile(result.
-          getPredfile(),
-          "Paste");
+      // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt",
+      // "File");
+      jalview.io.JPredFile prediction = new jalview.io.JPredFile(result
+              .getPredfile(), "Paste");
       SequenceI[] preds = prediction.getSeqsAsArray();
       jalview.bin.Cache.log.debug("Got prediction profile.");
 
-      if ( (this.msa != null) && (result.getAligfile() != null))
+      if ((this.msa != null) && (result.getAligfile() != null))
       {
         jalview.bin.Cache.log.debug("Getting associated alignment.");
-        // we ignore the returned alignment if we only predicted on a single sequence
-        String format = new jalview.io.IdentifyFile().Identify(result.
-            getAligfile(),
-            "Paste");
+        // we ignore the returned alignment if we only predicted on a single
+        // sequence
+        String format = new jalview.io.IdentifyFile().Identify(result
+                .getAligfile(), "Paste");
 
         if (jalview.io.FormatAdapter.isValidFormat(format))
         {
           SequenceI sqs[];
           if (predMap != null)
           {
-            Object[] alandcolsel = input.getAlignmentAndColumnSelection(
-                getGapChar());
+            Object[] alandcolsel = input
+                    .getAlignmentAndColumnSelection(getGapChar());
             sqs = (SequenceI[]) alandcolsel[0];
             al = new Alignment(sqs);
             alcsel = (ColumnSelection) alandcolsel[1];
@@ -96,33 +124,31 @@ class JPredThread
           else
           {
             al = new FormatAdapter().readFile(result.getAligfile(),
-                                              "Paste", format);
+                    "Paste", format);
             sqs = new SequenceI[al.getHeight()];
 
             for (int i = 0, j = al.getHeight(); i < j; i++)
             {
               sqs[i] = al.getSequenceAt(i);
             }
-            if (!jalview.analysis.SeqsetUtils.deuniquify( (Hashtable)
-                SequenceInfo, sqs))
+            if (!jalview.analysis.SeqsetUtils.deuniquify(
+                    (Hashtable) SequenceInfo, sqs))
             {
               throw (new Exception(
-                  "Couldn't recover sequence properties for alignment."));
+                      "Couldn't recover sequence properties for alignment."));
             }
           }
           FirstSeq = 0;
           al.setDataset(null);
 
           jalview.io.JnetAnnotationMaker.add_annotation(prediction, al,
-              FirstSeq,
-              false, predMap);
+                  FirstSeq, false, predMap);
 
         }
         else
         {
-          throw (new Exception(
-              "Unknown format " + format + " for file : \n" +
-              result.getAligfile()));
+          throw (new Exception("Unknown format " + format
+                  + " for file : \n" + result.getAligfile()));
         }
       }
       else
@@ -132,38 +158,36 @@ class JPredThread
         if (predMap != null)
         {
           char gc = getGapChar();
-          SequenceI[] sqs = (SequenceI[]) ( (java.lang.Object[]) input.
-                                           getAlignmentAndColumnSelection(gc))[
-              0];
+          SequenceI[] sqs = (SequenceI[]) ((java.lang.Object[]) input
+                  .getAlignmentAndColumnSelection(gc))[0];
           if (this.msaIndex >= sqs.length)
           {
-            throw new Error("Implementation Error! Invalid msaIndex for JPredJob on parent MSA input object!");
+            throw new Error(
+                    "Implementation Error! Invalid msaIndex for JPredJob on parent MSA input object!");
           }
 
-          /////
-          //Uses RemoveGapsCommand
-          /////
+          // ///
+          // Uses RemoveGapsCommand
+          // ///
           new jalview.commands.RemoveGapsCommand("Remove Gaps",
-                                                 new SequenceI[]
-                                                 {sqs[msaIndex]},
-                                                 currentView);
+                  new SequenceI[]
+                  { sqs[msaIndex] }, currentView);
 
           SequenceI profileseq = al.getSequenceAt(FirstSeq);
           profileseq.setSequence(sqs[msaIndex].getSequenceAsString());
         }
 
-        if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
-            al.getSequenceAt(FirstSeq), SequenceInfo))
+        if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(al
+                .getSequenceAt(FirstSeq), SequenceInfo))
         {
           throw (new Exception(
-              "Couldn't recover sequence properties for JNet Query sequence!"));
+                  "Couldn't recover sequence properties for JNet Query sequence!"));
         }
         else
         {
           al.setDataset(null);
           jalview.io.JnetAnnotationMaker.add_annotation(prediction, al,
-              FirstSeq,
-              true, predMap);
+                  FirstSeq, true, predMap);
           SequenceI profileseq = al.getSequenceAt(0); // this includes any gaps.
           alignToProfileSeq(al, profileseq);
           if (predMap != null)
@@ -175,12 +199,14 @@ class JPredThread
         }
       }
       return new Object[]
-          {
-          al, alcsel}; // , FirstSeq, noMsa};
+      { al, alcsel }; // , FirstSeq, noMsa};
     }
 
     /**
-     * Given an alignment where all other sequences except profileseq are aligned to the ungapped profileseq, insert gaps in the other sequences to realign them with the residues in profileseq
+     * Given an alignment where all other sequences except profileseq are
+     * aligned to the ungapped profileseq, insert gaps in the other sequences to
+     * realign them with the residues in profileseq
+     * 
      * @param al
      * @param profileseq
      */
@@ -206,19 +232,19 @@ class JPredThread
             {
               // pad gaps
               sq = sq + sb;
-              while ( (diff = gapMap[r] - sq.length()) > 0)
+              while ((diff = gapMap[r] - sq.length()) > 0)
               {
-                sq = sq +
-                    ( (diff >= sb.length()) ? sb.toString() :
-                     sb.substring(0, diff));
+                sq = sq
+                        + ((diff >= sb.length()) ? sb.toString() : sb
+                                .substring(0, diff));
               }
               al.getSequenceAt(s).setSequence(sq);
             }
             else
             {
-              al.getSequenceAt(s).setSequence(sq.substring(0, gapMap[r]) +
-                                              sb.toString() +
-                                              sq.substring(gapMap[r]));
+              al.getSequenceAt(s).setSequence(
+                      sq.substring(0, gapMap[r]) + sb.toString()
+                              + sq.substring(gapMap[r]));
             }
           }
         }
@@ -227,25 +253,29 @@ class JPredThread
     }
 
     /**
-     * Add gaps into the sequences aligned to profileseq under the given AlignmentView
+     * Add gaps into the sequences aligned to profileseq under the given
+     * AlignmentView
+     * 
      * @param profileseq
      * @param al
      * @param input
      */
     private ColumnSelection propagateInsertions(SequenceI profileseq,
-                                                Alignment al,
-                                                AlignmentView input)
+            Alignment al, AlignmentView input)
     {
       char gc = al.getGapCharacter();
       Object[] alandcolsel = input.getAlignmentAndColumnSelection(gc);
       ColumnSelection nview = (ColumnSelection) alandcolsel[1];
       SequenceI origseq;
-      nview.pruneDeletions(ShiftList.parseMap( (origseq = ( (SequenceI[])
-          alandcolsel[0])[0]).gapMap())); // recover original prediction sequence's mapping to view.
+      nview.pruneDeletions(ShiftList
+              .parseMap((origseq = ((SequenceI[]) alandcolsel[0])[0])
+                      .gapMap())); // recover original prediction sequence's
+                                    // mapping to view.
       int[] viscontigs = nview.getVisibleContigs(0, profileseq.getLength());
       int spos = 0;
       int offset = 0;
-      //  input.pruneDeletions(ShiftList.parseMap(((SequenceI[]) alandcolsel[0])[0].gapMap()))
+      // input.pruneDeletions(ShiftList.parseMap(((SequenceI[])
+      // alandcolsel[0])[0].gapMap()))
       // add profile to visible contigs
       for (int v = 0; v < viscontigs.length; v += 2)
       {
@@ -270,28 +300,28 @@ class JPredThread
                 {
                   // pad gaps
                   sq = sq + sb;
-                  while ( (diff = spos + offset - sq.length() - 1) > 0)
+                  while ((diff = spos + offset - sq.length() - 1) > 0)
                   {
-                    sq = sq +
-                        ( (diff >= sb.length()) ? sb.toString() :
-                         sb.substring(0, diff));
+                    sq = sq
+                            + ((diff >= sb.length()) ? sb.toString() : sb
+                                    .substring(0, diff));
                   }
                 }
                 sq += sb.toString();
               }
               else
               {
-                al.getSequenceAt(s).setSequence(sq.substring(0, spos + offset) +
-                                                sb.toString() +
-                                                sq.substring(spos + offset));
+                al.getSequenceAt(s).setSequence(
+                        sq.substring(0, spos + offset) + sb.toString()
+                                + sq.substring(spos + offset));
               }
             }
           }
-          //offset+=sb.length();
+          // offset+=sb.length();
         }
         spos = viscontigs[v + 1] + 1;
       }
-      if ( (offset + spos) < profileseq.getLength())
+      if ((offset + spos) < profileseq.getLength())
       {
         StringBuffer sb = new StringBuffer();
         for (int s = 0, ns = profileseq.getLength() - spos - offset; s < ns; s++)
@@ -305,8 +335,9 @@ class JPredThread
           int diff = origseq.getLength() - sq.length();
           while (diff > 0)
           {
-            sq = sq +
-                ( (diff >= sb.length()) ? sb.toString() : sb.substring(0, diff));
+            sq = sq
+                    + ((diff >= sb.length()) ? sb.toString() : sb
+                            .substring(0, diff));
             diff = origseq.getLength() - sq.length();
           }
         }
@@ -318,8 +349,8 @@ class JPredThread
     {
       super();
       this.predMap = delMap;
-      String sq = AlignSeq.extractGaps(Comparison.GapChars,
-                                       seq.getSequenceAsString());
+      String sq = AlignSeq.extractGaps(Comparison.GapChars, seq
+              .getSequenceAsString());
       if (sq.length() >= 20)
       {
         this.SequenceInfo = SequenceInfo;
@@ -345,18 +376,22 @@ class JPredThread
   }
 
   ext.vamsas.Jpred server;
+
   String altitle = "";
-  JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server,
-              String wsurl, AlignmentView alview, AlignFrame alframe)
+
+  JPredThread(WebserviceInfo wsinfo, String altitle,
+          ext.vamsas.Jpred server, String wsurl, AlignmentView alview,
+          AlignFrame alframe)
   {
     super(alframe, wsinfo, alview, wsurl);
     this.altitle = altitle;
     this.server = server;
   }
 
-  JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server,
-              String wsurl, Hashtable SequenceInfo, SequenceI seq, int[] delMap,
-              AlignmentView alview, AlignFrame alframe)
+  JPredThread(WebserviceInfo wsinfo, String altitle,
+          ext.vamsas.Jpred server, String wsurl, Hashtable SequenceInfo,
+          SequenceI seq, int[] delMap, AlignmentView alview,
+          AlignFrame alframe)
   {
     this(wsinfo, altitle, server, wsurl, alview, alframe);
     JPredJob job = new JPredJob(SequenceInfo, seq, delMap);
@@ -364,23 +399,22 @@ class JPredThread
     {
       OutputHeader = wsInfo.getProgressText();
       jobs = new WSJob[]
-          {
-          job};
+      { job };
       job.jobnum = 0;
     }
   }
 
-  JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server,
-              Hashtable SequenceInfo, SequenceI[] msf, int[] delMap,
-              AlignmentView alview, AlignFrame alframe, String wsurl)
+  JPredThread(WebserviceInfo wsinfo, String altitle,
+          ext.vamsas.Jpred server, Hashtable SequenceInfo, SequenceI[] msf,
+          int[] delMap, AlignmentView alview, AlignFrame alframe,
+          String wsurl)
   {
     this(wsinfo, altitle, server, wsurl, alview, alframe);
     JPredJob job = new JPredJob(SequenceInfo, msf, delMap);
     if (job.hasValidInput())
     {
       jobs = new WSJob[]
-          {
-          job};
+      { job };
       OutputHeader = wsInfo.getProgressText();
       job.jobnum = 0;
     }
@@ -388,10 +422,11 @@ class JPredThread
 
   void StartJob(WSJob j)
   {
-    if (! (j instanceof JPredJob))
+    if (!(j instanceof JPredJob))
     {
-      throw new Error("Implementation error - StartJob(JpredJob) called on " +
-                      j.getClass());
+      throw new Error(
+              "Implementation error - StartJob(JpredJob) called on "
+                      + j.getClass());
     }
     try
     {
@@ -400,20 +435,20 @@ class JPredThread
       {
         job.jobId = server.predictOnMsa(job.msa);
       }
-      else
-      if (job.sequence != null)
+      else if (job.sequence != null)
       {
-        job.jobId = server.predict(job.sequence); // debug like : job.jobId = "/jobs/www-jpred/jp_Yatat29";//
+        job.jobId = server.predict(job.sequence); // debug like : job.jobId =
+                                                  // "/jobs/www-jpred/jp_Yatat29";//
       }
 
       if (job.jobId != null)
       {
         if (job.jobId.startsWith("Broken"))
         {
-          job.result = (vamsas.objects.simple.Result)new JpredResult();
+          job.result = (vamsas.objects.simple.Result) new JpredResult();
           job.result.setInvalid(true);
           job.result.setStatus("Submission " + job.jobId);
-          throw new Exception(job.jobId); 
+          throw new Exception(job.jobId);
         }
         else
         {
@@ -426,21 +461,23 @@ class JPredThread
       {
         throw new Exception("Server timed out - try again later\n");
       }
-    }
-    catch (Exception e)
+    } catch (Exception e)
     {
       // kill the whole job.
       wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
       if (e.getMessage().indexOf("Exception") > -1)
       {
-        wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_SERVERERROR);
-        wsInfo.setProgressText(j.jobnum,
-                               "Failed to submit the prediction. (Just close the window)\n"
-                               +
-                               "It is most likely that there is a problem with the server.\n");
-        System.err.println(
-            "JPredWS Client: Failed to submit the prediction. Quite possibly because of a server error - see below)\n" +
-            e.getMessage() + "\n");
+        wsInfo
+                .setStatus(j.jobnum,
+                        WebserviceInfo.STATE_STOPPED_SERVERERROR);
+        wsInfo
+                .setProgressText(
+                        j.jobnum,
+                        "Failed to submit the prediction. (Just close the window)\n"
+                                + "It is most likely that there is a problem with the server.\n");
+        System.err
+                .println("JPredWS Client: Failed to submit the prediction. Quite possibly because of a server error - see below)\n"
+                        + e.getMessage() + "\n");
 
         jalview.bin.Cache.log.warn("Server Exception", e);
       }
@@ -449,11 +486,11 @@ class JPredThread
         wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
         // JBPNote - this could be a popup informing the user of the problem.
         wsInfo.appendProgressText(j.jobnum,
-                                  "Failed to submit the prediction:\n"
-                                  + e.getMessage() +
-                                  wsInfo.getProgressText());
+                "Failed to submit the prediction:\n" + e.getMessage()
+                        + wsInfo.getProgressText());
 
-        jalview.bin.Cache.log.debug("Failed Submission of job " + j.jobnum, e);
+        jalview.bin.Cache.log.debug("Failed Submission of job " + j.jobnum,
+                e);
 
       }
       j.allowedServerExceptions = -1;
@@ -470,39 +507,37 @@ class JPredThread
       for (int j = 0; j < jobs.length; j++)
       {
         finalState.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
-        if (jobs[j].submitted && jobs[j].subjobComplete && jobs[j].hasResults())
+        if (jobs[j].submitted && jobs[j].subjobComplete
+                && jobs[j].hasResults())
         {
           results++;
         }
       }
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
 
-      Cache.log.error("Unexpected exception when processing results for " +
-                      altitle, ex);
+      Cache.log.error("Unexpected exception when processing results for "
+              + altitle, ex);
       wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
     }
     if (results > 0)
     {
       wsInfo.showResultsNewFrame
-          .addActionListener(new java.awt.event.ActionListener()
-      {
-        public void actionPerformed(
-            java.awt.event.ActionEvent evt)
-        {
-          displayResults(true);
-        }
-      });
+              .addActionListener(new java.awt.event.ActionListener()
+              {
+                public void actionPerformed(java.awt.event.ActionEvent evt)
+                {
+                  displayResults(true);
+                }
+              });
       wsInfo.mergeResults
-          .addActionListener(new java.awt.event.ActionListener()
-      {
-        public void actionPerformed(
-            java.awt.event.ActionEvent evt)
-        {
-          displayResults(false);
-        }
-      });
+              .addActionListener(new java.awt.event.ActionListener()
+              {
+                public void actionPerformed(java.awt.event.ActionEvent evt)
+                {
+                  displayResults(false);
+                }
+              });
       wsInfo.setResultsReady();
     }
     else
@@ -525,7 +560,8 @@ class JPredThread
 
         if (j.hasResults())
         {
-          // hack - we only deal with all single seuqence predictions or all profile predictions
+          // hack - we only deal with all single seuqence predictions or all
+          // profile predictions
           msa = (j.msa != null) ? true : msa;
           try
           {
@@ -540,20 +576,16 @@ class JPredThread
             {
               // do merge with other job results
               throw new Error(
-                  "Multiple JNet subjob merging not yet implemented.");
+                      "Multiple JNet subjob merging not yet implemented.");
             }
-          }
-          catch (Exception e)
+          } catch (Exception e)
           {
             jalview.bin.Cache.log.error(
-                "JNet Client: JPred Annotation Parse Error",
-                e);
+                    "JNet Client: JPred Annotation Parse Error", e);
             wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
-            wsInfo.appendProgressText(j.jobnum,
-                                      OutputHeader + "\n" +
-                                      j.result.getStatus() +
-                                      "\nInvalid JNet job result data!\n" +
-                                      e.getMessage());
+            wsInfo.appendProgressText(j.jobnum, OutputHeader + "\n"
+                    + j.result.getStatus()
+                    + "\nInvalid JNet job result data!\n" + e.getMessage());
             j.result.setBroken(true);
           }
         }
@@ -568,37 +600,37 @@ class JPredThread
           {
             if (res[1] != null)
             {
-              af = new AlignFrame( (Alignment) res[0], (ColumnSelection) res[1],
-                                  AlignFrame.DEFAULT_WIDTH,
-                                  AlignFrame.DEFAULT_HEIGHT);
+              af = new AlignFrame((Alignment) res[0],
+                      (ColumnSelection) res[1], AlignFrame.DEFAULT_WIDTH,
+                      AlignFrame.DEFAULT_HEIGHT);
             }
             else
             {
-              af = new AlignFrame( (Alignment) res[0], AlignFrame.DEFAULT_WIDTH,
-                                  AlignFrame.DEFAULT_HEIGHT);
+              af = new AlignFrame((Alignment) res[0],
+                      AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
             }
           }
           else
           {
-            /*java.lang.Object[] alandcolsel = input.getAlignmentAndColumnSelection(alignFrame.getViewport().getGapCharacter());
-             if (((SequenceI[])alandcolsel[0])[0].getLength()!=res.getWidth()) {
-              if (msa) {
-                throw new Error("Implementation Error! ColumnSelection from input alignment will not map to result alignment!");
-              }
-                         }
-                         if (!msa) {
-              // update hidden regions to account for loss of gaps in profile. - if any
-              // gapMap returns insert list, interpreted as delete list by pruneDeletions
-              //((ColumnSelection) alandcolsel[1]).pruneDeletions(ShiftList.parseMap(((SequenceI[]) alandcolsel[0])[0].gapMap()));
-                         }*/
-
-            af = new AlignFrame( (Alignment) res[0], (ColumnSelection) res[1],
-                                AlignFrame.DEFAULT_WIDTH,
-                                AlignFrame.DEFAULT_HEIGHT);
+            /*
+             * java.lang.Object[] alandcolsel =
+             * input.getAlignmentAndColumnSelection(alignFrame.getViewport().getGapCharacter());
+             * if (((SequenceI[])alandcolsel[0])[0].getLength()!=res.getWidth()) {
+             * if (msa) { throw new Error("Implementation Error! ColumnSelection
+             * from input alignment will not map to result alignment!"); } } if
+             * (!msa) { // update hidden regions to account for loss of gaps in
+             * profile. - if any // gapMap returns insert list, interpreted as
+             * delete list by pruneDeletions //((ColumnSelection)
+             * alandcolsel[1]).pruneDeletions(ShiftList.parseMap(((SequenceI[])
+             * alandcolsel[0])[0].gapMap())); }
+             */
+
+            af = new AlignFrame((Alignment) res[0],
+                    (ColumnSelection) res[1], AlignFrame.DEFAULT_WIDTH,
+                    AlignFrame.DEFAULT_HEIGHT);
           }
-          Desktop.addInternalFrame(af, altitle,
-                                   AlignFrame.DEFAULT_WIDTH,
-                                   AlignFrame.DEFAULT_HEIGHT);
+          Desktop.addInternalFrame(af, altitle, AlignFrame.DEFAULT_WIDTH,
+                  AlignFrame.DEFAULT_HEIGHT);
         }
         else
         {
@@ -608,8 +640,7 @@ class JPredThread
     }
   }
 
-  void pollJob(WSJob job)
-      throws Exception
+  void pollJob(WSJob job) throws Exception
   {
     job.result = server.getresult(job.jobId);
   }
diff --git a/src/jalview/ws/MsaWSClient.java b/src/jalview/ws/MsaWSClient.java
index 63e60d7..089b243 100755
--- a/src/jalview/ws/MsaWSClient.java
+++ b/src/jalview/ws/MsaWSClient.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -29,56 +29,61 @@ import jalview.gui.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class MsaWSClient
-    extends WSClient
+public class MsaWSClient extends WSClient
 {
   /**
    * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
    */
   ext.vamsas.MuscleWS server;
+
   AlignFrame alignFrame;
 
   /**
-   * Creates a new MsaWSClient object that uses a service
-   * given by an externally retrieved ServiceHandle
-   *
-   * @param sh service handle of type AbstractName(MsaWS)
-   * @param altitle DOCUMENT ME!
-   * @param msa DOCUMENT ME!
-   * @param submitGaps DOCUMENT ME!
-   * @param preserveOrder DOCUMENT ME!
+   * Creates a new MsaWSClient object that uses a service given by an externally
+   * retrieved ServiceHandle
+   * 
+   * @param sh
+   *                service handle of type AbstractName(MsaWS)
+   * @param altitle
+   *                DOCUMENT ME!
+   * @param msa
+   *                DOCUMENT ME!
+   * @param submitGaps
+   *                DOCUMENT ME!
+   * @param preserveOrder
+   *                DOCUMENT ME!
    */
 
   public MsaWSClient(ext.vamsas.ServiceHandle sh, String altitle,
-                     jalview.datamodel.AlignmentView msa,
-                     boolean submitGaps, boolean preserveOrder,
-                     Alignment seqdataset,
-                     AlignFrame _alignFrame)
+          jalview.datamodel.AlignmentView msa, boolean submitGaps,
+          boolean preserveOrder, Alignment seqdataset,
+          AlignFrame _alignFrame)
   {
     super();
     alignFrame = _alignFrame;
     if (!sh.getAbstractName().equals("MsaWS"))
     {
-      JOptionPane.showMessageDialog(Desktop.desktop,
-                                    "The Service called \n" + sh.getName() +
-                                    "\nis not a \nMultiple Sequence Alignment Service !",
-                                    "Internal Jalview Error",
-                                    JOptionPane.WARNING_MESSAGE);
+      JOptionPane
+              .showMessageDialog(
+                      Desktop.desktop,
+                      "The Service called \n"
+                              + sh.getName()
+                              + "\nis not a \nMultiple Sequence Alignment Service !",
+                      "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);
 
       return;
     }
 
-    if ( (wsInfo = setWebService(sh)) == null)
+    if ((wsInfo = setWebService(sh)) == null)
     {
       JOptionPane.showMessageDialog(Desktop.desktop,
-                                    "The Multiple Sequence Alignment Service named " +
-                                    sh.getName() +
-                                    " is unknown", "Internal Jalview Error",
-                                    JOptionPane.WARNING_MESSAGE);
+              "The Multiple Sequence Alignment Service named "
+                      + sh.getName() + " is unknown",
+              "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);
 
       return;
     }
@@ -93,26 +98,25 @@ public class MsaWSClient
   }
 
   private void startMsaWSClient(String altitle, AlignmentView msa,
-                                boolean submitGaps, boolean preserveOrder,
-                                Alignment seqdataset)
+          boolean submitGaps, boolean preserveOrder, Alignment seqdataset)
   {
     if (!locateWebService())
     {
       return;
     }
 
-    wsInfo.setProgressText( ( (submitGaps) ? "Re-alignment" : "Alignment") +
-                           " of " + altitle + "\nJob details\n");
+    wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment")
+            + " of " + altitle + "\nJob details\n");
     String jobtitle = WebServiceName.toLowerCase();
     if (jobtitle.endsWith("alignment"))
     {
       if (submitGaps
-          && (!jobtitle.endsWith("realignment")
-              || jobtitle.indexOf("profile") == -1))
+              && (!jobtitle.endsWith("realignment") || jobtitle
+                      .indexOf("profile") == -1))
       {
         int pos = jobtitle.indexOf("alignment");
-        jobtitle = WebServiceName.substring(0, pos) + "re-alignment of " +
-            altitle;
+        jobtitle = WebServiceName.substring(0, pos) + "re-alignment of "
+                + altitle;
       }
       else
       {
@@ -121,23 +125,20 @@ public class MsaWSClient
     }
     else
     {
-      jobtitle = WebServiceName + (submitGaps ? " re" : " ") + "alignment of " +
-          altitle;
+      jobtitle = WebServiceName + (submitGaps ? " re" : " ")
+              + "alignment of " + altitle;
     }
 
-    MsaWSThread msathread = new MsaWSThread(server, WsURL, wsInfo, alignFrame,
-                                            WebServiceName,
-                                            jobtitle,
-                                            msa,
-                                            submitGaps, preserveOrder,
-                                            seqdataset);
+    MsaWSThread msathread = new MsaWSThread(server, WsURL, wsInfo,
+            alignFrame, WebServiceName, jobtitle, msa, submitGaps,
+            preserveOrder, seqdataset);
     wsInfo.setthisService(msathread);
     msathread.start();
   }
 
   /**
    * Initializes the server field with a valid service implementation.
-   *
+   * 
    * @return true if service was located.
    */
   private boolean locateWebService()
@@ -148,14 +149,13 @@ public class MsaWSClient
     try
     {
       this.server = (MuscleWS) loc.getMuscleWS(new java.net.URL(WsURL));
-      ( (MuscleWSSoapBindingStub)this.server).setTimeout(60000); // One minute timeout
-    }
-    catch (Exception ex)
+      ((MuscleWSSoapBindingStub) this.server).setTimeout(60000); // One minute
+                                                                  // timeout
+    } catch (Exception ex)
     {
-      wsInfo.setProgressText("Serious! " + WebServiceName +
-                             " Service location failed\nfor URL :" + WsURL +
-                             "\n" +
-                             ex.getMessage());
+      wsInfo.setProgressText("Serious! " + WebServiceName
+              + " Service location failed\nfor URL :" + WsURL + "\n"
+              + ex.getMessage());
       wsInfo.setStatus(WebserviceInfo.ERROR);
       ex.printStackTrace();
 
@@ -176,16 +176,22 @@ public class MsaWSClient
   {
     return "Multiple Sequence Alignment";
   }
+
   /**
-   * look at ourselves and work out if we are a service that can take a profile and align to it 
+   * look at ourselves and work out if we are a service that can take a profile
+   * and align to it
+   * 
    * @return true if we can send gapped sequences to the alignment service
    */
   private boolean canSubmitGaps()
   {
-    // TODO: query service or extract service handle props to check if we can realign
+    // TODO: query service or extract service handle props to check if we can
+    // realign
     return (WebServiceName.indexOf("lustal") > -1); // cheat!
   }
-  public void attachWSMenuEntry(JMenu msawsmenu, final ServiceHandle serviceHandle, final AlignFrame alignFrame)
+
+  public void attachWSMenuEntry(JMenu msawsmenu,
+          final ServiceHandle serviceHandle, final AlignFrame alignFrame)
   {
     setWebService(serviceHandle, true); // headless
     JMenuItem method = new JMenuItem(WebServiceName);
@@ -195,29 +201,28 @@ public class MsaWSClient
       public void actionPerformed(ActionEvent e)
       {
         AlignmentView msa = alignFrame.gatherSequencesForAlignment();
-        new jalview.ws.MsaWSClient(serviceHandle, alignFrame.getTitle(), msa,
-                                   false, true,
-                                   alignFrame.getViewport().getAlignment().getDataset(),
-                                   alignFrame);
+        new jalview.ws.MsaWSClient(serviceHandle, alignFrame.getTitle(),
+                msa, false, true, alignFrame.getViewport().getAlignment()
+                        .getDataset(), alignFrame);
 
       }
 
     });
-    msawsmenu.add(method);    
+    msawsmenu.add(method);
     if (canSubmitGaps())
     {
       // We know that ClustalWS can accept partial alignments for refinement.
-      final JMenuItem methodR = new JMenuItem(serviceHandle.getName()+" Realign");
+      final JMenuItem methodR = new JMenuItem(serviceHandle.getName()
+              + " Realign");
       methodR.setToolTipText(WsURL);
-        methodR.addActionListener(new ActionListener()
+      methodR.addActionListener(new ActionListener()
       {
         public void actionPerformed(ActionEvent e)
         {
           AlignmentView msa = alignFrame.gatherSequencesForAlignment();
-          new jalview.ws.MsaWSClient(serviceHandle, alignFrame.getTitle(), msa,
-                                     true, true,
-                                     alignFrame.getViewport().getAlignment().getDataset(),
-                                     alignFrame);
+          new jalview.ws.MsaWSClient(serviceHandle, alignFrame.getTitle(),
+                  msa, true, true, alignFrame.getViewport().getAlignment()
+                          .getDataset(), alignFrame);
 
         }
 
diff --git a/src/jalview/ws/MsaWSThread.java b/src/jalview/ws/MsaWSThread.java
index 8d373ac..3f05213 100644
--- a/src/jalview/ws/MsaWSThread.java
+++ b/src/jalview/ws/MsaWSThread.java
@@ -1,721 +1,714 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.ws;
-
-import java.util.*;
-
-import jalview.analysis.*;
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.datamodel.Alignment;
-import jalview.gui.*;
-import vamsas.objects.simple.MsaResult;
-
-/**
- * <p>
- * Title:
- * </p>
- *
- * <p>
- * Description:
- * </p>
- *
- * <p>
- * Copyright: Copyright (c) 2004
- * </p>
- *
- * <p>
- * Company: Dundee University
- * </p>
- *
- * @author not attributable
- * @version 1.0
- */
-class MsaWSThread
-    extends WSThread implements WSClientI
-{
-  boolean submitGaps = false; // pass sequences including gaps to alignment
-
-  // service
-
-  boolean preserveOrder = true; // and always store and recover sequence
-
-  // order
-
-  class MsaWSJob
-      extends WSThread.WSJob
-  {
-    // hold special input for this
-    vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.
-        SequenceSet();
-
-    /**
-     * MsaWSJob
-     *
-     * @param jobNum
-     *            int
-     * @param jobId
-     *            String
-     */
-    public MsaWSJob(int jobNum, SequenceI[] inSeqs)
-    {
-      this.jobnum = jobNum;
-      if (!prepareInput(inSeqs, 2))
-      {
-        submitted = true;
-        subjobComplete = true;
-        result = new MsaResult();
-        result.setFinished(true);
-        result.setStatus("Job never ran - input returned to user.");
-      }
-
-    }
-
-    Hashtable SeqNames = new Hashtable();
-    Vector emptySeqs = new Vector();
-    /**
-     * prepare input sequences for MsaWS service
-     * @param seqs jalview sequences to be prepared
-     * @param minlen minimum number of residues required for this MsaWS service
-     * @return true if seqs contains sequences to be submitted to service.
-     */
-    private boolean prepareInput(SequenceI[] seqs, int minlen)
-    {
-      int nseqs = 0;
-      if (minlen < 0)
-      {
-        throw new Error("Implementation error: minlen must be zero or more.");
-      }
-      for (int i = 0; i < seqs.length; i++)
-      {
-        if (seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
-        {
-          nseqs++;
-        }
-      }
-      boolean valid = nseqs > 1; // need at least two seqs
-      vamsas.objects.simple.Sequence[] seqarray =
-          (valid)
-          ? new vamsas.objects.simple.Sequence[nseqs]
-          : null;
-      for (int i = 0, n = 0; i < seqs.length; i++)
-      {
-
-        String newname = jalview.analysis.SeqsetUtils.unique_name(i); // same
-        // for
-        // any
-        // subjob
-        SeqNames.put(newname, jalview.analysis.SeqsetUtils
-                     .SeqCharacterHash(seqs[i]));
-        if (valid && seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
-        {
-          seqarray[n] = new vamsas.objects.simple.Sequence();
-          seqarray[n].setId(newname);
-          seqarray[n++].setSeq( (submitGaps) ? seqs[i].getSequenceAsString()
-                               : AlignSeq.extractGaps(
-                                   jalview.util.Comparison.GapChars, seqs[i]
-                                   .getSequenceAsString()));
-        }
-        else
-        {
-          String empty = null;
-          if (seqs[i].getEnd() >= seqs[i].getStart())
-          {
-            empty = (submitGaps) ? seqs[i].getSequenceAsString()
-                : AlignSeq.extractGaps(
-                    jalview.util.Comparison.GapChars, seqs[i]
-                    .getSequenceAsString());
-          }
-          emptySeqs.add(new String[]
-                        {newname, empty});
-        }
-      }
-      this.seqs = new vamsas.objects.simple.SequenceSet();
-      this.seqs.setSeqs(seqarray);
-      return valid;
-    }
-
-    /**
-     *
-     * @return true if getAlignment will return a valid alignment result.
-     */
-    public boolean hasResults()
-    {
-      if (subjobComplete && result != null && result.isFinished()
-          && ( (MsaResult) result).getMsa() != null &&
-          ( (MsaResult) result).getMsa().getSeqs() != null)
-      {
-        return true;
-      }
-      return false;
-    }
-
-    public Object[] getAlignment()
-    {
-
-      if (result != null && result.isFinished())
-      {
-        SequenceI[] alseqs = null;
-        char alseq_gapchar = '-';
-        int alseq_l = 0;
-        if ( ( (MsaResult) result).getMsa() != null)
-        {
-          alseqs = getVamsasAlignment( ( (MsaResult) result).getMsa());
-          alseq_gapchar = ( (MsaResult) result).getMsa().getGapchar().charAt(0);
-          alseq_l = alseqs.length;
-        }
-        if (emptySeqs.size() > 0)
-        {
-          SequenceI[] t_alseqs = new SequenceI[alseq_l + emptySeqs.size()];
-          // get width
-          int i, w = 0;
-          if (alseq_l > 0)
-          {
-            for (i = 0, w = alseqs[0].getLength(); i < alseq_l; i++)
-            {
-              if (w < alseqs[i].getLength())
-              {
-                w = alseqs[i].getLength();
-              }
-              t_alseqs[i] = alseqs[i];
-              alseqs[i] = null;
-            }
-          }
-          // check that aligned width is at least as wide as emptySeqs width.
-          int ow = w, nw = w;
-          for (i = 0, w = emptySeqs.size(); i < w; i++)
-          {
-            String[] es = (String[]) emptySeqs.get(i);
-            if (es != null && es[1] != null)
-            {
-              int sw = es[1].length();
-              if (nw < sw)
-              {
-                nw = sw;
-              }
-            }
-          }
-          // make a gapped string.
-          StringBuffer insbuff = new StringBuffer(w);
-          for (i = 0; i < nw; i++)
-          {
-            insbuff.append(alseq_gapchar);
-          }
-          if (ow < nw)
-          {
-            for (i = 0; i < alseq_l; i++)
-            {
-              int sw = t_alseqs[i].getLength();
-              if (nw > sw)
-              {
-                // pad at end
-                alseqs[i].setSequence(t_alseqs[i].getSequenceAsString() +
-                                      insbuff.substring(0, sw - nw));
-              }
-            }
-          }
-          for (i = 0, w = emptySeqs.size(); i < w; i++)
-          {
-            String[] es = (String[]) emptySeqs.get(i);
-            if (es[1] == null)
-            {
-              t_alseqs[i +
-                  alseq_l] = new jalview.datamodel.Sequence(es[0],
-                  insbuff.toString(), 1, 0);
-            }
-            else
-            {
-              if (es[1].length() < nw)
-              {
-                t_alseqs[i +
-                    alseq_l] = new jalview.datamodel.Sequence(es[0],
-                    es[1] + insbuff.substring(0, nw - es[1].length()), 1,
-                    1 + es[1].length());
-              }
-              else
-              {
-                t_alseqs[i +
-                    alseq_l] = new jalview.datamodel.Sequence(es[0], es[1]);
-              }
-            }
-          }
-          alseqs = t_alseqs;
-        }
-        AlignmentOrder msaorder = new AlignmentOrder(alseqs);
-        // always recover the order - makes parseResult()'s life easier.
-        jalview.analysis.AlignmentSorter.recoverOrder(alseqs);
-        // account for any missing sequences
-        jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs);
-        return new Object[]
-            {
-            alseqs, msaorder};
-      }
-      return null;
-    }
-
-    /**
-     * mark subjob as cancelled and set result object appropriatly
-     */
-    void cancel()
-    {
-      cancelled = true;
-      subjobComplete = true;
-      result = null;
-    }
-
-    /**
-     *
-     * @return boolean true if job can be submitted.
-     */
-    boolean hasValidInput()
-    {
-      if (seqs.getSeqs() != null)
-      {
-        return true;
-      }
-      return false;
-    }
-  }
-
-  String alTitle; // name which will be used to form new alignment window.
-  Alignment dataset; // dataset to which the new alignment will be
-
-  // associated.
-
-  ext.vamsas.MuscleWS server = null;
-  /**
-   * set basic options for this (group) of Msa jobs
-   *
-   * @param subgaps
-   *            boolean
-   * @param presorder
-   *            boolean
-   */
-  MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl,
-              WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
-              AlignmentView alview,
-              String wsname, boolean subgaps, boolean presorder)
-  {
-    super(alFrame, wsinfo, alview, wsname, wsUrl);
-    this.server = server;
-    this.submitGaps = subgaps;
-    this.preserveOrder = presorder;
-  }
-
-  /**
-   * create one or more Msa jobs to align visible seuqences in _msa
-   *
-   * @param title
-   *            String
-   * @param _msa
-   *            AlignmentView
-   * @param subgaps
-   *            boolean
-   * @param presorder
-   *            boolean
-   * @param seqset
-   *            Alignment
-   */
-  MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl,
-              WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
-              String wsname, String title, AlignmentView _msa, boolean subgaps,
-              boolean presorder, Alignment seqset)
-  {
-    this(server, wsUrl, wsinfo, alFrame, _msa, wsname, subgaps, presorder);
-    OutputHeader = wsInfo.getProgressText();
-    alTitle = title;
-    dataset = seqset;
-
-    SequenceI[][] conmsa = _msa.getVisibleContigs('-');
-    if (conmsa != null)
-    {
-      int njobs = conmsa.length;
-      jobs = new MsaWSJob[njobs];
-      for (int j = 0; j < njobs; j++)
-      {
-        if (j != 0)
-        {
-          jobs[j] = new MsaWSJob(wsinfo.addJobPane(), conmsa[j]);
-        }
-        else
-        {
-          jobs[j] = new MsaWSJob(0, conmsa[j]);
-        }
-        if (njobs > 0)
-        {
-          wsinfo.setProgressName("region " + jobs[j].jobnum, jobs[j].jobnum);
-        }
-        wsinfo.setProgressText(jobs[j].jobnum, OutputHeader);
-      }
-    }
-  }
-
-  public boolean isCancellable()
-  {
-    return true;
-  }
-
-  public void cancelJob()
-  {
-    if (!jobComplete && jobs != null)
-    {
-      boolean cancelled = true;
-      for (int job = 0; job < jobs.length; job++)
-      {
-        if (jobs[job].submitted && !jobs[job].subjobComplete)
-        {
-          String cancelledMessage = "";
-          try
-          {
-            vamsas.objects.simple.WsJobId cancelledJob = server
-                .cancel(jobs[job].jobId);
-            if (cancelledJob.getStatus() == 2)
-            {
-              // CANCELLED_JOB
-              cancelledMessage = "Job cancelled.";
-              ( (MsaWSJob) jobs[job]).cancel();
-              wsInfo.setStatus(jobs[job].jobnum,
-                               WebserviceInfo.STATE_CANCELLED_OK);
-            }
-            else if (cancelledJob.getStatus() == 3)
-            {
-              // VALID UNSTOPPABLE JOB
-              cancelledMessage +=
-                  "Server cannot cancel this job. just close the window.\n";
-              cancelled = false;
-              // wsInfo.setStatus(jobs[job].jobnum,
-              //                 WebserviceInfo.STATE_RUNNING);
-            }
-
-            if (cancelledJob.getJobId() != null)
-            {
-              cancelledMessage += ("[" + cancelledJob.getJobId() + "]");
-            }
-
-            cancelledMessage += "\n";
-          }
-          catch (Exception exc)
-          {
-            cancelledMessage +=
-                ("\nProblems cancelling the job : Exception received...\n"
-                 + exc + "\n");
-            Cache.log.warn("Exception whilst cancelling " + jobs[job].jobId,
-                           exc);
-          }
-          wsInfo.setProgressText(jobs[job].jobnum, OutputHeader
-                                 + cancelledMessage + "\n");
-        }
-      }
-      if (cancelled)
-      {
-        wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);
-        jobComplete = true;
-      }
-      this.interrupt(); // kick thread to update job states.
-    }
-    else
-    {
-      if (!jobComplete)
-      {
-        wsInfo
-            .setProgressText(OutputHeader
-                             + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
-      }
-    }
-  }
-
-  void pollJob(WSJob job)
-      throws Exception
-  {
-    ( (MsaWSJob) job).result = server.getResult( ( (MsaWSJob) job).jobId);
-  }
-
-  void StartJob(WSJob job)
-  {
-    if (! (job instanceof MsaWSJob))
-    {
-      throw new Error("StartJob(MsaWSJob) called on a WSJobInstance " +
-                      job.getClass());
-    }
-    MsaWSJob j = (MsaWSJob) job;
-    if (j.submitted)
-    {
-      if (Cache.log.isDebugEnabled())
-      {
-        Cache.log.debug("Tried to submit an already submitted job " + j.jobId);
-      }
-      return;
-    }
-    if (j.seqs.getSeqs() == null)
-    {
-      // special case - selection consisted entirely of empty sequences...
-      j.submitted = true;
-      j.result = new MsaResult();
-      j.result.setFinished(true);
-      j.result.setStatus("Empty Alignment Job");
-      ( (MsaResult) j.result).setMsa(null);
-    }
-    try
-    {
-      vamsas.objects.simple.WsJobId jobsubmit = server.align(j.seqs);
-
-      if ( (jobsubmit != null) && (jobsubmit.getStatus() == 1))
-      {
-        j.jobId = jobsubmit.getJobId();
-        j.submitted = true;
-        j.subjobComplete = false;
-        // System.out.println(WsURL + " Job Id '" + jobId + "'");
-      }
-      else
-      {
-        if (jobsubmit == null)
-        {
-          throw new Exception(
-              "Server at "
-              + WsUrl
-              +
-              " returned null object, it probably cannot be contacted. Try again later ?");
-        }
-
-        throw new Exception(jobsubmit.getJobId());
-      }
-    }
-    catch (Exception e)
-    {
-      // TODO: JBPNote catch timeout or other fault types explicitly
-      // For unexpected errors
-      System.err
-          .println(WebServiceName
-                   + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
-                   + "When contacting Server:" + WsUrl + "\n"
-                   + e.toString() + "\n");
-      j.allowedServerExceptions = 0;
-      wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
-      wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_SERVERERROR);
-      wsInfo
-          .appendProgressText(
-              j.jobnum,
-              "Failed to submit sequences for alignment.\n"
-              + "It is most likely that there is a problem with the server.\n"
-              + "Just close the window\n");
-
-      // e.printStackTrace(); // TODO: JBPNote DEBUG
-    }
-  }
-
-  private jalview.datamodel.Sequence[] getVamsasAlignment(
-      vamsas.objects.simple.Alignment valign)
-  {
-    // TODO: refactor to helper class for vamsas.objects.simple objects
-    vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();
-    jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.
-        length];
-
-    for (int i = 0, j = seqs.length; i < j; i++)
-    {
-      msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(), seqs[i]
-                                              .getSeq());
-    }
-
-    return msa;
-  }
-
-  void parseResult()
-  {
-    int results = 0; // number of result sets received
-    JobStateSummary finalState = new JobStateSummary();
-    try
-    {
-      for (int j = 0; j < jobs.length; j++)
-      {
-        finalState.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
-        if (jobs[j].submitted && jobs[j].subjobComplete && jobs[j].hasResults())
-        {
-          results++;
-          vamsas.objects.simple.Alignment valign = ( (MsaResult) jobs[j].result).
-              getMsa();
-          if (valign != null)
-          {
-            wsInfo.appendProgressText(jobs[j].jobnum,
-                                      "\nAlignment Object Method Notes\n");
-            String[] lines = valign.getMethod();
-            for (int line = 0; line < lines.length; line++)
-            {
-              wsInfo.appendProgressText(jobs[j].jobnum, lines[line] + "\n");
-            }
-            // JBPNote The returned files from a webservice could be
-            //  hidden behind icons in the monitor window that,
-            // when clicked, pop up their corresponding data
-          }
-        }
-      }
-    }
-    catch (Exception ex)
-    {
-
-      Cache.log.error("Unexpected exception when processing results for " +
-                      alTitle, ex);
-      wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
-    }
-    if (results > 0)
-    {
-      wsInfo.showResultsNewFrame
-          .addActionListener(new java.awt.event.ActionListener()
-      {
-        public void actionPerformed(
-            java.awt.event.ActionEvent evt)
-        {
-          displayResults(true);
-        }
-      });
-      wsInfo.mergeResults
-          .addActionListener(new java.awt.event.ActionListener()
-      {
-        public void actionPerformed(
-            java.awt.event.ActionEvent evt)
-        {
-          displayResults(false);
-        }
-      });
-      wsInfo.setResultsReady();
-    }
-    else
-    {
-      wsInfo.setFinishedNoResults();
-    }
-  }
-
-  void displayResults(boolean newFrame)
-  {
-    // view input or result data for each block
-    Vector alorders = new Vector();
-    SequenceI[][] results = new SequenceI[jobs.length][];
-    AlignmentOrder[] orders = new AlignmentOrder[jobs.length];
-    for (int j = 0; j < jobs.length; j++)
-    {
-      if (jobs[j].hasResults())
-      {
-        Object[] res = ( (MsaWSJob) jobs[j]).getAlignment();
-        alorders.add(res[1]);
-        results[j] = (SequenceI[]) res[0];
-        orders[j] = (AlignmentOrder) res[1];
-         
-//    SequenceI[] alignment = input.getUpdated
-      }
-      else
-      {
-        results[j] = null;
-      }
-    }
-    Object[] newview = input.getUpdatedView(results, orders, getGapChar());
-    // trash references to original result data
-    for (int j = 0; j < jobs.length; j++)
-    {
-      results[j] = null;
-      orders[j] = null;
-    }
-    SequenceI[] alignment = (SequenceI[]) newview[0];
-    ColumnSelection columnselection = (ColumnSelection) newview[1];
-    Alignment al = new Alignment(alignment);
-    // TODO: add 'provenance' property to alignment from the method notes accompanying each subjob
-    if (dataset != null)
-    {
-      al.setDataset(dataset);
-    }
-
-    propagateDatasetMappings(al);
-    // JBNote- TODO: warn user if a block is input rather than aligned data ?
-
-    if (newFrame)
-    {
-      AlignFrame af = new AlignFrame(al, columnselection,
-                                     AlignFrame.DEFAULT_WIDTH,
-                                     AlignFrame.DEFAULT_HEIGHT);
-
-      // initialise with same renderer settings as in parent alignframe.
-      af.getFeatureRenderer().transferSettings(
-          this.featureSettings);
-      // update orders
-      if (alorders.size() > 0)
-      {
-        if (alorders.size() == 1)
-        {
-          af.addSortByOrderMenuItem(WebServiceName + " Ordering",
-                                    (AlignmentOrder) alorders.get(0));
-        }
-        else
-        {
-          // construct a non-redundant ordering set
-          Vector names = new Vector();
-          for (int i = 0, l = alorders.size(); i < l; i++)
-          {
-            String orderName = new String(" Region " + i);
-            int j = i + 1;
-
-            while (j < l)
-            {
-              if ( ( (AlignmentOrder) alorders.get(i)).equals( ( (
-                  AlignmentOrder) alorders.get(j))))
-              {
-                alorders.remove(j);
-                l--;
-                orderName += "," + j;
-              }
-              else
-              {
-                j++;
-              }
-            }
-
-            if (i == 0 && j == 1)
-            {
-              names.add(new String(""));
-            }
-            else
-            {
-              names.add(orderName);
-            }
-          }
-          for (int i = 0, l = alorders.size(); i < l; i++)
-          {
-            af.addSortByOrderMenuItem(WebServiceName
-                                      + ( (String) names.get(i)) +
-                                      " Ordering",
-                                      (AlignmentOrder) alorders.get(i));
-          }
-        }
-      }
-
-      Desktop.addInternalFrame(af, alTitle,
-                               AlignFrame.DEFAULT_WIDTH,
-                               AlignFrame.DEFAULT_HEIGHT);
-
-    }
-    else
-    {
-      System.out.println("MERGE WITH OLD FRAME");
-      // TODO: modify alignment in original frame, replacing old for new alignment using the commands.EditCommand model to ensure the update can be undone
-    }
-  }
-
-  public boolean canMergeResults()
-  {
-    return false;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.ws;
+
+import java.util.*;
+
+import jalview.analysis.*;
+import jalview.bin.*;
+import jalview.datamodel.*;
+import jalview.datamodel.Alignment;
+import jalview.gui.*;
+import vamsas.objects.simple.MsaResult;
+
+/**
+ * <p>
+ * Title:
+ * </p>
+ * 
+ * <p>
+ * Description:
+ * </p>
+ * 
+ * <p>
+ * Copyright: Copyright (c) 2004
+ * </p>
+ * 
+ * <p>
+ * Company: Dundee University
+ * </p>
+ * 
+ * @author not attributable
+ * @version 1.0
+ */
+class MsaWSThread extends WSThread implements WSClientI
+{
+  boolean submitGaps = false; // pass sequences including gaps to alignment
+
+  // service
+
+  boolean preserveOrder = true; // and always store and recover sequence
+
+  // order
+
+  class MsaWSJob extends WSThread.WSJob
+  {
+    // hold special input for this
+    vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.SequenceSet();
+
+    /**
+     * MsaWSJob
+     * 
+     * @param jobNum
+     *                int
+     * @param jobId
+     *                String
+     */
+    public MsaWSJob(int jobNum, SequenceI[] inSeqs)
+    {
+      this.jobnum = jobNum;
+      if (!prepareInput(inSeqs, 2))
+      {
+        submitted = true;
+        subjobComplete = true;
+        result = new MsaResult();
+        result.setFinished(true);
+        result.setStatus("Job never ran - input returned to user.");
+      }
+
+    }
+
+    Hashtable SeqNames = new Hashtable();
+
+    Vector emptySeqs = new Vector();
+
+    /**
+     * prepare input sequences for MsaWS service
+     * 
+     * @param seqs
+     *                jalview sequences to be prepared
+     * @param minlen
+     *                minimum number of residues required for this MsaWS service
+     * @return true if seqs contains sequences to be submitted to service.
+     */
+    private boolean prepareInput(SequenceI[] seqs, int minlen)
+    {
+      int nseqs = 0;
+      if (minlen < 0)
+      {
+        throw new Error(
+                "Implementation error: minlen must be zero or more.");
+      }
+      for (int i = 0; i < seqs.length; i++)
+      {
+        if (seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
+        {
+          nseqs++;
+        }
+      }
+      boolean valid = nseqs > 1; // need at least two seqs
+      vamsas.objects.simple.Sequence[] seqarray = (valid) ? new vamsas.objects.simple.Sequence[nseqs]
+              : null;
+      for (int i = 0, n = 0; i < seqs.length; i++)
+      {
+
+        String newname = jalview.analysis.SeqsetUtils.unique_name(i); // same
+        // for
+        // any
+        // subjob
+        SeqNames.put(newname, jalview.analysis.SeqsetUtils
+                .SeqCharacterHash(seqs[i]));
+        if (valid && seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
+        {
+          seqarray[n] = new vamsas.objects.simple.Sequence();
+          seqarray[n].setId(newname);
+          seqarray[n++].setSeq((submitGaps) ? seqs[i].getSequenceAsString()
+                  : AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
+                          seqs[i].getSequenceAsString()));
+        }
+        else
+        {
+          String empty = null;
+          if (seqs[i].getEnd() >= seqs[i].getStart())
+          {
+            empty = (submitGaps) ? seqs[i].getSequenceAsString() : AlignSeq
+                    .extractGaps(jalview.util.Comparison.GapChars, seqs[i]
+                            .getSequenceAsString());
+          }
+          emptySeqs.add(new String[]
+          { newname, empty });
+        }
+      }
+      this.seqs = new vamsas.objects.simple.SequenceSet();
+      this.seqs.setSeqs(seqarray);
+      return valid;
+    }
+
+    /**
+     * 
+     * @return true if getAlignment will return a valid alignment result.
+     */
+    public boolean hasResults()
+    {
+      if (subjobComplete && result != null && result.isFinished()
+              && ((MsaResult) result).getMsa() != null
+              && ((MsaResult) result).getMsa().getSeqs() != null)
+      {
+        return true;
+      }
+      return false;
+    }
+
+    public Object[] getAlignment()
+    {
+
+      if (result != null && result.isFinished())
+      {
+        SequenceI[] alseqs = null;
+        char alseq_gapchar = '-';
+        int alseq_l = 0;
+        if (((MsaResult) result).getMsa() != null)
+        {
+          alseqs = getVamsasAlignment(((MsaResult) result).getMsa());
+          alseq_gapchar = ((MsaResult) result).getMsa().getGapchar()
+                  .charAt(0);
+          alseq_l = alseqs.length;
+        }
+        if (emptySeqs.size() > 0)
+        {
+          SequenceI[] t_alseqs = new SequenceI[alseq_l + emptySeqs.size()];
+          // get width
+          int i, w = 0;
+          if (alseq_l > 0)
+          {
+            for (i = 0, w = alseqs[0].getLength(); i < alseq_l; i++)
+            {
+              if (w < alseqs[i].getLength())
+              {
+                w = alseqs[i].getLength();
+              }
+              t_alseqs[i] = alseqs[i];
+              alseqs[i] = null;
+            }
+          }
+          // check that aligned width is at least as wide as emptySeqs width.
+          int ow = w, nw = w;
+          for (i = 0, w = emptySeqs.size(); i < w; i++)
+          {
+            String[] es = (String[]) emptySeqs.get(i);
+            if (es != null && es[1] != null)
+            {
+              int sw = es[1].length();
+              if (nw < sw)
+              {
+                nw = sw;
+              }
+            }
+          }
+          // make a gapped string.
+          StringBuffer insbuff = new StringBuffer(w);
+          for (i = 0; i < nw; i++)
+          {
+            insbuff.append(alseq_gapchar);
+          }
+          if (ow < nw)
+          {
+            for (i = 0; i < alseq_l; i++)
+            {
+              int sw = t_alseqs[i].getLength();
+              if (nw > sw)
+              {
+                // pad at end
+                alseqs[i].setSequence(t_alseqs[i].getSequenceAsString()
+                        + insbuff.substring(0, sw - nw));
+              }
+            }
+          }
+          for (i = 0, w = emptySeqs.size(); i < w; i++)
+          {
+            String[] es = (String[]) emptySeqs.get(i);
+            if (es[1] == null)
+            {
+              t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(es[0],
+                      insbuff.toString(), 1, 0);
+            }
+            else
+            {
+              if (es[1].length() < nw)
+              {
+                t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(
+                        es[0],
+                        es[1] + insbuff.substring(0, nw - es[1].length()),
+                        1, 1 + es[1].length());
+              }
+              else
+              {
+                t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(
+                        es[0], es[1]);
+              }
+            }
+          }
+          alseqs = t_alseqs;
+        }
+        AlignmentOrder msaorder = new AlignmentOrder(alseqs);
+        // always recover the order - makes parseResult()'s life easier.
+        jalview.analysis.AlignmentSorter.recoverOrder(alseqs);
+        // account for any missing sequences
+        jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs);
+        return new Object[]
+        { alseqs, msaorder };
+      }
+      return null;
+    }
+
+    /**
+     * mark subjob as cancelled and set result object appropriatly
+     */
+    void cancel()
+    {
+      cancelled = true;
+      subjobComplete = true;
+      result = null;
+    }
+
+    /**
+     * 
+     * @return boolean true if job can be submitted.
+     */
+    boolean hasValidInput()
+    {
+      if (seqs.getSeqs() != null)
+      {
+        return true;
+      }
+      return false;
+    }
+  }
+
+  String alTitle; // name which will be used to form new alignment window.
+
+  Alignment dataset; // dataset to which the new alignment will be
+
+  // associated.
+
+  ext.vamsas.MuscleWS server = null;
+
+  /**
+   * set basic options for this (group) of Msa jobs
+   * 
+   * @param subgaps
+   *                boolean
+   * @param presorder
+   *                boolean
+   */
+  MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl,
+          WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
+          AlignmentView alview, String wsname, boolean subgaps,
+          boolean presorder)
+  {
+    super(alFrame, wsinfo, alview, wsname, wsUrl);
+    this.server = server;
+    this.submitGaps = subgaps;
+    this.preserveOrder = presorder;
+  }
+
+  /**
+   * create one or more Msa jobs to align visible seuqences in _msa
+   * 
+   * @param title
+   *                String
+   * @param _msa
+   *                AlignmentView
+   * @param subgaps
+   *                boolean
+   * @param presorder
+   *                boolean
+   * @param seqset
+   *                Alignment
+   */
+  MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl,
+          WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
+          String wsname, String title, AlignmentView _msa, boolean subgaps,
+          boolean presorder, Alignment seqset)
+  {
+    this(server, wsUrl, wsinfo, alFrame, _msa, wsname, subgaps, presorder);
+    OutputHeader = wsInfo.getProgressText();
+    alTitle = title;
+    dataset = seqset;
+
+    SequenceI[][] conmsa = _msa.getVisibleContigs('-');
+    if (conmsa != null)
+    {
+      int njobs = conmsa.length;
+      jobs = new MsaWSJob[njobs];
+      for (int j = 0; j < njobs; j++)
+      {
+        if (j != 0)
+        {
+          jobs[j] = new MsaWSJob(wsinfo.addJobPane(), conmsa[j]);
+        }
+        else
+        {
+          jobs[j] = new MsaWSJob(0, conmsa[j]);
+        }
+        if (njobs > 0)
+        {
+          wsinfo
+                  .setProgressName("region " + jobs[j].jobnum,
+                          jobs[j].jobnum);
+        }
+        wsinfo.setProgressText(jobs[j].jobnum, OutputHeader);
+      }
+    }
+  }
+
+  public boolean isCancellable()
+  {
+    return true;
+  }
+
+  public void cancelJob()
+  {
+    if (!jobComplete && jobs != null)
+    {
+      boolean cancelled = true;
+      for (int job = 0; job < jobs.length; job++)
+      {
+        if (jobs[job].submitted && !jobs[job].subjobComplete)
+        {
+          String cancelledMessage = "";
+          try
+          {
+            vamsas.objects.simple.WsJobId cancelledJob = server
+                    .cancel(jobs[job].jobId);
+            if (cancelledJob.getStatus() == 2)
+            {
+              // CANCELLED_JOB
+              cancelledMessage = "Job cancelled.";
+              ((MsaWSJob) jobs[job]).cancel();
+              wsInfo.setStatus(jobs[job].jobnum,
+                      WebserviceInfo.STATE_CANCELLED_OK);
+            }
+            else if (cancelledJob.getStatus() == 3)
+            {
+              // VALID UNSTOPPABLE JOB
+              cancelledMessage += "Server cannot cancel this job. just close the window.\n";
+              cancelled = false;
+              // wsInfo.setStatus(jobs[job].jobnum,
+              // WebserviceInfo.STATE_RUNNING);
+            }
+
+            if (cancelledJob.getJobId() != null)
+            {
+              cancelledMessage += ("[" + cancelledJob.getJobId() + "]");
+            }
+
+            cancelledMessage += "\n";
+          } catch (Exception exc)
+          {
+            cancelledMessage += ("\nProblems cancelling the job : Exception received...\n"
+                    + exc + "\n");
+            Cache.log.warn(
+                    "Exception whilst cancelling " + jobs[job].jobId, exc);
+          }
+          wsInfo.setProgressText(jobs[job].jobnum, OutputHeader
+                  + cancelledMessage + "\n");
+        }
+      }
+      if (cancelled)
+      {
+        wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);
+        jobComplete = true;
+      }
+      this.interrupt(); // kick thread to update job states.
+    }
+    else
+    {
+      if (!jobComplete)
+      {
+        wsInfo
+                .setProgressText(OutputHeader
+                        + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
+      }
+    }
+  }
+
+  void pollJob(WSJob job) throws Exception
+  {
+    ((MsaWSJob) job).result = server.getResult(((MsaWSJob) job).jobId);
+  }
+
+  void StartJob(WSJob job)
+  {
+    if (!(job instanceof MsaWSJob))
+    {
+      throw new Error("StartJob(MsaWSJob) called on a WSJobInstance "
+              + job.getClass());
+    }
+    MsaWSJob j = (MsaWSJob) job;
+    if (j.submitted)
+    {
+      if (Cache.log.isDebugEnabled())
+      {
+        Cache.log.debug("Tried to submit an already submitted job "
+                + j.jobId);
+      }
+      return;
+    }
+    if (j.seqs.getSeqs() == null)
+    {
+      // special case - selection consisted entirely of empty sequences...
+      j.submitted = true;
+      j.result = new MsaResult();
+      j.result.setFinished(true);
+      j.result.setStatus("Empty Alignment Job");
+      ((MsaResult) j.result).setMsa(null);
+    }
+    try
+    {
+      vamsas.objects.simple.WsJobId jobsubmit = server.align(j.seqs);
+
+      if ((jobsubmit != null) && (jobsubmit.getStatus() == 1))
+      {
+        j.jobId = jobsubmit.getJobId();
+        j.submitted = true;
+        j.subjobComplete = false;
+        // System.out.println(WsURL + " Job Id '" + jobId + "'");
+      }
+      else
+      {
+        if (jobsubmit == null)
+        {
+          throw new Exception(
+                  "Server at "
+                          + WsUrl
+                          + " returned null object, it probably cannot be contacted. Try again later ?");
+        }
+
+        throw new Exception(jobsubmit.getJobId());
+      }
+    } catch (Exception e)
+    {
+      // TODO: JBPNote catch timeout or other fault types explicitly
+      // For unexpected errors
+      System.err
+              .println(WebServiceName
+                      + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
+                      + "When contacting Server:" + WsUrl + "\n"
+                      + e.toString() + "\n");
+      j.allowedServerExceptions = 0;
+      wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+      wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_SERVERERROR);
+      wsInfo
+              .appendProgressText(
+                      j.jobnum,
+                      "Failed to submit sequences for alignment.\n"
+                              + "It is most likely that there is a problem with the server.\n"
+                              + "Just close the window\n");
+
+      // e.printStackTrace(); // TODO: JBPNote DEBUG
+    }
+  }
+
+  private jalview.datamodel.Sequence[] getVamsasAlignment(
+          vamsas.objects.simple.Alignment valign)
+  {
+    // TODO: refactor to helper class for vamsas.objects.simple objects
+    vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();
+    jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.length];
+
+    for (int i = 0, j = seqs.length; i < j; i++)
+    {
+      msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(), seqs[i]
+              .getSeq());
+    }
+
+    return msa;
+  }
+
+  void parseResult()
+  {
+    int results = 0; // number of result sets received
+    JobStateSummary finalState = new JobStateSummary();
+    try
+    {
+      for (int j = 0; j < jobs.length; j++)
+      {
+        finalState.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
+        if (jobs[j].submitted && jobs[j].subjobComplete
+                && jobs[j].hasResults())
+        {
+          results++;
+          vamsas.objects.simple.Alignment valign = ((MsaResult) jobs[j].result)
+                  .getMsa();
+          if (valign != null)
+          {
+            wsInfo.appendProgressText(jobs[j].jobnum,
+                    "\nAlignment Object Method Notes\n");
+            String[] lines = valign.getMethod();
+            for (int line = 0; line < lines.length; line++)
+            {
+              wsInfo.appendProgressText(jobs[j].jobnum, lines[line] + "\n");
+            }
+            // JBPNote The returned files from a webservice could be
+            // hidden behind icons in the monitor window that,
+            // when clicked, pop up their corresponding data
+          }
+        }
+      }
+    } catch (Exception ex)
+    {
+
+      Cache.log.error("Unexpected exception when processing results for "
+              + alTitle, ex);
+      wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+    }
+    if (results > 0)
+    {
+      wsInfo.showResultsNewFrame
+              .addActionListener(new java.awt.event.ActionListener()
+              {
+                public void actionPerformed(java.awt.event.ActionEvent evt)
+                {
+                  displayResults(true);
+                }
+              });
+      wsInfo.mergeResults
+              .addActionListener(new java.awt.event.ActionListener()
+              {
+                public void actionPerformed(java.awt.event.ActionEvent evt)
+                {
+                  displayResults(false);
+                }
+              });
+      wsInfo.setResultsReady();
+    }
+    else
+    {
+      wsInfo.setFinishedNoResults();
+    }
+  }
+
+  void displayResults(boolean newFrame)
+  {
+    // view input or result data for each block
+    Vector alorders = new Vector();
+    SequenceI[][] results = new SequenceI[jobs.length][];
+    AlignmentOrder[] orders = new AlignmentOrder[jobs.length];
+    for (int j = 0; j < jobs.length; j++)
+    {
+      if (jobs[j].hasResults())
+      {
+        Object[] res = ((MsaWSJob) jobs[j]).getAlignment();
+        alorders.add(res[1]);
+        results[j] = (SequenceI[]) res[0];
+        orders[j] = (AlignmentOrder) res[1];
+
+        // SequenceI[] alignment = input.getUpdated
+      }
+      else
+      {
+        results[j] = null;
+      }
+    }
+    Object[] newview = input.getUpdatedView(results, orders, getGapChar());
+    // trash references to original result data
+    for (int j = 0; j < jobs.length; j++)
+    {
+      results[j] = null;
+      orders[j] = null;
+    }
+    SequenceI[] alignment = (SequenceI[]) newview[0];
+    ColumnSelection columnselection = (ColumnSelection) newview[1];
+    Alignment al = new Alignment(alignment);
+    // TODO: add 'provenance' property to alignment from the method notes
+    // accompanying each subjob
+    if (dataset != null)
+    {
+      al.setDataset(dataset);
+    }
+
+    propagateDatasetMappings(al);
+    // JBNote- TODO: warn user if a block is input rather than aligned data ?
+
+    if (newFrame)
+    {
+      AlignFrame af = new AlignFrame(al, columnselection,
+              AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+
+      // initialise with same renderer settings as in parent alignframe.
+      af.getFeatureRenderer().transferSettings(this.featureSettings);
+      // update orders
+      if (alorders.size() > 0)
+      {
+        if (alorders.size() == 1)
+        {
+          af.addSortByOrderMenuItem(WebServiceName + " Ordering",
+                  (AlignmentOrder) alorders.get(0));
+        }
+        else
+        {
+          // construct a non-redundant ordering set
+          Vector names = new Vector();
+          for (int i = 0, l = alorders.size(); i < l; i++)
+          {
+            String orderName = new String(" Region " + i);
+            int j = i + 1;
+
+            while (j < l)
+            {
+              if (((AlignmentOrder) alorders.get(i))
+                      .equals(((AlignmentOrder) alorders.get(j))))
+              {
+                alorders.remove(j);
+                l--;
+                orderName += "," + j;
+              }
+              else
+              {
+                j++;
+              }
+            }
+
+            if (i == 0 && j == 1)
+            {
+              names.add(new String(""));
+            }
+            else
+            {
+              names.add(orderName);
+            }
+          }
+          for (int i = 0, l = alorders.size(); i < l; i++)
+          {
+            af.addSortByOrderMenuItem(WebServiceName
+                    + ((String) names.get(i)) + " Ordering",
+                    (AlignmentOrder) alorders.get(i));
+          }
+        }
+      }
+
+      Desktop.addInternalFrame(af, alTitle, AlignFrame.DEFAULT_WIDTH,
+              AlignFrame.DEFAULT_HEIGHT);
+
+    }
+    else
+    {
+      System.out.println("MERGE WITH OLD FRAME");
+      // TODO: modify alignment in original frame, replacing old for new
+      // alignment using the commands.EditCommand model to ensure the update can
+      // be undone
+    }
+  }
+
+  public boolean canMergeResults()
+  {
+    return false;
+  }
+}
diff --git a/src/jalview/ws/SeqSearchWSClient.java b/src/jalview/ws/SeqSearchWSClient.java
index e52cefd..9b6023c 100644
--- a/src/jalview/ws/SeqSearchWSClient.java
+++ b/src/jalview/ws/SeqSearchWSClient.java
@@ -1,294 +1,316 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.ws;
-
-import java.awt.Component;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.StringTokenizer;
-import java.util.Vector;
-
-import javax.swing.*;
-
-import ext.vamsas.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class SeqSearchWSClient
-    extends WSClient
-{
-  /**
-   * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
-   */
-  ext.vamsas.SeqSearchI server;
-  AlignFrame alignFrame;
-
-  /**
-   * Creates a new MsaWSClient object that uses a service
-   * given by an externally retrieved ServiceHandle
-   *
-   * @param sh service handle of type AbstractName(MsaWS)
-   * @param altitle DOCUMENT ME!
-   * @param msa DOCUMENT ME!
-   * @param submitGaps DOCUMENT ME!
-   * @param preserveOrder DOCUMENT ME!
-   */
-
-  public SeqSearchWSClient(ext.vamsas.ServiceHandle sh, String altitle,
-                     jalview.datamodel.AlignmentView msa, String db,
-                     Alignment seqdataset,
-                     AlignFrame _alignFrame)
-  {
-    super();
-    alignFrame = _alignFrame;
-    // can generalise the two errors below for metadata mapping from interface name to service client name
-    if (!sh.getAbstractName().equals(this.getServiceActionKey()))
-    {
-      JOptionPane.showMessageDialog(Desktop.desktop,
-                                    "The Service called \n" + sh.getName() +
-                                    "\nis not a \nSequence Search Service !",
-                                    "Internal Jalview Error",
-                                    JOptionPane.WARNING_MESSAGE);
-
-      return;
-    }
-
-    if ( (wsInfo = setWebService(sh)) == null)
-    {
-      JOptionPane.showMessageDialog(Desktop.desktop,
-                                    "The Sequence Search Service named " +
-                                    sh.getName() +
-                                    " is unknown", "Internal Jalview Error",
-                                    JOptionPane.WARNING_MESSAGE);
-
-      return;
-    }
-    startSeqSearchClient(altitle, msa, db, seqdataset);
-
-  }
-  /**
- * non-process web service interaction - use this for calling HEADLESS synchronous service methods
- * @param sh
- */
-  public SeqSearchWSClient(ServiceHandle sh)
-  {
-    setWebService(sh, true);
-  }
-
-  public SeqSearchWSClient()
-  {
-
-    super();
-    // add a class reference to the list
-  }
-  private void startSeqSearchClient(String altitle, AlignmentView msa,
-                                String db,
-                                Alignment seqdataset)
-  {
-    if (!locateWebService())
-    {
-      return;
-    }
-    String visdb = (db==null || db == "") ? "default" : db; // need a visible name for a sequence db
-    boolean profileSearch = msa.getSequences().length>2 ? true : false;
-    // single sequence or profile from alignment view
-    wsInfo.setProgressText( "Searching "+visdb+(!profileSearch ? " with sequence "+msa.getSequences()[0].getRefSeq().getName()
-              : " with profile") +
-                           " from " + altitle + "\nJob details\n");
-    
-    String jobtitle = WebServiceName+((WebServiceName.indexOf("earch")>-1) ? " " : " search ")+" of "+visdb+(!profileSearch ? " with sequence "+msa.getSequences()[0].getRefSeq().getName()
-            : " with profile") +
-            " from " + altitle;
-    SeqSearchWSThread ssthread = new SeqSearchWSThread(server, WsURL, wsInfo, alignFrame,
-                                            WebServiceName,
-                                            jobtitle,
-                                            msa,
-                                            db,
-                                            seqdataset);
-    wsInfo.setthisService(ssthread);
-    ssthread.start();
-  }
-
-  /**
-   * Initializes the server field with a valid service implementation.
-   *
-   * @return true if service was located.
-   */
-  private boolean locateWebService()
-  {
-    // this can be abstracted using reflection
-    // TODO: MuscleWS transmuted to generic MsaWS client
-    SeqSearchServiceLocator loc = new SeqSearchServiceLocator(); // Default
-
-    try
-    {
-      this.server = (SeqSearchI) loc.getSeqSearchService(new java.net.URL(WsURL));
-      ( (SeqSearchServiceSoapBindingStub)this.server).setTimeout(60000); // One minute timeout
-    }
-    catch (Exception ex)
-    {
-      wsInfo.setProgressText("Serious! " + WebServiceName +
-                             " Service location failed\nfor URL :" + WsURL +
-                             "\n" +
-                             ex.getMessage());
-      wsInfo.setStatus(WebserviceInfo.ERROR);
-      ex.printStackTrace();
-
-      return false;
-    }
-
-    loc.getEngine().setOption("axis", "1");
-
-    return true;
-  }
-
-  protected String getServiceActionKey()
-  {
-    return "SeqSearch";
-  }
-
-  protected String getServiceActionDescription()
-  {
-    return "Sequence Database Search";
-  }
-  // simple caching of db parameters for each service endpoint
-  private static Hashtable dbParamsForEndpoint;
-  static { 
-    dbParamsForEndpoint = new Hashtable();
-  }
-  public String[] getSupportedDatabases() throws Exception
-  {
-    
-    // check that we haven't already been to this service endpoint
-    if (dbParamsForEndpoint.containsKey(WsURL))
-    {
-      return (String[]) dbParamsForEndpoint.get(WsURL);
-    }
-    if (!locateWebService())
-    {
-      throw new Exception("Cannot contact service endpoint at "+WsURL); 
-    }
-    String database = server.getDatabase();
-    if (database==null)
-    {
-      dbParamsForEndpoint.put(WsURL, new String[] {});
-      return null;
-    }
-    StringTokenizer en = new StringTokenizer(database.trim(), ",| ");
-    String[] dbs = new String[en.countTokens()];
-    for (int i=0; i<dbs.length; i++)
-    {
-      dbs[i++] = en.nextToken().trim();
-    }
-    dbParamsForEndpoint.put(WsURL, dbs);
-    return dbs;
-  }
-  public void attachWSMenuEntry(JMenu wsmenu, final ServiceHandle sh,
-          final AlignFrame af)
-  {
-    // look for existing database service submenus on wsmenu
-    Hashtable dbsrchs = new Hashtable();
-    Vector newdbsrch = new Vector();
-    Component entries[] =  wsmenu.getComponents();
-    for (int i = 0; entries!=null && i<entries.length; i++)
-    {
-      if (entries[i] instanceof JMenu)
-      {
-        dbsrchs.put(entries[i].getName(), entries[i]);
-      }
-    }
-    JMenu defmenu=(JMenu) dbsrchs.get("Default Database");
-    if (defmenu==null)
-    {
-      dbsrchs.put("Default Database", defmenu = new JMenu("Default Database"));
-      newdbsrch.addElement(defmenu);
-    }
-      
-      String dbs[] = null;
-      try {
-        dbs = new jalview.ws.SeqSearchWSClient(sh).getSupportedDatabases();
-      } catch (Exception e)
-      {
-        jalview.bin.Cache.log.warn("Database list request failed, so disabling SeqSearch Service client "+sh.getName()+" at "+sh.getEndpointURL(), e);
-        return;
-      }
-      JMenuItem method;
-      // do default entry
-      defmenu.add(method = new JMenuItem(sh.getName()));
-      method.setToolTipText(sh.getEndpointURL());
-      method.addActionListener(new ActionListener()
-      {
-        public void actionPerformed(ActionEvent e)
-        {
-          // use same input gatherer as for secondary structure prediction
-          // we could actually parameterise the gatherer method here...
-          AlignmentView msa = af.gatherSeqOrMsaForSecStrPrediction();
-          new jalview.ws.SeqSearchWSClient(sh, af.getTitle(), msa, null, 
-                  af.getViewport().getAlignment().getDataset(),
-                  af);
-          }
-        }
-      );
-      // add entry for each database the service supports
-      for (int db=0; dbs!=null && db<dbs.length; db++)
-      {
-        JMenu dbmenu = (JMenu) dbsrchs.get(dbs[db]);
-        if (dbmenu==null)
-        {
-          dbsrchs.put(dbs[db], dbmenu = new JMenu(dbs[db]));
-          newdbsrch.addElement(dbmenu);
-        }
-        // add the client handler code for this service
-        dbmenu.add(method = new JMenuItem(sh.getName()));
-        method.setToolTipText(sh.getEndpointURL());
-        final String searchdb = dbs[db];
-        method.addActionListener(new ActionListener()
-        {
-          public void actionPerformed(ActionEvent e)
-          {
-            AlignmentView msa = af.gatherSeqOrMsaForSecStrPrediction();
-            new jalview.ws.SeqSearchWSClient(sh, af.getTitle(), msa, searchdb, 
-                      af.getViewport().getAlignment().getDataset(),
-                      af);
-          }
-        });
-      }
-    // add the databases onto the seqsearch menu
-    Enumeration e = newdbsrch.elements();
-    while (e.hasMoreElements())
-    {
-      Object el = e.nextElement();
-      if (el instanceof JMenu)
-      {
-        wsmenu.add((JMenu) el);
-      } else {
-        wsmenu.add((JMenuItem) el);
-      }
-    }
-    
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.ws;
+
+import java.awt.Component;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import javax.swing.*;
+
+import ext.vamsas.*;
+import jalview.datamodel.*;
+import jalview.gui.*;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class SeqSearchWSClient extends WSClient
+{
+  /**
+   * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
+   */
+  ext.vamsas.SeqSearchI server;
+
+  AlignFrame alignFrame;
+
+  /**
+   * Creates a new MsaWSClient object that uses a service given by an externally
+   * retrieved ServiceHandle
+   * 
+   * @param sh
+   *                service handle of type AbstractName(MsaWS)
+   * @param altitle
+   *                DOCUMENT ME!
+   * @param msa
+   *                DOCUMENT ME!
+   * @param submitGaps
+   *                DOCUMENT ME!
+   * @param preserveOrder
+   *                DOCUMENT ME!
+   */
+
+  public SeqSearchWSClient(ext.vamsas.ServiceHandle sh, String altitle,
+          jalview.datamodel.AlignmentView msa, String db,
+          Alignment seqdataset, AlignFrame _alignFrame)
+  {
+    super();
+    alignFrame = _alignFrame;
+    // can generalise the two errors below for metadata mapping from interface
+    // name to service client name
+    if (!sh.getAbstractName().equals(this.getServiceActionKey()))
+    {
+      JOptionPane.showMessageDialog(Desktop.desktop,
+              "The Service called \n" + sh.getName()
+                      + "\nis not a \nSequence Search Service !",
+              "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);
+
+      return;
+    }
+
+    if ((wsInfo = setWebService(sh)) == null)
+    {
+      JOptionPane.showMessageDialog(Desktop.desktop,
+              "The Sequence Search Service named " + sh.getName()
+                      + " is unknown", "Internal Jalview Error",
+              JOptionPane.WARNING_MESSAGE);
+
+      return;
+    }
+    startSeqSearchClient(altitle, msa, db, seqdataset);
+
+  }
+
+  /**
+   * non-process web service interaction - use this for calling HEADLESS
+   * synchronous service methods
+   * 
+   * @param sh
+   */
+  public SeqSearchWSClient(ServiceHandle sh)
+  {
+    setWebService(sh, true);
+  }
+
+  public SeqSearchWSClient()
+  {
+
+    super();
+    // add a class reference to the list
+  }
+
+  private void startSeqSearchClient(String altitle, AlignmentView msa,
+          String db, Alignment seqdataset)
+  {
+    if (!locateWebService())
+    {
+      return;
+    }
+    String visdb = (db == null || db == "") ? "default" : db; // need a visible
+                                                              // name for a
+                                                              // sequence db
+    boolean profileSearch = msa.getSequences().length > 2 ? true : false;
+    // single sequence or profile from alignment view
+    wsInfo.setProgressText("Searching "
+            + visdb
+            + (!profileSearch ? " with sequence "
+                    + msa.getSequences()[0].getRefSeq().getName()
+                    : " with profile") + " from " + altitle
+            + "\nJob details\n");
+
+    String jobtitle = WebServiceName
+            + ((WebServiceName.indexOf("earch") > -1) ? " " : " search ")
+            + " of "
+            + visdb
+            + (!profileSearch ? " with sequence "
+                    + msa.getSequences()[0].getRefSeq().getName()
+                    : " with profile") + " from " + altitle;
+    SeqSearchWSThread ssthread = new SeqSearchWSThread(server, WsURL,
+            wsInfo, alignFrame, WebServiceName, jobtitle, msa, db,
+            seqdataset);
+    wsInfo.setthisService(ssthread);
+    ssthread.start();
+  }
+
+  /**
+   * Initializes the server field with a valid service implementation.
+   * 
+   * @return true if service was located.
+   */
+  private boolean locateWebService()
+  {
+    // this can be abstracted using reflection
+    // TODO: MuscleWS transmuted to generic MsaWS client
+    SeqSearchServiceLocator loc = new SeqSearchServiceLocator(); // Default
+
+    try
+    {
+      this.server = (SeqSearchI) loc.getSeqSearchService(new java.net.URL(
+              WsURL));
+      ((SeqSearchServiceSoapBindingStub) this.server).setTimeout(60000); // One
+                                                                          // minute
+                                                                          // timeout
+    } catch (Exception ex)
+    {
+      wsInfo.setProgressText("Serious! " + WebServiceName
+              + " Service location failed\nfor URL :" + WsURL + "\n"
+              + ex.getMessage());
+      wsInfo.setStatus(WebserviceInfo.ERROR);
+      ex.printStackTrace();
+
+      return false;
+    }
+
+    loc.getEngine().setOption("axis", "1");
+
+    return true;
+  }
+
+  protected String getServiceActionKey()
+  {
+    return "SeqSearch";
+  }
+
+  protected String getServiceActionDescription()
+  {
+    return "Sequence Database Search";
+  }
+
+  // simple caching of db parameters for each service endpoint
+  private static Hashtable dbParamsForEndpoint;
+  static
+  {
+    dbParamsForEndpoint = new Hashtable();
+  }
+
+  public String[] getSupportedDatabases() throws Exception
+  {
+
+    // check that we haven't already been to this service endpoint
+    if (dbParamsForEndpoint.containsKey(WsURL))
+    {
+      return (String[]) dbParamsForEndpoint.get(WsURL);
+    }
+    if (!locateWebService())
+    {
+      throw new Exception("Cannot contact service endpoint at " + WsURL);
+    }
+    String database = server.getDatabase();
+    if (database == null)
+    {
+      dbParamsForEndpoint.put(WsURL, new String[]
+      {});
+      return null;
+    }
+    StringTokenizer en = new StringTokenizer(database.trim(), ",| ");
+    String[] dbs = new String[en.countTokens()];
+    for (int i = 0; i < dbs.length; i++)
+    {
+      dbs[i++] = en.nextToken().trim();
+    }
+    dbParamsForEndpoint.put(WsURL, dbs);
+    return dbs;
+  }
+
+  public void attachWSMenuEntry(JMenu wsmenu, final ServiceHandle sh,
+          final AlignFrame af)
+  {
+    // look for existing database service submenus on wsmenu
+    Hashtable dbsrchs = new Hashtable();
+    Vector newdbsrch = new Vector();
+    Component entries[] = wsmenu.getComponents();
+    for (int i = 0; entries != null && i < entries.length; i++)
+    {
+      if (entries[i] instanceof JMenu)
+      {
+        dbsrchs.put(entries[i].getName(), entries[i]);
+      }
+    }
+    JMenu defmenu = (JMenu) dbsrchs.get("Default Database");
+    if (defmenu == null)
+    {
+      dbsrchs.put("Default Database", defmenu = new JMenu(
+              "Default Database"));
+      newdbsrch.addElement(defmenu);
+    }
+
+    String dbs[] = null;
+    try
+    {
+      dbs = new jalview.ws.SeqSearchWSClient(sh).getSupportedDatabases();
+    } catch (Exception e)
+    {
+      jalview.bin.Cache.log.warn(
+              "Database list request failed, so disabling SeqSearch Service client "
+                      + sh.getName() + " at " + sh.getEndpointURL(), e);
+      return;
+    }
+    JMenuItem method;
+    // do default entry
+    defmenu.add(method = new JMenuItem(sh.getName()));
+    method.setToolTipText(sh.getEndpointURL());
+    method.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        // use same input gatherer as for secondary structure prediction
+        // we could actually parameterise the gatherer method here...
+        AlignmentView msa = af.gatherSeqOrMsaForSecStrPrediction();
+        new jalview.ws.SeqSearchWSClient(sh, af.getTitle(), msa, null, af
+                .getViewport().getAlignment().getDataset(), af);
+      }
+    });
+    // add entry for each database the service supports
+    for (int db = 0; dbs != null && db < dbs.length; db++)
+    {
+      JMenu dbmenu = (JMenu) dbsrchs.get(dbs[db]);
+      if (dbmenu == null)
+      {
+        dbsrchs.put(dbs[db], dbmenu = new JMenu(dbs[db]));
+        newdbsrch.addElement(dbmenu);
+      }
+      // add the client handler code for this service
+      dbmenu.add(method = new JMenuItem(sh.getName()));
+      method.setToolTipText(sh.getEndpointURL());
+      final String searchdb = dbs[db];
+      method.addActionListener(new ActionListener()
+      {
+        public void actionPerformed(ActionEvent e)
+        {
+          AlignmentView msa = af.gatherSeqOrMsaForSecStrPrediction();
+          new jalview.ws.SeqSearchWSClient(sh, af.getTitle(), msa,
+                  searchdb, af.getViewport().getAlignment().getDataset(),
+                  af);
+        }
+      });
+    }
+    // add the databases onto the seqsearch menu
+    Enumeration e = newdbsrch.elements();
+    while (e.hasMoreElements())
+    {
+      Object el = e.nextElement();
+      if (el instanceof JMenu)
+      {
+        wsmenu.add((JMenu) el);
+      }
+      else
+      {
+        wsmenu.add((JMenuItem) el);
+      }
+    }
+
+  }
+}
diff --git a/src/jalview/ws/SeqSearchWSThread.java b/src/jalview/ws/SeqSearchWSThread.java
index 07686fe..0c34518 100644
--- a/src/jalview/ws/SeqSearchWSThread.java
+++ b/src/jalview/ws/SeqSearchWSThread.java
@@ -1,667 +1,679 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.ws;
-
-import java.util.*;
-
-import jalview.analysis.*;
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import jalview.io.NewickFile;
-import vamsas.objects.simple.MsaResult;
-import vamsas.objects.simple.SeqSearchResult;
-
-/**
- * <p>
- * Title:
- * </p>
- *
- * <p>
- * Description:
- * </p>
- *
- * <p>
- * Copyright: Copyright (c) 2004
- * </p>
- *
- * <p>
- * Company: Dundee University
- * </p>
- *
- * @author not attributable
- * @version 1.0
- */
-class SeqSearchWSThread
-    extends WSThread implements WSClientI
-{
-  String dbs=null;
-  boolean profile=false;
-
-  class SeqSearchWSJob
-      extends WSThread.WSJob
-  {
-    // hold special input for this
-    vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.
-        SequenceSet();
-
-    /**
-     * MsaWSJob
-     *
-     * @param jobNum
-     *            int
-     * @param jobId
-     *            String
-     */
-    public SeqSearchWSJob(int jobNum, SequenceI[] inSeqs)
-    {
-      this.jobnum = jobNum;
-      if (!prepareInput(inSeqs, 2))
-      {
-        submitted = true;
-        subjobComplete = true;
-        result = new MsaResult();
-        result.setFinished(true);
-        result.setStatus("Job never ran - input returned to user.");
-      }
-
-    }
-
-    Hashtable SeqNames = new Hashtable();
-    Vector emptySeqs = new Vector();
-    /**
-     * prepare input sequences for service
-     * @param seqs jalview sequences to be prepared
-     * @param minlen minimum number of residues required for this MsaWS service
-     * @return true if seqs contains sequences to be submitted to service.
-     */
-    private boolean prepareInput(SequenceI[] seqs, int minlen)
-    {
-      int nseqs = 0;
-      if (minlen < 0)
-      {
-        throw new Error("Implementation error: minlen must be zero or more.");
-      }
-      for (int i = 0; i < seqs.length; i++)
-      {
-        if (seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
-        {
-          nseqs++;
-        }
-      }
-      boolean valid = nseqs >= 1; // need at least one sequence for valid input TODO: generalise
-      vamsas.objects.simple.Sequence[] seqarray =
-          (valid)
-          ? new vamsas.objects.simple.Sequence[nseqs]
-          : null;
-      boolean submitGaps = (nseqs==1) ? false : true; // profile is submitted with gaps  
-      for (int i = 0, n = 0; i < seqs.length; i++)
-      {
-
-        String newname = jalview.analysis.SeqsetUtils.unique_name(i); // same
-        // for
-        // any
-        // subjob
-        SeqNames.put(newname, jalview.analysis.SeqsetUtils
-                     .SeqCharacterHash(seqs[i]));
-        if (valid && seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
-        {
-          seqarray[n] = new vamsas.objects.simple.Sequence();
-          seqarray[n].setId(newname);
-          seqarray[n++].setSeq( (submitGaps) ? seqs[i].getSequenceAsString()
-                               : AlignSeq.extractGaps(
-                                   jalview.util.Comparison.GapChars, seqs[i]
-                                   .getSequenceAsString()));
-        }
-        else
-        {
-          String empty = null;
-          if (seqs[i].getEnd() >= seqs[i].getStart())
-          {
-            empty = (submitGaps) ? seqs[i].getSequenceAsString()
-                : AlignSeq.extractGaps(
-                    jalview.util.Comparison.GapChars, seqs[i]
-                    .getSequenceAsString());
-          }
-          emptySeqs.add(new String[]
-                        {newname, empty});
-        }
-      }
-      if (submitGaps)
-      {
-        // almost certainly have to remove gapped columns here
-      }
-      this.seqs = new vamsas.objects.simple.SequenceSet();
-      this.seqs.setSeqs(seqarray);
-      return valid;
-    }
-
-    /**
-     *
-     * @return true if getAlignment will return a valid alignment result.
-     */
-    public boolean hasResults()
-    {
-      if (subjobComplete && result != null && result.isFinished()
-          && ( (SeqSearchResult) result).getAlignment() != null &&
-          ( (SeqSearchResult) result).getAlignment().getSeqs() != null)
-      {
-        return true;
-      }
-      return false;
-    }
-
-    /**
-     * return sequence search results for display
-     * @return null or { Alignment(+features and annotation), NewickFile)}
-     */
-    public Object[] getAlignment(Alignment dataset, Hashtable featureColours)
-    {
-
-      if (result != null && result.isFinished())
-      {
-        SequenceI[] alseqs = null;
-        //char alseq_gapchar = '-';
-        //int alseq_l = 0;
-        if ( ( (SeqSearchResult) result).getAlignment() != null)
-        {
-          alseqs = getVamsasAlignment( ( (SeqSearchResult) result).getAlignment());
-          //alseq_gapchar = ( (SeqSearchResult) result).getAlignment().getGapchar().charAt(0);
-          //alseq_l = alseqs.length;
-        }
-        /**
-         * what has to be done. 1 - annotate returned alignment with annotation file and sequence features file, and associate any tree-nodes.
-         * 2. connect alignment back to any associated dataset: 2.a. deuniquify recovers sequence information - but additionally, 
-         * relocations must be made from the returned aligned sequence back to the dataset.
-         */
-        // construct annotated alignment as it would be done by the jalview applet
-        jalview.datamodel.Alignment al = new Alignment(alseqs);
-        // al.setDataset(dataset);
-        // make dataset
-        String inFile=null;
-        try {
-          inFile = ((SeqSearchResult) result).getAnnotation();
-          if (inFile!=null && inFile.length()>0)
-          {
-            new jalview.io.AnnotationFile().readAnnotationFile(al, inFile, jalview.io.AppletFormatAdapter.PASTE);
-          }
-          }
-        catch (Exception e)
-        {
-          System.err.println("Failed to parse the annotation file associated with the alignment.");
-          System.err.println(">>>EOF"+inFile+"\n<<<EOF\n");
-          e.printStackTrace(System.err);
-        }
-        
-        try {
-          inFile = ((SeqSearchResult) result).getFeatures();
-          if (inFile!=null && inFile.length()>0)
-          {
-            jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(inFile, jalview.io.AppletFormatAdapter.PASTE);
-            ff.parse(al, featureColours, false);
-          }
-        }
-        catch (Exception e)
-        {
-          System.err.println("Failed to parse the Features file associated with the alignment.");
-          System.err.println(">>>EOF"+inFile+"\n<<<EOF\n");
-          e.printStackTrace(System.err);
-        }
-        jalview.io.NewickFile nf=null;
-        try {
-          inFile = ((SeqSearchResult) result).getNewickTree();
-          if (inFile!=null && inFile.length()>0)
-          {
-            nf = new jalview.io.NewickFile(inFile, jalview.io.AppletFormatAdapter.PASTE);
-            if (!nf.isValid()) {
-              nf.close();
-              nf = null;
-            }
-          }
-        }
-        catch (Exception e)
-        {
-          System.err.println("Failed to parse the treeFile associated with the alignment.");
-          System.err.println(">>>EOF"+inFile+"\n<<<EOF\n");
-          e.printStackTrace(System.err);
-        }
-        
-        /* TODO: housekeeping w.r.t. recovery of dataset and annotation references for input sequences, and then dataset sequence creation for new sequences retrieved from service
-         * // finally, attempt to de-uniquify to recover input sequence identity, and try to map back onto dataset
-        Note: this
-        jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs, true);
-        will NOT WORK - the returned alignment may contain multiple versions of the input sequence, each being a subsequence of the original.
-        deuniquify also removes existing annotation and features added in the previous step...
-        al.setDataset(dataset);
-        // add in new sequences retrieved from sequence search which are not already in dataset.
-        // trigger a 'fetchDBids' to annotate sequences with database ids...
-        */
-
-        return new Object[]
-            {
-            al, nf};
-      }
-      return null;
-    }
-
-    /**
-     * mark subjob as cancelled and set result object appropriatly
-     */
-    void cancel()
-    {
-      cancelled = true;
-      subjobComplete = true;
-      result = null;
-    }
-
-    /**
-     *
-     * @return boolean true if job can be submitted.
-     */
-    boolean hasValidInput()
-    {
-      if (seqs.getSeqs() != null)
-      {
-        return true;
-      }
-      return false;
-    }
-  }
-
-  String alTitle; // name which will be used to form new alignment window.
-  Alignment dataset; // dataset to which the new alignment will be
-
-  // associated.
-
-  ext.vamsas.SeqSearchI server = null;
-
-  private String dbArg;
-  /**
-   * set basic options for this (group) of Msa jobs
-   *
-   * @param subgaps
-   *            boolean
-   * @param presorder
-   *            boolean
-   */
-  SeqSearchWSThread(ext.vamsas.SeqSearchI server, String wsUrl,
-              WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
-              AlignmentView alview,
-              String wsname, String db)
-  {
-    super(alFrame, wsinfo, alview, wsname, wsUrl);
-    this.server = server;
-    this.dbArg = db;
-  }
-
-  /**
-   * create one or more Msa jobs to align visible seuqences in _msa
-   *
-   * @param title
-   *            String
-   * @param _msa
-   *            AlignmentView
-   * @param subgaps
-   *            boolean
-   * @param presorder
-   *            boolean
-   * @param seqset
-   *            Alignment
-   */
-  SeqSearchWSThread(ext.vamsas.SeqSearchI server, String wsUrl,
-              WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
-              String wsname, String title, AlignmentView _msa, String db, Alignment seqset)
-  {
-    this(server, wsUrl, wsinfo, alFrame, _msa, wsname, db);
-    OutputHeader = wsInfo.getProgressText();
-    alTitle = title;
-    dataset = seqset;
-
-    SequenceI[][] conmsa = _msa.getVisibleContigs('-');
-    if (conmsa != null)
-    {
-      int njobs = conmsa.length;
-      jobs = new SeqSearchWSJob[njobs];
-      for (int j = 0; j < njobs; j++)
-      {
-        if (j != 0)
-        {
-          jobs[j] = new SeqSearchWSJob(wsinfo.addJobPane(), conmsa[j]);
-        }
-        else
-        {
-          jobs[j] = new SeqSearchWSJob(0, conmsa[j]);
-        }
-        if (njobs > 0)
-        {
-          wsinfo.setProgressName("region " + jobs[j].jobnum, jobs[j].jobnum);
-        }
-        wsinfo.setProgressText(jobs[j].jobnum, OutputHeader);
-      }
-    }
-  }
-
-  public boolean isCancellable()
-  {
-    return true;
-  }
-
-  public void cancelJob()
-  {
-    if (!jobComplete && jobs != null)
-    {
-      boolean cancelled = true;
-      for (int job = 0; job < jobs.length; job++)
-      {
-        if (jobs[job].submitted && !jobs[job].subjobComplete)
-        {
-          String cancelledMessage = "";
-          try
-          {
-            vamsas.objects.simple.WsJobId cancelledJob = server
-                .cancel(jobs[job].jobId);
-            if (cancelledJob.getStatus() == 2)
-            {
-              // CANCELLED_JOB
-              cancelledMessage = "Job cancelled.";
-              ( (SeqSearchWSJob) jobs[job]).cancel();
-              wsInfo.setStatus(jobs[job].jobnum,
-                               WebserviceInfo.STATE_CANCELLED_OK);
-            }
-            else if (cancelledJob.getStatus() == 3)
-            {
-              // VALID UNSTOPPABLE JOB
-              cancelledMessage +=
-                  "Server cannot cancel this job. just close the window.\n";
-              cancelled = false;
-              // wsInfo.setStatus(jobs[job].jobnum,
-              //                 WebserviceInfo.STATE_RUNNING);
-            }
-
-            if (cancelledJob.getJobId() != null)
-            {
-              cancelledMessage += ("[" + cancelledJob.getJobId() + "]");
-            }
-
-            cancelledMessage += "\n";
-          }
-          catch (Exception exc)
-          {
-            cancelledMessage +=
-                ("\nProblems cancelling the job : Exception received...\n"
-                 + exc + "\n");
-            Cache.log.warn("Exception whilst cancelling " + jobs[job].jobId,
-                           exc);
-          }
-          wsInfo.setProgressText(jobs[job].jobnum, OutputHeader
-                                 + cancelledMessage + "\n");
-        }
-      }
-      if (cancelled)
-      {
-        wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);
-        jobComplete = true;
-      }
-      this.interrupt(); // kick thread to update job states.
-    }
-    else
-    {
-      if (!jobComplete)
-      {
-        wsInfo
-            .setProgressText(OutputHeader
-                             + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
-      }
-    }
-  }
-
-  void pollJob(WSJob job)
-      throws Exception
-  {
-    ( (SeqSearchWSJob) job).result = server.getResult( ( (SeqSearchWSJob) job).jobId);
-  }
-
-  void StartJob(WSJob job)
-  {
-    if (! (job instanceof SeqSearchWSJob))
-    {
-      throw new Error("StartJob(MsaWSJob) called on a WSJobInstance " +
-                      job.getClass());
-    }
-    SeqSearchWSJob j = (SeqSearchWSJob) job;
-    if (j.submitted)
-    {
-      if (Cache.log.isDebugEnabled())
-      {
-        Cache.log.debug("Tried to submit an already submitted job " + j.jobId);
-      }
-      return;
-    }
-    if (j.seqs.getSeqs() == null)
-    {
-      // special case - selection consisted entirely of empty sequences...
-      j.submitted = true;
-      j.result = new MsaResult();
-      j.result.setFinished(true);
-      j.result.setStatus("Empty Alignment Job");
-      ( (MsaResult) j.result).setMsa(null);
-    }
-    try
-    {
-      vamsas.objects.simple.WsJobId jobsubmit = server.search(j.seqs.getSeqs()[0], dbArg);
-
-      if ( (jobsubmit != null) && (jobsubmit.getStatus() == 1))
-      {
-        j.jobId = jobsubmit.getJobId();
-        j.submitted = true;
-        j.subjobComplete = false;
-        // System.out.println(WsURL + " Job Id '" + jobId + "'");
-      }
-      else
-      {
-        if (jobsubmit == null)
-        {
-          throw new Exception(
-              "Server at "
-              + WsUrl
-              +
-              " returned null object, it probably cannot be contacted. Try again later ?");
-        }
-
-        throw new Exception(jobsubmit.getJobId());
-      }
-    }
-    catch (Exception e)
-    {
-      // TODO: JBPNote catch timeout or other fault types explicitly
-      // For unexpected errors
-      System.err
-          .println(WebServiceName
-                   + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
-                   + "When contacting Server:" + WsUrl + "\n"
-                   + e.toString() + "\n");
-      j.allowedServerExceptions = 0;
-      wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
-      wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_SERVERERROR);
-      wsInfo
-          .appendProgressText(
-              j.jobnum,
-              "Failed to submit sequences for alignment.\n"
-              + "It is most likely that there is a problem with the server.\n"
-              + "Just close the window\n");
-
-      // e.printStackTrace(); // TODO: JBPNote DEBUG
-    }
-  }
-
-  private jalview.datamodel.Sequence[] getVamsasAlignment(
-      vamsas.objects.simple.Alignment valign)
-  {
-    vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();
-    jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.
-        length];
-
-    for (int i = 0, j = seqs.length; i < j; i++)
-    {
-      msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(), seqs[i]
-                                              .getSeq());
-    }
-
-    return msa;
-  }
-
-  void parseResult()
-  {
-    int results = 0; // number of result sets received
-    JobStateSummary finalState = new JobStateSummary();
-    try
-    {
-      for (int j = 0; j < jobs.length; j++)
-      {
-        finalState.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
-        if (jobs[j].submitted && jobs[j].subjobComplete && jobs[j].hasResults())
-        {
-          results++;
-          vamsas.objects.simple.Alignment valign = ( (SeqSearchResult) jobs[j].result).
-              getAlignment();
-          if (valign != null)
-          {
-            wsInfo.appendProgressText(jobs[j].jobnum,
-                                      "\nAlignment Object Method Notes\n");
-            String[] lines = valign.getMethod();
-            for (int line = 0; line < lines.length; line++)
-            {
-              wsInfo.appendProgressText(jobs[j].jobnum, lines[line] + "\n");
-            }
-            // JBPNote The returned files from a webservice could be
-            //  hidden behind icons in the monitor window that,
-            // when clicked, pop up their corresponding data
-          }
-        }
-      }
-    }
-    catch (Exception ex)
-    {
-
-      Cache.log.error("Unexpected exception when processing results for " +
-                      alTitle, ex);
-      wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
-    }
-    if (results > 0)
-    {
-      wsInfo.showResultsNewFrame
-          .addActionListener(new java.awt.event.ActionListener()
-      {
-        public void actionPerformed(
-            java.awt.event.ActionEvent evt)
-        {
-          displayResults(true);
-        }
-      });
-      wsInfo.mergeResults
-          .addActionListener(new java.awt.event.ActionListener()
-      {
-        public void actionPerformed(
-            java.awt.event.ActionEvent evt)
-        {
-          displayResults(false);
-        }
-      });
-      wsInfo.setResultsReady();
-    }
-    else
-    {
-      wsInfo.setFinishedNoResults();
-    }
-  }
-
-  void displayResults(boolean newFrame)
-  {
-    if (!newFrame)
-    {
-      System.err.println("MERGE WITH OLD FRAME NOT IMPLEMENTED");
-      return;
-    }
-    // each subjob is an independent alignment for the moment
-    //Alignment al[] = new Alignment[jobs.length];
-    //NewickFile nf[] = new NewickFile[jobs.length];
-    for (int j = 0; j < jobs.length; j++)
-    {
-      Hashtable featureColours = new Hashtable();
-      Alignment al=null;
-      NewickFile nf = null;
-      if (jobs[j].hasResults())
-      {
-        Object[] res = ( (SeqSearchWSJob) jobs[j]).getAlignment(dataset, featureColours);
-        if (res==null) { continue; };
-        al = (Alignment) res[0];
-        nf = (NewickFile) res[1];
-      }
-      else
-      {
-        al = null;
-        nf = null;
-        continue;
-      }
-    /*
-     * We can't map new alignment back with insertions from input's hidden regions until dataset mapping is sorted out...
-     * but basically it goes like this:
-     1. Merge each domain hit back onto the visible segments in the same way as a Jnet prediction is mapped back
-     
-     Object[] newview = input.getUpdatedView(results, orders, getGapChar());
-    // trash references to original result data
-    for (int j = 0; j < jobs.length; j++)
-    {
-      results[j] = null;
-      orders[j] = null;
-    }
-    SequenceI[] alignment = (SequenceI[]) newview[0];
-    ColumnSelection columnselection = (ColumnSelection) newview[1];
-    Alignment al = new Alignment(alignment);
-
-    if (dataset != null)
-    {
-      al.setDataset(dataset);
-    }
-
-    propagateDatasetMappings(al);
-    }
-    */
-      
-      AlignFrame af = new AlignFrame(al,//  columnselection,
-              AlignFrame.DEFAULT_WIDTH,
-              AlignFrame.DEFAULT_HEIGHT);
-      if (nf!=null)
-      {
-        af.ShowNewickTree(nf, "Tree from "+this.alTitle);
-      }
-      // initialise with same renderer settings as in parent alignframe.
-      af.getFeatureRenderer().transferSettings(
-              this.featureSettings);
-      Desktop.addInternalFrame(af, alTitle,
-              AlignFrame.DEFAULT_WIDTH,
-              AlignFrame.DEFAULT_HEIGHT);
-    }
-  }
-
-  public boolean canMergeResults()
-  {
-    return false;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.ws;
+
+import java.util.*;
+
+import jalview.analysis.*;
+import jalview.bin.*;
+import jalview.datamodel.*;
+import jalview.gui.*;
+import jalview.io.NewickFile;
+import vamsas.objects.simple.MsaResult;
+import vamsas.objects.simple.SeqSearchResult;
+
+/**
+ * <p>
+ * Title:
+ * </p>
+ * 
+ * <p>
+ * Description:
+ * </p>
+ * 
+ * <p>
+ * Copyright: Copyright (c) 2004
+ * </p>
+ * 
+ * <p>
+ * Company: Dundee University
+ * </p>
+ * 
+ * @author not attributable
+ * @version 1.0
+ */
+class SeqSearchWSThread extends WSThread implements WSClientI
+{
+  String dbs = null;
+
+  boolean profile = false;
+
+  class SeqSearchWSJob extends WSThread.WSJob
+  {
+    // hold special input for this
+    vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.SequenceSet();
+
+    /**
+     * MsaWSJob
+     * 
+     * @param jobNum
+     *                int
+     * @param jobId
+     *                String
+     */
+    public SeqSearchWSJob(int jobNum, SequenceI[] inSeqs)
+    {
+      this.jobnum = jobNum;
+      if (!prepareInput(inSeqs, 2))
+      {
+        submitted = true;
+        subjobComplete = true;
+        result = new MsaResult();
+        result.setFinished(true);
+        result.setStatus("Job never ran - input returned to user.");
+      }
+
+    }
+
+    Hashtable SeqNames = new Hashtable();
+
+    Vector emptySeqs = new Vector();
+
+    /**
+     * prepare input sequences for service
+     * 
+     * @param seqs
+     *                jalview sequences to be prepared
+     * @param minlen
+     *                minimum number of residues required for this MsaWS service
+     * @return true if seqs contains sequences to be submitted to service.
+     */
+    private boolean prepareInput(SequenceI[] seqs, int minlen)
+    {
+      int nseqs = 0;
+      if (minlen < 0)
+      {
+        throw new Error(
+                "Implementation error: minlen must be zero or more.");
+      }
+      for (int i = 0; i < seqs.length; i++)
+      {
+        if (seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
+        {
+          nseqs++;
+        }
+      }
+      boolean valid = nseqs >= 1; // need at least one sequence for valid input
+                                  // TODO: generalise
+      vamsas.objects.simple.Sequence[] seqarray = (valid) ? new vamsas.objects.simple.Sequence[nseqs]
+              : null;
+      boolean submitGaps = (nseqs == 1) ? false : true; // profile is submitted
+                                                        // with gaps
+      for (int i = 0, n = 0; i < seqs.length; i++)
+      {
+
+        String newname = jalview.analysis.SeqsetUtils.unique_name(i); // same
+        // for
+        // any
+        // subjob
+        SeqNames.put(newname, jalview.analysis.SeqsetUtils
+                .SeqCharacterHash(seqs[i]));
+        if (valid && seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
+        {
+          seqarray[n] = new vamsas.objects.simple.Sequence();
+          seqarray[n].setId(newname);
+          seqarray[n++].setSeq((submitGaps) ? seqs[i].getSequenceAsString()
+                  : AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
+                          seqs[i].getSequenceAsString()));
+        }
+        else
+        {
+          String empty = null;
+          if (seqs[i].getEnd() >= seqs[i].getStart())
+          {
+            empty = (submitGaps) ? seqs[i].getSequenceAsString() : AlignSeq
+                    .extractGaps(jalview.util.Comparison.GapChars, seqs[i]
+                            .getSequenceAsString());
+          }
+          emptySeqs.add(new String[]
+          { newname, empty });
+        }
+      }
+      if (submitGaps)
+      {
+        // almost certainly have to remove gapped columns here
+      }
+      this.seqs = new vamsas.objects.simple.SequenceSet();
+      this.seqs.setSeqs(seqarray);
+      return valid;
+    }
+
+    /**
+     * 
+     * @return true if getAlignment will return a valid alignment result.
+     */
+    public boolean hasResults()
+    {
+      if (subjobComplete
+              && result != null
+              && result.isFinished()
+              && ((SeqSearchResult) result).getAlignment() != null
+              && ((SeqSearchResult) result).getAlignment().getSeqs() != null)
+      {
+        return true;
+      }
+      return false;
+    }
+
+    /**
+     * return sequence search results for display
+     * 
+     * @return null or { Alignment(+features and annotation), NewickFile)}
+     */
+    public Object[] getAlignment(Alignment dataset, Hashtable featureColours)
+    {
+
+      if (result != null && result.isFinished())
+      {
+        SequenceI[] alseqs = null;
+        // char alseq_gapchar = '-';
+        // int alseq_l = 0;
+        if (((SeqSearchResult) result).getAlignment() != null)
+        {
+          alseqs = getVamsasAlignment(((SeqSearchResult) result)
+                  .getAlignment());
+          // alseq_gapchar = ( (SeqSearchResult)
+          // result).getAlignment().getGapchar().charAt(0);
+          // alseq_l = alseqs.length;
+        }
+        /**
+         * what has to be done. 1 - annotate returned alignment with annotation
+         * file and sequence features file, and associate any tree-nodes. 2.
+         * connect alignment back to any associated dataset: 2.a. deuniquify
+         * recovers sequence information - but additionally, relocations must be
+         * made from the returned aligned sequence back to the dataset.
+         */
+        // construct annotated alignment as it would be done by the jalview
+        // applet
+        jalview.datamodel.Alignment al = new Alignment(alseqs);
+        // al.setDataset(dataset);
+        // make dataset
+        String inFile = null;
+        try
+        {
+          inFile = ((SeqSearchResult) result).getAnnotation();
+          if (inFile != null && inFile.length() > 0)
+          {
+            new jalview.io.AnnotationFile().readAnnotationFile(al, inFile,
+                    jalview.io.AppletFormatAdapter.PASTE);
+          }
+        } catch (Exception e)
+        {
+          System.err
+                  .println("Failed to parse the annotation file associated with the alignment.");
+          System.err.println(">>>EOF" + inFile + "\n<<<EOF\n");
+          e.printStackTrace(System.err);
+        }
+
+        try
+        {
+          inFile = ((SeqSearchResult) result).getFeatures();
+          if (inFile != null && inFile.length() > 0)
+          {
+            jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(
+                    inFile, jalview.io.AppletFormatAdapter.PASTE);
+            ff.parse(al, featureColours, false);
+          }
+        } catch (Exception e)
+        {
+          System.err
+                  .println("Failed to parse the Features file associated with the alignment.");
+          System.err.println(">>>EOF" + inFile + "\n<<<EOF\n");
+          e.printStackTrace(System.err);
+        }
+        jalview.io.NewickFile nf = null;
+        try
+        {
+          inFile = ((SeqSearchResult) result).getNewickTree();
+          if (inFile != null && inFile.length() > 0)
+          {
+            nf = new jalview.io.NewickFile(inFile,
+                    jalview.io.AppletFormatAdapter.PASTE);
+            if (!nf.isValid())
+            {
+              nf.close();
+              nf = null;
+            }
+          }
+        } catch (Exception e)
+        {
+          System.err
+                  .println("Failed to parse the treeFile associated with the alignment.");
+          System.err.println(">>>EOF" + inFile + "\n<<<EOF\n");
+          e.printStackTrace(System.err);
+        }
+
+        /*
+         * TODO: housekeeping w.r.t. recovery of dataset and annotation
+         * references for input sequences, and then dataset sequence creation
+         * for new sequences retrieved from service // finally, attempt to
+         * de-uniquify to recover input sequence identity, and try to map back
+         * onto dataset Note: this
+         * jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs, true); will
+         * NOT WORK - the returned alignment may contain multiple versions of
+         * the input sequence, each being a subsequence of the original.
+         * deuniquify also removes existing annotation and features added in the
+         * previous step... al.setDataset(dataset); // add in new sequences
+         * retrieved from sequence search which are not already in dataset. //
+         * trigger a 'fetchDBids' to annotate sequences with database ids...
+         */
+
+        return new Object[]
+        { al, nf };
+      }
+      return null;
+    }
+
+    /**
+     * mark subjob as cancelled and set result object appropriatly
+     */
+    void cancel()
+    {
+      cancelled = true;
+      subjobComplete = true;
+      result = null;
+    }
+
+    /**
+     * 
+     * @return boolean true if job can be submitted.
+     */
+    boolean hasValidInput()
+    {
+      if (seqs.getSeqs() != null)
+      {
+        return true;
+      }
+      return false;
+    }
+  }
+
+  String alTitle; // name which will be used to form new alignment window.
+
+  Alignment dataset; // dataset to which the new alignment will be
+
+  // associated.
+
+  ext.vamsas.SeqSearchI server = null;
+
+  private String dbArg;
+
+  /**
+   * set basic options for this (group) of Msa jobs
+   * 
+   * @param subgaps
+   *                boolean
+   * @param presorder
+   *                boolean
+   */
+  SeqSearchWSThread(ext.vamsas.SeqSearchI server, String wsUrl,
+          WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
+          AlignmentView alview, String wsname, String db)
+  {
+    super(alFrame, wsinfo, alview, wsname, wsUrl);
+    this.server = server;
+    this.dbArg = db;
+  }
+
+  /**
+   * create one or more Msa jobs to align visible seuqences in _msa
+   * 
+   * @param title
+   *                String
+   * @param _msa
+   *                AlignmentView
+   * @param subgaps
+   *                boolean
+   * @param presorder
+   *                boolean
+   * @param seqset
+   *                Alignment
+   */
+  SeqSearchWSThread(ext.vamsas.SeqSearchI server, String wsUrl,
+          WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
+          String wsname, String title, AlignmentView _msa, String db,
+          Alignment seqset)
+  {
+    this(server, wsUrl, wsinfo, alFrame, _msa, wsname, db);
+    OutputHeader = wsInfo.getProgressText();
+    alTitle = title;
+    dataset = seqset;
+
+    SequenceI[][] conmsa = _msa.getVisibleContigs('-');
+    if (conmsa != null)
+    {
+      int njobs = conmsa.length;
+      jobs = new SeqSearchWSJob[njobs];
+      for (int j = 0; j < njobs; j++)
+      {
+        if (j != 0)
+        {
+          jobs[j] = new SeqSearchWSJob(wsinfo.addJobPane(), conmsa[j]);
+        }
+        else
+        {
+          jobs[j] = new SeqSearchWSJob(0, conmsa[j]);
+        }
+        if (njobs > 0)
+        {
+          wsinfo
+                  .setProgressName("region " + jobs[j].jobnum,
+                          jobs[j].jobnum);
+        }
+        wsinfo.setProgressText(jobs[j].jobnum, OutputHeader);
+      }
+    }
+  }
+
+  public boolean isCancellable()
+  {
+    return true;
+  }
+
+  public void cancelJob()
+  {
+    if (!jobComplete && jobs != null)
+    {
+      boolean cancelled = true;
+      for (int job = 0; job < jobs.length; job++)
+      {
+        if (jobs[job].submitted && !jobs[job].subjobComplete)
+        {
+          String cancelledMessage = "";
+          try
+          {
+            vamsas.objects.simple.WsJobId cancelledJob = server
+                    .cancel(jobs[job].jobId);
+            if (cancelledJob.getStatus() == 2)
+            {
+              // CANCELLED_JOB
+              cancelledMessage = "Job cancelled.";
+              ((SeqSearchWSJob) jobs[job]).cancel();
+              wsInfo.setStatus(jobs[job].jobnum,
+                      WebserviceInfo.STATE_CANCELLED_OK);
+            }
+            else if (cancelledJob.getStatus() == 3)
+            {
+              // VALID UNSTOPPABLE JOB
+              cancelledMessage += "Server cannot cancel this job. just close the window.\n";
+              cancelled = false;
+              // wsInfo.setStatus(jobs[job].jobnum,
+              // WebserviceInfo.STATE_RUNNING);
+            }
+
+            if (cancelledJob.getJobId() != null)
+            {
+              cancelledMessage += ("[" + cancelledJob.getJobId() + "]");
+            }
+
+            cancelledMessage += "\n";
+          } catch (Exception exc)
+          {
+            cancelledMessage += ("\nProblems cancelling the job : Exception received...\n"
+                    + exc + "\n");
+            Cache.log.warn(
+                    "Exception whilst cancelling " + jobs[job].jobId, exc);
+          }
+          wsInfo.setProgressText(jobs[job].jobnum, OutputHeader
+                  + cancelledMessage + "\n");
+        }
+      }
+      if (cancelled)
+      {
+        wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);
+        jobComplete = true;
+      }
+      this.interrupt(); // kick thread to update job states.
+    }
+    else
+    {
+      if (!jobComplete)
+      {
+        wsInfo
+                .setProgressText(OutputHeader
+                        + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
+      }
+    }
+  }
+
+  void pollJob(WSJob job) throws Exception
+  {
+    ((SeqSearchWSJob) job).result = server
+            .getResult(((SeqSearchWSJob) job).jobId);
+  }
+
+  void StartJob(WSJob job)
+  {
+    if (!(job instanceof SeqSearchWSJob))
+    {
+      throw new Error("StartJob(MsaWSJob) called on a WSJobInstance "
+              + job.getClass());
+    }
+    SeqSearchWSJob j = (SeqSearchWSJob) job;
+    if (j.submitted)
+    {
+      if (Cache.log.isDebugEnabled())
+      {
+        Cache.log.debug("Tried to submit an already submitted job "
+                + j.jobId);
+      }
+      return;
+    }
+    if (j.seqs.getSeqs() == null)
+    {
+      // special case - selection consisted entirely of empty sequences...
+      j.submitted = true;
+      j.result = new MsaResult();
+      j.result.setFinished(true);
+      j.result.setStatus("Empty Alignment Job");
+      ((MsaResult) j.result).setMsa(null);
+    }
+    try
+    {
+      vamsas.objects.simple.WsJobId jobsubmit = server.search(j.seqs
+              .getSeqs()[0], dbArg);
+
+      if ((jobsubmit != null) && (jobsubmit.getStatus() == 1))
+      {
+        j.jobId = jobsubmit.getJobId();
+        j.submitted = true;
+        j.subjobComplete = false;
+        // System.out.println(WsURL + " Job Id '" + jobId + "'");
+      }
+      else
+      {
+        if (jobsubmit == null)
+        {
+          throw new Exception(
+                  "Server at "
+                          + WsUrl
+                          + " returned null object, it probably cannot be contacted. Try again later ?");
+        }
+
+        throw new Exception(jobsubmit.getJobId());
+      }
+    } catch (Exception e)
+    {
+      // TODO: JBPNote catch timeout or other fault types explicitly
+      // For unexpected errors
+      System.err
+              .println(WebServiceName
+                      + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
+                      + "When contacting Server:" + WsUrl + "\n"
+                      + e.toString() + "\n");
+      j.allowedServerExceptions = 0;
+      wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+      wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_SERVERERROR);
+      wsInfo
+              .appendProgressText(
+                      j.jobnum,
+                      "Failed to submit sequences for alignment.\n"
+                              + "It is most likely that there is a problem with the server.\n"
+                              + "Just close the window\n");
+
+      // e.printStackTrace(); // TODO: JBPNote DEBUG
+    }
+  }
+
+  private jalview.datamodel.Sequence[] getVamsasAlignment(
+          vamsas.objects.simple.Alignment valign)
+  {
+    vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();
+    jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.length];
+
+    for (int i = 0, j = seqs.length; i < j; i++)
+    {
+      msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(), seqs[i]
+              .getSeq());
+    }
+
+    return msa;
+  }
+
+  void parseResult()
+  {
+    int results = 0; // number of result sets received
+    JobStateSummary finalState = new JobStateSummary();
+    try
+    {
+      for (int j = 0; j < jobs.length; j++)
+      {
+        finalState.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
+        if (jobs[j].submitted && jobs[j].subjobComplete
+                && jobs[j].hasResults())
+        {
+          results++;
+          vamsas.objects.simple.Alignment valign = ((SeqSearchResult) jobs[j].result)
+                  .getAlignment();
+          if (valign != null)
+          {
+            wsInfo.appendProgressText(jobs[j].jobnum,
+                    "\nAlignment Object Method Notes\n");
+            String[] lines = valign.getMethod();
+            for (int line = 0; line < lines.length; line++)
+            {
+              wsInfo.appendProgressText(jobs[j].jobnum, lines[line] + "\n");
+            }
+            // JBPNote The returned files from a webservice could be
+            // hidden behind icons in the monitor window that,
+            // when clicked, pop up their corresponding data
+          }
+        }
+      }
+    } catch (Exception ex)
+    {
+
+      Cache.log.error("Unexpected exception when processing results for "
+              + alTitle, ex);
+      wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+    }
+    if (results > 0)
+    {
+      wsInfo.showResultsNewFrame
+              .addActionListener(new java.awt.event.ActionListener()
+              {
+                public void actionPerformed(java.awt.event.ActionEvent evt)
+                {
+                  displayResults(true);
+                }
+              });
+      wsInfo.mergeResults
+              .addActionListener(new java.awt.event.ActionListener()
+              {
+                public void actionPerformed(java.awt.event.ActionEvent evt)
+                {
+                  displayResults(false);
+                }
+              });
+      wsInfo.setResultsReady();
+    }
+    else
+    {
+      wsInfo.setFinishedNoResults();
+    }
+  }
+
+  void displayResults(boolean newFrame)
+  {
+    if (!newFrame)
+    {
+      System.err.println("MERGE WITH OLD FRAME NOT IMPLEMENTED");
+      return;
+    }
+    // each subjob is an independent alignment for the moment
+    // Alignment al[] = new Alignment[jobs.length];
+    // NewickFile nf[] = new NewickFile[jobs.length];
+    for (int j = 0; j < jobs.length; j++)
+    {
+      Hashtable featureColours = new Hashtable();
+      Alignment al = null;
+      NewickFile nf = null;
+      if (jobs[j].hasResults())
+      {
+        Object[] res = ((SeqSearchWSJob) jobs[j]).getAlignment(dataset,
+                featureColours);
+        if (res == null)
+        {
+          continue;
+        }
+        ;
+        al = (Alignment) res[0];
+        nf = (NewickFile) res[1];
+      }
+      else
+      {
+        al = null;
+        nf = null;
+        continue;
+      }
+      /*
+       * We can't map new alignment back with insertions from input's hidden
+       * regions until dataset mapping is sorted out... but basically it goes
+       * like this: 1. Merge each domain hit back onto the visible segments in
+       * the same way as a Jnet prediction is mapped back
+       * 
+       * Object[] newview = input.getUpdatedView(results, orders, getGapChar()); //
+       * trash references to original result data for (int j = 0; j <
+       * jobs.length; j++) { results[j] = null; orders[j] = null; } SequenceI[]
+       * alignment = (SequenceI[]) newview[0]; ColumnSelection columnselection =
+       * (ColumnSelection) newview[1]; Alignment al = new Alignment(alignment);
+       * 
+       * if (dataset != null) { al.setDataset(dataset); }
+       * 
+       * propagateDatasetMappings(al); }
+       */
+
+      AlignFrame af = new AlignFrame(al,// columnselection,
+              AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+      if (nf != null)
+      {
+        af.ShowNewickTree(nf, "Tree from " + this.alTitle);
+      }
+      // initialise with same renderer settings as in parent alignframe.
+      af.getFeatureRenderer().transferSettings(this.featureSettings);
+      Desktop.addInternalFrame(af, alTitle, AlignFrame.DEFAULT_WIDTH,
+              AlignFrame.DEFAULT_HEIGHT);
+    }
+  }
+
+  public boolean canMergeResults()
+  {
+    return false;
+  }
+}
diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index 0d93cb8..b20ebbb 100644
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.ws;
 
 import java.util.ArrayList;
@@ -19,7 +37,8 @@ import jalview.ws.seqfetcher.DbSourceProxy;
 /**
  * This is the the concrete implementation of the sequence retrieval interface
  * and abstract class in jalview.ws.seqfetcher. This implements the run-time
- * discovery of sequence database clients, and provides a hardwired main for testing all registered handlers. 
+ * discovery of sequence database clients, and provides a hardwired main for
+ * testing all registered handlers.
  * 
  */
 public class SequenceFetcher extends ASequenceFetcher
@@ -38,17 +57,22 @@ public class SequenceFetcher extends ASequenceFetcher
     addDBRefSourceImpl(jalview.ws.dbsources.UnprotName.class);
     addDBRefSourceImpl(jalview.ws.dbsources.Pdb.class);
     addDBRefSourceImpl(jalview.ws.dbsources.PfamFull.class);
-    addDBRefSourceImpl(jalview.ws.dbsources.PfamSeed.class); // ensures Seed alignment is 'default' for PFAM
+    addDBRefSourceImpl(jalview.ws.dbsources.PfamSeed.class); // ensures Seed
+                                                              // alignment is
+                                                              // 'default' for
+                                                              // PFAM
     registerDasSequenceSources();
   }
+
   /**
-   * return an ordered list of database sources suitable for using in a GUI element
+   * return an ordered list of database sources suitable for using in a GUI
+   * element
    */
-  public String[] getOrderedSupportedSources() {
+  public String[] getOrderedSupportedSources()
+  {
     String[] srcs = this.getSupportedDb();
-    ArrayList dassrc = new ArrayList(),
-      nondas=new ArrayList();
-    for (int i=0;i<srcs.length;i++)
+    ArrayList dassrc = new ArrayList(), nondas = new ArrayList();
+    for (int i = 0; i < srcs.length; i++)
     {
       String nm = getSourceProxy(srcs[i]).getDbName();
       if (getSourceProxy(srcs[i]) instanceof jalview.ws.dbsources.DasSequenceSource)
@@ -57,21 +81,25 @@ public class SequenceFetcher extends ASequenceFetcher
         {
           nm = nm.substring(4);
         }
-        dassrc.add(new String[] { srcs[i], nm.toUpperCase()} );
-      } else {
-        nondas.add(new String[] { srcs[i], nm.toUpperCase()} );
+        dassrc.add(new String[]
+        { srcs[i], nm.toUpperCase() });
+      }
+      else
+      {
+        nondas.add(new String[]
+        { srcs[i], nm.toUpperCase() });
       }
     }
     Object[] sorted = nondas.toArray();
     String[] tosort = new String[sorted.length];
     nondas.clear();
-    for (int j=0;j<sorted.length;j++)
+    for (int j = 0; j < sorted.length; j++)
     {
       tosort[j] = ((String[]) sorted[j])[1];
     }
     jalview.util.QuickSort.sort(tosort, sorted);
-    int i=0;
-    for (int j=sorted.length-1;j>=0; j--,i++)
+    int i = 0;
+    for (int j = sorted.length - 1; j >= 0; j--, i++)
     {
       srcs[i] = ((String[]) sorted[j])[0];
       sorted[j] = null;
@@ -80,20 +108,22 @@ public class SequenceFetcher extends ASequenceFetcher
     sorted = dassrc.toArray();
     tosort = new String[sorted.length];
     dassrc.clear();
-    for (int j=0;j<sorted.length;j++)
+    for (int j = 0; j < sorted.length; j++)
     {
       tosort[j] = ((String[]) sorted[j])[1];
     }
     jalview.util.QuickSort.sort(tosort, sorted);
-    for (int j=sorted.length-1;j>=0; j--,i++)
+    for (int j = sorted.length - 1; j >= 0; j--, i++)
     {
       srcs[i] = ((String[]) sorted[j])[0];
       sorted[j] = null;
     }
     return srcs;
   }
+
   /**
    * simple run method to test dbsources.
+   * 
    * @param argv
    */
   public static void main(String[] argv)
@@ -101,12 +131,12 @@ public class SequenceFetcher extends ASequenceFetcher
     AlignmentI ds = null;
     Vector noProds = new Vector();
     String usage = "SequenceFetcher.main [<DBNAME> <ACCNO>]\n"
-      +"With no arguments, all DbSources will be queried with their test Accession number.\n"
-      +"If given two arguments, SequenceFetcher will try to find the DbFetcher corresponding to <DBNAME> and retrieve <ACCNO> from it.";
+            + "With no arguments, all DbSources will be queried with their test Accession number.\n"
+            + "If given two arguments, SequenceFetcher will try to find the DbFetcher corresponding to <DBNAME> and retrieve <ACCNO> from it.";
     if (argv != null && argv.length > 0)
     {
       DbSourceProxy sp = new SequenceFetcher().getSourceProxy(argv[0]);
-      if (sp!=null)
+      if (sp != null)
       {
         AlignmentI al = null;
         try
@@ -115,40 +145,46 @@ public class SequenceFetcher extends ASequenceFetcher
         } catch (Exception e)
         {
           e.printStackTrace();
-          System.err.println("Error when retrieving "+argv[1]+" from "+argv[0]+"\nUsage: "+usage);
+          System.err.println("Error when retrieving " + argv[1] + " from "
+                  + argv[0] + "\nUsage: " + usage);
         }
         SequenceI[] prod = al.getSequencesArray();
-        if (al!=null)
+        if (al != null)
         {
           for (int p = 0; p < prod.length; p++)
           {
             System.out.println("Prod " + p + ": "
-                    + prod[p].getDisplayId(true) + " : "+prod[p].getDescription());
+                    + prod[p].getDisplayId(true) + " : "
+                    + prod[p].getDescription());
           }
         }
         return;
-      } else {
-        System.err.println("Can't resolve "+argv[0]+" as a database name. Allowed values are :\n"+new SequenceFetcher().getSupportedDb());
       }
-      System.out
-              .println(usage);
+      else
+      {
+        System.err.println("Can't resolve " + argv[0]
+                + " as a database name. Allowed values are :\n"
+                + new SequenceFetcher().getSupportedDb());
+      }
+      System.out.println(usage);
     }
     ASequenceFetcher sfetcher = new SequenceFetcher();
     String[] dbSources = sfetcher.getSupportedDb();
-    for (int dbsource=0; dbsource<dbSources.length;dbsource++)
+    for (int dbsource = 0; dbsource < dbSources.length; dbsource++)
     {
       String db = dbSources[dbsource];
       // skip me
       if (db.equals(DBRefSource.PDB))
         continue;
       DbSourceProxy sp = sfetcher.getSourceProxy(db);
-      System.out
-              .println("Source: "+sp.getDbName()+" (" + db + "): retrieving test:" + sp.getTestQuery());
+      System.out.println("Source: " + sp.getDbName() + " (" + db
+              + "): retrieving test:" + sp.getTestQuery());
       AlignmentI al = null;
       try
       {
         al = sp.getSequenceRecords(sp.getTestQuery());
-        if (al != null && al.getHeight() > 0 && sp.getDbSourceProperties()!=null)
+        if (al != null && al.getHeight() > 0
+                && sp.getDbSourceProperties() != null)
         {
           boolean dna = sp.getDbSourceProperties().containsKey(
                   DBRefSource.DNACODINGSEQDB)
@@ -248,7 +284,8 @@ public class SequenceFetcher extends ASequenceFetcher
         Alignment prodal = jalview.analysis.CrossRef.findXrefSequences(
                 seqs, dna, null, ds);
         System.out.println("Found "
-                + ((prodal == null) ? "no" : "" + prodal.getHeight()) + " products");
+                + ((prodal == null) ? "no" : "" + prodal.getHeight())
+                + " products");
         if (prodal != null)
         {
           SequenceI[] prod = prodal.getSequencesArray(); // note
@@ -262,7 +299,7 @@ public class SequenceFetcher extends ASequenceFetcher
           // mapping
           // (if
           // present)
-            for (int p = 0; p < prod.length; p++)
+          for (int p = 0; p < prod.length; p++)
           {
             System.out.println("Prod " + p + ": "
                     + prod[p].getDisplayId(true));
@@ -272,53 +309,67 @@ public class SequenceFetcher extends ASequenceFetcher
 
     }
   }
+
   /**
-   * query the currently defined DAS source registry for sequence sources and add a DasSequenceSource instance for each source to the SequenceFetcher source list.
+   * query the currently defined DAS source registry for sequence sources and
+   * add a DasSequenceSource instance for each source to the SequenceFetcher
+   * source list.
    */
-  public void registerDasSequenceSources() {
-    DasSource[] sources = jalview.ws.DasSequenceFeatureFetcher.getDASSources();
-    for (int s=0;s<sources.length; s++)
+  public void registerDasSequenceSources()
+  {
+    DasSource[] sources = jalview.ws.DasSequenceFeatureFetcher
+            .getDASSources();
+    for (int s = 0; s < sources.length; s++)
     {
-      Das1Source d1s=null;
+      Das1Source d1s = null;
       if (sources[s].hasCapability("sequence"))
       {
         if (sources[s] instanceof Das2Source)
         {
-          if (((Das2Source)sources[s]).hasDas1Capabilities()) {
-            try {
-              d1s = org.biojava.dasobert.das2.DasSourceConverter.toDas1Source((Das2Source) sources[s]);
+          if (((Das2Source) sources[s]).hasDas1Capabilities())
+          {
+            try
+            {
+              d1s = org.biojava.dasobert.das2.DasSourceConverter
+                      .toDas1Source((Das2Source) sources[s]);
             } catch (Exception e)
             {
-              System.err.println("Ignoring DAS2 sequence source "+sources[s].getNickname()+" - couldn't map to Das1Source.\n");
+              System.err.println("Ignoring DAS2 sequence source "
+                      + sources[s].getNickname()
+                      + " - couldn't map to Das1Source.\n");
               e.printStackTrace();
             }
           }
-        } else {
+        }
+        else
+        {
           if (sources[s] instanceof Das1Source)
-          { 
+          {
             d1s = (Das1Source) sources[s];
           }
         }
       }
-      if (d1s!=null)
+      if (d1s != null)
       {
         DasCoordinateSystem[] css = d1s.getCoordinateSystem();
-        for (int c=0;c<css.length;c++)
+        for (int c = 0; c < css.length; c++)
         {
-          try {
-            addDbRefSourceImpl(
-                    new jalview.ws.dbsources.DasSequenceSource("das:"+d1s.getNickname()+" ("+css[c].getName()+")",
-                            css[c].getName(),d1s, css[c]));
+          try
+          {
+            addDbRefSourceImpl(new jalview.ws.dbsources.DasSequenceSource(
+                    "das:" + d1s.getNickname() + " (" + css[c].getName()
+                            + ")", css[c].getName(), d1s, css[c]));
           } catch (Exception e)
           {
-            System.err.println("Ignoring sequence coord system "+c+" ("+
-                    css[c].getName()+") for source "+d1s.getNickname()
+            System.err.println("Ignoring sequence coord system " + c + " ("
+                    + css[c].getName() + ") for source "
+                    + d1s.getNickname()
                     + "- threw exception when constructing fetcher.\n");
             e.printStackTrace();
           }
         }
       }
-          
+
     }
   }
 
diff --git a/src/jalview/ws/WSClient.java b/src/jalview/ws/WSClient.java
index 91fd4b0..e883ea4 100755
--- a/src/jalview/ws/WSClient.java
+++ b/src/jalview/ws/WSClient.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -26,33 +26,41 @@ import jalview.gui.*;
 public abstract class WSClient
 {
   /**
-   * WSClient holds the basic attributes that are displayed to the user
-   * for all jalview web service clients
+   * WSClient holds the basic attributes that are displayed to the user for all
+   * jalview web service clients
    */
   /**
    * displayed name for this web service
    */
   protected String WebServiceName;
+
   /**
-   * specific job title (e.g. 'ClustalW Alignment of Selection from Aligment from Cut and Paste input')
+   * specific job title (e.g. 'ClustalW Alignment of Selection from Aligment
+   * from Cut and Paste input')
    */
   protected String WebServiceJobTitle;
+
   /**
-   * String giving additional information such as method citations for this service 
+   * String giving additional information such as method citations for this
+   * service
    */
   protected String WebServiceReference;
+
   /**
    * Service endpoint
    */
   protected String WsURL;
+
   /**
    * Web service information used to initialise the WSClient attributes
    */
   protected WebserviceInfo wsInfo;
+
   /**
-   * total number of jobs managed by this web service client instance. 
+   * total number of jobs managed by this web service client instance.
    */
   int jobsRunning = 0;
+
   /**
    * TODO: this is really service metadata, and should be moved elsewhere.
    * mappings between abstract interface names and menu entries
@@ -63,11 +71,14 @@ public abstract class WSClient
     ServiceActions.put("MsaWS", "Multiple Sequence Alignment");
     ServiceActions.put("SecStrPred", "Secondary Structure Prediction");
   };
+
   public WSClient()
   {
   }
+
   /**
    * initialise WSClient service information attributes from the service handle
+   * 
    * @param sh
    * @return the service instance information GUI for this client and job.
    */
@@ -75,23 +86,29 @@ public abstract class WSClient
   {
     return setWebService(sh, false);
   }
+
   /**
    * original service handle that this client was derived from
    */
-  ServiceHandle serviceHandle=null;
-    /**
-     * initialise WSClient service information attributes from the service handle
-     * @param sh
-     * @param headless true implies no GUI objects will be created.
-     * @return the service instance information GUI for this client and job.
-     */
+  ServiceHandle serviceHandle = null;
+
+  /**
+   * initialise WSClient service information attributes from the service handle
+   * 
+   * @param sh
+   * @param headless
+   *                true implies no GUI objects will be created.
+   * @return the service instance information GUI for this client and job.
+   */
   protected WebserviceInfo setWebService(ServiceHandle sh, boolean headless)
   {
     WebServiceName = sh.getName();
     if (ServiceActions.containsKey(sh.getAbstractName()))
     {
-      WebServiceJobTitle = sh.getName(); // TODO: control sh.Name specification properly
-      // add this for short names. +(String) ServiceActions.get(sh.getAbstractName());
+      WebServiceJobTitle = sh.getName(); // TODO: control sh.Name specification
+                                          // properly
+      // add this for short names. +(String)
+      // ServiceActions.get(sh.getAbstractName());
     }
     else
     {
@@ -103,31 +120,43 @@ public abstract class WSClient
     WebserviceInfo wsInfo = null;
     if (!headless)
     {
-      wsInfo = new WebserviceInfo(WebServiceJobTitle,
-                                               WebServiceReference);
+      wsInfo = new WebserviceInfo(WebServiceJobTitle, WebServiceReference);
     }
     return wsInfo;
   }
+
   /**
-   * convenience method to pass the serviceHandle reference that instantiated this 
-   * service on to the menu entry constructor
-   * @param wsmenu the menu to which any menu entries/sub menus are to be attached
-   * @param alignFrame the alignFrame instance that provides input data for the service
+   * convenience method to pass the serviceHandle reference that instantiated
+   * this service on to the menu entry constructor
+   * 
+   * @param wsmenu
+   *                the menu to which any menu entries/sub menus are to be
+   *                attached
+   * @param alignFrame
+   *                the alignFrame instance that provides input data for the
+   *                service
    */
   public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
   {
-    if (serviceHandle==null)
+    if (serviceHandle == null)
     {
-      throw new Error("IMPLEMENTATION ERROR: cannot attach WS Menu Entry without service handle reference!");
+      throw new Error(
+              "IMPLEMENTATION ERROR: cannot attach WS Menu Entry without service handle reference!");
     }
     attachWSMenuEntry(wsmenu, serviceHandle, alignFrame);
   }
+
   /**
-   * method implemented by each WSClient implementation that creates menu entries that enact their service
-   * using data from alignFrame.
-   * @param wsmenu where new menu entries (and submenus) are to be attached
-   * @param serviceHandle the serviceHandle document for the service that entries are created for
+   * method implemented by each WSClient implementation that creates menu
+   * entries that enact their service using data from alignFrame.
+   * 
+   * @param wsmenu
+   *                where new menu entries (and submenus) are to be attached
+   * @param serviceHandle
+   *                the serviceHandle document for the service that entries are
+   *                created for
    * @param alignFrame
    */
-  public abstract void attachWSMenuEntry(JMenu wsmenu, final ServiceHandle serviceHandle, final AlignFrame alignFrame);
+  public abstract void attachWSMenuEntry(JMenu wsmenu,
+          final ServiceHandle serviceHandle, final AlignFrame alignFrame);
 }
diff --git a/src/jalview/ws/WSClientI.java b/src/jalview/ws/WSClientI.java
index 92b7bb3..8e78ba5 100755
--- a/src/jalview/ws/WSClientI.java
+++ b/src/jalview/ws/WSClientI.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -22,23 +22,26 @@ public interface WSClientI
 {
   /**
    * basic interface supported by web service clients used by
-   * jalview.gui.WebserviceInfo to discover GUI properties and
-   * pass events back to the client. 
+   * jalview.gui.WebserviceInfo to discover GUI properties and pass events back
+   * to the client.
    * 
    */
   /**
-   * TODO: change this to be a WS Job Panel GUI 'attribute' 
+   * TODO: change this to be a WS Job Panel GUI 'attribute'
+   * 
    * @return boolean true if a job cancel button should be shown
    */
   boolean isCancellable();
 
   /**
-   * TODO: change this to be a WS Job Panel GUI 'attribute' 
+   * TODO: change this to be a WS Job Panel GUI 'attribute'
+   * 
    * @return boolean true if results can be merged into the source of input data
    */
   boolean canMergeResults();
+
   /**
-   * instruct client to cancel the job. This is also used by the GUI to  
+   * instruct client to cancel the job. This is also used by the GUI to
    */
   void cancelJob();
 }
diff --git a/src/jalview/ws/WSThread.java b/src/jalview/ws/WSThread.java
index a9e9b0b..72d1e4f 100644
--- a/src/jalview/ws/WSThread.java
+++ b/src/jalview/ws/WSThread.java
@@ -1,449 +1,480 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.ws;
-
-import javax.swing.*;
-
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import jalview.gui.FeatureRenderer.FeatureRendererSettings;
-
-public abstract class WSThread
-    extends Thread
-{
-  /**
-   * Generic properties for Web Service Client threads.
-   */
-  /**
-   * view that this job was associated with
-   */
-  AlignmentI currentView = null;
-  /**
-   * feature settings from view that job was associated with
-   */
-  FeatureRendererSettings featureSettings = null;
-  /**
-   * metadata about this web service
-   */
-  WebserviceInfo wsInfo = null;
-  /**
-   * original input data for this job
-   */
-  AlignmentView input = null;
-  /**
-   * dataset sequence relationships to be propagated onto new results
-   */
-  AlignedCodonFrame[] codonframe = null;
-  /**
-   * are there jobs still running in this thread.
-   */
-  boolean jobComplete = false;
-  
-  abstract class WSJob
-  {
-    /**
-     * Generic properties for an individual job within a Web Service Client thread
-     */
-    int jobnum = 0; // WebServiceInfo pane for this job
-    String jobId; // ws job ticket
-    /**
-     * has job been cancelled
-     */
-    boolean cancelled = false;
-    /**
-     * number of exceptions left before job dies
-     */
-    int allowedServerExceptions = 3;
-    /**
-     * has job been submitted
-     */
-    boolean submitted = false;
-    /**
-     * are all sub-jobs complete
-     */
-    boolean subjobComplete = false;
-    /**
-     *
-     * @return true if job has completed and valid results are available
-     */
-    abstract boolean hasResults();
-
-    /**
-     *
-     * @return boolean true if job can be submitted.
-     */
-    abstract boolean hasValidInput();
-
-    /**
-     * The last result object returned by the service.
-     */
-    vamsas.objects.simple.Result result;
-  }
-
-  class JobStateSummary
-  {
-    /**
-     * number of jobs running
-     */
-    int running = 0;
-    /**
-     * number of jobs queued
-     */
-    int queuing = 0;
-    /**
-     * number of jobs finished
-     */
-    int finished = 0;
-    /**
-     * number of jobs failed
-     */
-    int error = 0;
-    /**
-     * number of jobs stopped due to server error
-     */
-    int serror = 0;
-    /**
-     * number of jobs cancelled
-     */
-    int cancelled = 0;
-    /**
-     * number of jobs finished with results
-     */
-    int results = 0;
-    /**
-     * processes WSJob and updates job status counters and WebService status displays
-     * @param wsInfo
-     * @param OutputHeader
-     * @param j
-     */
-    void updateJobPanelState(WebserviceInfo wsInfo, String OutputHeader,
-                             WSJob j)
-    {
-      if (j.result != null)
-      {
-        String progheader = "";
-        // Parse state of job[j]
-        if (j.result.isRunning())
-        {
-          running++;
-          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_RUNNING);
-        }
-        else if (j.result.isQueued())
-        {
-          queuing++;
-          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_QUEUING);
-        }
-        else if (j.result.isFinished())
-        {
-          finished++;
-          j.subjobComplete = true;
-          if (j.hasResults())
-          {
-            results++;
-          }
-          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_OK);
-        }
-        else if (j.result.isFailed())
-        {
-          progheader += "Job failed.\n";
-          j.subjobComplete = true;
-          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
-          error++;
-        }
-        else if (j.result.isServerError())
-        {
-          serror++;
-          j.subjobComplete = true;
-          wsInfo.setStatus(j.jobnum,
-                           WebserviceInfo.STATE_STOPPED_SERVERERROR);
-        }
-        else if (j.result.isBroken() || j.result.isFailed())
-        {
-          error++;
-          j.subjobComplete = true;
-          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
-        }
-        // and pass on any sub-job messages to the user
-        wsInfo.setProgressText(j.jobnum, OutputHeader);
-        wsInfo.appendProgressText(j.jobnum, progheader);
-        if (j.result.getStatus() != null)
-        {
-          wsInfo.appendProgressText(j.jobnum, j.result.getStatus());
-        }
-      }
-      else
-      {
-        if (j.submitted && j.subjobComplete)
-        {
-          if (j.allowedServerExceptions == 0)
-          {
-            serror++;
-          }
-          else if (j.result == null)
-          {
-            error++;
-          }
-        }
-      }
-    }
-  }
-  /**
-   * one or more jobs being managed by this thread.
-   */
-  WSJob jobs[] = null;
-  /**
-   * full name of service
-   */
-  String WebServiceName = null;
-  String OutputHeader;
-  String WsUrl = null;
-  /**
-   * query web service for status of job.
-   * on return, job.result must not be null - if it is then it will be
-   * assumed that the job status query timed out and a server exception
-   * will be logged.
-   * @param job
-   * @throws Exception will be logged as a server exception for this job
-   */
-  abstract void pollJob(WSJob job)
-      throws Exception;
-
-  public void run()
-  {
-    JobStateSummary jstate = null;
-    if (jobs == null)
-    {
-      jobComplete = true;
-    }
-    while (!jobComplete)
-    {
-      jstate = new JobStateSummary();
-      for (int j = 0; j < jobs.length; j++)
-      {
-
-        if (!jobs[j].submitted && jobs[j].hasValidInput())
-        {
-          StartJob(jobs[j]);
-        }
-
-        if (jobs[j].submitted && !jobs[j].subjobComplete)
-        {
-          try
-          {
-            pollJob(jobs[j]);
-            if (jobs[j].result == null)
-            {
-              throw (new Exception(
-                  "Timed out when communicating with server\nTry again later.\n"));
-            }
-            jalview.bin.Cache.log.debug("Job " + j + " Result state " +
-                                        jobs[j].result.getState()
-                                        + "(ServerError=" +
-                                        jobs[j].result.isServerError() + ")");
-          }
-          catch (Exception ex)
-          {
-            // Deal with Transaction exceptions
-            wsInfo.appendProgressText(jobs[j].jobnum, "\n" + WebServiceName
-                                      + " Server exception!\n" + ex.getMessage());
-            Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum
-                           + ") Server exception: " + ex.getMessage());
-
-            if (jobs[j].allowedServerExceptions > 0)
-            {
-              jobs[j].allowedServerExceptions--;
-              Cache.log.debug("Sleeping after a server exception.");
-              try
-              {
-                Thread.sleep(5000);
-              }
-              catch (InterruptedException ex1)
-              {
-              }
-            }
-            else
-            {
-              Cache.log.warn("Dropping job " + j + " " + jobs[j].jobId);
-              jobs[j].subjobComplete = true;
-              wsInfo.setStatus(jobs[j].jobnum,
-                               WebserviceInfo.STATE_STOPPED_SERVERERROR);
-            }
-          }
-          catch (OutOfMemoryError er)
-          {
-            jobComplete = true;
-            jobs[j].subjobComplete = true;
-            jobs[j].result = null; // may contain out of date result object
-            wsInfo.setStatus(jobs[j].jobnum,
-                             WebserviceInfo.STATE_STOPPED_ERROR);
-            JOptionPane
-                .showInternalMessageDialog(
-                    Desktop.desktop,
-                    "Out of memory handling result for job !!"
-                    +
-                    "\nSee help files for increasing Java Virtual Machine memory.",
-                    "Out of memory", JOptionPane.WARNING_MESSAGE);
-            Cache.log.error("Out of memory when retrieving Job " + j + " id:" +
-                            WsUrl + "/" + jobs[j].jobId, er);
-            System.gc();
-          }
-        }
-        jstate.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
-      }
-      // Decide on overall state based on collected jobs[] states
-      if (jstate.running > 0)
-      {
-        wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
-      }
-      else if (jstate.queuing > 0)
-      {
-        wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
-      }
-      else
-      {
-        jobComplete = true;
-        if (jstate.finished > 0)
-        {
-          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
-        }
-        else if (jstate.error > 0)
-        {
-          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
-        }
-        else if (jstate.serror > 0)
-        {
-          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
-        }
-      }
-      if (!jobComplete)
-      {
-        try
-        {
-          Thread.sleep(5000);
-        }
-        catch (InterruptedException e)
-        {
-          Cache.log.debug("Interrupted sleep waiting for next job poll.", e);
-        }
-        // System.out.println("I'm alive "+alTitle);
-      }
-    }
-    if (jobComplete && jobs != null)
-    {
-      parseResult(); // tidy up and make results available to user
-    }
-    else
-    {
-      Cache.log.debug("WebServiceJob poll loop finished with no jobs created.");
-      wsInfo.setFinishedNoResults();
-    }
-  }
-
-  /**
-   * submit job to web service
-   * @param job
-   */
-  abstract void StartJob(WSJob job);
-
-  /**
-   * process the set of WSJob objects into a set of results, and tidy up.
-   */
-  abstract void parseResult();
-
-  /**
-   * helper function to conserve dataset references to sequence objects returned from web services
-   * 1. Propagates AlCodonFrame data from <code>codonframe</code> to <code>al</code>
-   * @param al
-   */
-  protected void propagateDatasetMappings(Alignment al)
-  {
-    if (codonframe!=null)
-    {
-      SequenceI[] alignment = al.getSequencesArray();
-      for (int sq = 0; sq<alignment.length; sq++)
-      {
-        for (int i=0; i<codonframe.length; i++)
-        {
-          if (codonframe[i]!=null &&
-                  codonframe[i].involvesSequence(alignment[sq]))
-          {
-            al.addCodonFrame(codonframe[i]);
-            codonframe[i] = null;
-            break;
-          }
-        }
-      }
-    }
-  }
-
-  /**
-   * 
-   * @param alignFrame reference for copying mappings across
-   * @param wsInfo gui attachment point
-   * @param input input data for the calculation
-   * @param webServiceName name of service
-   * @param wsUrl  url of the service being invoked
-   */
-  public WSThread(AlignFrame alignFrame, WebserviceInfo wsinfo,
-          AlignmentView input, String webServiceName,
-          String wsUrl)
-  {
-    this(alignFrame, wsinfo, input, wsUrl);
-    WebServiceName = webServiceName;
-  }
-  char defGapChar = '-';
-  /**
-   * 
-   * @return gap character to use for any alignment generation
-   */
-  public char getGapChar()
-  {
-    return defGapChar;
-  }
-
-  /**
-   * 
-   * @param alframe - reference for copying mappings and display styles across
-   * @param wsinfo2 - gui attachment point
-   * @param alview - input data for the calculation
-   * @param wsurl2 - url of the service being invoked
-   */
-  public WSThread(AlignFrame alframe, WebserviceInfo wsinfo2,
-          AlignmentView alview, String wsurl2)
-  {
-    super();
-    // this.alignFrame = alframe;
-    currentView = alframe.getCurrentView().getAlignment();
-    featureSettings = alframe.getFeatureRenderer().getSettings();
-    defGapChar = alframe.getViewport().getGapCharacter();
-    this.wsInfo = wsinfo2;
-    this.input = alview;
-    WsUrl = wsurl2;
-    if (alframe!=null)
-    {
-      AlignedCodonFrame[] cf = alframe.getViewport().getAlignment().getCodonFrames();
-      if (cf!=null)
-      {
-        codonframe = new AlignedCodonFrame[cf.length];
-        System.arraycopy(cf, 0, codonframe, 0, cf.length);
-      }
-    }
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.ws;
+
+import javax.swing.*;
+
+import jalview.bin.*;
+import jalview.datamodel.*;
+import jalview.gui.*;
+import jalview.gui.FeatureRenderer.FeatureRendererSettings;
+
+public abstract class WSThread extends Thread
+{
+  /**
+   * Generic properties for Web Service Client threads.
+   */
+  /**
+   * view that this job was associated with
+   */
+  AlignmentI currentView = null;
+
+  /**
+   * feature settings from view that job was associated with
+   */
+  FeatureRendererSettings featureSettings = null;
+
+  /**
+   * metadata about this web service
+   */
+  WebserviceInfo wsInfo = null;
+
+  /**
+   * original input data for this job
+   */
+  AlignmentView input = null;
+
+  /**
+   * dataset sequence relationships to be propagated onto new results
+   */
+  AlignedCodonFrame[] codonframe = null;
+
+  /**
+   * are there jobs still running in this thread.
+   */
+  boolean jobComplete = false;
+
+  abstract class WSJob
+  {
+    /**
+     * Generic properties for an individual job within a Web Service Client
+     * thread
+     */
+    int jobnum = 0; // WebServiceInfo pane for this job
+
+    String jobId; // ws job ticket
+
+    /**
+     * has job been cancelled
+     */
+    boolean cancelled = false;
+
+    /**
+     * number of exceptions left before job dies
+     */
+    int allowedServerExceptions = 3;
+
+    /**
+     * has job been submitted
+     */
+    boolean submitted = false;
+
+    /**
+     * are all sub-jobs complete
+     */
+    boolean subjobComplete = false;
+
+    /**
+     * 
+     * @return true if job has completed and valid results are available
+     */
+    abstract boolean hasResults();
+
+    /**
+     * 
+     * @return boolean true if job can be submitted.
+     */
+    abstract boolean hasValidInput();
+
+    /**
+     * The last result object returned by the service.
+     */
+    vamsas.objects.simple.Result result;
+  }
+
+  class JobStateSummary
+  {
+    /**
+     * number of jobs running
+     */
+    int running = 0;
+
+    /**
+     * number of jobs queued
+     */
+    int queuing = 0;
+
+    /**
+     * number of jobs finished
+     */
+    int finished = 0;
+
+    /**
+     * number of jobs failed
+     */
+    int error = 0;
+
+    /**
+     * number of jobs stopped due to server error
+     */
+    int serror = 0;
+
+    /**
+     * number of jobs cancelled
+     */
+    int cancelled = 0;
+
+    /**
+     * number of jobs finished with results
+     */
+    int results = 0;
+
+    /**
+     * processes WSJob and updates job status counters and WebService status
+     * displays
+     * 
+     * @param wsInfo
+     * @param OutputHeader
+     * @param j
+     */
+    void updateJobPanelState(WebserviceInfo wsInfo, String OutputHeader,
+            WSJob j)
+    {
+      if (j.result != null)
+      {
+        String progheader = "";
+        // Parse state of job[j]
+        if (j.result.isRunning())
+        {
+          running++;
+          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_RUNNING);
+        }
+        else if (j.result.isQueued())
+        {
+          queuing++;
+          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_QUEUING);
+        }
+        else if (j.result.isFinished())
+        {
+          finished++;
+          j.subjobComplete = true;
+          if (j.hasResults())
+          {
+            results++;
+          }
+          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_OK);
+        }
+        else if (j.result.isFailed())
+        {
+          progheader += "Job failed.\n";
+          j.subjobComplete = true;
+          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
+          error++;
+        }
+        else if (j.result.isServerError())
+        {
+          serror++;
+          j.subjobComplete = true;
+          wsInfo.setStatus(j.jobnum,
+                  WebserviceInfo.STATE_STOPPED_SERVERERROR);
+        }
+        else if (j.result.isBroken() || j.result.isFailed())
+        {
+          error++;
+          j.subjobComplete = true;
+          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
+        }
+        // and pass on any sub-job messages to the user
+        wsInfo.setProgressText(j.jobnum, OutputHeader);
+        wsInfo.appendProgressText(j.jobnum, progheader);
+        if (j.result.getStatus() != null)
+        {
+          wsInfo.appendProgressText(j.jobnum, j.result.getStatus());
+        }
+      }
+      else
+      {
+        if (j.submitted && j.subjobComplete)
+        {
+          if (j.allowedServerExceptions == 0)
+          {
+            serror++;
+          }
+          else if (j.result == null)
+          {
+            error++;
+          }
+        }
+      }
+    }
+  }
+
+  /**
+   * one or more jobs being managed by this thread.
+   */
+  WSJob jobs[] = null;
+
+  /**
+   * full name of service
+   */
+  String WebServiceName = null;
+
+  String OutputHeader;
+
+  String WsUrl = null;
+
+  /**
+   * query web service for status of job. on return, job.result must not be null -
+   * if it is then it will be assumed that the job status query timed out and a
+   * server exception will be logged.
+   * 
+   * @param job
+   * @throws Exception
+   *                 will be logged as a server exception for this job
+   */
+  abstract void pollJob(WSJob job) throws Exception;
+
+  public void run()
+  {
+    JobStateSummary jstate = null;
+    if (jobs == null)
+    {
+      jobComplete = true;
+    }
+    while (!jobComplete)
+    {
+      jstate = new JobStateSummary();
+      for (int j = 0; j < jobs.length; j++)
+      {
+
+        if (!jobs[j].submitted && jobs[j].hasValidInput())
+        {
+          StartJob(jobs[j]);
+        }
+
+        if (jobs[j].submitted && !jobs[j].subjobComplete)
+        {
+          try
+          {
+            pollJob(jobs[j]);
+            if (jobs[j].result == null)
+            {
+              throw (new Exception(
+                      "Timed out when communicating with server\nTry again later.\n"));
+            }
+            jalview.bin.Cache.log.debug("Job " + j + " Result state "
+                    + jobs[j].result.getState() + "(ServerError="
+                    + jobs[j].result.isServerError() + ")");
+          } catch (Exception ex)
+          {
+            // Deal with Transaction exceptions
+            wsInfo.appendProgressText(jobs[j].jobnum, "\n" + WebServiceName
+                    + " Server exception!\n" + ex.getMessage());
+            Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum
+                    + ") Server exception: " + ex.getMessage());
+
+            if (jobs[j].allowedServerExceptions > 0)
+            {
+              jobs[j].allowedServerExceptions--;
+              Cache.log.debug("Sleeping after a server exception.");
+              try
+              {
+                Thread.sleep(5000);
+              } catch (InterruptedException ex1)
+              {
+              }
+            }
+            else
+            {
+              Cache.log.warn("Dropping job " + j + " " + jobs[j].jobId);
+              jobs[j].subjobComplete = true;
+              wsInfo.setStatus(jobs[j].jobnum,
+                      WebserviceInfo.STATE_STOPPED_SERVERERROR);
+            }
+          } catch (OutOfMemoryError er)
+          {
+            jobComplete = true;
+            jobs[j].subjobComplete = true;
+            jobs[j].result = null; // may contain out of date result object
+            wsInfo.setStatus(jobs[j].jobnum,
+                    WebserviceInfo.STATE_STOPPED_ERROR);
+            Cache.log.error("Out of memory when retrieving Job " + j
+                    + " id:" + WsUrl + "/" + jobs[j].jobId, er);
+            new jalview.gui.OOMWarning("retrieving result for "
+                    + WebServiceName, er);
+            System.gc();
+          }
+        }
+        jstate.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
+      }
+      // Decide on overall state based on collected jobs[] states
+      if (jstate.running > 0)
+      {
+        wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
+      }
+      else if (jstate.queuing > 0)
+      {
+        wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
+      }
+      else
+      {
+        jobComplete = true;
+        if (jstate.finished > 0)
+        {
+          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
+        }
+        else if (jstate.error > 0)
+        {
+          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+        }
+        else if (jstate.serror > 0)
+        {
+          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+        }
+      }
+      if (!jobComplete)
+      {
+        try
+        {
+          Thread.sleep(5000);
+        } catch (InterruptedException e)
+        {
+          Cache.log
+                  .debug("Interrupted sleep waiting for next job poll.", e);
+        }
+        // System.out.println("I'm alive "+alTitle);
+      }
+    }
+    if (jobComplete && jobs != null)
+    {
+      parseResult(); // tidy up and make results available to user
+    }
+    else
+    {
+      Cache.log
+              .debug("WebServiceJob poll loop finished with no jobs created.");
+      wsInfo.setFinishedNoResults();
+    }
+  }
+
+  /**
+   * submit job to web service
+   * 
+   * @param job
+   */
+  abstract void StartJob(WSJob job);
+
+  /**
+   * process the set of WSJob objects into a set of results, and tidy up.
+   */
+  abstract void parseResult();
+
+  /**
+   * helper function to conserve dataset references to sequence objects returned
+   * from web services 1. Propagates AlCodonFrame data from
+   * <code>codonframe</code> to <code>al</code>
+   * 
+   * @param al
+   */
+  protected void propagateDatasetMappings(Alignment al)
+  {
+    if (codonframe != null)
+    {
+      SequenceI[] alignment = al.getSequencesArray();
+      for (int sq = 0; sq < alignment.length; sq++)
+      {
+        for (int i = 0; i < codonframe.length; i++)
+        {
+          if (codonframe[i] != null
+                  && codonframe[i].involvesSequence(alignment[sq]))
+          {
+            al.addCodonFrame(codonframe[i]);
+            codonframe[i] = null;
+            break;
+          }
+        }
+      }
+    }
+  }
+
+  /**
+   * 
+   * @param alignFrame
+   *                reference for copying mappings across
+   * @param wsInfo
+   *                gui attachment point
+   * @param input
+   *                input data for the calculation
+   * @param webServiceName
+   *                name of service
+   * @param wsUrl
+   *                url of the service being invoked
+   */
+  public WSThread(AlignFrame alignFrame, WebserviceInfo wsinfo,
+          AlignmentView input, String webServiceName, String wsUrl)
+  {
+    this(alignFrame, wsinfo, input, wsUrl);
+    WebServiceName = webServiceName;
+  }
+
+  char defGapChar = '-';
+
+  /**
+   * 
+   * @return gap character to use for any alignment generation
+   */
+  public char getGapChar()
+  {
+    return defGapChar;
+  }
+
+  /**
+   * 
+   * @param alframe -
+   *                reference for copying mappings and display styles across
+   * @param wsinfo2 -
+   *                gui attachment point
+   * @param alview -
+   *                input data for the calculation
+   * @param wsurl2 -
+   *                url of the service being invoked
+   */
+  public WSThread(AlignFrame alframe, WebserviceInfo wsinfo2,
+          AlignmentView alview, String wsurl2)
+  {
+    super();
+    // this.alignFrame = alframe;
+    currentView = alframe.getCurrentView().getAlignment();
+    featureSettings = alframe.getFeatureRenderer().getSettings();
+    defGapChar = alframe.getViewport().getGapCharacter();
+    this.wsInfo = wsinfo2;
+    this.input = alview;
+    WsUrl = wsurl2;
+    if (alframe != null)
+    {
+      AlignedCodonFrame[] cf = alframe.getViewport().getAlignment()
+              .getCodonFrames();
+      if (cf != null)
+      {
+        codonframe = new AlignedCodonFrame[cf.length];
+        System.arraycopy(cf, 0, codonframe, 0, cf.length);
+      }
+    }
+  }
+}
diff --git a/src/jalview/ws/dbsources/DasSequenceSource.java b/src/jalview/ws/dbsources/DasSequenceSource.java
index accb0b9..9283c66 100644
--- a/src/jalview/ws/dbsources/DasSequenceSource.java
+++ b/src/jalview/ws/dbsources/DasSequenceSource.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.ws.dbsources;
 
 import java.util.Hashtable;
@@ -17,38 +35,52 @@ import jalview.ws.seqfetcher.*;
 import jalview.datamodel.AlignmentI;
 
 /**
- * an instance of this class is created for each unique DAS Sequence source (ie one capable of handling the 'sequence' for a particular MapMaster)
- *  
+ * an instance of this class is created for each unique DAS Sequence source (ie
+ * one capable of handling the 'sequence' for a particular MapMaster)
+ * 
  * @author JimP
- *
+ * 
  */
 public class DasSequenceSource extends DbSourceProxyImpl implements
         DbSourceProxy
 {
-  protected Das1Source source=null;
-  protected String dbname="DASCS";
-  protected String dbrefname="das:source";
+  protected Das1Source source = null;
+
+  protected String dbname = "DASCS";
+
+  protected String dbrefname = "das:source";
+
   protected DasCoordinateSystem coordsys = null;
+
   /**
    * create a new DbSource proxy for a DAS 1 source
-   * @param dbnbame Human Readable Name to use when fetching from this source
-   * @param dbrefname DbRefName for DbRefs attached to sequences retrieved from this source
-   * @param source Das1Source
-   * @param coordsys specific coordinate system to use for this source
-   * @throws Exception if source is not capable of the 'sequence' command
+   * 
+   * @param dbnbame
+   *                Human Readable Name to use when fetching from this source
+   * @param dbrefname
+   *                DbRefName for DbRefs attached to sequences retrieved from
+   *                this source
+   * @param source
+   *                Das1Source
+   * @param coordsys
+   *                specific coordinate system to use for this source
+   * @throws Exception
+   *                 if source is not capable of the 'sequence' command
    */
-  public DasSequenceSource(String dbname, String dbrefname, Das1Source source,
-            DasCoordinateSystem coordsys) throws Exception
+  public DasSequenceSource(String dbname, String dbrefname,
+          Das1Source source, DasCoordinateSystem coordsys) throws Exception
   {
     if (!source.hasCapability("sequence"))
     {
-      throw new Exception("Source "+source.getNickname()+" does not support the sequence command.");
+      throw new Exception("Source " + source.getNickname()
+              + " does not support the sequence command.");
     }
     this.source = source;
     this.dbname = dbname;
-    this.dbrefname=dbrefname;
+    this.dbrefname = dbrefname;
     this.coordsys = coordsys;
   }
+
   public String getAccessionSeparator()
   {
     // cope with single sequences only
@@ -57,14 +89,14 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
 
   public Regex getAccessionValidator()
   {
-    /** ? **/
+    /** ? * */
     return Regex.perlCode("\\S+");
   }
 
   public String getDbName()
   {
     // TODO: map to
-     return dbname+" (DAS)";
+    return dbname + " (DAS)";
   }
 
   public String getDbSource()
@@ -79,20 +111,37 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
 
   public AlignmentI getSequenceRecords(String queries) throws Exception
   {
-    SequenceThread seqfetcher = new org.biojava.dasobert.das.SequenceThread(queries, source);
-    DasSequenceSourceListener ourlistener = new DasSequenceSourceListener(this, queries);
+    SequenceThread seqfetcher = new org.biojava.dasobert.das.SequenceThread(
+            queries, source);
+    DasSequenceSourceListener ourlistener = new DasSequenceSourceListener(
+            this, queries);
     seqfetcher.addSequenceListener(ourlistener);
     seqfetcher.start();
-    try { Thread.sleep(5); } catch (Exception e) {};
+    try
+    {
+      Thread.sleep(5);
+    } catch (Exception e)
+    {
+    }
+    ;
     while (ourlistener.isNotCalled() && seqfetcher.isAlive())
     {
-      try { Thread.sleep(5); } catch (Exception e) { };
+      try
+      {
+        Thread.sleep(5);
+      } catch (Exception e)
+      {
+      }
+      ;
     }
     if (ourlistener.isNotCalled() || ourlistener.hasNoSequences())
     {
-      System.err.println("Sequence Query to "+source.getNickname()+" with '"+queries+"' returned no sequences.");
+      System.err.println("Sequence Query to " + source.getNickname()
+              + " with '" + queries + "' returned no sequences.");
       return null;
-    } else {
+    }
+    else
+    {
       return ourlistener.getSequences();
     }
   }
@@ -101,13 +150,15 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
   {
     return coordsys.getTestCode();
   }
+
   public boolean isValidReference(String accession)
   {
     // TODO try to validate an accession against source
     // We don't really know how to do this without querying source
-    
+
     return true;
   }
+
   /**
    * @return the source
    */
@@ -115,6 +166,7 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
   {
     return source;
   }
+
   /**
    * @return the coordsys
    */
diff --git a/src/jalview/ws/dbsources/EbiFileRetrievedProxy.java b/src/jalview/ws/dbsources/EbiFileRetrievedProxy.java
index dc73e74..de2a034 100644
--- a/src/jalview/ws/dbsources/EbiFileRetrievedProxy.java
+++ b/src/jalview/ws/dbsources/EbiFileRetrievedProxy.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.ws.dbsources;
 
 import java.io.BufferedReader;
@@ -19,17 +37,18 @@ public abstract class EbiFileRetrievedProxy extends DbSourceProxyImpl
 
   public StringBuffer getRawRecords()
   {
-    if (file==null)
+    if (file == null)
       return null;
-    StringBuffer bf=null;
-    try {
+    StringBuffer bf = null;
+    try
+    {
       File f = new File(file);
       if (f.exists())
       {
         bf = new StringBuffer();
         BufferedReader breader = new BufferedReader(new FileReader(f));
-        String line=null;
-        while (breader.ready() && (line = breader.readLine())!=null)
+        String line = null;
+        while (breader.ready() && (line = breader.readLine()) != null)
         {
           bf.append(line);
         }
@@ -37,7 +56,7 @@ public abstract class EbiFileRetrievedProxy extends DbSourceProxyImpl
       }
     } catch (Exception e)
     {
-      System.err.println("Warning: problems reading temp file "+file);
+      System.err.println("Warning: problems reading temp file " + file);
       return null;
     }
     return bf;
diff --git a/src/jalview/ws/dbsources/EmblCdsSouce.java b/src/jalview/ws/dbsources/EmblCdsSouce.java
index 65b4e21..1ac5c76 100644
--- a/src/jalview/ws/dbsources/EmblCdsSouce.java
+++ b/src/jalview/ws/dbsources/EmblCdsSouce.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.ws.dbsources;
 
 import java.util.Hashtable;
@@ -11,14 +29,15 @@ import jalview.ws.seqfetcher.DbSourceProxy;
 public class EmblCdsSouce extends EmblXmlSource implements DbSourceProxy
 {
 
-  public EmblCdsSouce() {
+  public EmblCdsSouce()
+  {
     super();
-    addDbSourceProperty(DBRefSource.CODINGSEQDB); 
+    addDbSourceProperty(DBRefSource.CODINGSEQDB);
   }
-  
+
   public String getAccessionSeparator()
   {
-   return null;
+    return null;
   }
 
   public Regex getAccessionValidator()
@@ -34,12 +53,13 @@ public class EmblCdsSouce extends EmblXmlSource implements DbSourceProxy
 
   public String getDbVersion()
   {
-    return "0"; // TODO : this is dynamically set for a returned record - not tied to proxy
+    return "0"; // TODO : this is dynamically set for a returned record - not
+                // tied to proxy
   }
 
   public AlignmentI getSequenceRecords(String queries) throws Exception
-  { 
-    if (queries.indexOf(".")>-1)
+  {
+    if (queries.indexOf(".") > -1)
     {
       queries = queries.substring(0, queries.indexOf("."));
     }
@@ -51,6 +71,7 @@ public class EmblCdsSouce extends EmblXmlSource implements DbSourceProxy
     // TODO Auto-generated method stub
     return true;
   }
+
   /**
    * cDNA for LDHA_CHICK swissprot sequence
    */
@@ -58,6 +79,7 @@ public class EmblCdsSouce extends EmblXmlSource implements DbSourceProxy
   {
     return "CAA37824";
   }
+
   public String getDbName()
   {
     return "EMBL (CDS)";
diff --git a/src/jalview/ws/dbsources/EmblSource.java b/src/jalview/ws/dbsources/EmblSource.java
index 2858c23..5eac1c0 100644
--- a/src/jalview/ws/dbsources/EmblSource.java
+++ b/src/jalview/ws/dbsources/EmblSource.java
@@ -1,5 +1,20 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
  * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
 package jalview.ws.dbsources;
 
@@ -21,17 +36,20 @@ import jalview.ws.seqfetcher.DbSourceProxyImpl;
 
 /**
  * @author JimP
- *
+ * 
  */
 public class EmblSource extends EmblXmlSource implements DbSourceProxy
 {
 
-  public EmblSource() {
+  public EmblSource()
+  {
     addDbSourceProperty(DBRefSource.DNASEQDB);
     addDbSourceProperty(DBRefSource.CODINGSEQDB);
   }
-  
-  /* (non-Javadoc)
+
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
    */
   public String getAccessionSeparator()
@@ -40,7 +58,9 @@ public class EmblSource extends EmblXmlSource implements DbSourceProxy
     return null;
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#getAccessionValidator()
    */
   public Regex getAccessionValidator()
@@ -49,14 +69,19 @@ public class EmblSource extends EmblXmlSource implements DbSourceProxy
     return null;
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#getDbSource()
    */
   public String getDbSource()
   {
     return DBRefSource.EMBL;
   }
-  /* (non-Javadoc)
+
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#getDbVersion()
    */
   public String getDbVersion()
@@ -65,14 +90,19 @@ public class EmblSource extends EmblXmlSource implements DbSourceProxy
     return "0";
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
    */
   public AlignmentI getSequenceRecords(String queries) throws Exception
   {
     return getEmblSequenceRecords(DBRefSource.EMBL, queries);
   }
-  /* (non-Javadoc)
+
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
    */
   public boolean isValidReference(String accession)
@@ -82,7 +112,7 @@ public class EmblSource extends EmblXmlSource implements DbSourceProxy
   }
 
   /**
-   * return LHD_CHICK coding gene 
+   * return LHD_CHICK coding gene
    */
   public String getTestQuery()
   {
@@ -91,6 +121,6 @@ public class EmblSource extends EmblXmlSource implements DbSourceProxy
 
   public String getDbName()
   {
-    return "EMBL"; //getDbSource();
+    return "EMBL"; // getDbSource();
   }
 }
diff --git a/src/jalview/ws/dbsources/EmblXmlSource.java b/src/jalview/ws/dbsources/EmblXmlSource.java
index 68a2424..61f2d8b 100644
--- a/src/jalview/ws/dbsources/EmblXmlSource.java
+++ b/src/jalview/ws/dbsources/EmblXmlSource.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.ws.dbsources;
 
 import jalview.datamodel.Alignment;
@@ -22,89 +40,124 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
   {
     super();
   }
+
   /**
    * retrieve and parse an emblxml file
-   * @param emprefx either EMBL or EMBLCDS strings are allowed - anything else will not retrieve emblxml
+   * 
+   * @param emprefx
+   *                either EMBL or EMBLCDS strings are allowed - anything else
+   *                will not retrieve emblxml
    * @param query
    * @return
    * @throws Exception
    */
-  public AlignmentI getEmblSequenceRecords(String emprefx, String query) throws Exception
+  public AlignmentI getEmblSequenceRecords(String emprefx, String query)
+          throws Exception
   {
     startQuery();
     EBIFetchClient dbFetch = new EBIFetchClient();
-    File reply; 
-    try {
-      reply = dbFetch.fetchDataAsFile(
-            emprefx.toLowerCase() + ":" + query.trim(),
-          "emblxml",null);
-    }
-    catch (Exception e)
+    File reply;
+    try
+    {
+      reply = dbFetch.fetchDataAsFile(emprefx.toLowerCase() + ":"
+              + query.trim(), "emblxml", null);
+    } catch (Exception e)
     {
       stopQuery();
-      throw new Exception("EBI EMBL XML retrieval failed on "+emprefx.toLowerCase()+":"+query.trim(),e);
+      throw new Exception("EBI EMBL XML retrieval failed on "
+              + emprefx.toLowerCase() + ":" + query.trim(), e);
     }
     return getEmblSequenceRecords(emprefx, query, reply);
   }
+
   /**
    * parse an emblxml file stored locally
-   * @param emprefx either EMBL or EMBLCDS strings are allowed - anything else will not retrieve emblxml
+   * 
+   * @param emprefx
+   *                either EMBL or EMBLCDS strings are allowed - anything else
+   *                will not retrieve emblxml
    * @param query
-   * @param file the EMBL XML file containing the results of a query
+   * @param file
+   *                the EMBL XML file containing the results of a query
    * @return
    * @throws Exception
    */
-  public AlignmentI getEmblSequenceRecords(String emprefx, String query, File reply) throws Exception
+  public AlignmentI getEmblSequenceRecords(String emprefx, String query,
+          File reply) throws Exception
   {
     SequenceI seqs[] = null;
     StringBuffer result = new StringBuffer();
     if (reply != null && reply.exists())
+    {
+      efile = null;
+      file = reply.getAbsolutePath();
+      if (reply.length() > 25)
       {
-        efile=null;
-        file = reply.getAbsolutePath();
-        if (reply.length()>25)
-        {
-            efile = jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply);
-        } else {
-          result.append("# No EMBL record retrieved for "+emprefx.toLowerCase()+":"+query.trim());
-        }
+        efile = jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply);
       }
-      if (efile!=null) {
-        for (Iterator i=efile.getEntries().iterator(); i.hasNext(); ) {
-          EmblEntry entry = (EmblEntry) i.next();
-          SequenceI[] seqparts = entry.getSequences(false, true, emprefx); // TODO: use !fetchNa,!fetchPeptide here instead - see todo in emblEntry
-          if (seqparts!=null) {
-            SequenceI[] newseqs = null;
-            int si=0;
-            if (seqs==null) {
-              newseqs = new SequenceI[seqparts.length];
-            } else {
-              newseqs  = new SequenceI[seqs.length+seqparts.length];
-  
-              for (;si<seqs.length; si++) {
-                newseqs[si] = seqs[si];
-                seqs[si] = null;
-              }
-            }
-            for (int j=0;j<seqparts.length; si++, j++) {
-              newseqs[si] = seqparts[j].deriveSequence(); // place DBReferences on dataset and refer
+      else
+      {
+        result.append("# No EMBL record retrieved for "
+                + emprefx.toLowerCase() + ":" + query.trim());
+      }
+    }
+    if (efile != null)
+    {
+      for (Iterator i = efile.getEntries().iterator(); i.hasNext();)
+      {
+        EmblEntry entry = (EmblEntry) i.next();
+        SequenceI[] seqparts = entry.getSequences(false, true, emprefx); // TODO:
+                                                                          // use
+                                                                          // !fetchNa,!fetchPeptide
+                                                                          // here
+                                                                          // instead
+                                                                          // -
+                                                                          // see
+                                                                          // todo
+                                                                          // in
+                                                                          // emblEntry
+        if (seqparts != null)
+        {
+          SequenceI[] newseqs = null;
+          int si = 0;
+          if (seqs == null)
+          {
+            newseqs = new SequenceI[seqparts.length];
+          }
+          else
+          {
+            newseqs = new SequenceI[seqs.length + seqparts.length];
+
+            for (; si < seqs.length; si++)
+            {
+              newseqs[si] = seqs[si];
+              seqs[si] = null;
             }
-            seqs=newseqs;
-  
           }
+          for (int j = 0; j < seqparts.length; si++, j++)
+          {
+            newseqs[si] = seqparts[j].deriveSequence(); // place DBReferences on
+                                                        // dataset and refer
+          }
+          seqs = newseqs;
+
         }
-      } else {
-        result=null;
       }
-    AlignmentI al =null;
-    if (seqs!=null && seqs.length>0)
+    }
+    else
+    {
+      result = null;
+    }
+    AlignmentI al = null;
+    if (seqs != null && seqs.length > 0)
     {
       al = new Alignment(seqs);
-      result.append("# Successfully parsed the "+emprefx+" queries into an Alignment");
+      result.append("# Successfully parsed the " + emprefx
+              + " queries into an Alignment");
       results = result;
     }
     stopQuery();
     return al;
   }
 
-}
\ No newline at end of file
+}
diff --git a/src/jalview/ws/dbsources/GeneDbSource.java b/src/jalview/ws/dbsources/GeneDbSource.java
index 7cea532..ab779f6 100644
--- a/src/jalview/ws/dbsources/GeneDbSource.java
+++ b/src/jalview/ws/dbsources/GeneDbSource.java
@@ -1,5 +1,20 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
  * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
 package jalview.ws.dbsources;
 
@@ -20,6 +35,7 @@ import jalview.ws.seqfetcher.DbSourceProxy;
 import jalview.ws.seqfetcher.DbSourceProxyImpl;
 
 /**
+ * Test class for accessing GeneDB - not yet finished.
  * @author JimP
  *
  */
@@ -93,6 +109,6 @@ public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
 
   public String getDbName()
   {
-    return getDbSource();
+    return "GeneDB"; // getDbSource();
   }
 }
diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index e6d46da..754176c 100644
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -1,5 +1,20 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
  * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
 package jalview.ws.dbsources;
 
@@ -27,16 +42,19 @@ import jalview.ws.seqfetcher.DbSourceProxyImpl;
 
 /**
  * @author JimP
- *
+ * 
  */
 public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
 {
-  public Pdb() {
+  public Pdb()
+  {
     super();
     addDbSourceProperty(DBRefSource.PROTSEQDB);
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
    */
   public String getAccessionSeparator()
@@ -45,7 +63,9 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
     return null;
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#getAccessionValidator()
    */
   public Regex getAccessionValidator()
@@ -53,7 +73,9 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
     return new Regex("([1-9][0-9A-Za-z]{3}):?([ _A-Za-z0-9]?)");
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#getDbSource()
    */
   public String getDbSource()
@@ -61,14 +83,19 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
     return DBRefSource.PDB;
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#getDbVersion()
    */
   public String getDbVersion()
   {
     return "0";
   }
-  /* (non-Javadoc)
+
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
    */
   public AlignmentI getSequenceRecords(String queries) throws Exception
@@ -88,18 +115,17 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
     }
     if (queries.length() > 4 && chain == null)
     {
-      chain = queries.substring(4,5);
+      chain = queries.substring(4, 5);
       id = queries.substring(0, 4);
     }
     if (!isValidReference(id))
     {
-      System.err.println("Ignoring invalid pdb query: '"+id+"'");
+      System.err.println("Ignoring invalid pdb query: '" + id + "'");
       stopQuery();
       return null;
     }
     EBIFetchClient ebi = new EBIFetchClient();
-    file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw")
-            .getAbsolutePath();
+    file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw").getAbsolutePath();
     stopQuery();
     if (file == null)
     {
@@ -107,7 +133,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
     }
     try
     {
-      
+
       PDBfile pdbfile = new PDBfile(file,
               jalview.io.AppletFormatAdapter.FILE);
       for (int i = 0; i < pdbfile.chains.size(); i++)
@@ -117,27 +143,27 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
                         .toUpperCase().equals(chain))
         {
           PDBChain pdbchain = (PDBChain) pdbfile.chains.elementAt(i);
-          // Get the Chain's Sequence - who's dataset includes any special features added from the PDB file
+          // Get the Chain's Sequence - who's dataset includes any special
+          // features added from the PDB file
           SequenceI sq = pdbchain.sequence;
-          // Specially formatted name for the PDB chain sequences retrieved from the PDB
-          sq.setName(jalview.datamodel.DBRefSource.PDB+"|" + id + "|" + sq.getName());
+          // Specially formatted name for the PDB chain sequences retrieved from
+          // the PDB
+          sq.setName(jalview.datamodel.DBRefSource.PDB + "|" + id + "|"
+                  + sq.getName());
           // Might need to add more metadata to the PDBEntry object
           // like below
           /*
-           * PDBEntry entry = new PDBEntry();
-           // Construct the PDBEntry
-           entry.setId(id);
-           if (entry.getProperty() == null)
-           entry.setProperty(new Hashtable());
-           entry.getProperty().put("chains",
-           pdbchain.id
-           + "=" + sq.getStart()
-           + "-" + sq.getEnd());
-           sq.getDatasetSequence().addPDBId(entry);
+           * PDBEntry entry = new PDBEntry(); // Construct the PDBEntry
+           * entry.setId(id); if (entry.getProperty() == null)
+           * entry.setProperty(new Hashtable());
+           * entry.getProperty().put("chains", pdbchain.id + "=" + sq.getStart() +
+           * "-" + sq.getEnd()); sq.getDatasetSequence().addPDBId(entry);
            */
           // Add PDB DB Refs
-          // We make a DBRefEtntry because we have obtained the PDB file from a verifiable source
-          // JBPNote - PDB DBRefEntry should also carry the chain and mapping information
+          // We make a DBRefEtntry because we have obtained the PDB file from a
+          // verifiable source
+          // JBPNote - PDB DBRefEntry should also carry the chain and mapping
+          // information
           DBRefEntry dbentry = new DBRefEntry(getDbSource(),
                   getDbVersion(), id + pdbchain.id);
           sq.addDBRef(dbentry);
@@ -166,7 +192,9 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
     return new Alignment(results);
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
    */
   public boolean isValidReference(String accession)
diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java
index 4136e62..91ffbca 100644
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -1,5 +1,20 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
  * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
 package jalview.ws.dbsources;
 
@@ -14,23 +29,29 @@ import jalview.io.FastaFile;
 import jalview.io.StockholmFile;
 import jalview.ws.seqfetcher.DbSourceProxy;
 import jalview.ws.seqfetcher.DbSourceProxyImpl;
+
 /**
- * TODO: later PFAM is a complex datasource - it could return a tree in addition to an alignment
- * TODO: create interface to pass alignment properties and tree back to sequence fetcher
+ * TODO: later PFAM is a complex datasource - it could return a tree in addition
+ * to an alignment TODO: create interface to pass alignment properties and tree
+ * back to sequence fetcher
+ * 
  * @author JimP
- *
+ * 
  */
-abstract public class Pfam extends DbSourceProxyImpl implements DbSourceProxy
+abstract public class Pfam extends DbSourceProxyImpl implements
+        DbSourceProxy
 {
 
   public Pfam()
   {
     super();
-    // all extensions of this PFAM source base class are DOMAINDB sources 
+    // all extensions of this PFAM source base class are DOMAINDB sources
     addDbSourceProperty(jalview.datamodel.DBRefSource.DOMAINDB);
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
    */
   public String getAccessionSeparator()
@@ -39,7 +60,9 @@ abstract public class Pfam extends DbSourceProxyImpl implements DbSourceProxy
     return null;
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#getAccessionValidator()
    */
   public Regex getAccessionValidator()
@@ -48,27 +71,28 @@ abstract public class Pfam extends DbSourceProxyImpl implements DbSourceProxy
     return null;
   }
 
-  /* (non-Javadoc)
-   * @see jalview.ws.DbSourceProxy#getDbSource()
-  public String getDbSource()
-  {
-    ** this doesn't work - DbSource is key for the hash of DbSourceProxy instances - 1:many mapping for DbSource to proxy will be lost.
-    ** suggest : PFAM is an 'alignment' source - means proxy is higher level than a sequence source.
-    return jalview.datamodel.DBRefSource.PFAM;
-  }
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.DbSourceProxy#getDbSource() public String getDbSource() { *
+   *      this doesn't work - DbSource is key for the hash of DbSourceProxy
+   *      instances - 1:many mapping for DbSource to proxy will be lost. *
+   *      suggest : PFAM is an 'alignment' source - means proxy is higher level
+   *      than a sequence source. return jalview.datamodel.DBRefSource.PFAM; }
    */
 
-  
-  /* (non-Javadoc)
-   * @see jalview.ws.DbSourceProxy#getDbSourceProperties()
-  public Hashtable getDbSourceProperties()
-  {
-    
-    return null;
-  }
- */
-  
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.DbSourceProxy#getDbSourceProperties() public Hashtable
+   *      getDbSourceProperties() {
+   * 
+   * return null; }
+   */
+
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#getDbVersion()
    */
   public String getDbVersion()
@@ -76,46 +100,55 @@ abstract public class Pfam extends DbSourceProxyImpl implements DbSourceProxy
     // TODO Auto-generated method stub
     return null;
   }
+
   /**
    * 
    * @return PFAM URL stub for this DbSource
    */
   protected abstract String getPFAMURL();
-  /* (non-Javadoc)
+
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
    */
   public AlignmentI getSequenceRecords(String queries) throws Exception
   {
-    // TODO: this is not a perfect implementation. We need to be able to add individual references to each sequence in each family alignment that's retrieved. 
+    // TODO: this is not a perfect implementation. We need to be able to add
+    // individual references to each sequence in each family alignment that's
+    // retrieved.
     startQuery();
-    AlignmentI rcds = new jalview.io.FormatAdapter().readFile(getPFAMURL()+queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,"STH");
-    for (int s=0,sNum=rcds.getHeight(); s<sNum;s++)
+    AlignmentI rcds = new jalview.io.FormatAdapter().readFile(getPFAMURL()
+            + queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,
+            "STH");
+    for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
     {
-      rcds.getSequenceAt(s).addDBRef(new DBRefEntry(jalview.datamodel.DBRefSource.PFAM,
-              // getDbSource(), 
-              getDbVersion(), queries.trim().toUpperCase()));
+      rcds.getSequenceAt(s).addDBRef(
+              new DBRefEntry(jalview.datamodel.DBRefSource.PFAM,
+              // getDbSource(),
+                      getDbVersion(), queries.trim().toUpperCase()));
       if (!getDbSource().equals(jalview.datamodel.DBRefSource.PFAM))
-      {         // add the specific ref too
+      { // add the specific ref too
         rcds.getSequenceAt(s).addDBRef(
-                new DBRefEntry( getDbSource(), 
-                        getDbVersion(), queries.trim().toUpperCase()));
+                new DBRefEntry(getDbSource(), getDbVersion(), queries
+                        .trim().toUpperCase()));
       }
     }
     stopQuery();
     return rcds;
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
    */
   public boolean isValidReference(String accession)
   {
-    return accession.indexOf("PF")==0;
+    return accession.indexOf("PF") == 0;
   }
 
-
-  /*public String getDbName()
-  {
-    return "PFAM"; // getDbSource();
-  } */
+  /*
+   * public String getDbName() { return "PFAM"; // getDbSource(); }
+   */
 }
diff --git a/src/jalview/ws/dbsources/PfamFull.java b/src/jalview/ws/dbsources/PfamFull.java
index 3d3ab53..25e08fc 100644
--- a/src/jalview/ws/dbsources/PfamFull.java
+++ b/src/jalview/ws/dbsources/PfamFull.java
@@ -1,5 +1,20 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
  * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
 package jalview.ws.dbsources;
 
@@ -7,7 +22,7 @@ import jalview.ws.seqfetcher.DbSourceProxy;
 
 /**
  * flyweight class specifying retrieval of Full family alignments from PFAM
- *
+ * 
  */
 public class PfamFull extends Pfam implements DbSourceProxy
 {
@@ -16,7 +31,9 @@ public class PfamFull extends Pfam implements DbSourceProxy
     super();
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.dbsources.Pfam#getPFAMURL()
    */
   protected String getPFAMURL()
@@ -24,20 +41,24 @@ public class PfamFull extends Pfam implements DbSourceProxy
     return "http://pfam.sanger.ac.uk/family/alignment/download/format?alnType=full&format=stockholm&order=t&case=l&gaps=default&entry=";
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.seqfetcher.DbSourceProxy#getDbName()
    */
   public String getDbName()
   {
     return "PFAM (Full)";
   }
+
   public String getDbSource()
   {
     return getDbName(); // so we have unique DbSource string.
   }
+
   public String getTestQuery()
   {
-    return "PF00535"; // TODO: Pick a better full alignment to retrieve.
+    return "PF03760";
   }
 
 }
diff --git a/src/jalview/ws/dbsources/PfamSeed.java b/src/jalview/ws/dbsources/PfamSeed.java
index e0e2b4f..5cde798 100644
--- a/src/jalview/ws/dbsources/PfamSeed.java
+++ b/src/jalview/ws/dbsources/PfamSeed.java
@@ -1,5 +1,20 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
  * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
 package jalview.ws.dbsources;
 
@@ -7,8 +22,9 @@ import jalview.ws.seqfetcher.DbSourceProxy;
 
 /**
  * flyweight class specifying retrieval of Seed alignments from PFAM
+ * 
  * @author JimP
- *
+ * 
  */
 public class PfamSeed extends Pfam implements DbSourceProxy
 {
@@ -17,7 +33,9 @@ public class PfamSeed extends Pfam implements DbSourceProxy
     super();
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.dbsources.Pfam#getPFAMURL()
    */
   protected String getPFAMURL()
@@ -25,20 +43,24 @@ public class PfamSeed extends Pfam implements DbSourceProxy
     return "http://pfam.sanger.ac.uk/family/alignment/download/format?alnType=seed&format=stockholm&order=t&case=l&gaps=default&entry=";
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.seqfetcher.DbSourceProxy#getDbName()
    */
   public String getDbName()
   {
     return "PFAM (Seed)";
   }
+
   public String getDbSource()
   {
     return jalview.datamodel.DBRefSource.PFAM; // archetype source
   }
+
   public String getTestQuery()
   {
-    return "PF00535";
+    return "PF03760";
   }
 
 }
diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index f29a555..ab0b10c 100644
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -1,5 +1,20 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
  * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
 package jalview.ws.dbsources;
 
@@ -36,11 +51,12 @@ import jalview.ws.seqfetcher.DbSourceProxyImpl;
  */
 public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
 {
-  public Uniprot() {
+  public Uniprot()
+  {
     super();
     addDbSourceProperty(DBRefSource.SEQDB, DBRefSource.SEQDB);
     addDbSourceProperty(DBRefSource.PROTSEQDB);
-//    addDbSourceProperty(DBRefSource.MULTIACC, new Integer(50));
+    // addDbSourceProperty(DBRefSource.MULTIACC, new Integer(50));
   }
 
   /*
@@ -91,7 +107,8 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
     try
     {
       // 1. Load the mapping information from the file
-      org.exolab.castor.mapping.Mapping map = new org.exolab.castor.mapping.Mapping(uni.getClass().getClassLoader());
+      org.exolab.castor.mapping.Mapping map = new org.exolab.castor.mapping.Mapping(
+              uni.getClass().getClassLoader());
       java.net.URL url = getClass().getResource("/uniprot_mapping.xml");
       map.loadMapping(url);
 
@@ -101,8 +118,7 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
       unmar.setMapping(map);
 
       uni = (UniprotFile) unmar.unmarshal(new FileReader(file));
-    }
-    catch (Exception e)
+    } catch (Exception e)
     {
       System.out.println("Error getUniprotEntries() " + e);
     }
@@ -120,11 +136,12 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
     startQuery();
     try
     {
-      Alignment al=null;
+      Alignment al = null;
       ebi = new EBIFetchClient();
-      StringBuffer result=new StringBuffer();
+      StringBuffer result = new StringBuffer();
       // uniprotxml parameter required since december 2007
-      File file = ebi.fetchDataAsFile("uniprot:" + queries, "uniprotxml", null);
+      File file = ebi.fetchDataAsFile("uniprot:" + queries, "uniprotxml",
+              null);
       Vector entries = getUniprotEntries(file);
 
       if (entries != null)
@@ -149,12 +166,13 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
             name.append(en2.nextElement());
           }
 
-          if (entry.getProtein()!=null && entry.getProtein().getName()!=null)
+          if (entry.getProtein() != null
+                  && entry.getProtein().getName() != null)
           {
-              for (int nm=0,nmSize=entry.getProtein().getName().size(); nm<nmSize;nm++)
-              {
-                name.append(" " + entry.getProtein().getName().elementAt(nm));
-              }
+            for (int nm = 0, nmSize = entry.getProtein().getName().size(); nm < nmSize; nm++)
+            {
+              name.append(" " + entry.getProtein().getName().elementAt(nm));
+            }
           }
 
           result.append(name + "\n"
@@ -164,11 +182,13 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
 
         // Then read in the features and apply them to the dataset
         al = parseResult(result.toString());
-        if (al!=null)
+        if (al != null)
         {
           // Decorate the alignment with database entries.
           addUniprotXrefs(al, entries);
-        } else {
+        }
+        else
+        {
           results = result;
         }
       }
@@ -177,7 +197,7 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
     } catch (Exception e)
     {
       stopQuery();
-      throw(e);
+      throw (e);
     }
   }
 
@@ -185,9 +205,9 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
    * add an ordered set of UniprotEntry objects to an ordered set of seuqences.
    * 
    * @param al -
-   *          a sequence of n sequences
+   *                a sequence of n sequences
    * @param entries
-   *          a seuqence of n uniprot entries to be analysed.
+   *                a seuqence of n uniprot entries to be analysed.
    */
   public void addUniprotXrefs(Alignment al, Vector entries)
   {
@@ -203,17 +223,17 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
         DBRefEntry dbr = new DBRefEntry();
         dbr.setSource(pdb.getType());
         dbr.setAccessionId(pdb.getId());
-        dbr.setVersion(DBRefSource.UNIPROT+":"+getDbVersion());
+        dbr.setVersion(DBRefSource.UNIPROT + ":" + getDbVersion());
         dbxrefs.addElement(dbr);
         if (!pdb.getType().equals("PDB"))
         {
           continue;
         }
-        
+
         onlyPdbEntries.addElement(pdb);
       }
       SequenceI sq = al.getSequenceAt(i);
-      while (sq.getDatasetSequence()!=null)
+      while (sq.getDatasetSequence() != null)
       {
         sq = sq.getDatasetSequence();
       }
@@ -222,16 +242,15 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
       while (en2.hasMoreElements())
       {
         // we always add as uniprot if we retrieved from uniprot or uniprot name
-        sq.addDBRef(
-                new DBRefEntry(DBRefSource.UNIPROT, getDbVersion(), en2.nextElement()
-                        .toString()));
+        sq.addDBRef(new DBRefEntry(DBRefSource.UNIPROT, getDbVersion(), en2
+                .nextElement().toString()));
       }
       en2 = dbxrefs.elements();
       while (en2.hasMoreElements())
       {
-     // we always add as uniprot if we retrieved from uniprot or uniprot name
+        // we always add as uniprot if we retrieved from uniprot or uniprot name
         sq.addDBRef((DBRefEntry) en2.nextElement());
-                    
+
       }
       sq.setPDBId(onlyPdbEntries);
       if (entry.getFeature() != null)
@@ -256,6 +275,7 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
   {
     return true;
   }
+
   /**
    * return LDHA_CHICK uniprot entry
    */
@@ -263,6 +283,7 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
   {
     return "P00340";
   }
+
   public String getDbName()
   {
     return "Uniprot"; // getDbSource();
diff --git a/src/jalview/ws/dbsources/UnprotName.java b/src/jalview/ws/dbsources/UnprotName.java
index 4fbbe97..c827b03 100644
--- a/src/jalview/ws/dbsources/UnprotName.java
+++ b/src/jalview/ws/dbsources/UnprotName.java
@@ -1,19 +1,42 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.ws.dbsources;
 
 /**
- * Canonical Uniprot fetcher instance specifically retrieving UP_NAME references.
+ * Canonical Uniprot fetcher instance specifically retrieving UP_NAME
+ * references.
+ * 
  * @author JimP
- *
+ * 
  */
-public class UnprotName extends Uniprot implements jalview.ws.seqfetcher.DbSourceProxy
+public class UnprotName extends Uniprot implements
+        jalview.ws.seqfetcher.DbSourceProxy
 {
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.dbsources.Uniprot#getDbSource()
    */
   public String getDbSource()
   {
     return jalview.datamodel.DBRefSource.UP_NAME;
   }
-  
+
 }
diff --git a/src/jalview/ws/dbsources/das/DasSequenceSourceListener.java b/src/jalview/ws/dbsources/das/DasSequenceSourceListener.java
index fa961f0..e036404 100644
--- a/src/jalview/ws/dbsources/das/DasSequenceSourceListener.java
+++ b/src/jalview/ws/dbsources/das/DasSequenceSourceListener.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.ws.dbsources.das;
 
 import jalview.datamodel.AlignmentI;
@@ -11,25 +29,32 @@ import org.biojava.dasobert.eventmodel.SequenceEvent;
 import org.biojava.dasobert.eventmodel.SequenceListener;
 
 /**
- * Listen for sequence fetch events from a dasobert SequenceThread started with a 
- * query string and collect sequences returned from the DAS sequence source. 
+ * Listen for sequence fetch events from a dasobert SequenceThread started with
+ * a query string and collect sequences returned from the DAS sequence source.
+ * 
  * @author JimP
- *
+ * 
  */
 public class DasSequenceSourceListener implements SequenceListener
 {
-  
+
   String ourAccession = null;
-  DasSequenceSource oursource=null;
+
+  DasSequenceSource oursource = null;
+
   /**
    * 
-   * @param source the DAS Sequence DbProxy object containing database details for this source
-   * @param query the query string sent to the das source that we should be listening for.
+   * @param source
+   *                the DAS Sequence DbProxy object containing database details
+   *                for this source
+   * @param query
+   *                the query string sent to the das source that we should be
+   *                listening for.
    */
   public DasSequenceSourceListener(DasSequenceSource source, String query)
   {
-    oursource=source;
-    ourAccession=query;
+    oursource = source;
+    ourAccession = query;
   }
 
   public void clearSelection()
@@ -37,32 +62,39 @@ public class DasSequenceSourceListener implements SequenceListener
     // TODO Auto-generated method stub
 
   }
+
   java.util.Vector seqs = null;
+
   public void newSequence(SequenceEvent e)
   {
     if (!e.getAccessionCode().equals(ourAccession))
     {
-      System.err.println("Warning - received sequence event for strange accession code ("
-              +e.getAccessionCode()+") - we expected "+ourAccession);
-      
+      System.err
+              .println("Warning - received sequence event for strange accession code ("
+                      + e.getAccessionCode()
+                      + ") - we expected "
+                      + ourAccession);
+
       return;
     }
-    if (seqs==null)
+    if (seqs == null)
     {
-      if (e.getSequence().length()==0)
+      if (e.getSequence().length() == 0)
       {
         System.err.println("Empty sequence returned for accession code ("
-                +e.getAccessionCode()+") from "+oursource.getDbName());
-        called=true;
-        noSequences=true;
+                + e.getAccessionCode() + ") from " + oursource.getDbName());
+        called = true;
+        noSequences = true;
         return;
       }
       seqs = new java.util.Vector();
     }
     Sequence sq = new Sequence(e.getAccessionCode(), e.getSequence());
-    sq.addDBRef(new DBRefEntry(oursource.getDbSource(), oursource.getDbVersion()+":"+e.getVersion(), e.getAccessionCode()));
+    sq.addDBRef(new DBRefEntry(oursource.getDbSource(), oursource
+            .getDbVersion()
+            + ":" + e.getVersion(), e.getAccessionCode()));
     seqs.addElement(sq);
-    called=true;
+    called = true;
   }
 
   public void selectedSeqPosition(int position)
@@ -88,19 +120,25 @@ public class DasSequenceSourceListener implements SequenceListener
     // TODO Auto-generated method stub
 
   }
-  boolean noSequences=false;
+
+  boolean noSequences = false;
+
   public void noObjectFound(String accessionCode)
   {
     if (accessionCode.equals(ourAccession))
     {
-      noSequences=true;
+      noSequences = true;
       called = true;
     }
   }
-  public boolean hasNoSequences() {
+
+  public boolean hasNoSequences()
+  {
     return noSequences;
   }
-  boolean called=false;
+
+  boolean called = false;
+
   public boolean isNotCalled()
   {
     return !called;
@@ -108,10 +146,10 @@ public class DasSequenceSourceListener implements SequenceListener
 
   public AlignmentI getSequences()
   {
-    if (noSequences || seqs!=null && seqs.size()==0)
+    if (noSequences || seqs != null && seqs.size() == 0)
       return null;
     SequenceI[] sqs = new SequenceI[seqs.size()];
-    for (int i=0,iSize=seqs.size(); i<iSize;i++)
+    for (int i = 0, iSize = seqs.size(); i < iSize; i++)
     {
       sqs[i] = (SequenceI) seqs.elementAt(i);
     }
@@ -120,11 +158,9 @@ public class DasSequenceSourceListener implements SequenceListener
     {
       java.util.Vector src = new java.util.Vector();
       src.addElement(oursource.getSource());
-      new jalview.ws.DasSequenceFeatureFetcher(sqs, 
-              null,
-              src, false, false);
+      new jalview.ws.DasSequenceFeatureFetcher(sqs, null, src, false, false);
     }
-    
+
     return al;
   }
 
diff --git a/src/jalview/ws/ebi/EBIFetchClient.java b/src/jalview/ws/ebi/EBIFetchClient.java
index e9aff35..d5ab2e1 100644
--- a/src/jalview/ws/ebi/EBIFetchClient.java
+++ b/src/jalview/ws/ebi/EBIFetchClient.java
@@ -1,235 +1,240 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.ws.ebi;
-
-import java.io.*;
-import java.util.*;
-import javax.xml.namespace.*;
-import javax.xml.rpc.*;
-
-import org.apache.axis.client.Call;
-import org.apache.axis.client.Service;
-import org.apache.axis.encoding.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class EBIFetchClient
-{
-  Call call;
-  String format = "default";
-  String style = "raw";
-
-  /**
-   * Creates a new EBIFetchClient object.
-   */
-  public EBIFetchClient()
-  {
-    try
-    {
-      call = (Call)new Service().createCall();
-      call.setTargetEndpointAddress(new java.net.URL(
-          "http://www.ebi.ac.uk/ws/services/Dbfetch"));
-    }
-    catch (Exception ex)
-    {
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public String[] getSupportedDBs()
-  {
-    try
-    {
-      call.setOperationName(new QName("urn:Dbfetch", "getSupportedDBs"));
-      call.setReturnType(XMLType.SOAP_ARRAY);
-
-      return (String[]) call.invoke(new Object[]
-                                    {});
-    }
-    catch (Exception ex)
-    {
-      return null;
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public String[] getSupportedFormats()
-  {
-    try
-    {
-      call.setOperationName(new QName("urn:Dbfetch", "getSupportedFormats"));
-      call.setReturnType(XMLType.SOAP_ARRAY);
-
-      return (String[]) call.invoke(new Object[]
-                                    {});
-    }
-    catch (Exception ex)
-    {
-      return null;
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public String[] getSupportedStyles()
-  {
-    try
-    {
-      call.setOperationName(new QName("urn:Dbfetch", "getSupportedStyles"));
-      call.setReturnType(XMLType.SOAP_ARRAY);
-
-      return (String[]) call.invoke(new Object[]
-                                    {});
-    }
-    catch (Exception ex)
-    {
-      return null;
-    }
-  }
-
-
-  public File fetchDataAsFile(String ids, String f, String s)
-  {
-    String[] data = fetchData(ids, f, s);
-    File outFile = null;
-    try
-    {
-      outFile = File.createTempFile("jalview", ".xml");
-      outFile.deleteOnExit();
-      PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
-      int index = 0;
-      while (index < data.length)
-      {
-        out.println(data[index]);
-        index++;
-      }
-      out.close();
-    }
-    catch (Exception ex)
-    {}
-    return outFile;
-  }
-
-  /**
-   * Single DB multiple record retrieval
-   *
-   * @param ids db:query1;query2;query3
-   * @param f raw/xml
-   * @param s ?
-   *
-   * @return Raw string array result of query set
-   */
-  public String[] fetchData(String ids, String f, String s)
-  {
-    // Need to split
-    // ids of the form uniprot:25KD_SARPE;ADHR_DROPS;
-    StringTokenizer queries = new StringTokenizer(ids, ";");
-    String db = null;
-    StringBuffer querystring = null;
-    while (queries.hasMoreTokens())
-    {
-      String query = queries.nextToken();
-      int p;
-      if ( (p = query.indexOf(':')) > -1)
-      {
-        db = query.substring(0, p);
-        query = query.substring(p + 1);
-      }
-      if (querystring == null)
-      {
-        querystring = new StringBuffer(query);
-      }
-      else
-      {
-        querystring.append("," + query);
-      }
-    }
-    if (db == null)
-    {
-      System.err.println("Invalid Query string : '" + ids +
-                         "'\nShould be of form 'dbname:q1;q2;q3;q4'");
-    }
-    return fetchBatch(querystring.toString(), db, f, s);
-  }
-
-  public String[] fetchBatch(String ids, String db, String f, String s)
-  {
-    // max 50 ids can be added at one time
-    try
-    {
-      //call.setOperationName(new QName("urn:Dbfetch", "fetchData"));
-      call.setOperationName(new QName("urn:Dbfetch", "fetchBatch"));
-      call.addParameter("ids", XMLType.XSD_STRING, ParameterMode.IN);
-      call.addParameter("db", XMLType.XSD_STRING, ParameterMode.IN);
-      call.addParameter("format", XMLType.XSD_STRING, ParameterMode.IN);
-      call.addParameter("style", XMLType.XSD_STRING, ParameterMode.IN);
-      call.setReturnType(XMLType.SOAP_ARRAY);
-
-      if (f != null)
-      {
-        format = f;
-      }
-
-      if (s != null)
-      {
-        style = s;
-      }
-
-      try
-      {
-        return (String[]) call.invoke(new Object[]
-                                      {ids.toLowerCase(), db.toLowerCase(),
-                                      format, style});
-      }
-      catch (OutOfMemoryError er)
-      {
-        System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + db + ":\n" +
-                           ids);
-      }
-      return null;
-    }
-    catch (Exception ex)
-    {
-      if (ex.getMessage().startsWith(
-          "uk.ac.ebi.jdbfetch.exceptions.DbfNoEntryFoundException"))
-      {
-        return null;
-      }
-      System.err.println("Unexpected exception when retrieving from " + db +
-                         "\nQuery was : '" + ids + "'");
-      ex.printStackTrace(System.err);
-      return null;
-    }
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.ws.ebi;
+
+import java.io.*;
+import java.util.*;
+import javax.xml.namespace.*;
+import javax.xml.rpc.*;
+
+import org.apache.axis.client.Call;
+import org.apache.axis.client.Service;
+import org.apache.axis.encoding.*;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class EBIFetchClient
+{
+  Call call;
+
+  String format = "default";
+
+  String style = "raw";
+
+  /**
+   * Creates a new EBIFetchClient object.
+   */
+  public EBIFetchClient()
+  {
+    try
+    {
+      call = (Call) new Service().createCall();
+      call.setTargetEndpointAddress(new java.net.URL(
+              "http://www.ebi.ac.uk/ws/services/Dbfetch"));
+    } catch (Exception ex)
+    {
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public String[] getSupportedDBs()
+  {
+    try
+    {
+      call.setOperationName(new QName("urn:Dbfetch", "getSupportedDBs"));
+      call.setReturnType(XMLType.SOAP_ARRAY);
+
+      return (String[]) call.invoke(new Object[]
+      {});
+    } catch (Exception ex)
+    {
+      return null;
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public String[] getSupportedFormats()
+  {
+    try
+    {
+      call
+              .setOperationName(new QName("urn:Dbfetch",
+                      "getSupportedFormats"));
+      call.setReturnType(XMLType.SOAP_ARRAY);
+
+      return (String[]) call.invoke(new Object[]
+      {});
+    } catch (Exception ex)
+    {
+      return null;
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public String[] getSupportedStyles()
+  {
+    try
+    {
+      call.setOperationName(new QName("urn:Dbfetch", "getSupportedStyles"));
+      call.setReturnType(XMLType.SOAP_ARRAY);
+
+      return (String[]) call.invoke(new Object[]
+      {});
+    } catch (Exception ex)
+    {
+      return null;
+    }
+  }
+
+  public File fetchDataAsFile(String ids, String f, String s)
+          throws OutOfMemoryError
+  {
+    String[] data = fetchData(ids, f, s);
+    // TODO: after JV 2.4 - test data==null and pass error(s) back up if
+    // possible (OutOfMemoryErrors are usual problem)
+    File outFile = null;
+    try
+    {
+      outFile = File.createTempFile("jalview", ".xml");
+      outFile.deleteOnExit();
+      PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
+      int index = 0;
+      while (index < data.length)
+      {
+        out.println(data[index]);
+        index++;
+      }
+      out.close();
+    } catch (Exception ex)
+    {
+    }
+    return outFile;
+  }
+
+  /**
+   * Single DB multiple record retrieval
+   * 
+   * @param ids
+   *                db:query1;query2;query3
+   * @param f
+   *                raw/xml
+   * @param s ?
+   * 
+   * @return Raw string array result of query set
+   */
+  public String[] fetchData(String ids, String f, String s)
+          throws OutOfMemoryError
+  {
+    // Need to split
+    // ids of the form uniprot:25KD_SARPE;ADHR_DROPS;
+    StringTokenizer queries = new StringTokenizer(ids, ";");
+    String db = null;
+    StringBuffer querystring = null;
+    while (queries.hasMoreTokens())
+    {
+      String query = queries.nextToken();
+      int p;
+      if ((p = query.indexOf(':')) > -1)
+      {
+        db = query.substring(0, p);
+        query = query.substring(p + 1);
+      }
+      if (querystring == null)
+      {
+        querystring = new StringBuffer(query);
+      }
+      else
+      {
+        querystring.append("," + query);
+      }
+    }
+    if (db == null)
+    {
+      System.err.println("Invalid Query string : '" + ids
+              + "'\nShould be of form 'dbname:q1;q2;q3;q4'");
+    }
+    return fetchBatch(querystring.toString(), db, f, s);
+  }
+
+  public String[] fetchBatch(String ids, String db, String f, String s)
+          throws OutOfMemoryError
+  {
+    // max 50 ids can be added at one time
+    try
+    {
+      // call.setOperationName(new QName("urn:Dbfetch", "fetchData"));
+      call.setOperationName(new QName("urn:Dbfetch", "fetchBatch"));
+      call.addParameter("ids", XMLType.XSD_STRING, ParameterMode.IN);
+      call.addParameter("db", XMLType.XSD_STRING, ParameterMode.IN);
+      call.addParameter("format", XMLType.XSD_STRING, ParameterMode.IN);
+      call.addParameter("style", XMLType.XSD_STRING, ParameterMode.IN);
+      call.setReturnType(XMLType.SOAP_ARRAY);
+
+      if (f != null)
+      {
+        format = f;
+      }
+
+      if (s != null)
+      {
+        style = s;
+      }
+
+      try
+      {
+        return (String[]) call.invoke(new Object[]
+        { ids.toLowerCase(), db.toLowerCase(), format, style });
+      } catch (OutOfMemoryError er)
+      {
+
+        System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + db
+                + ":\n" + ids);
+        throw er;
+      }
+      // return null;
+    } catch (Exception ex)
+    {
+      if (ex.getMessage().startsWith(
+              "uk.ac.ebi.jdbfetch.exceptions.DbfNoEntryFoundException"))
+      {
+        return null;
+      }
+      System.err.println("Unexpected exception when retrieving from " + db
+              + "\nQuery was : '" + ids + "'");
+      ex.printStackTrace(System.err);
+      return null;
+    }
+  }
+}
diff --git a/src/jalview/ws/seqfetcher/ASequenceFetcher.java b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
index 0785ea2..8a8cf44 100644
--- a/src/jalview/ws/seqfetcher/ASequenceFetcher.java
+++ b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.ws.seqfetcher;
 
 import jalview.datamodel.AlignmentI;
@@ -86,10 +104,10 @@ public class ASequenceFetcher
                   "Don't know how to fetch from this database :" + db);
         DbSourceProxy fetcher = getSourceProxy(db);
         boolean doMultiple = fetcher.getAccessionSeparator() != null; // No
-                                                                      // separator
-                                                                      // - no
-                                                                      // Multiple
-                                                                      // Queries
+        // separator
+        // - no
+        // Multiple
+        // Queries
         Enumeration qs = query.elements();
         while (qs.hasMoreElements())
         {
@@ -98,20 +116,22 @@ public class ASequenceFetcher
           {
             qsb.append((String) qs.nextElement());
             if (qs.hasMoreElements() && doMultiple) // and not reached limit for
-                                                    // multiple queries at one
-                                                    // time for this source
+            // multiple queries at one
+            // time for this source
             {
               qsb.append(fetcher.getAccessionSeparator());
             }
           } while (doMultiple && qs.hasMoreElements());
-          
-          AlignmentI seqset=null;
-          try {
+
+          AlignmentI seqset = null;
+          try
+          {
             // create a fetcher and go to it
             seqset = fetcher.getSequenceRecords(qsb.toString());
           } catch (Exception ex)
           {
-            System.err.println("Failed to retrieve the following from "+db);
+            System.err.println("Failed to retrieve the following from "
+                    + db);
             System.err.println(qsb);
             ex.printStackTrace(System.err);
           }
@@ -176,7 +196,7 @@ public class ASequenceFetcher
     {
       ret = new SequenceI[rseqs.size()];
       Enumeration sqs = rseqs.elements();
-      int si=0;
+      int si = 0;
       while (sqs.hasMoreElements())
       {
         SequenceI s = (SequenceI) sqs.nextElement();
@@ -191,8 +211,8 @@ public class ASequenceFetcher
    * Retrieve an instance of the proxy for the given source
    * 
    * @param db
-   *          database source string TODO: add version string/wildcard for
-   *          retrieval of specific DB source/version combinations.
+   *                database source string TODO: add version string/wildcard for
+   *                retrieval of specific DB source/version combinations.
    * @return an instance of DbSourceProxy for that db.
    */
   public DbSourceProxy getSourceProxy(String db)
@@ -215,11 +235,11 @@ public class ASequenceFetcher
   protected void addDBRefSourceImpl(Class dbSourceProxy)
           throws java.lang.IllegalArgumentException
   {
-    DbSourceProxy proxy = null; 
+    DbSourceProxy proxy = null;
     try
     {
-      Object proxyObj = dbSourceProxy.getConstructor(
-              null).newInstance(null);
+      Object proxyObj = dbSourceProxy.getConstructor(null)
+              .newInstance(null);
       if (!DbSourceProxy.class.isInstance(proxyObj))
       {
         throw new IllegalArgumentException(
@@ -227,20 +247,21 @@ public class ASequenceFetcher
                         + " does not implement the jalview.ws.seqfetcher.DbSourceProxy");
       }
       proxy = (DbSourceProxy) proxyObj;
-    } 
-    catch (IllegalArgumentException e)
+    } catch (IllegalArgumentException e)
     {
       throw e;
-    }
-    catch (Exception e)
+    } catch (Exception e)
     {
       // Serious problems if this happens.
       throw new Error("DBRefSource Implementation Exception", e);
     }
     addDbRefSourceImpl(proxy);
   }
+
   /**
-   * add the properly initialised DbSourceProxy object 'proxy' to the list of sequence fetchers
+   * add the properly initialised DbSourceProxy object 'proxy' to the list of
+   * sequence fetchers
+   * 
    * @param proxy
    */
   protected void addDbRefSourceImpl(DbSourceProxy proxy)
@@ -257,6 +278,7 @@ public class ASequenceFetcher
 
   /**
    * test if the database handler for dbName contains the given dbProperty
+   * 
    * @param dbName
    * @param dbProperty
    * @return true if proxy has the given property
@@ -265,9 +287,9 @@ public class ASequenceFetcher
   {
     // TODO: decide if invalidDbName exception is thrown here.
     DbSourceProxy proxy = getSourceProxy(dbName);
-    if (proxy!=null)
+    if (proxy != null)
     {
-      if (proxy.getDbSourceProperties()!=null)
+      if (proxy.getDbSourceProperties() != null)
       {
         return proxy.getDbSourceProperties().containsKey(dbProperty);
       }
@@ -275,4 +297,4 @@ public class ASequenceFetcher
     return false;
   }
 
-}
\ No newline at end of file
+}
diff --git a/src/jalview/ws/seqfetcher/DbSourceProxy.java b/src/jalview/ws/seqfetcher/DbSourceProxy.java
index f0e81fa..25fbcbf 100644
--- a/src/jalview/ws/seqfetcher/DbSourceProxy.java
+++ b/src/jalview/ws/seqfetcher/DbSourceProxy.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.ws.seqfetcher;
 
 import jalview.datamodel.AlignmentI;
@@ -5,12 +23,16 @@ import jalview.datamodel.AlignmentI;
 import java.util.Hashtable;
 
 import com.stevesoft.pat.Regex;
+
 /**
- * generic Reference Retrieval interface for a particular database source/version as cited in DBRefEntry.
- * TODO: add/define property to describe max number of queries that this source can cope with at once.
- * TODO: add/define mechanism for retrieval of Trees and distance matrices from a database (unify with io)
+ * generic Reference Retrieval interface for a particular database
+ * source/version as cited in DBRefEntry. TODO: add/define property to describe
+ * max number of queries that this source can cope with at once. TODO:
+ * add/define mechanism for retrieval of Trees and distance matrices from a
+ * database (unify with io)
+ * 
  * @author JimP
- *
+ * 
  */
 public interface DbSourceProxy
 {
@@ -19,61 +41,83 @@ public interface DbSourceProxy
    * @return source string constant used for this DB source
    */
   public String getDbSource();
+
   /**
-   * Short meaningful name for this data source for
-   * display in menus or selection boxes. 
+   * Short meaningful name for this data source for display in menus or
+   * selection boxes.
+   * 
    * @return String
    */
   public String getDbName();
+
   /**
    * 
    * @return version string for this database.
    */
   public String getDbVersion();
+
   /**
-   * Separator between individual accession queries for a database that allows multiple IDs
-   * to be fetched in a single query. Null implies that only a single ID can be fetched at a time.
-   * @return string for separating concatenated queries (as individually validated by the accession validator)
+   * Separator between individual accession queries for a database that allows
+   * multiple IDs to be fetched in a single query. Null implies that only a
+   * single ID can be fetched at a time.
+   * 
+   * @return string for separating concatenated queries (as individually
+   *         validated by the accession validator)
    */
   public String getAccessionSeparator();
+
   /**
-   * Regular expression for checking form of query string understood by this source.
+   * Regular expression for checking form of query string understood by this
+   * source.
+   * 
    * @return null or a validation regex
    */
   public Regex getAccessionValidator();
+
   /**
-   * DbSource properties hash - define the capabilities of this source
-   * Property hash methods defined in DbSourceProxyImpl.
-   * See constants in jalview.datamodel.DBRefSource for definition of properties.
-   * @return 
+   * DbSource properties hash - define the capabilities of this source Property
+   * hash methods defined in DbSourceProxyImpl. See constants in
+   * jalview.datamodel.DBRefSource for definition of properties.
+   * 
+   * @return
    */
   public Hashtable getDbSourceProperties();
+
   /**
    * 
-   * @return a test/example query that can be used to validate retrieval and parsing mechanisms
+   * @return a test/example query that can be used to validate retrieval and
+   *         parsing mechanisms
    */
   public String getTestQuery();
+
   /**
    * optionally implemented
+   * 
    * @param accession
    * @return
    */
   public boolean isValidReference(String accession);
+
   /**
-   * make one or more queries to the database
-   * and attempt to parse the response into an alignment
+   * make one or more queries to the database and attempt to parse the response
+   * into an alignment
+   * 
    * @param queries
    * @return null if queries were successful but result was not parsable
-   * @throws Exception TODO
+   * @throws Exception
+   *                 TODO
    */
   public AlignmentI getSequenceRecords(String queries) throws Exception;
+
   /**
    * 
    * @return true if a query is currently being made
    */
   public boolean queryInProgress();
+
   /**
    * get the raw reponse from the last set of queries
+   * 
    * @return one or more string buffers for each individual query
    */
   public StringBuffer getRawRecords();
diff --git a/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java b/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
index 21272be..10aaf7d 100644
--- a/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
+++ b/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.ws.seqfetcher;
 
 import jalview.datamodel.Alignment;
@@ -11,7 +29,7 @@ import java.util.Hashtable;
  * common methods for implementations of the DbSourceProxy interface.
  * 
  * @author JimP
- *
+ * 
  */
 public abstract class DbSourceProxyImpl implements DbSourceProxy
 {
@@ -19,14 +37,19 @@ public abstract class DbSourceProxyImpl implements DbSourceProxy
   {
     // default constructor - do nothing probably.
   }
-  private Hashtable props=null;
-  /* (non-Javadoc)
+
+  private Hashtable props = null;
+
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#getDbSourceProperties()
    */
   public Hashtable getDbSourceProperties()
   {
     return props;
   }
+
   protected void addDbSourceProperty(Object propname)
   {
     addDbSourceProperty(propname, propname);
@@ -34,14 +57,17 @@ public abstract class DbSourceProxyImpl implements DbSourceProxy
 
   protected void addDbSourceProperty(Object propname, Object propvalue)
   {
-    if (props==null)
+    if (props == null)
     {
       props = new Hashtable();
     }
     props.put(propname, propvalue);
   }
-  boolean queryInProgress=false;
+
+  boolean queryInProgress = false;
+
   protected StringBuffer results = null;
+
   /*
    * (non-Javadoc)
    * 
@@ -52,45 +78,51 @@ public abstract class DbSourceProxyImpl implements DbSourceProxy
     return results;
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#queryInProgress()
    */
   public boolean queryInProgress()
   {
     return queryInProgress;
   }
+
   /**
    * call to set the queryInProgress flag
-   *
+   * 
    */
   protected void startQuery()
   {
-    queryInProgress=true;
+    queryInProgress = true;
   }
+
   /**
    * call to clear the queryInProgress flag
-   *
+   * 
    */
   protected void stopQuery()
   {
-    queryInProgress=false;
+    queryInProgress = false;
   }
 
   /**
    * create an alignment from raw text file...
+   * 
    * @param result
    * @return null or a valid alignment
    * @throws Exception
    */
-  protected Alignment parseResult(String result) throws Exception {
+  protected Alignment parseResult(String result) throws Exception
+  {
     Alignment sequences = null;
     String format = new IdentifyFile().Identify(result, "Paste");
     if (FormatAdapter.isValidFormat(format))
     {
       sequences = new FormatAdapter().readFile(result.toString(), "Paste",
-            format);
+              format);
     }
     return sequences;
   }
-  
+
 }
diff --git a/src/org/biojava/dasobert/das/DAS_FeatureRetrieve.java b/src/org/biojava/dasobert/das/DAS_FeatureRetrieve.java
index 21ccee1..7d35dea 100755
--- a/src/org/biojava/dasobert/das/DAS_FeatureRetrieve.java
+++ b/src/org/biojava/dasobert/das/DAS_FeatureRetrieve.java
@@ -34,23 +34,27 @@ import org.xml.sax.*;
 
 /**
  * A class to perform a DAS features request
- *
- * @author Andreas Prlic
- * Adapted for jalview use.
- * @author Andrew Waterhouse 
- * Updated to Das 1.53e feature spec.
+ * 
+ * @author Andreas Prlic Adapted for jalview use.
+ * @author Andrew Waterhouse Updated to Das 1.53e feature spec.
  * @author Jim Procter
  */
 public class DAS_FeatureRetrieve
 {
   String version;
+
   List features;
+
   Logger logger;
+
   int comeBackLater;
+
   URL url;
+
   /**
-   * @param url the URL the features should be downloaded from
-   *
+   * @param url
+   *                the URL the features should be downloaded from
+   * 
    */
   public DAS_FeatureRetrieve(URL url)
   {
@@ -63,10 +67,11 @@ public class DAS_FeatureRetrieve
     reload();
   }
 
-  /** contact the DAS-feature server again. Usually
-   * it is not necessary to call this again, because the constructor already does, but
-   * if comeBackLater > -1 this should be called again.
-   *
+  /**
+   * contact the DAS-feature server again. Usually it is not necessary to call
+   * this again, because the constructor already does, but if comeBackLater > -1
+   * this should be called again.
+   * 
    */
   public void reload()
   {
@@ -78,8 +83,7 @@ public class DAS_FeatureRetrieve
       try
       {
         dasInStream = open(url);
-      }
-      catch (Exception e)
+      } catch (Exception e)
       {
         comeBackLater = -1;
         System.out.println("NO RESPONSE FROM " + url);
@@ -87,8 +91,7 @@ public class DAS_FeatureRetrieve
         return;
       }
 
-      SAXParserFactory spfactory =
-          SAXParserFactory.newInstance();
+      SAXParserFactory spfactory = SAXParserFactory.newInstance();
 
       spfactory.setValidating(false);
 
@@ -96,10 +99,8 @@ public class DAS_FeatureRetrieve
 
       try
       {
-        saxParser =
-            spfactory.newSAXParser();
-      }
-      catch (ParserConfigurationException e)
+        saxParser = spfactory.newSAXParser();
+      } catch (ParserConfigurationException e)
       {
         e.printStackTrace();
       }
@@ -117,27 +118,28 @@ public class DAS_FeatureRetrieve
 
       XMLReader xmlreader = saxParser.getXMLReader();
 
-      //XMLReader xmlreader = XMLReaderFactory.createXMLReader();
+      // XMLReader xmlreader = XMLReaderFactory.createXMLReader();
       try
       {
         xmlreader.setFeature("http://xml.org/sax/features/validation",
-                             validation);
-      }
-      catch (SAXException e)
+                validation);
+      } catch (SAXException e)
       {
         logger.log(Level.FINE, "Cannot set validation " + validation);
       }
 
       try
       {
-        xmlreader.setFeature(
-            "http://apache.org/xml/features/nonvalidating/load-external-dtd",
-            validation);
-      }
-      catch (SAXNotRecognizedException e)
+        xmlreader
+                .setFeature(
+                        "http://apache.org/xml/features/nonvalidating/load-external-dtd",
+                        validation);
+      } catch (SAXNotRecognizedException e)
       {
         e.printStackTrace();
-        logger.log(Level.FINE, "Cannot set load-external-dtd " + validation);
+        logger
+                .log(Level.FINE, "Cannot set load-external-dtd "
+                        + validation);
 
       }
 
@@ -152,30 +154,30 @@ public class DAS_FeatureRetrieve
       {
         xmlreader.parse(insource);
         features = cont_handle.get_features();
-                version  = cont_handle.getVersion();
-                
+        version = cont_handle.getVersion();
+
         comeBackLater = cont_handle.getComBackLater();
-      }
-      catch (Exception e)
+      } catch (Exception e)
       {
-        System.out.println("Error parsing response from: " + url + "\n" + e);
+        System.out
+                .println("Error parsing response from: " + url + "\n" + e);
         logger.log(Level.FINE, "error while parsing response from " + url);
         comeBackLater = -1;
         features = new ArrayList();
       }
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       ex.printStackTrace();
       comeBackLater = -1;
     }
   }
 
-  /** open HttpURLConnection. Recommended way to open
-   * HttpURLConnections, since this take care of setting timeouts
-   * properly for java 1.4 and 1.5*/
+  /**
+   * open HttpURLConnection. Recommended way to open HttpURLConnections, since
+   * this take care of setting timeouts properly for java 1.4 and 1.5
+   */
   public static HttpURLConnection openHttpURLConnection(URL url)
-      throws IOException, ConnectException
+          throws IOException, ConnectException
   {
     HttpURLConnection huc = null;
     huc = (HttpURLConnection) url.openConnection();
@@ -185,18 +187,20 @@ public class DAS_FeatureRetrieve
     String os_arch = java.lang.System.getProperty("os.arch");
     String VERSION = "1.0";
 
-    String userAgent = "Jalview " + VERSION + "(" + os_name + "; " + os_arch +
-        " ; " + os_version + ")";
-    //e.g. "Mozilla/5.0 (Windows; U; Win98; en-US; rv:1.7.2) Gecko/20040803"
+    String userAgent = "Jalview " + VERSION + "(" + os_name + "; "
+            + os_arch + " ; " + os_version + ")";
+    // e.g. "Mozilla/5.0 (Windows; U; Win98; en-US; rv:1.7.2) Gecko/20040803"
     huc.addRequestProperty("User-Agent", userAgent);
-    //logger.finest("opening "+url);
-
+    // logger.finest("opening "+url);
 
     int timeout = 10000;
-    System.setProperty("sun.net.client.defaultConnectTimeout", timeout + "");
+    System
+            .setProperty("sun.net.client.defaultConnectTimeout", timeout
+                    + "");
     System.setProperty("sun.net.client.defaultReadTimeout", timeout + "");
 
-    // use reflection to determine if get and set timeout methods for urlconnection are available
+    // use reflection to determine if get and set timeout methods for
+    // urlconnection are available
     // seems java 1.5 does not watch the System properties any longer...
     // and java 1.4 did not provide these...
     // for 1.4 see setSystemProperties
@@ -204,33 +208,31 @@ public class DAS_FeatureRetrieve
     try
     {
       // try to use reflection to set timeout property
-      Class urlconnectionClass = Class.forName("java.net.HttpURLConnection");
+      Class urlconnectionClass = Class
+              .forName("java.net.HttpURLConnection");
 
       Method setconnecttimeout = urlconnectionClass.getMethod(
-          "setConnectTimeout", new Class[]
-          {int.class}
-          );
+              "setConnectTimeout", new Class[]
+              { int.class });
       setconnecttimeout.invoke(huc, new Object[]
-                               {new Integer(timeout)});
+      { new Integer(timeout) });
 
       Method setreadtimeout = urlconnectionClass.getMethod(
-          "setReadTimeout", new Class[]
-          {int.class}
-          );
+              "setReadTimeout", new Class[]
+              { int.class });
       setreadtimeout.invoke(huc, new Object[]
-                            {new Integer(timeout)});
-      //System.out.println("successfully set java 1.5 timeout");
-    }
-    catch (Exception e)
+      { new Integer(timeout) });
+      // System.out.println("successfully set java 1.5 timeout");
+    } catch (Exception e)
     {
-      //e.printStackTrace();
+      // e.printStackTrace();
       // most likely it was a NoSuchMEthodException and we are running java 1.4.
     }
     return huc;
   }
 
-  private InputStream open(URL url)
-      throws java.io.IOException, java.net.ConnectException
+  private InputStream open(URL url) throws java.io.IOException,
+          java.net.ConnectException
   {
     InputStream inStream = null;
 
@@ -242,32 +244,37 @@ public class DAS_FeatureRetrieve
 
   }
 
-  /** returns a List of Features
-   * @return a List of Maps containing the features*/
+  /**
+   * returns a List of Features
+   * 
+   * @return a List of Maps containing the features
+   */
   public List get_features()
   {
 
     return features;
-    }
-    
-    
-    /** Get the version string of the reference object.
-     * If it does not match the version string that is obtained from the 
-     * reference server there is a version problem!
-     *  
-     * @return version string. (e.g. a MD5 digest of the reference sequence)
-     */
-    public String getVersion() {
-		return version;
-	}
-
-
-	public void setVersion(String version) {
-		this.version = version;
   }
 
-  /** returns the comeBackLater value - if a server returned suchh -
-   *
+  /**
+   * Get the version string of the reference object. If it does not match the
+   * version string that is obtained from the reference server there is a
+   * version problem!
+   * 
+   * @return version string. (e.g. a MD5 digest of the reference sequence)
+   */
+  public String getVersion()
+  {
+    return version;
+  }
+
+  public void setVersion(String version)
+  {
+    this.version = version;
+  }
+
+  /**
+   * returns the comeBackLater value - if a server returned suchh -
+   * 
    * @return comeBackLater in seconds, or -1 if not provided by server
    */
   public int getComeBackLater()
diff --git a/src/org/biojava/dasobert/das/DAS_Feature_Handler.java b/src/org/biojava/dasobert/das/DAS_Feature_Handler.java
index eed54e8..b6badc7 100755
--- a/src/org/biojava/dasobert/das/DAS_Feature_Handler.java
+++ b/src/org/biojava/dasobert/das/DAS_Feature_Handler.java
@@ -30,83 +30,94 @@ import org.xml.sax.helpers.*;
 
 /**
  * a class to parse the response of a DAS - Feature request
- * @author Andreas Prlic
- * Adapted for jalview use.
- * @author Andrew Waterhouse 
- * Updated to Das 1.53e feature spec.
+ * 
+ * @author Andreas Prlic Adapted for jalview use.
+ * @author Andrew Waterhouse Updated to Das 1.53e feature spec.
  * @author Jim Procter
-
+ * 
  */
-public class DAS_Feature_Handler
-    extends DefaultHandler
+public class DAS_Feature_Handler extends DefaultHandler
 {
 
   /**
-   *
+   * 
    */
   List features;
+
   boolean first_flag;
+
   HashMap feature;
+
   String featurefield;
+
   StringBuffer characterdata;
+
   String dasCommand;
 
   int comeBackLater;
 
   int maxFeatures;
 
-	String segmentId ;
-	String version;
-	String type_id;
-	String type_category;
-	
-	
-	public DAS_Feature_Handler() {
+  String segmentId;
+
+  String version;
+
+  String type_id;
+
+  String type_category;
+
+  public DAS_Feature_Handler()
+  {
     super();
 
     features = new ArrayList();
     first_flag = true;
     featurefield = "";
-		characterdata = new StringBuffer();
+    characterdata = new StringBuffer();
     dasCommand = "";
     comeBackLater = -1;
     maxFeatures = -1;
-		segmentId = "";
-		version   = "";
-		type_id = "";
-		type_category="";
-	}
-
-	
-	
-	/** get the id information specified int the SEGMENT field of the DAS response
-	 * 
-	 * @return the segmentId or an emtpy string if not available
-	 */
-	public String getSegmentId() {
-		return segmentId;
-	}
-
-	/** get the version informationspecified in the SEGMENT field of the DAS response
-	 * 
-	 * @return the version information of an empty string if not available 
-	 */
-	public String getVersion() {
-		return version;
+    segmentId = "";
+    version = "";
+    type_id = "";
+    type_category = "";
+  }
+
+  /**
+   * get the id information specified int the SEGMENT field of the DAS response
+   * 
+   * @return the segmentId or an emtpy string if not available
+   */
+  public String getSegmentId()
+  {
+    return segmentId;
   }
-	
-	public boolean isMD5Checksum(){
 
-		if ((version != null) && (version.length() == 32))
-			return true;
-		return false;
-	}
+  /**
+   * get the version informationspecified in the SEGMENT field of the DAS
+   * response
+   * 
+   * @return the version information of an empty string if not available
+   */
+  public String getVersion()
+  {
+    return version;
+  }
+
+  public boolean isMD5Checksum()
+  {
 
+    if ((version != null) && (version.length() == 32))
+      return true;
+    return false;
+  }
 
-  /** specifies a maximum number of features to be downloaded. if a
-    server returns more, they will be ignored.  default is to load
-    all features
-       @param max the maximium number of features to be downloaded
+  /**
+   * specifies a maximum number of features to be downloaded. if a server
+   * returns more, they will be ignored. default is to load all features
+   * 
+   * @param max
+   *                the maximium number of features to be downloaded
    */
 
   public void setMaxFeatures(int max)
@@ -142,67 +153,74 @@ public class DAS_Feature_Handler
   void start_feature(String uri, String name, String qName, Attributes atts)
   {
 
-		if (( maxFeatures > 0 ) && ( features.size() > maxFeatures ) ) {
-			characterdata = new StringBuffer();
+    if ((maxFeatures > 0) && (features.size() > maxFeatures))
+    {
+      characterdata = new StringBuffer();
       return;
     }
     feature = new HashMap();
     String id = atts.getValue("id");
     feature.put("id", id);
     feature.put("dassource", dasCommand);
-		characterdata = new StringBuffer();
+    characterdata = new StringBuffer();
   }
 
   void add_featuredata(String uri, String name, String qName)
   {
-    //System.out.println("featurefield "+featurefield+ " data "+characterdata);
+    // System.out.println("featurefield "+featurefield+ " data "+characterdata);
     // NOTE can have multiple lines ..
 
-    if ( (maxFeatures > 0) && (features.size() > maxFeatures))
+    if ((maxFeatures > 0) && (features.size() > maxFeatures))
     {
       return;
     }
 
     String data = (String) feature.get(featurefield);
-		String featureText = characterdata.toString();
-		if (data != null){
-			featureText = data + " " + featureText;
+    String featureText = characterdata.toString();
+    if (data != null)
+    {
+      featureText = data + " " + featureText;
     }
 
-		if ( qName.equals("TYPE")){
-			if ( featureText.length() < 1)
-				featureText = type_id;
-		
-			feature.put("TYPE_ID",type_id);
-			feature.put("TYPE_CATEGORY", type_category);
-			type_id = "";
-			type_category="";
-		}
-		
-		
-		feature.put(featurefield,featureText);
+    if (qName.equals("TYPE"))
+    {
+      if (featureText.length() < 1)
+        featureText = type_id;
+
+      feature.put("TYPE_ID", type_id);
+      feature.put("TYPE_CATEGORY", type_category);
+      type_id = "";
+      type_category = "";
+    }
+
+    feature.put(featurefield, featureText);
     featurefield = "";
-		characterdata = new StringBuffer();
+    characterdata = new StringBuffer();
   }
 
-  private void addLink(String uri, String name, String qName, Attributes atts)
+  private void addLink(String uri, String name, String qName,
+          Attributes atts)
   {
     String href = atts.getValue("href");
     feature.put("LINK", href);
-		characterdata= new StringBuffer();
+    characterdata = new StringBuffer();
     featurefield = "LINK-TEXT";
 
   }
 
-	private void addGroup(String uri, String name, String qName, Attributes atts) {
-		String id = atts.getValue("id");
-		feature.put("GROUP",id);
-		characterdata= new StringBuffer();
-		featurefield = "GROUP";
-	}
-	
-	public void startElement (String uri, String name, String qName, Attributes atts){
-    //System.out.println("new element "+qName);
+  private void addGroup(String uri, String name, String qName,
+          Attributes atts)
+  {
+    String id = atts.getValue("id");
+    feature.put("GROUP", id);
+    characterdata = new StringBuffer();
+    featurefield = "GROUP";
+  }
+
+  public void startElement(String uri, String name, String qName,
+          Attributes atts)
+  {
+    // System.out.println("new element "+qName);
 
     if (qName.equals("FEATURE"))
     {
@@ -211,32 +229,34 @@ public class DAS_Feature_Handler
     else if (qName.equals("LINK"))
     {
       addLink(uri, name, qName, atts);
-		 } else if ( qName.equals("GROUP"))
-			{ addGroup(uri,name,qName, atts); }
-    else if (qName.equals("METHOD") ||
-             qName.equals("TYPE") ||
-             qName.equals("START") ||
-             qName.equals("END") ||
-             qName.equals("NOTE") ||
-				qName.equals("SCORE") ||
-				qName.equals("ORIENTATION") 				
-		){
+    }
+    else if (qName.equals("GROUP"))
+    {
+      addGroup(uri, name, qName, atts);
+    }
+    else if (qName.equals("METHOD") || qName.equals("TYPE")
+            || qName.equals("START") || qName.equals("END")
+            || qName.equals("NOTE") || qName.equals("SCORE")
+            || qName.equals("ORIENTATION"))
+    {
       characterdata = new StringBuffer();
       featurefield = qName;
-		} else if (qName.equals("SEGMENT")){
-			String id = atts.getValue("id");
-			if (id != null)
-				segmentId = id;
-	String v = atts.getValue("version");
-			if ( v != null)
-				version = v;
-			
-			
-		}
-		if ( qName.equals("TYPE")){
-			type_id      = atts.getValue("id");
-			type_category= atts.getValue("category");
-		}
+    }
+    else if (qName.equals("SEGMENT"))
+    {
+      String id = atts.getValue("id");
+      if (id != null)
+        segmentId = id;
+      String v = atts.getValue("version");
+      if (v != null)
+        version = v;
+
+    }
+    if (qName.equals("TYPE"))
+    {
+      type_id = atts.getValue("id");
+      type_category = atts.getValue("category");
+    }
 
   }
 
@@ -251,16 +271,12 @@ public class DAS_Feature_Handler
   public void endElement(String uri, String name, String qName)
   {
 
-    if (qName.equals("METHOD") ||
-        qName.equals("TYPE") ||
-        qName.equals("START") ||
-        qName.equals("END") ||
-        qName.equals("NOTE") ||
-        qName.equals("LINK") ||
-				qName.equals("SCORE") ||
-				qName.equals("ORIENTATION") ||
-				qName.equals("GROUP")
-		) {
+    if (qName.equals("METHOD") || qName.equals("TYPE")
+            || qName.equals("START") || qName.equals("END")
+            || qName.equals("NOTE") || qName.equals("LINK")
+            || qName.equals("SCORE") || qName.equals("ORIENTATION")
+            || qName.equals("GROUP"))
+    {
       add_featuredata(uri, name, qName);
     }
     else if (qName.equals("FEATURE"))
@@ -281,16 +297,18 @@ public class DAS_Feature_Handler
     }
   }
 
-	public void characters (char ch[], int start, int length){
-		if ( maxFeatures > 0)
-			if ( features.size() > maxFeatures )
-				return;
+  public void characters(char ch[], int start, int length)
+  {
+    if (maxFeatures > 0)
+      if (features.size() > maxFeatures)
+        return;
 
-		for (int i = start; i < start + length; i++) {
+    for (int i = start; i < start + length; i++)
+    {
 
-			characterdata.append(ch[i]);
-		}
+      characterdata.append(ch[i]);
+    }
 
-	}
+  }
 
 }
diff --git a/src/org/biojava/dasobert/das/DAS_Sequence_Handler.java b/src/org/biojava/dasobert/das/DAS_Sequence_Handler.java
index 0e3f5b5..fe5be8b 100755
--- a/src/org/biojava/dasobert/das/DAS_Sequence_Handler.java
+++ b/src/org/biojava/dasobert/das/DAS_Sequence_Handler.java
@@ -23,123 +23,139 @@
  */
 package org.biojava.dasobert.das;
 
-
 import org.xml.sax.helpers.DefaultHandler;
-import org.xml.sax.Attributes            ;
-import java.util.logging.*                ;
+import org.xml.sax.Attributes;
+import java.util.logging.*;
 
 /**
  * a class that parses the XML response of a DAS - sequence command.
+ * 
  * @author Andreas Prlic
- *
+ * 
  */
-public class DAS_Sequence_Handler extends DefaultHandler {
-
-	StringBuffer sequence ;
-	int length ;
-
-	int maxLength;
-	String version;
-
-	boolean dna_flag; 
-	/**
-	 * 
-	 */
-	public DAS_Sequence_Handler() {
-		super();
-
-		sequence = new StringBuffer() ;
-		length = 0;
-		dna_flag = false ;
-		maxLength = -1;
-		version = "";
-	}
-
-
-
-	/** set a maximum length of sequence that should be loaded
-	 * default: -1. if -1 no length restriction is being supplied
-	 * @return the maximum length or -1 if no restriction
-	 */
-	public int getMaxLength() {
-		return maxLength;
-	}
-
-
-
-	/** set a maximum length of sequence that should be loaded
-	 * default: -1. if -1 no length restriction is being supplied
-	 * @param maxLength the maximum length or -1 if unrestricted
-	 */
-	public void setMaxLength(int maxLength) {
-		this.maxLength = maxLength;
-	}
-
-
-
-
-	public void startElement (String uri, String name, String qName, Attributes atts){
-
-		if ( qName.equals("SEQUENCE")){
-			version = atts.getValue("version");
-			String lenstr 	= atts.getValue("stop");
-			length = Integer.parseInt(lenstr);
-			dna_flag = true ;
-		}
-
-	}
-
-	public void characters (char ch[], int start, int length){		
-
-		if (maxLength > 0)
-			if ( sequence.length() > maxLength)
-				return;
-
-		if (dna_flag) 
-			for (int i = start; i < start + length; i++) {
-
-				// all sorts of characters can be found in "seqeunces" ... ignore them...
-				switch (ch[i]) {
-				case '\\':
-					//System.out.print("\\\\");
-					break;
-				case '"':
-					//System.out.print("\\\"");
-					break;
-				case '\n':
-					//System.out.print("\\n");
-					break;
-				case '\r':
-					//System.out.print("\\r");
-					break;
-				case '\t':
-					//System.out.print("\\t");
-					break;
-				case ' ':
-					break;
-				default:
-					sequence = sequence.append(ch[i]);
-
-				break;
-				}
-			}
-
-	}
-
-	public String get_sequence() {
-
-		if ( maxLength < 0) {		
-			if ( length != sequence.length()) {	
-				Logger logger  = Logger.getLogger("org.biojava.spice");
-				logger.warning("Sequence does not match specified length!");
-			}
-		}
-
-		return sequence.toString();
-	}
-
-	public String getVersion() {
-		return version;
-	}
+public class DAS_Sequence_Handler extends DefaultHandler
+{
+
+  StringBuffer sequence;
+
+  int length;
+
+  int maxLength;
+
+  String version;
+
+  boolean dna_flag;
+
+  /**
+   * 
+   */
+  public DAS_Sequence_Handler()
+  {
+    super();
+
+    sequence = new StringBuffer();
+    length = 0;
+    dna_flag = false;
+    maxLength = -1;
+    version = "";
+  }
+
+  /**
+   * set a maximum length of sequence that should be loaded default: -1. if -1
+   * no length restriction is being supplied
+   * 
+   * @return the maximum length or -1 if no restriction
+   */
+  public int getMaxLength()
+  {
+    return maxLength;
+  }
+
+  /**
+   * set a maximum length of sequence that should be loaded default: -1. if -1
+   * no length restriction is being supplied
+   * 
+   * @param maxLength
+   *                the maximum length or -1 if unrestricted
+   */
+  public void setMaxLength(int maxLength)
+  {
+    this.maxLength = maxLength;
+  }
+
+  public void startElement(String uri, String name, String qName,
+          Attributes atts)
+  {
+
+    if (qName.equals("SEQUENCE"))
+    {
+      version = atts.getValue("version");
+      String lenstr = atts.getValue("stop");
+      length = Integer.parseInt(lenstr);
+      dna_flag = true;
+    }
+
+  }
+
+  public void characters(char ch[], int start, int length)
+  {
+
+    if (maxLength > 0)
+      if (sequence.length() > maxLength)
+        return;
+
+    if (dna_flag)
+      for (int i = start; i < start + length; i++)
+      {
+
+        // all sorts of characters can be found in "seqeunces" ... ignore
+        // them...
+        switch (ch[i])
+        {
+        case '\\':
+          // System.out.print("\\\\");
+          break;
+        case '"':
+          // System.out.print("\\\"");
+          break;
+        case '\n':
+          // System.out.print("\\n");
+          break;
+        case '\r':
+          // System.out.print("\\r");
+          break;
+        case '\t':
+          // System.out.print("\\t");
+          break;
+        case ' ':
+          break;
+        default:
+          sequence = sequence.append(ch[i]);
+
+          break;
+        }
+      }
+
+  }
+
+  public String get_sequence()
+  {
+
+    if (maxLength < 0)
+    {
+      if (length != sequence.length())
+      {
+        Logger logger = Logger.getLogger("org.biojava.spice");
+        logger.warning("Sequence does not match specified length!");
+      }
+    }
+
+    return sequence.toString();
+  }
+
+  public String getVersion()
+  {
+    return version;
+  }
 
 }
diff --git a/src/org/biojava/dasobert/das/FeatureThread.java b/src/org/biojava/dasobert/das/FeatureThread.java
index e7c9df9..172078b 100755
--- a/src/org/biojava/dasobert/das/FeatureThread.java
+++ b/src/org/biojava/dasobert/das/FeatureThread.java
@@ -31,20 +31,20 @@ import java.util.logging.*;
 import org.biojava.dasobert.dasregistry.*;
 import org.biojava.dasobert.eventmodel.*;
 
-/** a thread that connects to a DAS - Feature service and gets the features
- *
+/**
+ * a thread that connects to a DAS - Feature service and gets the features
+ * 
  * @author Andreas Prlic
  */
 
-
-
-public class FeatureThread
-    implements Runnable
+public class FeatureThread implements Runnable
 {
 
-  /** number of times the client tries to reconnect to the server if a "come back later" is returned.
-   * the server should provide a reasonable estimation how long it will take him to create results.
-   * if this number of requests is still not successfull, give up.
+  /**
+   * number of times the client tries to reconnect to the server if a "come back
+   * later" is returned. the server should provide a reasonable estimation how
+   * long it will take him to create results. if this number of requests is
+   * still not successfull, give up.
    */
   public static int MAX_COME_BACK_ITERATIONS = 5;
 
@@ -53,8 +53,11 @@ public class FeatureThread
   static Logger logger = Logger.getLogger("org.biojava.spice");
 
   Das1Source dasSource;
+
   String ac;
+
   List featureListeners;
+
   Thread thread;
 
   public FeatureThread(String accessionCode, Das1Source dasSource)
@@ -91,8 +94,7 @@ public class FeatureThread
       try
       {
         cmd = new URL(queryString);
-      }
-      catch (MalformedURLException e)
+      } catch (MalformedURLException e)
       {
         logger.warning("got MalformedURL from das source " + dasSource);
         e.printStackTrace();
@@ -104,7 +106,7 @@ public class FeatureThread
 
       int comeBackLater = ftmp.getComeBackLater();
       int securityCounter = 0;
-      while ( (thread == me) && (comeBackLater > 0))
+      while ((thread == me) && (comeBackLater > 0))
       {
         securityCounter++;
         if (securityCounter >= MAX_COME_BACK_ITERATIONS)
@@ -118,8 +120,7 @@ public class FeatureThread
         try
         {
           wait(comeBackLater);
-        }
-        catch (InterruptedException e)
+        } catch (InterruptedException e)
         {
           comeBackLater = -1;
           break;
@@ -129,7 +130,7 @@ public class FeatureThread
         comeBackLater = ftmp.getComeBackLater();
       }
 
-      if (! (thread == me))
+      if (!(thread == me))
       {
         break;
       }
@@ -140,9 +141,10 @@ public class FeatureThread
       // a fallback mechanism to prevent DAS sources from bringing down spice
       if (features.size() > MAX_NR_FEATURES)
       {
-        logger.warning("DAS source returned more than " + MAX_NR_FEATURES +
-                       "features. " +
-                       " throwing away excess features at " + cmd);
+        logger
+                .warning("DAS source returned more than " + MAX_NR_FEATURES
+                        + "features. "
+                        + " throwing away excess features at " + cmd);
         features = features.subList(0, MAX_NR_FEATURES);
       }
 
@@ -175,8 +177,9 @@ public class FeatureThread
     }
   }
 
-  /** the Annotation server requested to be queried again in a while
-   *
+  /**
+   * the Annotation server requested to be queried again in a while
+   * 
    * @param comeBackLater
    */
   private void notifyComeBackLater(int comeBackLater)
diff --git a/src/org/biojava/dasobert/das/SequenceThread.java b/src/org/biojava/dasobert/das/SequenceThread.java
index efdd50f..76008b6 100755
--- a/src/org/biojava/dasobert/das/SequenceThread.java
+++ b/src/org/biojava/dasobert/das/SequenceThread.java
@@ -41,228 +41,253 @@ import org.xml.sax.SAXNotRecognizedException;
 import org.xml.sax.XMLReader;
 import java.util.*;
 
-/** a thread that gets the sequence from a DAS server
+/**
+ * a thread that gets the sequence from a DAS server
  * 
  * @author Andreas Prlic
- *
+ * 
  */
-public class SequenceThread 
-extends Thread {
-    
-    Das1Source[] sequenceServers;
-    String sp_accession;
-    List seqListeners;
-    String version ;
-    
-    static Logger logger = Logger.getLogger("org.biojava.spice");
-    
-     public SequenceThread(String sp_accession,Das1Source ds ) {
-        super();
-        Das1Source[] dss =new Das1Source[1];
-	dss[0] = ds;
-        this.sp_accession = sp_accession;
-        this.sequenceServers =dss ;
-        clearSequenceListeners();
+public class SequenceThread extends Thread
+{
+
+  Das1Source[] sequenceServers;
+
+  String sp_accession;
+
+  List seqListeners;
+
+  String version;
+
+  static Logger logger = Logger.getLogger("org.biojava.spice");
+
+  public SequenceThread(String sp_accession, Das1Source ds)
+  {
+    super();
+    Das1Source[] dss = new Das1Source[1];
+    dss[0] = ds;
+    this.sp_accession = sp_accession;
+    this.sequenceServers = dss;
+    clearSequenceListeners();
+    version = "";
+  }
+
+  public SequenceThread(String sp_accession, Das1Source[] ds)
+  {
+    super();
+
+    this.sp_accession = sp_accession;
+    this.sequenceServers = ds;
+    clearSequenceListeners();
+  }
+
+  public void clearSequenceListeners()
+  {
+    seqListeners = new ArrayList();
+  }
+
+  public void addSequenceListener(SequenceListener lis)
+  {
+    seqListeners.add(lis);
+  }
+
+  public void run()
+  {
+    getSequence();
+  }
+
+  public void getSequence()
+  {
+
+    boolean gotSequence = false;
+
+    for (int i = 0; i < sequenceServers.length; i++)
+    {
+
+      if (gotSequence)
+        break;
+
+      Das1Source ds = sequenceServers[i];
+      String url = ds.getUrl();
+      char lastChar = url.charAt(url.length() - 1);
+      if (!(lastChar == '/'))
+        url += "/";
+      String dascmd = url + "sequence?segment=";
+      String connstr = dascmd + sp_accession;
+
+      try
+      {
         version = "";
+
+        String sequence = retrieveSequence(connstr);
+        // bug in aristotle das source?
+        sequence.replaceAll(" ", "");
+        gotSequence = true;
+        // set the sequence ...
+
+        triggerNewSequence(sp_accession, sequence, ds, version);
+
+        return;
+      } catch (Exception ex)
+      {
+        ex.printStackTrace();
+        logger.warning(ex.getMessage());
+
+        // triggerException(ex);
+
+      }
     }
-    public SequenceThread(String sp_accession,Das1Source[] ds ) {
-        super();
-        
-        this.sp_accession = sp_accession;
-        this.sequenceServers =ds ;
-        clearSequenceListeners();
-    }
-    
-    public void clearSequenceListeners(){
-        seqListeners = new ArrayList();
-    }
-    
-    public void addSequenceListener(SequenceListener lis){
-        seqListeners.add(lis);
-    }
-    
-    public void run() {
-        getSequence();
+
+    logger
+            .log(
+                    Level.WARNING,
+                    "could not retreive UniProt sequence from any available DAS sequence server");
+
+    triggerNoSequence(sp_accession);
+
+  }
+
+  // private void triggerException(Exception e){
+  // Iterator iter = seqListeners.iterator();
+  // while (iter.hasNext()){
+  // SequenceListener li = (SequenceListener)iter.next();
+  // li.exceptionOccured(e);
+  // }
+  // }
+
+  private void triggerNewSequence(String sp_accession, String sequence,
+          Das1Source source, String version)
+  {
+
+    Iterator iter = seqListeners.iterator();
+    while (iter.hasNext())
+    {
+      SequenceListener li = (SequenceListener) iter.next();
+      // SequenceEvent event = new SequenceEvent(sequence);
+      SequenceEvent event = new SequenceEvent(sp_accession, sequence,
+              version);
+      event.setSource(source);
+      li.newSequence(event);
     }
-    
-    public void getSequence( ){
-        
-        boolean gotSequence = false ;
-        
-        for ( int i = 0 ; i< sequenceServers.length; i++){
-            
-            if ( gotSequence ) break ;
-            
-            Das1Source ds = sequenceServers[i];
-            String url = ds.getUrl() ;
-            char lastChar = url.charAt(url.length()-1);      
-            if ( ! (lastChar == '/') ) 
-                url +="/" ;
-            String dascmd = url + "sequence?segment=";
-            String connstr = dascmd + sp_accession ;
-            
-            try {
-                version = "";
-                
-                String sequence = retrieveSequence(connstr);
-                // bug in aristotle das source?
-                sequence.replaceAll(" ","");
-                gotSequence = true ;
-                // set the sequence ...
-                
-                triggerNewSequence(sp_accession,sequence,ds,version);
-                
-                
-                return;
-            }
-            catch (Exception ex) {
-                ex.printStackTrace();     
-                logger.warning(ex.getMessage());
-                
-                //triggerException(ex);
-                
-            }       
-        }
-        
-        logger.log(Level.WARNING,"could not retreive UniProt sequence from any available DAS sequence server");
-        
-        triggerNoSequence(sp_accession);
-        
+  }
+
+  private void triggerNoSequence(String ac)
+  {
+
+    Iterator iter = seqListeners.iterator();
+    while (iter.hasNext())
+    {
+      SequenceListener li = (SequenceListener) iter.next();
+      li.noObjectFound(ac);
     }
 
-   
-    
-//    private void triggerException(Exception e){
-//        Iterator iter = seqListeners.iterator();
-//        while (iter.hasNext()){
-//           SequenceListener li = (SequenceListener)iter.next();
-//           li.exceptionOccured(e);
-//        }
-//    }
-    
-    private void triggerNewSequence(String sp_accession,String sequence,Das1Source source,String version){
-
-        Iterator iter = seqListeners.iterator();
-        while (iter.hasNext()){
-           SequenceListener li = (SequenceListener)iter.next();
-            //SequenceEvent event = new SequenceEvent(sequence);
-           SequenceEvent event = new SequenceEvent(sp_accession,sequence,version); 
-           event.setSource(source);
-           li.newSequence(event);
-        }
+  }
+
+  /**
+   * retrieve the Sequence from a DAS server.
+   * 
+   * @param connstr -
+   *                the DAS - request string. e.g.
+   *                http://www.ebi.ac.uk/das-srv/uniprot/das/aristotle/sequence?segment=P00280
+   * @return the requested Sequence
+   * @throws Exception
+   */
+  public String retrieveSequence(String connstr) throws Exception
+  {
+
+    // logger.finest("trying: " + connstr) ;
+    URL dasUrl = new URL(connstr);
+    // DAS_httpConnector dhtp = new DAS_httpConnector() ;
+    logger.info("requesting sequence from " + connstr);
+    InputStream dasInStream = open(dasUrl);
+
+    SAXParserFactory spfactory = SAXParserFactory.newInstance();
+
+    // never do this
+    // String vali = System.getProperty("XMLVALIDATION");
+    String vali = "false";
+    boolean validate = false;
+    if ((vali != null) && (vali.equals("true")))
+      validate = true;
+    spfactory.setValidating(validate);
+
+    SAXParser saxParser = null;
+
+    try
+    {
+      saxParser = spfactory.newSAXParser();
+    } catch (ParserConfigurationException e)
+    {
+      // e.printStackTrace();
+      logger.log(Level.FINER, "Uncaught exception", e);
     }
-    
-    private void triggerNoSequence(String ac){
-
-        Iterator iter = seqListeners.iterator();
-        while (iter.hasNext()){
-            SequenceListener li = (SequenceListener)iter.next();
-            li.noObjectFound(ac);
-        }
-    
+
+    XMLReader xmlreader = saxParser.getXMLReader();
+
+    try
+    {
+      xmlreader.setFeature("http://xml.org/sax/features/validation",
+              validate);
+    } catch (SAXException e)
+    {
+      logger.finer("Cannot set validation to " + validate);
+      logger.log(Level.FINER, "Uncaught exception", e);
     }
-    
-    /** retrieve the Sequence from a DAS server.  
-     * 
-     * @param connstr - the DAS - request string. e.g. http://www.ebi.ac.uk/das-srv/uniprot/das/aristotle/sequence?segment=P00280
-     * @return the requested Sequence
-     * @throws Exception
-     */
-    public String retrieveSequence( String connstr) 
-    throws Exception 
+
+    try
+    {
+      xmlreader
+              .setFeature(
+                      "http://apache.org/xml/features/nonvalidating/load-external-dtd",
+                      validate);
+    } catch (SAXNotRecognizedException e)
     {
-        
-        //logger.finest("trying: " + connstr) ;
-        URL dasUrl = new URL(connstr);
-        //DAS_httpConnector dhtp = new DAS_httpConnector() ;
-        logger.info("requesting sequence from " + connstr);
-        InputStream dasInStream =open(dasUrl); 
-        
-        
-        SAXParserFactory spfactory =
-            SAXParserFactory.newInstance();
-        
-	// never do this 
-        //String vali = System.getProperty("XMLVALIDATION");
-        String vali = "false";
-        boolean validate = false ;
-        if ((vali != null) && ( vali.equals("true")) ) 
-            validate = true ;
-        spfactory.setValidating(validate);
-        
-        SAXParser saxParser = null ;
-        
-        try{
-            saxParser =
-                spfactory.newSAXParser();
-        } catch (ParserConfigurationException e) {
-            //e.printStackTrace();
-            logger.log(Level.FINER,"Uncaught exception", e);
-        }
-        
-        XMLReader xmlreader = saxParser.getXMLReader();
-        
-        try {
-            xmlreader.setFeature("http://xml.org/sax/features/validation", validate);
-        } catch (SAXException e) {
-            logger.finer("Cannot set validation to " + validate); 
-            logger.log(Level.FINER,"Uncaught exception", e);
-        }
-        
-        try {
-            xmlreader.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd",validate);
-        } catch (SAXNotRecognizedException e){
-            //e.printStackTrace();
-            logger.finer("Cannot set load-external-dtd to" + validate); 
-            logger.log(Level.FINER,"Uncaught exception", e);
-            //System.err.println("Cannot set load-external-dtd to" + validate); 
-        }
-        
-        
-        //DAS_DNA_Handler cont_handle = new DAS_DNA_Handler() ;
-        DAS_Sequence_Handler cont_handle = new DAS_Sequence_Handler() ;
-        xmlreader.setContentHandler(cont_handle);
-        xmlreader.setErrorHandler(new org.xml.sax.helpers.DefaultHandler());
-        InputSource insource = new InputSource() ;
-        insource.setByteStream(dasInStream);
-        
-        xmlreader.parse(insource);
-        String sequence = cont_handle.get_sequence();
-        version = cont_handle.getVersion();
-        //logger.finest("Got sequence from DAS: " +sequence);
-        
-        logger.exiting(this.getClass().getName(), "retreiveSequence",  sequence);
-        return sequence ;
+      // e.printStackTrace();
+      logger.finer("Cannot set load-external-dtd to" + validate);
+      logger.log(Level.FINER, "Uncaught exception", e);
+      // System.err.println("Cannot set load-external-dtd to" + validate);
     }
-    
-    private InputStream open(URL url) {
-        {
-            
-            InputStream inStream = null;
-            try{
-                
-             
-               
-                
-                HttpURLConnection huc = null;
-             
-                huc = DAS_FeatureRetrieve.openHttpURLConnection(url);
-                
-                
-                logger.finest(huc.getResponseMessage());
-                
-                inStream = huc.getInputStream();
-                
-                
-            }
-            catch ( Exception ex){
-                ex.printStackTrace();
-                logger.log(Level.WARNING,"exception occured", ex);
-            }
-            
-            return inStream;
-        }
-        
+
+    // DAS_DNA_Handler cont_handle = new DAS_DNA_Handler() ;
+    DAS_Sequence_Handler cont_handle = new DAS_Sequence_Handler();
+    xmlreader.setContentHandler(cont_handle);
+    xmlreader.setErrorHandler(new org.xml.sax.helpers.DefaultHandler());
+    InputSource insource = new InputSource();
+    insource.setByteStream(dasInStream);
+
+    xmlreader.parse(insource);
+    String sequence = cont_handle.get_sequence();
+    version = cont_handle.getVersion();
+    // logger.finest("Got sequence from DAS: " +sequence);
+
+    logger.exiting(this.getClass().getName(), "retreiveSequence", sequence);
+    return sequence;
+  }
+
+  private InputStream open(URL url)
+  {
+    {
+
+      InputStream inStream = null;
+      try
+      {
+
+        HttpURLConnection huc = null;
+
+        huc = DAS_FeatureRetrieve.openHttpURLConnection(url);
+
+        logger.finest(huc.getResponseMessage());
+
+        inStream = huc.getInputStream();
+
+      } catch (Exception ex)
+      {
+        ex.printStackTrace();
+        logger.log(Level.WARNING, "exception occured", ex);
+      }
+
+      return inStream;
     }
-    
+
+  }
+
 }
diff --git a/src/org/biojava/dasobert/das2/Das2Capability.java b/src/org/biojava/dasobert/das2/Das2Capability.java
index 43fad73..e91bc77 100755
--- a/src/org/biojava/dasobert/das2/Das2Capability.java
+++ b/src/org/biojava/dasobert/das2/Das2Capability.java
@@ -41,8 +41,9 @@ public interface Das2Capability
 
   public String[] getFormats();
 
-  /** checks if this capability is actually of das1 style
-   *
+  /**
+   * checks if this capability is actually of das1 style
+   * 
    * @return boolean true if the capability is in DAS1 style
    */
   public boolean isDas1Style();
diff --git a/src/org/biojava/dasobert/das2/Das2CapabilityImpl.java b/src/org/biojava/dasobert/das2/Das2CapabilityImpl.java
index 5a061c7..196b681 100755
--- a/src/org/biojava/dasobert/das2/Das2CapabilityImpl.java
+++ b/src/org/biojava/dasobert/das2/Das2CapabilityImpl.java
@@ -22,12 +22,13 @@
  */
 package org.biojava.dasobert.das2;
 
-public class Das2CapabilityImpl
-    implements Das2Capability
+public class Das2CapabilityImpl implements Das2Capability
 {
 
   String capability;
+
   String[] formats;
+
   String queryId;
 
   public static String DAS1_CAPABILITY_PREFIX = "das1:";
@@ -52,8 +53,8 @@ public class Das2CapabilityImpl
     {
       return false;
     }
-    if (capability.substring(0,
-        DAS1_CAPABILITY_PREFIX.length()).equals(DAS1_CAPABILITY_PREFIX))
+    if (capability.substring(0, DAS1_CAPABILITY_PREFIX.length()).equals(
+            DAS1_CAPABILITY_PREFIX))
     {
       return true;
     }
diff --git a/src/org/biojava/dasobert/das2/Das2Source.java b/src/org/biojava/dasobert/das2/Das2Source.java
index 1d96298..71d59e0 100755
--- a/src/org/biojava/dasobert/das2/Das2Source.java
+++ b/src/org/biojava/dasobert/das2/Das2Source.java
@@ -24,18 +24,18 @@ package org.biojava.dasobert.das2;
 
 import org.biojava.dasobert.dasregistry.*;
 
-public interface Das2Source
-    extends DasSource
+public interface Das2Source extends DasSource
 {
 
   public Das2Capability[] getDas2Capabilities();
 
   public void setDas2Capabilities(Das2Capability[] capabilities);
 
-  /** test if this is a DAS1 source represented as a DAS2 source
-   *  if true - this source can be converted into a DAS1 source by using
-   *  DasSourceConverter.toDas1(Das2Source);
-   *
+  /**
+   * test if this is a DAS1 source represented as a DAS2 source if true - this
+   * source can be converted into a DAS1 source by using
+   * DasSourceConverter.toDas1(Das2Source);
+   * 
    * @return true if the DasSource has DAS1 capabilties
    */
   public boolean hasDas1Capabilities();
diff --git a/src/org/biojava/dasobert/das2/Das2SourceImpl.java b/src/org/biojava/dasobert/das2/Das2SourceImpl.java
index efdf40d..2f5a7ed 100755
--- a/src/org/biojava/dasobert/das2/Das2SourceImpl.java
+++ b/src/org/biojava/dasobert/das2/Das2SourceImpl.java
@@ -24,8 +24,7 @@ package org.biojava.dasobert.das2;
 
 import org.biojava.dasobert.dasregistry.*;
 
-public class Das2SourceImpl
-    extends Das1Source implements Das2Source
+public class Das2SourceImpl extends Das1Source implements Das2Source
 
 {
 
@@ -38,8 +37,9 @@ public class Das2SourceImpl
     capabilities = new Das2Capability[0];
   }
 
-  /**  compare if two DasSources are identical
-   *
+  /**
+   * compare if two DasSources are identical
+   * 
    */
   public boolean equals(DasSource other)
   {
@@ -49,13 +49,13 @@ public class Das2SourceImpl
       return true;
     }
 
-    if ( (other == null) || (other.getClass() != this.getClass()))
+    if ((other == null) || (other.getClass() != this.getClass()))
     {
       return false;
     }
 
     // to compare if two Das2Sources are identical we do the following:
-    //  we check the capabilities
+    // we check the capabilities
 
     Das2SourceImpl d2o = (Das2SourceImpl) other;
 
@@ -66,7 +66,7 @@ public class Das2SourceImpl
 
     Das2Capability[] othercaps = d2o.getDas2Capabilities();
 
-    if (! (capabilities.length == othercaps.length))
+    if (!(capabilities.length == othercaps.length))
     {
       return false;
     }
@@ -89,7 +89,7 @@ public class Das2SourceImpl
       }
     }
 
-    //TODO?
+    // TODO?
     // should we add a check for coordinate systems?
     // but we already check for the endpoints, that should be enough...
 
@@ -131,7 +131,7 @@ public class Das2SourceImpl
 
   public String[] getCapabilities()
   {
-    //todo mark as not needed / not appropriate ...
+    // todo mark as not needed / not appropriate ...
     return super.getCapabilities();
   }
 
diff --git a/src/org/biojava/dasobert/das2/DasSourceConverter.java b/src/org/biojava/dasobert/das2/DasSourceConverter.java
index 77cda0f..3e4d8e8 100755
--- a/src/org/biojava/dasobert/das2/DasSourceConverter.java
+++ b/src/org/biojava/dasobert/das2/DasSourceConverter.java
@@ -22,7 +22,7 @@
  */
 package org.biojava.dasobert.das2;
 
-//import org.biojava.bio.program.das.dasalignment.DASException;
+// import org.biojava.bio.program.das.dasalignment.DASException;
 import org.biojava.dasobert.dasregistry.*;
 
 public class DasSourceConverter
@@ -34,20 +34,22 @@ public class DasSourceConverter
 
   }
 
-  /** convert a das2 source to a das 1 source.
-   * This only will work if is passes the Das2Source.isDas1Source() test
-   * i.e. this is really a das1 server there
-   *
-   * @param das2source a DAS2Source to be converted
+  /**
+   * convert a das2 source to a das 1 source. This only will work if is passes
+   * the Das2Source.isDas1Source() test i.e. this is really a das1 server there
+   * 
+   * @param das2source
+   *                a DAS2Source to be converted
    * @return a Das1Source
    * @throws DASException
    */
   public static Das1Source toDas1Source(Das2Source das2source)
-      throws Exception
+          throws Exception
   {
     if (!das2source.hasDas1Capabilities())
     {
-      throw new Exception("this das source does not have das1 capabilitites");
+      throw new Exception(
+              "this das source does not have das1 capabilitites");
     }
 
     Das1Source ds = new Das1Source();
@@ -65,7 +67,8 @@ public class DasSourceConverter
     // convert the capabilitites to das1 capabiltities and get the url
     Das2Capability[] caps = das2source.getDas2Capabilities();
     String[] das1capabilitites = new String[caps.length];
-    int DASPREFIXLENGTH = Das2CapabilityImpl.DAS1_CAPABILITY_PREFIX.length();
+    int DASPREFIXLENGTH = Das2CapabilityImpl.DAS1_CAPABILITY_PREFIX
+            .length();
 
     for (int i = 0; i < caps.length; i++)
     {
@@ -78,7 +81,7 @@ public class DasSourceConverter
       String query_uri = cap.getQueryUri();
 
       String url = query_uri.substring(0,
-                                       (query_uri.length() - c.length() + DASPREFIXLENGTH));
+              (query_uri.length() - c.length() + DASPREFIXLENGTH));
       ds.setUrl(url);
     }
     ds.setCapabilities(das1capabilitites);
diff --git a/src/org/biojava/dasobert/das2/io/DAS2SourceHandler.java b/src/org/biojava/dasobert/das2/io/DAS2SourceHandler.java
index d8c61fa..0ee0b5e 100755
--- a/src/org/biojava/dasobert/das2/io/DAS2SourceHandler.java
+++ b/src/org/biojava/dasobert/das2/io/DAS2SourceHandler.java
@@ -29,20 +29,24 @@ import org.biojava.dasobert.dasregistry.*;
 import org.xml.sax.*;
 import org.xml.sax.helpers.*;
 
-/** a parser for the DAS2 sources response
- *
+/**
+ * a parser for the DAS2 sources response
+ * 
  * @author Andreas Prlic
  * @since 6:53:45 PM
  * @version %I% %G%
  */
-public class DAS2SourceHandler
-    extends DefaultHandler
+public class DAS2SourceHandler extends DefaultHandler
 {
 
   List sources;
+
   Das2Source currentSource;
+
   List coordinates;
+
   List capabilities;
+
   List labels;
 
   public static final String LABELPROPERTY = "label";
@@ -59,7 +63,7 @@ public class DAS2SourceHandler
   }
 
   private void startSource(String uri, String name, String qName,
-                           Attributes atts)
+          Attributes atts)
   {
 
     String id = atts.getValue("uri");
@@ -75,7 +79,7 @@ public class DAS2SourceHandler
   }
 
   private DasCoordinateSystem getCoordinateSystem(String uri, String name,
-                                                  String qname, Attributes atts)
+          String qname, Attributes atts)
   {
     // e.g. uri="http://das.sanger.ac.uk/dasregistry/coordsys/CS_LOCAL6"
     // source="Protein Sequence" authority="UniProt" test_range="P06213" />
@@ -97,9 +101,9 @@ public class DAS2SourceHandler
       String taxidstr = atts.getValue("taxid");
       int taxid = Integer.parseInt(taxidstr);
       dcs.setNCBITaxId(taxid);
+    } catch (Exception e)
+    {
     }
-    catch (Exception e)
-    {}
 
     String version = atts.getValue("version");
     if (version != null)
@@ -111,13 +115,13 @@ public class DAS2SourceHandler
   }
 
   public void startElement(String uri, String name, String qName,
-                           Attributes atts)
+          Attributes atts)
   {
-    //System.out.println("new element "+qName);
+    // System.out.println("new element "+qName);
 
     if (qName.equals("SOURCE"))
     {
-      //System.out.println("new Source " + atts.getValue(uri));
+      // System.out.println("new Source " + atts.getValue(uri));
       currentSource = new Das2SourceImpl();
       coordinates = new ArrayList();
       capabilities = new ArrayList();
@@ -147,10 +151,11 @@ public class DAS2SourceHandler
     }
   }
 
-  private Das2Capability getCapability(String uri, String name, String qName,
-                                       Attributes atts)
+  private Das2Capability getCapability(String uri, String name,
+          String qName, Attributes atts)
   {
-    // e.g <CAPABILITY type="features" query_id="http://das.biopackages.net/das/genome/yeast/S228C/feature" />
+    // e.g <CAPABILITY type="features"
+    // query_id="http://das.biopackages.net/das/genome/yeast/S228C/feature" />
     Das2Capability cap = new Das2CapabilityImpl();
 
     String type = atts.getValue("type");
@@ -162,7 +167,7 @@ public class DAS2SourceHandler
   }
 
   private void addProperty(String uri, String name, String qName,
-                           Attributes atts)
+          Attributes atts)
   {
     String pname = atts.getValue("name");
     String label = atts.getValue("value");
@@ -183,19 +188,20 @@ public class DAS2SourceHandler
   {
     if (qName.equals("SOURCE"))
     {
-      currentSource.setDas2Capabilities( (Das2Capability[]) capabilities.
-                                        toArray(new Das2Capability[capabilities.
-                                                size()]));
-      //System.out.println("got coordinates " + coordinates.size());
-      currentSource.setCoordinateSystem( (DasCoordinateSystem[]) coordinates.
-                                        toArray(new DasCoordinateSystem[
-                                                coordinates.size()]));
-
-      currentSource.setLabels( (String[]) labels.toArray(new String[labels.size()]));
+      currentSource.setDas2Capabilities((Das2Capability[]) capabilities
+              .toArray(new Das2Capability[capabilities.size()]));
+      // System.out.println("got coordinates " + coordinates.size());
+      currentSource.setCoordinateSystem((DasCoordinateSystem[]) coordinates
+              .toArray(new DasCoordinateSystem[coordinates.size()]));
+
+      currentSource.setLabels((String[]) labels.toArray(new String[labels
+              .size()]));
       labels.clear();
 
-      //System.out.println("Das2SourceHandler endElement name " + name + " uri " + uri + " qName " + qName);
-      //System.out.println("Das2SourceHandler adding to source: " + currentSource.getId());
+      // System.out.println("Das2SourceHandler endElement name " + name + " uri
+      // " + uri + " qName " + qName);
+      // System.out.println("Das2SourceHandler adding to source: " +
+      // currentSource.getId());
       sources.add(currentSource);
       currentSource = new Das2SourceImpl();
     }
@@ -203,7 +209,7 @@ public class DAS2SourceHandler
 
   public DasSource[] getSources()
   {
-    //System.out.println("Das2SourceHandler: source size: " + sources.size());
+    // System.out.println("Das2SourceHandler: source size: " + sources.size());
     return (DasSource[]) sources.toArray(new DasSource[sources.size()]);
   }
 
diff --git a/src/org/biojava/dasobert/das2/io/DasSourceReaderImpl.java b/src/org/biojava/dasobert/das2/io/DasSourceReaderImpl.java
index af403ed..6b6122a 100755
--- a/src/org/biojava/dasobert/das2/io/DasSourceReaderImpl.java
+++ b/src/org/biojava/dasobert/das2/io/DasSourceReaderImpl.java
@@ -30,8 +30,7 @@ import org.biojava.dasobert.das.*;
 import org.biojava.dasobert.dasregistry.*;
 import org.xml.sax.*;
 
-public class DasSourceReaderImpl
-    implements DasSourceReader
+public class DasSourceReaderImpl implements DasSourceReader
 {
 
   Exception loggedException;
@@ -44,8 +43,8 @@ public class DasSourceReaderImpl
     // open the stream to a server and then parse the result ...
   }
 
-  private InputStream open(URL url)
-      throws java.io.IOException, java.net.ConnectException
+  private InputStream open(URL url) throws java.io.IOException,
+          java.net.ConnectException
   {
     InputStream inStream = null;
 
@@ -66,8 +65,7 @@ public class DasSourceReaderImpl
       InputStream stream = open(url);
 
       sources = readDasSource(stream);
-    }
-    catch (Exception e)
+    } catch (Exception e)
     {
       e.printStackTrace();
       loggedException = e;
@@ -75,8 +73,9 @@ public class DasSourceReaderImpl
     return sources;
   }
 
-  /** read a DAS2 sources response and return a list of DAS sources.
-   *
+  /**
+   * read a DAS2 sources response and return a list of DAS sources.
+   * 
    */
   public DasSource[] readDasSource(InputStream stream)
   {
@@ -85,8 +84,7 @@ public class DasSourceReaderImpl
 
     try
     {
-      SAXParserFactory spfactory =
-          SAXParserFactory.newInstance();
+      SAXParserFactory spfactory = SAXParserFactory.newInstance();
 
       spfactory.setValidating(false);
 
@@ -94,10 +92,8 @@ public class DasSourceReaderImpl
 
       try
       {
-        saxParser =
-            spfactory.newSAXParser();
-      }
-      catch (ParserConfigurationException e)
+        saxParser = spfactory.newSAXParser();
+      } catch (ParserConfigurationException e)
       {
         e.printStackTrace();
         loggedException = e;
@@ -116,27 +112,26 @@ public class DasSourceReaderImpl
 
       XMLReader xmlreader = saxParser.getXMLReader();
 
-      //XMLReader xmlreader = XMLReaderFactory.createXMLReader();
+      // XMLReader xmlreader = XMLReaderFactory.createXMLReader();
       try
       {
         xmlreader.setFeature("http://xml.org/sax/features/validation",
-                             validation);
-      }
-      catch (SAXException e)
+                validation);
+      } catch (SAXException e)
       {
-        //logger.log(Level.FINE,"Cannot set validation " + validation);
+        // logger.log(Level.FINE,"Cannot set validation " + validation);
       }
 
       try
       {
-        xmlreader.setFeature(
-            "http://apache.org/xml/features/nonvalidating/load-external-dtd",
-            validation);
-      }
-      catch (SAXNotRecognizedException e)
+        xmlreader
+                .setFeature(
+                        "http://apache.org/xml/features/nonvalidating/load-external-dtd",
+                        validation);
+      } catch (SAXNotRecognizedException e)
       {
         e.printStackTrace();
-        //logger.log(Level.FINE,"Cannot set load-external-dtd "+validation);
+        // logger.log(Level.FINE,"Cannot set load-external-dtd "+validation);
 
       }
 
@@ -150,8 +145,7 @@ public class DasSourceReaderImpl
       xmlreader.parse(insource);
       sources = cont_handle.getSources();
 
-    }
-    catch (Exception e)
+    } catch (Exception e)
     {
       e.printStackTrace();
       loggedException = e;
@@ -178,8 +172,7 @@ public class DasSourceReaderImpl
         System.out.println(ds.toString());
       }
 
-    }
-    catch (Exception e)
+    } catch (Exception e)
     {
       e.printStackTrace();
     }
diff --git a/src/org/biojava/dasobert/dasregistry/Das1Source.java b/src/org/biojava/dasobert/dasregistry/Das1Source.java
index e7541b4..c46d709 100755
--- a/src/org/biojava/dasobert/dasregistry/Das1Source.java
+++ b/src/org/biojava/dasobert/dasregistry/Das1Source.java
@@ -25,31 +25,44 @@ package org.biojava.dasobert.dasregistry;
 
 import java.util.*;
 
-//import org.biojava.dasobert.das2.io.DasSourceWriter;
-//import org.biojava.dasobert.das2.io.DasSourceWriterImpl;
-//import org.biojava.utils.xml.PrettyXMLWriter;
+// import org.biojava.dasobert.das2.io.DasSourceWriter;
+// import org.biojava.dasobert.das2.io.DasSourceWriterImpl;
+// import org.biojava.utils.xml.PrettyXMLWriter;
 
-
-/** a simple Bean class to be returned via SOAP
+/**
+ * a simple Bean class to be returned via SOAP
+ * 
  * @author Andreas Prlic
  */
 
-public class Das1Source
-    implements DasSource
+public class Das1Source implements DasSource
 {
   String url;
+
   protected String nickname;
+
   String adminemail;
+
   String description;
+
   DasCoordinateSystem[] coordinateSystem;
+
   String[] capabilities;
+
   String[] labels;
+
   String helperurl;
+
   Date registerDate;
+
   Date leaseDate;
+
   String id;
+
   boolean local;
+
   Map properties;
+
   boolean alertAdmin;
 
   public static String EMPTY_ID = "UNK:-1";
@@ -60,13 +73,13 @@ public class Das1Source
     url = "";
     adminemail = "";
     description = "";
-    //String empty     = "" ;
+    // String empty = "" ;
     nickname = "";
     coordinateSystem = new DasCoordinateSystem[0];
-    //coordinateSystem[0] = new DasCoordinateSystem();
+    // coordinateSystem[0] = new DasCoordinateSystem();
     capabilities = new String[0];
     labels = new String[0];
-    //capabilities[0]  = empty ;
+    // capabilities[0] = empty ;
     registerDate = new Date();
     leaseDate = new Date();
     helperurl = "";
@@ -76,7 +89,7 @@ public class Das1Source
   public boolean equals(DasSource other)
   {
     System.out.println("Das1Source equals, comparing with other DasSource");
-    if (! (other instanceof Das1Source))
+    if (!(other instanceof Das1Source))
     {
       return false;
     }
@@ -104,25 +117,22 @@ public class Das1Source
     return h;
   }
 
-  /** the DAS2 string representation of this DAS source
-   *
-       public String toString() {
-
-      StringWriter writer = new StringWriter();
-
-      PrintWriter pw = new PrintWriter(writer);
-      PrettyXMLWriter xw = new PrettyXMLWriter(pw);
-
-      DasSourceWriter dswriter = new DasSourceWriterImpl();
-      try {
-          dswriter.writeDasSource(xw,this);
-      } catch (IOException e){
-          e.printStackTrace();
-      }
-
-      return writer.toString();
-
-       }
+  /**
+   * the DAS2 string representation of this DAS source
+   * 
+   * public String toString() {
+   * 
+   * StringWriter writer = new StringWriter();
+   * 
+   * PrintWriter pw = new PrintWriter(writer); PrettyXMLWriter xw = new
+   * PrettyXMLWriter(pw);
+   * 
+   * DasSourceWriter dswriter = new DasSourceWriterImpl(); try {
+   * dswriter.writeDasSource(xw,this); } catch (IOException e){
+   * e.printStackTrace(); }
+   * 
+   * return writer.toString();
+   *  }
    */
   public void setLocal(boolean flag)
   {
@@ -139,10 +149,10 @@ public class Das1Source
     id = i;
   }
 
-  /** get a the Id of the DasSource. The Id is a unique db
-   * identifier. The public DAS-Registry has Auto_Ids that look like
-   * DASSOURCE:12345; public look like XYZ:12345, where the XYZ
-   * prefix can be configured in the config file.
+  /**
+   * get a the Id of the DasSource. The Id is a unique db identifier. The public
+   * DAS-Registry has Auto_Ids that look like DASSOURCE:12345; public look like
+   * XYZ:12345, where the XYZ prefix can be configured in the config file.
    */
   public String getId()
   {
@@ -209,19 +219,23 @@ public class Das1Source
   {
     return capabilities;
   }
-    /** test if a this source has a particular capability
-     * 
-     * @param testCapability
-     * @return <code>true</code> if the server has this capability.
-     */
-    public boolean hasCapability(String testCapability){
-        for (int i=0 ; i< capabilities.length;i++){
-            String cap = capabilities[i];
-            if ( cap.equals(testCapability))
-                return true;
-        }
-        return false;
+
+  /**
+   * test if a this source has a particular capability
+   * 
+   * @param testCapability
+   * @return <code>true</code> if the server has this capability.
+   */
+  public boolean hasCapability(String testCapability)
+  {
+    for (int i = 0; i < capabilities.length; i++)
+    {
+      String cap = capabilities[i];
+      if (cap.equals(testCapability))
+        return true;
     }
+    return false;
+  }
 
   public DasCoordinateSystem[] getCoordinateSystem()
   {
@@ -276,12 +290,16 @@ public class Das1Source
   public boolean getAlertAdmin()
   {
     return alertAdmin;
-    }
-	public Map getProperties() {
-		return properties;
-	}
-	public void setProperties(Map properties) {
-		this.properties = properties;
-	}
+  }
+
+  public Map getProperties()
+  {
+    return properties;
+  }
+
+  public void setProperties(Map properties)
+  {
+    this.properties = properties;
+  }
 
 }
diff --git a/src/org/biojava/dasobert/dasregistry/DasCoordSysComparator.java b/src/org/biojava/dasobert/dasregistry/DasCoordSysComparator.java
index 3de3702..dbae74d 100755
--- a/src/org/biojava/dasobert/dasregistry/DasCoordSysComparator.java
+++ b/src/org/biojava/dasobert/dasregistry/DasCoordSysComparator.java
@@ -22,26 +22,26 @@
  *
  */
 
-
 package org.biojava.dasobert.dasregistry;
 
 import java.util.*;
 
-/** a comparator to sort DasSources
+/**
+ * a comparator to sort DasSources
+ * 
  * @author Andreas Prlic
  */
 
-
-public abstract class DasCoordSysComparator
-    implements Comparator
+public abstract class DasCoordSysComparator implements Comparator
 {
 
   private final String name;
+
   private static final Map COMPS_BY_NAME;
 
   public DasCoordSysComparator(String str)
   {
-    //System.out.println("new dasSourceComparator " + str);
+    // System.out.println("new dasSourceComparator " + str);
     name = str;
   }
 
@@ -60,23 +60,27 @@ public abstract class DasCoordSysComparator
       return ds.getUniqueId();
     }
   };
+
   public static final Comparator BY_CATEGORY = new DasCoordSysComparator(
-      "category")
+          "category")
   {
     protected Comparable getField(DasCoordinateSystem ds)
     {
       return ds.getCategory();
     }
   };
+
   public static final Comparator BY_ORGANISM = new DasCoordSysComparator(
-      "organism")
+          "organism")
   {
     protected Comparable getField(DasCoordinateSystem ds)
     {
       return ds.getOrganismName();
     }
   };
-  public static final Comparator BY_TAXID = new DasCoordSysComparator("taxid")
+
+  public static final Comparator BY_TAXID = new DasCoordSysComparator(
+          "taxid")
   {
     protected Comparable getField(DasCoordinateSystem ds)
     {
diff --git a/src/org/biojava/dasobert/dasregistry/DasCoordinateSystem.java b/src/org/biojava/dasobert/dasregistry/DasCoordinateSystem.java
index 48508d9..8936a16 100755
--- a/src/org/biojava/dasobert/dasregistry/DasCoordinateSystem.java
+++ b/src/org/biojava/dasobert/dasregistry/DasCoordinateSystem.java
@@ -23,18 +23,26 @@
  */
 package org.biojava.dasobert.dasregistry;
 
-/** a Bean to be returned via SOAP. It takes care of the DAS -  coordinate Systems
+/**
+ * a Bean to be returned via SOAP. It takes care of the DAS - coordinate Systems
+ * 
  * @author Andreas Prlic
  */
 public class DasCoordinateSystem
 {
 
   String name;
+
   String category;
+
   String organism_name;
+
   int ncbi_tax_id;
+
   String uniqueId;
+
   String version;
+
   String testCode;
 
   public DasCoordinateSystem()
@@ -51,17 +59,18 @@ public class DasCoordinateSystem
   public boolean equals(DasCoordinateSystem other)
   {
     boolean match = true;
-    System.out.println("comparing " + this.toString() + " to " + other.toString());
+    System.out.println("comparing " + this.toString() + " to "
+            + other.toString());
     // URI has piority
-    if ( (!uniqueId.equals("")) && (uniqueId.equals(other.getUniqueId())))
+    if ((!uniqueId.equals("")) && (uniqueId.equals(other.getUniqueId())))
     {
       return true;
     }
 
     if (ncbi_tax_id != other.getNCBITaxId())
     {
-      System.out.println("mismatch in ncbi tax id " + ncbi_tax_id + " != " +
-                         other.getNCBITaxId());
+      System.out.println("mismatch in ncbi tax id " + ncbi_tax_id + " != "
+              + other.getNCBITaxId());
       match = false;
     }
     if (!version.equals(other.getVersion()))
@@ -83,15 +92,16 @@ public class DasCoordinateSystem
 
     return match;
   }
-  
-    public int hashCode() {
-        int h = 7;
-        
-        h = 31 * h + ( null == name ? 0 : name.hashCode());
-        h = 31 * h + ( null == category ? 0 : category.hashCode());
-        
-        return h;
-    }
+
+  public int hashCode()
+  {
+    int h = 7;
+
+    h = 31 * h + (null == name ? 0 : name.hashCode());
+    h = 31 * h + (null == category ? 0 : category.hashCode());
+
+    return h;
+  }
 
   public Object clone()
   {
diff --git a/src/org/biojava/dasobert/dasregistry/DasSource.java b/src/org/biojava/dasobert/dasregistry/DasSource.java
index fffda83..892963b 100755
--- a/src/org/biojava/dasobert/dasregistry/DasSource.java
+++ b/src/org/biojava/dasobert/dasregistry/DasSource.java
@@ -31,25 +31,28 @@ public interface DasSource
 
   public boolean isLocal();
 
-  /** compare if two das sources are equal
-   *
+  /**
+   * compare if two das sources are equal
+   * 
    * @param ds
    * @return returns true if two DAS sources are equivalent
    */
   public boolean equals(DasSource ds);
 
-  /** classes that implement equals, should also implement hashKey
-   *
+  /**
+   * classes that implement equals, should also implement hashKey
+   * 
    * @return the hash code of a das source
    */
   public int hashCode();
 
   public void setId(String i);
 
-  /** get a the Id of the DasSource. The Id is a unique db
-   * identifier. The public DAS-Registry has Auto_Ids that look like
-   * DASSOURCE:12345; public look like XYZ:12345, where the XYZ
-   * prefix can be configured in the config file.
+  /**
+   * get a the Id of the DasSource. The Id is a unique db identifier. The public
+   * DAS-Registry has Auto_Ids that look like DASSOURCE:12345; public look like
+   * XYZ:12345, where the XYZ prefix can be configured in the config file.
+   * 
    * @return String the ID of a Das Source
    */
   public String getId();
@@ -67,12 +70,15 @@ public interface DasSource
   public void setCoordinateSystem(DasCoordinateSystem[] u);
 
   public void setCapabilities(String[] u);
-    /** test if a this source has a particular capability
-     * 
-     * @param testCapability
-     * @return <code>true</code> if the server has this capability.
-     */
-    public boolean hasCapability(String testCapability);
+
+  /**
+   * test if a this source has a particular capability
+   * 
+   * @param testCapability
+   * @return <code>true</code> if the server has this capability.
+   */
+  public boolean hasCapability(String testCapability);
+
   public String getUrl();
 
   public String getAdminemail();
@@ -100,24 +106,25 @@ public interface DasSource
   public String getHelperurl();
 
   // TestCode is now part of the coordinate system!
-  //public  void setTestCode(String code);
-  //public  String getTestCode();
+  // public void setTestCode(String code);
+  // public String getTestCode();
 
   public void setAlertAdmin(boolean flag);
 
   public boolean getAlertAdmin();
-      
-    /** set Properties for this DAS source, e.g. project name
-     * 
-     * @param properties
-     */
-    public void setProperties(Map properties);
-    
-    /** get Properties for this DAS source
-     * 
-     * @return Properties
-     */
-    public Map getProperties();
-  
+
+  /**
+   * set Properties for this DAS source, e.g. project name
+   * 
+   * @param properties
+   */
+  public void setProperties(Map properties);
+
+  /**
+   * get Properties for this DAS source
+   * 
+   * @return Properties
+   */
+  public Map getProperties();
 
 }
\ No newline at end of file
diff --git a/src/org/biojava/dasobert/dasregistry/DasSourceComparator.java b/src/org/biojava/dasobert/dasregistry/DasSourceComparator.java
index 3d95d1a..0d52fd9 100755
--- a/src/org/biojava/dasobert/dasregistry/DasSourceComparator.java
+++ b/src/org/biojava/dasobert/dasregistry/DasSourceComparator.java
@@ -22,27 +22,28 @@
  *
  */
 
-
 package org.biojava.dasobert.dasregistry;
 
 import java.util.*;
 
-/** a comparator to sort DasSources
+/**
+ * a comparator to sort DasSources
+ * 
  * @author Andreas Prlic, Thomas Down
  */
 
-
-public abstract class DasSourceComparator
-    implements Comparator
+public abstract class DasSourceComparator implements Comparator
 {
 
   private final String name;
+
   private static final Map COMPS_BY_NAME;
-    private static final int TWODAYS = 1000 * 60 * 60 * 24 * 2;
+
+  private static final int TWODAYS = 1000 * 60 * 60 * 24 * 2;
 
   public DasSourceComparator(String str)
   {
-    //System.out.println("new dasSourceComparator " + str);
+    // System.out.println("new dasSourceComparator " + str);
     name = str;
   }
 
@@ -55,41 +56,46 @@ public abstract class DasSourceComparator
   };
 
   public static final Comparator BY_NICKNAME = new DasSourceComparator(
-      "nickname")
+          "nickname")
   {
     protected Comparable getField(DasSource ds)
     {
       return ds.getNickname();
     }
   };
-      public static final Comparator BY_STATUS = new DasSourceComparator("status"){
-		protected Comparable getField(DasSource ds) {
-			
-			Date now = new Date();
-			
-			if (ds.getLeaseDate().getTime() < (now.getTime() - TWODAYS))
-				return new Integer(0);
-			return new Integer(1);
-		}
-	};
-    
-  
+
+  public static final Comparator BY_STATUS = new DasSourceComparator(
+          "status")
+  {
+    protected Comparable getField(DasSource ds)
+    {
+
+      Date now = new Date();
+
+      if (ds.getLeaseDate().getTime() < (now.getTime() - TWODAYS))
+        return new Integer(0);
+      return new Integer(1);
+    }
+  };
+
   public static final Comparator BY_REGISTER_DATE = new DasSourceComparator(
-      "registerdate")
+          "registerdate")
   {
     protected Comparable getField(DasSource ds)
     {
       return ds.getRegisterDate();
     }
   };
+
   public static final Comparator BY_LEASE_DATE = new DasSourceComparator(
-      "leasedate")
+          "leasedate")
   {
     protected Comparable getField(DasSource ds)
     {
       return ds.getLeaseDate();
     }
   };
+
   public static final Comparator BY_URL = new DasSourceComparator("url")
   {
     protected Comparable getField(DasSource ds)
@@ -97,24 +103,27 @@ public abstract class DasSourceComparator
       return ds.getUrl();
     }
   };
+
   public static final Comparator BY_ADMIN_EMAIL = new DasSourceComparator(
-      "adminemail")
+          "adminemail")
   {
     protected Comparable getField(DasSource ds)
     {
       return ds.getAdminemail();
     }
   };
+
   public static final Comparator BY_DESCRIPTION = new DasSourceComparator(
-      "description")
+          "description")
   {
     protected Comparable getField(DasSource ds)
     {
       return ds.getDescription();
     }
   };
+
   public static final Comparator BY_CAPABILITIES = new DasSourceComparator(
-      "capabilities")
+          "capabilities")
   {
     protected Comparable getField(DasSource ds)
     {
@@ -122,8 +131,9 @@ public abstract class DasSourceComparator
       return caps.length == 0 ? "" : caps[0];
     }
   };
+
   public static final Comparator BY_COORDINATE_SYSTEM = new DasSourceComparator(
-      "coordinateSystem")
+          "coordinateSystem")
   {
     protected Comparable getField(DasSource ds)
     {
@@ -143,9 +153,10 @@ public abstract class DasSourceComparator
     COMPS_BY_NAME.put(BY_ADMIN_EMAIL.toString(), BY_ADMIN_EMAIL);
     COMPS_BY_NAME.put(BY_DESCRIPTION.toString(), BY_DESCRIPTION);
     COMPS_BY_NAME.put(BY_CAPABILITIES.toString(), BY_CAPABILITIES);
-    COMPS_BY_NAME.put(BY_COORDINATE_SYSTEM.toString(), BY_COORDINATE_SYSTEM);
-    COMPS_BY_NAME.put(BY_STATUS.toString(),            BY_STATUS);
-    
+    COMPS_BY_NAME
+            .put(BY_COORDINATE_SYSTEM.toString(), BY_COORDINATE_SYSTEM);
+    COMPS_BY_NAME.put(BY_STATUS.toString(), BY_STATUS);
+
   }
 
   public static Comparator fromString(String name)
diff --git a/src/org/biojava/dasobert/eventmodel/AbstractDasEvent.java b/src/org/biojava/dasobert/eventmodel/AbstractDasEvent.java
index 9d8e101..d8cbebe 100644
--- a/src/org/biojava/dasobert/eventmodel/AbstractDasEvent.java
+++ b/src/org/biojava/dasobert/eventmodel/AbstractDasEvent.java
@@ -25,20 +25,19 @@ package org.biojava.dasobert.eventmodel;
 
 import org.biojava.dasobert.dasregistry.Das1Source;
 
-public class AbstractDasEvent {
+public class AbstractDasEvent
+{
 
-	Das1Source dasSource;
+  Das1Source dasSource;
 
-	public Das1Source getSource() {
-		return dasSource;
-	}
+  public Das1Source getSource()
+  {
+    return dasSource;
+  }
 
-	public void setSource(Das1Source source) {
-		this.dasSource = source;
-	}
-	
-	
+  public void setSource(Das1Source source)
+  {
+    this.dasSource = source;
+  }
 
-	
-	
 }
diff --git a/src/org/biojava/dasobert/eventmodel/FeatureEvent.java b/src/org/biojava/dasobert/eventmodel/FeatureEvent.java
index 26711bc..dd89ef3 100755
--- a/src/org/biojava/dasobert/eventmodel/FeatureEvent.java
+++ b/src/org/biojava/dasobert/eventmodel/FeatureEvent.java
@@ -30,9 +30,11 @@ public class FeatureEvent extends AbstractDasEvent
 {
 
   Map[] features;
+
   int comeBackLater;
-    String version;
-    
+
+  String version;
+
   public FeatureEvent(Map[] features, Das1Source dasSource, String version)
   {
     super();
@@ -52,17 +54,20 @@ public class FeatureEvent extends AbstractDasEvent
     this.comeBackLater = comeBackLater;
   }
 
-  /** get the features that have been found.
-   *
-   * do something like
-   * Map[] features = event.getFeatures();
+  /**
+   * get the features that have been found.
+   * 
+   * do something like Map[] features = event.getFeatures();
+   * 
    * <pre>
-   * for (int i = 0 ; i< features;i++) {
-   *      Map f = features[i];
-   *      String type = (String) f.get("TYPE") ;
-   *      System.out.println(type);
+   * for (int i = 0; i &lt; features; i++)
+   * {
+   *   Map f = features[i];
+   *   String type = (String) f.get(&quot;TYPE&quot;);
+   *   System.out.println(type);
    * }
    * </pre>
+   * 
    * @return a Map containng the features
    */
   public Map[] getFeatures()
@@ -70,17 +75,22 @@ public class FeatureEvent extends AbstractDasEvent
     return features;
   }
 
-    /** Get the version of the reference object that has been annotated.
-     * Compare the version string with the version string obtained from the reference server.
-     * If they don;t match there is a version problem between the annotation and the reference!
-     * @return the version string (e.g. an MD5 digest of the reference sequence)
-     */
-	public String getVersion() {
-		return version;
-	}
+  /**
+   * Get the version of the reference object that has been annotated. Compare
+   * the version string with the version string obtained from the reference
+   * server. If they don;t match there is a version problem between the
+   * annotation and the reference!
+   * 
+   * @return the version string (e.g. an MD5 digest of the reference sequence)
+   */
+  public String getVersion()
+  {
+    return version;
+  }
 
-	public void setVersion(String version) {
-		this.version = version;
-	}
+  public void setVersion(String version)
+  {
+    this.version = version;
+  }
 
 }
diff --git a/src/org/biojava/dasobert/eventmodel/FeatureListener.java b/src/org/biojava/dasobert/eventmodel/FeatureListener.java
index 1ae5827..235c486 100755
--- a/src/org/biojava/dasobert/eventmodel/FeatureListener.java
+++ b/src/org/biojava/dasobert/eventmodel/FeatureListener.java
@@ -22,22 +22,25 @@
  */
 package org.biojava.dasobert.eventmodel;
 
-//import org.biojava.spice.multipanel.eventmodel.FeatureEvent;
+// import org.biojava.spice.multipanel.eventmodel.FeatureEvent;
 
-/**  a feature listener that returns the raw features as returned by a DAS source.
- *
+/**
+ * a feature listener that returns the raw features as returned by a DAS source.
+ * 
  */
 public interface FeatureListener
 {
 
-  /** new features have been returned from the Annotation server
-   *
+  /**
+   * new features have been returned from the Annotation server
+   * 
    * @param e
    */
   public void newFeatures(FeatureEvent e);
 
-  /** the server says that he is busy and we should try again in x seconds
-   *
+  /**
+   * the server says that he is busy and we should try again in x seconds
+   * 
    * @param e
    */
   public void comeBackLater(FeatureEvent e);
diff --git a/src/org/biojava/dasobert/eventmodel/ObjectListener.java b/src/org/biojava/dasobert/eventmodel/ObjectListener.java
index b5acf89..a19ae4d 100755
--- a/src/org/biojava/dasobert/eventmodel/ObjectListener.java
+++ b/src/org/biojava/dasobert/eventmodel/ObjectListener.java
@@ -22,22 +22,26 @@
  */
 package org.biojava.dasobert.eventmodel;
 
-/** an interface for the listeners of new PDB code requested / new Uniprot code requested
- *
+/**
+ * an interface for the listeners of new PDB code requested / new Uniprot code
+ * requested
+ * 
  * @author Andreas Prlic
- *
+ * 
  */
 public interface ObjectListener
 {
 
-  /** a new object has been requested
-   *
+  /**
+   * a new object has been requested
+   * 
    * @param accessionCode
    */
   public void newObjectRequested(String accessionCode);
 
-  /** no object with that accessionCode has been found
-   *
+  /**
+   * no object with that accessionCode has been found
+   * 
    * @param accessionCode
    */
   public void noObjectFound(String accessionCode);
diff --git a/src/org/biojava/dasobert/eventmodel/SequenceEvent.java b/src/org/biojava/dasobert/eventmodel/SequenceEvent.java
index 1c4f38e..484cf49 100755
--- a/src/org/biojava/dasobert/eventmodel/SequenceEvent.java
+++ b/src/org/biojava/dasobert/eventmodel/SequenceEvent.java
@@ -26,9 +26,11 @@ public class SequenceEvent extends AbstractDasEvent
 {
 
   String sequence;
+
   String accessionCode;
+
   String version;
-  
+
   public SequenceEvent(String accessionCode, String seq, String version)
   {
     super();
@@ -47,13 +49,14 @@ public class SequenceEvent extends AbstractDasEvent
     return sequence;
   }
 
+  public String getVersion()
+  {
+    return version;
+  }
 
-	public String getVersion() {
-		return version;
-	}
-
-	public void setVersion(String version) {
-		this.version = version;
-	}
+  public void setVersion(String version)
+  {
+    this.version = version;
+  }
 
 }
diff --git a/src/org/biojava/dasobert/eventmodel/SequenceListener.java b/src/org/biojava/dasobert/eventmodel/SequenceListener.java
index c71a6d9..df3a687 100755
--- a/src/org/biojava/dasobert/eventmodel/SequenceListener.java
+++ b/src/org/biojava/dasobert/eventmodel/SequenceListener.java
@@ -22,35 +22,43 @@
  */
 package org.biojava.dasobert.eventmodel;
 
-/** An interface fore events related to selections of sequence
- * position, sequence range and locking of the selection.
- *
+/**
+ * An interface fore events related to selections of sequence position, sequence
+ * range and locking of the selection.
+ * 
  * @author Andreas Prlic
- *
+ * 
  */
-public interface SequenceListener
-    extends ObjectListener
+public interface SequenceListener extends ObjectListener
 {
 
   /* select a certain sequence position */
   public void selectedSeqPosition(int position);
 
-  /** select a certain range of a sequence
-   * @param start the start
-   * @param end the end of the range
-   * */
+  /**
+   * select a certain range of a sequence
+   * 
+   * @param start
+   *                the start
+   * @param end
+   *                the end of the range
+   */
   public void selectedSeqRange(int start, int end);
 
-  /** the current selecetion is locked and can not be changed
-   * @param flag true if selection should be locked
-   * */
+  /**
+   * the current selecetion is locked and can not be changed
+   * 
+   * @param flag
+   *                true if selection should be locked
+   */
   public void selectionLocked(boolean flag);
 
   public void newSequence(SequenceEvent e);
 
-  /** clear what has been selected
-   *
-   *
+  /**
+   * clear what has been selected
+   * 
+   * 
    */
   public void clearSelection();
 }
diff --git a/src/org/biojava/dasobert/feature/AbstractFeatureTrack.java b/src/org/biojava/dasobert/feature/AbstractFeatureTrack.java
index af6236f..0ad2df7 100644
--- a/src/org/biojava/dasobert/feature/AbstractFeatureTrack.java
+++ b/src/org/biojava/dasobert/feature/AbstractFeatureTrack.java
@@ -26,175 +26,253 @@ import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
 
-/** An Abstract class representing a Feature as being diplayed in the SeqFeaturePanel 
- *  A feature corresponds to everything that is visible in a "line" and can contain one or multiple Segments.
+/**
+ * An Abstract class representing a Feature as being diplayed in the
+ * SeqFeaturePanel A feature corresponds to everything that is visible in a
+ * "line" and can contain one or multiple Segments.
  * 
  * 
  * @author Andreas Prlic
- *
+ * 
  */
-public abstract class AbstractFeatureTrack implements FeatureTrack,Cloneable {
-
-	String name;
-	String method;
-	String type;
-	List  segments ;
-	String note;
-	String link;
-	String source;
-	String score;
-	String orientation;
-	String typeID;
-	String typeCategory;
-
-	public AbstractFeatureTrack() {
-		source = "Unknown";
-		method = "Unknown";
-		type   = "Unknown";
-		note   = "";
-		link   = "";
-		score  = "";
-		orientation = null;
-		segments = new ArrayList();
-
-	}
-
-	public abstract Object clone();
-
-
-	public String toString() {
-		String str = "Feature: method: " + method +" type: " + type ;
-		if ( name != null)
-			str += " name: " + name;
-		
-		if (( note != null) && (! note.equals("null")))
-		{
-			if (note.length() > 40)
-				str += "note: " +note.substring(0,39) + "...";
-			else
-				str += " note: "+note;
-		}
-		str += " # segments: " + segments.size() ;
-		return str ;
-	}
-
-
-	/** returns true if the specified sequence position is within the range of this Feature
-	 * 
-	 * @param seqPosition the position to check
-	 * @return true if the position is within the ranges of the segments of this feature
-	 */
-	public boolean overlaps(int seqPosition){
-		List segments = getSegments();
-		Iterator iter =segments.iterator();
-
-		while (iter.hasNext()){
-
-			Segment seg = (Segment) iter.next();
-			if ( seg.overlaps(seqPosition) )
-				return true;                                     
-		}
-
-		return false;
-	}
-
-	public void setSource(String s) { source = s;}
-	public String getSource() { return source; };
-
-
-	public void setName(String nam) { name = nam; }
-	public String getName() { return name; }
-
-	public void setMethod(String methd) { method = methd ; }
-	public String getMethod() { return method ; }
-
-	public void setType(String typ) { type = typ ; }
-	public String getType() { return type ; }
-
-	public void setNote(String nte) { 
-		if (nte != null)
-			note = nte; 
-		}
-	public String getNote() { return note ; }
-
-	public void setLink(String lnk) { link = lnk;}
-	public String getLink() { return link;}
-
-	public void setScore(String s){ score = s;}
-	public String getScore() { return score;}
-
-	/** add a segment to this feature */
-	public void addSegment(int start, int end, String name) {
-		Segment s = new SegmentImpl() ;
-		s.setStart(start);
-		s.setEnd(end) ;
-		s.setName(name);
-		s.setParent(this);
-		segments.add(s);
-	}
-
-	public void addSegment( Segment s ){
-		s.setParent(this);
-		segments.add(s);
-	}
-
-	public List getSegments() {
-		return segments ;
-	}
-
-
-	public String getOrientation() {
-		return orientation;
-	}
-
-	public void setOrientation(String orientation) {
-		this.orientation = orientation;
-	}
-
-	/** test if two features are equivalent 
-	 * important: only comares type,method and source.
-	 * The individual segments are not compared!
-	 * 
-	 * */
-	public  boolean equals(FeatureTrack feat) {
-//		if ( note == null) {
-		//  if (( feat.getNote() == null ) || 
-		// ( feat.getNote().equals(""))) {
-		//} else if ( this.note.equals(feat.getNote())){
-		//  return true;
-		//}
-		if ( this.type.equals(feat.getType())){
-			if ( this.method.equals(feat.getMethod())){
-				if ( this.source.equals(feat.getSource())){										
-					if (this.note.equals(feat.getNote())){
-						return true;
-					}
-				}
-			}
-		}
-		return false;
-
-	}
-	public String getTypeCategory() {
-		// TODO Auto-generated method stub
-		return typeCategory;
-	}
-
-	public String getTypeID() {
-		// TODO Auto-generated method stub
-		return typeID;
-	}
-
-	public void setTypeCategory(String typeCategory) {
-		this.typeCategory = typeCategory;
-		
-	}
-
-	public void setTypeID(String typeID) {
-		this.typeID = typeID;
-		
-	}
-	
-
+public abstract class AbstractFeatureTrack implements FeatureTrack,
+        Cloneable
+{
+
+  String name;
+
+  String method;
+
+  String type;
+
+  List segments;
+
+  String note;
+
+  String link;
+
+  String source;
+
+  String score;
+
+  String orientation;
+
+  String typeID;
+
+  String typeCategory;
+
+  public AbstractFeatureTrack()
+  {
+    source = "Unknown";
+    method = "Unknown";
+    type = "Unknown";
+    note = "";
+    link = "";
+    score = "";
+    orientation = null;
+    segments = new ArrayList();
+
+  }
+
+  public abstract Object clone();
+
+  public String toString()
+  {
+    String str = "Feature: method: " + method + " type: " + type;
+    if (name != null)
+      str += " name: " + name;
+
+    if ((note != null) && (!note.equals("null")))
+    {
+      if (note.length() > 40)
+        str += "note: " + note.substring(0, 39) + "...";
+      else
+        str += " note: " + note;
+    }
+    str += " # segments: " + segments.size();
+    return str;
+  }
+
+  /**
+   * returns true if the specified sequence position is within the range of this
+   * Feature
+   * 
+   * @param seqPosition
+   *                the position to check
+   * @return true if the position is within the ranges of the segments of this
+   *         feature
+   */
+  public boolean overlaps(int seqPosition)
+  {
+    List segments = getSegments();
+    Iterator iter = segments.iterator();
+
+    while (iter.hasNext())
+    {
+
+      Segment seg = (Segment) iter.next();
+      if (seg.overlaps(seqPosition))
+        return true;
+    }
+
+    return false;
+  }
+
+  public void setSource(String s)
+  {
+    source = s;
+  }
+
+  public String getSource()
+  {
+    return source;
+  };
+
+  public void setName(String nam)
+  {
+    name = nam;
+  }
+
+  public String getName()
+  {
+    return name;
+  }
+
+  public void setMethod(String methd)
+  {
+    method = methd;
+  }
+
+  public String getMethod()
+  {
+    return method;
+  }
+
+  public void setType(String typ)
+  {
+    type = typ;
+  }
+
+  public String getType()
+  {
+    return type;
+  }
+
+  public void setNote(String nte)
+  {
+    if (nte != null)
+      note = nte;
+  }
+
+  public String getNote()
+  {
+    return note;
+  }
+
+  public void setLink(String lnk)
+  {
+    link = lnk;
+  }
+
+  public String getLink()
+  {
+    return link;
+  }
+
+  public void setScore(String s)
+  {
+    score = s;
+  }
+
+  public String getScore()
+  {
+    return score;
+  }
+
+  /** add a segment to this feature */
+  public void addSegment(int start, int end, String name)
+  {
+    Segment s = new SegmentImpl();
+    s.setStart(start);
+    s.setEnd(end);
+    s.setName(name);
+    s.setParent(this);
+    segments.add(s);
+  }
+
+  public void addSegment(Segment s)
+  {
+    s.setParent(this);
+    segments.add(s);
+  }
+
+  public List getSegments()
+  {
+    return segments;
+  }
+
+  public String getOrientation()
+  {
+    return orientation;
+  }
+
+  public void setOrientation(String orientation)
+  {
+    this.orientation = orientation;
+  }
+
+  /**
+   * test if two features are equivalent important: only comares type,method and
+   * source. The individual segments are not compared!
+   * 
+   */
+  public boolean equals(FeatureTrack feat)
+  {
+    // if ( note == null) {
+    // if (( feat.getNote() == null ) ||
+    // ( feat.getNote().equals(""))) {
+    // } else if ( this.note.equals(feat.getNote())){
+    // return true;
+    // }
+    if (this.type.equals(feat.getType()))
+    {
+      if (this.method.equals(feat.getMethod()))
+      {
+        if (this.source.equals(feat.getSource()))
+        {
+          if (this.note.equals(feat.getNote()))
+          {
+            return true;
+          }
+        }
+      }
+    }
+    return false;
+
+  }
+
+  public String getTypeCategory()
+  {
+    // TODO Auto-generated method stub
+    return typeCategory;
+  }
+
+  public String getTypeID()
+  {
+    // TODO Auto-generated method stub
+    return typeID;
+  }
+
+  public void setTypeCategory(String typeCategory)
+  {
+    this.typeCategory = typeCategory;
+
+  }
+
+  public void setTypeID(String typeID)
+  {
+    this.typeID = typeID;
+
+  }
 
 }
diff --git a/src/org/biojava/dasobert/feature/AbstractSegment.java b/src/org/biojava/dasobert/feature/AbstractSegment.java
index daa7f75..12c5e1d 100644
--- a/src/org/biojava/dasobert/feature/AbstractSegment.java
+++ b/src/org/biojava/dasobert/feature/AbstractSegment.java
@@ -25,139 +25,232 @@ package org.biojava.dasobert.feature;
 
 import java.awt.Color;
 
-public abstract class AbstractSegment implements Segment,Cloneable {
-	int start   ;
-	int end     ;
-	String name ;
-	Color color ;
-	FeatureTrack parent ;
-	String txtColor ;
-	String note;
-
-	public abstract Object clone();
-	
-	/* (non-Javadoc)
-	 * @see org.biojava.spice.feature.SegmentIF#toString()
-	 */
-	public String toString() {
-		String str = "Segment: " +name + " " +start + " " + end ;
-		if ( ( note != null ) && ( ! note.equals("null")))
-			if ( note.length() >40)
-				str += note.substring(0,39)+"...";
-			else
-				str += note;
-		return str ;
-	}
-
-	/* (non-Javadoc)
-	 * @see org.biojava.spice.feature.SegmentIF#getNote()
-	 */
-	public String getNote() {
-		return note;
-	}
-
-	/* (non-Javadoc)
-	 * @see org.biojava.spice.feature.SegmentIF#setNote(java.lang.String)
-	 */
-	public void setNote(String note) {
-		this.note = note;
-	}
-
-	/* (non-Javadoc)
-	 * @see org.biojava.spice.feature.SegmentIF#setStart(int)
-	 */
-	public void setStart(int strt) {start = strt ; }
-	/* (non-Javadoc)
-	 * @see org.biojava.spice.feature.SegmentIF#getStart()
-	 */
-	public int  getStart() {return start ;}
-
-	/* (non-Javadoc)
-	 * @see org.biojava.spice.feature.SegmentIF#setEnd(int)
-	 */
-	public void setEnd(int ed) { end = ed;}
-	/* (non-Javadoc)
-	 * @see org.biojava.spice.feature.SegmentIF#getEnd()
-	 */
-	public int getEnd() { return end;}
-
-	/* (non-Javadoc)
-	 * @see org.biojava.spice.feature.SegmentIF#setName(java.lang.String)
-	 */
-	public void setName(String nam) { name = nam;}
-	/* (non-Javadoc)
-	 * @see org.biojava.spice.feature.SegmentIF#getName()
-	 */
-	public String getName() { return name ; }
-
-	/* (non-Javadoc)
-	 * @see org.biojava.spice.feature.SegmentIF#setColor(java.awt.Color)
-	 */
-	public void setColor(Color col) { color = col; }
-	/* (non-Javadoc)
-	 * @see org.biojava.spice.feature.SegmentIF#getColor()
-	 */
-	public Color getColor() { return color ; }
-
-	/* (non-Javadoc)
-	 * @see org.biojava.spice.feature.SegmentIF#setParent(org.biojava.spice.feature.Feature)
-	 */
-	public void setParent(FeatureTrack f) { parent = f;}
-	/* (non-Javadoc)
-	 * @see org.biojava.spice.feature.SegmentIF#getParent()
-	 */
-	public FeatureTrack getParent(){ return parent;}
-
-	/* (non-Javadoc)
-	 * @see org.biojava.spice.feature.SegmentIF#setTxtColor(java.lang.String)
-	 */
-	public void setTxtColor(String str) { txtColor = str; }
-	/* (non-Javadoc)
-	 * @see org.biojava.spice.feature.SegmentIF#getTxtColor()
-	 */
-	public String getTxtColor() { return txtColor;}
-
-
-	/* (non-Javadoc)
-	 * @see org.biojava.spice.feature.SegmentIF#overlaps(int)
-	 */
-	public boolean overlaps(int seqPosition){
-		if ( ( getStart() <= seqPosition) && ( getEnd() >= seqPosition)){
-			return true;             
-		}   
-		return false;
-	}
-
-
-
-	/* (non-Javadoc)
-	 * @see org.biojava.spice.feature.SegmentIF#overlaps(org.biojava.spice.feature.Segment)
-	 */
-	public boolean overlaps(Segment segment){
-		if (! (this.start <= this.end )) 
-			throw new IndexOutOfBoundsException("start > end for segment" + this);
-
-		if ( ! (segment.getStart() <= segment.getEnd() ))
-			throw new IndexOutOfBoundsException("start > end for segment" + segment);
-
-		// start must be in region of other
-		if ( this.start >= segment.getStart()){
-			if ( this.start <= segment.getEnd()){
-				return true;
-			}
-		}
-		// or end must be in region of other..
-		if ( this.end >= segment.getStart() ) {
-			if ( this.end <= segment.getEnd()){
-				return true;
-			}
-		}
-
-		if ( this.start <= segment.getStart() ) {
-			if ( this.end >= segment.getEnd() ) {
-				return true;
-			}
-		}
-		return false;
-	}
+public abstract class AbstractSegment implements Segment, Cloneable
+{
+  int start;
+
+  int end;
+
+  String name;
+
+  Color color;
+
+  FeatureTrack parent;
+
+  String txtColor;
+
+  String note;
+
+  public abstract Object clone();
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see org.biojava.spice.feature.SegmentIF#toString()
+   */
+  public String toString()
+  {
+    String str = "Segment: " + name + " " + start + " " + end;
+    if ((note != null) && (!note.equals("null")))
+      if (note.length() > 40)
+        str += note.substring(0, 39) + "...";
+      else
+        str += note;
+    return str;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see org.biojava.spice.feature.SegmentIF#getNote()
+   */
+  public String getNote()
+  {
+    return note;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see org.biojava.spice.feature.SegmentIF#setNote(java.lang.String)
+   */
+  public void setNote(String note)
+  {
+    this.note = note;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see org.biojava.spice.feature.SegmentIF#setStart(int)
+   */
+  public void setStart(int strt)
+  {
+    start = strt;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see org.biojava.spice.feature.SegmentIF#getStart()
+   */
+  public int getStart()
+  {
+    return start;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see org.biojava.spice.feature.SegmentIF#setEnd(int)
+   */
+  public void setEnd(int ed)
+  {
+    end = ed;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see org.biojava.spice.feature.SegmentIF#getEnd()
+   */
+  public int getEnd()
+  {
+    return end;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see org.biojava.spice.feature.SegmentIF#setName(java.lang.String)
+   */
+  public void setName(String nam)
+  {
+    name = nam;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see org.biojava.spice.feature.SegmentIF#getName()
+   */
+  public String getName()
+  {
+    return name;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see org.biojava.spice.feature.SegmentIF#setColor(java.awt.Color)
+   */
+  public void setColor(Color col)
+  {
+    color = col;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see org.biojava.spice.feature.SegmentIF#getColor()
+   */
+  public Color getColor()
+  {
+    return color;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see org.biojava.spice.feature.SegmentIF#setParent(org.biojava.spice.feature.Feature)
+   */
+  public void setParent(FeatureTrack f)
+  {
+    parent = f;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see org.biojava.spice.feature.SegmentIF#getParent()
+   */
+  public FeatureTrack getParent()
+  {
+    return parent;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see org.biojava.spice.feature.SegmentIF#setTxtColor(java.lang.String)
+   */
+  public void setTxtColor(String str)
+  {
+    txtColor = str;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see org.biojava.spice.feature.SegmentIF#getTxtColor()
+   */
+  public String getTxtColor()
+  {
+    return txtColor;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see org.biojava.spice.feature.SegmentIF#overlaps(int)
+   */
+  public boolean overlaps(int seqPosition)
+  {
+    if ((getStart() <= seqPosition) && (getEnd() >= seqPosition))
+    {
+      return true;
+    }
+    return false;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see org.biojava.spice.feature.SegmentIF#overlaps(org.biojava.spice.feature.Segment)
+   */
+  public boolean overlaps(Segment segment)
+  {
+    if (!(this.start <= this.end))
+      throw new IndexOutOfBoundsException("start > end for segment" + this);
+
+    if (!(segment.getStart() <= segment.getEnd()))
+      throw new IndexOutOfBoundsException("start > end for segment"
+              + segment);
+
+    // start must be in region of other
+    if (this.start >= segment.getStart())
+    {
+      if (this.start <= segment.getEnd())
+      {
+        return true;
+      }
+    }
+    // or end must be in region of other..
+    if (this.end >= segment.getStart())
+    {
+      if (this.end <= segment.getEnd())
+      {
+        return true;
+      }
+    }
+
+    if (this.start <= segment.getStart())
+    {
+      if (this.end >= segment.getEnd())
+      {
+        return true;
+      }
+    }
+    return false;
+  }
 }
diff --git a/src/org/biojava/dasobert/feature/FeatureComparator.java b/src/org/biojava/dasobert/feature/FeatureComparator.java
index 900d196..2b75c22 100644
--- a/src/org/biojava/dasobert/feature/FeatureComparator.java
+++ b/src/org/biojava/dasobert/feature/FeatureComparator.java
@@ -22,60 +22,66 @@
  *
  */
 
+package org.biojava.dasobert.feature;
 
-package org.biojava.dasobert.feature ;
-
-import java.util.Comparator ;
+import java.util.Comparator;
 import java.util.Iterator;
 import java.util.List;
 
-
-/** a comparator to sort Features byt type
+/**
+ * a comparator to sort Features byt type
+ * 
  * @author Andreas Prlic
  */
 
-public class FeatureComparator 
-implements Comparator
+public class FeatureComparator implements Comparator
 {
 
-	public FeatureComparator() {
-	}
+  public FeatureComparator()
+  {
+  }
 
-	public int compare(Object a, Object b) {
-		FeatureTrack x = (FeatureTrack) a;
-		FeatureTrack y = (FeatureTrack) b;
+  public int compare(Object a, Object b)
+  {
+    FeatureTrack x = (FeatureTrack) a;
+    FeatureTrack y = (FeatureTrack) b;
 
-		String typea = x.getType();
-		String typeb = y.getType();
+    String typea = x.getType();
+    String typeb = y.getType();
 
-		if ( ! typea.equals(typeb))
-			return typea.compareTo(typeb);
+    if (!typea.equals(typeb))
+      return typea.compareTo(typeb);
 
-		List s1 = x.getSegments();
-		List s2 = y.getSegments();
+    List s1 = x.getSegments();
+    List s2 = y.getSegments();
 
-		Iterator iter1 = s1.iterator();
-		Iterator iter2 = s2.iterator();
+    Iterator iter1 = s1.iterator();
+    Iterator iter2 = s2.iterator();
 
-		while (iter1.hasNext()){
-			Segment seg1 = (Segment)iter1.next();
-			int start1 = seg1.getStart();
+    while (iter1.hasNext())
+    {
+      Segment seg1 = (Segment) iter1.next();
+      int start1 = seg1.getStart();
 
-			while (iter2.hasNext()){
-				Segment seg2 = (Segment)iter2.next();
-				int start2 = seg2.getStart();
+      while (iter2.hasNext())
+      {
+        Segment seg2 = (Segment) iter2.next();
+        int start2 = seg2.getStart();
 
-				if ( start1 < start2){
-					return -1;
-				} if ( start1 > start2){
-					return 1;
-				}
+        if (start1 < start2)
+        {
+          return -1;
+        }
+        if (start1 > start2)
+        {
+          return 1;
+        }
 
-			}
-		}
+      }
+    }
 
-		return 0;
+    return 0;
 
-	}
+  }
 
 }
diff --git a/src/org/biojava/dasobert/feature/FeatureMapComparator.java b/src/org/biojava/dasobert/feature/FeatureMapComparator.java
index 8aa747b..aa38981 100644
--- a/src/org/biojava/dasobert/feature/FeatureMapComparator.java
+++ b/src/org/biojava/dasobert/feature/FeatureMapComparator.java
@@ -22,48 +22,47 @@
  *
  */
 
+package org.biojava.dasobert.feature;
 
-package org.biojava.dasobert.feature ;
+import java.util.Comparator;
+import java.util.Map;
 
-import java.util.Comparator ;
-import java.util.Map ;
-
-/** a comparator to sort Features if they are still in a Map ( sorts by type )
+/**
+ * a comparator to sort Features if they are still in a Map ( sorts by type )
+ * 
  * @author Andreas Prlic
  */
 
-public class FeatureMapComparator 
-    implements Comparator
+public class FeatureMapComparator implements Comparator
 {
 
-    public FeatureMapComparator() {
-    }
+  public FeatureMapComparator()
+  {
+  }
 
-    public int compare(Object a, Object b) {
-	Map x = (Map) a;
-	Map y = (Map) b;
+  public int compare(Object a, Object b)
+  {
+    Map x = (Map) a;
+    Map y = (Map) b;
 
-	String typea = (String)x.get("TYPE");
-	String typeb = (String)y.get("TYPE");
-	
-	
+    String typea = (String) x.get("TYPE");
+    String typeb = (String) y.get("TYPE");
 
-	if ( isSecstruc(typea) && isSecstruc(typeb)) {
-	    return 0 ;
-	}
-	return typea.compareTo(typeb);
+    if (isSecstruc(typea) && isSecstruc(typeb))
+    {
+      return 0;
     }
+    return typea.compareTo(typeb);
+  }
 
-    public boolean isSecstruc(String type) {
-	if ( type.equals("HELIX") 
-	     ||
-	     type.equals("STRAND") 
-	     ||
-	     type.equals("TURN") 
-	     ) {
-	    return true ;
-	}
-	return false ;
+  public boolean isSecstruc(String type)
+  {
+    if (type.equals("HELIX") || type.equals("STRAND")
+            || type.equals("TURN"))
+    {
+      return true;
     }
+    return false;
+  }
 
 }
diff --git a/src/org/biojava/dasobert/feature/FeatureTrack.java b/src/org/biojava/dasobert/feature/FeatureTrack.java
index 42136ee..e7b6bbd 100644
--- a/src/org/biojava/dasobert/feature/FeatureTrack.java
+++ b/src/org/biojava/dasobert/feature/FeatureTrack.java
@@ -28,86 +28,100 @@ import java.util.List;
  * A feature corresponds to a track in Ensembl
  * 
  * @author Andreas Prlic
- *
+ * 
  */
-public interface FeatureTrack {
-    
-	
-	public Object clone();
-	
-    /** returns true if the specified sequence position is within the range of this Feature
-     * 
-     * @param seqPosition the position to check
-     * @return true if the position is within the ranges of the segments of this feature
-     */
-    public boolean overlaps(int seqPosition);
-    
-    public  String toString();
-
-    public  void setSource(String s);
-
-    public  String getSource();
-
-    public  void setName(String nam);
-
-    public  String getName();
-
-    public  void setMethod(String methd);
-
-    public  String getMethod();
-
-    public  void setType(String typ);
-
-    public  String getType();
-
-    public  void setNote(String nte);
-
-    public  String getNote();
-
-    public  void setLink(String lnk);
-
-    public  String getLink();
-    
-    public  void setScore(String score);
-    
-    public  String getScore();
-    
-    public void setOrientation(String orientation);
-    
-    public String getOrientation();
-    
-    /** test if two features are equivalent
-     * 
-     * @param feat feature to compare with 
-     * @return true if equivalend
-     */
-    public abstract boolean equals(FeatureTrack feat);
-
-    /** add a segment to this feature
-     * 
-     * @param start position
-     * @param end position 
-     * @param name of feature
-     */
-    public abstract void addSegment(int start, int end, String name);
-
-    public abstract void addSegment(Segment s);
-
-    public abstract List getSegments();
-    
-    /** set the data from the DAS - type - id field
-     * (used for Ontology support)
-     * @param typeID
-     */
-    public void setTypeID(String typeID);
-    
-    /** set the data from the DAS - type - category field
-     * (used for Ontology support)
-     * @param typeCategory
-     */
-    public void setTypeCategory(String typeCategory);
-    
-    public String getTypeID();
-    public String getTypeCategory();
-   
+public interface FeatureTrack
+{
+
+  public Object clone();
+
+  /**
+   * returns true if the specified sequence position is within the range of this
+   * Feature
+   * 
+   * @param seqPosition
+   *                the position to check
+   * @return true if the position is within the ranges of the segments of this
+   *         feature
+   */
+  public boolean overlaps(int seqPosition);
+
+  public String toString();
+
+  public void setSource(String s);
+
+  public String getSource();
+
+  public void setName(String nam);
+
+  public String getName();
+
+  public void setMethod(String methd);
+
+  public String getMethod();
+
+  public void setType(String typ);
+
+  public String getType();
+
+  public void setNote(String nte);
+
+  public String getNote();
+
+  public void setLink(String lnk);
+
+  public String getLink();
+
+  public void setScore(String score);
+
+  public String getScore();
+
+  public void setOrientation(String orientation);
+
+  public String getOrientation();
+
+  /**
+   * test if two features are equivalent
+   * 
+   * @param feat
+   *                feature to compare with
+   * @return true if equivalend
+   */
+  public abstract boolean equals(FeatureTrack feat);
+
+  /**
+   * add a segment to this feature
+   * 
+   * @param start
+   *                position
+   * @param end
+   *                position
+   * @param name
+   *                of feature
+   */
+  public abstract void addSegment(int start, int end, String name);
+
+  public abstract void addSegment(Segment s);
+
+  public abstract List getSegments();
+
+  /**
+   * set the data from the DAS - type - id field (used for Ontology support)
+   * 
+   * @param typeID
+   */
+  public void setTypeID(String typeID);
+
+  /**
+   * set the data from the DAS - type - category field (used for Ontology
+   * support)
+   * 
+   * @param typeCategory
+   */
+  public void setTypeCategory(String typeCategory);
+
+  public String getTypeID();
+
+  public String getTypeCategory();
+
 }
\ No newline at end of file
diff --git a/src/org/biojava/dasobert/feature/FeatureTrackConverter.java b/src/org/biojava/dasobert/feature/FeatureTrackConverter.java
index d7dee86..4818e10 100644
--- a/src/org/biojava/dasobert/feature/FeatureTrackConverter.java
+++ b/src/org/biojava/dasobert/feature/FeatureTrackConverter.java
@@ -29,462 +29,498 @@ import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 
-
-
-/** converts the features from their "raw" representation as a Map
- * into a Feature class
+/**
+ * converts the features from their "raw" representation as a Map into a Feature
+ * class
+ * 
  * @author Andreas Prlic
- *
+ * 
  */
-public class FeatureTrackConverter {
-
-	public static final Color HELIX_COLOR  = new Color(255,51,51);
-	public static final Color STRAND_COLOR = new Color(255,204,51);
-	public static final Color TURN_COLOR   = new Color(204,204,204); 
-
+public class FeatureTrackConverter
+{
 
-	// some  annotation types, for which there is a special treatment
-	public static final String DISULFID_TYPE = "DISULFID";
-	public static final String SECSTRUC_TYPE = "SECSTRUC";
-	public static final String METAL_TYPE    = "METAL";
-	public static final String MSD_SITE_TYPE = "MSD_SITE";
+  public static final Color HELIX_COLOR = new Color(255, 51, 51);
 
-	String type;
-	public static final String TYPE_HISTOGRAM = "histogram";
-	public static final String TYPE_DEFAULT   = "default";
+  public static final Color STRAND_COLOR = new Color(255, 204, 51);
 
+  public static final Color TURN_COLOR = new Color(204, 204, 204);
 
-	// rotate between these colors
-	public static final  Color[] entColors = new Color []{
-		new Color(51,51,255), // blue
-		new Color(102,255,255),    // cyan
-		new Color(153,255,153), // green
-		new Color(153,255,153), // green
-		new Color(255,153,153), // pink
-		new Color(255,51,51),   // red
-		new Color(255,51,255)    // pink 
-	};
-
-	public static final String[] txtColors = new String[] { 
-		"blue",
-		"pink",
-		"green",
-		"yellow",
-		"red",
-		"cyan",
-	"pink"};
+  // some annotation types, for which there is a special treatment
+  public static final String DISULFID_TYPE = "DISULFID";
 
-	Map[] stylesheet;
+  public static final String SECSTRUC_TYPE = "SECSTRUC";
 
-	boolean isHistogram = false;
+  public static final String METAL_TYPE = "METAL";
 
+  public static final String MSD_SITE_TYPE = "MSD_SITE";
 
-	public FeatureTrackConverter(){
-		type = TYPE_DEFAULT;	
-		stylesheet = new Map[0];
-	}
-
-	public FeatureTrackConverter(Map[] stylesheet){
-
-		if (stylesheet == null)
-			stylesheet = new Map[0];
-
-		this.stylesheet = stylesheet;
-
-	}
-
-
-	public FeatureTrackConverter(Map[] stylesheet, boolean isHistogram){
-		this(stylesheet);
-		this.isHistogram = isHistogram;
-		if ( isHistogram)
-			type = TYPE_HISTOGRAM;
-	}
-	public String getType() {
-		return type;
-	}
+  String type;
 
-	public void setType(String type) {
-		if ( type.equals(TYPE_HISTOGRAM))
-			isHistogram = true;
-		this.type = type;
-	}
+  public static final String TYPE_HISTOGRAM = "histogram";
 
-	public boolean isHistogram() {
-		return isHistogram;
-	}
-
-
-	public void setHistogram(boolean isHistogram) {
-		this.isHistogram = isHistogram;
-	}
-
-	
-
-	
-
-	public  FeatureTrack[] convertMap2Features(Map[] mapfeatures){
-		List features = new ArrayList();
-
-		boolean first = true ;
-		boolean secstruc = false ;
-		boolean isGroup  = false;
-
-		FeatureTrack feat = null ;
-		Segment segment   = null ;
-
-		int featuresCounter = 0;
-		String prevGroup = null;
-
-		for (int i = 0 ; i< mapfeatures.length;i++) {
-
-			Map currentFeatureMap = mapfeatures[i];
-			String type = (String) currentFeatureMap.get("TYPE") ;
-
-			
-			
-			String group = (String) currentFeatureMap.get("GROUP");
-			if ( group != null){
-				if ( prevGroup != null) {
-					if ( group.equals(prevGroup)){
-						feat.setName(group);
-						isGroup = true;
-					} else {
-						isGroup = false;
-					}
-				} else {
-					isGroup = false;
-				}
-			} else {
-				isGroup = false;
-			}			
-
-			// we are skipping literature references for the moment 
-			// TODO: add a display to spice for non-positional features
-			//
-			if ( type.equals("reference") || type.equals("GOA")){
-				continue ;
-			}
-
-			if (! first) 
-			{
-				// if not first feature
-
-				if ( (! secstruc ) && (! isGroup) )  {             
-
-					// if not secondary structure and not in a group ...
-					features = testAddFeatures(features,feat);
-
-
-				} else if ( ! 
-						(
-								type.equals("HELIX")  || 
-								type.equals("STRAND") || 
-								type.equals("TURN")  
-						) 
-				)
-				{
-					// end of secondary structure
-					secstruc = false ;
-					if ( feat != null && (! isGroup)) {						
-						features = testAddFeatures(features,feat);                        
-					}
-
-				}
-			} // end of not first
-
-			first = false ;             
-			if ( (! secstruc) && (! isGroup)) {				
-				featuresCounter +=1;
-				feat = getNewFeat(currentFeatureMap);       
-			}
-
-
-
-
-			if (type.equals("STRAND")){
-				secstruc = true ;				
-				currentFeatureMap.put("colorTxt","yellow");
-				feat.setName("SECSTRUC");       
-				feat.setType("SECSTRUC");
-			}
-
-			else if (type.equals("HELIX")) {
-				secstruc = true ;				
-				currentFeatureMap.put("colorTxt","red");
-				feat.setName("SECSTRUC");
-				feat.setType("SECSTRUC");
-			}   
-
-			else if (type.equals("TURN")) {
-				secstruc = true ;				
-				currentFeatureMap.put("colorTxt","white");
-
-				feat.setName("SECSTRUC");
-				feat.setType("SECSTRUC");
-			}     
-			else {
-				secstruc = false ;				
-				currentFeatureMap.put("colorTxt",txtColors[featuresCounter%txtColors.length]);
-				if ( ! isGroup) {
-					try {
-						feat.setName(type);
-					
-					} catch ( NullPointerException e) {
-						//e.printStackTrace();
-						feat.setName("null");
-					}
-				}
-			}
-
-			segment = getNewSegment(currentFeatureMap);
-
-			feat.addSegment(segment);       
-			prevGroup = group;
-		}   
-
-		if ( feat != null)  
-			features =testAddFeatures(features,feat);
-
-
-		return (FeatureTrack[]) features.toArray(new FeatureTrack[features.size()]);
-	}
-
-	/**	 test if this features is added as a new feature to the features list, 
-	 * or if it is joint with an already existing one...
-	 * 
-	 * @param features
-	 * @param newFeature
-	 * @return a List of FeatureTrack objects
-	 */
-	protected  List testAddFeatures(List features,FeatureTrack newFeature){
-		
-		//System.out.println("testing " + newFeature + " " + newFeature.getScore());   
-		Iterator iter = features.iterator();
-
-
-		if ( isHistogramFeatureType(newFeature)) {  
-			
-			// return histogram type features
-			type = TYPE_HISTOGRAM;
-
-			Segment seg = getHistogramSegmentFromFeature(newFeature);
-
-			while (iter.hasNext()){
-				FeatureTrack knownFeature = (FeatureTrack) iter.next() ;
-				String knownType = knownFeature.getType();
-
-				//System.out.println("found histogram style " + feat);
-				// set type of this DAS source to being HISTOGRAM style
-
-
-				if ( knownType.equals(newFeature.getType())){
-					// convert the feature into a HistogramSegment and add to the already known feature
-
-					knownFeature.addSegment(seg);
-					// we can return now
-					return features;
-				}
-
-
-			}
-			// we could not link this to any existing feature
-			// convert it to a new HistogramFeature
-			HistogramFeature hfeat = new HistogramFeature();
-
-			hfeat.setLink(newFeature.getLink());
-			hfeat.setMethod(newFeature.getMethod());
-			hfeat.setName(newFeature.getName());
-			hfeat.setNote(newFeature.getNote());
-			hfeat.setScore("0");
-			hfeat.setSource(newFeature.getSource());
-			hfeat.addSegment(seg);
-			hfeat.setType(newFeature.getType());
-
-			newFeature = hfeat;
-			features.add(newFeature);
-			return features;
-		} 
-
-
-
-		while (iter.hasNext()){
-			FeatureTrack knownFeature = (FeatureTrack) iter.next() ;
-			// this only compares method source and type ...
-			boolean sameFeat = false;
-			if ( knownFeature.equals(newFeature))
-				sameFeat = true;
-
-			if ( ( knownFeature.getSource().equals(newFeature.getSource() )) &&
-					( knownFeature.getMethod().equals(newFeature.getMethod())) &&
-					( knownFeature.getNote().equals(newFeature.getNote())) &&
-					isSecondaryStructureFeat(knownFeature) && 
-					isSecondaryStructureFeat(newFeature))
-				sameFeat =true;
-
-			if ( sameFeat) {
-
-				// seems to be of same type, method and source, so check if the segments can be joined
-
-				List tmpsegs = knownFeature.getSegments();
-				Iterator segiter = tmpsegs.iterator();
-				List newsegs = newFeature.getSegments();
-				Iterator newsegsiter = newsegs.iterator();
-				boolean overlap = false;
-				while (newsegsiter.hasNext()){
-					Segment newseg = (Segment)newsegsiter.next();
-
-
-					while (segiter.hasNext()){
-						Segment tmpseg = (Segment) segiter.next();
-
-						if (  tmpseg.overlaps(newseg))
-							overlap = true;
-					}
-				}
-
-				if ( ! overlap){
-					// add all new segments to old features...
-					newsegsiter = newsegs.iterator();
-					while (newsegsiter.hasNext()){
-						Segment newseg = (Segment)newsegsiter.next();
-						knownFeature.addSegment(newseg);
-					}
-
-					return features;
-				} 
-			}
-
-		}
-
-		//      if we get here, the  features could not be joint with any other one, so there is always some overlap
-		// add to the list of known features
-		features.add(newFeature);
-		return features;
-	}
-
-	private FeatureTrack getNewFeat(Map currentFeatureMap) {
-		FeatureTrack feat = new FeatureTrackImpl();
-		//logger.finest(currentFeatureMap);
-		//System.out.println("DrawableDasSource " + currentFeatureMap);
-		feat.setSource((String)currentFeatureMap.get("dassource"));
-		feat.setName(  (String)currentFeatureMap.get("NAME"));
-		feat.setType(  (String)currentFeatureMap.get("TYPE"));
-		feat.setLink(  (String)currentFeatureMap.get("LINK"));
-		feat.setNote(  (String)currentFeatureMap.get("NOTE"));
-		
-		String typeID       = (String) currentFeatureMap.get("TYPE_ID");
-		String typeCategory = (String) currentFeatureMap.get("TYPE_CATEGORY");
-		feat.setTypeID(typeID);
-		feat.setTypeCategory(typeCategory);
-		
-		String method = (String)currentFeatureMap.get("METHOD");
-		if ( method == null) { method = "";}
-		feat.setMethod(method);
-		feat.setScore( (String)currentFeatureMap.get("SCORE"));
-		return feat ;
-	}
-
-	private Segment getNewSegment(Map featureMap) {
-		Segment s = new SegmentImpl();
-		String sstart = (String)featureMap.get("START") ;
-		String send   = (String)featureMap.get("END")   ;
-		int start = Integer.parseInt(sstart) ;
-		int end   = Integer.parseInt(send)   ;
-		s.setStart(start);
-		s.setEnd(end);
-		s.setName((String)featureMap.get("TYPE"));
-		s.setTxtColor((String)featureMap.get("colorTxt"));  
-		s.setColor((Color)featureMap.get("color"));
-		s.setNote((String) featureMap.get("NOTE"));
-		return s ;
-
-	}
-
-	private boolean isSecondaryStructureFeat(FeatureTrack feat){
-		String type = feat.getType();
-		if (
-				type.equals("HELIX")  || 
-				type.equals("STRAND") || 
-				type.equals("TURN")
-		) return true;
-		return false;
-	}
-
-	private boolean isHistogramFeatureType(FeatureTrack feat){
-		String ftype = feat.getType();
-
-		Map[] style = stylesheet;
-
-		//System.out.println("is HistogramFeature type " + ftype + " " + style );
-
-
-		// todo : move this info into a config file...
-
-		if ( ftype.equals("hydrophobicity")){
-			return true;
-		}
-		if ( getType().equals(TYPE_HISTOGRAM) )
-			return true;
-
-
-
-		if (style != null ) {
-
-			for ( int i =0; i< style.length ; i++){
-				Map m = style[i];
-
-				// make sure the stylesheet is for this feature type
-				String styleType = (String) m.get("type");
-				if ( styleType != null) {
-					if ( ! styleType.equals(ftype)){
-						continue;
-					}
-				} else {
-					continue;
-				}
-
-				String type = (String) m.get("style");
-				if ( type != null) {
-					//System.out.println("stylesheet type " + type);
-					if ( type.equals("gradient") || ( type.equals("lineplot")) || ( type.equals("histogram"))){
-
-						return true;
-					}
-				}
-			}
-		}
-
-		return false;
-	}
-
-
-	private HistogramSegment getHistogramSegmentFromFeature(FeatureTrack feat){
-		HistogramSegment s = new HistogramSegment();
-
-		double score = 0.0;
-
-		try {
-			score = Double.parseDouble(feat.getScore());
-
-		} catch (Exception e){
-			//e.printStackTrace();
-		}
-		s.setScore(score);		
-		List segments = feat.getSegments();
-		if (segments.size() > 0){
-			Segment seg = (Segment) segments.get(0);
-			s.setName(seg.getName());
-			s.setStart(seg.getStart());
-			s.setEnd(seg.getEnd());
-			s.setNote(seg.getNote());
-			s.setColor(seg.getColor());
-			s.setTxtColor(seg.getTxtColor());
-		}
-
-
-		return s;
-	}
+  public static final String TYPE_DEFAULT = "default";
 
+  // rotate between these colors
+  public static final Color[] entColors = new Color[]
+  { new Color(51, 51, 255), // blue
+      new Color(102, 255, 255), // cyan
+      new Color(153, 255, 153), // green
+      new Color(153, 255, 153), // green
+      new Color(255, 153, 153), // pink
+      new Color(255, 51, 51), // red
+      new Color(255, 51, 255) // pink
+  };
+
+  public static final String[] txtColors = new String[]
+  { "blue", "pink", "green", "yellow", "red", "cyan", "pink" };
+
+  Map[] stylesheet;
+
+  boolean isHistogram = false;
+
+  public FeatureTrackConverter()
+  {
+    type = TYPE_DEFAULT;
+    stylesheet = new Map[0];
+  }
+
+  public FeatureTrackConverter(Map[] stylesheet)
+  {
+
+    if (stylesheet == null)
+      stylesheet = new Map[0];
+
+    this.stylesheet = stylesheet;
+
+  }
+
+  public FeatureTrackConverter(Map[] stylesheet, boolean isHistogram)
+  {
+    this(stylesheet);
+    this.isHistogram = isHistogram;
+    if (isHistogram)
+      type = TYPE_HISTOGRAM;
+  }
+
+  public String getType()
+  {
+    return type;
+  }
+
+  public void setType(String type)
+  {
+    if (type.equals(TYPE_HISTOGRAM))
+      isHistogram = true;
+    this.type = type;
+  }
+
+  public boolean isHistogram()
+  {
+    return isHistogram;
+  }
+
+  public void setHistogram(boolean isHistogram)
+  {
+    this.isHistogram = isHistogram;
+  }
+
+  public FeatureTrack[] convertMap2Features(Map[] mapfeatures)
+  {
+    List features = new ArrayList();
+
+    boolean first = true;
+    boolean secstruc = false;
+    boolean isGroup = false;
+
+    FeatureTrack feat = null;
+    Segment segment = null;
+
+    int featuresCounter = 0;
+    String prevGroup = null;
+
+    for (int i = 0; i < mapfeatures.length; i++)
+    {
+
+      Map currentFeatureMap = mapfeatures[i];
+      String type = (String) currentFeatureMap.get("TYPE");
+
+      String group = (String) currentFeatureMap.get("GROUP");
+      if (group != null)
+      {
+        if (prevGroup != null)
+        {
+          if (group.equals(prevGroup))
+          {
+            feat.setName(group);
+            isGroup = true;
+          }
+          else
+          {
+            isGroup = false;
+          }
+        }
+        else
+        {
+          isGroup = false;
+        }
+      }
+      else
+      {
+        isGroup = false;
+      }
+
+      // we are skipping literature references for the moment
+      // TODO: add a display to spice for non-positional features
+      //
+      if (type.equals("reference") || type.equals("GOA"))
+      {
+        continue;
+      }
+
+      if (!first)
+      {
+        // if not first feature
+
+        if ((!secstruc) && (!isGroup))
+        {
+
+          // if not secondary structure and not in a group ...
+          features = testAddFeatures(features, feat);
+
+        }
+        else if (!(type.equals("HELIX") || type.equals("STRAND") || type
+                .equals("TURN")))
+        {
+          // end of secondary structure
+          secstruc = false;
+          if (feat != null && (!isGroup))
+          {
+            features = testAddFeatures(features, feat);
+          }
+
+        }
+      } // end of not first
+
+      first = false;
+      if ((!secstruc) && (!isGroup))
+      {
+        featuresCounter += 1;
+        feat = getNewFeat(currentFeatureMap);
+      }
+
+      if (type.equals("STRAND"))
+      {
+        secstruc = true;
+        currentFeatureMap.put("colorTxt", "yellow");
+        feat.setName("SECSTRUC");
+        feat.setType("SECSTRUC");
+      }
+
+      else if (type.equals("HELIX"))
+      {
+        secstruc = true;
+        currentFeatureMap.put("colorTxt", "red");
+        feat.setName("SECSTRUC");
+        feat.setType("SECSTRUC");
+      }
+
+      else if (type.equals("TURN"))
+      {
+        secstruc = true;
+        currentFeatureMap.put("colorTxt", "white");
+
+        feat.setName("SECSTRUC");
+        feat.setType("SECSTRUC");
+      }
+      else
+      {
+        secstruc = false;
+        currentFeatureMap.put("colorTxt", txtColors[featuresCounter
+                % txtColors.length]);
+        if (!isGroup)
+        {
+          try
+          {
+            feat.setName(type);
+
+          } catch (NullPointerException e)
+          {
+            // e.printStackTrace();
+            feat.setName("null");
+          }
+        }
+      }
+
+      segment = getNewSegment(currentFeatureMap);
+
+      feat.addSegment(segment);
+      prevGroup = group;
+    }
+
+    if (feat != null)
+      features = testAddFeatures(features, feat);
+
+    return (FeatureTrack[]) features.toArray(new FeatureTrack[features
+            .size()]);
+  }
+
+  /**
+   * test if this features is added as a new feature to the features list, or if
+   * it is joint with an already existing one...
+   * 
+   * @param features
+   * @param newFeature
+   * @return a List of FeatureTrack objects
+   */
+  protected List testAddFeatures(List features, FeatureTrack newFeature)
+  {
+
+    // System.out.println("testing " + newFeature + " " +
+    // newFeature.getScore());
+    Iterator iter = features.iterator();
+
+    if (isHistogramFeatureType(newFeature))
+    {
+
+      // return histogram type features
+      type = TYPE_HISTOGRAM;
+
+      Segment seg = getHistogramSegmentFromFeature(newFeature);
+
+      while (iter.hasNext())
+      {
+        FeatureTrack knownFeature = (FeatureTrack) iter.next();
+        String knownType = knownFeature.getType();
+
+        // System.out.println("found histogram style " + feat);
+        // set type of this DAS source to being HISTOGRAM style
+
+        if (knownType.equals(newFeature.getType()))
+        {
+          // convert the feature into a HistogramSegment and add to the already
+          // known feature
+
+          knownFeature.addSegment(seg);
+          // we can return now
+          return features;
+        }
+
+      }
+      // we could not link this to any existing feature
+      // convert it to a new HistogramFeature
+      HistogramFeature hfeat = new HistogramFeature();
+
+      hfeat.setLink(newFeature.getLink());
+      hfeat.setMethod(newFeature.getMethod());
+      hfeat.setName(newFeature.getName());
+      hfeat.setNote(newFeature.getNote());
+      hfeat.setScore("0");
+      hfeat.setSource(newFeature.getSource());
+      hfeat.addSegment(seg);
+      hfeat.setType(newFeature.getType());
+
+      newFeature = hfeat;
+      features.add(newFeature);
+      return features;
+    }
+
+    while (iter.hasNext())
+    {
+      FeatureTrack knownFeature = (FeatureTrack) iter.next();
+      // this only compares method source and type ...
+      boolean sameFeat = false;
+      if (knownFeature.equals(newFeature))
+        sameFeat = true;
+
+      if ((knownFeature.getSource().equals(newFeature.getSource()))
+              && (knownFeature.getMethod().equals(newFeature.getMethod()))
+              && (knownFeature.getNote().equals(newFeature.getNote()))
+              && isSecondaryStructureFeat(knownFeature)
+              && isSecondaryStructureFeat(newFeature))
+        sameFeat = true;
+
+      if (sameFeat)
+      {
+
+        // seems to be of same type, method and source, so check if the segments
+        // can be joined
+
+        List tmpsegs = knownFeature.getSegments();
+        Iterator segiter = tmpsegs.iterator();
+        List newsegs = newFeature.getSegments();
+        Iterator newsegsiter = newsegs.iterator();
+        boolean overlap = false;
+        while (newsegsiter.hasNext())
+        {
+          Segment newseg = (Segment) newsegsiter.next();
+
+          while (segiter.hasNext())
+          {
+            Segment tmpseg = (Segment) segiter.next();
+
+            if (tmpseg.overlaps(newseg))
+              overlap = true;
+          }
+        }
+
+        if (!overlap)
+        {
+          // add all new segments to old features...
+          newsegsiter = newsegs.iterator();
+          while (newsegsiter.hasNext())
+          {
+            Segment newseg = (Segment) newsegsiter.next();
+            knownFeature.addSegment(newseg);
+          }
+
+          return features;
+        }
+      }
+
+    }
+
+    // if we get here, the features could not be joint with any other one, so
+    // there is always some overlap
+    // add to the list of known features
+    features.add(newFeature);
+    return features;
+  }
+
+  private FeatureTrack getNewFeat(Map currentFeatureMap)
+  {
+    FeatureTrack feat = new FeatureTrackImpl();
+    // logger.finest(currentFeatureMap);
+    // System.out.println("DrawableDasSource " + currentFeatureMap);
+    feat.setSource((String) currentFeatureMap.get("dassource"));
+    feat.setName((String) currentFeatureMap.get("NAME"));
+    feat.setType((String) currentFeatureMap.get("TYPE"));
+    feat.setLink((String) currentFeatureMap.get("LINK"));
+    feat.setNote((String) currentFeatureMap.get("NOTE"));
+
+    String typeID = (String) currentFeatureMap.get("TYPE_ID");
+    String typeCategory = (String) currentFeatureMap.get("TYPE_CATEGORY");
+    feat.setTypeID(typeID);
+    feat.setTypeCategory(typeCategory);
+
+    String method = (String) currentFeatureMap.get("METHOD");
+    if (method == null)
+    {
+      method = "";
+    }
+    feat.setMethod(method);
+    feat.setScore((String) currentFeatureMap.get("SCORE"));
+    return feat;
+  }
+
+  private Segment getNewSegment(Map featureMap)
+  {
+    Segment s = new SegmentImpl();
+    String sstart = (String) featureMap.get("START");
+    String send = (String) featureMap.get("END");
+    int start = Integer.parseInt(sstart);
+    int end = Integer.parseInt(send);
+    s.setStart(start);
+    s.setEnd(end);
+    s.setName((String) featureMap.get("TYPE"));
+    s.setTxtColor((String) featureMap.get("colorTxt"));
+    s.setColor((Color) featureMap.get("color"));
+    s.setNote((String) featureMap.get("NOTE"));
+    return s;
+
+  }
+
+  private boolean isSecondaryStructureFeat(FeatureTrack feat)
+  {
+    String type = feat.getType();
+    if (type.equals("HELIX") || type.equals("STRAND")
+            || type.equals("TURN"))
+      return true;
+    return false;
+  }
+
+  private boolean isHistogramFeatureType(FeatureTrack feat)
+  {
+    String ftype = feat.getType();
+
+    Map[] style = stylesheet;
+
+    // System.out.println("is HistogramFeature type " + ftype + " " + style );
+
+    // todo : move this info into a config file...
+
+    if (ftype.equals("hydrophobicity"))
+    {
+      return true;
+    }
+    if (getType().equals(TYPE_HISTOGRAM))
+      return true;
+
+    if (style != null)
+    {
+
+      for (int i = 0; i < style.length; i++)
+      {
+        Map m = style[i];
+
+        // make sure the stylesheet is for this feature type
+        String styleType = (String) m.get("type");
+        if (styleType != null)
+        {
+          if (!styleType.equals(ftype))
+          {
+            continue;
+          }
+        }
+        else
+        {
+          continue;
+        }
+
+        String type = (String) m.get("style");
+        if (type != null)
+        {
+          // System.out.println("stylesheet type " + type);
+          if (type.equals("gradient") || (type.equals("lineplot"))
+                  || (type.equals("histogram")))
+          {
+
+            return true;
+          }
+        }
+      }
+    }
+
+    return false;
+  }
+
+  private HistogramSegment getHistogramSegmentFromFeature(FeatureTrack feat)
+  {
+    HistogramSegment s = new HistogramSegment();
+
+    double score = 0.0;
+
+    try
+    {
+      score = Double.parseDouble(feat.getScore());
+
+    } catch (Exception e)
+    {
+      // e.printStackTrace();
+    }
+    s.setScore(score);
+    List segments = feat.getSegments();
+    if (segments.size() > 0)
+    {
+      Segment seg = (Segment) segments.get(0);
+      s.setName(seg.getName());
+      s.setStart(seg.getStart());
+      s.setEnd(seg.getEnd());
+      s.setNote(seg.getNote());
+      s.setColor(seg.getColor());
+      s.setTxtColor(seg.getTxtColor());
+    }
+
+    return s;
+  }
 
 }
diff --git a/src/org/biojava/dasobert/feature/FeatureTrackImpl.java b/src/org/biojava/dasobert/feature/FeatureTrackImpl.java
index 8eaf6f8..a13fbb3 100644
--- a/src/org/biojava/dasobert/feature/FeatureTrackImpl.java
+++ b/src/org/biojava/dasobert/feature/FeatureTrackImpl.java
@@ -26,48 +26,43 @@ package org.biojava.dasobert.feature;
 
 import java.util.Iterator;
 
-/** a class to store FeatureData and to visualize them
- * coordinate system of features is always UniProt !
- * PDBresnum features served by DAS need to be converted into UniProt coord sys first.
- *
- * a feature consists of one or several segments.
- * segmetns cotnains <start> and <end> information.
- *
+/**
+ * a class to store FeatureData and to visualize them coordinate system of
+ * features is always UniProt ! PDBresnum features served by DAS need to be
+ * converted into UniProt coord sys first.
+ * 
+ * a feature consists of one or several segments. segmetns cotnains <start> and
+ * <end> information.
+ * 
  * @author Andreas Prlic
  */
-public class FeatureTrackImpl 
-extends AbstractFeatureTrack
-implements FeatureTrack
+public class FeatureTrackImpl extends AbstractFeatureTrack implements
+        FeatureTrack
 
 {
-   
-	
-	 public Object clone(){
-	    	
-	    	FeatureTrack f = new FeatureTrackImpl();
-	    	f.setName(name);
-	    	f.setMethod(method);
-	    	f.setType(type);
-	    	f.setNote(note);
-	    	f.setLink(link);
-	    	f.setSource(source);
-	    	f.setScore(score);
-	    	
-	    	Iterator iter = segments.iterator();
-	    	
-	    	while (iter.hasNext()){
-	    		Segment s = (Segment) iter.next();
-	    		f.addSegment((Segment)s.clone());
-	    	}
-	    	
-	    	return f;
-	    	
-	    }
 
-	
-	
-}
+  public Object clone()
+  {
 
+    FeatureTrack f = new FeatureTrackImpl();
+    f.setName(name);
+    f.setMethod(method);
+    f.setType(type);
+    f.setNote(note);
+    f.setLink(link);
+    f.setSource(source);
+    f.setScore(score);
 
+    Iterator iter = segments.iterator();
 
+    while (iter.hasNext())
+    {
+      Segment s = (Segment) iter.next();
+      f.addSegment((Segment) s.clone());
+    }
 
+    return f;
+
+  }
+
+}
diff --git a/src/org/biojava/dasobert/feature/HistogramFeature.java b/src/org/biojava/dasobert/feature/HistogramFeature.java
index ef26891..8663081 100644
--- a/src/org/biojava/dasobert/feature/HistogramFeature.java
+++ b/src/org/biojava/dasobert/feature/HistogramFeature.java
@@ -23,80 +23,73 @@
 
 package org.biojava.dasobert.feature;
 
-
 import java.util.Iterator;
 
-/** a class that represents Histogram Style features
- * in addition to normal features they know about Max and Minimum scores for the whole line
- * Histogram feautes have only one (Histogram) Segment, which contains the scores for each position
- *  
+/**
+ * a class that represents Histogram Style features in addition to normal
+ * features they know about Max and Minimum scores for the whole line Histogram
+ * feautes have only one (Histogram) Segment, which contains the scores for each
+ * position
+ * 
  * @author Andreas Prlic
- *
+ * 
  */
-public class HistogramFeature 
-	extends AbstractFeatureTrack {
-	
-	double max;
-	double min;
-	
-	public HistogramFeature() {
-		super();
-		// TODO Auto-generated constructor stub
-	}
-	
-	
-	
-	public double getMax() {
-		return max;
-	}
-
-
-
-	public void setMax(double max) {
-		this.max = max;
-	}
-
-
-
-	public double getMin() {
-		return min;
-	}
-
-
-
-	public void setMin(double min) {
-		this.min = min;
-	}
-
-
-
-	public Object clone() {
-		
-		HistogramFeature f = new HistogramFeature();
-		
-		f.setName(name);
-    	f.setMethod(method);
-    	f.setType(type);
-    	f.setNote(note);
-    	f.setLink(link);
-    	f.setSource(source);
-    	f.setScore(score);
-    	
-    	Iterator iter = segments.iterator();
-    	
-    	while (iter.hasNext()){
-    		Segment s = (Segment) iter.next();
-    		f.addSegment((Segment)s.clone());
-    	}
-    	
-    	return f;
-		
-		
-	}
-	
-	
-	
-	
-	
+public class HistogramFeature extends AbstractFeatureTrack
+{
+
+  double max;
+
+  double min;
+
+  public HistogramFeature()
+  {
+    super();
+    // TODO Auto-generated constructor stub
+  }
+
+  public double getMax()
+  {
+    return max;
+  }
+
+  public void setMax(double max)
+  {
+    this.max = max;
+  }
+
+  public double getMin()
+  {
+    return min;
+  }
+
+  public void setMin(double min)
+  {
+    this.min = min;
+  }
+
+  public Object clone()
+  {
+
+    HistogramFeature f = new HistogramFeature();
+
+    f.setName(name);
+    f.setMethod(method);
+    f.setType(type);
+    f.setNote(note);
+    f.setLink(link);
+    f.setSource(source);
+    f.setScore(score);
+
+    Iterator iter = segments.iterator();
+
+    while (iter.hasNext())
+    {
+      Segment s = (Segment) iter.next();
+      f.addSegment((Segment) s.clone());
+    }
+
+    return f;
+
+  }
 
 }
diff --git a/src/org/biojava/dasobert/feature/HistogramSegment.java b/src/org/biojava/dasobert/feature/HistogramSegment.java
index 2b0fd8b..7a7ea25 100644
--- a/src/org/biojava/dasobert/feature/HistogramSegment.java
+++ b/src/org/biojava/dasobert/feature/HistogramSegment.java
@@ -23,43 +23,45 @@
 
 package org.biojava.dasobert.feature;
 
-/** a Histogram segment is an extension of the standard Segment with a score
+/**
+ * a Histogram segment is an extension of the standard Segment with a score
  * 
  * @author Andreas Prlic
- *
- */ 
-public class HistogramSegment extends AbstractSegment {
+ * 
+ */
+public class HistogramSegment extends AbstractSegment
+{
+
+  double score;
+
+  public HistogramSegment()
+  {
+    super();
+
+  }
+
+  public double getScore()
+  {
+    return score;
+  }
+
+  public void setScore(double score)
+  {
+    this.score = score;
+  }
+
+  public Object clone()
+  {
 
-	double score;
-	
-	public HistogramSegment() {
-		super();
-		
-	}
+    Segment s = new HistogramSegment();
+    s.setStart(start);
+    s.setEnd(end);
+    s.setName(name);
+    s.setColor(color);
+    s.setTxtColor(txtColor);
+    s.setNote(note);
+    return s;
 
-	public double getScore() {
-		return score;
-	}
+  }
 
-	public void setScore(double score) {
-		this.score = score;
-	}
-	
-	
-	public Object clone(){
-        
-        Segment s = new HistogramSegment();
-        s.setStart(start);
-        s.setEnd(end);
-        s.setName(name);
-        s.setColor(color);
-        s.setTxtColor(txtColor);
-        s.setNote(note);
-        return s;
-        
-    }
-	
-	
-	
-	
 }
diff --git a/src/org/biojava/dasobert/feature/Segment.java b/src/org/biojava/dasobert/feature/Segment.java
index f2a0bb6..78e2840 100644
--- a/src/org/biojava/dasobert/feature/Segment.java
+++ b/src/org/biojava/dasobert/feature/Segment.java
@@ -22,59 +22,63 @@
  *
  */
 
-package org.biojava.dasobert.feature ;
+package org.biojava.dasobert.feature;
 
 import java.awt.Color;
 
-
 /** a class to keep track of location information for a feature */
-public interface Segment  {
-  
-	public Object clone();
-	
-	public  String toString();
+public interface Segment
+{
+
+  public Object clone();
+
+  public String toString();
 
-	public  String getNote();
+  public String getNote();
 
-	public  void setNote(String note);
+  public void setNote(String note);
 
-	public  void setStart(int strt);
+  public void setStart(int strt);
 
-	public  int getStart();
+  public int getStart();
 
-	public  void setEnd(int ed);
+  public void setEnd(int ed);
 
-	public  int getEnd();
+  public int getEnd();
 
-	public  void setName(String nam);
+  public void setName(String nam);
 
-	public  String getName();
+  public String getName();
 
-	public  void setColor(Color col);
+  public void setColor(Color col);
 
-	public  Color getColor();
+  public Color getColor();
 
-	public  void setParent(FeatureTrack f);
+  public void setParent(FeatureTrack f);
 
-	public  FeatureTrack getParent();
+  public FeatureTrack getParent();
 
-	public  void setTxtColor(String str);
+  public void setTxtColor(String str);
 
-	public  String getTxtColor();
+  public String getTxtColor();
 
-	/** returns true if the specified sequence position is within the range of this Segment
-	 * 
-	 * @param seqPosition the position to check
-	 * @return true if seqPos >= start && seqPos <= end
-	 */
-	public  boolean overlaps(int seqPosition);
+  /**
+   * returns true if the specified sequence position is within the range of this
+   * Segment
+   * 
+   * @param seqPosition
+   *                the position to check
+   * @return true if seqPos >= start && seqPos <= end
+   */
+  public boolean overlaps(int seqPosition);
 
-	/** tests if two segments are overlapping
-	 * 
-	 * @param segment to compare with
-	 * @return true if segments overlap
-	 */
-	public  boolean overlaps(Segment segment);
+  /**
+   * tests if two segments are overlapping
+   * 
+   * @param segment
+   *                to compare with
+   * @return true if segments overlap
+   */
+  public boolean overlaps(Segment segment);
 
-    
 }
diff --git a/src/org/biojava/dasobert/feature/SegmentComparator.java b/src/org/biojava/dasobert/feature/SegmentComparator.java
index 535576f..68a2c16 100644
--- a/src/org/biojava/dasobert/feature/SegmentComparator.java
+++ b/src/org/biojava/dasobert/feature/SegmentComparator.java
@@ -25,19 +25,21 @@ package org.biojava.dasobert.feature;
 
 import java.util.Comparator;
 
-public class SegmentComparator implements Comparator {
-
-	public int compare(Object arg0, Object arg1) {
-		
-		Segment s1 = (Segment) arg0;
-		Segment s2 = (Segment) arg1;
-		
-		if (s1.getStart() < s2.getStart())
-			return -1;
-		if (s1.getStart() > s2.getStart())
-			return 1;		
-		
-		return 0;
-	}
+public class SegmentComparator implements Comparator
+{
+
+  public int compare(Object arg0, Object arg1)
+  {
+
+    Segment s1 = (Segment) arg0;
+    Segment s2 = (Segment) arg1;
+
+    if (s1.getStart() < s2.getStart())
+      return -1;
+    if (s1.getStart() > s2.getStart())
+      return 1;
+
+    return 0;
+  }
 
 }
diff --git a/src/org/biojava/dasobert/feature/SegmentImpl.java b/src/org/biojava/dasobert/feature/SegmentImpl.java
index 5a0585f..dba25e9 100644
--- a/src/org/biojava/dasobert/feature/SegmentImpl.java
+++ b/src/org/biojava/dasobert/feature/SegmentImpl.java
@@ -25,54 +25,59 @@ package org.biojava.dasobert.feature;
 
 import java.awt.Color;
 
-public class SegmentImpl extends AbstractSegment  {
+public class SegmentImpl extends AbstractSegment
+{
 
-    public SegmentImpl() {
-    	super();
-        start = 0 ;
-        end   = 0 ;
-        name  = "Unknown";
-        color = Color.white ;
-        txtColor = "white" ;
-        parent = null ;
-        note = "";
-    }
-    
-    public boolean equals(Segment s){
-        if ( s == null)
-            return false;
-        
-        if (    ( start == s.getStart() ) &&
-                ( end == s.getEnd() ) &&
-                ( name.equals(s.getName()))               
-                )      
+  public SegmentImpl()
+  {
+    super();
+    start = 0;
+    end = 0;
+    name = "Unknown";
+    color = Color.white;
+    txtColor = "white";
+    parent = null;
+    note = "";
+  }
+
+  public boolean equals(Segment s)
+  {
+    if (s == null)
+      return false;
+
+    if ((start == s.getStart()) && (end == s.getEnd())
+            && (name.equals(s.getName())))
+    {
+      if (note == null)
+      {
+        if (s.getNote() == null)
+          return true;
+      }
+      else
+      {
+        if (s.getNote() != null)
         {
-            if ( note == null) {
-                if (s.getNote() == null)
-                    return true;
-            } else {
-                if (s.getNote() != null){
-                    if (s.getNote().equals(note))
-                        return true;
-                }
-            }
-            
+          if (s.getNote().equals(note))
+            return true;
         }
-        
-        
-        return false;
-    }
-    
-    public Object clone(){
-        
-        Segment s = new SegmentImpl();
-        s.setStart(start);
-        s.setEnd(end);
-        s.setName(name);
-        s.setColor(color);
-        s.setTxtColor(txtColor);
-        s.setNote(note);
-        return s;
-        
+      }
+
     }
+
+    return false;
+  }
+
+  public Object clone()
+  {
+
+    Segment s = new SegmentImpl();
+    s.setStart(start);
+    s.setEnd(end);
+    s.setName(name);
+    s.setColor(color);
+    s.setTxtColor(txtColor);
+    s.setNote(note);
+    return s;
+
+  }
 }
diff --git a/src/org/jibble/epsgraphics/EpsDocument.java b/src/org/jibble/epsgraphics/EpsDocument.java
index a53df85..0674d05 100755
--- a/src/org/jibble/epsgraphics/EpsDocument.java
+++ b/src/org/jibble/epsgraphics/EpsDocument.java
@@ -1,266 +1,267 @@
-/*
- Copyright Paul James Mutton, 2001-2004, http://www.jibble.org/
-
- This file is part of EpsGraphics2D.
-
- This software is dual-licensed, allowing you to choose between the GNU
- General Public License (GPL) and the www.jibble.org Commercial License.
- Since the GPL may be too restrictive for use in a proprietary application,
- a commercial license is also provided. Full license information can be
- found at http://www.jibble.org/licenses/
-
- $Author$
- $Id$
-
- */
-
-package org.jibble.epsgraphics;
-
-import java.io.*;
-import java.util.*;
-
-/**
- * This represents an EPS document. Several EpsGraphics2D objects may point
- * to the same EpsDocument.
- *  <p>
- * Copyright Paul Mutton,
- *           <a href="http://www.jibble.org/">http://www.jibble.org/</a>
- *
- */
-public class EpsDocument
-{
-
-  /**
-   * Constructs an empty EpsDevice.
-   */
-  public EpsDocument(String title)
-  {
-    _title = title;
-    minX = Float.POSITIVE_INFINITY;
-    minY = Float.POSITIVE_INFINITY;
-    maxX = Float.NEGATIVE_INFINITY;
-    maxY = Float.NEGATIVE_INFINITY;
-    _stringWriter = new StringWriter();
-    _bufferedWriter = new BufferedWriter(_stringWriter);
-  }
-
-  /**
-   * Constructs an empty EpsDevice that writes directly to a file.
-   * Bounds must be set before use.
-   */
-  public EpsDocument(String title, OutputStream outputStream, int minX,
-                     int minY, int maxX, int maxY)
-      throws IOException
-  {
-    _title = title;
-    this.minX = minX;
-    this.minY = minY;
-    this.maxX = maxX;
-    this.maxY = maxY;
-    _bufferedWriter = new BufferedWriter(new OutputStreamWriter(outputStream));
-    write(_bufferedWriter);
-  }
-
-  /**
-   * Returns the title of the EPS document.
-   */
-  public synchronized String getTitle()
-  {
-    return _title;
-  }
-
-  /**
-   * Updates the bounds of the current EPS document.
-   */
-  public synchronized void updateBounds(double x, double y)
-  {
-    if (x > maxX)
-    {
-      maxX = (float) x;
-    }
-    if (x < minX)
-    {
-      minX = (float) x;
-    }
-    if (y > maxY)
-    {
-      maxY = (float) y;
-    }
-    if (y < minY)
-    {
-      minY = (float) y;
-    }
-  }
-
-  /**
-   * Appends a line to the EpsDocument.  A new line character is added
-   * to the end of the line when it is added.
-   */
-  public synchronized void append(EpsGraphics2D g, String line)
-  {
-    if (_lastG == null)
-    {
-      _lastG = g;
-    }
-    else if (g != _lastG)
-    {
-      EpsGraphics2D lastG = _lastG;
-      _lastG = g;
-      // We are being drawn on with a different EpsGraphics2D context.
-      // We may need to update the clip, etc from this new context.
-      if (g.getClip() != lastG.getClip())
-      {
-        g.setClip(g.getClip());
-      }
-      if (!g.getColor().equals(lastG.getColor()))
-      {
-        g.setColor(g.getColor());
-      }
-      if (!g.getBackground().equals(lastG.getBackground()))
-      {
-        g.setBackground(g.getBackground());
-      }
-      // We don't need this, as this only affects the stroke and font,
-      // which are dealt with separately later on.
-      //if (!g.getTransform().equals(lastG.getTransform())) {
-      //    g.setTransform(g.getTransform());
-      //}
-      if (!g.getPaint().equals(lastG.getPaint()))
-      {
-        g.setPaint(g.getPaint());
-      }
-      if (!g.getComposite().equals(lastG.getComposite()))
-      {
-        g.setComposite(g.getComposite());
-      }
-      if (!g.getComposite().equals(lastG.getComposite()))
-      {
-        g.setComposite(g.getComposite());
-      }
-      if (!g.getFont().equals(lastG.getFont()))
-      {
-        g.setFont(g.getFont());
-      }
-      if (!g.getStroke().equals(lastG.getStroke()))
-      {
-        g.setStroke(g.getStroke());
-      }
-    }
-    _lastG = g;
-
-    try
-    {
-      _bufferedWriter.write(line + "\n");
-    }
-    catch (IOException e)
-    {
-      throw new EpsException("Could not write to the output file: " + e);
-    }
-  }
-
-  /**
-   * Outputs the contents of the EPS document to the specified
-   * Writer, complete with headers and bounding box.
-   */
-  public synchronized void write(Writer writer)
-      throws IOException
-  {
-    float offsetX = -minX;
-    float offsetY = -minY;
-
-    writer.write("%!PS-Adobe-3.0 EPSF-3.0\n");
-    writer.write("%%Creator: Jalview " +
-                 jalview.bin.Cache.getProperty("VERSION") + " \n");
-    writer.write("%%Title: " + _title + "\n");
-    writer.write("%%CreationDate: " + new Date() + "\n");
-    writer.write("%%BoundingBox: 0 0 " + ( (int) Math.ceil(maxX + offsetX)) +
-                 " " + ( (int) Math.ceil(maxY + offsetY)) + "\n");
-    writer.write("%%DocumentData: Clean7Bit\n");
-    writer.write("%%DocumentProcessColors: Black\n");
-    writer.write("%%ColorUsage: Color\n");
-    writer.write("%%Origin: 0 0\n");
-    writer.write("%%Pages: 1\n");
-    writer.write("%%Page: 1 1\n");
-    writer.write("%%EndComments\n\n");
-
-    writer.write("gsave\n");
-
-    if (_stringWriter != null)
-    {
-      writer.write(offsetX + " " + (offsetY) + " translate\n");
-
-      _bufferedWriter.flush();
-      StringBuffer buffer = _stringWriter.getBuffer();
-      for (int i = 0; i < buffer.length(); i++)
-      {
-        writer.write(buffer.charAt(i));
-      }
-
-      writeFooter(writer);
-    }
-    else
-    {
-      writer.write(offsetX + " " + ( (maxY - minY) - offsetY) + " translate\n");
-    }
-
-    writer.flush();
-  }
-
-  private void writeFooter(Writer writer)
-      throws IOException
-  {
-    writer.write("grestore\n");
-    if (isClipSet())
-    {
-      writer.write("grestore\n");
-    }
-    writer.write("showpage\n");
-    writer.write("\n");
-    writer.write("%%EOF");
-    writer.flush();
-  }
-
-  public synchronized void flush()
-      throws IOException
-  {
-    _bufferedWriter.flush();
-  }
-
-  public synchronized void close()
-      throws IOException
-  {
-    if (_stringWriter == null)
-    {
-      writeFooter(_bufferedWriter);
-      _bufferedWriter.flush();
-      _bufferedWriter.close();
-    }
-  }
-
-  public boolean isClipSet()
-  {
-    return _isClipSet;
-  }
-
-  public void setClipSet(boolean isClipSet)
-  {
-    _isClipSet = isClipSet;
-  }
-
-  private float minX;
-  private float minY;
-  private float maxX;
-  private float maxY;
-
-  private boolean _isClipSet = false;
-
-  private String _title;
-  private StringWriter _stringWriter;
-  private BufferedWriter _bufferedWriter = null;
-
-  // We need to remember which was the last EpsGraphics2D object to use
-  // us, as we need to replace the clipping region if another EpsGraphics2D
-  // object tries to use us.
-  private EpsGraphics2D _lastG = null;
-
-}
+/*
+ Copyright Paul James Mutton, 2001-2004, http://www.jibble.org/
+
+ This file is part of EpsGraphics2D.
+
+ This software is dual-licensed, allowing you to choose between the GNU
+ General Public License (GPL) and the www.jibble.org Commercial License.
+ Since the GPL may be too restrictive for use in a proprietary application,
+ a commercial license is also provided. Full license information can be
+ found at http://www.jibble.org/licenses/
+
+ $Author$
+ $Id$
+
+ */
+
+package org.jibble.epsgraphics;
+
+import java.io.*;
+import java.util.*;
+
+/**
+ * This represents an EPS document. Several EpsGraphics2D objects may point to
+ * the same EpsDocument.
+ * <p>
+ * Copyright Paul Mutton, <a
+ * href="http://www.jibble.org/">http://www.jibble.org/</a>
+ * 
+ */
+public class EpsDocument
+{
+
+  /**
+   * Constructs an empty EpsDevice.
+   */
+  public EpsDocument(String title)
+  {
+    _title = title;
+    minX = Float.POSITIVE_INFINITY;
+    minY = Float.POSITIVE_INFINITY;
+    maxX = Float.NEGATIVE_INFINITY;
+    maxY = Float.NEGATIVE_INFINITY;
+    _stringWriter = new StringWriter();
+    _bufferedWriter = new BufferedWriter(_stringWriter);
+  }
+
+  /**
+   * Constructs an empty EpsDevice that writes directly to a file. Bounds must
+   * be set before use.
+   */
+  public EpsDocument(String title, OutputStream outputStream, int minX,
+          int minY, int maxX, int maxY) throws IOException
+  {
+    _title = title;
+    this.minX = minX;
+    this.minY = minY;
+    this.maxX = maxX;
+    this.maxY = maxY;
+    _bufferedWriter = new BufferedWriter(new OutputStreamWriter(
+            outputStream));
+    write(_bufferedWriter);
+  }
+
+  /**
+   * Returns the title of the EPS document.
+   */
+  public synchronized String getTitle()
+  {
+    return _title;
+  }
+
+  /**
+   * Updates the bounds of the current EPS document.
+   */
+  public synchronized void updateBounds(double x, double y)
+  {
+    if (x > maxX)
+    {
+      maxX = (float) x;
+    }
+    if (x < minX)
+    {
+      minX = (float) x;
+    }
+    if (y > maxY)
+    {
+      maxY = (float) y;
+    }
+    if (y < minY)
+    {
+      minY = (float) y;
+    }
+  }
+
+  /**
+   * Appends a line to the EpsDocument. A new line character is added to the end
+   * of the line when it is added.
+   */
+  public synchronized void append(EpsGraphics2D g, String line)
+  {
+    if (_lastG == null)
+    {
+      _lastG = g;
+    }
+    else if (g != _lastG)
+    {
+      EpsGraphics2D lastG = _lastG;
+      _lastG = g;
+      // We are being drawn on with a different EpsGraphics2D context.
+      // We may need to update the clip, etc from this new context.
+      if (g.getClip() != lastG.getClip())
+      {
+        g.setClip(g.getClip());
+      }
+      if (!g.getColor().equals(lastG.getColor()))
+      {
+        g.setColor(g.getColor());
+      }
+      if (!g.getBackground().equals(lastG.getBackground()))
+      {
+        g.setBackground(g.getBackground());
+      }
+      // We don't need this, as this only affects the stroke and font,
+      // which are dealt with separately later on.
+      // if (!g.getTransform().equals(lastG.getTransform())) {
+      // g.setTransform(g.getTransform());
+      // }
+      if (!g.getPaint().equals(lastG.getPaint()))
+      {
+        g.setPaint(g.getPaint());
+      }
+      if (!g.getComposite().equals(lastG.getComposite()))
+      {
+        g.setComposite(g.getComposite());
+      }
+      if (!g.getComposite().equals(lastG.getComposite()))
+      {
+        g.setComposite(g.getComposite());
+      }
+      if (!g.getFont().equals(lastG.getFont()))
+      {
+        g.setFont(g.getFont());
+      }
+      if (!g.getStroke().equals(lastG.getStroke()))
+      {
+        g.setStroke(g.getStroke());
+      }
+    }
+    _lastG = g;
+
+    try
+    {
+      _bufferedWriter.write(line + "\n");
+    } catch (IOException e)
+    {
+      throw new EpsException("Could not write to the output file: " + e);
+    }
+  }
+
+  /**
+   * Outputs the contents of the EPS document to the specified Writer, complete
+   * with headers and bounding box.
+   */
+  public synchronized void write(Writer writer) throws IOException
+  {
+    float offsetX = -minX;
+    float offsetY = -minY;
+
+    writer.write("%!PS-Adobe-3.0 EPSF-3.0\n");
+    writer.write("%%Creator: Jalview "
+            + jalview.bin.Cache.getProperty("VERSION") + " \n");
+    writer.write("%%Title: " + _title + "\n");
+    writer.write("%%CreationDate: " + new Date() + "\n");
+    writer.write("%%BoundingBox: 0 0 " + ((int) Math.ceil(maxX + offsetX))
+            + " " + ((int) Math.ceil(maxY + offsetY)) + "\n");
+    writer.write("%%DocumentData: Clean7Bit\n");
+    writer.write("%%DocumentProcessColors: Black\n");
+    writer.write("%%ColorUsage: Color\n");
+    writer.write("%%Origin: 0 0\n");
+    writer.write("%%Pages: 1\n");
+    writer.write("%%Page: 1 1\n");
+    writer.write("%%EndComments\n\n");
+
+    writer.write("gsave\n");
+
+    if (_stringWriter != null)
+    {
+      writer.write(offsetX + " " + (offsetY) + " translate\n");
+
+      _bufferedWriter.flush();
+      StringBuffer buffer = _stringWriter.getBuffer();
+      for (int i = 0; i < buffer.length(); i++)
+      {
+        writer.write(buffer.charAt(i));
+      }
+
+      writeFooter(writer);
+    }
+    else
+    {
+      writer.write(offsetX + " " + ((maxY - minY) - offsetY)
+              + " translate\n");
+    }
+
+    writer.flush();
+  }
+
+  private void writeFooter(Writer writer) throws IOException
+  {
+    writer.write("grestore\n");
+    if (isClipSet())
+    {
+      writer.write("grestore\n");
+    }
+    writer.write("showpage\n");
+    writer.write("\n");
+    writer.write("%%EOF");
+    writer.flush();
+  }
+
+  public synchronized void flush() throws IOException
+  {
+    _bufferedWriter.flush();
+  }
+
+  public synchronized void close() throws IOException
+  {
+    if (_stringWriter == null)
+    {
+      writeFooter(_bufferedWriter);
+      _bufferedWriter.flush();
+      _bufferedWriter.close();
+    }
+  }
+
+  public boolean isClipSet()
+  {
+    return _isClipSet;
+  }
+
+  public void setClipSet(boolean isClipSet)
+  {
+    _isClipSet = isClipSet;
+  }
+
+  private float minX;
+
+  private float minY;
+
+  private float maxX;
+
+  private float maxY;
+
+  private boolean _isClipSet = false;
+
+  private String _title;
+
+  private StringWriter _stringWriter;
+
+  private BufferedWriter _bufferedWriter = null;
+
+  // We need to remember which was the last EpsGraphics2D object to use
+  // us, as we need to replace the clipping region if another EpsGraphics2D
+  // object tries to use us.
+  private EpsGraphics2D _lastG = null;
+
+}
diff --git a/src/org/jibble/epsgraphics/EpsException.java b/src/org/jibble/epsgraphics/EpsException.java
index c9ae519..c860500 100755
--- a/src/org/jibble/epsgraphics/EpsException.java
+++ b/src/org/jibble/epsgraphics/EpsException.java
@@ -1,28 +1,27 @@
-/*
- Copyright Paul James Mutton, 2001-2004, http://www.jibble.org/
-
- This file is part of EpsGraphics2D.
-
- This software is dual-licensed, allowing you to choose between the GNU
- General Public License (GPL) and the www.jibble.org Commercial License.
- Since the GPL may be too restrictive for use in a proprietary application,
- a commercial license is also provided. Full license information can be
- found at http://www.jibble.org/licenses/
-
- $Author$
- $Id$
-
- */
-
-package org.jibble.epsgraphics;
-
-public class EpsException
-    extends RuntimeException
-{
-
-  public EpsException(String message)
-  {
-    super(message);
-  }
-
+/*
+ Copyright Paul James Mutton, 2001-2004, http://www.jibble.org/
+
+ This file is part of EpsGraphics2D.
+
+ This software is dual-licensed, allowing you to choose between the GNU
+ General Public License (GPL) and the www.jibble.org Commercial License.
+ Since the GPL may be too restrictive for use in a proprietary application,
+ a commercial license is also provided. Full license information can be
+ found at http://www.jibble.org/licenses/
+
+ $Author$
+ $Id$
+
+ */
+
+package org.jibble.epsgraphics;
+
+public class EpsException extends RuntimeException
+{
+
+  public EpsException(String message)
+  {
+    super(message);
+  }
+
 }
\ No newline at end of file
diff --git a/src/org/jibble/epsgraphics/EpsGraphics2D.java b/src/org/jibble/epsgraphics/EpsGraphics2D.java
index 45eeb5b..63b10d9 100755
--- a/src/org/jibble/epsgraphics/EpsGraphics2D.java
+++ b/src/org/jibble/epsgraphics/EpsGraphics2D.java
@@ -1,1445 +1,1444 @@
-/*
- Copyright Paul James Mutton, 2001-2004, http://www.jibble.org/
-
- This file is part of EpsGraphics2D.
-
- This software is dual-licensed, allowing you to choose between the GNU
- General Public License (GPL) and the www.jibble.org Commercial License.
- Since the GPL may be too restrictive for use in a proprietary application,
- a commercial license is also provided. Full license information can be
- found at http://www.jibble.org/licenses/
-
- $Author$
- $Id$
-
- */
-
-package org.jibble.epsgraphics;
-
-import java.io.*;
-import java.text.*;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.font.*;
-import java.awt.geom.*;
-import java.awt.image.*;
-import java.awt.image.renderable.*;
-
-/**
- * EpsGraphics2D is suitable for creating high quality EPS graphics for
- * use in documents and papers, and can be used just like a standard
- * Graphics2D object.
- *  <p>
- * Many Java programs use Graphics2D to draw stuff on the screen, and while
- * it is easy to save the output as a png or jpeg file, it is a little
- * harder to export it as an EPS for including in a document or paper.
- *  <p>
- * This class makes the whole process extremely easy, because you can use
- * it as if it's a Graphics2D object.  The only difference is that all of
- * the implemented methods create EPS output, which means the diagrams you
- * draw can be resized without leading to any of the jagged edges you may
- * see when resizing pixel-based images, such as jpeg and png files.
- *  <p>
- *   Example usage:
- *  <p>
- * <pre>    Graphics2D g = new EpsGraphics2D();
- *    g.setColor(Color.black);
- *
- *    // Line thickness 2.
- *    g.setStroke(new BasicStroke(2.0f));
- *
- *    // Draw a line.
- *    g.drawLine(10, 10, 50, 10);
- *
- *    // Fill a rectangle in blue
- *    g.setColor(Color.blue);
- *    g.fillRect(10, 0, 20, 20);
- *
- *    // Get the EPS output.
- *    String output = g.toString();</pre>
- *  <p>
- * You do not need to worry about the size of the canvas when drawing on a
- * EpsGraphics2D object.  The bounding box of the EPS document will
- * automatically resize to accomodate new items that you draw.
- *  <p>
- * Not all methods are implemented yet.  Those that are not are clearly
- * labelled.
- *  <p>
- * Copyright Paul Mutton,
- *           <a href="http://www.jibble.org/">http://www.jibble.org/</a>
- *
- */
-public class EpsGraphics2D
-    extends java.awt.Graphics2D
-{
-
-  public static final String VERSION = "0.8.8";
-
-  /**
-   * Constructs a new EPS document that is initially empty and can be
-   * drawn on like a Graphics2D object.  The EPS document is stored in
-   * memory.
-   */
-  public EpsGraphics2D()
-  {
-    this("Untitled");
-  }
-
-  /**
-   * Constructs a new EPS document that is initially empty and can be
-   * drawn on like a Graphics2D object.  The EPS document is stored in
-   * memory.
-   */
-  public EpsGraphics2D(String title)
-  {
-    _document = new EpsDocument(title);
-    _backgroundColor = Color.white;
-    _clip = null;
-    _transform = new AffineTransform();
-    _clipTransform = new AffineTransform();
-    _accurateTextMode = true;
-    setColor(Color.black);
-    setPaint(Color.black);
-    setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR));
-    setFont(Font.decode(null));
-    setStroke(new BasicStroke());
-  }
-
-  /**
-   * Constructs a new EPS document that is initially empty and can be
-   * drawn on like a Graphics2D object. The EPS document is written to
-   * the file as it goes, which reduces memory usage. The bounding box of
-   * the document is fixed and specified at construction time by
-   * minX,minY,maxX,maxY. The file is flushed and closed when the close()
-   * method is called.
-   */
-  public EpsGraphics2D(String title, File file, int minX, int minY, int maxX,
-                       int maxY)
-      throws IOException
-  {
-    this(title, new FileOutputStream(file), minX, minY, maxX, maxY);
-  }
-
-  /**
-   * Constructs a new EPS document that is initially empty and can be
-   * drawn on like a Graphics2D object. The EPS document is written to
-   * the output stream as it goes, which reduces memory usage. The
-   * bounding box of the document is fixed and specified at construction
-   * time by minX,minY,maxX,maxY. The output stream is flushed and closed
-   * when the close() method is called.
-   */
-  public EpsGraphics2D(String title, OutputStream outputStream, int minX,
-                       int minY, int maxX, int maxY)
-      throws IOException
-  {
-    this(title);
-    _document = new EpsDocument(title, outputStream, minX, minY, maxX, maxY);
-  }
-
-  /**
-   * Constructs a new EpsGraphics2D instance that is a copy of the
-   * supplied argument and points at the same EpsDocument.
-   */
-  protected EpsGraphics2D(EpsGraphics2D g)
-  {
-    _document = g._document;
-    _backgroundColor = g._backgroundColor;
-    _clip = g._clip;
-    _clipTransform = (AffineTransform) g._clipTransform.clone();
-    _transform = (AffineTransform) g._transform.clone();
-    _color = g._color;
-    _paint = g._paint;
-    _composite = g._composite;
-    _font = g._font;
-    _stroke = g._stroke;
-    _accurateTextMode = g._accurateTextMode;
-  }
-
-  /**
-   * This method is called to indicate that a particular method is not
-   * supported yet.  The stack trace is printed to the standard output.
-   */
-  private void methodNotSupported()
-  {
-    EpsException e = new EpsException(
-        "Method not currently supported by EpsGraphics2D version " + VERSION);
-    e.printStackTrace(System.err);
-  }
-
-  /////////////// Specialist methods ///////////////////////
-
-
-  /**
-   * Sets whether to use accurate text mode when rendering text in EPS.
-   * This is enabled (true) by default. When accurate text mode is used,
-   * all text will be rendered in EPS to appear exactly the same as it
-   * would do when drawn with a Graphics2D context. With accurate text
-   * mode enabled, it is not necessary for the EPS viewer to have the
-   * required font installed.
-   * <p>
-   * Turning off accurate text mode will require the EPS viewer to have
-   * the necessary fonts installed. If you are using a lot of text, you
-   * will find that this significantly reduces the file size of your EPS
-   * documents.  AffineTransforms can only affect the starting point of
-   * text using this simpler text mode - all text will be horizontal.
-   */
-  public void setAccurateTextMode(boolean b)
-  {
-    _accurateTextMode = b;
-  }
-
-  /**
-   * Returns whether accurate text mode is being used.
-   */
-  public boolean getAccurateTextMode()
-  {
-    return _accurateTextMode;
-  }
-
-  /**
-   * Flushes the buffered contents of this EPS document to the underlying
-   * OutputStream it is being written to.
-   */
-  public void flush()
-      throws IOException
-  {
-    _document.flush();
-  }
-
-  /**
-   * Closes the EPS file being output to the underlying OutputStream.
-   * The OutputStream is automatically flushed before being closed.
-   * If you forget to do this, the file may be incomplete.
-   */
-  public void close()
-      throws IOException
-  {
-    flush();
-    _document.close();
-  }
-
-  /**
-   * Appends a line to the EpsDocument.
-   */
-  private void append(String line)
-  {
-    _document.append(this, line);
-  }
-
-  /**
-   * Returns the point after it has been transformed by the transformation.
-   */
-  private Point2D transform(float x, float y)
-  {
-    Point2D result = new Point2D.Float(x, y);
-    result = _transform.transform(result, result);
-    result.setLocation(result.getX(), -result.getY());
-    return result;
-  }
-
-  /**
-   * Appends the commands required to draw a shape on the EPS document.
-   */
-  private void draw(Shape s, String action)
-  {
-
-    if (s != null)
-    {
-
-      //Rectangle2D userBounds = s.getBounds2D();
-      if (!_transform.isIdentity())
-      {
-        s = _transform.createTransformedShape(s);
-      }
-
-      // Update the bounds.
-      if (!action.equals("clip"))
-      {
-        Rectangle2D shapeBounds = s.getBounds2D();
-        Rectangle2D visibleBounds = shapeBounds;
-        if (_clip != null)
-        {
-          Rectangle2D clipBounds = _clip.getBounds2D();
-          visibleBounds = shapeBounds.createIntersection(clipBounds);
-        }
-        float lineRadius = _stroke.getLineWidth() / 2;
-        float minX = (float) visibleBounds.getMinX() - lineRadius;
-        float minY = (float) visibleBounds.getMinY() - lineRadius;
-        float maxX = (float) visibleBounds.getMaxX() + lineRadius;
-        float maxY = (float) visibleBounds.getMaxY() + lineRadius;
-        _document.updateBounds(minX, -minY);
-        _document.updateBounds(maxX, -maxY);
-      }
-
-      append("newpath");
-      int type = 0;
-      float[] coords = new float[6];
-      PathIterator it = s.getPathIterator(null);
-      float x0 = 0;
-      float y0 = 0;
-      int count = 0;
-      while (!it.isDone())
-      {
-        type = it.currentSegment(coords);
-        float x1 = coords[0];
-        float y1 = -coords[1];
-        float x2 = coords[2];
-        float y2 = -coords[3];
-        float x3 = coords[4];
-        float y3 = -coords[5];
-
-        if (type == PathIterator.SEG_CLOSE)
-        {
-          append("closepath");
-          count++;
-        }
-        else if (type == PathIterator.SEG_CUBICTO)
-        {
-          append(x1 + " " + y1 + " " + x2 + " " + y2 + " " + x3 + " " + y3 +
-                 " curveto");
-          count++;
-          x0 = x3;
-          y0 = y3;
-        }
-        else if (type == PathIterator.SEG_LINETO)
-        {
-          append(x1 + " " + y1 + " lineto");
-          count++;
-          x0 = x1;
-          y0 = y1;
-        }
-        else if (type == PathIterator.SEG_MOVETO)
-        {
-          append(x1 + " " + y1 + " moveto");
-          count++;
-          x0 = x1;
-          y0 = y1;
-        }
-        else if (type == PathIterator.SEG_QUADTO)
-        {
-          // Convert the quad curve into a cubic.
-          float _x1 = x0 + 2 / 3f * (x1 - x0);
-          float _y1 = y0 + 2 / 3f * (y1 - y0);
-          float _x2 = x1 + 1 / 3f * (x2 - x1);
-          float _y2 = y1 + 1 / 3f * (y2 - y1);
-          float _x3 = x2;
-          float _y3 = y2;
-          append(_x1 + " " + _y1 + " " + _x2 + " " + _y2 + " " + _x3 + " " +
-                 _y3 + " curveto");
-          count++;
-          x0 = _x3;
-          y0 = _y3;
-        }
-        else if (type == PathIterator.WIND_EVEN_ODD)
-        {
-          // Ignore.
-        }
-        else if (type == PathIterator.WIND_NON_ZERO)
-        {
-          // Ignore.
-        }
-        it.next();
-      }
-      append(action);
-      append("newpath");
-    }
-  }
-
-  /**
-   * Returns a hex string that always contains two characters.
-   */
-  private String toHexString(int n)
-  {
-    String result = Integer.toString(n, 16);
-    while (result.length() < 2)
-    {
-      result = "0" + result;
-    }
-    return result;
-  }
-
-  /////////////// Graphics2D methods ///////////////////////
-
-
-  /**
-   * Draws a 3D rectangle outline.  If it is raised, light appears to come
-   * from the top left.
-   */
-  public void draw3DRect(int x, int y, int width, int height, boolean raised)
-  {
-    Color originalColor = getColor();
-    Stroke originalStroke = getStroke();
-
-    setStroke(new BasicStroke(1.0f));
-
-    if (raised)
-    {
-      setColor(originalColor.brighter());
-    }
-    else
-    {
-      setColor(originalColor.darker());
-    }
-
-    drawLine(x, y, x + width, y);
-    drawLine(x, y, x, y + height);
-
-    if (raised)
-    {
-      setColor(originalColor.darker());
-    }
-    else
-    {
-      setColor(originalColor.brighter());
-    }
-
-    drawLine(x + width, y + height, x, y + height);
-    drawLine(x + width, y + height, x + width, y);
-
-    setColor(originalColor);
-    setStroke(originalStroke);
-  }
-
-  /**
-   * Fills a 3D rectangle.  If raised, it has bright fill and light appears
-   * to come from the top left.
-   */
-  public void fill3DRect(int x, int y, int width, int height, boolean raised)
-  {
-    Color originalColor = getColor();
-
-    if (raised)
-    {
-      setColor(originalColor.brighter());
-    }
-    else
-    {
-      setColor(originalColor.darker());
-    }
-    draw(new Rectangle(x, y, width, height), "fill");
-    setColor(originalColor);
-    draw3DRect(x, y, width, height, raised);
-  }
-
-  /**
-   * Draws a Shape on the EPS document.
-   */
-  public void draw(Shape s)
-  {
-    draw(s, "stroke");
-  }
-
-  /**
-   * Draws an Image on the EPS document.
-   */
-  public boolean drawImage(Image img, AffineTransform xform, ImageObserver obs)
-  {
-    AffineTransform at = getTransform();
-    transform(xform);
-    boolean st = drawImage(img, 0, 0, obs);
-    setTransform(at);
-    return st;
-  }
-
-  /**
-   * Draws a BufferedImage on the EPS document.
-   */
-  public void drawImage(BufferedImage img, BufferedImageOp op, int x, int y)
-  {
-    BufferedImage img1 = op.filter(img, null);
-    drawImage(img1, new AffineTransform(1f, 0f, 0f, 1f, x, y), null);
-  }
-
-  /**
-   * Draws a RenderedImage on the EPS document.
-   */
-  public void drawRenderedImage(RenderedImage img, AffineTransform xform)
-  {
-    Hashtable properties = new Hashtable();
-    String[] names = img.getPropertyNames();
-    for (int i = 0; i < names.length; i++)
-    {
-      properties.put(names[i], img.getProperty(names[i]));
-    }
-
-    ColorModel cm = img.getColorModel();
-    WritableRaster wr = img.copyData(null);
-    BufferedImage img1 = new BufferedImage(cm, wr, cm.isAlphaPremultiplied(),
-                                           properties);
-    AffineTransform at = AffineTransform.getTranslateInstance(img.getMinX(),
-        img.getMinY());
-    at.preConcatenate(xform);
-    drawImage(img1, at, null);
-  }
-
-  /**
-   * Draws a RenderableImage by invoking its createDefaultRendering method.
-   */
-  public void drawRenderableImage(RenderableImage img, AffineTransform xform)
-  {
-    drawRenderedImage(img.createDefaultRendering(), xform);
-  }
-
-  /**
-   * Draws a string at (x,y)
-   */
-  public void drawString(String str, int x, int y)
-  {
-    drawString(str, (float) x, (float) y);
-  }
-
-  /**
-   * Draws a string at (x,y)
-   */
-  public void drawString(String s, float x, float y)
-  {
-    if (s != null && s.length() > 0)
-    {
-      AttributedString as = new AttributedString(s);
-      as.addAttribute(TextAttribute.FONT, getFont());
-      drawString(as.getIterator(), x, y);
-    }
-  }
-
-  /**
-   * Draws the characters of an AttributedCharacterIterator, starting from
-   * (x,y).
-   */
-  public void drawString(AttributedCharacterIterator iterator, int x, int y)
-  {
-    drawString(iterator, (float) x, (float) y);
-  }
-
-  /**
-   * Draws the characters of an AttributedCharacterIterator, starting from
-   * (x,y).
-   */
-  public void drawString(AttributedCharacterIterator iterator, float x, float y)
-  {
-    if (getAccurateTextMode())
-    {
-      TextLayout layout = new TextLayout(iterator, getFontRenderContext());
-      Shape shape = layout.getOutline(AffineTransform.getTranslateInstance(x, y));
-      draw(shape, "fill");
-    }
-    else
-    {
-      append("newpath");
-      Point2D location = transform(x, y);
-      append(location.getX() + " " + location.getY() + " moveto");
-      StringBuffer buffer = new StringBuffer();
-      for (char ch = iterator.first(); ch != CharacterIterator.DONE;
-           ch = iterator.next())
-      {
-        if (ch == '(' || ch == ')')
-        {
-          buffer.append('\\');
-        }
-        buffer.append(ch);
-      }
-      append("(" + buffer.toString() + ") show");
-    }
-  }
-
-  /**
-   * Draws a GlyphVector at (x,y)
-   */
-  public void drawGlyphVector(GlyphVector g, float x, float y)
-  {
-    Shape shape = g.getOutline(x, y);
-    draw(shape, "fill");
-  }
-
-  /**
-   * Fills a Shape on the EPS document.
-   */
-  public void fill(Shape s)
-  {
-    draw(s, "fill");
-  }
-
-  /**
-   * Checks whether or not the specified Shape intersects the specified
-   * Rectangle, which is in device space.
-   */
-  public boolean hit(Rectangle rect, Shape s, boolean onStroke)
-  {
-    return s.intersects(rect);
-  }
-
-  /**
-   * Returns the device configuration associated with this EpsGraphics2D
-   * object.
-   */
-  public GraphicsConfiguration getDeviceConfiguration()
-  {
-    GraphicsConfiguration gc = null;
-    GraphicsEnvironment ge = GraphicsEnvironment.getLocalGraphicsEnvironment();
-    GraphicsDevice[] gds = ge.getScreenDevices();
-    for (int i = 0; i < gds.length; i++)
-    {
-      GraphicsDevice gd = gds[i];
-      GraphicsConfiguration[] gcs = gd.getConfigurations();
-      if (gcs.length > 0)
-      {
-        return gcs[0];
-      }
-    }
-    return gc;
-  }
-
-  /**
-   * Sets the Composite to be used by this EpsGraphics2D.  EpsGraphics2D
-   * does not make use of these.
-   */
-  public void setComposite(Composite comp)
-  {
-    _composite = comp;
-  }
-
-  /**
-   * Sets the Paint attribute for the EpsGraphics2D object.  Only Paint
-   * objects of type Color are respected by EpsGraphics2D.
-   */
-  public void setPaint(Paint paint)
-  {
-    _paint = paint;
-    if (paint instanceof Color)
-    {
-      setColor( (Color) paint);
-    }
-  }
-
-  /**
-   * Sets the stroke.  Only accepts BasicStroke objects (or subclasses of
-   * BasicStroke).
-   */
-  public void setStroke(Stroke s)
-  {
-    if (s instanceof BasicStroke)
-    {
-      _stroke = (BasicStroke) s;
-
-      append(_stroke.getLineWidth() + " setlinewidth");
-      float miterLimit = _stroke.getMiterLimit();
-      if (miterLimit < 1.0f)
-      {
-        miterLimit = 1;
-      }
-      append(miterLimit + " setmiterlimit");
-      append(_stroke.getLineJoin() + " setlinejoin");
-      append(_stroke.getEndCap() + " setlinecap");
-
-      StringBuffer dashes = new StringBuffer();
-      dashes.append("[ ");
-      float[] dashArray = _stroke.getDashArray();
-      if (dashArray != null)
-      {
-        for (int i = 0; i < dashArray.length; i++)
-        {
-          dashes.append( (dashArray[i]) + " ");
-        }
-      }
-      dashes.append("]");
-      append(dashes.toString() + " 0 setdash");
-    }
-  }
-
-  /**
-   * Sets a rendering hint. These are not used by EpsGraphics2D.
-   */
-  public void setRenderingHint(RenderingHints.Key hintKey, Object hintValue)
-  {
-    // Do nothing.
-  }
-
-  /**
-   * Returns the value of a single preference for the rendering
-   * algorithms.  Rendering hints are not used by EpsGraphics2D.
-   */
-  public Object getRenderingHint(RenderingHints.Key hintKey)
-  {
-    return null;
-  }
-
-  /**
-   * Sets the rendering hints.  These are ignored by EpsGraphics2D.
-   */
-  public void setRenderingHints(Map hints)
-  {
-    // Do nothing.
-  }
-
-  /**
-   * Adds rendering hints.  These are ignored by EpsGraphics2D.
-   */
-  public void addRenderingHints(Map hints)
-  {
-    // Do nothing.
-  }
-
-  /**
-   * Returns the preferences for the rendering algorithms.
-   */
-  public RenderingHints getRenderingHints()
-  {
-    return new RenderingHints(null);
-  }
-
-  /**
-   * Translates the origin of the EpsGraphics2D context to the point (x,y)
-   * in the current coordinate system.
-   */
-  public void translate(int x, int y)
-  {
-    translate( (double) x, (double) y);
-  }
-
-  /**
-   * Concatenates the current EpsGraphics2D Transformation with a
-   * translation transform.
-   */
-  public void translate(double tx, double ty)
-  {
-    transform(AffineTransform.getTranslateInstance(tx, ty));
-  }
-
-  /**
-   * Concatenates the current EpsGraphics2D Transform with a rotation
-   * transform.
-   */
-  public void rotate(double theta)
-  {
-    rotate(theta, 0, 0);
-  }
-
-  /**
-   * Concatenates the current EpsGraphics2D Transform with a translated
-   * rotation transform.
-   */
-  public void rotate(double theta, double x, double y)
-  {
-    transform(AffineTransform.getRotateInstance(theta, x, y));
-  }
-
-  /**
-   * Concatenates the current EpsGraphics2D Transform with a scaling
-   * transformation.
-   */
-  public void scale(double sx, double sy)
-  {
-    transform(AffineTransform.getScaleInstance(sx, sy));
-  }
-
-  /**
-   * Concatenates the current EpsGraphics2D Transform with a shearing
-   * transform.
-   */
-  public void shear(double shx, double shy)
-  {
-    transform(AffineTransform.getShearInstance(shx, shy));
-  }
-
-  /**
-   * Composes an AffineTransform object with the Transform in this
-   * EpsGraphics2D according to the rule last-specified-first-applied.
-   */
-  public void transform(AffineTransform Tx)
-  {
-    _transform.concatenate(Tx);
-    setTransform(getTransform());
-  }
-
-  /**
-   * Sets the AffineTransform to be used by this EpsGraphics2D.
-   */
-  public void setTransform(AffineTransform Tx)
-  {
-    if (Tx == null)
-    {
-      _transform = new AffineTransform();
-    }
-    else
-    {
-      _transform = new AffineTransform(Tx);
-    }
-    // Need to update the stroke and font so they know the scale changed
-    setStroke(getStroke());
-    setFont(getFont());
-  }
-
-  /**
-   * Gets the AffineTransform used by this EpsGraphics2D.
-   */
-  public AffineTransform getTransform()
-  {
-    return new AffineTransform(_transform);
-  }
-
-  /**
-   * Returns the current Paint of the EpsGraphics2D object.
-   */
-  public Paint getPaint()
-  {
-    return _paint;
-  }
-
-  /**
-   * returns the current Composite of the EpsGraphics2D object.
-   */
-  public Composite getComposite()
-  {
-    return _composite;
-  }
-
-  /**
-   * Sets the background color to be used by the clearRect method.
-   */
-  public void setBackground(Color color)
-  {
-    if (color == null)
-    {
-      color = Color.black;
-    }
-    _backgroundColor = color;
-  }
-
-  /**
-   * Gets the background color that is used by the clearRect method.
-   */
-  public Color getBackground()
-  {
-    return _backgroundColor;
-  }
-
-  /**
-   * Returns the Stroke currently used.  Guaranteed to be an instance of
-   * BasicStroke.
-   */
-  public Stroke getStroke()
-  {
-    return _stroke;
-  }
-
-  /**
-   * Intersects the current clip with the interior of the specified Shape
-   * and sets the clip to the resulting intersection.
-   */
-  public void clip(Shape s)
-  {
-    if (_clip == null)
-    {
-      setClip(s);
-    }
-    else
-    {
-      Area area = new Area(_clip);
-      area.intersect(new Area(s));
-      setClip(area);
-    }
-  }
-
-  /**
-   * Returns the FontRenderContext.
-   */
-  public FontRenderContext getFontRenderContext()
-  {
-    return _fontRenderContext;
-  }
-
-  /////////////// Graphics methods ///////////////////////
-
-
-  /**
-   * Returns a new Graphics object that is identical to this EpsGraphics2D.
-   */
-  public Graphics create()
-  {
-    return new EpsGraphics2D(this);
-  }
-
-  /**
-   * Returns an EpsGraphics2D object based on this
-   * Graphics object, but with a new translation and clip
-   * area.
-   */
-  public Graphics create(int x, int y, int width, int height)
-  {
-    Graphics g = create();
-    g.translate(x, y);
-    g.clipRect(0, 0, width, height);
-    return g;
-  }
-
-  /**
-   * Returns the current Color.  This will be a default value (black)
-   * until it is changed using the setColor method.
-   */
-  public Color getColor()
-  {
-    return _color;
-  }
-
-  /**
-   * Sets the Color to be used when drawing all future shapes, text, etc.
-   */
-  public void setColor(Color c)
-  {
-    if (c == null)
-    {
-      c = Color.black;
-    }
-    _color = c;
-    append( (c.getRed() / 255f) + " " + (c.getGreen() / 255f) + " " +
-           (c.getBlue() / 255f) + " setrgbcolor");
-  }
-
-  /**
-   * Sets the paint mode of this EpsGraphics2D object to overwrite the
-   * destination EpsDocument with the current color.
-   */
-  public void setPaintMode()
-  {
-    // Do nothing - paint mode is the only method supported anyway.
-  }
-
-  /**
-   * <b><i><font color="red">Not implemented</font></i></b> - performs no action.
-   */
-  public void setXORMode(Color c1)
-  {
-    methodNotSupported();
-  }
-
-  /**
-   * Returns the Font currently being used.
-   */
-  public Font getFont()
-  {
-    return _font;
-  }
-
-  /**
-   * Sets the Font to be used in future text.
-   */
-  public void setFont(Font font)
-  {
-    if (font == null)
-    {
-      font = Font.decode(null);
-    }
-    _font = font;
-    append("/" + _font.getPSName() + " findfont " + ( (int) _font.getSize()) +
-           " scalefont setfont");
-  }
-
-  /**
-   * Gets the font metrics of the current font.
-   */
-  public FontMetrics getFontMetrics()
-  {
-    return getFontMetrics(getFont());
-  }
-
-  /**
-   * Gets the font metrics for the specified font.
-   */
-  public FontMetrics getFontMetrics(Font f)
-  {
-    BufferedImage image = new BufferedImage(1, 1, BufferedImage.TYPE_INT_RGB);
-    Graphics g = image.getGraphics();
-    return g.getFontMetrics(f);
-  }
-
-  /**
-   * Returns the bounding rectangle of the current clipping area.
-   */
-  public Rectangle getClipBounds()
-  {
-    if (_clip == null)
-    {
-      return null;
-    }
-    Rectangle rect = getClip().getBounds();
-    return rect;
-  }
-
-  /**
-   * Intersects the current clip with the specified rectangle.
-   */
-  public void clipRect(int x, int y, int width, int height)
-  {
-    clip(new Rectangle(x, y, width, height));
-  }
-
-  /**
-   * Sets the current clip to the rectangle specified by the given
-   * coordinates.
-   */
-  public void setClip(int x, int y, int width, int height)
-  {
-    setClip(new Rectangle(x, y, width, height));
-  }
-
-  /**
-   * Gets the current clipping area.
-   */
-  public Shape getClip()
-  {
-    if (_clip == null)
-    {
-      return null;
-    }
-    else
-    {
-      try
-      {
-        AffineTransform t = _transform.createInverse();
-        t.concatenate(_clipTransform);
-        return t.createTransformedShape(_clip);
-      }
-      catch (Exception e)
-      {
-        throw new EpsException("Unable to get inverse of matrix: " + _transform);
-      }
-    }
-  }
-
-  /**
-   * Sets the current clipping area to an arbitrary clip shape.
-   */
-  public void setClip(Shape clip)
-  {
-    if (clip != null)
-    {
-      if (_document.isClipSet())
-      {
-        append("grestore");
-        append("gsave");
-      }
-      else
-      {
-        _document.setClipSet(true);
-        append("gsave");
-      }
-      draw(clip, "clip");
-      _clip = clip;
-      _clipTransform = (AffineTransform) _transform.clone();
-    }
-    else
-    {
-      if (_document.isClipSet())
-      {
-        append("grestore");
-        _document.setClipSet(false);
-      }
-      _clip = null;
-    }
-  }
-
-  /**
-   * <b><i><font color="red">Not implemented</font></i></b> - performs no action.
-   */
-  public void copyArea(int x, int y, int width, int height, int dx, int dy)
-  {
-    methodNotSupported();
-  }
-
-  /**
-   * Draws a straight line from (x1,y1) to (x2,y2).
-   */
-  public void drawLine(int x1, int y1, int x2, int y2)
-  {
-    Shape shape = new Line2D.Float(x1, y1, x2, y2);
-    draw(shape);
-  }
-
-  /**
-   * Fills a rectangle with top-left corner placed at (x,y).
-   */
-  public void fillRect(int x, int y, int width, int height)
-  {
-    Shape shape = new Rectangle(x, y, width, height);
-    draw(shape, "fill");
-  }
-
-  /**
-   * Draws a rectangle with top-left corner placed at (x,y).
-   */
-  public void drawRect(int x, int y, int width, int height)
-  {
-    Shape shape = new Rectangle(x, y, width, height);
-    draw(shape);
-  }
-
-  /**
-   * Clears a rectangle with top-left corner placed at (x,y) using the
-   * current background color.
-   */
-  public void clearRect(int x, int y, int width, int height)
-  {
-    Color originalColor = getColor();
-
-    setColor(getBackground());
-    Shape shape = new Rectangle(x, y, width, height);
-    draw(shape, "fill");
-
-    setColor(originalColor);
-  }
-
-  /**
-   * Draws a rounded rectangle.
-   */
-  public void drawRoundRect(int x, int y, int width, int height, int arcWidth,
-                            int arcHeight)
-  {
-    Shape shape = new RoundRectangle2D.Float(x, y, width, height, arcWidth,
-                                             arcHeight);
-    draw(shape);
-  }
-
-  /**
-   * Fills a rounded rectangle.
-   */
-  public void fillRoundRect(int x, int y, int width, int height, int arcWidth,
-                            int arcHeight)
-  {
-    Shape shape = new RoundRectangle2D.Float(x, y, width, height, arcWidth,
-                                             arcHeight);
-    draw(shape, "fill");
-  }
-
-  /**
-   * Draws an oval.
-   */
-  public void drawOval(int x, int y, int width, int height)
-  {
-    Shape shape = new Ellipse2D.Float(x, y, width, height);
-    draw(shape);
-  }
-
-  /**
-   * Fills an oval.
-   */
-  public void fillOval(int x, int y, int width, int height)
-  {
-    Shape shape = new Ellipse2D.Float(x, y, width, height);
-    draw(shape, "fill");
-  }
-
-  /**
-   * Draws an arc.
-   */
-  public void drawArc(int x, int y, int width, int height, int startAngle,
-                      int arcAngle)
-  {
-    Shape shape = new Arc2D.Float(x, y, width, height, startAngle, arcAngle,
-                                  Arc2D.OPEN);
-    draw(shape);
-  }
-
-  /**
-   * Fills an arc.
-   */
-  public void fillArc(int x, int y, int width, int height, int startAngle,
-                      int arcAngle)
-  {
-    Shape shape = new Arc2D.Float(x, y, width, height, startAngle, arcAngle,
-                                  Arc2D.PIE);
-    draw(shape, "fill");
-  }
-
-  /**
-   * Draws a polyline.
-   */
-  public void drawPolyline(int[] xPoints, int[] yPoints, int nPoints)
-  {
-    if (nPoints > 0)
-    {
-      GeneralPath path = new GeneralPath();
-      path.moveTo(xPoints[0], yPoints[0]);
-      for (int i = 1; i < nPoints; i++)
-      {
-        path.lineTo(xPoints[i], yPoints[i]);
-      }
-      draw(path);
-    }
-  }
-
-  /**
-   * Draws a polygon made with the specified points.
-   */
-  public void drawPolygon(int[] xPoints, int[] yPoints, int nPoints)
-  {
-    Shape shape = new Polygon(xPoints, yPoints, nPoints);
-    draw(shape);
-  }
-
-  /**
-   * Draws a polygon.
-   */
-  public void drawPolygon(Polygon p)
-  {
-    draw(p);
-  }
-
-  /**
-   * Fills a polygon made with the specified points.
-   */
-  public void fillPolygon(int[] xPoints, int[] yPoints, int nPoints)
-  {
-    Shape shape = new Polygon(xPoints, yPoints, nPoints);
-    draw(shape, "fill");
-  }
-
-  /**
-   * Fills a polygon.
-   */
-  public void fillPolygon(Polygon p)
-  {
-    draw(p, "fill");
-  }
-
-  /**
-   * Draws the specified characters, starting from (x,y)
-   */
-  public void drawChars(char[] data, int offset, int length, int x, int y)
-  {
-    String string = new String(data, offset, length);
-    drawString(string, x, y);
-  }
-
-  /**
-   * Draws the specified bytes, starting from (x,y)
-   */
-  public void drawBytes(byte[] data, int offset, int length, int x, int y)
-  {
-    String string = new String(data, offset, length);
-    drawString(string, x, y);
-  }
-
-  /**
-   * Draws an image.
-   */
-  public boolean drawImage(Image img, int x, int y, ImageObserver observer)
-  {
-    return drawImage(img, x, y, Color.white, observer);
-  }
-
-  /**
-   * Draws an image.
-   */
-  public boolean drawImage(Image img, int x, int y, int width, int height,
-                           ImageObserver observer)
-  {
-    return drawImage(img, x, y, width, height, Color.white, observer);
-  }
-
-  /**
-   * Draws an image.
-   */
-  public boolean drawImage(Image img, int x, int y, Color bgcolor,
-                           ImageObserver observer)
-  {
-    int width = img.getWidth(null);
-    int height = img.getHeight(null);
-    return drawImage(img, x, y, width, height, bgcolor, observer);
-  }
-
-  /**
-   * Draws an image.
-   */
-  public boolean drawImage(Image img, int x, int y, int width, int height,
-                           Color bgcolor, ImageObserver observer)
-  {
-    return drawImage(img, x, y, x + width, y + height, 0, 0, width, height,
-                     bgcolor, observer);
-  }
-
-  /**
-   * Draws an image.
-   */
-  public boolean drawImage(Image img, int dx1, int dy1, int dx2, int dy2,
-                           int sx1, int sy1, int sx2, int sy2,
-                           ImageObserver observer)
-  {
-    return drawImage(img, dx1, dy1, dx2, dy2, sx1, sy1, sx2, sy2, Color.white,
-                     observer);
-  }
-
-  /**
-   * Draws an image.
-   */
-  public boolean drawImage(Image img, int dx1, int dy1, int dx2, int dy2,
-                           int sx1, int sy1, int sx2, int sy2, Color bgcolor,
-                           ImageObserver observer)
-  {
-    if (dx1 >= dx2)
-    {
-      throw new IllegalArgumentException("dx1 >= dx2");
-    }
-    if (sx1 >= sx2)
-    {
-      throw new IllegalArgumentException("sx1 >= sx2");
-    }
-    if (dy1 >= dy2)
-    {
-      throw new IllegalArgumentException("dy1 >= dy2");
-    }
-    if (sy1 >= sy2)
-    {
-      throw new IllegalArgumentException("sy1 >= sy2");
-    }
-
-    append("gsave");
-
-    int width = sx2 - sx1;
-    int height = sy2 - sy1;
-    int destWidth = dx2 - dx1;
-    int destHeight = dy2 - dy1;
-
-    int[] pixels = new int[width * height];
-    PixelGrabber pg = new PixelGrabber(img, sx1, sy1, sx2 - sx1, sy2 - sy1,
-                                       pixels, 0, width);
-    try
-    {
-      pg.grabPixels();
-    }
-    catch (InterruptedException e)
-    {
-      return false;
-    }
-
-    AffineTransform matrix = new AffineTransform(_transform);
-    matrix.translate(dx1, dy1);
-    matrix.scale(destWidth / (double) width, destHeight / (double) height);
-    double[] m = new double[6];
-    try
-    {
-      matrix = matrix.createInverse();
-    }
-    catch (Exception e)
-    {
-      throw new EpsException("Unable to get inverse of matrix: " + matrix);
-    }
-    matrix.scale(1, -1);
-    matrix.getMatrix(m);
-    append(width + " " + height + " 8 [" + m[0] + " " + m[1] + " " + m[2] + " " +
-           m[3] + " " + m[4] + " " + m[5] + "]");
-    // Fill the background to update the bounding box.
-    Color oldColor = getColor();
-    setColor(getBackground());
-    fillRect(dx1, dy1, destWidth, destHeight);
-    setColor(oldColor);
-    append("{currentfile 3 " + width + " mul string readhexstring pop} bind");
-    append("false 3 colorimage");
-    StringBuffer line = new StringBuffer();
-    for (int y = 0; y < height; y++)
-    {
-      for (int x = 0; x < width; x++)
-      {
-        Color color = new Color(pixels[x + width * y]);
-        line.append(toHexString(color.getRed()) + toHexString(color.getGreen()) +
-                    toHexString(color.getBlue()));
-        if (line.length() > 64)
-        {
-          append(line.toString());
-          line = new StringBuffer();
-        }
-      }
-    }
-    if (line.length() > 0)
-    {
-      append(line.toString());
-    }
-
-    append("grestore");
-
-    return true;
-  }
-
-  /**
-   * Disposes of all resources used by this EpsGraphics2D object.
-   * If this is the only remaining EpsGraphics2D instance pointing at
-   * a EpsDocument object, then the EpsDocument object shall become
-   * eligible for garbage collection.
-   */
-  public void dispose()
-  {
-    _document = null;
-  }
-
-  /**
-   * Finalizes the object.
-   */
-  public void finalize()
-  {
-    super.finalize();
-  }
-
-  /**
-   * Returns the entire contents of the EPS document, complete with
-   * headers and bounding box.  The returned String is suitable for
-   * being written directly to disk as an EPS file.
-   */
-  public String toString()
-  {
-    StringWriter writer = new StringWriter();
-    try
-    {
-      _document.write(writer);
-      _document.flush();
-      _document.close();
-    }
-    catch (IOException e)
-    {
-      throw new EpsException(e.toString());
-    }
-    return writer.toString();
-  }
-
-  /**
-   * Returns true if the specified rectangular area might intersect the
-   * current clipping area.
-   */
-  public boolean hitClip(int x, int y, int width, int height)
-  {
-    if (_clip == null)
-    {
-      return true;
-    }
-    Rectangle rect = new Rectangle(x, y, width, height);
-    return hit(rect, _clip, true);
-  }
-
-  /**
-   * Returns the bounding rectangle of the current clipping area.
-   */
-  public Rectangle getClipBounds(Rectangle r)
-  {
-    if (_clip == null)
-    {
-      return r;
-    }
-    Rectangle rect = getClipBounds();
-    r.setLocation( (int) rect.getX(), (int) rect.getY());
-    r.setSize( (int) rect.getWidth(), (int) rect.getHeight());
-    return r;
-  }
-
-  private Color _color;
-  private Color _backgroundColor;
-  private Paint _paint;
-  private Composite _composite;
-  private BasicStroke _stroke;
-  private Font _font;
-  private Shape _clip;
-  private AffineTransform _clipTransform;
-  private AffineTransform _transform;
-  private boolean _accurateTextMode;
-
-  private EpsDocument _document;
-
-  private static FontRenderContext _fontRenderContext = new FontRenderContext(null, false, true);
+/*
+ Copyright Paul James Mutton, 2001-2004, http://www.jibble.org/
+
+ This file is part of EpsGraphics2D.
+
+ This software is dual-licensed, allowing you to choose between the GNU
+ General Public License (GPL) and the www.jibble.org Commercial License.
+ Since the GPL may be too restrictive for use in a proprietary application,
+ a commercial license is also provided. Full license information can be
+ found at http://www.jibble.org/licenses/
+
+ $Author$
+ $Id$
+
+ */
+
+package org.jibble.epsgraphics;
+
+import java.io.*;
+import java.text.*;
+import java.util.*;
+
+import java.awt.*;
+import java.awt.font.*;
+import java.awt.geom.*;
+import java.awt.image.*;
+import java.awt.image.renderable.*;
+
+/**
+ * EpsGraphics2D is suitable for creating high quality EPS graphics for use in
+ * documents and papers, and can be used just like a standard Graphics2D object.
+ * <p>
+ * Many Java programs use Graphics2D to draw stuff on the screen, and while it
+ * is easy to save the output as a png or jpeg file, it is a little harder to
+ * export it as an EPS for including in a document or paper.
+ * <p>
+ * This class makes the whole process extremely easy, because you can use it as
+ * if it's a Graphics2D object. The only difference is that all of the
+ * implemented methods create EPS output, which means the diagrams you draw can
+ * be resized without leading to any of the jagged edges you may see when
+ * resizing pixel-based images, such as jpeg and png files.
+ * <p>
+ * Example usage:
+ * <p>
+ * 
+ * <pre>
+ * Graphics2D g = new EpsGraphics2D();
+ * g.setColor(Color.black);
+ * 
+ * // Line thickness 2.
+ * g.setStroke(new BasicStroke(2.0f));
+ * 
+ * // Draw a line.
+ * g.drawLine(10, 10, 50, 10);
+ * 
+ * // Fill a rectangle in blue
+ * g.setColor(Color.blue);
+ * g.fillRect(10, 0, 20, 20);
+ * 
+ * // Get the EPS output.
+ * String output = g.toString();
+ * </pre>
+ * 
+ * <p>
+ * You do not need to worry about the size of the canvas when drawing on a
+ * EpsGraphics2D object. The bounding box of the EPS document will automatically
+ * resize to accomodate new items that you draw.
+ * <p>
+ * Not all methods are implemented yet. Those that are not are clearly labelled.
+ * <p>
+ * Copyright Paul Mutton, <a
+ * href="http://www.jibble.org/">http://www.jibble.org/</a>
+ * 
+ */
+public class EpsGraphics2D extends java.awt.Graphics2D
+{
+
+  public static final String VERSION = "0.8.8";
+
+  /**
+   * Constructs a new EPS document that is initially empty and can be drawn on
+   * like a Graphics2D object. The EPS document is stored in memory.
+   */
+  public EpsGraphics2D()
+  {
+    this("Untitled");
+  }
+
+  /**
+   * Constructs a new EPS document that is initially empty and can be drawn on
+   * like a Graphics2D object. The EPS document is stored in memory.
+   */
+  public EpsGraphics2D(String title)
+  {
+    _document = new EpsDocument(title);
+    _backgroundColor = Color.white;
+    _clip = null;
+    _transform = new AffineTransform();
+    _clipTransform = new AffineTransform();
+    _accurateTextMode = true;
+    setColor(Color.black);
+    setPaint(Color.black);
+    setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR));
+    setFont(Font.decode(null));
+    setStroke(new BasicStroke());
+  }
+
+  /**
+   * Constructs a new EPS document that is initially empty and can be drawn on
+   * like a Graphics2D object. The EPS document is written to the file as it
+   * goes, which reduces memory usage. The bounding box of the document is fixed
+   * and specified at construction time by minX,minY,maxX,maxY. The file is
+   * flushed and closed when the close() method is called.
+   */
+  public EpsGraphics2D(String title, File file, int minX, int minY,
+          int maxX, int maxY) throws IOException
+  {
+    this(title, new FileOutputStream(file), minX, minY, maxX, maxY);
+  }
+
+  /**
+   * Constructs a new EPS document that is initially empty and can be drawn on
+   * like a Graphics2D object. The EPS document is written to the output stream
+   * as it goes, which reduces memory usage. The bounding box of the document is
+   * fixed and specified at construction time by minX,minY,maxX,maxY. The output
+   * stream is flushed and closed when the close() method is called.
+   */
+  public EpsGraphics2D(String title, OutputStream outputStream, int minX,
+          int minY, int maxX, int maxY) throws IOException
+  {
+    this(title);
+    _document = new EpsDocument(title, outputStream, minX, minY, maxX, maxY);
+  }
+
+  /**
+   * Constructs a new EpsGraphics2D instance that is a copy of the supplied
+   * argument and points at the same EpsDocument.
+   */
+  protected EpsGraphics2D(EpsGraphics2D g)
+  {
+    _document = g._document;
+    _backgroundColor = g._backgroundColor;
+    _clip = g._clip;
+    _clipTransform = (AffineTransform) g._clipTransform.clone();
+    _transform = (AffineTransform) g._transform.clone();
+    _color = g._color;
+    _paint = g._paint;
+    _composite = g._composite;
+    _font = g._font;
+    _stroke = g._stroke;
+    _accurateTextMode = g._accurateTextMode;
+  }
+
+  /**
+   * This method is called to indicate that a particular method is not supported
+   * yet. The stack trace is printed to the standard output.
+   */
+  private void methodNotSupported()
+  {
+    EpsException e = new EpsException(
+            "Method not currently supported by EpsGraphics2D version "
+                    + VERSION);
+    e.printStackTrace(System.err);
+  }
+
+  // ///////////// Specialist methods ///////////////////////
+
+  /**
+   * Sets whether to use accurate text mode when rendering text in EPS. This is
+   * enabled (true) by default. When accurate text mode is used, all text will
+   * be rendered in EPS to appear exactly the same as it would do when drawn
+   * with a Graphics2D context. With accurate text mode enabled, it is not
+   * necessary for the EPS viewer to have the required font installed.
+   * <p>
+   * Turning off accurate text mode will require the EPS viewer to have the
+   * necessary fonts installed. If you are using a lot of text, you will find
+   * that this significantly reduces the file size of your EPS documents.
+   * AffineTransforms can only affect the starting point of text using this
+   * simpler text mode - all text will be horizontal.
+   */
+  public void setAccurateTextMode(boolean b)
+  {
+    _accurateTextMode = b;
+  }
+
+  /**
+   * Returns whether accurate text mode is being used.
+   */
+  public boolean getAccurateTextMode()
+  {
+    return _accurateTextMode;
+  }
+
+  /**
+   * Flushes the buffered contents of this EPS document to the underlying
+   * OutputStream it is being written to.
+   */
+  public void flush() throws IOException
+  {
+    _document.flush();
+  }
+
+  /**
+   * Closes the EPS file being output to the underlying OutputStream. The
+   * OutputStream is automatically flushed before being closed. If you forget to
+   * do this, the file may be incomplete.
+   */
+  public void close() throws IOException
+  {
+    flush();
+    _document.close();
+  }
+
+  /**
+   * Appends a line to the EpsDocument.
+   */
+  private void append(String line)
+  {
+    _document.append(this, line);
+  }
+
+  /**
+   * Returns the point after it has been transformed by the transformation.
+   */
+  private Point2D transform(float x, float y)
+  {
+    Point2D result = new Point2D.Float(x, y);
+    result = _transform.transform(result, result);
+    result.setLocation(result.getX(), -result.getY());
+    return result;
+  }
+
+  /**
+   * Appends the commands required to draw a shape on the EPS document.
+   */
+  private void draw(Shape s, String action)
+  {
+
+    if (s != null)
+    {
+
+      // Rectangle2D userBounds = s.getBounds2D();
+      if (!_transform.isIdentity())
+      {
+        s = _transform.createTransformedShape(s);
+      }
+
+      // Update the bounds.
+      if (!action.equals("clip"))
+      {
+        Rectangle2D shapeBounds = s.getBounds2D();
+        Rectangle2D visibleBounds = shapeBounds;
+        if (_clip != null)
+        {
+          Rectangle2D clipBounds = _clip.getBounds2D();
+          visibleBounds = shapeBounds.createIntersection(clipBounds);
+        }
+        float lineRadius = _stroke.getLineWidth() / 2;
+        float minX = (float) visibleBounds.getMinX() - lineRadius;
+        float minY = (float) visibleBounds.getMinY() - lineRadius;
+        float maxX = (float) visibleBounds.getMaxX() + lineRadius;
+        float maxY = (float) visibleBounds.getMaxY() + lineRadius;
+        _document.updateBounds(minX, -minY);
+        _document.updateBounds(maxX, -maxY);
+      }
+
+      append("newpath");
+      int type = 0;
+      float[] coords = new float[6];
+      PathIterator it = s.getPathIterator(null);
+      float x0 = 0;
+      float y0 = 0;
+      int count = 0;
+      while (!it.isDone())
+      {
+        type = it.currentSegment(coords);
+        float x1 = coords[0];
+        float y1 = -coords[1];
+        float x2 = coords[2];
+        float y2 = -coords[3];
+        float x3 = coords[4];
+        float y3 = -coords[5];
+
+        if (type == PathIterator.SEG_CLOSE)
+        {
+          append("closepath");
+          count++;
+        }
+        else if (type == PathIterator.SEG_CUBICTO)
+        {
+          append(x1 + " " + y1 + " " + x2 + " " + y2 + " " + x3 + " " + y3
+                  + " curveto");
+          count++;
+          x0 = x3;
+          y0 = y3;
+        }
+        else if (type == PathIterator.SEG_LINETO)
+        {
+          append(x1 + " " + y1 + " lineto");
+          count++;
+          x0 = x1;
+          y0 = y1;
+        }
+        else if (type == PathIterator.SEG_MOVETO)
+        {
+          append(x1 + " " + y1 + " moveto");
+          count++;
+          x0 = x1;
+          y0 = y1;
+        }
+        else if (type == PathIterator.SEG_QUADTO)
+        {
+          // Convert the quad curve into a cubic.
+          float _x1 = x0 + 2 / 3f * (x1 - x0);
+          float _y1 = y0 + 2 / 3f * (y1 - y0);
+          float _x2 = x1 + 1 / 3f * (x2 - x1);
+          float _y2 = y1 + 1 / 3f * (y2 - y1);
+          float _x3 = x2;
+          float _y3 = y2;
+          append(_x1 + " " + _y1 + " " + _x2 + " " + _y2 + " " + _x3 + " "
+                  + _y3 + " curveto");
+          count++;
+          x0 = _x3;
+          y0 = _y3;
+        }
+        else if (type == PathIterator.WIND_EVEN_ODD)
+        {
+          // Ignore.
+        }
+        else if (type == PathIterator.WIND_NON_ZERO)
+        {
+          // Ignore.
+        }
+        it.next();
+      }
+      append(action);
+      append("newpath");
+    }
+  }
+
+  /**
+   * Returns a hex string that always contains two characters.
+   */
+  private String toHexString(int n)
+  {
+    String result = Integer.toString(n, 16);
+    while (result.length() < 2)
+    {
+      result = "0" + result;
+    }
+    return result;
+  }
+
+  // ///////////// Graphics2D methods ///////////////////////
+
+  /**
+   * Draws a 3D rectangle outline. If it is raised, light appears to come from
+   * the top left.
+   */
+  public void draw3DRect(int x, int y, int width, int height, boolean raised)
+  {
+    Color originalColor = getColor();
+    Stroke originalStroke = getStroke();
+
+    setStroke(new BasicStroke(1.0f));
+
+    if (raised)
+    {
+      setColor(originalColor.brighter());
+    }
+    else
+    {
+      setColor(originalColor.darker());
+    }
+
+    drawLine(x, y, x + width, y);
+    drawLine(x, y, x, y + height);
+
+    if (raised)
+    {
+      setColor(originalColor.darker());
+    }
+    else
+    {
+      setColor(originalColor.brighter());
+    }
+
+    drawLine(x + width, y + height, x, y + height);
+    drawLine(x + width, y + height, x + width, y);
+
+    setColor(originalColor);
+    setStroke(originalStroke);
+  }
+
+  /**
+   * Fills a 3D rectangle. If raised, it has bright fill and light appears to
+   * come from the top left.
+   */
+  public void fill3DRect(int x, int y, int width, int height, boolean raised)
+  {
+    Color originalColor = getColor();
+
+    if (raised)
+    {
+      setColor(originalColor.brighter());
+    }
+    else
+    {
+      setColor(originalColor.darker());
+    }
+    draw(new Rectangle(x, y, width, height), "fill");
+    setColor(originalColor);
+    draw3DRect(x, y, width, height, raised);
+  }
+
+  /**
+   * Draws a Shape on the EPS document.
+   */
+  public void draw(Shape s)
+  {
+    draw(s, "stroke");
+  }
+
+  /**
+   * Draws an Image on the EPS document.
+   */
+  public boolean drawImage(Image img, AffineTransform xform,
+          ImageObserver obs)
+  {
+    AffineTransform at = getTransform();
+    transform(xform);
+    boolean st = drawImage(img, 0, 0, obs);
+    setTransform(at);
+    return st;
+  }
+
+  /**
+   * Draws a BufferedImage on the EPS document.
+   */
+  public void drawImage(BufferedImage img, BufferedImageOp op, int x, int y)
+  {
+    BufferedImage img1 = op.filter(img, null);
+    drawImage(img1, new AffineTransform(1f, 0f, 0f, 1f, x, y), null);
+  }
+
+  /**
+   * Draws a RenderedImage on the EPS document.
+   */
+  public void drawRenderedImage(RenderedImage img, AffineTransform xform)
+  {
+    Hashtable properties = new Hashtable();
+    String[] names = img.getPropertyNames();
+    for (int i = 0; i < names.length; i++)
+    {
+      properties.put(names[i], img.getProperty(names[i]));
+    }
+
+    ColorModel cm = img.getColorModel();
+    WritableRaster wr = img.copyData(null);
+    BufferedImage img1 = new BufferedImage(cm, wr, cm
+            .isAlphaPremultiplied(), properties);
+    AffineTransform at = AffineTransform.getTranslateInstance(
+            img.getMinX(), img.getMinY());
+    at.preConcatenate(xform);
+    drawImage(img1, at, null);
+  }
+
+  /**
+   * Draws a RenderableImage by invoking its createDefaultRendering method.
+   */
+  public void drawRenderableImage(RenderableImage img, AffineTransform xform)
+  {
+    drawRenderedImage(img.createDefaultRendering(), xform);
+  }
+
+  /**
+   * Draws a string at (x,y)
+   */
+  public void drawString(String str, int x, int y)
+  {
+    drawString(str, (float) x, (float) y);
+  }
+
+  /**
+   * Draws a string at (x,y)
+   */
+  public void drawString(String s, float x, float y)
+  {
+    if (s != null && s.length() > 0)
+    {
+      AttributedString as = new AttributedString(s);
+      as.addAttribute(TextAttribute.FONT, getFont());
+      drawString(as.getIterator(), x, y);
+    }
+  }
+
+  /**
+   * Draws the characters of an AttributedCharacterIterator, starting from
+   * (x,y).
+   */
+  public void drawString(AttributedCharacterIterator iterator, int x, int y)
+  {
+    drawString(iterator, (float) x, (float) y);
+  }
+
+  /**
+   * Draws the characters of an AttributedCharacterIterator, starting from
+   * (x,y).
+   */
+  public void drawString(AttributedCharacterIterator iterator, float x,
+          float y)
+  {
+    if (getAccurateTextMode())
+    {
+      TextLayout layout = new TextLayout(iterator, getFontRenderContext());
+      Shape shape = layout.getOutline(AffineTransform.getTranslateInstance(
+              x, y));
+      draw(shape, "fill");
+    }
+    else
+    {
+      append("newpath");
+      Point2D location = transform(x, y);
+      append(location.getX() + " " + location.getY() + " moveto");
+      StringBuffer buffer = new StringBuffer();
+      for (char ch = iterator.first(); ch != CharacterIterator.DONE; ch = iterator
+              .next())
+      {
+        if (ch == '(' || ch == ')')
+        {
+          buffer.append('\\');
+        }
+        buffer.append(ch);
+      }
+      append("(" + buffer.toString() + ") show");
+    }
+  }
+
+  /**
+   * Draws a GlyphVector at (x,y)
+   */
+  public void drawGlyphVector(GlyphVector g, float x, float y)
+  {
+    Shape shape = g.getOutline(x, y);
+    draw(shape, "fill");
+  }
+
+  /**
+   * Fills a Shape on the EPS document.
+   */
+  public void fill(Shape s)
+  {
+    draw(s, "fill");
+  }
+
+  /**
+   * Checks whether or not the specified Shape intersects the specified
+   * Rectangle, which is in device space.
+   */
+  public boolean hit(Rectangle rect, Shape s, boolean onStroke)
+  {
+    return s.intersects(rect);
+  }
+
+  /**
+   * Returns the device configuration associated with this EpsGraphics2D object.
+   */
+  public GraphicsConfiguration getDeviceConfiguration()
+  {
+    GraphicsConfiguration gc = null;
+    GraphicsEnvironment ge = GraphicsEnvironment
+            .getLocalGraphicsEnvironment();
+    GraphicsDevice[] gds = ge.getScreenDevices();
+    for (int i = 0; i < gds.length; i++)
+    {
+      GraphicsDevice gd = gds[i];
+      GraphicsConfiguration[] gcs = gd.getConfigurations();
+      if (gcs.length > 0)
+      {
+        return gcs[0];
+      }
+    }
+    return gc;
+  }
+
+  /**
+   * Sets the Composite to be used by this EpsGraphics2D. EpsGraphics2D does not
+   * make use of these.
+   */
+  public void setComposite(Composite comp)
+  {
+    _composite = comp;
+  }
+
+  /**
+   * Sets the Paint attribute for the EpsGraphics2D object. Only Paint objects
+   * of type Color are respected by EpsGraphics2D.
+   */
+  public void setPaint(Paint paint)
+  {
+    _paint = paint;
+    if (paint instanceof Color)
+    {
+      setColor((Color) paint);
+    }
+  }
+
+  /**
+   * Sets the stroke. Only accepts BasicStroke objects (or subclasses of
+   * BasicStroke).
+   */
+  public void setStroke(Stroke s)
+  {
+    if (s instanceof BasicStroke)
+    {
+      _stroke = (BasicStroke) s;
+
+      append(_stroke.getLineWidth() + " setlinewidth");
+      float miterLimit = _stroke.getMiterLimit();
+      if (miterLimit < 1.0f)
+      {
+        miterLimit = 1;
+      }
+      append(miterLimit + " setmiterlimit");
+      append(_stroke.getLineJoin() + " setlinejoin");
+      append(_stroke.getEndCap() + " setlinecap");
+
+      StringBuffer dashes = new StringBuffer();
+      dashes.append("[ ");
+      float[] dashArray = _stroke.getDashArray();
+      if (dashArray != null)
+      {
+        for (int i = 0; i < dashArray.length; i++)
+        {
+          dashes.append((dashArray[i]) + " ");
+        }
+      }
+      dashes.append("]");
+      append(dashes.toString() + " 0 setdash");
+    }
+  }
+
+  /**
+   * Sets a rendering hint. These are not used by EpsGraphics2D.
+   */
+  public void setRenderingHint(RenderingHints.Key hintKey, Object hintValue)
+  {
+    // Do nothing.
+  }
+
+  /**
+   * Returns the value of a single preference for the rendering algorithms.
+   * Rendering hints are not used by EpsGraphics2D.
+   */
+  public Object getRenderingHint(RenderingHints.Key hintKey)
+  {
+    return null;
+  }
+
+  /**
+   * Sets the rendering hints. These are ignored by EpsGraphics2D.
+   */
+  public void setRenderingHints(Map hints)
+  {
+    // Do nothing.
+  }
+
+  /**
+   * Adds rendering hints. These are ignored by EpsGraphics2D.
+   */
+  public void addRenderingHints(Map hints)
+  {
+    // Do nothing.
+  }
+
+  /**
+   * Returns the preferences for the rendering algorithms.
+   */
+  public RenderingHints getRenderingHints()
+  {
+    return new RenderingHints(null);
+  }
+
+  /**
+   * Translates the origin of the EpsGraphics2D context to the point (x,y) in
+   * the current coordinate system.
+   */
+  public void translate(int x, int y)
+  {
+    translate((double) x, (double) y);
+  }
+
+  /**
+   * Concatenates the current EpsGraphics2D Transformation with a translation
+   * transform.
+   */
+  public void translate(double tx, double ty)
+  {
+    transform(AffineTransform.getTranslateInstance(tx, ty));
+  }
+
+  /**
+   * Concatenates the current EpsGraphics2D Transform with a rotation transform.
+   */
+  public void rotate(double theta)
+  {
+    rotate(theta, 0, 0);
+  }
+
+  /**
+   * Concatenates the current EpsGraphics2D Transform with a translated rotation
+   * transform.
+   */
+  public void rotate(double theta, double x, double y)
+  {
+    transform(AffineTransform.getRotateInstance(theta, x, y));
+  }
+
+  /**
+   * Concatenates the current EpsGraphics2D Transform with a scaling
+   * transformation.
+   */
+  public void scale(double sx, double sy)
+  {
+    transform(AffineTransform.getScaleInstance(sx, sy));
+  }
+
+  /**
+   * Concatenates the current EpsGraphics2D Transform with a shearing transform.
+   */
+  public void shear(double shx, double shy)
+  {
+    transform(AffineTransform.getShearInstance(shx, shy));
+  }
+
+  /**
+   * Composes an AffineTransform object with the Transform in this EpsGraphics2D
+   * according to the rule last-specified-first-applied.
+   */
+  public void transform(AffineTransform Tx)
+  {
+    _transform.concatenate(Tx);
+    setTransform(getTransform());
+  }
+
+  /**
+   * Sets the AffineTransform to be used by this EpsGraphics2D.
+   */
+  public void setTransform(AffineTransform Tx)
+  {
+    if (Tx == null)
+    {
+      _transform = new AffineTransform();
+    }
+    else
+    {
+      _transform = new AffineTransform(Tx);
+    }
+    // Need to update the stroke and font so they know the scale changed
+    setStroke(getStroke());
+    setFont(getFont());
+  }
+
+  /**
+   * Gets the AffineTransform used by this EpsGraphics2D.
+   */
+  public AffineTransform getTransform()
+  {
+    return new AffineTransform(_transform);
+  }
+
+  /**
+   * Returns the current Paint of the EpsGraphics2D object.
+   */
+  public Paint getPaint()
+  {
+    return _paint;
+  }
+
+  /**
+   * returns the current Composite of the EpsGraphics2D object.
+   */
+  public Composite getComposite()
+  {
+    return _composite;
+  }
+
+  /**
+   * Sets the background color to be used by the clearRect method.
+   */
+  public void setBackground(Color color)
+  {
+    if (color == null)
+    {
+      color = Color.black;
+    }
+    _backgroundColor = color;
+  }
+
+  /**
+   * Gets the background color that is used by the clearRect method.
+   */
+  public Color getBackground()
+  {
+    return _backgroundColor;
+  }
+
+  /**
+   * Returns the Stroke currently used. Guaranteed to be an instance of
+   * BasicStroke.
+   */
+  public Stroke getStroke()
+  {
+    return _stroke;
+  }
+
+  /**
+   * Intersects the current clip with the interior of the specified Shape and
+   * sets the clip to the resulting intersection.
+   */
+  public void clip(Shape s)
+  {
+    if (_clip == null)
+    {
+      setClip(s);
+    }
+    else
+    {
+      Area area = new Area(_clip);
+      area.intersect(new Area(s));
+      setClip(area);
+    }
+  }
+
+  /**
+   * Returns the FontRenderContext.
+   */
+  public FontRenderContext getFontRenderContext()
+  {
+    return _fontRenderContext;
+  }
+
+  // ///////////// Graphics methods ///////////////////////
+
+  /**
+   * Returns a new Graphics object that is identical to this EpsGraphics2D.
+   */
+  public Graphics create()
+  {
+    return new EpsGraphics2D(this);
+  }
+
+  /**
+   * Returns an EpsGraphics2D object based on this Graphics object, but with a
+   * new translation and clip area.
+   */
+  public Graphics create(int x, int y, int width, int height)
+  {
+    Graphics g = create();
+    g.translate(x, y);
+    g.clipRect(0, 0, width, height);
+    return g;
+  }
+
+  /**
+   * Returns the current Color. This will be a default value (black) until it is
+   * changed using the setColor method.
+   */
+  public Color getColor()
+  {
+    return _color;
+  }
+
+  /**
+   * Sets the Color to be used when drawing all future shapes, text, etc.
+   */
+  public void setColor(Color c)
+  {
+    if (c == null)
+    {
+      c = Color.black;
+    }
+    _color = c;
+    append((c.getRed() / 255f) + " " + (c.getGreen() / 255f) + " "
+            + (c.getBlue() / 255f) + " setrgbcolor");
+  }
+
+  /**
+   * Sets the paint mode of this EpsGraphics2D object to overwrite the
+   * destination EpsDocument with the current color.
+   */
+  public void setPaintMode()
+  {
+    // Do nothing - paint mode is the only method supported anyway.
+  }
+
+  /**
+   * <b><i><font color="red">Not implemented</font></i></b> - performs no
+   * action.
+   */
+  public void setXORMode(Color c1)
+  {
+    methodNotSupported();
+  }
+
+  /**
+   * Returns the Font currently being used.
+   */
+  public Font getFont()
+  {
+    return _font;
+  }
+
+  /**
+   * Sets the Font to be used in future text.
+   */
+  public void setFont(Font font)
+  {
+    if (font == null)
+    {
+      font = Font.decode(null);
+    }
+    _font = font;
+    append("/" + _font.getPSName() + " findfont " + ((int) _font.getSize())
+            + " scalefont setfont");
+  }
+
+  /**
+   * Gets the font metrics of the current font.
+   */
+  public FontMetrics getFontMetrics()
+  {
+    return getFontMetrics(getFont());
+  }
+
+  /**
+   * Gets the font metrics for the specified font.
+   */
+  public FontMetrics getFontMetrics(Font f)
+  {
+    BufferedImage image = new BufferedImage(1, 1,
+            BufferedImage.TYPE_INT_RGB);
+    Graphics g = image.getGraphics();
+    return g.getFontMetrics(f);
+  }
+
+  /**
+   * Returns the bounding rectangle of the current clipping area.
+   */
+  public Rectangle getClipBounds()
+  {
+    if (_clip == null)
+    {
+      return null;
+    }
+    Rectangle rect = getClip().getBounds();
+    return rect;
+  }
+
+  /**
+   * Intersects the current clip with the specified rectangle.
+   */
+  public void clipRect(int x, int y, int width, int height)
+  {
+    clip(new Rectangle(x, y, width, height));
+  }
+
+  /**
+   * Sets the current clip to the rectangle specified by the given coordinates.
+   */
+  public void setClip(int x, int y, int width, int height)
+  {
+    setClip(new Rectangle(x, y, width, height));
+  }
+
+  /**
+   * Gets the current clipping area.
+   */
+  public Shape getClip()
+  {
+    if (_clip == null)
+    {
+      return null;
+    }
+    else
+    {
+      try
+      {
+        AffineTransform t = _transform.createInverse();
+        t.concatenate(_clipTransform);
+        return t.createTransformedShape(_clip);
+      } catch (Exception e)
+      {
+        throw new EpsException("Unable to get inverse of matrix: "
+                + _transform);
+      }
+    }
+  }
+
+  /**
+   * Sets the current clipping area to an arbitrary clip shape.
+   */
+  public void setClip(Shape clip)
+  {
+    if (clip != null)
+    {
+      if (_document.isClipSet())
+      {
+        append("grestore");
+        append("gsave");
+      }
+      else
+      {
+        _document.setClipSet(true);
+        append("gsave");
+      }
+      draw(clip, "clip");
+      _clip = clip;
+      _clipTransform = (AffineTransform) _transform.clone();
+    }
+    else
+    {
+      if (_document.isClipSet())
+      {
+        append("grestore");
+        _document.setClipSet(false);
+      }
+      _clip = null;
+    }
+  }
+
+  /**
+   * <b><i><font color="red">Not implemented</font></i></b> - performs no
+   * action.
+   */
+  public void copyArea(int x, int y, int width, int height, int dx, int dy)
+  {
+    methodNotSupported();
+  }
+
+  /**
+   * Draws a straight line from (x1,y1) to (x2,y2).
+   */
+  public void drawLine(int x1, int y1, int x2, int y2)
+  {
+    Shape shape = new Line2D.Float(x1, y1, x2, y2);
+    draw(shape);
+  }
+
+  /**
+   * Fills a rectangle with top-left corner placed at (x,y).
+   */
+  public void fillRect(int x, int y, int width, int height)
+  {
+    Shape shape = new Rectangle(x, y, width, height);
+    draw(shape, "fill");
+  }
+
+  /**
+   * Draws a rectangle with top-left corner placed at (x,y).
+   */
+  public void drawRect(int x, int y, int width, int height)
+  {
+    Shape shape = new Rectangle(x, y, width, height);
+    draw(shape);
+  }
+
+  /**
+   * Clears a rectangle with top-left corner placed at (x,y) using the current
+   * background color.
+   */
+  public void clearRect(int x, int y, int width, int height)
+  {
+    Color originalColor = getColor();
+
+    setColor(getBackground());
+    Shape shape = new Rectangle(x, y, width, height);
+    draw(shape, "fill");
+
+    setColor(originalColor);
+  }
+
+  /**
+   * Draws a rounded rectangle.
+   */
+  public void drawRoundRect(int x, int y, int width, int height,
+          int arcWidth, int arcHeight)
+  {
+    Shape shape = new RoundRectangle2D.Float(x, y, width, height, arcWidth,
+            arcHeight);
+    draw(shape);
+  }
+
+  /**
+   * Fills a rounded rectangle.
+   */
+  public void fillRoundRect(int x, int y, int width, int height,
+          int arcWidth, int arcHeight)
+  {
+    Shape shape = new RoundRectangle2D.Float(x, y, width, height, arcWidth,
+            arcHeight);
+    draw(shape, "fill");
+  }
+
+  /**
+   * Draws an oval.
+   */
+  public void drawOval(int x, int y, int width, int height)
+  {
+    Shape shape = new Ellipse2D.Float(x, y, width, height);
+    draw(shape);
+  }
+
+  /**
+   * Fills an oval.
+   */
+  public void fillOval(int x, int y, int width, int height)
+  {
+    Shape shape = new Ellipse2D.Float(x, y, width, height);
+    draw(shape, "fill");
+  }
+
+  /**
+   * Draws an arc.
+   */
+  public void drawArc(int x, int y, int width, int height, int startAngle,
+          int arcAngle)
+  {
+    Shape shape = new Arc2D.Float(x, y, width, height, startAngle,
+            arcAngle, Arc2D.OPEN);
+    draw(shape);
+  }
+
+  /**
+   * Fills an arc.
+   */
+  public void fillArc(int x, int y, int width, int height, int startAngle,
+          int arcAngle)
+  {
+    Shape shape = new Arc2D.Float(x, y, width, height, startAngle,
+            arcAngle, Arc2D.PIE);
+    draw(shape, "fill");
+  }
+
+  /**
+   * Draws a polyline.
+   */
+  public void drawPolyline(int[] xPoints, int[] yPoints, int nPoints)
+  {
+    if (nPoints > 0)
+    {
+      GeneralPath path = new GeneralPath();
+      path.moveTo(xPoints[0], yPoints[0]);
+      for (int i = 1; i < nPoints; i++)
+      {
+        path.lineTo(xPoints[i], yPoints[i]);
+      }
+      draw(path);
+    }
+  }
+
+  /**
+   * Draws a polygon made with the specified points.
+   */
+  public void drawPolygon(int[] xPoints, int[] yPoints, int nPoints)
+  {
+    Shape shape = new Polygon(xPoints, yPoints, nPoints);
+    draw(shape);
+  }
+
+  /**
+   * Draws a polygon.
+   */
+  public void drawPolygon(Polygon p)
+  {
+    draw(p);
+  }
+
+  /**
+   * Fills a polygon made with the specified points.
+   */
+  public void fillPolygon(int[] xPoints, int[] yPoints, int nPoints)
+  {
+    Shape shape = new Polygon(xPoints, yPoints, nPoints);
+    draw(shape, "fill");
+  }
+
+  /**
+   * Fills a polygon.
+   */
+  public void fillPolygon(Polygon p)
+  {
+    draw(p, "fill");
+  }
+
+  /**
+   * Draws the specified characters, starting from (x,y)
+   */
+  public void drawChars(char[] data, int offset, int length, int x, int y)
+  {
+    String string = new String(data, offset, length);
+    drawString(string, x, y);
+  }
+
+  /**
+   * Draws the specified bytes, starting from (x,y)
+   */
+  public void drawBytes(byte[] data, int offset, int length, int x, int y)
+  {
+    String string = new String(data, offset, length);
+    drawString(string, x, y);
+  }
+
+  /**
+   * Draws an image.
+   */
+  public boolean drawImage(Image img, int x, int y, ImageObserver observer)
+  {
+    return drawImage(img, x, y, Color.white, observer);
+  }
+
+  /**
+   * Draws an image.
+   */
+  public boolean drawImage(Image img, int x, int y, int width, int height,
+          ImageObserver observer)
+  {
+    return drawImage(img, x, y, width, height, Color.white, observer);
+  }
+
+  /**
+   * Draws an image.
+   */
+  public boolean drawImage(Image img, int x, int y, Color bgcolor,
+          ImageObserver observer)
+  {
+    int width = img.getWidth(null);
+    int height = img.getHeight(null);
+    return drawImage(img, x, y, width, height, bgcolor, observer);
+  }
+
+  /**
+   * Draws an image.
+   */
+  public boolean drawImage(Image img, int x, int y, int width, int height,
+          Color bgcolor, ImageObserver observer)
+  {
+    return drawImage(img, x, y, x + width, y + height, 0, 0, width, height,
+            bgcolor, observer);
+  }
+
+  /**
+   * Draws an image.
+   */
+  public boolean drawImage(Image img, int dx1, int dy1, int dx2, int dy2,
+          int sx1, int sy1, int sx2, int sy2, ImageObserver observer)
+  {
+    return drawImage(img, dx1, dy1, dx2, dy2, sx1, sy1, sx2, sy2,
+            Color.white, observer);
+  }
+
+  /**
+   * Draws an image.
+   */
+  public boolean drawImage(Image img, int dx1, int dy1, int dx2, int dy2,
+          int sx1, int sy1, int sx2, int sy2, Color bgcolor,
+          ImageObserver observer)
+  {
+    if (dx1 >= dx2)
+    {
+      throw new IllegalArgumentException("dx1 >= dx2");
+    }
+    if (sx1 >= sx2)
+    {
+      throw new IllegalArgumentException("sx1 >= sx2");
+    }
+    if (dy1 >= dy2)
+    {
+      throw new IllegalArgumentException("dy1 >= dy2");
+    }
+    if (sy1 >= sy2)
+    {
+      throw new IllegalArgumentException("sy1 >= sy2");
+    }
+
+    append("gsave");
+
+    int width = sx2 - sx1;
+    int height = sy2 - sy1;
+    int destWidth = dx2 - dx1;
+    int destHeight = dy2 - dy1;
+
+    int[] pixels = new int[width * height];
+    PixelGrabber pg = new PixelGrabber(img, sx1, sy1, sx2 - sx1, sy2 - sy1,
+            pixels, 0, width);
+    try
+    {
+      pg.grabPixels();
+    } catch (InterruptedException e)
+    {
+      return false;
+    }
+
+    AffineTransform matrix = new AffineTransform(_transform);
+    matrix.translate(dx1, dy1);
+    matrix.scale(destWidth / (double) width, destHeight / (double) height);
+    double[] m = new double[6];
+    try
+    {
+      matrix = matrix.createInverse();
+    } catch (Exception e)
+    {
+      throw new EpsException("Unable to get inverse of matrix: " + matrix);
+    }
+    matrix.scale(1, -1);
+    matrix.getMatrix(m);
+    append(width + " " + height + " 8 [" + m[0] + " " + m[1] + " " + m[2]
+            + " " + m[3] + " " + m[4] + " " + m[5] + "]");
+    // Fill the background to update the bounding box.
+    Color oldColor = getColor();
+    setColor(getBackground());
+    fillRect(dx1, dy1, destWidth, destHeight);
+    setColor(oldColor);
+    append("{currentfile 3 " + width
+            + " mul string readhexstring pop} bind");
+    append("false 3 colorimage");
+    StringBuffer line = new StringBuffer();
+    for (int y = 0; y < height; y++)
+    {
+      for (int x = 0; x < width; x++)
+      {
+        Color color = new Color(pixels[x + width * y]);
+        line.append(toHexString(color.getRed())
+                + toHexString(color.getGreen())
+                + toHexString(color.getBlue()));
+        if (line.length() > 64)
+        {
+          append(line.toString());
+          line = new StringBuffer();
+        }
+      }
+    }
+    if (line.length() > 0)
+    {
+      append(line.toString());
+    }
+
+    append("grestore");
+
+    return true;
+  }
+
+  /**
+   * Disposes of all resources used by this EpsGraphics2D object. If this is the
+   * only remaining EpsGraphics2D instance pointing at a EpsDocument object,
+   * then the EpsDocument object shall become eligible for garbage collection.
+   */
+  public void dispose()
+  {
+    _document = null;
+  }
+
+  /**
+   * Finalizes the object.
+   */
+  public void finalize()
+  {
+    super.finalize();
+  }
+
+  /**
+   * Returns the entire contents of the EPS document, complete with headers and
+   * bounding box. The returned String is suitable for being written directly to
+   * disk as an EPS file.
+   */
+  public String toString()
+  {
+    StringWriter writer = new StringWriter();
+    try
+    {
+      _document.write(writer);
+      _document.flush();
+      _document.close();
+    } catch (IOException e)
+    {
+      throw new EpsException(e.toString());
+    }
+    return writer.toString();
+  }
+
+  /**
+   * Returns true if the specified rectangular area might intersect the current
+   * clipping area.
+   */
+  public boolean hitClip(int x, int y, int width, int height)
+  {
+    if (_clip == null)
+    {
+      return true;
+    }
+    Rectangle rect = new Rectangle(x, y, width, height);
+    return hit(rect, _clip, true);
+  }
+
+  /**
+   * Returns the bounding rectangle of the current clipping area.
+   */
+  public Rectangle getClipBounds(Rectangle r)
+  {
+    if (_clip == null)
+    {
+      return r;
+    }
+    Rectangle rect = getClipBounds();
+    r.setLocation((int) rect.getX(), (int) rect.getY());
+    r.setSize((int) rect.getWidth(), (int) rect.getHeight());
+    return r;
+  }
+
+  private Color _color;
+
+  private Color _backgroundColor;
+
+  private Paint _paint;
+
+  private Composite _composite;
+
+  private BasicStroke _stroke;
+
+  private Font _font;
+
+  private Shape _clip;
+
+  private AffineTransform _clipTransform;
+
+  private AffineTransform _transform;
+
+  private boolean _accurateTextMode;
+
+  private EpsDocument _document;
+
+  private static FontRenderContext _fontRenderContext = new FontRenderContext(
+          null, false, true);
 }
\ No newline at end of file
diff --git a/src/uk/ac/ebi/picr/model/CrossReference.java b/src/uk/ac/ebi/picr/model/CrossReference.java
index 04b50bf..58f8a8b 100644
--- a/src/uk/ac/ebi/picr/model/CrossReference.java
+++ b/src/uk/ac/ebi/picr/model/CrossReference.java
@@ -7,296 +7,314 @@
 
 package uk.ac.ebi.picr.model;
 
-public class CrossReference  implements java.io.Serializable {
-    private java.lang.String accession;
-    private java.lang.String accessionVersion;
-    private java.lang.String databaseDescription;
-    private java.lang.String databaseName;
-    private java.util.Calendar dateAdded;
-    private java.util.Calendar dateDeleted;
-    private boolean deleted;
-    private java.lang.String gi;
-    private java.lang.String taxonId;
-
-    public CrossReference() {
+public class CrossReference implements java.io.Serializable
+{
+  private java.lang.String accession;
+
+  private java.lang.String accessionVersion;
+
+  private java.lang.String databaseDescription;
+
+  private java.lang.String databaseName;
+
+  private java.util.Calendar dateAdded;
+
+  private java.util.Calendar dateDeleted;
+
+  private boolean deleted;
+
+  private java.lang.String gi;
+
+  private java.lang.String taxonId;
+
+  public CrossReference()
+  {
+  }
+
+  public CrossReference(java.lang.String accession,
+          java.lang.String accessionVersion,
+          java.lang.String databaseDescription,
+          java.lang.String databaseName, java.util.Calendar dateAdded,
+          java.util.Calendar dateDeleted, boolean deleted,
+          java.lang.String gi, java.lang.String taxonId)
+  {
+    this.accession = accession;
+    this.accessionVersion = accessionVersion;
+    this.databaseDescription = databaseDescription;
+    this.databaseName = databaseName;
+    this.dateAdded = dateAdded;
+    this.dateDeleted = dateDeleted;
+    this.deleted = deleted;
+    this.gi = gi;
+    this.taxonId = taxonId;
+  }
+
+  /**
+   * Gets the accession value for this CrossReference.
+   * 
+   * @return accession
+   */
+  public java.lang.String getAccession()
+  {
+    return accession;
+  }
+
+  /**
+   * Sets the accession value for this CrossReference.
+   * 
+   * @param accession
+   */
+  public void setAccession(java.lang.String accession)
+  {
+    this.accession = accession;
+  }
+
+  /**
+   * Gets the accessionVersion value for this CrossReference.
+   * 
+   * @return accessionVersion
+   */
+  public java.lang.String getAccessionVersion()
+  {
+    return accessionVersion;
+  }
+
+  /**
+   * Sets the accessionVersion value for this CrossReference.
+   * 
+   * @param accessionVersion
+   */
+  public void setAccessionVersion(java.lang.String accessionVersion)
+  {
+    this.accessionVersion = accessionVersion;
+  }
+
+  /**
+   * Gets the databaseDescription value for this CrossReference.
+   * 
+   * @return databaseDescription
+   */
+  public java.lang.String getDatabaseDescription()
+  {
+    return databaseDescription;
+  }
+
+  /**
+   * Sets the databaseDescription value for this CrossReference.
+   * 
+   * @param databaseDescription
+   */
+  public void setDatabaseDescription(java.lang.String databaseDescription)
+  {
+    this.databaseDescription = databaseDescription;
+  }
+
+  /**
+   * Gets the databaseName value for this CrossReference.
+   * 
+   * @return databaseName
+   */
+  public java.lang.String getDatabaseName()
+  {
+    return databaseName;
+  }
+
+  /**
+   * Sets the databaseName value for this CrossReference.
+   * 
+   * @param databaseName
+   */
+  public void setDatabaseName(java.lang.String databaseName)
+  {
+    this.databaseName = databaseName;
+  }
+
+  /**
+   * Gets the dateAdded value for this CrossReference.
+   * 
+   * @return dateAdded
+   */
+  public java.util.Calendar getDateAdded()
+  {
+    return dateAdded;
+  }
+
+  /**
+   * Sets the dateAdded value for this CrossReference.
+   * 
+   * @param dateAdded
+   */
+  public void setDateAdded(java.util.Calendar dateAdded)
+  {
+    this.dateAdded = dateAdded;
+  }
+
+  /**
+   * Gets the dateDeleted value for this CrossReference.
+   * 
+   * @return dateDeleted
+   */
+  public java.util.Calendar getDateDeleted()
+  {
+    return dateDeleted;
+  }
+
+  /**
+   * Sets the dateDeleted value for this CrossReference.
+   * 
+   * @param dateDeleted
+   */
+  public void setDateDeleted(java.util.Calendar dateDeleted)
+  {
+    this.dateDeleted = dateDeleted;
+  }
+
+  /**
+   * Gets the deleted value for this CrossReference.
+   * 
+   * @return deleted
+   */
+  public boolean isDeleted()
+  {
+    return deleted;
+  }
+
+  /**
+   * Sets the deleted value for this CrossReference.
+   * 
+   * @param deleted
+   */
+  public void setDeleted(boolean deleted)
+  {
+    this.deleted = deleted;
+  }
+
+  /**
+   * Gets the gi value for this CrossReference.
+   * 
+   * @return gi
+   */
+  public java.lang.String getGi()
+  {
+    return gi;
+  }
+
+  /**
+   * Sets the gi value for this CrossReference.
+   * 
+   * @param gi
+   */
+  public void setGi(java.lang.String gi)
+  {
+    this.gi = gi;
+  }
+
+  /**
+   * Gets the taxonId value for this CrossReference.
+   * 
+   * @return taxonId
+   */
+  public java.lang.String getTaxonId()
+  {
+    return taxonId;
+  }
+
+  /**
+   * Sets the taxonId value for this CrossReference.
+   * 
+   * @param taxonId
+   */
+  public void setTaxonId(java.lang.String taxonId)
+  {
+    this.taxonId = taxonId;
+  }
+
+  private java.lang.Object __equalsCalc = null;
+
+  public synchronized boolean equals(java.lang.Object obj)
+  {
+    if (!(obj instanceof CrossReference))
+      return false;
+    CrossReference other = (CrossReference) obj;
+    if (obj == null)
+      return false;
+    if (this == obj)
+      return true;
+    if (__equalsCalc != null)
+    {
+      return (__equalsCalc == obj);
     }
-
-    public CrossReference(
-           java.lang.String accession,
-           java.lang.String accessionVersion,
-           java.lang.String databaseDescription,
-           java.lang.String databaseName,
-           java.util.Calendar dateAdded,
-           java.util.Calendar dateDeleted,
-           boolean deleted,
-           java.lang.String gi,
-           java.lang.String taxonId) {
-           this.accession = accession;
-           this.accessionVersion = accessionVersion;
-           this.databaseDescription = databaseDescription;
-           this.databaseName = databaseName;
-           this.dateAdded = dateAdded;
-           this.dateDeleted = dateDeleted;
-           this.deleted = deleted;
-           this.gi = gi;
-           this.taxonId = taxonId;
+    __equalsCalc = obj;
+    boolean _equals;
+    _equals = true
+            && ((this.accession == null && other.getAccession() == null) || (this.accession != null && this.accession
+                    .equals(other.getAccession())))
+            && ((this.accessionVersion == null && other
+                    .getAccessionVersion() == null) || (this.accessionVersion != null && this.accessionVersion
+                    .equals(other.getAccessionVersion())))
+            && ((this.databaseDescription == null && other
+                    .getDatabaseDescription() == null) || (this.databaseDescription != null && this.databaseDescription
+                    .equals(other.getDatabaseDescription())))
+            && ((this.databaseName == null && other.getDatabaseName() == null) || (this.databaseName != null && this.databaseName
+                    .equals(other.getDatabaseName())))
+            && ((this.dateAdded == null && other.getDateAdded() == null) || (this.dateAdded != null && this.dateAdded
+                    .equals(other.getDateAdded())))
+            && ((this.dateDeleted == null && other.getDateDeleted() == null) || (this.dateDeleted != null && this.dateDeleted
+                    .equals(other.getDateDeleted())))
+            && this.deleted == other.isDeleted()
+            && ((this.gi == null && other.getGi() == null) || (this.gi != null && this.gi
+                    .equals(other.getGi())))
+            && ((this.taxonId == null && other.getTaxonId() == null) || (this.taxonId != null && this.taxonId
+                    .equals(other.getTaxonId())));
+    __equalsCalc = null;
+    return _equals;
+  }
+
+  private boolean __hashCodeCalc = false;
+
+  public synchronized int hashCode()
+  {
+    if (__hashCodeCalc)
+    {
+      return 0;
     }
-
-
-    /**
-     * Gets the accession value for this CrossReference.
-     * 
-     * @return accession
-     */
-    public java.lang.String getAccession() {
-        return accession;
+    __hashCodeCalc = true;
+    int _hashCode = 1;
+    if (getAccession() != null)
+    {
+      _hashCode += getAccession().hashCode();
     }
-
-
-    /**
-     * Sets the accession value for this CrossReference.
-     * 
-     * @param accession
-     */
-    public void setAccession(java.lang.String accession) {
-        this.accession = accession;
-    }
-
-
-    /**
-     * Gets the accessionVersion value for this CrossReference.
-     * 
-     * @return accessionVersion
-     */
-    public java.lang.String getAccessionVersion() {
-        return accessionVersion;
-    }
-
-
-    /**
-     * Sets the accessionVersion value for this CrossReference.
-     * 
-     * @param accessionVersion
-     */
-    public void setAccessionVersion(java.lang.String accessionVersion) {
-        this.accessionVersion = accessionVersion;
-    }
-
-
-    /**
-     * Gets the databaseDescription value for this CrossReference.
-     * 
-     * @return databaseDescription
-     */
-    public java.lang.String getDatabaseDescription() {
-        return databaseDescription;
+    if (getAccessionVersion() != null)
+    {
+      _hashCode += getAccessionVersion().hashCode();
     }
-
-
-    /**
-     * Sets the databaseDescription value for this CrossReference.
-     * 
-     * @param databaseDescription
-     */
-    public void setDatabaseDescription(java.lang.String databaseDescription) {
-        this.databaseDescription = databaseDescription;
+    if (getDatabaseDescription() != null)
+    {
+      _hashCode += getDatabaseDescription().hashCode();
     }
-
-
-    /**
-     * Gets the databaseName value for this CrossReference.
-     * 
-     * @return databaseName
-     */
-    public java.lang.String getDatabaseName() {
-        return databaseName;
+    if (getDatabaseName() != null)
+    {
+      _hashCode += getDatabaseName().hashCode();
     }
-
-
-    /**
-     * Sets the databaseName value for this CrossReference.
-     * 
-     * @param databaseName
-     */
-    public void setDatabaseName(java.lang.String databaseName) {
-        this.databaseName = databaseName;
+    if (getDateAdded() != null)
+    {
+      _hashCode += getDateAdded().hashCode();
     }
-
-
-    /**
-     * Gets the dateAdded value for this CrossReference.
-     * 
-     * @return dateAdded
-     */
-    public java.util.Calendar getDateAdded() {
-        return dateAdded;
+    if (getDateDeleted() != null)
+    {
+      _hashCode += getDateDeleted().hashCode();
     }
-
-
-    /**
-     * Sets the dateAdded value for this CrossReference.
-     * 
-     * @param dateAdded
-     */
-    public void setDateAdded(java.util.Calendar dateAdded) {
-        this.dateAdded = dateAdded;
+    _hashCode += (isDeleted() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+    if (getGi() != null)
+    {
+      _hashCode += getGi().hashCode();
     }
-
-
-    /**
-     * Gets the dateDeleted value for this CrossReference.
-     * 
-     * @return dateDeleted
-     */
-    public java.util.Calendar getDateDeleted() {
-        return dateDeleted;
-    }
-
-
-    /**
-     * Sets the dateDeleted value for this CrossReference.
-     * 
-     * @param dateDeleted
-     */
-    public void setDateDeleted(java.util.Calendar dateDeleted) {
-        this.dateDeleted = dateDeleted;
-    }
-
-
-    /**
-     * Gets the deleted value for this CrossReference.
-     * 
-     * @return deleted
-     */
-    public boolean isDeleted() {
-        return deleted;
-    }
-
-
-    /**
-     * Sets the deleted value for this CrossReference.
-     * 
-     * @param deleted
-     */
-    public void setDeleted(boolean deleted) {
-        this.deleted = deleted;
-    }
-
-
-    /**
-     * Gets the gi value for this CrossReference.
-     * 
-     * @return gi
-     */
-    public java.lang.String getGi() {
-        return gi;
-    }
-
-
-    /**
-     * Sets the gi value for this CrossReference.
-     * 
-     * @param gi
-     */
-    public void setGi(java.lang.String gi) {
-        this.gi = gi;
-    }
-
-
-    /**
-     * Gets the taxonId value for this CrossReference.
-     * 
-     * @return taxonId
-     */
-    public java.lang.String getTaxonId() {
-        return taxonId;
-    }
-
-
-    /**
-     * Sets the taxonId value for this CrossReference.
-     * 
-     * @param taxonId
-     */
-    public void setTaxonId(java.lang.String taxonId) {
-        this.taxonId = taxonId;
-    }
-
-    private java.lang.Object __equalsCalc = null;
-    public synchronized boolean equals(java.lang.Object obj) {
-        if (!(obj instanceof CrossReference)) return false;
-        CrossReference other = (CrossReference) obj;
-        if (obj == null) return false;
-        if (this == obj) return true;
-        if (__equalsCalc != null) {
-            return (__equalsCalc == obj);
-        }
-        __equalsCalc = obj;
-        boolean _equals;
-        _equals = true && 
-            ((this.accession==null && other.getAccession()==null) || 
-             (this.accession!=null &&
-              this.accession.equals(other.getAccession()))) &&
-            ((this.accessionVersion==null && other.getAccessionVersion()==null) || 
-             (this.accessionVersion!=null &&
-              this.accessionVersion.equals(other.getAccessionVersion()))) &&
-            ((this.databaseDescription==null && other.getDatabaseDescription()==null) || 
-             (this.databaseDescription!=null &&
-              this.databaseDescription.equals(other.getDatabaseDescription()))) &&
-            ((this.databaseName==null && other.getDatabaseName()==null) || 
-             (this.databaseName!=null &&
-              this.databaseName.equals(other.getDatabaseName()))) &&
-            ((this.dateAdded==null && other.getDateAdded()==null) || 
-             (this.dateAdded!=null &&
-              this.dateAdded.equals(other.getDateAdded()))) &&
-            ((this.dateDeleted==null && other.getDateDeleted()==null) || 
-             (this.dateDeleted!=null &&
-              this.dateDeleted.equals(other.getDateDeleted()))) &&
-            this.deleted == other.isDeleted() &&
-            ((this.gi==null && other.getGi()==null) || 
-             (this.gi!=null &&
-              this.gi.equals(other.getGi()))) &&
-            ((this.taxonId==null && other.getTaxonId()==null) || 
-             (this.taxonId!=null &&
-              this.taxonId.equals(other.getTaxonId())));
-        __equalsCalc = null;
-        return _equals;
-    }
-
-    private boolean __hashCodeCalc = false;
-    public synchronized int hashCode() {
-        if (__hashCodeCalc) {
-            return 0;
-        }
-        __hashCodeCalc = true;
-        int _hashCode = 1;
-        if (getAccession() != null) {
-            _hashCode += getAccession().hashCode();
-        }
-        if (getAccessionVersion() != null) {
-            _hashCode += getAccessionVersion().hashCode();
-        }
-        if (getDatabaseDescription() != null) {
-            _hashCode += getDatabaseDescription().hashCode();
-        }
-        if (getDatabaseName() != null) {
-            _hashCode += getDatabaseName().hashCode();
-        }
-        if (getDateAdded() != null) {
-            _hashCode += getDateAdded().hashCode();
-        }
-        if (getDateDeleted() != null) {
-            _hashCode += getDateDeleted().hashCode();
-        }
-        _hashCode += (isDeleted() ? Boolean.TRUE : Boolean.FALSE).hashCode();
-        if (getGi() != null) {
-            _hashCode += getGi().hashCode();
-        }
-        if (getTaxonId() != null) {
-            _hashCode += getTaxonId().hashCode();
-        }
-        __hashCodeCalc = false;
-        return _hashCode;
+    if (getTaxonId() != null)
+    {
+      _hashCode += getTaxonId().hashCode();
     }
+    __hashCodeCalc = false;
+    return _hashCode;
+  }
 
 }
diff --git a/src/uk/ac/ebi/picr/model/CrossReference_Helper.java b/src/uk/ac/ebi/picr/model/CrossReference_Helper.java
index 0613a0c..e07e14e 100644
--- a/src/uk/ac/ebi/picr/model/CrossReference_Helper.java
+++ b/src/uk/ac/ebi/picr/model/CrossReference_Helper.java
@@ -7,89 +7,109 @@
 
 package uk.ac.ebi.picr.model;
 
-public class CrossReference_Helper {
-    // Type metadata
-    private static org.apache.axis.description.TypeDesc typeDesc =
-        new org.apache.axis.description.TypeDesc(CrossReference.class, true);
+public class CrossReference_Helper
+{
+  // Type metadata
+  private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(
+          CrossReference.class, true);
 
-    static {
-        typeDesc.setXmlType(new javax.xml.namespace.QName("http://model.picr.ebi.ac.uk", "CrossReference"));
-        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("accession");
-        elemField.setXmlName(new javax.xml.namespace.QName("http://model.picr.ebi.ac.uk", "accession"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("accessionVersion");
-        elemField.setXmlName(new javax.xml.namespace.QName("http://model.picr.ebi.ac.uk", "accessionVersion"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("databaseDescription");
-        elemField.setXmlName(new javax.xml.namespace.QName("http://model.picr.ebi.ac.uk", "databaseDescription"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("databaseName");
-        elemField.setXmlName(new javax.xml.namespace.QName("http://model.picr.ebi.ac.uk", "databaseName"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("dateAdded");
-        elemField.setXmlName(new javax.xml.namespace.QName("http://model.picr.ebi.ac.uk", "dateAdded"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "dateTime"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("dateDeleted");
-        elemField.setXmlName(new javax.xml.namespace.QName("http://model.picr.ebi.ac.uk", "dateDeleted"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "dateTime"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("deleted");
-        elemField.setXmlName(new javax.xml.namespace.QName("http://model.picr.ebi.ac.uk", "deleted"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("gi");
-        elemField.setXmlName(new javax.xml.namespace.QName("http://model.picr.ebi.ac.uk", "gi"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("taxonId");
-        elemField.setXmlName(new javax.xml.namespace.QName("http://model.picr.ebi.ac.uk", "taxonId"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
-        typeDesc.addFieldDesc(elemField);
-    }
+  static
+  {
+    typeDesc.setXmlType(new javax.xml.namespace.QName(
+            "http://model.picr.ebi.ac.uk", "CrossReference"));
+    org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("accession");
+    elemField.setXmlName(new javax.xml.namespace.QName(
+            "http://model.picr.ebi.ac.uk", "accession"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "http://www.w3.org/2001/XMLSchema", "string"));
+    typeDesc.addFieldDesc(elemField);
+    elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("accessionVersion");
+    elemField.setXmlName(new javax.xml.namespace.QName(
+            "http://model.picr.ebi.ac.uk", "accessionVersion"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "http://www.w3.org/2001/XMLSchema", "string"));
+    typeDesc.addFieldDesc(elemField);
+    elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("databaseDescription");
+    elemField.setXmlName(new javax.xml.namespace.QName(
+            "http://model.picr.ebi.ac.uk", "databaseDescription"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "http://www.w3.org/2001/XMLSchema", "string"));
+    typeDesc.addFieldDesc(elemField);
+    elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("databaseName");
+    elemField.setXmlName(new javax.xml.namespace.QName(
+            "http://model.picr.ebi.ac.uk", "databaseName"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "http://www.w3.org/2001/XMLSchema", "string"));
+    typeDesc.addFieldDesc(elemField);
+    elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("dateAdded");
+    elemField.setXmlName(new javax.xml.namespace.QName(
+            "http://model.picr.ebi.ac.uk", "dateAdded"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "http://www.w3.org/2001/XMLSchema", "dateTime"));
+    typeDesc.addFieldDesc(elemField);
+    elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("dateDeleted");
+    elemField.setXmlName(new javax.xml.namespace.QName(
+            "http://model.picr.ebi.ac.uk", "dateDeleted"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "http://www.w3.org/2001/XMLSchema", "dateTime"));
+    typeDesc.addFieldDesc(elemField);
+    elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("deleted");
+    elemField.setXmlName(new javax.xml.namespace.QName(
+            "http://model.picr.ebi.ac.uk", "deleted"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "http://www.w3.org/2001/XMLSchema", "boolean"));
+    typeDesc.addFieldDesc(elemField);
+    elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("gi");
+    elemField.setXmlName(new javax.xml.namespace.QName(
+            "http://model.picr.ebi.ac.uk", "gi"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "http://www.w3.org/2001/XMLSchema", "string"));
+    typeDesc.addFieldDesc(elemField);
+    elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("taxonId");
+    elemField.setXmlName(new javax.xml.namespace.QName(
+            "http://model.picr.ebi.ac.uk", "taxonId"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "http://www.w3.org/2001/XMLSchema", "string"));
+    typeDesc.addFieldDesc(elemField);
+  }
 
-    /**
-     * Return type metadata object
-     */
-    public static org.apache.axis.description.TypeDesc getTypeDesc() {
-        return typeDesc;
-    }
+  /**
+   * Return type metadata object
+   */
+  public static org.apache.axis.description.TypeDesc getTypeDesc()
+  {
+    return typeDesc;
+  }
 
-    /**
-     * Get Custom Serializer
-     */
-    public static org.apache.axis.encoding.Serializer getSerializer(
-           java.lang.String mechType, 
-           java.lang.Class _javaType,  
-           javax.xml.namespace.QName _xmlType) {
-        return 
-          new  org.apache.axis.encoding.ser.BeanSerializer(
-            _javaType, _xmlType, typeDesc);
-    }
+  /**
+   * Get Custom Serializer
+   */
+  public static org.apache.axis.encoding.Serializer getSerializer(
+          java.lang.String mechType, java.lang.Class _javaType,
+          javax.xml.namespace.QName _xmlType)
+  {
+    return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,
+            _xmlType, typeDesc);
+  }
 
-    /**
-     * Get Custom Deserializer
-     */
-    public static org.apache.axis.encoding.Deserializer getDeserializer(
-           java.lang.String mechType, 
-           java.lang.Class _javaType,  
-           javax.xml.namespace.QName _xmlType) {
-        return 
-          new  org.apache.axis.encoding.ser.BeanDeserializer(
-            _javaType, _xmlType, typeDesc);
-    }
+  /**
+   * Get Custom Deserializer
+   */
+  public static org.apache.axis.encoding.Deserializer getDeserializer(
+          java.lang.String mechType, java.lang.Class _javaType,
+          javax.xml.namespace.QName _xmlType)
+  {
+    return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,
+            _xmlType, typeDesc);
+  }
 
 }
diff --git a/src/uk/ac/ebi/picr/model/UPEntry.java b/src/uk/ac/ebi/picr/model/UPEntry.java
index 2237ba8..b7ad7a6 100644
--- a/src/uk/ac/ebi/picr/model/UPEntry.java
+++ b/src/uk/ac/ebi/picr/model/UPEntry.java
@@ -7,245 +7,274 @@
 
 package uk.ac.ebi.picr.model;
 
-public class UPEntry  implements java.io.Serializable {
-    private java.lang.String CRC64;
-    private java.lang.String UPI;
-    private uk.ac.ebi.picr.model.CrossReference[] identicalCrossReferences;
-    private uk.ac.ebi.picr.model.CrossReference[] logicalCrossReferences;
-    private java.lang.String sequence;
-    private java.util.Calendar timestamp;
-
-    public UPEntry() {
+public class UPEntry implements java.io.Serializable
+{
+  private java.lang.String CRC64;
+
+  private java.lang.String UPI;
+
+  private uk.ac.ebi.picr.model.CrossReference[] identicalCrossReferences;
+
+  private uk.ac.ebi.picr.model.CrossReference[] logicalCrossReferences;
+
+  private java.lang.String sequence;
+
+  private java.util.Calendar timestamp;
+
+  public UPEntry()
+  {
+  }
+
+  public UPEntry(java.lang.String CRC64, java.lang.String UPI,
+          uk.ac.ebi.picr.model.CrossReference[] identicalCrossReferences,
+          uk.ac.ebi.picr.model.CrossReference[] logicalCrossReferences,
+          java.lang.String sequence, java.util.Calendar timestamp)
+  {
+    this.CRC64 = CRC64;
+    this.UPI = UPI;
+    this.identicalCrossReferences = identicalCrossReferences;
+    this.logicalCrossReferences = logicalCrossReferences;
+    this.sequence = sequence;
+    this.timestamp = timestamp;
+  }
+
+  /**
+   * Gets the CRC64 value for this UPEntry.
+   * 
+   * @return CRC64
+   */
+  public java.lang.String getCRC64()
+  {
+    return CRC64;
+  }
+
+  /**
+   * Sets the CRC64 value for this UPEntry.
+   * 
+   * @param CRC64
+   */
+  public void setCRC64(java.lang.String CRC64)
+  {
+    this.CRC64 = CRC64;
+  }
+
+  /**
+   * Gets the UPI value for this UPEntry.
+   * 
+   * @return UPI
+   */
+  public java.lang.String getUPI()
+  {
+    return UPI;
+  }
+
+  /**
+   * Sets the UPI value for this UPEntry.
+   * 
+   * @param UPI
+   */
+  public void setUPI(java.lang.String UPI)
+  {
+    this.UPI = UPI;
+  }
+
+  /**
+   * Gets the identicalCrossReferences value for this UPEntry.
+   * 
+   * @return identicalCrossReferences
+   */
+  public uk.ac.ebi.picr.model.CrossReference[] getIdenticalCrossReferences()
+  {
+    return identicalCrossReferences;
+  }
+
+  /**
+   * Sets the identicalCrossReferences value for this UPEntry.
+   * 
+   * @param identicalCrossReferences
+   */
+  public void setIdenticalCrossReferences(
+          uk.ac.ebi.picr.model.CrossReference[] identicalCrossReferences)
+  {
+    this.identicalCrossReferences = identicalCrossReferences;
+  }
+
+  public uk.ac.ebi.picr.model.CrossReference getIdenticalCrossReferences(
+          int i)
+  {
+    return this.identicalCrossReferences[i];
+  }
+
+  public void setIdenticalCrossReferences(int i,
+          uk.ac.ebi.picr.model.CrossReference _value)
+  {
+    this.identicalCrossReferences[i] = _value;
+  }
+
+  /**
+   * Gets the logicalCrossReferences value for this UPEntry.
+   * 
+   * @return logicalCrossReferences
+   */
+  public uk.ac.ebi.picr.model.CrossReference[] getLogicalCrossReferences()
+  {
+    return logicalCrossReferences;
+  }
+
+  /**
+   * Sets the logicalCrossReferences value for this UPEntry.
+   * 
+   * @param logicalCrossReferences
+   */
+  public void setLogicalCrossReferences(
+          uk.ac.ebi.picr.model.CrossReference[] logicalCrossReferences)
+  {
+    this.logicalCrossReferences = logicalCrossReferences;
+  }
+
+  public uk.ac.ebi.picr.model.CrossReference getLogicalCrossReferences(int i)
+  {
+    return this.logicalCrossReferences[i];
+  }
+
+  public void setLogicalCrossReferences(int i,
+          uk.ac.ebi.picr.model.CrossReference _value)
+  {
+    this.logicalCrossReferences[i] = _value;
+  }
+
+  /**
+   * Gets the sequence value for this UPEntry.
+   * 
+   * @return sequence
+   */
+  public java.lang.String getSequence()
+  {
+    return sequence;
+  }
+
+  /**
+   * Sets the sequence value for this UPEntry.
+   * 
+   * @param sequence
+   */
+  public void setSequence(java.lang.String sequence)
+  {
+    this.sequence = sequence;
+  }
+
+  /**
+   * Gets the timestamp value for this UPEntry.
+   * 
+   * @return timestamp
+   */
+  public java.util.Calendar getTimestamp()
+  {
+    return timestamp;
+  }
+
+  /**
+   * Sets the timestamp value for this UPEntry.
+   * 
+   * @param timestamp
+   */
+  public void setTimestamp(java.util.Calendar timestamp)
+  {
+    this.timestamp = timestamp;
+  }
+
+  private java.lang.Object __equalsCalc = null;
+
+  public synchronized boolean equals(java.lang.Object obj)
+  {
+    if (!(obj instanceof UPEntry))
+      return false;
+    UPEntry other = (UPEntry) obj;
+    if (obj == null)
+      return false;
+    if (this == obj)
+      return true;
+    if (__equalsCalc != null)
+    {
+      return (__equalsCalc == obj);
     }
-
-    public UPEntry(
-           java.lang.String CRC64,
-           java.lang.String UPI,
-           uk.ac.ebi.picr.model.CrossReference[] identicalCrossReferences,
-           uk.ac.ebi.picr.model.CrossReference[] logicalCrossReferences,
-           java.lang.String sequence,
-           java.util.Calendar timestamp) {
-           this.CRC64 = CRC64;
-           this.UPI = UPI;
-           this.identicalCrossReferences = identicalCrossReferences;
-           this.logicalCrossReferences = logicalCrossReferences;
-           this.sequence = sequence;
-           this.timestamp = timestamp;
-    }
-
-
-    /**
-     * Gets the CRC64 value for this UPEntry.
-     * 
-     * @return CRC64
-     */
-    public java.lang.String getCRC64() {
-        return CRC64;
-    }
-
-
-    /**
-     * Sets the CRC64 value for this UPEntry.
-     * 
-     * @param CRC64
-     */
-    public void setCRC64(java.lang.String CRC64) {
-        this.CRC64 = CRC64;
+    __equalsCalc = obj;
+    boolean _equals;
+    _equals = true
+            && ((this.CRC64 == null && other.getCRC64() == null) || (this.CRC64 != null && this.CRC64
+                    .equals(other.getCRC64())))
+            && ((this.UPI == null && other.getUPI() == null) || (this.UPI != null && this.UPI
+                    .equals(other.getUPI())))
+            && ((this.identicalCrossReferences == null && other
+                    .getIdenticalCrossReferences() == null) || (this.identicalCrossReferences != null && java.util.Arrays
+                    .equals(this.identicalCrossReferences, other
+                            .getIdenticalCrossReferences())))
+            && ((this.logicalCrossReferences == null && other
+                    .getLogicalCrossReferences() == null) || (this.logicalCrossReferences != null && java.util.Arrays
+                    .equals(this.logicalCrossReferences, other
+                            .getLogicalCrossReferences())))
+            && ((this.sequence == null && other.getSequence() == null) || (this.sequence != null && this.sequence
+                    .equals(other.getSequence())))
+            && ((this.timestamp == null && other.getTimestamp() == null) || (this.timestamp != null && this.timestamp
+                    .equals(other.getTimestamp())));
+    __equalsCalc = null;
+    return _equals;
+  }
+
+  private boolean __hashCodeCalc = false;
+
+  public synchronized int hashCode()
+  {
+    if (__hashCodeCalc)
+    {
+      return 0;
     }
-
-
-    /**
-     * Gets the UPI value for this UPEntry.
-     * 
-     * @return UPI
-     */
-    public java.lang.String getUPI() {
-        return UPI;
+    __hashCodeCalc = true;
+    int _hashCode = 1;
+    if (getCRC64() != null)
+    {
+      _hashCode += getCRC64().hashCode();
     }
-
-
-    /**
-     * Sets the UPI value for this UPEntry.
-     * 
-     * @param UPI
-     */
-    public void setUPI(java.lang.String UPI) {
-        this.UPI = UPI;
-    }
-
-
-    /**
-     * Gets the identicalCrossReferences value for this UPEntry.
-     * 
-     * @return identicalCrossReferences
-     */
-    public uk.ac.ebi.picr.model.CrossReference[] getIdenticalCrossReferences() {
-        return identicalCrossReferences;
-    }
-
-
-    /**
-     * Sets the identicalCrossReferences value for this UPEntry.
-     * 
-     * @param identicalCrossReferences
-     */
-    public void setIdenticalCrossReferences(uk.ac.ebi.picr.model.CrossReference[] identicalCrossReferences) {
-        this.identicalCrossReferences = identicalCrossReferences;
-    }
-
-    public uk.ac.ebi.picr.model.CrossReference getIdenticalCrossReferences(int i) {
-        return this.identicalCrossReferences[i];
-    }
-
-    public void setIdenticalCrossReferences(int i, uk.ac.ebi.picr.model.CrossReference _value) {
-        this.identicalCrossReferences[i] = _value;
-    }
-
-
-    /**
-     * Gets the logicalCrossReferences value for this UPEntry.
-     * 
-     * @return logicalCrossReferences
-     */
-    public uk.ac.ebi.picr.model.CrossReference[] getLogicalCrossReferences() {
-        return logicalCrossReferences;
-    }
-
-
-    /**
-     * Sets the logicalCrossReferences value for this UPEntry.
-     * 
-     * @param logicalCrossReferences
-     */
-    public void setLogicalCrossReferences(uk.ac.ebi.picr.model.CrossReference[] logicalCrossReferences) {
-        this.logicalCrossReferences = logicalCrossReferences;
+    if (getUPI() != null)
+    {
+      _hashCode += getUPI().hashCode();
     }
-
-    public uk.ac.ebi.picr.model.CrossReference getLogicalCrossReferences(int i) {
-        return this.logicalCrossReferences[i];
-    }
-
-    public void setLogicalCrossReferences(int i, uk.ac.ebi.picr.model.CrossReference _value) {
-        this.logicalCrossReferences[i] = _value;
-    }
-
-
-    /**
-     * Gets the sequence value for this UPEntry.
-     * 
-     * @return sequence
-     */
-    public java.lang.String getSequence() {
-        return sequence;
-    }
-
-
-    /**
-     * Sets the sequence value for this UPEntry.
-     * 
-     * @param sequence
-     */
-    public void setSequence(java.lang.String sequence) {
-        this.sequence = sequence;
-    }
-
-
-    /**
-     * Gets the timestamp value for this UPEntry.
-     * 
-     * @return timestamp
-     */
-    public java.util.Calendar getTimestamp() {
-        return timestamp;
-    }
-
-
-    /**
-     * Sets the timestamp value for this UPEntry.
-     * 
-     * @param timestamp
-     */
-    public void setTimestamp(java.util.Calendar timestamp) {
-        this.timestamp = timestamp;
-    }
-
-    private java.lang.Object __equalsCalc = null;
-    public synchronized boolean equals(java.lang.Object obj) {
-        if (!(obj instanceof UPEntry)) return false;
-        UPEntry other = (UPEntry) obj;
-        if (obj == null) return false;
-        if (this == obj) return true;
-        if (__equalsCalc != null) {
-            return (__equalsCalc == obj);
+    if (getIdenticalCrossReferences() != null)
+    {
+      for (int i = 0; i < java.lang.reflect.Array
+              .getLength(getIdenticalCrossReferences()); i++)
+      {
+        java.lang.Object obj = java.lang.reflect.Array.get(
+                getIdenticalCrossReferences(), i);
+        if (obj != null && !obj.getClass().isArray())
+        {
+          _hashCode += obj.hashCode();
         }
-        __equalsCalc = obj;
-        boolean _equals;
-        _equals = true && 
-            ((this.CRC64==null && other.getCRC64()==null) || 
-             (this.CRC64!=null &&
-              this.CRC64.equals(other.getCRC64()))) &&
-            ((this.UPI==null && other.getUPI()==null) || 
-             (this.UPI!=null &&
-              this.UPI.equals(other.getUPI()))) &&
-            ((this.identicalCrossReferences==null && other.getIdenticalCrossReferences()==null) || 
-             (this.identicalCrossReferences!=null &&
-              java.util.Arrays.equals(this.identicalCrossReferences, other.getIdenticalCrossReferences()))) &&
-            ((this.logicalCrossReferences==null && other.getLogicalCrossReferences()==null) || 
-             (this.logicalCrossReferences!=null &&
-              java.util.Arrays.equals(this.logicalCrossReferences, other.getLogicalCrossReferences()))) &&
-            ((this.sequence==null && other.getSequence()==null) || 
-             (this.sequence!=null &&
-              this.sequence.equals(other.getSequence()))) &&
-            ((this.timestamp==null && other.getTimestamp()==null) || 
-             (this.timestamp!=null &&
-              this.timestamp.equals(other.getTimestamp())));
-        __equalsCalc = null;
-        return _equals;
+      }
     }
-
-    private boolean __hashCodeCalc = false;
-    public synchronized int hashCode() {
-        if (__hashCodeCalc) {
-            return 0;
-        }
-        __hashCodeCalc = true;
-        int _hashCode = 1;
-        if (getCRC64() != null) {
-            _hashCode += getCRC64().hashCode();
-        }
-        if (getUPI() != null) {
-            _hashCode += getUPI().hashCode();
+    if (getLogicalCrossReferences() != null)
+    {
+      for (int i = 0; i < java.lang.reflect.Array
+              .getLength(getLogicalCrossReferences()); i++)
+      {
+        java.lang.Object obj = java.lang.reflect.Array.get(
+                getLogicalCrossReferences(), i);
+        if (obj != null && !obj.getClass().isArray())
+        {
+          _hashCode += obj.hashCode();
         }
-        if (getIdenticalCrossReferences() != null) {
-            for (int i=0;
-                 i<java.lang.reflect.Array.getLength(getIdenticalCrossReferences());
-                 i++) {
-                java.lang.Object obj = java.lang.reflect.Array.get(getIdenticalCrossReferences(), i);
-                if (obj != null &&
-                    !obj.getClass().isArray()) {
-                    _hashCode += obj.hashCode();
-                }
-            }
-        }
-        if (getLogicalCrossReferences() != null) {
-            for (int i=0;
-                 i<java.lang.reflect.Array.getLength(getLogicalCrossReferences());
-                 i++) {
-                java.lang.Object obj = java.lang.reflect.Array.get(getLogicalCrossReferences(), i);
-                if (obj != null &&
-                    !obj.getClass().isArray()) {
-                    _hashCode += obj.hashCode();
-                }
-            }
-        }
-        if (getSequence() != null) {
-            _hashCode += getSequence().hashCode();
-        }
-        if (getTimestamp() != null) {
-            _hashCode += getTimestamp().hashCode();
-        }
-        __hashCodeCalc = false;
-        return _hashCode;
+      }
+    }
+    if (getSequence() != null)
+    {
+      _hashCode += getSequence().hashCode();
+    }
+    if (getTimestamp() != null)
+    {
+      _hashCode += getTimestamp().hashCode();
     }
+    __hashCodeCalc = false;
+    return _hashCode;
+  }
 
 }
diff --git a/src/uk/ac/ebi/picr/model/UPEntry_Helper.java b/src/uk/ac/ebi/picr/model/UPEntry_Helper.java
index edb61d5..579a1b1 100644
--- a/src/uk/ac/ebi/picr/model/UPEntry_Helper.java
+++ b/src/uk/ac/ebi/picr/model/UPEntry_Helper.java
@@ -7,76 +7,90 @@
 
 package uk.ac.ebi.picr.model;
 
-public class UPEntry_Helper {
-    // Type metadata
-    private static org.apache.axis.description.TypeDesc typeDesc =
-        new org.apache.axis.description.TypeDesc(UPEntry.class, true);
+public class UPEntry_Helper
+{
+  // Type metadata
+  private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(
+          UPEntry.class, true);
 
-    static {
-        typeDesc.setXmlType(new javax.xml.namespace.QName("http://model.picr.ebi.ac.uk", "UPEntry"));
-        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("CRC64");
-        elemField.setXmlName(new javax.xml.namespace.QName("http://model.picr.ebi.ac.uk", "CRC64"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("UPI");
-        elemField.setXmlName(new javax.xml.namespace.QName("http://model.picr.ebi.ac.uk", "UPI"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("identicalCrossReferences");
-        elemField.setXmlName(new javax.xml.namespace.QName("http://model.picr.ebi.ac.uk", "identicalCrossReferences"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://model.picr.ebi.ac.uk", "CrossReference"));
-        elemField.setMinOccurs(0);
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("logicalCrossReferences");
-        elemField.setXmlName(new javax.xml.namespace.QName("http://model.picr.ebi.ac.uk", "logicalCrossReferences"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://model.picr.ebi.ac.uk", "CrossReference"));
-        elemField.setMinOccurs(0);
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("sequence");
-        elemField.setXmlName(new javax.xml.namespace.QName("http://model.picr.ebi.ac.uk", "sequence"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("timestamp");
-        elemField.setXmlName(new javax.xml.namespace.QName("http://model.picr.ebi.ac.uk", "timestamp"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "dateTime"));
-        typeDesc.addFieldDesc(elemField);
-    }
+  static
+  {
+    typeDesc.setXmlType(new javax.xml.namespace.QName(
+            "http://model.picr.ebi.ac.uk", "UPEntry"));
+    org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("CRC64");
+    elemField.setXmlName(new javax.xml.namespace.QName(
+            "http://model.picr.ebi.ac.uk", "CRC64"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "http://www.w3.org/2001/XMLSchema", "string"));
+    typeDesc.addFieldDesc(elemField);
+    elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("UPI");
+    elemField.setXmlName(new javax.xml.namespace.QName(
+            "http://model.picr.ebi.ac.uk", "UPI"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "http://www.w3.org/2001/XMLSchema", "string"));
+    typeDesc.addFieldDesc(elemField);
+    elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("identicalCrossReferences");
+    elemField.setXmlName(new javax.xml.namespace.QName(
+            "http://model.picr.ebi.ac.uk", "identicalCrossReferences"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "http://model.picr.ebi.ac.uk", "CrossReference"));
+    elemField.setMinOccurs(0);
+    typeDesc.addFieldDesc(elemField);
+    elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("logicalCrossReferences");
+    elemField.setXmlName(new javax.xml.namespace.QName(
+            "http://model.picr.ebi.ac.uk", "logicalCrossReferences"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "http://model.picr.ebi.ac.uk", "CrossReference"));
+    elemField.setMinOccurs(0);
+    typeDesc.addFieldDesc(elemField);
+    elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("sequence");
+    elemField.setXmlName(new javax.xml.namespace.QName(
+            "http://model.picr.ebi.ac.uk", "sequence"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "http://www.w3.org/2001/XMLSchema", "string"));
+    typeDesc.addFieldDesc(elemField);
+    elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("timestamp");
+    elemField.setXmlName(new javax.xml.namespace.QName(
+            "http://model.picr.ebi.ac.uk", "timestamp"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "http://www.w3.org/2001/XMLSchema", "dateTime"));
+    typeDesc.addFieldDesc(elemField);
+  }
 
-    /**
-     * Return type metadata object
-     */
-    public static org.apache.axis.description.TypeDesc getTypeDesc() {
-        return typeDesc;
-    }
+  /**
+   * Return type metadata object
+   */
+  public static org.apache.axis.description.TypeDesc getTypeDesc()
+  {
+    return typeDesc;
+  }
 
-    /**
-     * Get Custom Serializer
-     */
-    public static org.apache.axis.encoding.Serializer getSerializer(
-           java.lang.String mechType, 
-           java.lang.Class _javaType,  
-           javax.xml.namespace.QName _xmlType) {
-        return 
-          new  org.apache.axis.encoding.ser.BeanSerializer(
-            _javaType, _xmlType, typeDesc);
-    }
+  /**
+   * Get Custom Serializer
+   */
+  public static org.apache.axis.encoding.Serializer getSerializer(
+          java.lang.String mechType, java.lang.Class _javaType,
+          javax.xml.namespace.QName _xmlType)
+  {
+    return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,
+            _xmlType, typeDesc);
+  }
 
-    /**
-     * Get Custom Deserializer
-     */
-    public static org.apache.axis.encoding.Deserializer getDeserializer(
-           java.lang.String mechType, 
-           java.lang.Class _javaType,  
-           javax.xml.namespace.QName _xmlType) {
-        return 
-          new  org.apache.axis.encoding.ser.BeanDeserializer(
-            _javaType, _xmlType, typeDesc);
-    }
+  /**
+   * Get Custom Deserializer
+   */
+  public static org.apache.axis.encoding.Deserializer getDeserializer(
+          java.lang.String mechType, java.lang.Class _javaType,
+          javax.xml.namespace.QName _xmlType)
+  {
+    return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,
+            _xmlType, typeDesc);
+  }
 
 }
diff --git a/src/uk/ac/ebi/www/Data.java b/src/uk/ac/ebi/www/Data.java
index 9bb671e..d9e1037 100755
--- a/src/uk/ac/ebi/www/Data.java
+++ b/src/uk/ac/ebi/www/Data.java
@@ -7,10 +7,10 @@
 
 package uk.ac.ebi.www;
 
-public class Data
-    implements java.io.Serializable
+public class Data implements java.io.Serializable
 {
   private java.lang.String type;
+
   private java.lang.String content;
 
   public Data()
@@ -38,9 +38,10 @@ public class Data
   }
 
   private java.lang.Object __equalsCalc = null;
+
   public synchronized boolean equals(java.lang.Object obj)
   {
-    if (! (obj instanceof Data))
+    if (!(obj instanceof Data))
     {
       return false;
     }
@@ -59,18 +60,17 @@ public class Data
     }
     __equalsCalc = obj;
     boolean _equals;
-    _equals = true &&
-        ( (type == null && other.getType() == null) ||
-         (type != null &&
-          type.equals(other.getType()))) &&
-        ( (content == null && other.getContent() == null) ||
-         (content != null &&
-          content.equals(other.getContent())));
+    _equals = true
+            && ((type == null && other.getType() == null) || (type != null && type
+                    .equals(other.getType())))
+            && ((content == null && other.getContent() == null) || (content != null && content
+                    .equals(other.getContent())));
     __equalsCalc = null;
     return _equals;
   }
 
   private boolean __hashCodeCalc = false;
+
   public synchronized int hashCode()
   {
     if (__hashCodeCalc)
@@ -92,23 +92,22 @@ public class Data
   }
 
   // Type metadata
-  private static org.apache.axis.description.TypeDesc typeDesc =
-      new org.apache.axis.description.TypeDesc(Data.class);
+  private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(
+          Data.class);
 
   static
   {
-    org.apache.axis.description.FieldDesc field = new org.apache.axis.
-        description.ElementDesc();
+    org.apache.axis.description.FieldDesc field = new org.apache.axis.description.ElementDesc();
     field.setFieldName("type");
     field.setXmlName(new javax.xml.namespace.QName("", "type"));
     field.setXmlType(new javax.xml.namespace.QName(
-        "http://www.w3.org/2001/XMLSchema", "string"));
+            "http://www.w3.org/2001/XMLSchema", "string"));
     typeDesc.addFieldDesc(field);
     field = new org.apache.axis.description.ElementDesc();
     field.setFieldName("content");
     field.setXmlName(new javax.xml.namespace.QName("", "content"));
     field.setXmlType(new javax.xml.namespace.QName(
-        "http://www.w3.org/2001/XMLSchema", "string"));
+            "http://www.w3.org/2001/XMLSchema", "string"));
     typeDesc.addFieldDesc(field);
   };
 
@@ -124,26 +123,22 @@ public class Data
    * Get Custom Serializer
    */
   public static org.apache.axis.encoding.Serializer getSerializer(
-      java.lang.String mechType,
-      java.lang.Class _javaType,
-      javax.xml.namespace.QName _xmlType)
+          java.lang.String mechType, java.lang.Class _javaType,
+          javax.xml.namespace.QName _xmlType)
   {
-    return
-        new org.apache.axis.encoding.ser.BeanSerializer(
-            _javaType, _xmlType, typeDesc);
+    return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,
+            _xmlType, typeDesc);
   }
 
   /**
    * Get Custom Deserializer
    */
   public static org.apache.axis.encoding.Deserializer getDeserializer(
-      java.lang.String mechType,
-      java.lang.Class _javaType,
-      javax.xml.namespace.QName _xmlType)
+          java.lang.String mechType, java.lang.Class _javaType,
+          javax.xml.namespace.QName _xmlType)
   {
-    return
-        new org.apache.axis.encoding.ser.BeanDeserializer(
-            _javaType, _xmlType, typeDesc);
+    return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,
+            _xmlType, typeDesc);
   }
 
 }
diff --git a/src/uk/ac/ebi/www/InputParams.java b/src/uk/ac/ebi/www/InputParams.java
index 83d68a9..0284103 100755
--- a/src/uk/ac/ebi/www/InputParams.java
+++ b/src/uk/ac/ebi/www/InputParams.java
@@ -7,24 +7,38 @@
 
 package uk.ac.ebi.www;
 
-public class InputParams
-    implements java.io.Serializable
+public class InputParams implements java.io.Serializable
 {
   private java.lang.String program;
+
   private java.lang.String database;
+
   private java.lang.String matrix;
+
   private float exp;
+
   private boolean echofilter;
+
   private java.lang.String filter;
+
   private int numal;
+
   private int scores;
+
   private java.lang.String sensitivity;
+
   private java.lang.String sort;
+
   private java.lang.String stats;
+
   private java.lang.String strand;
+
   private java.lang.String outformat;
+
   private int topcombon;
+
   private boolean async;
+
   private java.lang.String email;
 
   public InputParams()
@@ -192,9 +206,10 @@ public class InputParams
   }
 
   private java.lang.Object __equalsCalc = null;
+
   public synchronized boolean equals(java.lang.Object obj)
   {
-    if (! (obj instanceof InputParams))
+    if (!(obj instanceof InputParams))
     {
       return false;
     }
@@ -213,48 +228,39 @@ public class InputParams
     }
     __equalsCalc = obj;
     boolean _equals;
-    _equals = true &&
-        ( (program == null && other.getProgram() == null) ||
-         (program != null &&
-          program.equals(other.getProgram()))) &&
-        ( (database == null && other.getDatabase() == null) ||
-         (database != null &&
-          database.equals(other.getDatabase()))) &&
-        ( (matrix == null && other.getMatrix() == null) ||
-         (matrix != null &&
-          matrix.equals(other.getMatrix()))) &&
-        exp == other.getExp() &&
-        echofilter == other.isEchofilter() &&
-        ( (filter == null && other.getFilter() == null) ||
-         (filter != null &&
-          filter.equals(other.getFilter()))) &&
-        numal == other.getNumal() &&
-        scores == other.getScores() &&
-        ( (sensitivity == null && other.getSensitivity() == null) ||
-         (sensitivity != null &&
-          sensitivity.equals(other.getSensitivity()))) &&
-        ( (sort == null && other.getSort() == null) ||
-         (sort != null &&
-          sort.equals(other.getSort()))) &&
-        ( (stats == null && other.getStats() == null) ||
-         (stats != null &&
-          stats.equals(other.getStats()))) &&
-        ( (strand == null && other.getStrand() == null) ||
-         (strand != null &&
-          strand.equals(other.getStrand()))) &&
-        ( (outformat == null && other.getOutformat() == null) ||
-         (outformat != null &&
-          outformat.equals(other.getOutformat()))) &&
-        topcombon == other.getTopcombon() &&
-        async == other.isAsync() &&
-        ( (email == null && other.getEmail() == null) ||
-         (email != null &&
-          email.equals(other.getEmail())));
+    _equals = true
+            && ((program == null && other.getProgram() == null) || (program != null && program
+                    .equals(other.getProgram())))
+            && ((database == null && other.getDatabase() == null) || (database != null && database
+                    .equals(other.getDatabase())))
+            && ((matrix == null && other.getMatrix() == null) || (matrix != null && matrix
+                    .equals(other.getMatrix())))
+            && exp == other.getExp()
+            && echofilter == other.isEchofilter()
+            && ((filter == null && other.getFilter() == null) || (filter != null && filter
+                    .equals(other.getFilter())))
+            && numal == other.getNumal()
+            && scores == other.getScores()
+            && ((sensitivity == null && other.getSensitivity() == null) || (sensitivity != null && sensitivity
+                    .equals(other.getSensitivity())))
+            && ((sort == null && other.getSort() == null) || (sort != null && sort
+                    .equals(other.getSort())))
+            && ((stats == null && other.getStats() == null) || (stats != null && stats
+                    .equals(other.getStats())))
+            && ((strand == null && other.getStrand() == null) || (strand != null && strand
+                    .equals(other.getStrand())))
+            && ((outformat == null && other.getOutformat() == null) || (outformat != null && outformat
+                    .equals(other.getOutformat())))
+            && topcombon == other.getTopcombon()
+            && async == other.isAsync()
+            && ((email == null && other.getEmail() == null) || (email != null && email
+                    .equals(other.getEmail())));
     __equalsCalc = null;
     return _equals;
   }
 
   private boolean __hashCodeCalc = false;
+
   public synchronized int hashCode()
   {
     if (__hashCodeCalc)
@@ -314,107 +320,106 @@ public class InputParams
   }
 
   // Type metadata
-  private static org.apache.axis.description.TypeDesc typeDesc =
-      new org.apache.axis.description.TypeDesc(InputParams.class);
+  private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(
+          InputParams.class);
 
   static
   {
-    org.apache.axis.description.FieldDesc field = new org.apache.axis.
-        description.ElementDesc();
+    org.apache.axis.description.FieldDesc field = new org.apache.axis.description.ElementDesc();
     field.setFieldName("program");
     field.setXmlName(new javax.xml.namespace.QName("", "program"));
     field.setXmlType(new javax.xml.namespace.QName(
-        "http://www.w3.org/2001/XMLSchema", "string"));
+            "http://www.w3.org/2001/XMLSchema", "string"));
     typeDesc.addFieldDesc(field);
     field = new org.apache.axis.description.ElementDesc();
     field.setFieldName("database");
     field.setXmlName(new javax.xml.namespace.QName("", "database"));
     field.setXmlType(new javax.xml.namespace.QName(
-        "http://www.w3.org/2001/XMLSchema", "string"));
+            "http://www.w3.org/2001/XMLSchema", "string"));
     typeDesc.addFieldDesc(field);
     field = new org.apache.axis.description.ElementDesc();
     field.setFieldName("matrix");
     field.setXmlName(new javax.xml.namespace.QName("", "matrix"));
     field.setXmlType(new javax.xml.namespace.QName(
-        "http://www.w3.org/2001/XMLSchema", "string"));
+            "http://www.w3.org/2001/XMLSchema", "string"));
     typeDesc.addFieldDesc(field);
     field = new org.apache.axis.description.ElementDesc();
     field.setFieldName("exp");
     field.setXmlName(new javax.xml.namespace.QName("", "exp"));
     field.setXmlType(new javax.xml.namespace.QName(
-        "http://www.w3.org/2001/XMLSchema", "float"));
+            "http://www.w3.org/2001/XMLSchema", "float"));
     typeDesc.addFieldDesc(field);
     field = new org.apache.axis.description.ElementDesc();
     field.setFieldName("echofilter");
     field.setXmlName(new javax.xml.namespace.QName("", "echofilter"));
     field.setXmlType(new javax.xml.namespace.QName(
-        "http://www.w3.org/2001/XMLSchema", "boolean"));
+            "http://www.w3.org/2001/XMLSchema", "boolean"));
     typeDesc.addFieldDesc(field);
     field = new org.apache.axis.description.ElementDesc();
     field.setFieldName("filter");
     field.setXmlName(new javax.xml.namespace.QName("", "filter"));
     field.setXmlType(new javax.xml.namespace.QName(
-        "http://www.w3.org/2001/XMLSchema", "string"));
+            "http://www.w3.org/2001/XMLSchema", "string"));
     typeDesc.addFieldDesc(field);
     field = new org.apache.axis.description.ElementDesc();
     field.setFieldName("numal");
     field.setXmlName(new javax.xml.namespace.QName("", "numal"));
     field.setXmlType(new javax.xml.namespace.QName(
-        "http://www.w3.org/2001/XMLSchema", "int"));
+            "http://www.w3.org/2001/XMLSchema", "int"));
     typeDesc.addFieldDesc(field);
     field = new org.apache.axis.description.ElementDesc();
     field.setFieldName("scores");
     field.setXmlName(new javax.xml.namespace.QName("", "scores"));
     field.setXmlType(new javax.xml.namespace.QName(
-        "http://www.w3.org/2001/XMLSchema", "int"));
+            "http://www.w3.org/2001/XMLSchema", "int"));
     typeDesc.addFieldDesc(field);
     field = new org.apache.axis.description.ElementDesc();
     field.setFieldName("sensitivity");
     field.setXmlName(new javax.xml.namespace.QName("", "sensitivity"));
     field.setXmlType(new javax.xml.namespace.QName(
-        "http://www.w3.org/2001/XMLSchema", "string"));
+            "http://www.w3.org/2001/XMLSchema", "string"));
     typeDesc.addFieldDesc(field);
     field = new org.apache.axis.description.ElementDesc();
     field.setFieldName("sort");
     field.setXmlName(new javax.xml.namespace.QName("", "sort"));
     field.setXmlType(new javax.xml.namespace.QName(
-        "http://www.w3.org/2001/XMLSchema", "string"));
+            "http://www.w3.org/2001/XMLSchema", "string"));
     typeDesc.addFieldDesc(field);
     field = new org.apache.axis.description.ElementDesc();
     field.setFieldName("stats");
     field.setXmlName(new javax.xml.namespace.QName("", "stats"));
     field.setXmlType(new javax.xml.namespace.QName(
-        "http://www.w3.org/2001/XMLSchema", "string"));
+            "http://www.w3.org/2001/XMLSchema", "string"));
     typeDesc.addFieldDesc(field);
     field = new org.apache.axis.description.ElementDesc();
     field.setFieldName("strand");
     field.setXmlName(new javax.xml.namespace.QName("", "strand"));
     field.setXmlType(new javax.xml.namespace.QName(
-        "http://www.w3.org/2001/XMLSchema", "string"));
+            "http://www.w3.org/2001/XMLSchema", "string"));
     typeDesc.addFieldDesc(field);
     field = new org.apache.axis.description.ElementDesc();
     field.setFieldName("outformat");
     field.setXmlName(new javax.xml.namespace.QName("", "outformat"));
     field.setXmlType(new javax.xml.namespace.QName(
-        "http://www.w3.org/2001/XMLSchema", "string"));
+            "http://www.w3.org/2001/XMLSchema", "string"));
     typeDesc.addFieldDesc(field);
     field = new org.apache.axis.description.ElementDesc();
     field.setFieldName("topcombon");
     field.setXmlName(new javax.xml.namespace.QName("", "topcombon"));
     field.setXmlType(new javax.xml.namespace.QName(
-        "http://www.w3.org/2001/XMLSchema", "int"));
+            "http://www.w3.org/2001/XMLSchema", "int"));
     typeDesc.addFieldDesc(field);
     field = new org.apache.axis.description.ElementDesc();
     field.setFieldName("async");
     field.setXmlName(new javax.xml.namespace.QName("", "async"));
     field.setXmlType(new javax.xml.namespace.QName(
-        "http://www.w3.org/2001/XMLSchema", "boolean"));
+            "http://www.w3.org/2001/XMLSchema", "boolean"));
     typeDesc.addFieldDesc(field);
     field = new org.apache.axis.description.ElementDesc();
     field.setFieldName("email");
     field.setXmlName(new javax.xml.namespace.QName("", "email"));
     field.setXmlType(new javax.xml.namespace.QName(
-        "http://www.w3.org/2001/XMLSchema", "string"));
+            "http://www.w3.org/2001/XMLSchema", "string"));
     typeDesc.addFieldDesc(field);
   };
 
@@ -430,26 +435,22 @@ public class InputParams
    * Get Custom Serializer
    */
   public static org.apache.axis.encoding.Serializer getSerializer(
-      java.lang.String mechType,
-      java.lang.Class _javaType,
-      javax.xml.namespace.QName _xmlType)
+          java.lang.String mechType, java.lang.Class _javaType,
+          javax.xml.namespace.QName _xmlType)
   {
-    return
-        new org.apache.axis.encoding.ser.BeanSerializer(
-            _javaType, _xmlType, typeDesc);
+    return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,
+            _xmlType, typeDesc);
   }
 
   /**
    * Get Custom Deserializer
    */
   public static org.apache.axis.encoding.Deserializer getDeserializer(
-      java.lang.String mechType,
-      java.lang.Class _javaType,
-      javax.xml.namespace.QName _xmlType)
+          java.lang.String mechType, java.lang.Class _javaType,
+          javax.xml.namespace.QName _xmlType)
   {
-    return
-        new org.apache.axis.encoding.ser.BeanDeserializer(
-            _javaType, _xmlType, typeDesc);
+    return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,
+            _xmlType, typeDesc);
   }
 
 }
diff --git a/src/uk/ac/ebi/www/WSFile.java b/src/uk/ac/ebi/www/WSFile.java
index 66bb1dc..0dd62b1 100755
--- a/src/uk/ac/ebi/www/WSFile.java
+++ b/src/uk/ac/ebi/www/WSFile.java
@@ -7,10 +7,10 @@
 
 package uk.ac.ebi.www;
 
-public class WSFile
-    implements java.io.Serializable
+public class WSFile implements java.io.Serializable
 {
   private java.lang.String type;
+
   private java.lang.String ext;
 
   public WSFile()
@@ -38,9 +38,10 @@ public class WSFile
   }
 
   private java.lang.Object __equalsCalc = null;
+
   public synchronized boolean equals(java.lang.Object obj)
   {
-    if (! (obj instanceof WSFile))
+    if (!(obj instanceof WSFile))
     {
       return false;
     }
@@ -59,18 +60,17 @@ public class WSFile
     }
     __equalsCalc = obj;
     boolean _equals;
-    _equals = true &&
-        ( (type == null && other.getType() == null) ||
-         (type != null &&
-          type.equals(other.getType()))) &&
-        ( (ext == null && other.getExt() == null) ||
-         (ext != null &&
-          ext.equals(other.getExt())));
+    _equals = true
+            && ((type == null && other.getType() == null) || (type != null && type
+                    .equals(other.getType())))
+            && ((ext == null && other.getExt() == null) || (ext != null && ext
+                    .equals(other.getExt())));
     __equalsCalc = null;
     return _equals;
   }
 
   private boolean __hashCodeCalc = false;
+
   public synchronized int hashCode()
   {
     if (__hashCodeCalc)
@@ -92,23 +92,22 @@ public class WSFile
   }
 
   // Type metadata
-  private static org.apache.axis.description.TypeDesc typeDesc =
-      new org.apache.axis.description.TypeDesc(WSFile.class);
+  private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(
+          WSFile.class);
 
   static
   {
-    org.apache.axis.description.FieldDesc field = new org.apache.axis.
-        description.ElementDesc();
+    org.apache.axis.description.FieldDesc field = new org.apache.axis.description.ElementDesc();
     field.setFieldName("type");
     field.setXmlName(new javax.xml.namespace.QName("", "type"));
     field.setXmlType(new javax.xml.namespace.QName(
-        "http://www.w3.org/2001/XMLSchema", "string"));
+            "http://www.w3.org/2001/XMLSchema", "string"));
     typeDesc.addFieldDesc(field);
     field = new org.apache.axis.description.ElementDesc();
     field.setFieldName("ext");
     field.setXmlName(new javax.xml.namespace.QName("", "ext"));
     field.setXmlType(new javax.xml.namespace.QName(
-        "http://www.w3.org/2001/XMLSchema", "string"));
+            "http://www.w3.org/2001/XMLSchema", "string"));
     typeDesc.addFieldDesc(field);
   };
 
@@ -124,26 +123,22 @@ public class WSFile
    * Get Custom Serializer
    */
   public static org.apache.axis.encoding.Serializer getSerializer(
-      java.lang.String mechType,
-      java.lang.Class _javaType,
-      javax.xml.namespace.QName _xmlType)
+          java.lang.String mechType, java.lang.Class _javaType,
+          javax.xml.namespace.QName _xmlType)
   {
-    return
-        new org.apache.axis.encoding.ser.BeanSerializer(
-            _javaType, _xmlType, typeDesc);
+    return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,
+            _xmlType, typeDesc);
   }
 
   /**
    * Get Custom Deserializer
    */
   public static org.apache.axis.encoding.Deserializer getDeserializer(
-      java.lang.String mechType,
-      java.lang.Class _javaType,
-      javax.xml.namespace.QName _xmlType)
+          java.lang.String mechType, java.lang.Class _javaType,
+          javax.xml.namespace.QName _xmlType)
   {
-    return
-        new org.apache.axis.encoding.ser.BeanDeserializer(
-            _javaType, _xmlType, typeDesc);
+    return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,
+            _xmlType, typeDesc);
   }
 
 }
diff --git a/src/uk/ac/ebi/www/WSWUBlast.java b/src/uk/ac/ebi/www/WSWUBlast.java
index e7f6f87..09d59a4 100755
--- a/src/uk/ac/ebi/www/WSWUBlast.java
+++ b/src/uk/ac/ebi/www/WSWUBlast.java
@@ -7,28 +7,26 @@
 
 package uk.ac.ebi.www;
 
-public interface WSWUBlast
-    extends java.rmi.Remote
+public interface WSWUBlast extends java.rmi.Remote
 {
   public java.lang.String runWUBlast(uk.ac.ebi.www.InputParams params,
-                                     uk.ac.ebi.www.Data[] content)
-      throws java.rmi.RemoteException;
+          uk.ac.ebi.www.Data[] content) throws java.rmi.RemoteException;
 
   public java.lang.String checkStatus(java.lang.String jobid)
-      throws java.rmi.RemoteException;
+          throws java.rmi.RemoteException;
 
   public byte[] poll(java.lang.String jobid, java.lang.String type)
-      throws java.rmi.RemoteException;
+          throws java.rmi.RemoteException;
 
   public uk.ac.ebi.www.WSFile[] getResults(java.lang.String jobid)
-      throws java.rmi.RemoteException;
+          throws java.rmi.RemoteException;
 
   public byte[] test(java.lang.String jobid, java.lang.String type)
-      throws java.rmi.RemoteException;
+          throws java.rmi.RemoteException;
 
   public byte[] polljob(java.lang.String jobid, java.lang.String outformat)
-      throws java.rmi.RemoteException;
+          throws java.rmi.RemoteException;
 
   public byte[] doWUBlast(uk.ac.ebi.www.InputParams params, byte[] content)
-      throws java.rmi.RemoteException;
+          throws java.rmi.RemoteException;
 }
diff --git a/src/uk/ac/ebi/www/WSWUBlastService.java b/src/uk/ac/ebi/www/WSWUBlastService.java
index bc65727..ececb65 100755
--- a/src/uk/ac/ebi/www/WSWUBlastService.java
+++ b/src/uk/ac/ebi/www/WSWUBlastService.java
@@ -7,14 +7,13 @@
 
 package uk.ac.ebi.www;
 
-public interface WSWUBlastService
-    extends javax.xml.rpc.Service
+public interface WSWUBlastService extends javax.xml.rpc.Service
 {
   public java.lang.String getWSWUBlastAddress();
 
   public uk.ac.ebi.www.WSWUBlast getWSWUBlast()
-      throws javax.xml.rpc.ServiceException;
+          throws javax.xml.rpc.ServiceException;
 
   public uk.ac.ebi.www.WSWUBlast getWSWUBlast(java.net.URL portAddress)
-      throws javax.xml.rpc.ServiceException;
+          throws javax.xml.rpc.ServiceException;
 }
diff --git a/src/uk/ac/ebi/www/WSWUBlastServiceLocator.java b/src/uk/ac/ebi/www/WSWUBlastServiceLocator.java
index 08f0509..6e8fca9 100755
--- a/src/uk/ac/ebi/www/WSWUBlastServiceLocator.java
+++ b/src/uk/ac/ebi/www/WSWUBlastServiceLocator.java
@@ -7,14 +7,12 @@
 
 package uk.ac.ebi.www;
 
-public class WSWUBlastServiceLocator
-    extends org.apache.axis.client.Service implements uk.ac.ebi.www.
-    WSWUBlastService
+public class WSWUBlastServiceLocator extends org.apache.axis.client.Service
+        implements uk.ac.ebi.www.WSWUBlastService
 {
 
   // Use to get a proxy class for WSWUBlast
-  private final java.lang.String WSWUBlast_address =
-      "http://www.ebi.ac.uk/~alabarga/cgi-bin/webservices/WSWUBlast";
+  private final java.lang.String WSWUBlast_address = "http://www.ebi.ac.uk/~alabarga/cgi-bin/webservices/WSWUBlast";
 
   public java.lang.String getWSWUBlastAddress()
   {
@@ -35,14 +33,13 @@ public class WSWUBlastServiceLocator
   }
 
   public uk.ac.ebi.www.WSWUBlast getWSWUBlast()
-      throws javax.xml.rpc.ServiceException
+          throws javax.xml.rpc.ServiceException
   {
     java.net.URL endpoint;
     try
     {
       endpoint = new java.net.URL(WSWUBlast_address);
-    }
-    catch (java.net.MalformedURLException e)
+    } catch (java.net.MalformedURLException e)
     {
       return null; // unlikely as URL was validated in WSDL2Java
     }
@@ -50,68 +47,64 @@ public class WSWUBlastServiceLocator
   }
 
   public uk.ac.ebi.www.WSWUBlast getWSWUBlast(java.net.URL portAddress)
-      throws javax.xml.rpc.ServiceException
+          throws javax.xml.rpc.ServiceException
   {
     try
     {
-      uk.ac.ebi.www.WSWUBlastSoapBindingStub _stub = new uk.ac.ebi.www.
-          WSWUBlastSoapBindingStub(portAddress, this);
+      uk.ac.ebi.www.WSWUBlastSoapBindingStub _stub = new uk.ac.ebi.www.WSWUBlastSoapBindingStub(
+              portAddress, this);
       _stub.setPortName(getWSWUBlastWSDDServiceName());
       return _stub;
-    }
-    catch (org.apache.axis.AxisFault e)
+    } catch (org.apache.axis.AxisFault e)
     {
       return null;
     }
   }
 
   /**
-   * For the given interface, get the stub implementation.
-   * If this service has no port for the given interface,
-   * then ServiceException is thrown.
+   * For the given interface, get the stub implementation. If this service has
+   * no port for the given interface, then ServiceException is thrown.
    */
   public java.rmi.Remote getPort(Class serviceEndpointInterface)
-      throws javax.xml.rpc.ServiceException
+          throws javax.xml.rpc.ServiceException
   {
     try
     {
-      if (uk.ac.ebi.www.WSWUBlast.class.isAssignableFrom(
-          serviceEndpointInterface))
+      if (uk.ac.ebi.www.WSWUBlast.class
+              .isAssignableFrom(serviceEndpointInterface))
       {
-        uk.ac.ebi.www.WSWUBlastSoapBindingStub _stub = new uk.ac.ebi.www.
-            WSWUBlastSoapBindingStub(new java.net.URL(WSWUBlast_address), this);
+        uk.ac.ebi.www.WSWUBlastSoapBindingStub _stub = new uk.ac.ebi.www.WSWUBlastSoapBindingStub(
+                new java.net.URL(WSWUBlast_address), this);
         _stub.setPortName(getWSWUBlastWSDDServiceName());
         return _stub;
       }
-    }
-    catch (java.lang.Throwable t)
+    } catch (java.lang.Throwable t)
     {
       throw new javax.xml.rpc.ServiceException(t);
     }
     throw new javax.xml.rpc.ServiceException(
-        "There is no stub implementation for the interface:  " +
-        (serviceEndpointInterface == null ? "null" :
-         serviceEndpointInterface.getName()));
+            "There is no stub implementation for the interface:  "
+                    + (serviceEndpointInterface == null ? "null"
+                            : serviceEndpointInterface.getName()));
   }
 
   /**
-   * For the given interface, get the stub implementation.
-   * If this service has no port for the given interface,
-   * then ServiceException is thrown.
+   * For the given interface, get the stub implementation. If this service has
+   * no port for the given interface, then ServiceException is thrown.
    */
   public java.rmi.Remote getPort(javax.xml.namespace.QName portName,
-                                 Class serviceEndpointInterface)
-      throws javax.xml.rpc.ServiceException
+          Class serviceEndpointInterface)
+          throws javax.xml.rpc.ServiceException
   {
     java.rmi.Remote _stub = getPort(serviceEndpointInterface);
-    ( (org.apache.axis.client.Stub) _stub).setPortName(portName);
+    ((org.apache.axis.client.Stub) _stub).setPortName(portName);
     return _stub;
   }
 
   public javax.xml.namespace.QName getServiceName()
   {
     return new javax.xml.namespace.QName("http://www.ebi.ac.uk/WSWUBlast",
-                                         "WSWUBlastService");
+            "WSWUBlastService");
   }
 
   private java.util.HashSet ports = null;
diff --git a/src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java b/src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java
index 842bf8b..a8157b8 100755
--- a/src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java
+++ b/src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java
@@ -7,30 +7,31 @@
 
 package uk.ac.ebi.www;
 
-public class WSWUBlastSoapBindingStub
-    extends org.apache.axis.client.Stub implements uk.ac.ebi.www.WSWUBlast
+public class WSWUBlastSoapBindingStub extends org.apache.axis.client.Stub
+        implements uk.ac.ebi.www.WSWUBlast
 {
   private java.util.Vector cachedSerClasses = new java.util.Vector();
+
   private java.util.Vector cachedSerQNames = new java.util.Vector();
+
   private java.util.Vector cachedSerFactories = new java.util.Vector();
+
   private java.util.Vector cachedDeserFactories = new java.util.Vector();
 
-  public WSWUBlastSoapBindingStub()
-      throws org.apache.axis.AxisFault
+  public WSWUBlastSoapBindingStub() throws org.apache.axis.AxisFault
   {
     this(null);
   }
 
   public WSWUBlastSoapBindingStub(java.net.URL endpointURL,
-                                  javax.xml.rpc.Service service)
-      throws org.apache.axis.AxisFault
+          javax.xml.rpc.Service service) throws org.apache.axis.AxisFault
   {
     this(service);
     super.cachedEndpoint = endpointURL;
   }
 
   public WSWUBlastSoapBindingStub(javax.xml.rpc.Service service)
-      throws org.apache.axis.AxisFault
+          throws org.apache.axis.AxisFault
   {
     if (service == null)
     {
@@ -43,21 +44,15 @@ public class WSWUBlastSoapBindingStub
     java.lang.Class cls;
     javax.xml.namespace.QName qName;
     java.lang.Class beansf = org.apache.axis.encoding.ser.BeanSerializerFactory.class;
-    java.lang.Class beandf = org.apache.axis.encoding.ser.
-        BeanDeserializerFactory.class;
+    java.lang.Class beandf = org.apache.axis.encoding.ser.BeanDeserializerFactory.class;
     java.lang.Class enumsf = org.apache.axis.encoding.ser.EnumSerializerFactory.class;
-    java.lang.Class enumdf = org.apache.axis.encoding.ser.
-        EnumDeserializerFactory.class;
-    java.lang.Class arraysf = org.apache.axis.encoding.ser.
-        ArraySerializerFactory.class;
-    java.lang.Class arraydf = org.apache.axis.encoding.ser.
-        ArrayDeserializerFactory.class;
-    java.lang.Class simplesf = org.apache.axis.encoding.ser.
-        SimpleSerializerFactory.class;
-    java.lang.Class simpledf = org.apache.axis.encoding.ser.
-        SimpleDeserializerFactory.class;
+    java.lang.Class enumdf = org.apache.axis.encoding.ser.EnumDeserializerFactory.class;
+    java.lang.Class arraysf = org.apache.axis.encoding.ser.ArraySerializerFactory.class;
+    java.lang.Class arraydf = org.apache.axis.encoding.ser.ArrayDeserializerFactory.class;
+    java.lang.Class simplesf = org.apache.axis.encoding.ser.SimpleSerializerFactory.class;
+    java.lang.Class simpledf = org.apache.axis.encoding.ser.SimpleDeserializerFactory.class;
     qName = new javax.xml.namespace.QName("http://www.ebi.ac.uk/WSWUBlast",
-                                          "inputParams");
+            "inputParams");
     cachedSerQNames.add(qName);
     cls = uk.ac.ebi.www.InputParams.class;
     cachedSerClasses.add(cls);
@@ -65,7 +60,7 @@ public class WSWUBlastSoapBindingStub
     cachedDeserFactories.add(beandf);
 
     qName = new javax.xml.namespace.QName("http://www.ebi.ac.uk/WSWUBlast",
-                                          "WSArrayofFile");
+            "WSArrayofFile");
     cachedSerQNames.add(qName);
     cls = uk.ac.ebi.www.WSFile[].class;
     cachedSerClasses.add(cls);
@@ -73,7 +68,7 @@ public class WSWUBlastSoapBindingStub
     cachedDeserFactories.add(arraydf);
 
     qName = new javax.xml.namespace.QName("http://www.ebi.ac.uk/WSWUBlast",
-                                          "WSArrayofData");
+            "WSArrayofData");
     cachedSerQNames.add(qName);
     cls = uk.ac.ebi.www.Data[].class;
     cachedSerClasses.add(cls);
@@ -81,7 +76,7 @@ public class WSWUBlastSoapBindingStub
     cachedDeserFactories.add(arraydf);
 
     qName = new javax.xml.namespace.QName("http://www.ebi.ac.uk/WSWUBlast",
-                                          "data");
+            "data");
     cachedSerQNames.add(qName);
     cls = uk.ac.ebi.www.Data.class;
     cachedSerClasses.add(cls);
@@ -89,7 +84,7 @@ public class WSWUBlastSoapBindingStub
     cachedDeserFactories.add(beandf);
 
     qName = new javax.xml.namespace.QName("http://www.ebi.ac.uk/WSWUBlast",
-                                          "WSFile");
+            "WSFile");
     cachedSerQNames.add(qName);
     cls = uk.ac.ebi.www.WSFile.class;
     cachedSerClasses.add(cls);
@@ -99,12 +94,12 @@ public class WSWUBlastSoapBindingStub
   }
 
   private org.apache.axis.client.Call createCall()
-      throws java.rmi.RemoteException
+          throws java.rmi.RemoteException
   {
     try
     {
-      org.apache.axis.client.Call _call =
-          (org.apache.axis.client.Call)super.service.createCall();
+      org.apache.axis.client.Call _call = (org.apache.axis.client.Call) super.service
+              .createCall();
       if (super.maintainSessionSet)
       {
         _call.setMaintainSession(super.maintainSession);
@@ -137,8 +132,8 @@ public class WSWUBlastSoapBindingStub
         {
           _call.setProperty(key, super.cachedProperties.get(key));
         }
-        //  else
-        //   _call.setScopedProperty(key, super.cachedProperties.get(key));
+        // else
+        // _call.setScopedProperty(key, super.cachedProperties.get(key));
       }
       // All the type mapping information is registered
       // when the first call is made.
@@ -154,27 +149,26 @@ public class WSWUBlastSoapBindingStub
           for (int i = 0; i < cachedSerFactories.size(); ++i)
           {
             java.lang.Class cls = (java.lang.Class) cachedSerClasses.get(i);
-            javax.xml.namespace.QName qName =
-                (javax.xml.namespace.QName) cachedSerQNames.get(i);
-            java.lang.Class sf = (java.lang.Class)
-                cachedSerFactories.get(i);
-            java.lang.Class df = (java.lang.Class)
-                cachedDeserFactories.get(i);
+            javax.xml.namespace.QName qName = (javax.xml.namespace.QName) cachedSerQNames
+                    .get(i);
+            java.lang.Class sf = (java.lang.Class) cachedSerFactories
+                    .get(i);
+            java.lang.Class df = (java.lang.Class) cachedDeserFactories
+                    .get(i);
             _call.registerTypeMapping(cls, qName, sf, df, false);
           }
         }
       }
       return _call;
-    }
-    catch (java.lang.Throwable t)
+    } catch (java.lang.Throwable t)
     {
       throw new org.apache.axis.AxisFault(
-          "Failure trying to get the Call object", t);
+              "Failure trying to get the Call object", t);
     }
   }
 
   public byte[] poll(java.lang.String jobid, java.lang.String type)
-      throws java.rmi.RemoteException
+          throws java.rmi.RemoteException
   {
     if (super.cachedEndpoint == null)
     {
@@ -182,25 +176,24 @@ public class WSWUBlastSoapBindingStub
     }
     org.apache.axis.client.Call _call = createCall();
     _call.addParameter(new javax.xml.namespace.QName("", "jobid"),
-                       new javax.
-                       xml.namespace.QName("http://www.w3.org/2001/XMLSchema",
-                                           "string"), java.lang.String.class,
-                       javax.xml.rpc.ParameterMode.IN);
+            new javax.xml.namespace.QName(
+                    "http://www.w3.org/2001/XMLSchema", "string"),
+            java.lang.String.class, javax.xml.rpc.ParameterMode.IN);
     _call.addParameter(new javax.xml.namespace.QName("", "type"),
-                       new javax.xml.
-                       namespace.QName("http://www.w3.org/2001/XMLSchema",
-                                       "string"), java.lang.String.class,
-                       javax.xml.rpc.ParameterMode.IN);
+            new javax.xml.namespace.QName(
+                    "http://www.w3.org/2001/XMLSchema", "string"),
+            java.lang.String.class, javax.xml.rpc.ParameterMode.IN);
     _call.setReturnType(new javax.xml.namespace.QName(
-        "http://www.w3.org/2001/XMLSchema", "base64Binary"), byte[].class);
+            "http://www.w3.org/2001/XMLSchema", "base64Binary"),
+            byte[].class);
     _call.setUseSOAPAction(true);
     _call.setSOAPActionURI("http://www.ebi.ac.uk/WSWUBlast#poll");
     _call.setOperationStyle("rpc");
     _call.setOperationName(new javax.xml.namespace.QName(
-        "http://www.ebi.ac.uk/WSWUBlast", "poll"));
+            "http://www.ebi.ac.uk/WSWUBlast", "poll"));
 
     java.lang.Object _resp = _call.invoke(new java.lang.Object[]
-                                          {jobid, type});
+    { jobid, type });
 
     if (_resp instanceof java.rmi.RemoteException)
     {
@@ -211,17 +204,16 @@ public class WSWUBlastSoapBindingStub
       try
       {
         return (byte[]) _resp;
-      }
-      catch (java.lang.Exception _exception)
+      } catch (java.lang.Exception _exception)
       {
-        return (byte[]) org.apache.axis.utils.JavaUtils.convert(_resp, byte[].class);
+        return (byte[]) org.apache.axis.utils.JavaUtils.convert(_resp,
+                byte[].class);
       }
     }
   }
 
   public java.lang.String runWUBlast(uk.ac.ebi.www.InputParams params,
-                                     uk.ac.ebi.www.Data[] content)
-      throws java.rmi.RemoteException
+          uk.ac.ebi.www.Data[] content) throws java.rmi.RemoteException
   {
     if (super.cachedEndpoint == null)
     {
@@ -229,26 +221,24 @@ public class WSWUBlastSoapBindingStub
     }
     org.apache.axis.client.Call _call = createCall();
     _call.addParameter(new javax.xml.namespace.QName("", "params"),
-                       new javax.
-                       xml.namespace.QName("http://www.ebi.ac.uk/WSWUBlast",
-                                           "inputParams"),
-                       uk.ac.ebi.www.InputParams.class,
-                       javax.xml.rpc.ParameterMode.IN);
+            new javax.xml.namespace.QName("http://www.ebi.ac.uk/WSWUBlast",
+                    "inputParams"), uk.ac.ebi.www.InputParams.class,
+            javax.xml.rpc.ParameterMode.IN);
     _call.addParameter(new javax.xml.namespace.QName("", "content"),
-                       new javax.
-                       xml.namespace.QName("http://www.ebi.ac.uk/WSWUBlast",
-                                           "WSArrayofData"), uk.ac.ebi.www.Data[].class,
-                       javax.xml.rpc.ParameterMode.IN);
+            new javax.xml.namespace.QName("http://www.ebi.ac.uk/WSWUBlast",
+                    "WSArrayofData"), uk.ac.ebi.www.Data[].class,
+            javax.xml.rpc.ParameterMode.IN);
     _call.setReturnType(new javax.xml.namespace.QName(
-        "http://www.w3.org/2001/XMLSchema", "string"), java.lang.String.class);
+            "http://www.w3.org/2001/XMLSchema", "string"),
+            java.lang.String.class);
     _call.setUseSOAPAction(true);
     _call.setSOAPActionURI("http://www.ebi.ac.uk/WSWUBlast#runWUBlast");
     _call.setOperationStyle("rpc");
     _call.setOperationName(new javax.xml.namespace.QName(
-        "http://www.ebi.ac.uk/WSWUBlast", "runWUBlast"));
+            "http://www.ebi.ac.uk/WSWUBlast", "runWUBlast"));
 
     java.lang.Object _resp = _call.invoke(new java.lang.Object[]
-                                          {params, content});
+    { params, content });
 
     if (_resp instanceof java.rmi.RemoteException)
     {
@@ -259,17 +249,16 @@ public class WSWUBlastSoapBindingStub
       try
       {
         return (java.lang.String) _resp;
-      }
-      catch (java.lang.Exception _exception)
+      } catch (java.lang.Exception _exception)
       {
-        return (java.lang.String) org.apache.axis.utils.JavaUtils.convert(_resp,
-            java.lang.String.class);
+        return (java.lang.String) org.apache.axis.utils.JavaUtils.convert(
+                _resp, java.lang.String.class);
       }
     }
   }
 
   public byte[] test(java.lang.String jobid, java.lang.String type)
-      throws java.rmi.RemoteException
+          throws java.rmi.RemoteException
   {
     if (super.cachedEndpoint == null)
     {
@@ -277,25 +266,24 @@ public class WSWUBlastSoapBindingStub
     }
     org.apache.axis.client.Call _call = createCall();
     _call.addParameter(new javax.xml.namespace.QName("", "jobid"),
-                       new javax.
-                       xml.namespace.QName("http://www.w3.org/2001/XMLSchema",
-                                           "string"), java.lang.String.class,
-                       javax.xml.rpc.ParameterMode.IN);
+            new javax.xml.namespace.QName(
+                    "http://www.w3.org/2001/XMLSchema", "string"),
+            java.lang.String.class, javax.xml.rpc.ParameterMode.IN);
     _call.addParameter(new javax.xml.namespace.QName("", "type"),
-                       new javax.xml.
-                       namespace.QName("http://www.w3.org/2001/XMLSchema",
-                                       "string"), java.lang.String.class,
-                       javax.xml.rpc.ParameterMode.IN);
+            new javax.xml.namespace.QName(
+                    "http://www.w3.org/2001/XMLSchema", "string"),
+            java.lang.String.class, javax.xml.rpc.ParameterMode.IN);
     _call.setReturnType(new javax.xml.namespace.QName(
-        "http://www.w3.org/2001/XMLSchema", "base64Binary"), byte[].class);
+            "http://www.w3.org/2001/XMLSchema", "base64Binary"),
+            byte[].class);
     _call.setUseSOAPAction(true);
     _call.setSOAPActionURI("http://www.ebi.ac.uk/WSWUBlast#test");
     _call.setOperationStyle("rpc");
     _call.setOperationName(new javax.xml.namespace.QName(
-        "http://www.ebi.ac.uk/WSWUBlast", "test"));
+            "http://www.ebi.ac.uk/WSWUBlast", "test"));
 
     java.lang.Object _resp = _call.invoke(new java.lang.Object[]
-                                          {jobid, type});
+    { jobid, type });
 
     if (_resp instanceof java.rmi.RemoteException)
     {
@@ -306,16 +294,16 @@ public class WSWUBlastSoapBindingStub
       try
       {
         return (byte[]) _resp;
-      }
-      catch (java.lang.Exception _exception)
+      } catch (java.lang.Exception _exception)
       {
-        return (byte[]) org.apache.axis.utils.JavaUtils.convert(_resp, byte[].class);
+        return (byte[]) org.apache.axis.utils.JavaUtils.convert(_resp,
+                byte[].class);
       }
     }
   }
 
   public java.lang.String checkStatus(java.lang.String jobid)
-      throws java.rmi.RemoteException
+          throws java.rmi.RemoteException
   {
     if (super.cachedEndpoint == null)
     {
@@ -323,20 +311,20 @@ public class WSWUBlastSoapBindingStub
     }
     org.apache.axis.client.Call _call = createCall();
     _call.addParameter(new javax.xml.namespace.QName("", "jobid"),
-                       new javax.
-                       xml.namespace.QName("http://www.w3.org/2001/XMLSchema",
-                                           "string"), java.lang.String.class,
-                       javax.xml.rpc.ParameterMode.IN);
+            new javax.xml.namespace.QName(
+                    "http://www.w3.org/2001/XMLSchema", "string"),
+            java.lang.String.class, javax.xml.rpc.ParameterMode.IN);
     _call.setReturnType(new javax.xml.namespace.QName(
-        "http://www.w3.org/2001/XMLSchema", "string"), java.lang.String.class);
+            "http://www.w3.org/2001/XMLSchema", "string"),
+            java.lang.String.class);
     _call.setUseSOAPAction(true);
     _call.setSOAPActionURI("http://www.ebi.ac.uk/WSWUBlast#checkStatus");
     _call.setOperationStyle("rpc");
     _call.setOperationName(new javax.xml.namespace.QName(
-        "http://www.ebi.ac.uk/WSWUBlast", "checkStatus"));
+            "http://www.ebi.ac.uk/WSWUBlast", "checkStatus"));
 
     java.lang.Object _resp = _call.invoke(new java.lang.Object[]
-                                          {jobid});
+    { jobid });
 
     if (_resp instanceof java.rmi.RemoteException)
     {
@@ -347,17 +335,16 @@ public class WSWUBlastSoapBindingStub
       try
       {
         return (java.lang.String) _resp;
-      }
-      catch (java.lang.Exception _exception)
+      } catch (java.lang.Exception _exception)
       {
-        return (java.lang.String) org.apache.axis.utils.JavaUtils.convert(_resp,
-            java.lang.String.class);
+        return (java.lang.String) org.apache.axis.utils.JavaUtils.convert(
+                _resp, java.lang.String.class);
       }
     }
   }
 
   public uk.ac.ebi.www.WSFile[] getResults(java.lang.String jobid)
-      throws java.rmi.RemoteException
+          throws java.rmi.RemoteException
   {
     if (super.cachedEndpoint == null)
     {
@@ -365,21 +352,20 @@ public class WSWUBlastSoapBindingStub
     }
     org.apache.axis.client.Call _call = createCall();
     _call.addParameter(new javax.xml.namespace.QName("", "jobid"),
-                       new javax.
-                       xml.namespace.QName("http://www.w3.org/2001/XMLSchema",
-                                           "string"), java.lang.String.class,
-                       javax.xml.rpc.ParameterMode.IN);
+            new javax.xml.namespace.QName(
+                    "http://www.w3.org/2001/XMLSchema", "string"),
+            java.lang.String.class, javax.xml.rpc.ParameterMode.IN);
     _call.setReturnType(new javax.xml.namespace.QName(
-        "http://www.ebi.ac.uk/WSWUBlast", "WSArrayofFile"),
-                        uk.ac.ebi.www.WSFile[].class);
+            "http://www.ebi.ac.uk/WSWUBlast", "WSArrayofFile"),
+            uk.ac.ebi.www.WSFile[].class);
     _call.setUseSOAPAction(true);
     _call.setSOAPActionURI("http://www.ebi.ac.uk/WSWUBlast#getResults");
     _call.setOperationStyle("rpc");
     _call.setOperationName(new javax.xml.namespace.QName(
-        "http://www.ebi.ac.uk/WSWUBlast", "getResults"));
+            "http://www.ebi.ac.uk/WSWUBlast", "getResults"));
 
     java.lang.Object _resp = _call.invoke(new java.lang.Object[]
-                                          {jobid});
+    { jobid });
 
     if (_resp instanceof java.rmi.RemoteException)
     {
@@ -390,17 +376,16 @@ public class WSWUBlastSoapBindingStub
       try
       {
         return (uk.ac.ebi.www.WSFile[]) _resp;
-      }
-      catch (java.lang.Exception _exception)
+      } catch (java.lang.Exception _exception)
       {
-        return (uk.ac.ebi.www.WSFile[]) org.apache.axis.utils.JavaUtils.convert(
-            _resp, uk.ac.ebi.www.WSFile[].class);
+        return (uk.ac.ebi.www.WSFile[]) org.apache.axis.utils.JavaUtils
+                .convert(_resp, uk.ac.ebi.www.WSFile[].class);
       }
     }
   }
 
   public byte[] polljob(java.lang.String jobid, java.lang.String outformat)
-      throws java.rmi.RemoteException
+          throws java.rmi.RemoteException
   {
     if (super.cachedEndpoint == null)
     {
@@ -408,26 +393,24 @@ public class WSWUBlastSoapBindingStub
     }
     org.apache.axis.client.Call _call = createCall();
     _call.addParameter(new javax.xml.namespace.QName("", "jobid"),
-                       new javax.
-                       xml.namespace.QName("http://www.w3.org/2001/XMLSchema",
-                                           "string"), java.lang.String.class,
-                       javax.xml.rpc.ParameterMode.IN);
+            new javax.xml.namespace.QName(
+                    "http://www.w3.org/2001/XMLSchema", "string"),
+            java.lang.String.class, javax.xml.rpc.ParameterMode.IN);
     _call.addParameter(new javax.xml.namespace.QName("", "outformat"),
-                       new
-                       javax.xml.namespace.QName(
-        "http://www.w3.org/2001/XMLSchema",
-        "string"), java.lang.String.class,
-                       javax.xml.rpc.ParameterMode.IN);
+            new javax.xml.namespace.QName(
+                    "http://www.w3.org/2001/XMLSchema", "string"),
+            java.lang.String.class, javax.xml.rpc.ParameterMode.IN);
     _call.setReturnType(new javax.xml.namespace.QName(
-        "http://www.w3.org/2001/XMLSchema", "base64Binary"), byte[].class);
+            "http://www.w3.org/2001/XMLSchema", "base64Binary"),
+            byte[].class);
     _call.setUseSOAPAction(true);
     _call.setSOAPActionURI("http://www.ebi.ac.uk/WSWUBlast#polljob");
     _call.setOperationStyle("rpc");
     _call.setOperationName(new javax.xml.namespace.QName(
-        "http://www.ebi.ac.uk/WSWUBlast", "polljob"));
+            "http://www.ebi.ac.uk/WSWUBlast", "polljob"));
 
     java.lang.Object _resp = _call.invoke(new java.lang.Object[]
-                                          {jobid, outformat});
+    { jobid, outformat });
 
     if (_resp instanceof java.rmi.RemoteException)
     {
@@ -438,16 +421,16 @@ public class WSWUBlastSoapBindingStub
       try
       {
         return (byte[]) _resp;
-      }
-      catch (java.lang.Exception _exception)
+      } catch (java.lang.Exception _exception)
       {
-        return (byte[]) org.apache.axis.utils.JavaUtils.convert(_resp, byte[].class);
+        return (byte[]) org.apache.axis.utils.JavaUtils.convert(_resp,
+                byte[].class);
       }
     }
   }
 
   public byte[] doWUBlast(uk.ac.ebi.www.InputParams params, byte[] content)
-      throws java.rmi.RemoteException
+          throws java.rmi.RemoteException
   {
     if (super.cachedEndpoint == null)
     {
@@ -455,26 +438,24 @@ public class WSWUBlastSoapBindingStub
     }
     org.apache.axis.client.Call _call = createCall();
     _call.addParameter(new javax.xml.namespace.QName("", "params"),
-                       new javax.
-                       xml.namespace.QName("http://www.ebi.ac.uk/WSWUBlast",
-                                           "inputParams"),
-                       uk.ac.ebi.www.InputParams.class,
-                       javax.xml.rpc.ParameterMode.IN);
+            new javax.xml.namespace.QName("http://www.ebi.ac.uk/WSWUBlast",
+                    "inputParams"), uk.ac.ebi.www.InputParams.class,
+            javax.xml.rpc.ParameterMode.IN);
     _call.addParameter(new javax.xml.namespace.QName("", "content"),
-                       new javax.
-                       xml.namespace.QName("http://www.w3.org/2001/XMLSchema",
-                                           "base64Binary"), byte[].class,
-                       javax.xml.rpc.ParameterMode.IN);
+            new javax.xml.namespace.QName(
+                    "http://www.w3.org/2001/XMLSchema", "base64Binary"),
+            byte[].class, javax.xml.rpc.ParameterMode.IN);
     _call.setReturnType(new javax.xml.namespace.QName(
-        "http://www.w3.org/2001/XMLSchema", "base64Binary"), byte[].class);
+            "http://www.w3.org/2001/XMLSchema", "base64Binary"),
+            byte[].class);
     _call.setUseSOAPAction(true);
     _call.setSOAPActionURI("http://www.ebi.ac.uk/WSWUBlast#doWUBlast");
     _call.setOperationStyle("rpc");
     _call.setOperationName(new javax.xml.namespace.QName(
-        "http://www.ebi.ac.uk/WSWUBlast", "doWUBlast"));
+            "http://www.ebi.ac.uk/WSWUBlast", "doWUBlast"));
 
     java.lang.Object _resp = _call.invoke(new java.lang.Object[]
-                                          {params, content});
+    { params, content });
 
     if (_resp instanceof java.rmi.RemoteException)
     {
@@ -485,10 +466,10 @@ public class WSWUBlastSoapBindingStub
       try
       {
         return (byte[]) _resp;
-      }
-      catch (java.lang.Exception _exception)
+      } catch (java.lang.Exception _exception)
       {
-        return (byte[]) org.apache.axis.utils.JavaUtils.convert(_resp, byte[].class);
+        return (byte[]) org.apache.axis.utils.JavaUtils.convert(_resp,
+                byte[].class);
       }
     }
   }
diff --git a/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperBindingStub.java b/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperBindingStub.java
index e31f288..ed401ad 100644
--- a/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperBindingStub.java
+++ b/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperBindingStub.java
@@ -7,248 +7,384 @@
 
 package uk.ac.ebi.www.picr.AccessionMappingService;
 
-public class AccessionMapperBindingStub extends org.apache.axis.client.Stub implements uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperInterface {
-    private java.util.Vector cachedSerClasses = new java.util.Vector();
-    private java.util.Vector cachedSerQNames = new java.util.Vector();
-    private java.util.Vector cachedSerFactories = new java.util.Vector();
-    private java.util.Vector cachedDeserFactories = new java.util.Vector();
-
-    static org.apache.axis.description.OperationDesc [] _operations;
-
-    static {
-        _operations = new org.apache.axis.description.OperationDesc[3];
-        _initOperationDesc1();
-    }
-
-    private static void _initOperationDesc1(){
-        org.apache.axis.description.OperationDesc oper;
-        oper = new org.apache.axis.description.OperationDesc();
-        oper.setName("getUPIForSequence");
-        oper.addParameter(new javax.xml.namespace.QName("http://www.ebi.ac.uk/picr/AccessionMappingService", "sequence"), new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"), java.lang.String.class, org.apache.axis.description.ParameterDesc.IN, false, false);
-        oper.addParameter(new javax.xml.namespace.QName("http://www.ebi.ac.uk/picr/AccessionMappingService", "searchDatabases"), new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"), java.lang.String[].class, org.apache.axis.description.ParameterDesc.IN, false, false);
-        oper.addParameter(new javax.xml.namespace.QName("http://www.ebi.ac.uk/picr/AccessionMappingService", "taxonId"), new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"), java.lang.String.class, org.apache.axis.description.ParameterDesc.IN, false, false);
-        oper.addParameter(new javax.xml.namespace.QName("http://www.ebi.ac.uk/picr/AccessionMappingService", "onlyActive"), new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"), boolean.class, org.apache.axis.description.ParameterDesc.IN, false, false);
-        oper.setReturnType(new javax.xml.namespace.QName("http://model.picr.ebi.ac.uk", "UPEntry"));
-        oper.setReturnClass(uk.ac.ebi.picr.model.UPEntry.class);
-        oper.setReturnQName(new javax.xml.namespace.QName("http://www.ebi.ac.uk/picr/AccessionMappingService", "getUPIForSequenceReturn"));
-        oper.setStyle(org.apache.axis.constants.Style.WRAPPED);
-        oper.setUse(org.apache.axis.constants.Use.LITERAL);
-        _operations[0] = oper;
-
-        oper = new org.apache.axis.description.OperationDesc();
-        oper.setName("getUPIForAccession");
-        oper.addParameter(new javax.xml.namespace.QName("http://www.ebi.ac.uk/picr/AccessionMappingService", "accession"), new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"), java.lang.String.class, org.apache.axis.description.ParameterDesc.IN, false, false);
-        oper.addParameter(new javax.xml.namespace.QName("http://www.ebi.ac.uk/picr/AccessionMappingService", "ac_version"), new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"), java.lang.String.class, org.apache.axis.description.ParameterDesc.IN, false, false);
-        oper.addParameter(new javax.xml.namespace.QName("http://www.ebi.ac.uk/picr/AccessionMappingService", "searchDatabases"), new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"), java.lang.String[].class, org.apache.axis.description.ParameterDesc.IN, false, false);
-        oper.addParameter(new javax.xml.namespace.QName("http://www.ebi.ac.uk/picr/AccessionMappingService", "taxonId"), new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"), java.lang.String.class, org.apache.axis.description.ParameterDesc.IN, false, false);
-        oper.addParameter(new javax.xml.namespace.QName("http://www.ebi.ac.uk/picr/AccessionMappingService", "onlyActive"), new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"), boolean.class, org.apache.axis.description.ParameterDesc.IN, false, false);
-        oper.setReturnType(new javax.xml.namespace.QName("http://model.picr.ebi.ac.uk", "UPEntry"));
-        oper.setReturnClass(uk.ac.ebi.picr.model.UPEntry[].class);
-        oper.setReturnQName(new javax.xml.namespace.QName("http://www.ebi.ac.uk/picr/AccessionMappingService", "getUPIForAccessionReturn"));
-        oper.setStyle(org.apache.axis.constants.Style.WRAPPED);
-        oper.setUse(org.apache.axis.constants.Use.LITERAL);
-        _operations[1] = oper;
-
-        oper = new org.apache.axis.description.OperationDesc();
-        oper.setName("getMappedDatabaseNames");
-        oper.setReturnType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
-        oper.setReturnClass(java.lang.String[].class);
-        oper.setReturnQName(new javax.xml.namespace.QName("http://www.ebi.ac.uk/picr/AccessionMappingService", "mappedDatabases"));
-        oper.setStyle(org.apache.axis.constants.Style.WRAPPED);
-        oper.setUse(org.apache.axis.constants.Use.LITERAL);
-        _operations[2] = oper;
+public class AccessionMapperBindingStub extends org.apache.axis.client.Stub
+        implements
+        uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperInterface
+{
+  private java.util.Vector cachedSerClasses = new java.util.Vector();
 
+  private java.util.Vector cachedSerQNames = new java.util.Vector();
+
+  private java.util.Vector cachedSerFactories = new java.util.Vector();
+
+  private java.util.Vector cachedDeserFactories = new java.util.Vector();
+
+  static org.apache.axis.description.OperationDesc[] _operations;
+
+  static
+  {
+    _operations = new org.apache.axis.description.OperationDesc[3];
+    _initOperationDesc1();
+  }
+
+  private static void _initOperationDesc1()
+  {
+    org.apache.axis.description.OperationDesc oper;
+    oper = new org.apache.axis.description.OperationDesc();
+    oper.setName("getUPIForSequence");
+    oper.addParameter(
+            new javax.xml.namespace.QName(
+                    "http://www.ebi.ac.uk/picr/AccessionMappingService",
+                    "sequence"), new javax.xml.namespace.QName(
+                    "http://www.w3.org/2001/XMLSchema", "string"),
+            java.lang.String.class,
+            org.apache.axis.description.ParameterDesc.IN, false, false);
+    oper.addParameter(new javax.xml.namespace.QName(
+            "http://www.ebi.ac.uk/picr/AccessionMappingService",
+            "searchDatabases"), new javax.xml.namespace.QName(
+            "http://www.w3.org/2001/XMLSchema", "string"),
+            java.lang.String[].class,
+            org.apache.axis.description.ParameterDesc.IN, false, false);
+    oper.addParameter(
+            new javax.xml.namespace.QName(
+                    "http://www.ebi.ac.uk/picr/AccessionMappingService",
+                    "taxonId"), new javax.xml.namespace.QName(
+                    "http://www.w3.org/2001/XMLSchema", "string"),
+            java.lang.String.class,
+            org.apache.axis.description.ParameterDesc.IN, false, false);
+    oper.addParameter(new javax.xml.namespace.QName(
+            "http://www.ebi.ac.uk/picr/AccessionMappingService",
+            "onlyActive"), new javax.xml.namespace.QName(
+            "http://www.w3.org/2001/XMLSchema", "boolean"), boolean.class,
+            org.apache.axis.description.ParameterDesc.IN, false, false);
+    oper.setReturnType(new javax.xml.namespace.QName(
+            "http://model.picr.ebi.ac.uk", "UPEntry"));
+    oper.setReturnClass(uk.ac.ebi.picr.model.UPEntry.class);
+    oper.setReturnQName(new javax.xml.namespace.QName(
+            "http://www.ebi.ac.uk/picr/AccessionMappingService",
+            "getUPIForSequenceReturn"));
+    oper.setStyle(org.apache.axis.constants.Style.WRAPPED);
+    oper.setUse(org.apache.axis.constants.Use.LITERAL);
+    _operations[0] = oper;
+
+    oper = new org.apache.axis.description.OperationDesc();
+    oper.setName("getUPIForAccession");
+    oper.addParameter(new javax.xml.namespace.QName(
+            "http://www.ebi.ac.uk/picr/AccessionMappingService",
+            "accession"), new javax.xml.namespace.QName(
+            "http://www.w3.org/2001/XMLSchema", "string"),
+            java.lang.String.class,
+            org.apache.axis.description.ParameterDesc.IN, false, false);
+    oper.addParameter(new javax.xml.namespace.QName(
+            "http://www.ebi.ac.uk/picr/AccessionMappingService",
+            "ac_version"), new javax.xml.namespace.QName(
+            "http://www.w3.org/2001/XMLSchema", "string"),
+            java.lang.String.class,
+            org.apache.axis.description.ParameterDesc.IN, false, false);
+    oper.addParameter(new javax.xml.namespace.QName(
+            "http://www.ebi.ac.uk/picr/AccessionMappingService",
+            "searchDatabases"), new javax.xml.namespace.QName(
+            "http://www.w3.org/2001/XMLSchema", "string"),
+            java.lang.String[].class,
+            org.apache.axis.description.ParameterDesc.IN, false, false);
+    oper.addParameter(
+            new javax.xml.namespace.QName(
+                    "http://www.ebi.ac.uk/picr/AccessionMappingService",
+                    "taxonId"), new javax.xml.namespace.QName(
+                    "http://www.w3.org/2001/XMLSchema", "string"),
+            java.lang.String.class,
+            org.apache.axis.description.ParameterDesc.IN, false, false);
+    oper.addParameter(new javax.xml.namespace.QName(
+            "http://www.ebi.ac.uk/picr/AccessionMappingService",
+            "onlyActive"), new javax.xml.namespace.QName(
+            "http://www.w3.org/2001/XMLSchema", "boolean"), boolean.class,
+            org.apache.axis.description.ParameterDesc.IN, false, false);
+    oper.setReturnType(new javax.xml.namespace.QName(
+            "http://model.picr.ebi.ac.uk", "UPEntry"));
+    oper.setReturnClass(uk.ac.ebi.picr.model.UPEntry[].class);
+    oper.setReturnQName(new javax.xml.namespace.QName(
+            "http://www.ebi.ac.uk/picr/AccessionMappingService",
+            "getUPIForAccessionReturn"));
+    oper.setStyle(org.apache.axis.constants.Style.WRAPPED);
+    oper.setUse(org.apache.axis.constants.Use.LITERAL);
+    _operations[1] = oper;
+
+    oper = new org.apache.axis.description.OperationDesc();
+    oper.setName("getMappedDatabaseNames");
+    oper.setReturnType(new javax.xml.namespace.QName(
+            "http://www.w3.org/2001/XMLSchema", "string"));
+    oper.setReturnClass(java.lang.String[].class);
+    oper.setReturnQName(new javax.xml.namespace.QName(
+            "http://www.ebi.ac.uk/picr/AccessionMappingService",
+            "mappedDatabases"));
+    oper.setStyle(org.apache.axis.constants.Style.WRAPPED);
+    oper.setUse(org.apache.axis.constants.Use.LITERAL);
+    _operations[2] = oper;
+
+  }
+
+  public AccessionMapperBindingStub() throws org.apache.axis.AxisFault
+  {
+    this(null);
+  }
+
+  public AccessionMapperBindingStub(java.net.URL endpointURL,
+          javax.xml.rpc.Service service) throws org.apache.axis.AxisFault
+  {
+    this(service);
+    super.cachedEndpoint = endpointURL;
+  }
+
+  public AccessionMapperBindingStub(javax.xml.rpc.Service service)
+          throws org.apache.axis.AxisFault
+  {
+    if (service == null)
+    {
+      super.service = new org.apache.axis.client.Service();
+    }
+    else
+    {
+      super.service = service;
     }
+    java.lang.Class cls;
+    javax.xml.namespace.QName qName;
+    java.lang.Class beansf = org.apache.axis.encoding.ser.BeanSerializerFactory.class;
+    java.lang.Class beandf = org.apache.axis.encoding.ser.BeanDeserializerFactory.class;
+    java.lang.Class enumsf = org.apache.axis.encoding.ser.EnumSerializerFactory.class;
+    java.lang.Class enumdf = org.apache.axis.encoding.ser.EnumDeserializerFactory.class;
+    java.lang.Class arraysf = org.apache.axis.encoding.ser.ArraySerializerFactory.class;
+    java.lang.Class arraydf = org.apache.axis.encoding.ser.ArrayDeserializerFactory.class;
+    java.lang.Class simplesf = org.apache.axis.encoding.ser.SimpleSerializerFactory.class;
+    java.lang.Class simpledf = org.apache.axis.encoding.ser.SimpleDeserializerFactory.class;
+    java.lang.Class simplelistsf = org.apache.axis.encoding.ser.SimpleListSerializerFactory.class;
+    java.lang.Class simplelistdf = org.apache.axis.encoding.ser.SimpleListDeserializerFactory.class;
+    qName = new javax.xml.namespace.QName("http://model.picr.ebi.ac.uk",
+            "UPEntry");
+    cachedSerQNames.add(qName);
+    cls = uk.ac.ebi.picr.model.UPEntry.class;
+    cachedSerClasses.add(cls);
+    cachedSerFactories.add(beansf);
+    cachedDeserFactories.add(beandf);
 
-    public AccessionMapperBindingStub() throws org.apache.axis.AxisFault {
-         this(null);
+    qName = new javax.xml.namespace.QName("http://model.picr.ebi.ac.uk",
+            "CrossReference");
+    cachedSerQNames.add(qName);
+    cls = uk.ac.ebi.picr.model.CrossReference.class;
+    cachedSerClasses.add(cls);
+    cachedSerFactories.add(beansf);
+    cachedDeserFactories.add(beandf);
+
+  }
+
+  protected org.apache.axis.client.Call createCall()
+          throws java.rmi.RemoteException
+  {
+    try
+    {
+      org.apache.axis.client.Call _call = (org.apache.axis.client.Call) super.service
+              .createCall();
+      if (super.maintainSessionSet)
+      {
+        _call.setMaintainSession(super.maintainSession);
+      }
+      if (super.cachedUsername != null)
+      {
+        _call.setUsername(super.cachedUsername);
+      }
+      if (super.cachedPassword != null)
+      {
+        _call.setPassword(super.cachedPassword);
+      }
+      if (super.cachedEndpoint != null)
+      {
+        _call.setTargetEndpointAddress(super.cachedEndpoint);
+      }
+      if (super.cachedTimeout != null)
+      {
+        _call.setTimeout(super.cachedTimeout);
+      }
+      if (super.cachedPortName != null)
+      {
+        _call.setPortName(super.cachedPortName);
+      }
+      java.util.Enumeration keys = super.cachedProperties.keys();
+      while (keys.hasMoreElements())
+      {
+        java.lang.String key = (java.lang.String) keys.nextElement();
+        _call.setProperty(key, super.cachedProperties.get(key));
+      }
+      // All the type mapping information is registered
+      // when the first call is made.
+      // The type mapping information is actually registered in
+      // the TypeMappingRegistry of the service, which
+      // is the reason why registration is only needed for the first call.
+      synchronized (this)
+      {
+        if (firstCall())
+        {
+          // must set encoding style before registering serializers
+          _call.setEncodingStyle(null);
+          for (int i = 0; i < cachedSerFactories.size(); ++i)
+          {
+            java.lang.Class cls = (java.lang.Class) cachedSerClasses.get(i);
+            javax.xml.namespace.QName qName = (javax.xml.namespace.QName) cachedSerQNames
+                    .get(i);
+            java.lang.Class sf = (java.lang.Class) cachedSerFactories
+                    .get(i);
+            java.lang.Class df = (java.lang.Class) cachedDeserFactories
+                    .get(i);
+            _call.registerTypeMapping(cls, qName, sf, df, false);
+          }
+        }
+      }
+      return _call;
+    } catch (java.lang.Throwable _t)
+    {
+      throw new org.apache.axis.AxisFault(
+              "Failure trying to get the Call object", _t);
     }
+  }
 
-    public AccessionMapperBindingStub(java.net.URL endpointURL, javax.xml.rpc.Service service) throws org.apache.axis.AxisFault {
-         this(service);
-         super.cachedEndpoint = endpointURL;
+  public uk.ac.ebi.picr.model.UPEntry getUPIForSequence(
+          java.lang.String sequence, java.lang.String[] searchDatabases,
+          java.lang.String taxonId, boolean onlyActive)
+          throws java.rmi.RemoteException
+  {
+    if (super.cachedEndpoint == null)
+    {
+      throw new org.apache.axis.NoEndPointException();
     }
+    org.apache.axis.client.Call _call = createCall();
+    _call.setOperation(_operations[0]);
+    _call.setUseSOAPAction(true);
+    _call.setSOAPActionURI("getUPIForSequence");
+    _call.setEncodingStyle(null);
+    _call.setProperty(org.apache.axis.client.Call.SEND_TYPE_ATTR,
+            Boolean.FALSE);
+    _call.setProperty(org.apache.axis.AxisEngine.PROP_DOMULTIREFS,
+            Boolean.FALSE);
+    _call
+            .setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+    _call.setOperationName(new javax.xml.namespace.QName(
+            "http://www.ebi.ac.uk/picr/AccessionMappingService",
+            "getUPIForSequence"));
 
-    public AccessionMapperBindingStub(javax.xml.rpc.Service service) throws org.apache.axis.AxisFault {
-        if (service == null) {
-            super.service = new org.apache.axis.client.Service();
-        } else {
-            super.service = service;
-        }
-            java.lang.Class cls;
-            javax.xml.namespace.QName qName;
-            java.lang.Class beansf = org.apache.axis.encoding.ser.BeanSerializerFactory.class;
-            java.lang.Class beandf = org.apache.axis.encoding.ser.BeanDeserializerFactory.class;
-            java.lang.Class enumsf = org.apache.axis.encoding.ser.EnumSerializerFactory.class;
-            java.lang.Class enumdf = org.apache.axis.encoding.ser.EnumDeserializerFactory.class;
-            java.lang.Class arraysf = org.apache.axis.encoding.ser.ArraySerializerFactory.class;
-            java.lang.Class arraydf = org.apache.axis.encoding.ser.ArrayDeserializerFactory.class;
-            java.lang.Class simplesf = org.apache.axis.encoding.ser.SimpleSerializerFactory.class;
-            java.lang.Class simpledf = org.apache.axis.encoding.ser.SimpleDeserializerFactory.class;
-            java.lang.Class simplelistsf = org.apache.axis.encoding.ser.SimpleListSerializerFactory.class;
-            java.lang.Class simplelistdf = org.apache.axis.encoding.ser.SimpleListDeserializerFactory.class;
-            qName = new javax.xml.namespace.QName("http://model.picr.ebi.ac.uk", "UPEntry");
-            cachedSerQNames.add(qName);
-            cls = uk.ac.ebi.picr.model.UPEntry.class;
-            cachedSerClasses.add(cls);
-            cachedSerFactories.add(beansf);
-            cachedDeserFactories.add(beandf);
-
-            qName = new javax.xml.namespace.QName("http://model.picr.ebi.ac.uk", "CrossReference");
-            cachedSerQNames.add(qName);
-            cls = uk.ac.ebi.picr.model.CrossReference.class;
-            cachedSerClasses.add(cls);
-            cachedSerFactories.add(beansf);
-            cachedDeserFactories.add(beandf);
+    setRequestHeaders(_call);
+    setAttachments(_call);
+    java.lang.Object _resp = _call
+            .invoke(new java.lang.Object[]
+            { sequence, searchDatabases, taxonId,
+                new java.lang.Boolean(onlyActive) });
 
+    if (_resp instanceof java.rmi.RemoteException)
+    {
+      throw (java.rmi.RemoteException) _resp;
     }
+    else
+    {
+      extractAttachments(_call);
+      try
+      {
+        return (uk.ac.ebi.picr.model.UPEntry) _resp;
+      } catch (java.lang.Exception _exception)
+      {
+        return (uk.ac.ebi.picr.model.UPEntry) org.apache.axis.utils.JavaUtils
+                .convert(_resp, uk.ac.ebi.picr.model.UPEntry.class);
+      }
+    }
+  }
 
-    protected org.apache.axis.client.Call createCall() throws java.rmi.RemoteException {
-        try {
-            org.apache.axis.client.Call _call =
-                    (org.apache.axis.client.Call) super.service.createCall();
-            if (super.maintainSessionSet) {
-                _call.setMaintainSession(super.maintainSession);
-            }
-            if (super.cachedUsername != null) {
-                _call.setUsername(super.cachedUsername);
-            }
-            if (super.cachedPassword != null) {
-                _call.setPassword(super.cachedPassword);
-            }
-            if (super.cachedEndpoint != null) {
-                _call.setTargetEndpointAddress(super.cachedEndpoint);
-            }
-            if (super.cachedTimeout != null) {
-                _call.setTimeout(super.cachedTimeout);
-            }
-            if (super.cachedPortName != null) {
-                _call.setPortName(super.cachedPortName);
-            }
-            java.util.Enumeration keys = super.cachedProperties.keys();
-            while (keys.hasMoreElements()) {
-                java.lang.String key = (java.lang.String) keys.nextElement();
-                _call.setProperty(key, super.cachedProperties.get(key));
-            }
-            // All the type mapping information is registered
-            // when the first call is made.
-            // The type mapping information is actually registered in
-            // the TypeMappingRegistry of the service, which
-            // is the reason why registration is only needed for the first call.
-            synchronized (this) {
-                if (firstCall()) {
-                    // must set encoding style before registering serializers
-                    _call.setEncodingStyle(null);
-                    for (int i = 0; i < cachedSerFactories.size(); ++i) {
-                        java.lang.Class cls = (java.lang.Class) cachedSerClasses.get(i);
-                        javax.xml.namespace.QName qName =
-                                (javax.xml.namespace.QName) cachedSerQNames.get(i);
-                        java.lang.Class sf = (java.lang.Class)
-                                 cachedSerFactories.get(i);
-                        java.lang.Class df = (java.lang.Class)
-                                 cachedDeserFactories.get(i);
-                        _call.registerTypeMapping(cls, qName, sf, df, false);
-                    }
-                }
-            }
-            return _call;
-        }
-        catch (java.lang.Throwable _t) {
-            throw new org.apache.axis.AxisFault("Failure trying to get the Call object", _t);
-        }
+  public uk.ac.ebi.picr.model.UPEntry[] getUPIForAccession(
+          java.lang.String accession, java.lang.String ac_version,
+          java.lang.String[] searchDatabases, java.lang.String taxonId,
+          boolean onlyActive) throws java.rmi.RemoteException
+  {
+    if (super.cachedEndpoint == null)
+    {
+      throw new org.apache.axis.NoEndPointException();
     }
+    org.apache.axis.client.Call _call = createCall();
+    _call.setOperation(_operations[1]);
+    _call.setUseSOAPAction(true);
+    _call.setSOAPActionURI("getUPIForAccession");
+    _call.setEncodingStyle(null);
+    _call.setProperty(org.apache.axis.client.Call.SEND_TYPE_ATTR,
+            Boolean.FALSE);
+    _call.setProperty(org.apache.axis.AxisEngine.PROP_DOMULTIREFS,
+            Boolean.FALSE);
+    _call
+            .setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+    _call.setOperationName(new javax.xml.namespace.QName(
+            "http://www.ebi.ac.uk/picr/AccessionMappingService",
+            "getUPIForAccession"));
 
-    public uk.ac.ebi.picr.model.UPEntry getUPIForSequence(java.lang.String sequence, java.lang.String[] searchDatabases, java.lang.String taxonId, boolean onlyActive) throws java.rmi.RemoteException {
-        if (super.cachedEndpoint == null) {
-            throw new org.apache.axis.NoEndPointException();
-        }
-        org.apache.axis.client.Call _call = createCall();
-        _call.setOperation(_operations[0]);
-        _call.setUseSOAPAction(true);
-        _call.setSOAPActionURI("getUPIForSequence");
-        _call.setEncodingStyle(null);
-        _call.setProperty(org.apache.axis.client.Call.SEND_TYPE_ATTR, Boolean.FALSE);
-        _call.setProperty(org.apache.axis.AxisEngine.PROP_DOMULTIREFS, Boolean.FALSE);
-        _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
-        _call.setOperationName(new javax.xml.namespace.QName("http://www.ebi.ac.uk/picr/AccessionMappingService", "getUPIForSequence"));
-
-        setRequestHeaders(_call);
-        setAttachments(_call);
-        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {sequence, searchDatabases, taxonId, new java.lang.Boolean(onlyActive)});
-
-        if (_resp instanceof java.rmi.RemoteException) {
-            throw (java.rmi.RemoteException)_resp;
-        }
-        else {
-            extractAttachments(_call);
-            try {
-                return (uk.ac.ebi.picr.model.UPEntry) _resp;
-            } catch (java.lang.Exception _exception) {
-                return (uk.ac.ebi.picr.model.UPEntry) org.apache.axis.utils.JavaUtils.convert(_resp, uk.ac.ebi.picr.model.UPEntry.class);
-            }
-        }
+    setRequestHeaders(_call);
+    setAttachments(_call);
+    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
+    { accession, ac_version, searchDatabases, taxonId,
+        new java.lang.Boolean(onlyActive) });
+
+    if (_resp instanceof java.rmi.RemoteException)
+    {
+      throw (java.rmi.RemoteException) _resp;
+    }
+    else
+    {
+      extractAttachments(_call);
+      try
+      {
+        return (uk.ac.ebi.picr.model.UPEntry[]) _resp;
+      } catch (java.lang.Exception _exception)
+      {
+        return (uk.ac.ebi.picr.model.UPEntry[]) org.apache.axis.utils.JavaUtils
+                .convert(_resp, uk.ac.ebi.picr.model.UPEntry[].class);
+      }
     }
+  }
 
-    public uk.ac.ebi.picr.model.UPEntry[] getUPIForAccession(java.lang.String accession, java.lang.String ac_version, java.lang.String[] searchDatabases, java.lang.String taxonId, boolean onlyActive) throws java.rmi.RemoteException {
-        if (super.cachedEndpoint == null) {
-            throw new org.apache.axis.NoEndPointException();
-        }
-        org.apache.axis.client.Call _call = createCall();
-        _call.setOperation(_operations[1]);
-        _call.setUseSOAPAction(true);
-        _call.setSOAPActionURI("getUPIForAccession");
-        _call.setEncodingStyle(null);
-        _call.setProperty(org.apache.axis.client.Call.SEND_TYPE_ATTR, Boolean.FALSE);
-        _call.setProperty(org.apache.axis.AxisEngine.PROP_DOMULTIREFS, Boolean.FALSE);
-        _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
-        _call.setOperationName(new javax.xml.namespace.QName("http://www.ebi.ac.uk/picr/AccessionMappingService", "getUPIForAccession"));
-
-        setRequestHeaders(_call);
-        setAttachments(_call);
-        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {accession, ac_version, searchDatabases, taxonId, new java.lang.Boolean(onlyActive)});
-
-        if (_resp instanceof java.rmi.RemoteException) {
-            throw (java.rmi.RemoteException)_resp;
-        }
-        else {
-            extractAttachments(_call);
-            try {
-                return (uk.ac.ebi.picr.model.UPEntry[]) _resp;
-            } catch (java.lang.Exception _exception) {
-                return (uk.ac.ebi.picr.model.UPEntry[]) org.apache.axis.utils.JavaUtils.convert(_resp, uk.ac.ebi.picr.model.UPEntry[].class);
-            }
-        }
+  public java.lang.String[] getMappedDatabaseNames()
+          throws java.rmi.RemoteException
+  {
+    if (super.cachedEndpoint == null)
+    {
+      throw new org.apache.axis.NoEndPointException();
     }
+    org.apache.axis.client.Call _call = createCall();
+    _call.setOperation(_operations[2]);
+    _call.setUseSOAPAction(true);
+    _call.setSOAPActionURI("getMappedDatabaseNames");
+    _call.setEncodingStyle(null);
+    _call.setProperty(org.apache.axis.client.Call.SEND_TYPE_ATTR,
+            Boolean.FALSE);
+    _call.setProperty(org.apache.axis.AxisEngine.PROP_DOMULTIREFS,
+            Boolean.FALSE);
+    _call
+            .setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+    _call.setOperationName(new javax.xml.namespace.QName(
+            "http://www.ebi.ac.uk/picr/AccessionMappingService",
+            "getMappedDatabaseNames"));
 
-    public java.lang.String[] getMappedDatabaseNames() throws java.rmi.RemoteException {
-        if (super.cachedEndpoint == null) {
-            throw new org.apache.axis.NoEndPointException();
-        }
-        org.apache.axis.client.Call _call = createCall();
-        _call.setOperation(_operations[2]);
-        _call.setUseSOAPAction(true);
-        _call.setSOAPActionURI("getMappedDatabaseNames");
-        _call.setEncodingStyle(null);
-        _call.setProperty(org.apache.axis.client.Call.SEND_TYPE_ATTR, Boolean.FALSE);
-        _call.setProperty(org.apache.axis.AxisEngine.PROP_DOMULTIREFS, Boolean.FALSE);
-        _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
-        _call.setOperationName(new javax.xml.namespace.QName("http://www.ebi.ac.uk/picr/AccessionMappingService", "getMappedDatabaseNames"));
-
-        setRequestHeaders(_call);
-        setAttachments(_call);
-        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {});
-
-        if (_resp instanceof java.rmi.RemoteException) {
-            throw (java.rmi.RemoteException)_resp;
-        }
-        else {
-            extractAttachments(_call);
-            try {
-                return (java.lang.String[]) _resp;
-            } catch (java.lang.Exception _exception) {
-                return (java.lang.String[]) org.apache.axis.utils.JavaUtils.convert(_resp, java.lang.String[].class);
-            }
-        }
+    setRequestHeaders(_call);
+    setAttachments(_call);
+    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
+    {});
+
+    if (_resp instanceof java.rmi.RemoteException)
+    {
+      throw (java.rmi.RemoteException) _resp;
+    }
+    else
+    {
+      extractAttachments(_call);
+      try
+      {
+        return (java.lang.String[]) _resp;
+      } catch (java.lang.Exception _exception)
+      {
+        return (java.lang.String[]) org.apache.axis.utils.JavaUtils
+                .convert(_resp, java.lang.String[].class);
+      }
     }
+  }
 
 }
diff --git a/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperInterface.java b/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperInterface.java
index 9ddf349..faf327b 100644
--- a/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperInterface.java
+++ b/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperInterface.java
@@ -7,8 +7,18 @@
 
 package uk.ac.ebi.www.picr.AccessionMappingService;
 
-public interface AccessionMapperInterface extends java.rmi.Remote {
-    public uk.ac.ebi.picr.model.UPEntry getUPIForSequence(java.lang.String sequence, java.lang.String[] searchDatabases, java.lang.String taxonId, boolean onlyActive) throws java.rmi.RemoteException;
-    public uk.ac.ebi.picr.model.UPEntry[] getUPIForAccession(java.lang.String accession, java.lang.String ac_version, java.lang.String[] searchDatabases, java.lang.String taxonId, boolean onlyActive) throws java.rmi.RemoteException;
-    public java.lang.String[] getMappedDatabaseNames() throws java.rmi.RemoteException;
+public interface AccessionMapperInterface extends java.rmi.Remote
+{
+  public uk.ac.ebi.picr.model.UPEntry getUPIForSequence(
+          java.lang.String sequence, java.lang.String[] searchDatabases,
+          java.lang.String taxonId, boolean onlyActive)
+          throws java.rmi.RemoteException;
+
+  public uk.ac.ebi.picr.model.UPEntry[] getUPIForAccession(
+          java.lang.String accession, java.lang.String ac_version,
+          java.lang.String[] searchDatabases, java.lang.String taxonId,
+          boolean onlyActive) throws java.rmi.RemoteException;
+
+  public java.lang.String[] getMappedDatabaseNames()
+          throws java.rmi.RemoteException;
 }
diff --git a/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperService.java b/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperService.java
index 1f08f84..a234689 100644
--- a/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperService.java
+++ b/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperService.java
@@ -7,10 +7,13 @@
 
 package uk.ac.ebi.www.picr.AccessionMappingService;
 
-public interface AccessionMapperService extends javax.xml.rpc.Service {
-    public java.lang.String getAccessionMapperPortAddress();
+public interface AccessionMapperService extends javax.xml.rpc.Service
+{
+  public java.lang.String getAccessionMapperPortAddress();
 
-    public uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperInterface getAccessionMapperPort() throws javax.xml.rpc.ServiceException;
+  public uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperInterface getAccessionMapperPort()
+          throws javax.xml.rpc.ServiceException;
 
-    public uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperInterface getAccessionMapperPort(java.net.URL portAddress) throws javax.xml.rpc.ServiceException;
+  public uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperInterface getAccessionMapperPort(
+          java.net.URL portAddress) throws javax.xml.rpc.ServiceException;
 }
diff --git a/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperServiceLocator.java b/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperServiceLocator.java
index 4da3262..debb3c9 100644
--- a/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperServiceLocator.java
+++ b/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperServiceLocator.java
@@ -7,130 +7,173 @@
 
 package uk.ac.ebi.www.picr.AccessionMappingService;
 
-public class AccessionMapperServiceLocator extends org.apache.axis.client.Service implements uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperService {
-
-    public AccessionMapperServiceLocator() {
+public class AccessionMapperServiceLocator extends
+        org.apache.axis.client.Service implements
+        uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperService
+{
+
+  public AccessionMapperServiceLocator()
+  {
+  }
+
+  public AccessionMapperServiceLocator(
+          org.apache.axis.EngineConfiguration config)
+  {
+    super(config);
+  }
+
+  // Use to get a proxy class for AccessionMapperPort
+  private java.lang.String AccessionMapperPort_address = "http://www.ebi.ac.uk:80/Tools/picr/service";
+
+  public java.lang.String getAccessionMapperPortAddress()
+  {
+    return AccessionMapperPort_address;
+  }
+
+  // The WSDD service name defaults to the port name.
+  private java.lang.String AccessionMapperPortWSDDServiceName = "AccessionMapperPort";
+
+  public java.lang.String getAccessionMapperPortWSDDServiceName()
+  {
+    return AccessionMapperPortWSDDServiceName;
+  }
+
+  public void setAccessionMapperPortWSDDServiceName(java.lang.String name)
+  {
+    AccessionMapperPortWSDDServiceName = name;
+  }
+
+  public uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperInterface getAccessionMapperPort()
+          throws javax.xml.rpc.ServiceException
+  {
+    java.net.URL endpoint;
+    try
+    {
+      endpoint = new java.net.URL(AccessionMapperPort_address);
+    } catch (java.net.MalformedURLException e)
+    {
+      throw new javax.xml.rpc.ServiceException(e);
     }
-
-
-    public AccessionMapperServiceLocator(org.apache.axis.EngineConfiguration config) {
-        super(config);
+    return getAccessionMapperPort(endpoint);
+  }
+
+  public uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperInterface getAccessionMapperPort(
+          java.net.URL portAddress) throws javax.xml.rpc.ServiceException
+  {
+    try
+    {
+      uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperBindingStub _stub = new uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperBindingStub(
+              portAddress, this);
+      _stub.setPortName(getAccessionMapperPortWSDDServiceName());
+      return _stub;
+    } catch (org.apache.axis.AxisFault e)
+    {
+      return null;
     }
-
-    // Use to get a proxy class for AccessionMapperPort
-    private java.lang.String AccessionMapperPort_address = "http://www.ebi.ac.uk:80/Tools/picr/service";
-
-    public java.lang.String getAccessionMapperPortAddress() {
-        return AccessionMapperPort_address;
+  }
+
+  public void setAccessionMapperPortEndpointAddress(java.lang.String address)
+  {
+    AccessionMapperPort_address = address;
+  }
+
+  /**
+   * For the given interface, get the stub implementation. If this service has
+   * no port for the given interface, then ServiceException is thrown.
+   */
+  public java.rmi.Remote getPort(Class serviceEndpointInterface)
+          throws javax.xml.rpc.ServiceException
+  {
+    try
+    {
+      if (uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperInterface.class
+              .isAssignableFrom(serviceEndpointInterface))
+      {
+        uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperBindingStub _stub = new uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperBindingStub(
+                new java.net.URL(AccessionMapperPort_address), this);
+        _stub.setPortName(getAccessionMapperPortWSDDServiceName());
+        return _stub;
+      }
+    } catch (java.lang.Throwable t)
+    {
+      throw new javax.xml.rpc.ServiceException(t);
     }
-
-    // The WSDD service name defaults to the port name.
-    private java.lang.String AccessionMapperPortWSDDServiceName = "AccessionMapperPort";
-
-    public java.lang.String getAccessionMapperPortWSDDServiceName() {
-        return AccessionMapperPortWSDDServiceName;
+    throw new javax.xml.rpc.ServiceException(
+            "There is no stub implementation for the interface:  "
+                    + (serviceEndpointInterface == null ? "null"
+                            : serviceEndpointInterface.getName()));
+  }
+
+  /**
+   * For the given interface, get the stub implementation. If this service has
+   * no port for the given interface, then ServiceException is thrown.
+   */
+  public java.rmi.Remote getPort(javax.xml.namespace.QName portName,
+          Class serviceEndpointInterface)
+          throws javax.xml.rpc.ServiceException
+  {
+    if (portName == null)
+    {
+      return getPort(serviceEndpointInterface);
     }
-
-    public void setAccessionMapperPortWSDDServiceName(java.lang.String name) {
-        AccessionMapperPortWSDDServiceName = name;
+    java.lang.String inputPortName = portName.getLocalPart();
+    if ("AccessionMapperPort".equals(inputPortName))
+    {
+      return getAccessionMapperPort();
     }
-
-    public uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperInterface getAccessionMapperPort() throws javax.xml.rpc.ServiceException {
-       java.net.URL endpoint;
-        try {
-            endpoint = new java.net.URL(AccessionMapperPort_address);
-        }
-        catch (java.net.MalformedURLException e) {
-            throw new javax.xml.rpc.ServiceException(e);
-        }
-        return getAccessionMapperPort(endpoint);
+    else
+    {
+      java.rmi.Remote _stub = getPort(serviceEndpointInterface);
+      ((org.apache.axis.client.Stub) _stub).setPortName(portName);
+      return _stub;
     }
-
-    public uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperInterface getAccessionMapperPort(java.net.URL portAddress) throws javax.xml.rpc.ServiceException {
-        try {
-            uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperBindingStub _stub = new uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperBindingStub(portAddress, this);
-            _stub.setPortName(getAccessionMapperPortWSDDServiceName());
-            return _stub;
-        }
-        catch (org.apache.axis.AxisFault e) {
-            return null;
-        }
+  }
+
+  public javax.xml.namespace.QName getServiceName()
+  {
+    return new javax.xml.namespace.QName(
+            "http://www.ebi.ac.uk/picr/AccessionMappingService",
+            "AccessionMapperService");
+  }
+
+  private java.util.HashSet ports = null;
+
+  public java.util.Iterator getPorts()
+  {
+    if (ports == null)
+    {
+      ports = new java.util.HashSet();
+      ports.add(new javax.xml.namespace.QName(
+              "http://www.ebi.ac.uk/picr/AccessionMappingService",
+              "AccessionMapperPort"));
     }
-
-    public void setAccessionMapperPortEndpointAddress(java.lang.String address) {
-        AccessionMapperPort_address = address;
+    return ports.iterator();
+  }
+
+  /**
+   * Set the endpoint address for the specified port name.
+   */
+  public void setEndpointAddress(java.lang.String portName,
+          java.lang.String address) throws javax.xml.rpc.ServiceException
+  {
+    if ("AccessionMapperPort".equals(portName))
+    {
+      setAccessionMapperPortEndpointAddress(address);
     }
-
-    /**
-     * For the given interface, get the stub implementation.
-     * If this service has no port for the given interface,
-     * then ServiceException is thrown.
-     */
-    public java.rmi.Remote getPort(Class serviceEndpointInterface) throws javax.xml.rpc.ServiceException {
-        try {
-            if (uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperInterface.class.isAssignableFrom(serviceEndpointInterface)) {
-                uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperBindingStub _stub = new uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperBindingStub(new java.net.URL(AccessionMapperPort_address), this);
-                _stub.setPortName(getAccessionMapperPortWSDDServiceName());
-                return _stub;
-            }
-        }
-        catch (java.lang.Throwable t) {
-            throw new javax.xml.rpc.ServiceException(t);
-        }
-        throw new javax.xml.rpc.ServiceException("There is no stub implementation for the interface:  " + (serviceEndpointInterface == null ? "null" : serviceEndpointInterface.getName()));
-    }
-
-    /**
-     * For the given interface, get the stub implementation.
-     * If this service has no port for the given interface,
-     * then ServiceException is thrown.
-     */
-    public java.rmi.Remote getPort(javax.xml.namespace.QName portName, Class serviceEndpointInterface) throws javax.xml.rpc.ServiceException {
-        if (portName == null) {
-            return getPort(serviceEndpointInterface);
-        }
-        java.lang.String inputPortName = portName.getLocalPart();
-        if ("AccessionMapperPort".equals(inputPortName)) {
-            return getAccessionMapperPort();
-        }
-        else  {
-            java.rmi.Remote _stub = getPort(serviceEndpointInterface);
-            ((org.apache.axis.client.Stub) _stub).setPortName(portName);
-            return _stub;
-        }
-    }
-
-    public javax.xml.namespace.QName getServiceName() {
-        return new javax.xml.namespace.QName("http://www.ebi.ac.uk/picr/AccessionMappingService", "AccessionMapperService");
-    }
-
-    private java.util.HashSet ports = null;
-
-    public java.util.Iterator getPorts() {
-        if (ports == null) {
-            ports = new java.util.HashSet();
-            ports.add(new javax.xml.namespace.QName("http://www.ebi.ac.uk/picr/AccessionMappingService", "AccessionMapperPort"));
-        }
-        return ports.iterator();
-    }
-
-    /**
-    * Set the endpoint address for the specified port name.
-    */
-    public void setEndpointAddress(java.lang.String portName, java.lang.String address) throws javax.xml.rpc.ServiceException {
-        if ("AccessionMapperPort".equals(portName)) {
-            setAccessionMapperPortEndpointAddress(address);
-        }
-        else { // Unknown Port Name
-            throw new javax.xml.rpc.ServiceException(" Cannot set Endpoint Address for Unknown Port" + portName);
-        }
-    }
-
-    /**
-    * Set the endpoint address for the specified port name.
-    */
-    public void setEndpointAddress(javax.xml.namespace.QName portName, java.lang.String address) throws javax.xml.rpc.ServiceException {
-        setEndpointAddress(portName.getLocalPart(), address);
+    else
+    { // Unknown Port Name
+      throw new javax.xml.rpc.ServiceException(
+              " Cannot set Endpoint Address for Unknown Port" + portName);
     }
+  }
+
+  /**
+   * Set the endpoint address for the specified port name.
+   */
+  public void setEndpointAddress(javax.xml.namespace.QName portName,
+          java.lang.String address) throws javax.xml.rpc.ServiceException
+  {
+    setEndpointAddress(portName.getLocalPart(), address);
+  }
 
 }
diff --git a/src/vamsas/IMsaWS.java b/src/vamsas/IMsaWS.java
index 7d02a94..93d6289 100755
--- a/src/vamsas/IMsaWS.java
+++ b/src/vamsas/IMsaWS.java
@@ -1,37 +1,32 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package vamsas;
 
 import vamsas.objects.simple.*;
 
 public interface IMsaWS
 {
-  public WsJobId align(SequenceSet s)
-      throws Exception;
+  public WsJobId align(SequenceSet s) throws Exception;
 
-  public Alignment getalign(String job_id)
-      throws Exception;
+  public Alignment getalign(String job_id) throws Exception;
 
-  public MsaResult getResult(String job_id)
-      throws Exception;
+  public MsaResult getResult(String job_id) throws Exception;
 
-  public WsJobId cancel(String jobId)
-      throws Exception;
+  public WsJobId cancel(String jobId) throws Exception;
 }
diff --git a/src/vamsas/objects/simple/Alignment.java b/src/vamsas/objects/simple/Alignment.java
index 18fa20c..0eb9256 100755
--- a/src/vamsas/objects/simple/Alignment.java
+++ b/src/vamsas/objects/simple/Alignment.java
@@ -1,140 +1,163 @@
-/**
- * Alignment.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package vamsas.objects.simple;
 
-public class Alignment  extends vamsas.objects.simple.Object  implements java.io.Serializable {
-    private java.lang.String gapchar;
-    private java.lang.String[] method;
-    private vamsas.objects.simple.SequenceSet seqs;
-
-    public Alignment() {
-    }
-
-    public Alignment(
-           java.lang.String gapchar,
-           java.lang.String[] method,
-           vamsas.objects.simple.SequenceSet seqs) {
-           this.gapchar = gapchar;
-           this.method = method;
-           this.seqs = seqs;
-    }
-
-
-    /**
-     * Gets the gapchar value for this Alignment.
-     * 
-     * @return gapchar
-     */
-    public java.lang.String getGapchar() {
-        return gapchar;
-    }
-
-
-    /**
-     * Sets the gapchar value for this Alignment.
-     * 
-     * @param gapchar
-     */
-    public void setGapchar(java.lang.String gapchar) {
-        this.gapchar = gapchar;
-    }
-
-
-    /**
-     * Gets the method value for this Alignment.
-     * 
-     * @return method
-     */
-    public java.lang.String[] getMethod() {
-        return method;
+public class Alignment extends vamsas.objects.simple.Object implements
+        java.io.Serializable
+{
+  private java.lang.String gapchar;
+
+  private java.lang.String[] method;
+
+  private vamsas.objects.simple.SequenceSet seqs;
+
+  public Alignment()
+  {
+  }
+
+  public Alignment(java.lang.String gapchar, java.lang.String[] method,
+          vamsas.objects.simple.SequenceSet seqs)
+  {
+    this.gapchar = gapchar;
+    this.method = method;
+    this.seqs = seqs;
+  }
+
+  /**
+   * Gets the gapchar value for this Alignment.
+   * 
+   * @return gapchar
+   */
+  public java.lang.String getGapchar()
+  {
+    return gapchar;
+  }
+
+  /**
+   * Sets the gapchar value for this Alignment.
+   * 
+   * @param gapchar
+   */
+  public void setGapchar(java.lang.String gapchar)
+  {
+    this.gapchar = gapchar;
+  }
+
+  /**
+   * Gets the method value for this Alignment.
+   * 
+   * @return method
+   */
+  public java.lang.String[] getMethod()
+  {
+    return method;
+  }
+
+  /**
+   * Sets the method value for this Alignment.
+   * 
+   * @param method
+   */
+  public void setMethod(java.lang.String[] method)
+  {
+    this.method = method;
+  }
+
+  /**
+   * Gets the seqs value for this Alignment.
+   * 
+   * @return seqs
+   */
+  public vamsas.objects.simple.SequenceSet getSeqs()
+  {
+    return seqs;
+  }
+
+  /**
+   * Sets the seqs value for this Alignment.
+   * 
+   * @param seqs
+   */
+  public void setSeqs(vamsas.objects.simple.SequenceSet seqs)
+  {
+    this.seqs = seqs;
+  }
+
+  private java.lang.Object __equalsCalc = null;
+
+  public synchronized boolean equals(java.lang.Object obj)
+  {
+    if (!(obj instanceof Alignment))
+      return false;
+    Alignment other = (Alignment) obj;
+    if (obj == null)
+      return false;
+    if (this == obj)
+      return true;
+    if (__equalsCalc != null)
+    {
+      return (__equalsCalc == obj);
     }
-
-
-    /**
-     * Sets the method value for this Alignment.
-     * 
-     * @param method
-     */
-    public void setMethod(java.lang.String[] method) {
-        this.method = method;
+    __equalsCalc = obj;
+    boolean _equals;
+    _equals = super.equals(obj)
+            && ((this.gapchar == null && other.getGapchar() == null) || (this.gapchar != null && this.gapchar
+                    .equals(other.getGapchar())))
+            && ((this.method == null && other.getMethod() == null) || (this.method != null && java.util.Arrays
+                    .equals(this.method, other.getMethod())))
+            && ((this.seqs == null && other.getSeqs() == null) || (this.seqs != null && this.seqs
+                    .equals(other.getSeqs())));
+    __equalsCalc = null;
+    return _equals;
+  }
+
+  private boolean __hashCodeCalc = false;
+
+  public synchronized int hashCode()
+  {
+    if (__hashCodeCalc)
+    {
+      return 0;
     }
-
-
-    /**
-     * Gets the seqs value for this Alignment.
-     * 
-     * @return seqs
-     */
-    public vamsas.objects.simple.SequenceSet getSeqs() {
-        return seqs;
-    }
-
-
-    /**
-     * Sets the seqs value for this Alignment.
-     * 
-     * @param seqs
-     */
-    public void setSeqs(vamsas.objects.simple.SequenceSet seqs) {
-        this.seqs = seqs;
+    __hashCodeCalc = true;
+    int _hashCode = super.hashCode();
+    if (getGapchar() != null)
+    {
+      _hashCode += getGapchar().hashCode();
     }
-
-    private java.lang.Object __equalsCalc = null;
-    public synchronized boolean equals(java.lang.Object obj) {
-        if (!(obj instanceof Alignment)) return false;
-        Alignment other = (Alignment) obj;
-        if (obj == null) return false;
-        if (this == obj) return true;
-        if (__equalsCalc != null) {
-            return (__equalsCalc == obj);
+    if (getMethod() != null)
+    {
+      for (int i = 0; i < java.lang.reflect.Array.getLength(getMethod()); i++)
+      {
+        java.lang.Object obj = java.lang.reflect.Array.get(getMethod(), i);
+        if (obj != null && !obj.getClass().isArray())
+        {
+          _hashCode += obj.hashCode();
         }
-        __equalsCalc = obj;
-        boolean _equals;
-        _equals = super.equals(obj) && 
-            ((this.gapchar==null && other.getGapchar()==null) || 
-             (this.gapchar!=null &&
-              this.gapchar.equals(other.getGapchar()))) &&
-            ((this.method==null && other.getMethod()==null) || 
-             (this.method!=null &&
-              java.util.Arrays.equals(this.method, other.getMethod()))) &&
-            ((this.seqs==null && other.getSeqs()==null) || 
-             (this.seqs!=null &&
-              this.seqs.equals(other.getSeqs())));
-        __equalsCalc = null;
-        return _equals;
+      }
     }
-
-    private boolean __hashCodeCalc = false;
-    public synchronized int hashCode() {
-        if (__hashCodeCalc) {
-            return 0;
-        }
-        __hashCodeCalc = true;
-        int _hashCode = super.hashCode();
-        if (getGapchar() != null) {
-            _hashCode += getGapchar().hashCode();
-        }
-        if (getMethod() != null) {
-            for (int i=0;
-                 i<java.lang.reflect.Array.getLength(getMethod());
-                 i++) {
-                java.lang.Object obj = java.lang.reflect.Array.get(getMethod(), i);
-                if (obj != null &&
-                    !obj.getClass().isArray()) {
-                    _hashCode += obj.hashCode();
-                }
-            }
-        }
-        if (getSeqs() != null) {
-            _hashCode += getSeqs().hashCode();
-        }
-        __hashCodeCalc = false;
-        return _hashCode;
+    if (getSeqs() != null)
+    {
+      _hashCode += getSeqs().hashCode();
     }
+    __hashCodeCalc = false;
+    return _hashCode;
+  }
 
 }
diff --git a/src/vamsas/objects/simple/Alignment_Helper.java b/src/vamsas/objects/simple/Alignment_Helper.java
index 5a54fe0..7bd91d0 100755
--- a/src/vamsas/objects/simple/Alignment_Helper.java
+++ b/src/vamsas/objects/simple/Alignment_Helper.java
@@ -1,65 +1,81 @@
-/**
- * Alignment_Helper.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package vamsas.objects.simple;
 
-public class Alignment_Helper {
-    // Type metadata
-    private static org.apache.axis.description.TypeDesc typeDesc =
-        new org.apache.axis.description.TypeDesc(Alignment.class, true);
+public class Alignment_Helper
+{
+  // Type metadata
+  private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(
+          Alignment.class, true);
 
-    static {
-        typeDesc.setXmlType(new javax.xml.namespace.QName("simple.objects.vamsas", "Alignment"));
-        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("gapchar");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "gapchar"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://schemas.xmlsoap.org/soap/encoding/", "string"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("method");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "method"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://schemas.xmlsoap.org/soap/encoding/", "string"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("seqs");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "seqs"));
-        elemField.setXmlType(new javax.xml.namespace.QName("simple.objects.vamsas", "SequenceSet"));
-        typeDesc.addFieldDesc(elemField);
-    }
+  static
+  {
+    typeDesc.setXmlType(new javax.xml.namespace.QName(
+            "simple.objects.vamsas", "Alignment"));
+    org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("gapchar");
+    elemField.setXmlName(new javax.xml.namespace.QName("", "gapchar"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "http://schemas.xmlsoap.org/soap/encoding/", "string"));
+    typeDesc.addFieldDesc(elemField);
+    elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("method");
+    elemField.setXmlName(new javax.xml.namespace.QName("", "method"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "http://schemas.xmlsoap.org/soap/encoding/", "string"));
+    typeDesc.addFieldDesc(elemField);
+    elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("seqs");
+    elemField.setXmlName(new javax.xml.namespace.QName("", "seqs"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "simple.objects.vamsas", "SequenceSet"));
+    typeDesc.addFieldDesc(elemField);
+  }
 
-    /**
-     * Return type metadata object
-     */
-    public static org.apache.axis.description.TypeDesc getTypeDesc() {
-        return typeDesc;
-    }
+  /**
+   * Return type metadata object
+   */
+  public static org.apache.axis.description.TypeDesc getTypeDesc()
+  {
+    return typeDesc;
+  }
 
-    /**
-     * Get Custom Serializer
-     */
-    public static org.apache.axis.encoding.Serializer getSerializer(
-           java.lang.String mechType, 
-           java.lang.Class _javaType,  
-           javax.xml.namespace.QName _xmlType) {
-        return 
-          new  org.apache.axis.encoding.ser.BeanSerializer(
-            _javaType, _xmlType, typeDesc);
-    }
+  /**
+   * Get Custom Serializer
+   */
+  public static org.apache.axis.encoding.Serializer getSerializer(
+          java.lang.String mechType, java.lang.Class _javaType,
+          javax.xml.namespace.QName _xmlType)
+  {
+    return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,
+            _xmlType, typeDesc);
+  }
 
-    /**
-     * Get Custom Deserializer
-     */
-    public static org.apache.axis.encoding.Deserializer getDeserializer(
-           java.lang.String mechType, 
-           java.lang.Class _javaType,  
-           javax.xml.namespace.QName _xmlType) {
-        return 
-          new  org.apache.axis.encoding.ser.BeanDeserializer(
-            _javaType, _xmlType, typeDesc);
-    }
+  /**
+   * Get Custom Deserializer
+   */
+  public static org.apache.axis.encoding.Deserializer getDeserializer(
+          java.lang.String mechType, java.lang.Class _javaType,
+          javax.xml.namespace.QName _xmlType)
+  {
+    return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,
+            _xmlType, typeDesc);
+  }
 
 }
diff --git a/src/vamsas/objects/simple/JpredResult.java b/src/vamsas/objects/simple/JpredResult.java
index 26eb6b7..f294d51 100755
--- a/src/vamsas/objects/simple/JpredResult.java
+++ b/src/vamsas/objects/simple/JpredResult.java
@@ -1,25 +1,35 @@
-/**
- * JpredResult.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package vamsas.objects.simple;
 
-public class JpredResult
-    extends vamsas.objects.simple.Result implements java.io.Serializable
+public class JpredResult extends vamsas.objects.simple.Result implements
+        java.io.Serializable
 {
   private java.lang.String aligfile;
+
   private java.lang.String predfile;
 
   public JpredResult()
   {
   }
 
-  public JpredResult(
-      java.lang.String aligfile,
-      java.lang.String predfile)
+  public JpredResult(java.lang.String aligfile, java.lang.String predfile)
   {
     this.aligfile = aligfile;
     this.predfile = predfile;
@@ -27,7 +37,7 @@ public class JpredResult
 
   /**
    * Gets the aligfile value for this JpredResult.
-   *
+   * 
    * @return aligfile
    */
   public java.lang.String getAligfile()
@@ -37,7 +47,7 @@ public class JpredResult
 
   /**
    * Sets the aligfile value for this JpredResult.
-   *
+   * 
    * @param aligfile
    */
   public void setAligfile(java.lang.String aligfile)
@@ -47,7 +57,7 @@ public class JpredResult
 
   /**
    * Gets the predfile value for this JpredResult.
-   *
+   * 
    * @return predfile
    */
   public java.lang.String getPredfile()
@@ -57,7 +67,7 @@ public class JpredResult
 
   /**
    * Sets the predfile value for this JpredResult.
-   *
+   * 
    * @param predfile
    */
   public void setPredfile(java.lang.String predfile)
@@ -66,9 +76,10 @@ public class JpredResult
   }
 
   private java.lang.Object __equalsCalc = null;
+
   public synchronized boolean equals(java.lang.Object obj)
   {
-    if (! (obj instanceof JpredResult))
+    if (!(obj instanceof JpredResult))
     {
       return false;
     }
@@ -87,18 +98,17 @@ public class JpredResult
     }
     __equalsCalc = obj;
     boolean _equals;
-    _equals = super.equals(obj) &&
-        ( (this.aligfile == null && other.getAligfile() == null) ||
-         (this.aligfile != null &&
-          this.aligfile.equals(other.getAligfile()))) &&
-        ( (this.predfile == null && other.getPredfile() == null) ||
-         (this.predfile != null &&
-          this.predfile.equals(other.getPredfile())));
+    _equals = super.equals(obj)
+            && ((this.aligfile == null && other.getAligfile() == null) || (this.aligfile != null && this.aligfile
+                    .equals(other.getAligfile())))
+            && ((this.predfile == null && other.getPredfile() == null) || (this.predfile != null && this.predfile
+                    .equals(other.getPredfile())));
     __equalsCalc = null;
     return _equals;
   }
 
   private boolean __hashCodeCalc = false;
+
   public synchronized int hashCode()
   {
     if (__hashCodeCalc)
diff --git a/src/vamsas/objects/simple/JpredResult_Helper.java b/src/vamsas/objects/simple/JpredResult_Helper.java
index 12dff09..edc1fc3 100755
--- a/src/vamsas/objects/simple/JpredResult_Helper.java
+++ b/src/vamsas/objects/simple/JpredResult_Helper.java
@@ -1,34 +1,44 @@
-/**
- * JpredResult_Helper.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package vamsas.objects.simple;
 
 public class JpredResult_Helper
 {
   // Type metadata
-  private static org.apache.axis.description.TypeDesc typeDesc =
-      new org.apache.axis.description.TypeDesc(JpredResult.class, true);
+  private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(
+          JpredResult.class, true);
 
   static
   {
     typeDesc.setXmlType(new javax.xml.namespace.QName(
-        "http://simple.objects.vamsas", "JpredResult"));
-    org.apache.axis.description.ElementDesc elemField = new org.apache.axis.
-        description.ElementDesc();
+            "http://simple.objects.vamsas", "JpredResult"));
+    org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
     elemField.setFieldName("aligfile");
     elemField.setXmlName(new javax.xml.namespace.QName("", "aligfile"));
     elemField.setXmlType(new javax.xml.namespace.QName(
-        "http://schemas.xmlsoap.org/soap/encoding/", "string"));
+            "http://schemas.xmlsoap.org/soap/encoding/", "string"));
     typeDesc.addFieldDesc(elemField);
     elemField = new org.apache.axis.description.ElementDesc();
     elemField.setFieldName("predfile");
     elemField.setXmlName(new javax.xml.namespace.QName("", "predfile"));
     elemField.setXmlType(new javax.xml.namespace.QName(
-        "http://schemas.xmlsoap.org/soap/encoding/", "string"));
+            "http://schemas.xmlsoap.org/soap/encoding/", "string"));
     typeDesc.addFieldDesc(elemField);
   }
 
@@ -44,26 +54,22 @@ public class JpredResult_Helper
    * Get Custom Serializer
    */
   public static org.apache.axis.encoding.Serializer getSerializer(
-      java.lang.String mechType,
-      java.lang.Class _javaType,
-      javax.xml.namespace.QName _xmlType)
+          java.lang.String mechType, java.lang.Class _javaType,
+          javax.xml.namespace.QName _xmlType)
   {
-    return
-        new org.apache.axis.encoding.ser.BeanSerializer(
-            _javaType, _xmlType, typeDesc);
+    return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,
+            _xmlType, typeDesc);
   }
 
   /**
    * Get Custom Deserializer
    */
   public static org.apache.axis.encoding.Deserializer getDeserializer(
-      java.lang.String mechType,
-      java.lang.Class _javaType,
-      javax.xml.namespace.QName _xmlType)
+          java.lang.String mechType, java.lang.Class _javaType,
+          javax.xml.namespace.QName _xmlType)
   {
-    return
-        new org.apache.axis.encoding.ser.BeanDeserializer(
-            _javaType, _xmlType, typeDesc);
+    return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,
+            _xmlType, typeDesc);
   }
 
 }
diff --git a/src/vamsas/objects/simple/MsaResult.java b/src/vamsas/objects/simple/MsaResult.java
index c8327dd..3b9bb2a 100755
--- a/src/vamsas/objects/simple/MsaResult.java
+++ b/src/vamsas/objects/simple/MsaResult.java
@@ -1,119 +1,132 @@
-/**
- * MsaResult.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package vamsas.objects.simple;
-
-public class MsaResult
-    extends vamsas.objects.simple.Result implements java.io.Serializable
-{
-  private vamsas.objects.simple.Alignment msa;
-  private java.lang.Object __equalsCalc = null;
-  private boolean __hashCodeCalc = false;
-
-  public MsaResult()
-  {
-  }
-
-  public MsaResult(vamsas.objects.simple.Alignment msa)
-  {
-    this.msa = msa;
-  }
-
-  /**
-   * Gets the msa value for this MsaResult.
-   *
-   * @return msa
-   */
-  public vamsas.objects.simple.Alignment getMsa()
-  {
-    return msa;
-  }
-
-  /**
-   * Sets the msa value for this MsaResult.
-   *
-   * @param msa
-   */
-  public void setMsa(vamsas.objects.simple.Alignment msa)
-  {
-    this.msa = msa;
-  }
-
-  public synchronized boolean equals(java.lang.Object obj)
-  {
-    if (! (obj instanceof MsaResult))
-    {
-      return false;
-    }
-
-    MsaResult other = (MsaResult) obj;
-
-    if (obj == null)
-    {
-      return false;
-    }
-
-    if (this == obj)
-    {
-      return true;
-    }
-
-    if (__equalsCalc != null)
-    {
-      return (__equalsCalc == obj);
-    }
-
-    __equalsCalc = obj;
-
-    boolean _equals;
-    _equals = super.equals(obj) &&
-        ( ( (this.msa == null) && (other.getMsa() == null)) ||
-         ( (this.msa != null) && this.msa.equals(other.getMsa())));
-    __equalsCalc = null;
-
-    return _equals;
-  }
-
-  public synchronized int hashCode()
-  {
-    if (__hashCodeCalc)
-    {
-      return 0;
-    }
-
-    __hashCodeCalc = true;
-
-    int _hashCode = super.hashCode();
-
-    if (getMsa() != null)
-    {
-      _hashCode += getMsa().hashCode();
-    }
-
-    __hashCodeCalc = false;
-
-    return _hashCode;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package vamsas.objects.simple;
+
+public class MsaResult extends vamsas.objects.simple.Result implements
+        java.io.Serializable
+{
+  private vamsas.objects.simple.Alignment msa;
+
+  private java.lang.Object __equalsCalc = null;
+
+  private boolean __hashCodeCalc = false;
+
+  public MsaResult()
+  {
+  }
+
+  public MsaResult(vamsas.objects.simple.Alignment msa)
+  {
+    this.msa = msa;
+  }
+
+  /**
+   * Gets the msa value for this MsaResult.
+   * 
+   * @return msa
+   */
+  public vamsas.objects.simple.Alignment getMsa()
+  {
+    return msa;
+  }
+
+  /**
+   * Sets the msa value for this MsaResult.
+   * 
+   * @param msa
+   */
+  public void setMsa(vamsas.objects.simple.Alignment msa)
+  {
+    this.msa = msa;
+  }
+
+  public synchronized boolean equals(java.lang.Object obj)
+  {
+    if (!(obj instanceof MsaResult))
+    {
+      return false;
+    }
+
+    MsaResult other = (MsaResult) obj;
+
+    if (obj == null)
+    {
+      return false;
+    }
+
+    if (this == obj)
+    {
+      return true;
+    }
+
+    if (__equalsCalc != null)
+    {
+      return (__equalsCalc == obj);
+    }
+
+    __equalsCalc = obj;
+
+    boolean _equals;
+    _equals = super.equals(obj)
+            && (((this.msa == null) && (other.getMsa() == null)) || ((this.msa != null) && this.msa
+                    .equals(other.getMsa())));
+    __equalsCalc = null;
+
+    return _equals;
+  }
+
+  public synchronized int hashCode()
+  {
+    if (__hashCodeCalc)
+    {
+      return 0;
+    }
+
+    __hashCodeCalc = true;
+
+    int _hashCode = super.hashCode();
+
+    if (getMsa() != null)
+    {
+      _hashCode += getMsa().hashCode();
+    }
+
+    __hashCodeCalc = false;
+
+    return _hashCode;
+  }
+}
diff --git a/src/vamsas/objects/simple/MsaResult_Helper.java b/src/vamsas/objects/simple/MsaResult_Helper.java
index b43e05b..3065aeb 100755
--- a/src/vamsas/objects/simple/MsaResult_Helper.java
+++ b/src/vamsas/objects/simple/MsaResult_Helper.java
@@ -1,78 +1,87 @@
-/**
- * MsaResult_Helper.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package vamsas.objects.simple;
-
-public class MsaResult_Helper
-{
-  // Type metadata
-  private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.
-      axis.description.TypeDesc(MsaResult.class,
-                                true);
-
-  static
-  {
-    typeDesc.setXmlType(new javax.xml.namespace.QName(
-        "simple.objects.vamsas", "MsaResult"));
-
-    org.apache.axis.description.ElementDesc elemField = new org.apache.axis.
-        description.ElementDesc();
-    elemField.setFieldName("msa");
-    elemField.setXmlName(new javax.xml.namespace.QName("", "msa"));
-    elemField.setXmlType(new javax.xml.namespace.QName(
-        "simple.objects.vamsas", "Alignment"));
-    typeDesc.addFieldDesc(elemField);
-  }
-
-  /**
-   * Return type metadata object
-   */
-  public static org.apache.axis.description.TypeDesc getTypeDesc()
-  {
-    return typeDesc;
-  }
-
-  /**
-   * Get Custom Serializer
-   */
-  public static org.apache.axis.encoding.Serializer getSerializer(
-      java.lang.String mechType, java.lang.Class _javaType,
-      javax.xml.namespace.QName _xmlType)
-  {
-    return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,
-        _xmlType, typeDesc);
-  }
-
-  /**
-   * Get Custom Deserializer
-   */
-  public static org.apache.axis.encoding.Deserializer getDeserializer(
-      java.lang.String mechType, java.lang.Class _javaType,
-      javax.xml.namespace.QName _xmlType)
-  {
-    return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,
-        _xmlType, typeDesc);
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package vamsas.objects.simple;
+
+public class MsaResult_Helper
+{
+  // Type metadata
+  private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(
+          MsaResult.class, true);
+
+  static
+  {
+    typeDesc.setXmlType(new javax.xml.namespace.QName(
+            "simple.objects.vamsas", "MsaResult"));
+
+    org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("msa");
+    elemField.setXmlName(new javax.xml.namespace.QName("", "msa"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "simple.objects.vamsas", "Alignment"));
+    typeDesc.addFieldDesc(elemField);
+  }
+
+  /**
+   * Return type metadata object
+   */
+  public static org.apache.axis.description.TypeDesc getTypeDesc()
+  {
+    return typeDesc;
+  }
+
+  /**
+   * Get Custom Serializer
+   */
+  public static org.apache.axis.encoding.Serializer getSerializer(
+          java.lang.String mechType, java.lang.Class _javaType,
+          javax.xml.namespace.QName _xmlType)
+  {
+    return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,
+            _xmlType, typeDesc);
+  }
+
+  /**
+   * Get Custom Deserializer
+   */
+  public static org.apache.axis.encoding.Deserializer getDeserializer(
+          java.lang.String mechType, java.lang.Class _javaType,
+          javax.xml.namespace.QName _xmlType)
+  {
+    return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,
+            _xmlType, typeDesc);
+  }
+}
diff --git a/src/vamsas/objects/simple/Msfalignment.java b/src/vamsas/objects/simple/Msfalignment.java
index 242b14f..a2b179e 100755
--- a/src/vamsas/objects/simple/Msfalignment.java
+++ b/src/vamsas/objects/simple/Msfalignment.java
@@ -1,25 +1,34 @@
-/**
- * Msfalignment.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package vamsas.objects.simple;
 
-public class Msfalignment
-    implements java.io.Serializable
+public class Msfalignment implements java.io.Serializable
 {
   private java.lang.String msf;
+
   private java.lang.String notes;
 
   public Msfalignment()
   {
   }
 
-  public Msfalignment(
-      java.lang.String msf,
-      java.lang.String notes)
+  public Msfalignment(java.lang.String msf, java.lang.String notes)
   {
     this.msf = msf;
     this.notes = notes;
@@ -27,7 +36,7 @@ public class Msfalignment
 
   /**
    * Gets the msf value for this Msfalignment.
-   *
+   * 
    * @return msf
    */
   public java.lang.String getMsf()
@@ -37,7 +46,7 @@ public class Msfalignment
 
   /**
    * Sets the msf value for this Msfalignment.
-   *
+   * 
    * @param msf
    */
   public void setMsf(java.lang.String msf)
@@ -47,7 +56,7 @@ public class Msfalignment
 
   /**
    * Gets the notes value for this Msfalignment.
-   *
+   * 
    * @return notes
    */
   public java.lang.String getNotes()
@@ -57,7 +66,7 @@ public class Msfalignment
 
   /**
    * Sets the notes value for this Msfalignment.
-   *
+   * 
    * @param notes
    */
   public void setNotes(java.lang.String notes)
@@ -66,9 +75,10 @@ public class Msfalignment
   }
 
   private java.lang.Object __equalsCalc = null;
+
   public synchronized boolean equals(java.lang.Object obj)
   {
-    if (! (obj instanceof Msfalignment))
+    if (!(obj instanceof Msfalignment))
     {
       return false;
     }
@@ -87,18 +97,17 @@ public class Msfalignment
     }
     __equalsCalc = obj;
     boolean _equals;
-    _equals = true &&
-        ( (this.msf == null && other.getMsf() == null) ||
-         (this.msf != null &&
-          this.msf.equals(other.getMsf()))) &&
-        ( (this.notes == null && other.getNotes() == null) ||
-         (this.notes != null &&
-          this.notes.equals(other.getNotes())));
+    _equals = true
+            && ((this.msf == null && other.getMsf() == null) || (this.msf != null && this.msf
+                    .equals(other.getMsf())))
+            && ((this.notes == null && other.getNotes() == null) || (this.notes != null && this.notes
+                    .equals(other.getNotes())));
     __equalsCalc = null;
     return _equals;
   }
 
   private boolean __hashCodeCalc = false;
+
   public synchronized int hashCode()
   {
     if (__hashCodeCalc)
diff --git a/src/vamsas/objects/simple/Msfalignment_Helper.java b/src/vamsas/objects/simple/Msfalignment_Helper.java
index 9b9288d..96fbca0 100755
--- a/src/vamsas/objects/simple/Msfalignment_Helper.java
+++ b/src/vamsas/objects/simple/Msfalignment_Helper.java
@@ -1,34 +1,44 @@
-/**
- * Msfalignment_Helper.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package vamsas.objects.simple;
 
 public class Msfalignment_Helper
 {
   // Type metadata
-  private static org.apache.axis.description.TypeDesc typeDesc =
-      new org.apache.axis.description.TypeDesc(Msfalignment.class, true);
+  private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(
+          Msfalignment.class, true);
 
   static
   {
     typeDesc.setXmlType(new javax.xml.namespace.QName(
-        "http://simple.objects.vamsas", "Msfalignment"));
-    org.apache.axis.description.ElementDesc elemField = new org.apache.axis.
-        description.ElementDesc();
+            "http://simple.objects.vamsas", "Msfalignment"));
+    org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
     elemField.setFieldName("msf");
     elemField.setXmlName(new javax.xml.namespace.QName("", "msf"));
     elemField.setXmlType(new javax.xml.namespace.QName(
-        "http://schemas.xmlsoap.org/soap/encoding/", "string"));
+            "http://schemas.xmlsoap.org/soap/encoding/", "string"));
     typeDesc.addFieldDesc(elemField);
     elemField = new org.apache.axis.description.ElementDesc();
     elemField.setFieldName("notes");
     elemField.setXmlName(new javax.xml.namespace.QName("", "notes"));
     elemField.setXmlType(new javax.xml.namespace.QName(
-        "http://schemas.xmlsoap.org/soap/encoding/", "string"));
+            "http://schemas.xmlsoap.org/soap/encoding/", "string"));
     typeDesc.addFieldDesc(elemField);
   }
 
@@ -44,26 +54,22 @@ public class Msfalignment_Helper
    * Get Custom Serializer
    */
   public static org.apache.axis.encoding.Serializer getSerializer(
-      java.lang.String mechType,
-      java.lang.Class _javaType,
-      javax.xml.namespace.QName _xmlType)
+          java.lang.String mechType, java.lang.Class _javaType,
+          javax.xml.namespace.QName _xmlType)
   {
-    return
-        new org.apache.axis.encoding.ser.BeanSerializer(
-            _javaType, _xmlType, typeDesc);
+    return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,
+            _xmlType, typeDesc);
   }
 
   /**
    * Get Custom Deserializer
    */
   public static org.apache.axis.encoding.Deserializer getDeserializer(
-      java.lang.String mechType,
-      java.lang.Class _javaType,
-      javax.xml.namespace.QName _xmlType)
+          java.lang.String mechType, java.lang.Class _javaType,
+          javax.xml.namespace.QName _xmlType)
   {
-    return
-        new org.apache.axis.encoding.ser.BeanDeserializer(
-            _javaType, _xmlType, typeDesc);
+    return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,
+            _xmlType, typeDesc);
   }
 
 }
diff --git a/src/vamsas/objects/simple/Object.java b/src/vamsas/objects/simple/Object.java
index 4bf69bd..81d954a 100755
--- a/src/vamsas/objects/simple/Object.java
+++ b/src/vamsas/objects/simple/Object.java
@@ -1,42 +1,64 @@
-/**
- * Object.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package vamsas.objects.simple;
 
-public abstract class Object  implements java.io.Serializable {
+public abstract class Object implements java.io.Serializable
+{
 
-    public Object() {
-    }
+  public Object()
+  {
+  }
 
-    private java.lang.Object __equalsCalc = null;
-    public synchronized boolean equals(java.lang.Object obj) {
-        if (!(obj instanceof Object)) return false;
-        Object other = (Object) obj;
-        if (obj == null) return false;
-        if (this == obj) return true;
-        if (__equalsCalc != null) {
-            return (__equalsCalc == obj);
-        }
-        __equalsCalc = obj;
-        boolean _equals;
-        _equals = true;
-        __equalsCalc = null;
-        return _equals;
+  private java.lang.Object __equalsCalc = null;
+
+  public synchronized boolean equals(java.lang.Object obj)
+  {
+    if (!(obj instanceof Object))
+      return false;
+    Object other = (Object) obj;
+    if (obj == null)
+      return false;
+    if (this == obj)
+      return true;
+    if (__equalsCalc != null)
+    {
+      return (__equalsCalc == obj);
     }
+    __equalsCalc = obj;
+    boolean _equals;
+    _equals = true;
+    __equalsCalc = null;
+    return _equals;
+  }
+
+  private boolean __hashCodeCalc = false;
 
-    private boolean __hashCodeCalc = false;
-    public synchronized int hashCode() {
-        if (__hashCodeCalc) {
-            return 0;
-        }
-        __hashCodeCalc = true;
-        int _hashCode = 1;
-        __hashCodeCalc = false;
-        return _hashCode;
+  public synchronized int hashCode()
+  {
+    if (__hashCodeCalc)
+    {
+      return 0;
     }
+    __hashCodeCalc = true;
+    int _hashCode = 1;
+    __hashCodeCalc = false;
+    return _hashCode;
+  }
 
 }
diff --git a/src/vamsas/objects/simple/Object_Helper.java b/src/vamsas/objects/simple/Object_Helper.java
index a1b944c..6ea63e7 100755
--- a/src/vamsas/objects/simple/Object_Helper.java
+++ b/src/vamsas/objects/simple/Object_Helper.java
@@ -1,50 +1,63 @@
-/**
- * Object_Helper.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package vamsas.objects.simple;
 
-public class Object_Helper {
-    // Type metadata
-    private static org.apache.axis.description.TypeDesc typeDesc =
-        new org.apache.axis.description.TypeDesc(Object.class, true);
+public class Object_Helper
+{
+  // Type metadata
+  private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(
+          Object.class, true);
 
-    static {
-        typeDesc.setXmlType(new javax.xml.namespace.QName("http://simple.objects.vamsas", "Object"));
-    }
+  static
+  {
+    typeDesc.setXmlType(new javax.xml.namespace.QName(
+            "http://simple.objects.vamsas", "Object"));
+  }
 
-    /**
-     * Return type metadata object
-     */
-    public static org.apache.axis.description.TypeDesc getTypeDesc() {
-        return typeDesc;
-    }
+  /**
+   * Return type metadata object
+   */
+  public static org.apache.axis.description.TypeDesc getTypeDesc()
+  {
+    return typeDesc;
+  }
 
-    /**
-     * Get Custom Serializer
-     */
-    public static org.apache.axis.encoding.Serializer getSerializer(
-           java.lang.String mechType, 
-           java.lang.Class _javaType,  
-           javax.xml.namespace.QName _xmlType) {
-        return 
-          new  org.apache.axis.encoding.ser.BeanSerializer(
-            _javaType, _xmlType, typeDesc);
-    }
+  /**
+   * Get Custom Serializer
+   */
+  public static org.apache.axis.encoding.Serializer getSerializer(
+          java.lang.String mechType, java.lang.Class _javaType,
+          javax.xml.namespace.QName _xmlType)
+  {
+    return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,
+            _xmlType, typeDesc);
+  }
 
-    /**
-     * Get Custom Deserializer
-     */
-    public static org.apache.axis.encoding.Deserializer getDeserializer(
-           java.lang.String mechType, 
-           java.lang.Class _javaType,  
-           javax.xml.namespace.QName _xmlType) {
-        return 
-          new  org.apache.axis.encoding.ser.BeanDeserializer(
-            _javaType, _xmlType, typeDesc);
-    }
+  /**
+   * Get Custom Deserializer
+   */
+  public static org.apache.axis.encoding.Deserializer getDeserializer(
+          java.lang.String mechType, java.lang.Class _javaType,
+          javax.xml.namespace.QName _xmlType)
+  {
+    return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,
+            _xmlType, typeDesc);
+  }
 
 }
diff --git a/src/vamsas/objects/simple/Result.java b/src/vamsas/objects/simple/Result.java
index b349019..84df25d 100755
--- a/src/vamsas/objects/simple/Result.java
+++ b/src/vamsas/objects/simple/Result.java
@@ -1,324 +1,350 @@
-/**
- * Result.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package vamsas.objects.simple;
 
-public class Result  implements java.io.Serializable {
-    private boolean broken;
-    private boolean failed;
-    private boolean finished;
-    private boolean invalid;
-    private boolean jobFailed;
-    private boolean queued;
-    private boolean running;
-    private boolean serverError;
-    private int state;
-    private java.lang.String status;
-    private boolean suspended;
-
-    public Result() {
-    }
-
-    public Result(
-           boolean broken,
-           boolean failed,
-           boolean finished,
-           boolean invalid,
-           boolean jobFailed,
-           boolean queued,
-           boolean running,
-           boolean serverError,
-           int state,
-           java.lang.String status,
-           boolean suspended) {
-           this.broken = broken;
-           this.failed = failed;
-           this.finished = finished;
-           this.invalid = invalid;
-           this.jobFailed = jobFailed;
-           this.queued = queued;
-           this.running = running;
-           this.serverError = serverError;
-           this.state = state;
-           this.status = status;
-           this.suspended = suspended;
-    }
-
-
-    /**
-     * Gets the broken value for this Result.
-     * 
-     * @return broken
-     */
-    public boolean isBroken() {
-        return broken;
-    }
-
-
-    /**
-     * Sets the broken value for this Result.
-     * 
-     * @param broken
-     */
-    public void setBroken(boolean broken) {
-        this.broken = broken;
-    }
-
-
-    /**
-     * Gets the failed value for this Result.
-     * 
-     * @return failed
-     */
-    public boolean isFailed() {
-        return failed;
-    }
-
-
-    /**
-     * Sets the failed value for this Result.
-     * 
-     * @param failed
-     */
-    public void setFailed(boolean failed) {
-        this.failed = failed;
-    }
-
-
-    /**
-     * Gets the finished value for this Result.
-     * 
-     * @return finished
-     */
-    public boolean isFinished() {
-        return finished;
+public class Result implements java.io.Serializable
+{
+  private boolean broken;
+
+  private boolean failed;
+
+  private boolean finished;
+
+  private boolean invalid;
+
+  private boolean jobFailed;
+
+  private boolean queued;
+
+  private boolean running;
+
+  private boolean serverError;
+
+  private int state;
+
+  private java.lang.String status;
+
+  private boolean suspended;
+
+  public Result()
+  {
+  }
+
+  public Result(boolean broken, boolean failed, boolean finished,
+          boolean invalid, boolean jobFailed, boolean queued,
+          boolean running, boolean serverError, int state,
+          java.lang.String status, boolean suspended)
+  {
+    this.broken = broken;
+    this.failed = failed;
+    this.finished = finished;
+    this.invalid = invalid;
+    this.jobFailed = jobFailed;
+    this.queued = queued;
+    this.running = running;
+    this.serverError = serverError;
+    this.state = state;
+    this.status = status;
+    this.suspended = suspended;
+  }
+
+  /**
+   * Gets the broken value for this Result.
+   * 
+   * @return broken
+   */
+  public boolean isBroken()
+  {
+    return broken;
+  }
+
+  /**
+   * Sets the broken value for this Result.
+   * 
+   * @param broken
+   */
+  public void setBroken(boolean broken)
+  {
+    this.broken = broken;
+  }
+
+  /**
+   * Gets the failed value for this Result.
+   * 
+   * @return failed
+   */
+  public boolean isFailed()
+  {
+    return failed;
+  }
+
+  /**
+   * Sets the failed value for this Result.
+   * 
+   * @param failed
+   */
+  public void setFailed(boolean failed)
+  {
+    this.failed = failed;
+  }
+
+  /**
+   * Gets the finished value for this Result.
+   * 
+   * @return finished
+   */
+  public boolean isFinished()
+  {
+    return finished;
+  }
+
+  /**
+   * Sets the finished value for this Result.
+   * 
+   * @param finished
+   */
+  public void setFinished(boolean finished)
+  {
+    this.finished = finished;
+  }
+
+  /**
+   * Gets the invalid value for this Result.
+   * 
+   * @return invalid
+   */
+  public boolean isInvalid()
+  {
+    return invalid;
+  }
+
+  /**
+   * Sets the invalid value for this Result.
+   * 
+   * @param invalid
+   */
+  public void setInvalid(boolean invalid)
+  {
+    this.invalid = invalid;
+  }
+
+  /**
+   * Gets the jobFailed value for this Result.
+   * 
+   * @return jobFailed
+   */
+  public boolean isJobFailed()
+  {
+    return jobFailed;
+  }
+
+  /**
+   * Sets the jobFailed value for this Result.
+   * 
+   * @param jobFailed
+   */
+  public void setJobFailed(boolean jobFailed)
+  {
+    this.jobFailed = jobFailed;
+  }
+
+  /**
+   * Gets the queued value for this Result.
+   * 
+   * @return queued
+   */
+  public boolean isQueued()
+  {
+    return queued;
+  }
+
+  /**
+   * Sets the queued value for this Result.
+   * 
+   * @param queued
+   */
+  public void setQueued(boolean queued)
+  {
+    this.queued = queued;
+  }
+
+  /**
+   * Gets the running value for this Result.
+   * 
+   * @return running
+   */
+  public boolean isRunning()
+  {
+    return running;
+  }
+
+  /**
+   * Sets the running value for this Result.
+   * 
+   * @param running
+   */
+  public void setRunning(boolean running)
+  {
+    this.running = running;
+  }
+
+  /**
+   * Gets the serverError value for this Result.
+   * 
+   * @return serverError
+   */
+  public boolean isServerError()
+  {
+    return serverError;
+  }
+
+  /**
+   * Sets the serverError value for this Result.
+   * 
+   * @param serverError
+   */
+  public void setServerError(boolean serverError)
+  {
+    this.serverError = serverError;
+  }
+
+  /**
+   * Gets the state value for this Result.
+   * 
+   * @return state
+   */
+  public int getState()
+  {
+    return state;
+  }
+
+  /**
+   * Sets the state value for this Result.
+   * 
+   * @param state
+   */
+  public void setState(int state)
+  {
+    this.state = state;
+  }
+
+  /**
+   * Gets the status value for this Result.
+   * 
+   * @return status
+   */
+  public java.lang.String getStatus()
+  {
+    return status;
+  }
+
+  /**
+   * Sets the status value for this Result.
+   * 
+   * @param status
+   */
+  public void setStatus(java.lang.String status)
+  {
+    this.status = status;
+  }
+
+  /**
+   * Gets the suspended value for this Result.
+   * 
+   * @return suspended
+   */
+  public boolean isSuspended()
+  {
+    return suspended;
+  }
+
+  /**
+   * Sets the suspended value for this Result.
+   * 
+   * @param suspended
+   */
+  public void setSuspended(boolean suspended)
+  {
+    this.suspended = suspended;
+  }
+
+  private java.lang.Object __equalsCalc = null;
+
+  public synchronized boolean equals(java.lang.Object obj)
+  {
+    if (!(obj instanceof Result))
+      return false;
+    Result other = (Result) obj;
+    if (obj == null)
+      return false;
+    if (this == obj)
+      return true;
+    if (__equalsCalc != null)
+    {
+      return (__equalsCalc == obj);
     }
-
-
-    /**
-     * Sets the finished value for this Result.
-     * 
-     * @param finished
-     */
-    public void setFinished(boolean finished) {
-        this.finished = finished;
-    }
-
-
-    /**
-     * Gets the invalid value for this Result.
-     * 
-     * @return invalid
-     */
-    public boolean isInvalid() {
-        return invalid;
-    }
-
-
-    /**
-     * Sets the invalid value for this Result.
-     * 
-     * @param invalid
-     */
-    public void setInvalid(boolean invalid) {
-        this.invalid = invalid;
-    }
-
-
-    /**
-     * Gets the jobFailed value for this Result.
-     * 
-     * @return jobFailed
-     */
-    public boolean isJobFailed() {
-        return jobFailed;
-    }
-
-
-    /**
-     * Sets the jobFailed value for this Result.
-     * 
-     * @param jobFailed
-     */
-    public void setJobFailed(boolean jobFailed) {
-        this.jobFailed = jobFailed;
+    __equalsCalc = obj;
+    boolean _equals;
+    _equals = true
+            && this.broken == other.isBroken()
+            && this.failed == other.isFailed()
+            && this.finished == other.isFinished()
+            && this.invalid == other.isInvalid()
+            && this.jobFailed == other.isJobFailed()
+            && this.queued == other.isQueued()
+            && this.running == other.isRunning()
+            && this.serverError == other.isServerError()
+            && this.state == other.getState()
+            && ((this.status == null && other.getStatus() == null) || (this.status != null && this.status
+                    .equals(other.getStatus())))
+            && this.suspended == other.isSuspended();
+    __equalsCalc = null;
+    return _equals;
+  }
+
+  private boolean __hashCodeCalc = false;
+
+  public synchronized int hashCode()
+  {
+    if (__hashCodeCalc)
+    {
+      return 0;
     }
-
-
-    /**
-     * Gets the queued value for this Result.
-     * 
-     * @return queued
-     */
-    public boolean isQueued() {
-        return queued;
-    }
-
-
-    /**
-     * Sets the queued value for this Result.
-     * 
-     * @param queued
-     */
-    public void setQueued(boolean queued) {
-        this.queued = queued;
-    }
-
-
-    /**
-     * Gets the running value for this Result.
-     * 
-     * @return running
-     */
-    public boolean isRunning() {
-        return running;
-    }
-
-
-    /**
-     * Sets the running value for this Result.
-     * 
-     * @param running
-     */
-    public void setRunning(boolean running) {
-        this.running = running;
-    }
-
-
-    /**
-     * Gets the serverError value for this Result.
-     * 
-     * @return serverError
-     */
-    public boolean isServerError() {
-        return serverError;
-    }
-
-
-    /**
-     * Sets the serverError value for this Result.
-     * 
-     * @param serverError
-     */
-    public void setServerError(boolean serverError) {
-        this.serverError = serverError;
-    }
-
-
-    /**
-     * Gets the state value for this Result.
-     * 
-     * @return state
-     */
-    public int getState() {
-        return state;
-    }
-
-
-    /**
-     * Sets the state value for this Result.
-     * 
-     * @param state
-     */
-    public void setState(int state) {
-        this.state = state;
-    }
-
-
-    /**
-     * Gets the status value for this Result.
-     * 
-     * @return status
-     */
-    public java.lang.String getStatus() {
-        return status;
-    }
-
-
-    /**
-     * Sets the status value for this Result.
-     * 
-     * @param status
-     */
-    public void setStatus(java.lang.String status) {
-        this.status = status;
-    }
-
-
-    /**
-     * Gets the suspended value for this Result.
-     * 
-     * @return suspended
-     */
-    public boolean isSuspended() {
-        return suspended;
-    }
-
-
-    /**
-     * Sets the suspended value for this Result.
-     * 
-     * @param suspended
-     */
-    public void setSuspended(boolean suspended) {
-        this.suspended = suspended;
-    }
-
-    private java.lang.Object __equalsCalc = null;
-    public synchronized boolean equals(java.lang.Object obj) {
-        if (!(obj instanceof Result)) return false;
-        Result other = (Result) obj;
-        if (obj == null) return false;
-        if (this == obj) return true;
-        if (__equalsCalc != null) {
-            return (__equalsCalc == obj);
-        }
-        __equalsCalc = obj;
-        boolean _equals;
-        _equals = true && 
-            this.broken == other.isBroken() &&
-            this.failed == other.isFailed() &&
-            this.finished == other.isFinished() &&
-            this.invalid == other.isInvalid() &&
-            this.jobFailed == other.isJobFailed() &&
-            this.queued == other.isQueued() &&
-            this.running == other.isRunning() &&
-            this.serverError == other.isServerError() &&
-            this.state == other.getState() &&
-            ((this.status==null && other.getStatus()==null) || 
-             (this.status!=null &&
-              this.status.equals(other.getStatus()))) &&
-            this.suspended == other.isSuspended();
-        __equalsCalc = null;
-        return _equals;
-    }
-
-    private boolean __hashCodeCalc = false;
-    public synchronized int hashCode() {
-        if (__hashCodeCalc) {
-            return 0;
-        }
-        __hashCodeCalc = true;
-        int _hashCode = 1;
-        _hashCode += (isBroken() ? Boolean.TRUE : Boolean.FALSE).hashCode();
-        _hashCode += (isFailed() ? Boolean.TRUE : Boolean.FALSE).hashCode();
-        _hashCode += (isFinished() ? Boolean.TRUE : Boolean.FALSE).hashCode();
-        _hashCode += (isInvalid() ? Boolean.TRUE : Boolean.FALSE).hashCode();
-        _hashCode += (isJobFailed() ? Boolean.TRUE : Boolean.FALSE).hashCode();
-        _hashCode += (isQueued() ? Boolean.TRUE : Boolean.FALSE).hashCode();
-        _hashCode += (isRunning() ? Boolean.TRUE : Boolean.FALSE).hashCode();
-        _hashCode += (isServerError() ? Boolean.TRUE : Boolean.FALSE).hashCode();
-        _hashCode += getState();
-        if (getStatus() != null) {
-            _hashCode += getStatus().hashCode();
-        }
-        _hashCode += (isSuspended() ? Boolean.TRUE : Boolean.FALSE).hashCode();
-        __hashCodeCalc = false;
-        return _hashCode;
+    __hashCodeCalc = true;
+    int _hashCode = 1;
+    _hashCode += (isBroken() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+    _hashCode += (isFailed() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+    _hashCode += (isFinished() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+    _hashCode += (isInvalid() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+    _hashCode += (isJobFailed() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+    _hashCode += (isQueued() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+    _hashCode += (isRunning() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+    _hashCode += (isServerError() ? Boolean.TRUE : Boolean.FALSE)
+            .hashCode();
+    _hashCode += getState();
+    if (getStatus() != null)
+    {
+      _hashCode += getStatus().hashCode();
     }
+    _hashCode += (isSuspended() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+    __hashCodeCalc = false;
+    return _hashCode;
+  }
 
 }
diff --git a/src/vamsas/objects/simple/Result_Helper.java b/src/vamsas/objects/simple/Result_Helper.java
index 14ed2b5..011ebf9 100755
--- a/src/vamsas/objects/simple/Result_Helper.java
+++ b/src/vamsas/objects/simple/Result_Helper.java
@@ -1,105 +1,129 @@
-/**
- * Result_Helper.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package vamsas.objects.simple;
 
-public class Result_Helper {
-    // Type metadata
-    private static org.apache.axis.description.TypeDesc typeDesc =
-        new org.apache.axis.description.TypeDesc(Result.class, true);
+public class Result_Helper
+{
+  // Type metadata
+  private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(
+          Result.class, true);
 
-    static {
-        typeDesc.setXmlType(new javax.xml.namespace.QName("simple.objects.vamsas", "Result"));
-        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("broken");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "broken"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("failed");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "failed"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("finished");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "finished"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("invalid");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "invalid"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("jobFailed");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "jobFailed"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("queued");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "queued"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("running");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "running"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("serverError");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "serverError"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("state");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "state"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "int"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("status");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "status"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://schemas.xmlsoap.org/soap/encoding/", "string"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("suspended");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "suspended"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
-        typeDesc.addFieldDesc(elemField);
-    }
+  static
+  {
+    typeDesc.setXmlType(new javax.xml.namespace.QName(
+            "simple.objects.vamsas", "Result"));
+    org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("broken");
+    elemField.setXmlName(new javax.xml.namespace.QName("", "broken"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "http://www.w3.org/2001/XMLSchema", "boolean"));
+    typeDesc.addFieldDesc(elemField);
+    elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("failed");
+    elemField.setXmlName(new javax.xml.namespace.QName("", "failed"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "http://www.w3.org/2001/XMLSchema", "boolean"));
+    typeDesc.addFieldDesc(elemField);
+    elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("finished");
+    elemField.setXmlName(new javax.xml.namespace.QName("", "finished"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "http://www.w3.org/2001/XMLSchema", "boolean"));
+    typeDesc.addFieldDesc(elemField);
+    elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("invalid");
+    elemField.setXmlName(new javax.xml.namespace.QName("", "invalid"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "http://www.w3.org/2001/XMLSchema", "boolean"));
+    typeDesc.addFieldDesc(elemField);
+    elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("jobFailed");
+    elemField.setXmlName(new javax.xml.namespace.QName("", "jobFailed"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "http://www.w3.org/2001/XMLSchema", "boolean"));
+    typeDesc.addFieldDesc(elemField);
+    elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("queued");
+    elemField.setXmlName(new javax.xml.namespace.QName("", "queued"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "http://www.w3.org/2001/XMLSchema", "boolean"));
+    typeDesc.addFieldDesc(elemField);
+    elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("running");
+    elemField.setXmlName(new javax.xml.namespace.QName("", "running"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "http://www.w3.org/2001/XMLSchema", "boolean"));
+    typeDesc.addFieldDesc(elemField);
+    elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("serverError");
+    elemField.setXmlName(new javax.xml.namespace.QName("", "serverError"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "http://www.w3.org/2001/XMLSchema", "boolean"));
+    typeDesc.addFieldDesc(elemField);
+    elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("state");
+    elemField.setXmlName(new javax.xml.namespace.QName("", "state"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "http://www.w3.org/2001/XMLSchema", "int"));
+    typeDesc.addFieldDesc(elemField);
+    elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("status");
+    elemField.setXmlName(new javax.xml.namespace.QName("", "status"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "http://schemas.xmlsoap.org/soap/encoding/", "string"));
+    typeDesc.addFieldDesc(elemField);
+    elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("suspended");
+    elemField.setXmlName(new javax.xml.namespace.QName("", "suspended"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "http://www.w3.org/2001/XMLSchema", "boolean"));
+    typeDesc.addFieldDesc(elemField);
+  }
 
-    /**
-     * Return type metadata object
-     */
-    public static org.apache.axis.description.TypeDesc getTypeDesc() {
-        return typeDesc;
-    }
+  /**
+   * Return type metadata object
+   */
+  public static org.apache.axis.description.TypeDesc getTypeDesc()
+  {
+    return typeDesc;
+  }
 
-    /**
-     * Get Custom Serializer
-     */
-    public static org.apache.axis.encoding.Serializer getSerializer(
-           java.lang.String mechType, 
-           java.lang.Class _javaType,  
-           javax.xml.namespace.QName _xmlType) {
-        return 
-          new  org.apache.axis.encoding.ser.BeanSerializer(
-            _javaType, _xmlType, typeDesc);
-    }
+  /**
+   * Get Custom Serializer
+   */
+  public static org.apache.axis.encoding.Serializer getSerializer(
+          java.lang.String mechType, java.lang.Class _javaType,
+          javax.xml.namespace.QName _xmlType)
+  {
+    return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,
+            _xmlType, typeDesc);
+  }
 
-    /**
-     * Get Custom Deserializer
-     */
-    public static org.apache.axis.encoding.Deserializer getDeserializer(
-           java.lang.String mechType, 
-           java.lang.Class _javaType,  
-           javax.xml.namespace.QName _xmlType) {
-        return 
-          new  org.apache.axis.encoding.ser.BeanDeserializer(
-            _javaType, _xmlType, typeDesc);
-    }
+  /**
+   * Get Custom Deserializer
+   */
+  public static org.apache.axis.encoding.Deserializer getDeserializer(
+          java.lang.String mechType, java.lang.Class _javaType,
+          javax.xml.namespace.QName _xmlType)
+  {
+    return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,
+            _xmlType, typeDesc);
+  }
 
 }
diff --git a/src/vamsas/objects/simple/Secstructpred.java b/src/vamsas/objects/simple/Secstructpred.java
index 8b334f4..93c8467 100755
--- a/src/vamsas/objects/simple/Secstructpred.java
+++ b/src/vamsas/objects/simple/Secstructpred.java
@@ -1,14 +1,24 @@
-/**
- * Secstructpred.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package vamsas.objects.simple;
 
-public class Secstructpred
-    implements java.io.Serializable
+public class Secstructpred implements java.io.Serializable
 {
   private java.lang.String output;
 
@@ -16,15 +26,14 @@ public class Secstructpred
   {
   }
 
-  public Secstructpred(
-      java.lang.String output)
+  public Secstructpred(java.lang.String output)
   {
     this.output = output;
   }
 
   /**
    * Gets the output value for this Secstructpred.
-   *
+   * 
    * @return output
    */
   public java.lang.String getOutput()
@@ -34,7 +43,7 @@ public class Secstructpred
 
   /**
    * Sets the output value for this Secstructpred.
-   *
+   * 
    * @param output
    */
   public void setOutput(java.lang.String output)
@@ -43,9 +52,10 @@ public class Secstructpred
   }
 
   private java.lang.Object __equalsCalc = null;
+
   public synchronized boolean equals(java.lang.Object obj)
   {
-    if (! (obj instanceof Secstructpred))
+    if (!(obj instanceof Secstructpred))
     {
       return false;
     }
@@ -64,15 +74,14 @@ public class Secstructpred
     }
     __equalsCalc = obj;
     boolean _equals;
-    _equals = true &&
-        ( (this.output == null && other.getOutput() == null) ||
-         (this.output != null &&
-          this.output.equals(other.getOutput())));
+    _equals = true && ((this.output == null && other.getOutput() == null) || (this.output != null && this.output
+            .equals(other.getOutput())));
     __equalsCalc = null;
     return _equals;
   }
 
   private boolean __hashCodeCalc = false;
+
   public synchronized int hashCode()
   {
     if (__hashCodeCalc)
diff --git a/src/vamsas/objects/simple/Secstructpred_Helper.java b/src/vamsas/objects/simple/Secstructpred_Helper.java
index 7e2ef3d..1052f69 100755
--- a/src/vamsas/objects/simple/Secstructpred_Helper.java
+++ b/src/vamsas/objects/simple/Secstructpred_Helper.java
@@ -1,28 +1,38 @@
-/**
- * Secstructpred_Helper.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package vamsas.objects.simple;
 
 public class Secstructpred_Helper
 {
   // Type metadata
-  private static org.apache.axis.description.TypeDesc typeDesc =
-      new org.apache.axis.description.TypeDesc(Secstructpred.class, true);
+  private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(
+          Secstructpred.class, true);
 
   static
   {
     typeDesc.setXmlType(new javax.xml.namespace.QName(
-        "http://simple.objects.vamsas", "Secstructpred"));
-    org.apache.axis.description.ElementDesc elemField = new org.apache.axis.
-        description.ElementDesc();
+            "http://simple.objects.vamsas", "Secstructpred"));
+    org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
     elemField.setFieldName("output");
     elemField.setXmlName(new javax.xml.namespace.QName("", "output"));
     elemField.setXmlType(new javax.xml.namespace.QName(
-        "http://schemas.xmlsoap.org/soap/encoding/", "string"));
+            "http://schemas.xmlsoap.org/soap/encoding/", "string"));
     typeDesc.addFieldDesc(elemField);
   }
 
@@ -38,26 +48,22 @@ public class Secstructpred_Helper
    * Get Custom Serializer
    */
   public static org.apache.axis.encoding.Serializer getSerializer(
-      java.lang.String mechType,
-      java.lang.Class _javaType,
-      javax.xml.namespace.QName _xmlType)
+          java.lang.String mechType, java.lang.Class _javaType,
+          javax.xml.namespace.QName _xmlType)
   {
-    return
-        new org.apache.axis.encoding.ser.BeanSerializer(
-            _javaType, _xmlType, typeDesc);
+    return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,
+            _xmlType, typeDesc);
   }
 
   /**
    * Get Custom Deserializer
    */
   public static org.apache.axis.encoding.Deserializer getDeserializer(
-      java.lang.String mechType,
-      java.lang.Class _javaType,
-      javax.xml.namespace.QName _xmlType)
+          java.lang.String mechType, java.lang.Class _javaType,
+          javax.xml.namespace.QName _xmlType)
   {
-    return
-        new org.apache.axis.encoding.ser.BeanDeserializer(
-            _javaType, _xmlType, typeDesc);
+    return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,
+            _xmlType, typeDesc);
   }
 
 }
diff --git a/src/vamsas/objects/simple/SeqSearchResult.java b/src/vamsas/objects/simple/SeqSearchResult.java
index 4d75aad..c902117 100644
--- a/src/vamsas/objects/simple/SeqSearchResult.java
+++ b/src/vamsas/objects/simple/SeqSearchResult.java
@@ -1,161 +1,186 @@
-/**
- * SeqSearchResult.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package vamsas.objects.simple;
 
-public class SeqSearchResult  extends vamsas.objects.simple.Result  implements java.io.Serializable {
-    private vamsas.objects.simple.Alignment alignment;
-    private java.lang.String annotation;
-    private java.lang.String features;
-    private java.lang.String newickTree;
-
-    public SeqSearchResult() {
+public class SeqSearchResult extends vamsas.objects.simple.Result implements
+        java.io.Serializable
+{
+  private vamsas.objects.simple.Alignment alignment;
+
+  private java.lang.String annotation;
+
+  private java.lang.String features;
+
+  private java.lang.String newickTree;
+
+  public SeqSearchResult()
+  {
+  }
+
+  public SeqSearchResult(vamsas.objects.simple.Alignment alignment,
+          java.lang.String annotation, java.lang.String features,
+          java.lang.String newickTree)
+  {
+    this.alignment = alignment;
+    this.annotation = annotation;
+    this.features = features;
+    this.newickTree = newickTree;
+  }
+
+  /**
+   * Gets the alignment value for this SeqSearchResult.
+   * 
+   * @return alignment
+   */
+  public vamsas.objects.simple.Alignment getAlignment()
+  {
+    return alignment;
+  }
+
+  /**
+   * Sets the alignment value for this SeqSearchResult.
+   * 
+   * @param alignment
+   */
+  public void setAlignment(vamsas.objects.simple.Alignment alignment)
+  {
+    this.alignment = alignment;
+  }
+
+  /**
+   * Gets the annotation value for this SeqSearchResult.
+   * 
+   * @return annotation
+   */
+  public java.lang.String getAnnotation()
+  {
+    return annotation;
+  }
+
+  /**
+   * Sets the annotation value for this SeqSearchResult.
+   * 
+   * @param annotation
+   */
+  public void setAnnotation(java.lang.String annotation)
+  {
+    this.annotation = annotation;
+  }
+
+  /**
+   * Gets the features value for this SeqSearchResult.
+   * 
+   * @return features
+   */
+  public java.lang.String getFeatures()
+  {
+    return features;
+  }
+
+  /**
+   * Sets the features value for this SeqSearchResult.
+   * 
+   * @param features
+   */
+  public void setFeatures(java.lang.String features)
+  {
+    this.features = features;
+  }
+
+  /**
+   * Gets the newickTree value for this SeqSearchResult.
+   * 
+   * @return newickTree
+   */
+  public java.lang.String getNewickTree()
+  {
+    return newickTree;
+  }
+
+  /**
+   * Sets the newickTree value for this SeqSearchResult.
+   * 
+   * @param newickTree
+   */
+  public void setNewickTree(java.lang.String newickTree)
+  {
+    this.newickTree = newickTree;
+  }
+
+  private java.lang.Object __equalsCalc = null;
+
+  public synchronized boolean equals(java.lang.Object obj)
+  {
+    if (!(obj instanceof SeqSearchResult))
+      return false;
+    SeqSearchResult other = (SeqSearchResult) obj;
+    if (obj == null)
+      return false;
+    if (this == obj)
+      return true;
+    if (__equalsCalc != null)
+    {
+      return (__equalsCalc == obj);
     }
-
-    public SeqSearchResult(
-           vamsas.objects.simple.Alignment alignment,
-           java.lang.String annotation,
-           java.lang.String features,
-           java.lang.String newickTree) {
-           this.alignment = alignment;
-           this.annotation = annotation;
-           this.features = features;
-           this.newickTree = newickTree;
+    __equalsCalc = obj;
+    boolean _equals;
+    _equals = super.equals(obj)
+            && ((this.alignment == null && other.getAlignment() == null) || (this.alignment != null && this.alignment
+                    .equals(other.getAlignment())))
+            && ((this.annotation == null && other.getAnnotation() == null) || (this.annotation != null && this.annotation
+                    .equals(other.getAnnotation())))
+            && ((this.features == null && other.getFeatures() == null) || (this.features != null && this.features
+                    .equals(other.getFeatures())))
+            && ((this.newickTree == null && other.getNewickTree() == null) || (this.newickTree != null && this.newickTree
+                    .equals(other.getNewickTree())));
+    __equalsCalc = null;
+    return _equals;
+  }
+
+  private boolean __hashCodeCalc = false;
+
+  public synchronized int hashCode()
+  {
+    if (__hashCodeCalc)
+    {
+      return 0;
     }
-
-
-    /**
-     * Gets the alignment value for this SeqSearchResult.
-     * 
-     * @return alignment
-     */
-    public vamsas.objects.simple.Alignment getAlignment() {
-        return alignment;
-    }
-
-
-    /**
-     * Sets the alignment value for this SeqSearchResult.
-     * 
-     * @param alignment
-     */
-    public void setAlignment(vamsas.objects.simple.Alignment alignment) {
-        this.alignment = alignment;
+    __hashCodeCalc = true;
+    int _hashCode = super.hashCode();
+    if (getAlignment() != null)
+    {
+      _hashCode += getAlignment().hashCode();
     }
-
-
-    /**
-     * Gets the annotation value for this SeqSearchResult.
-     * 
-     * @return annotation
-     */
-    public java.lang.String getAnnotation() {
-        return annotation;
+    if (getAnnotation() != null)
+    {
+      _hashCode += getAnnotation().hashCode();
     }
-
-
-    /**
-     * Sets the annotation value for this SeqSearchResult.
-     * 
-     * @param annotation
-     */
-    public void setAnnotation(java.lang.String annotation) {
-        this.annotation = annotation;
+    if (getFeatures() != null)
+    {
+      _hashCode += getFeatures().hashCode();
     }
-
-
-    /**
-     * Gets the features value for this SeqSearchResult.
-     * 
-     * @return features
-     */
-    public java.lang.String getFeatures() {
-        return features;
-    }
-
-
-    /**
-     * Sets the features value for this SeqSearchResult.
-     * 
-     * @param features
-     */
-    public void setFeatures(java.lang.String features) {
-        this.features = features;
-    }
-
-
-    /**
-     * Gets the newickTree value for this SeqSearchResult.
-     * 
-     * @return newickTree
-     */
-    public java.lang.String getNewickTree() {
-        return newickTree;
-    }
-
-
-    /**
-     * Sets the newickTree value for this SeqSearchResult.
-     * 
-     * @param newickTree
-     */
-    public void setNewickTree(java.lang.String newickTree) {
-        this.newickTree = newickTree;
-    }
-
-    private java.lang.Object __equalsCalc = null;
-    public synchronized boolean equals(java.lang.Object obj) {
-        if (!(obj instanceof SeqSearchResult)) return false;
-        SeqSearchResult other = (SeqSearchResult) obj;
-        if (obj == null) return false;
-        if (this == obj) return true;
-        if (__equalsCalc != null) {
-            return (__equalsCalc == obj);
-        }
-        __equalsCalc = obj;
-        boolean _equals;
-        _equals = super.equals(obj) && 
-            ((this.alignment==null && other.getAlignment()==null) || 
-             (this.alignment!=null &&
-              this.alignment.equals(other.getAlignment()))) &&
-            ((this.annotation==null && other.getAnnotation()==null) || 
-             (this.annotation!=null &&
-              this.annotation.equals(other.getAnnotation()))) &&
-            ((this.features==null && other.getFeatures()==null) || 
-             (this.features!=null &&
-              this.features.equals(other.getFeatures()))) &&
-            ((this.newickTree==null && other.getNewickTree()==null) || 
-             (this.newickTree!=null &&
-              this.newickTree.equals(other.getNewickTree())));
-        __equalsCalc = null;
-        return _equals;
-    }
-
-    private boolean __hashCodeCalc = false;
-    public synchronized int hashCode() {
-        if (__hashCodeCalc) {
-            return 0;
-        }
-        __hashCodeCalc = true;
-        int _hashCode = super.hashCode();
-        if (getAlignment() != null) {
-            _hashCode += getAlignment().hashCode();
-        }
-        if (getAnnotation() != null) {
-            _hashCode += getAnnotation().hashCode();
-        }
-        if (getFeatures() != null) {
-            _hashCode += getFeatures().hashCode();
-        }
-        if (getNewickTree() != null) {
-            _hashCode += getNewickTree().hashCode();
-        }
-        __hashCodeCalc = false;
-        return _hashCode;
+    if (getNewickTree() != null)
+    {
+      _hashCode += getNewickTree().hashCode();
     }
+    __hashCodeCalc = false;
+    return _hashCode;
+  }
 
 }
diff --git a/src/vamsas/objects/simple/SeqSearchResult_Helper.java b/src/vamsas/objects/simple/SeqSearchResult_Helper.java
index 3f6e30d..3e10bab 100644
--- a/src/vamsas/objects/simple/SeqSearchResult_Helper.java
+++ b/src/vamsas/objects/simple/SeqSearchResult_Helper.java
@@ -1,70 +1,87 @@
-/**
- * SeqSearchResult_Helper.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package vamsas.objects.simple;
 
-public class SeqSearchResult_Helper {
-    // Type metadata
-    private static org.apache.axis.description.TypeDesc typeDesc =
-        new org.apache.axis.description.TypeDesc(SeqSearchResult.class, true);
+public class SeqSearchResult_Helper
+{
+  // Type metadata
+  private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(
+          SeqSearchResult.class, true);
 
-    static {
-        typeDesc.setXmlType(new javax.xml.namespace.QName("simple.objects.vamsas", "SeqSearchResult"));
-        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("alignment");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "alignment"));
-        elemField.setXmlType(new javax.xml.namespace.QName("simple.objects.vamsas", "Alignment"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("annotation");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "annotation"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://schemas.xmlsoap.org/soap/encoding/", "string"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("features");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "features"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://schemas.xmlsoap.org/soap/encoding/", "string"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("newickTree");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "newickTree"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://schemas.xmlsoap.org/soap/encoding/", "string"));
-        typeDesc.addFieldDesc(elemField);
-    }
+  static
+  {
+    typeDesc.setXmlType(new javax.xml.namespace.QName(
+            "simple.objects.vamsas", "SeqSearchResult"));
+    org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("alignment");
+    elemField.setXmlName(new javax.xml.namespace.QName("", "alignment"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "simple.objects.vamsas", "Alignment"));
+    typeDesc.addFieldDesc(elemField);
+    elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("annotation");
+    elemField.setXmlName(new javax.xml.namespace.QName("", "annotation"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "http://schemas.xmlsoap.org/soap/encoding/", "string"));
+    typeDesc.addFieldDesc(elemField);
+    elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("features");
+    elemField.setXmlName(new javax.xml.namespace.QName("", "features"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "http://schemas.xmlsoap.org/soap/encoding/", "string"));
+    typeDesc.addFieldDesc(elemField);
+    elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("newickTree");
+    elemField.setXmlName(new javax.xml.namespace.QName("", "newickTree"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "http://schemas.xmlsoap.org/soap/encoding/", "string"));
+    typeDesc.addFieldDesc(elemField);
+  }
 
-    /**
-     * Return type metadata object
-     */
-    public static org.apache.axis.description.TypeDesc getTypeDesc() {
-        return typeDesc;
-    }
+  /**
+   * Return type metadata object
+   */
+  public static org.apache.axis.description.TypeDesc getTypeDesc()
+  {
+    return typeDesc;
+  }
 
-    /**
-     * Get Custom Serializer
-     */
-    public static org.apache.axis.encoding.Serializer getSerializer(
-           java.lang.String mechType, 
-           java.lang.Class _javaType,  
-           javax.xml.namespace.QName _xmlType) {
-        return 
-          new  org.apache.axis.encoding.ser.BeanSerializer(
-            _javaType, _xmlType, typeDesc);
-    }
+  /**
+   * Get Custom Serializer
+   */
+  public static org.apache.axis.encoding.Serializer getSerializer(
+          java.lang.String mechType, java.lang.Class _javaType,
+          javax.xml.namespace.QName _xmlType)
+  {
+    return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,
+            _xmlType, typeDesc);
+  }
 
-    /**
-     * Get Custom Deserializer
-     */
-    public static org.apache.axis.encoding.Deserializer getDeserializer(
-           java.lang.String mechType, 
-           java.lang.Class _javaType,  
-           javax.xml.namespace.QName _xmlType) {
-        return 
-          new  org.apache.axis.encoding.ser.BeanDeserializer(
-            _javaType, _xmlType, typeDesc);
-    }
+  /**
+   * Get Custom Deserializer
+   */
+  public static org.apache.axis.encoding.Deserializer getDeserializer(
+          java.lang.String mechType, java.lang.Class _javaType,
+          javax.xml.namespace.QName _xmlType)
+  {
+    return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,
+            _xmlType, typeDesc);
+  }
 
 }
diff --git a/src/vamsas/objects/simple/Sequence.java b/src/vamsas/objects/simple/Sequence.java
index d2eccb0..40c8ea0 100755
--- a/src/vamsas/objects/simple/Sequence.java
+++ b/src/vamsas/objects/simple/Sequence.java
@@ -1,103 +1,125 @@
-/**
- * Sequence.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package vamsas.objects.simple;
 
-public class Sequence  implements java.io.Serializable {
-    private java.lang.String id;
-    private java.lang.String seq;
+public class Sequence implements java.io.Serializable
+{
+  private java.lang.String id;
 
-    public Sequence() {
-    }
+  private java.lang.String seq;
 
-    public Sequence(
-           java.lang.String id,
-           java.lang.String seq) {
-           this.id = id;
-           this.seq = seq;
-    }
+  public Sequence()
+  {
+  }
 
+  public Sequence(java.lang.String id, java.lang.String seq)
+  {
+    this.id = id;
+    this.seq = seq;
+  }
 
-    /**
-     * Gets the id value for this Sequence.
-     * 
-     * @return id
-     */
-    public java.lang.String getId() {
-        return id;
-    }
+  /**
+   * Gets the id value for this Sequence.
+   * 
+   * @return id
+   */
+  public java.lang.String getId()
+  {
+    return id;
+  }
 
+  /**
+   * Sets the id value for this Sequence.
+   * 
+   * @param id
+   */
+  public void setId(java.lang.String id)
+  {
+    this.id = id;
+  }
 
-    /**
-     * Sets the id value for this Sequence.
-     * 
-     * @param id
-     */
-    public void setId(java.lang.String id) {
-        this.id = id;
-    }
+  /**
+   * Gets the seq value for this Sequence.
+   * 
+   * @return seq
+   */
+  public java.lang.String getSeq()
+  {
+    return seq;
+  }
+
+  /**
+   * Sets the seq value for this Sequence.
+   * 
+   * @param seq
+   */
+  public void setSeq(java.lang.String seq)
+  {
+    this.seq = seq;
+  }
 
+  private java.lang.Object __equalsCalc = null;
 
-    /**
-     * Gets the seq value for this Sequence.
-     * 
-     * @return seq
-     */
-    public java.lang.String getSeq() {
-        return seq;
+  public synchronized boolean equals(java.lang.Object obj)
+  {
+    if (!(obj instanceof Sequence))
+      return false;
+    Sequence other = (Sequence) obj;
+    if (obj == null)
+      return false;
+    if (this == obj)
+      return true;
+    if (__equalsCalc != null)
+    {
+      return (__equalsCalc == obj);
     }
+    __equalsCalc = obj;
+    boolean _equals;
+    _equals = true
+            && ((this.id == null && other.getId() == null) || (this.id != null && this.id
+                    .equals(other.getId())))
+            && ((this.seq == null && other.getSeq() == null) || (this.seq != null && this.seq
+                    .equals(other.getSeq())));
+    __equalsCalc = null;
+    return _equals;
+  }
 
+  private boolean __hashCodeCalc = false;
 
-    /**
-     * Sets the seq value for this Sequence.
-     * 
-     * @param seq
-     */
-    public void setSeq(java.lang.String seq) {
-        this.seq = seq;
+  public synchronized int hashCode()
+  {
+    if (__hashCodeCalc)
+    {
+      return 0;
     }
-
-    private java.lang.Object __equalsCalc = null;
-    public synchronized boolean equals(java.lang.Object obj) {
-        if (!(obj instanceof Sequence)) return false;
-        Sequence other = (Sequence) obj;
-        if (obj == null) return false;
-        if (this == obj) return true;
-        if (__equalsCalc != null) {
-            return (__equalsCalc == obj);
-        }
-        __equalsCalc = obj;
-        boolean _equals;
-        _equals = true && 
-            ((this.id==null && other.getId()==null) || 
-             (this.id!=null &&
-              this.id.equals(other.getId()))) &&
-            ((this.seq==null && other.getSeq()==null) || 
-             (this.seq!=null &&
-              this.seq.equals(other.getSeq())));
-        __equalsCalc = null;
-        return _equals;
+    __hashCodeCalc = true;
+    int _hashCode = 1;
+    if (getId() != null)
+    {
+      _hashCode += getId().hashCode();
     }
-
-    private boolean __hashCodeCalc = false;
-    public synchronized int hashCode() {
-        if (__hashCodeCalc) {
-            return 0;
-        }
-        __hashCodeCalc = true;
-        int _hashCode = 1;
-        if (getId() != null) {
-            _hashCode += getId().hashCode();
-        }
-        if (getSeq() != null) {
-            _hashCode += getSeq().hashCode();
-        }
-        __hashCodeCalc = false;
-        return _hashCode;
+    if (getSeq() != null)
+    {
+      _hashCode += getSeq().hashCode();
     }
+    __hashCodeCalc = false;
+    return _hashCode;
+  }
 
 }
diff --git a/src/vamsas/objects/simple/SequenceSet.java b/src/vamsas/objects/simple/SequenceSet.java
index 62e58b4..d8416b8 100755
--- a/src/vamsas/objects/simple/SequenceSet.java
+++ b/src/vamsas/objects/simple/SequenceSet.java
@@ -1,82 +1,102 @@
-/**
- * SequenceSet.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package vamsas.objects.simple;
 
-public class SequenceSet  implements java.io.Serializable {
-    private vamsas.objects.simple.Sequence[] seqs;
+public class SequenceSet implements java.io.Serializable
+{
+  private vamsas.objects.simple.Sequence[] seqs;
 
-    public SequenceSet() {
-    }
+  public SequenceSet()
+  {
+  }
 
-    public SequenceSet(
-           vamsas.objects.simple.Sequence[] seqs) {
-           this.seqs = seqs;
-    }
+  public SequenceSet(vamsas.objects.simple.Sequence[] seqs)
+  {
+    this.seqs = seqs;
+  }
 
+  /**
+   * Gets the seqs value for this SequenceSet.
+   * 
+   * @return seqs
+   */
+  public vamsas.objects.simple.Sequence[] getSeqs()
+  {
+    return seqs;
+  }
 
-    /**
-     * Gets the seqs value for this SequenceSet.
-     * 
-     * @return seqs
-     */
-    public vamsas.objects.simple.Sequence[] getSeqs() {
-        return seqs;
-    }
+  /**
+   * Sets the seqs value for this SequenceSet.
+   * 
+   * @param seqs
+   */
+  public void setSeqs(vamsas.objects.simple.Sequence[] seqs)
+  {
+    this.seqs = seqs;
+  }
 
+  private java.lang.Object __equalsCalc = null;
 
-    /**
-     * Sets the seqs value for this SequenceSet.
-     * 
-     * @param seqs
-     */
-    public void setSeqs(vamsas.objects.simple.Sequence[] seqs) {
-        this.seqs = seqs;
+  public synchronized boolean equals(java.lang.Object obj)
+  {
+    if (!(obj instanceof SequenceSet))
+      return false;
+    SequenceSet other = (SequenceSet) obj;
+    if (obj == null)
+      return false;
+    if (this == obj)
+      return true;
+    if (__equalsCalc != null)
+    {
+      return (__equalsCalc == obj);
     }
+    __equalsCalc = obj;
+    boolean _equals;
+    _equals = true && ((this.seqs == null && other.getSeqs() == null) || (this.seqs != null && java.util.Arrays
+            .equals(this.seqs, other.getSeqs())));
+    __equalsCalc = null;
+    return _equals;
+  }
 
-    private java.lang.Object __equalsCalc = null;
-    public synchronized boolean equals(java.lang.Object obj) {
-        if (!(obj instanceof SequenceSet)) return false;
-        SequenceSet other = (SequenceSet) obj;
-        if (obj == null) return false;
-        if (this == obj) return true;
-        if (__equalsCalc != null) {
-            return (__equalsCalc == obj);
-        }
-        __equalsCalc = obj;
-        boolean _equals;
-        _equals = true && 
-            ((this.seqs==null && other.getSeqs()==null) || 
-             (this.seqs!=null &&
-              java.util.Arrays.equals(this.seqs, other.getSeqs())));
-        __equalsCalc = null;
-        return _equals;
-    }
+  private boolean __hashCodeCalc = false;
 
-    private boolean __hashCodeCalc = false;
-    public synchronized int hashCode() {
-        if (__hashCodeCalc) {
-            return 0;
-        }
-        __hashCodeCalc = true;
-        int _hashCode = 1;
-        if (getSeqs() != null) {
-            for (int i=0;
-                 i<java.lang.reflect.Array.getLength(getSeqs());
-                 i++) {
-                java.lang.Object obj = java.lang.reflect.Array.get(getSeqs(), i);
-                if (obj != null &&
-                    !obj.getClass().isArray()) {
-                    _hashCode += obj.hashCode();
-                }
-            }
+  public synchronized int hashCode()
+  {
+    if (__hashCodeCalc)
+    {
+      return 0;
+    }
+    __hashCodeCalc = true;
+    int _hashCode = 1;
+    if (getSeqs() != null)
+    {
+      for (int i = 0; i < java.lang.reflect.Array.getLength(getSeqs()); i++)
+      {
+        java.lang.Object obj = java.lang.reflect.Array.get(getSeqs(), i);
+        if (obj != null && !obj.getClass().isArray())
+        {
+          _hashCode += obj.hashCode();
         }
-        __hashCodeCalc = false;
-        return _hashCode;
+      }
     }
+    __hashCodeCalc = false;
+    return _hashCode;
+  }
 
 }
diff --git a/src/vamsas/objects/simple/SequenceSet_Helper.java b/src/vamsas/objects/simple/SequenceSet_Helper.java
index 77586ba..5ad832f 100755
--- a/src/vamsas/objects/simple/SequenceSet_Helper.java
+++ b/src/vamsas/objects/simple/SequenceSet_Helper.java
@@ -1,55 +1,69 @@
-/**
- * SequenceSet_Helper.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package vamsas.objects.simple;
 
-public class SequenceSet_Helper {
-    // Type metadata
-    private static org.apache.axis.description.TypeDesc typeDesc =
-        new org.apache.axis.description.TypeDesc(SequenceSet.class, true);
+public class SequenceSet_Helper
+{
+  // Type metadata
+  private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(
+          SequenceSet.class, true);
 
-    static {
-        typeDesc.setXmlType(new javax.xml.namespace.QName("simple.objects.vamsas", "SequenceSet"));
-        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("seqs");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "seqs"));
-        elemField.setXmlType(new javax.xml.namespace.QName("simple.objects.vamsas", "Sequence"));
-        typeDesc.addFieldDesc(elemField);
-    }
+  static
+  {
+    typeDesc.setXmlType(new javax.xml.namespace.QName(
+            "simple.objects.vamsas", "SequenceSet"));
+    org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("seqs");
+    elemField.setXmlName(new javax.xml.namespace.QName("", "seqs"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "simple.objects.vamsas", "Sequence"));
+    typeDesc.addFieldDesc(elemField);
+  }
 
-    /**
-     * Return type metadata object
-     */
-    public static org.apache.axis.description.TypeDesc getTypeDesc() {
-        return typeDesc;
-    }
+  /**
+   * Return type metadata object
+   */
+  public static org.apache.axis.description.TypeDesc getTypeDesc()
+  {
+    return typeDesc;
+  }
 
-    /**
-     * Get Custom Serializer
-     */
-    public static org.apache.axis.encoding.Serializer getSerializer(
-           java.lang.String mechType, 
-           java.lang.Class _javaType,  
-           javax.xml.namespace.QName _xmlType) {
-        return 
-          new  org.apache.axis.encoding.ser.BeanSerializer(
-            _javaType, _xmlType, typeDesc);
-    }
+  /**
+   * Get Custom Serializer
+   */
+  public static org.apache.axis.encoding.Serializer getSerializer(
+          java.lang.String mechType, java.lang.Class _javaType,
+          javax.xml.namespace.QName _xmlType)
+  {
+    return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,
+            _xmlType, typeDesc);
+  }
 
-    /**
-     * Get Custom Deserializer
-     */
-    public static org.apache.axis.encoding.Deserializer getDeserializer(
-           java.lang.String mechType, 
-           java.lang.Class _javaType,  
-           javax.xml.namespace.QName _xmlType) {
-        return 
-          new  org.apache.axis.encoding.ser.BeanDeserializer(
-            _javaType, _xmlType, typeDesc);
-    }
+  /**
+   * Get Custom Deserializer
+   */
+  public static org.apache.axis.encoding.Deserializer getDeserializer(
+          java.lang.String mechType, java.lang.Class _javaType,
+          javax.xml.namespace.QName _xmlType)
+  {
+    return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,
+            _xmlType, typeDesc);
+  }
 
 }
diff --git a/src/vamsas/objects/simple/Sequence_Helper.java b/src/vamsas/objects/simple/Sequence_Helper.java
index f675384..f45ff0c 100755
--- a/src/vamsas/objects/simple/Sequence_Helper.java
+++ b/src/vamsas/objects/simple/Sequence_Helper.java
@@ -1,60 +1,75 @@
-/**
- * Sequence_Helper.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package vamsas.objects.simple;
 
-public class Sequence_Helper {
-    // Type metadata
-    private static org.apache.axis.description.TypeDesc typeDesc =
-        new org.apache.axis.description.TypeDesc(Sequence.class, true);
+public class Sequence_Helper
+{
+  // Type metadata
+  private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(
+          Sequence.class, true);
 
-    static {
-        typeDesc.setXmlType(new javax.xml.namespace.QName("simple.objects.vamsas", "Sequence"));
-        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("id");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "id"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://schemas.xmlsoap.org/soap/encoding/", "string"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("seq");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "seq"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://schemas.xmlsoap.org/soap/encoding/", "string"));
-        typeDesc.addFieldDesc(elemField);
-    }
+  static
+  {
+    typeDesc.setXmlType(new javax.xml.namespace.QName(
+            "simple.objects.vamsas", "Sequence"));
+    org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("id");
+    elemField.setXmlName(new javax.xml.namespace.QName("", "id"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "http://schemas.xmlsoap.org/soap/encoding/", "string"));
+    typeDesc.addFieldDesc(elemField);
+    elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("seq");
+    elemField.setXmlName(new javax.xml.namespace.QName("", "seq"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "http://schemas.xmlsoap.org/soap/encoding/", "string"));
+    typeDesc.addFieldDesc(elemField);
+  }
 
-    /**
-     * Return type metadata object
-     */
-    public static org.apache.axis.description.TypeDesc getTypeDesc() {
-        return typeDesc;
-    }
+  /**
+   * Return type metadata object
+   */
+  public static org.apache.axis.description.TypeDesc getTypeDesc()
+  {
+    return typeDesc;
+  }
 
-    /**
-     * Get Custom Serializer
-     */
-    public static org.apache.axis.encoding.Serializer getSerializer(
-           java.lang.String mechType, 
-           java.lang.Class _javaType,  
-           javax.xml.namespace.QName _xmlType) {
-        return 
-          new  org.apache.axis.encoding.ser.BeanSerializer(
-            _javaType, _xmlType, typeDesc);
-    }
+  /**
+   * Get Custom Serializer
+   */
+  public static org.apache.axis.encoding.Serializer getSerializer(
+          java.lang.String mechType, java.lang.Class _javaType,
+          javax.xml.namespace.QName _xmlType)
+  {
+    return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,
+            _xmlType, typeDesc);
+  }
 
-    /**
-     * Get Custom Deserializer
-     */
-    public static org.apache.axis.encoding.Deserializer getDeserializer(
-           java.lang.String mechType, 
-           java.lang.Class _javaType,  
-           javax.xml.namespace.QName _xmlType) {
-        return 
-          new  org.apache.axis.encoding.ser.BeanDeserializer(
-            _javaType, _xmlType, typeDesc);
-    }
+  /**
+   * Get Custom Deserializer
+   */
+  public static org.apache.axis.encoding.Deserializer getDeserializer(
+          java.lang.String mechType, java.lang.Class _javaType,
+          javax.xml.namespace.QName _xmlType)
+  {
+    return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,
+            _xmlType, typeDesc);
+  }
 
 }
diff --git a/src/vamsas/objects/simple/WsJobId.java b/src/vamsas/objects/simple/WsJobId.java
index 4bc1f2e..cce5388 100755
--- a/src/vamsas/objects/simple/WsJobId.java
+++ b/src/vamsas/objects/simple/WsJobId.java
@@ -1,99 +1,121 @@
-/**
- * WsJobId.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package vamsas.objects.simple;
 
-public class WsJobId  implements java.io.Serializable {
-    private java.lang.String jobId;
-    private int status;
+public class WsJobId implements java.io.Serializable
+{
+  private java.lang.String jobId;
 
-    public WsJobId() {
-    }
+  private int status;
 
-    public WsJobId(
-           java.lang.String jobId,
-           int status) {
-           this.jobId = jobId;
-           this.status = status;
-    }
+  public WsJobId()
+  {
+  }
 
+  public WsJobId(java.lang.String jobId, int status)
+  {
+    this.jobId = jobId;
+    this.status = status;
+  }
 
-    /**
-     * Gets the jobId value for this WsJobId.
-     * 
-     * @return jobId
-     */
-    public java.lang.String getJobId() {
-        return jobId;
-    }
+  /**
+   * Gets the jobId value for this WsJobId.
+   * 
+   * @return jobId
+   */
+  public java.lang.String getJobId()
+  {
+    return jobId;
+  }
 
+  /**
+   * Sets the jobId value for this WsJobId.
+   * 
+   * @param jobId
+   */
+  public void setJobId(java.lang.String jobId)
+  {
+    this.jobId = jobId;
+  }
 
-    /**
-     * Sets the jobId value for this WsJobId.
-     * 
-     * @param jobId
-     */
-    public void setJobId(java.lang.String jobId) {
-        this.jobId = jobId;
-    }
+  /**
+   * Gets the status value for this WsJobId.
+   * 
+   * @return status
+   */
+  public int getStatus()
+  {
+    return status;
+  }
 
+  /**
+   * Sets the status value for this WsJobId.
+   * 
+   * @param status
+   */
+  public void setStatus(int status)
+  {
+    this.status = status;
+  }
 
-    /**
-     * Gets the status value for this WsJobId.
-     * 
-     * @return status
-     */
-    public int getStatus() {
-        return status;
-    }
-
+  private java.lang.Object __equalsCalc = null;
 
-    /**
-     * Sets the status value for this WsJobId.
-     * 
-     * @param status
-     */
-    public void setStatus(int status) {
-        this.status = status;
+  public synchronized boolean equals(java.lang.Object obj)
+  {
+    if (!(obj instanceof WsJobId))
+      return false;
+    WsJobId other = (WsJobId) obj;
+    if (obj == null)
+      return false;
+    if (this == obj)
+      return true;
+    if (__equalsCalc != null)
+    {
+      return (__equalsCalc == obj);
     }
+    __equalsCalc = obj;
+    boolean _equals;
+    _equals = true
+            && ((this.jobId == null && other.getJobId() == null) || (this.jobId != null && this.jobId
+                    .equals(other.getJobId())))
+            && this.status == other.getStatus();
+    __equalsCalc = null;
+    return _equals;
+  }
 
-    private java.lang.Object __equalsCalc = null;
-    public synchronized boolean equals(java.lang.Object obj) {
-        if (!(obj instanceof WsJobId)) return false;
-        WsJobId other = (WsJobId) obj;
-        if (obj == null) return false;
-        if (this == obj) return true;
-        if (__equalsCalc != null) {
-            return (__equalsCalc == obj);
-        }
-        __equalsCalc = obj;
-        boolean _equals;
-        _equals = true && 
-            ((this.jobId==null && other.getJobId()==null) || 
-             (this.jobId!=null &&
-              this.jobId.equals(other.getJobId()))) &&
-            this.status == other.getStatus();
-        __equalsCalc = null;
-        return _equals;
-    }
+  private boolean __hashCodeCalc = false;
 
-    private boolean __hashCodeCalc = false;
-    public synchronized int hashCode() {
-        if (__hashCodeCalc) {
-            return 0;
-        }
-        __hashCodeCalc = true;
-        int _hashCode = 1;
-        if (getJobId() != null) {
-            _hashCode += getJobId().hashCode();
-        }
-        _hashCode += getStatus();
-        __hashCodeCalc = false;
-        return _hashCode;
+  public synchronized int hashCode()
+  {
+    if (__hashCodeCalc)
+    {
+      return 0;
+    }
+    __hashCodeCalc = true;
+    int _hashCode = 1;
+    if (getJobId() != null)
+    {
+      _hashCode += getJobId().hashCode();
     }
+    _hashCode += getStatus();
+    __hashCodeCalc = false;
+    return _hashCode;
+  }
 
 }
diff --git a/src/vamsas/objects/simple/WsJobId_Helper.java b/src/vamsas/objects/simple/WsJobId_Helper.java
index 3988ce9..77272d7 100755
--- a/src/vamsas/objects/simple/WsJobId_Helper.java
+++ b/src/vamsas/objects/simple/WsJobId_Helper.java
@@ -1,60 +1,75 @@
-/**
- * WsJobId_Helper.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package vamsas.objects.simple;
 
-public class WsJobId_Helper {
-    // Type metadata
-    private static org.apache.axis.description.TypeDesc typeDesc =
-        new org.apache.axis.description.TypeDesc(WsJobId.class, true);
+public class WsJobId_Helper
+{
+  // Type metadata
+  private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(
+          WsJobId.class, true);
 
-    static {
-        typeDesc.setXmlType(new javax.xml.namespace.QName("simple.objects.vamsas", "WsJobId"));
-        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("jobId");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "jobId"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://schemas.xmlsoap.org/soap/encoding/", "string"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("status");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "status"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "int"));
-        typeDesc.addFieldDesc(elemField);
-    }
+  static
+  {
+    typeDesc.setXmlType(new javax.xml.namespace.QName(
+            "simple.objects.vamsas", "WsJobId"));
+    org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("jobId");
+    elemField.setXmlName(new javax.xml.namespace.QName("", "jobId"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "http://schemas.xmlsoap.org/soap/encoding/", "string"));
+    typeDesc.addFieldDesc(elemField);
+    elemField = new org.apache.axis.description.ElementDesc();
+    elemField.setFieldName("status");
+    elemField.setXmlName(new javax.xml.namespace.QName("", "status"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+            "http://www.w3.org/2001/XMLSchema", "int"));
+    typeDesc.addFieldDesc(elemField);
+  }
 
-    /**
-     * Return type metadata object
-     */
-    public static org.apache.axis.description.TypeDesc getTypeDesc() {
-        return typeDesc;
-    }
+  /**
+   * Return type metadata object
+   */
+  public static org.apache.axis.description.TypeDesc getTypeDesc()
+  {
+    return typeDesc;
+  }
 
-    /**
-     * Get Custom Serializer
-     */
-    public static org.apache.axis.encoding.Serializer getSerializer(
-           java.lang.String mechType, 
-           java.lang.Class _javaType,  
-           javax.xml.namespace.QName _xmlType) {
-        return 
-          new  org.apache.axis.encoding.ser.BeanSerializer(
-            _javaType, _xmlType, typeDesc);
-    }
+  /**
+   * Get Custom Serializer
+   */
+  public static org.apache.axis.encoding.Serializer getSerializer(
+          java.lang.String mechType, java.lang.Class _javaType,
+          javax.xml.namespace.QName _xmlType)
+  {
+    return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,
+            _xmlType, typeDesc);
+  }
 
-    /**
-     * Get Custom Deserializer
-     */
-    public static org.apache.axis.encoding.Deserializer getDeserializer(
-           java.lang.String mechType, 
-           java.lang.Class _javaType,  
-           javax.xml.namespace.QName _xmlType) {
-        return 
-          new  org.apache.axis.encoding.ser.BeanDeserializer(
-            _javaType, _xmlType, typeDesc);
-    }
+  /**
+   * Get Custom Deserializer
+   */
+  public static org.apache.axis.encoding.Deserializer getDeserializer(
+          java.lang.String mechType, java.lang.Class _javaType,
+          javax.xml.namespace.QName _xmlType)
+  {
+    return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,
+            _xmlType, typeDesc);
+  }
 
 }
diff --git a/utils/.cvsignore b/utils/.cvsignore
new file mode 100644
index 0000000..70565c7
--- /dev/null
+++ b/utils/.cvsignore
@@ -0,0 +1 @@
+help2Website.class
diff --git a/utils/help2Website.java b/utils/help2Website.java
index 7a666ad..6bb4dfc 100755
--- a/utils/help2Website.java
+++ b/utils/help2Website.java
@@ -1,95 +1,113 @@
-import java.io.*;
-import java.util.*;
-
-public class help2Website
-{
-
-	public static void main(String [] args)
-	{
-		String line = "";
-		try{
-			Hashtable targets = new Hashtable();
-
-			File toc = new File("helpTOC.xml");
-			File jhm = new File("help.jhm");
-
-			BufferedReader in = new BufferedReader(new FileReader(jhm));
-
-			PrintWriter out = new PrintWriter(new FileWriter("helpTOC.html"));
-			out.println("<html><head><title>Jalview - Help </title></head>\n"
-			+"<body bgcolor=#F1F1F1>\n"
-			+"<p><center><strong>Contents</strong></center></p>\n");
-
-
-			StringTokenizer st;
-			StringBuffer indent = new StringBuffer();
-			String target, url, text;
-			while( (line = in.readLine()) != null)
-			{
-				if(line.indexOf("target")==-1)
-					continue;
-
-
-				st = new StringTokenizer(line, "\"");
-				st.nextToken(); //<mapID target="
-
-				target = st.nextToken();
-				st.nextToken(); //" url="
-
-				url = st.nextToken();
-				targets.put(target, url);
-			}
-
-			in = new BufferedReader(new FileReader(toc));
-			while( (line = in.readLine()) != null)
-			{
-				if(line.indexOf("</tocitem>")!=-1)
-					indent.setLength(indent.length()-18);
-
-				if(line.indexOf("<tocitem")==-1)
-					continue;
-
-				st = new StringTokenizer(line, "\"");
-				st.nextToken();
-
-				text = st.nextToken();
-				st.nextToken();
-
-				target = st.nextToken();
-
-				if(targets.get(target)!=null)
-					out.println("<br>"+indent+"<a href=\""
-							+ targets.get(target)
-							+"\" target=bodyframe>"
-							+text
-							+"</a>");
-				else
-					out.println("<br>"+indent+text);
-
-
-				if(line.indexOf("/>")==-1)
-					indent.append("&nbsp;&nbsp;&nbsp;");
-
-			}
-
-			out.println("</body>\n</html>");
-
-
-			out.close();
-
-		}
-
-		catch(Exception ex)
-		{
-
-			ex.printStackTrace();
-
-			System.out.println("\n"+line+"\n");
-
-			System.out.println("Usage: move to Help directory. help2Website will read"
-			+"\nhelpTOC.xml and help.jhm producing output helpTOC.html");
-		}
-	}
-
-
-}
\ No newline at end of file
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+import java.io.*;
+import java.util.*;
+
+public class help2Website
+{
+
+	public static void main(String [] args)
+	{
+		String line = "";
+		try{
+			Hashtable targets = new Hashtable();
+
+			File toc = new File("helpTOC.xml");
+			File jhm = new File("help.jhm");
+
+			BufferedReader in = new BufferedReader(new FileReader(jhm));
+
+			PrintWriter out = new PrintWriter(new FileWriter("helpTOC.html"));
+			out.println("<html><head><title>Jalview - Help </title></head>\n"
+			+"<body bgcolor=#F1F1F1>\n"
+			+"<p><center><strong>Contents</strong></center></p>\n");
+
+
+			StringTokenizer st;
+			StringBuffer indent = new StringBuffer();
+			String target, url, text;
+			while( (line = in.readLine()) != null)
+			{
+				if(line.indexOf("target")==-1)
+					continue;
+
+
+				st = new StringTokenizer(line, "\"");
+				st.nextToken(); //<mapID target="
+
+				target = st.nextToken();
+				st.nextToken(); //" url="
+
+				url = st.nextToken();
+				targets.put(target, url);
+			}
+
+			in = new BufferedReader(new FileReader(toc));
+			while( (line = in.readLine()) != null)
+			{
+				if(line.indexOf("</tocitem>")!=-1)
+					indent.setLength(indent.length()-18);
+
+				if(line.indexOf("<tocitem")==-1)
+					continue;
+
+				st = new StringTokenizer(line, "\"");
+				st.nextToken();
+
+				text = st.nextToken();
+				st.nextToken();
+
+				target = st.nextToken();
+
+				if(targets.get(target)!=null)
+					out.println("<br>"+indent+"<a href=\""
+							+ targets.get(target)
+							+"\" target=bodyframe>"
+							+text
+							+"</a>");
+				else
+					out.println("<br>"+indent+text);
+
+
+				if(line.indexOf("/>")==-1)
+					indent.append("&nbsp;&nbsp;&nbsp;");
+
+			}
+
+			out.println("</body>\n</html>");
+
+
+			out.close();
+
+		}
+
+		catch(Exception ex)
+		{
+
+			ex.printStackTrace();
+
+			System.out.println("\n"+line+"\n");
+
+			System.out.println("Usage: move to Help directory. help2Website will read"
+			+"\nhelpTOC.xml and help.jhm producing output helpTOC.html");
+		}
+	}
+
+
+}
-- 
1.7.10.2